# HG changeset patch # User cstrittmatter # Date 1588354243 14400 # Node ID e6437d4236937b7228e9d9bb24eb207812d9c791 # Parent 43f6b7f6ebb3748b08901cdc10a8f13741827318 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty diff -r 43f6b7f6ebb3 -r e6437d423693 LICENSE --- a/LICENSE Thu Apr 30 21:47:42 2020 -0400 +++ b/LICENSE Fri May 01 13:30:43 2020 -0400 @@ -1,21 +1,339 @@ -MIT License +GNU GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. By contrast, the GNU General Public +License is intended to guarantee your freedom to share and change free +software--to make sure the software is free for all its users. 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If this is what you want to do, use the GNU Lesser General +Public License instead of this License. diff -r 43f6b7f6ebb3 -r e6437d423693 README.md --- a/README.md Thu Apr 30 21:47:42 2020 -0400 +++ b/README.md Fri May 01 13:30:43 2020 -0400 @@ -1,51 +1,117 @@ -[![DOI](https://zenodo.org/badge/97020646.svg)](https://zenodo.org/badge/latestdoi/97020646) +# SeqSero2 v1.1.1 +Salmonella serotype prediction from genome sequencing data. + +Online version: http://www.denglab.info/SeqSero2 + +# Introduction +SeqSero2 is a pipeline for Salmonella serotype prediction from raw sequencing reads or genome assemblies -# SalmID -Rapid tool to check taxonomic ID of single isolate samples. Currently only IDs Salmonella species and subspecies, and some common contaminants (Listeria, Escherichia). +# Dependencies +SeqSero2 has three workflows: + +(A) Allele micro-assembly (default). This workflow takes raw reads as input and performs targeted assembly of serotype determinant alleles. Assembled alleles are used to predict serotype and flag potential inter-serotype contamination in sequencing data (i.e., presence of reads from multiple serotypes due to, for example, cross or carryover contamination during sequencing). -## Requirements: -Python 3 +Allele micro-assembly workflow depends on: + +1. Python 3; + +2. Biopython 1.73; + +3. [Burrows-Wheeler Aligner v0.7.12](http://sourceforge.net/projects/bio-bwa/files/); -## Installation: -The easy way with homebrew ([Linux](http://linuxbrew.sh/) or [MacOS](https://brew.sh/)): -``` -brew install brewsci/bio/salmid -``` -Big thanks to [Torsten Seemann](https://tseemann.github.io/) for including this in homebrew! +4. [Samtools v1.8](http://sourceforge.net/projects/samtools/files/samtools/); + +5. [NCBI BLAST v2.2.28+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download); + +6. [SRA Toolkit v2.8.0](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software); + +7. [SPAdes v3.9.0](http://bioinf.spbau.ru/spades); + +8. [Bedtools v2.17.0](http://bedtools.readthedocs.io/en/latest/); -Alternatively download from GitHub: +9. [SalmID v0.11](https://github.com/hcdenbakker/SalmID). + + +(B) Raw reads k-mer. This workflow takes raw reads as input and performs rapid serotype prediction based on unique k-mers of serotype determinants. -```bash -git clone https://github.com/hcdenbakker/SalmID.git -``` +Raw reads k-mer workflow (originally SeqSeroK) depends on: -build a wheel using [poetry](https://poetry.eustace.io/): +1. Python 3; +2. [SRA Toolkit](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software) (optional, just used to fastq-dump sra files); + + +(C) Genome assembly k-mer. This workflow takes genome assemblies as input and the rest of the workflow largely overlaps with the raw reads k-mer workflow -```bash -cd SalmID -poetry build +# Installation +### Conda +To install the latest SeqSero2 Conda package (recommended): +``` +conda install -c bioconda seqsero2=1.1.1 ``` - -and install using `pip` - -```bash -pip install dist/salmid*.whl +### Git +To install the SeqSero2 git repository locally: ``` - -To execute: +git clone https://github.com/denglab/SeqSero2.git +cd SeqSero2 +python3 -m pip install --user . ``` -SalmID.py -e .fastq.gz -``` -This will perform a SalmID run on all fastq.gz files in the current directory. -``` -SalmID.py -i your_fastq_gz.fastq.gz -``` -This will perform a SalmID run on an individual file (i.e., your_fastq_gz.fastq.gz) -``` -SalmID.py -d directory_with_data -e _1.fastq.gz -``` -This will perform a SalmID run on all files in directory 'directory_with_data' with extension '_1.fastq.gz' +### Other options +Third party SeqSero2 installations (may not be the latest version of SeqSero2): \ +https://github.com/B-UMMI/docker-images/tree/master/seqsero2 \ +https://github.com/denglab/SeqSero2/issues/13 + + +# Executing the code +Make sure all SeqSero2 and its dependency executables are added to your path (e.g. to ~/.bashrc). Then type SeqSero2_package.py to get detailed instructions. + + Usage: SeqSero2_package.py + + -m (which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a) + + -t (input data type, '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore fasta, '6'for nanopore fastq) + + -i (/path/to/input/file) + + -p (number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1) -## Todo's and thoughts for future releases: -- Provide coverage estimates for genomes in sample based on kmer frequencies -- Write code to use SalmID on long read (minion, pacbio) platforms + -b (algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default "mem" mode) + + -d (output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number) + + -c (if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files) + + -n (optional, to specify a sample name in the report output) + + -s (if '-s' was flagged, SeqSero2 will not output header in SeqSero_result.tsv) + + --check (use '--check' flag to check the required dependencies) + + -v, --version (show program's version number and exit) + + +# Examples +Allele mode: + + # Allele workflow ("-m a", default), for separated paired-end raw reads ("-t 2"), use 10 threads in mapping and assembly ("-p 10") + SeqSero2_package.py -p 10 -t 2 -i R1.fastq.gz R2.fastq.gz + +K-mer mode: + + # Raw reads k-mer ("-m k"), for separated paired-end raw reads ("-t 2") + SeqSero2_package.py -m k -t 2 -i R1.fastq.gz R2.fastq.gz + + # Genome assembly k-mer ("-t 4", genome assemblies only predicted by the k-mer workflow, "-m k") + SeqSero2_package.py -m k -t 4 -i assembly.fasta + +# Output +Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode). + + +# Citation +Zhang S, Den-Bakker HC, Li S, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X. +SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data. +**Appl Environ Microbiology. 2019 Sep; 85(23):e01746-19.** [PMID: 31540993](https://aem.asm.org/content/early/2019/09/17/AEM.01746-19.long) + +Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X. +Salmonella serotype determination utilizing high-throughput genome sequencing data. +**J Clin Microbiol. 2015 May;53(5):1685-92.** [PMID: 25762776](http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15) diff -r 43f6b7f6ebb3 -r e6437d423693 SeqSero2.egg-info/PKG-INFO --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2.egg-info/PKG-INFO Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,132 @@ +Metadata-Version: 1.1 +Name: SeqSero2 +Version: 1.1.1 +Summary: Salmonella serotyping +Home-page: https://github.com/denglab/SeqSero2/ +Author: Shaokang Zhang, Hendrik C Den-Bakker and Xiangyu Deng +Author-email: zskzsk@uga.edu, Hendrik.DenBakker@uga.edu, xdeng@uga.edu +License: GPLv2 +Description: # SeqSero2 v1.1.1 + Salmonella serotype prediction from genome sequencing data. + + Online version: http://www.denglab.info/SeqSero2 + + # Introduction + SeqSero2 is a pipeline for Salmonella serotype prediction from raw sequencing reads or genome assemblies + + # Dependencies + SeqSero2 has three workflows: + + (A) Allele micro-assembly (default). This workflow takes raw reads as input and performs targeted assembly of serotype determinant alleles. Assembled alleles are used to predict serotype and flag potential inter-serotype contamination in sequencing data (i.e., presence of reads from multiple serotypes due to, for example, cross or carryover contamination during sequencing). + + Allele micro-assembly workflow depends on: + + 1. Python 3; + + 2. Biopython 1.73; + + 3. [Burrows-Wheeler Aligner v0.7.12](http://sourceforge.net/projects/bio-bwa/files/); + + 4. [Samtools v1.8](http://sourceforge.net/projects/samtools/files/samtools/); + + 5. [NCBI BLAST v2.2.28+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download); + + 6. [SRA Toolkit v2.8.0](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software); + + 7. [SPAdes v3.9.0](http://bioinf.spbau.ru/spades); + + 8. [Bedtools v2.17.0](http://bedtools.readthedocs.io/en/latest/); + + 9. [SalmID v0.11](https://github.com/hcdenbakker/SalmID). + + + (B) Raw reads k-mer. This workflow takes raw reads as input and performs rapid serotype prediction based on unique k-mers of serotype determinants. + + Raw reads k-mer workflow (originally SeqSeroK) depends on: + + 1. Python 3; + 2. [SRA Toolkit](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software) (optional, just used to fastq-dump sra files); + + + (C) Genome assembly k-mer. This workflow takes genome assemblies as input and the rest of the workflow largely overlaps with the raw reads k-mer workflow + + # Installation + ### Conda + To install the latest SeqSero2 Conda package (recommended): + ``` + conda install -c bioconda seqsero2=1.1.1 + ``` + ### Git + To install the SeqSero2 git repository locally: + ``` + git clone https://github.com/denglab/SeqSero2.git + cd SeqSero2 + python3 -m pip install --user . + ``` + ### Other options + Third party SeqSero2 installations (may not be the latest version of SeqSero2): \ + https://github.com/B-UMMI/docker-images/tree/master/seqsero2 \ + https://github.com/denglab/SeqSero2/issues/13 + + + # Executing the code + Make sure all SeqSero2 and its dependency executables are added to your path (e.g. to ~/.bashrc). Then type SeqSero2_package.py to get detailed instructions. + + Usage: SeqSero2_package.py + + -m (which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a) + + -t (input data type, '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore fasta, '6'for nanopore fastq) + + -i (/path/to/input/file) + + -p (number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1) + + -b (algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default "mem" mode) + + -d (output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number) + + -c (if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files) + + -n (optional, to specify a sample name in the report output) + + -s (if '-s' was flagged, SeqSero2 will not output header in SeqSero_result.tsv) + + --check (use '--check' flag to check the required dependencies) + + -v, --version (show program's version number and exit) + + + # Examples + Allele mode: + + # Allele workflow ("-m a", default), for separated paired-end raw reads ("-t 2"), use 10 threads in mapping and assembly ("-p 10") + SeqSero2_package.py -p 10 -t 2 -i R1.fastq.gz R2.fastq.gz + + K-mer mode: + + # Raw reads k-mer ("-m k"), for separated paired-end raw reads ("-t 2") + SeqSero2_package.py -m k -t 2 -i R1.fastq.gz R2.fastq.gz + + # Genome assembly k-mer ("-t 4", genome assemblies only predicted by the k-mer workflow, "-m k") + SeqSero2_package.py -m k -t 4 -i assembly.fasta + + # Output + Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode). + + + # Citation + Zhang S, Den-Bakker HC, Li S, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X. + SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data. + **Appl Environ Microbiology. 2019 Sep; 85(23):e01746-19.** [PMID: 31540993](https://aem.asm.org/content/early/2019/09/17/AEM.01746-19.long) + + Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X. + Salmonella serotype determination utilizing high-throughput genome sequencing data. + **J Clin Microbiol. 2015 May;53(5):1685-92.** [PMID: 25762776](http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15) + +Keywords: Salmonella serotyping bioinformatics WGS +Platform: UNKNOWN +Classifier: Development Status :: 3 - Alpha +Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2) +Classifier: Programming Language :: Python :: 3 +Classifier: Topic :: Text Processing :: Linguistic diff -r 43f6b7f6ebb3 -r e6437d423693 SeqSero2.egg-info/SOURCES.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2.egg-info/SOURCES.txt Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,19 @@ +LICENSE +MANIFEST.in +README.md +setup.py +version.py +SeqSero2.egg-info/PKG-INFO +SeqSero2.egg-info/SOURCES.txt +SeqSero2.egg-info/dependency_links.txt +SeqSero2.egg-info/not-zip-safe +SeqSero2.egg-info/requires.txt +SeqSero2.egg-info/top_level.txt +bin/Initial_Conditions.py +bin/SeqSero2_package.py +bin/SeqSero2_update_kmer_database.py +bin/deinterleave_fastq.sh +seqsero2_db/H_and_O_and_specific_genes.fasta +seqsero2_db/antigens.pickle +seqsero2_db/invA_mers_dict +seqsero2_db/special.pickle \ No newline at end of file diff -r 43f6b7f6ebb3 -r e6437d423693 SeqSero2.egg-info/dependency_links.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2.egg-info/dependency_links.txt Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,1 @@ + diff -r 43f6b7f6ebb3 -r e6437d423693 SeqSero2.egg-info/not-zip-safe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2.egg-info/not-zip-safe Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,1 @@ + diff -r 43f6b7f6ebb3 -r e6437d423693 SeqSero2.egg-info/requires.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2.egg-info/requires.txt Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,1 @@ +biopython==1.73 diff -r 43f6b7f6ebb3 -r e6437d423693 SeqSero2.egg-info/top_level.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2.egg-info/top_level.txt Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,1 @@ + diff -r 43f6b7f6ebb3 -r e6437d423693 SeqSero2_package.py --- a/SeqSero2_package.py Thu Apr 30 21:47:42 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1473 +0,0 @@ -#!/usr/bin/env python3 - -import sys -import time -import random -import os -import subprocess -import gzip -import io -import pickle -import argparse -import itertools -import math -from distutils.version import LooseVersion -from distutils.spawn import find_executable - -try: - from .version import SeqSero2_version -except Exception: #ImportError - from version import SeqSero2_version - -### SeqSero Kmer -def parse_args(): - "Parse the input arguments, use '-h' for help." - parser = argparse.ArgumentParser(usage='SeqSero2_package.py -t -m -i [-d ] [-p ] [-b ]\n\nDevelopper: Shaokang Zhang (zskzsk@uga.edu), Hendrik C Den-Bakker (Hendrik.DenBakker@uga.edu) and Xiangyu Deng (xdeng@uga.edu)\n\nContact email:seqsero@gmail.com\n\nVersion: v1.0.2')#add "-m " in future - parser.add_argument("-i",nargs="+",help=": path/to/input_data",type=os.path.abspath) ### ed_SL_05282019: add 'type=os.path.abspath' to generate absolute path of input data. - parser.add_argument("-t",choices=['1','2','3','4','5','6'],help=": '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore fasta, '6' for nanopore fastq") - parser.add_argument("-b",choices=['sam','mem'],default="mem",help=": algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default 'mem' mode") - parser.add_argument("-p",default="1",help=": number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1") - parser.add_argument("-m",choices=['k','a'],default="a",help=": which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a") - parser.add_argument("-d",help=": output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number") - parser.add_argument("-c",action="store_true",help=": if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files") - parser.add_argument("--check",action="store_true",help=": use '--check' flag to check the required dependencies") - parser.add_argument('-v', '--version', action='version', version='%(prog)s ' + SeqSero2_version) - return parser.parse_args() - -### ed_SL_05282019: check paths of dependencies -check_dependencies = parse_args().check -dependencies = ['bwa','samtools','blastn','fastq-dump','spades.py','bedtools','SalmID.py'] -if check_dependencies: - for item in dependencies: - ext_path = find_executable(item) - if ext_path is not None: - print ("Using "+item+" - "+ext_path) - else: - print ("ERROR: can not find "+item+" in PATH") - sys.exit() -### end of --check - -def reverse_complement(sequence): - complement = { - 'A': 'T', - 'C': 'G', - 'G': 'C', - 'T': 'A', - 'N': 'N', - 'M': 'K', - 'R': 'Y', - 'W': 'W', - 'S': 'S', - 'Y': 'R', - 'K': 'M', - 'V': 'B', - 'H': 'D', - 'D': 'H', - 'B': 'V' - } - return "".join(complement[base] for base in reversed(sequence)) - - -def createKmerDict_reads(list_of_strings, kmer): - kmer_table = {} - for string in list_of_strings: - sequence = string.strip('\n') - for i in range(len(sequence) - kmer + 1): - new_mer = sequence[i:i + kmer].upper() - new_mer_rc = reverse_complement(new_mer) - if new_mer in kmer_table: - kmer_table[new_mer.upper()] += 1 - else: - kmer_table[new_mer.upper()] = 1 - if new_mer_rc in kmer_table: - kmer_table[new_mer_rc.upper()] += 1 - else: - kmer_table[new_mer_rc.upper()] = 1 - return kmer_table - - -def multifasta_dict(multifasta): - multifasta_list = [ - line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0 - ] - headers = [i for i in multifasta_list if i[0] == '>'] - multifasta_dict = {} - for h in headers: - start = multifasta_list.index(h) - for element in multifasta_list[start + 1:]: - if element[0] == '>': - break - else: - if h[1:] in multifasta_dict: - multifasta_dict[h[1:]] += element - else: - multifasta_dict[h[1:]] = element - return multifasta_dict - - -def multifasta_single_string(multifasta): - multifasta_list = [ - line.strip() for line in open(multifasta, 'r') - if (len(line.strip()) > 0) and (line.strip()[0] != '>') - ] - return ''.join(multifasta_list) - - -def chunk_a_long_sequence(long_sequence, chunk_size=60): - chunk_list = [] - steps = len(long_sequence) // 60 #how many chunks - for i in range(steps): - chunk_list.append(long_sequence[i * chunk_size:(i + 1) * chunk_size]) - chunk_list.append(long_sequence[steps * chunk_size:len(long_sequence)]) - return chunk_list - - -def target_multifasta_kmerizer(multifasta, k, kmerDict): - forward_length = 300 #if find the target, put forward 300 bases - reverse_length = 2200 #if find the target, put backward 2200 bases - chunk_size = 60 #it will firstly chunk the single long sequence to multiple smaller sequences, it controls the size of those smaller sequences - target_mers = [] - long_single_string = multifasta_single_string(multifasta) - multifasta_list = chunk_a_long_sequence(long_single_string, chunk_size) - unit_length = len(multifasta_list[0]) - forward_lines = int(forward_length / unit_length) + 1 - reverse_lines = int(forward_length / unit_length) + 1 - start_num = 0 - end_num = 0 - for i in range(len(multifasta_list)): - if i not in range(start_num, end_num): #avoid computational repetition - line = multifasta_list[i] - start = int((len(line) - k) // 2) - s1 = line[start:k + start] - if s1 in kmerDict: #detect it is a potential read or not (use the middle part) - if i - forward_lines >= 0: - start_num = i - forward_lines - else: - start_num = 0 - if i + reverse_lines <= len(multifasta_list) - 1: - end_num = i + reverse_lines - else: - end_num = len(multifasta_list) - 1 - target_list = [ - x.strip() for x in multifasta_list[start_num:end_num] - ] - target_line = "".join(target_list) - target_mers += [ - k1 for k1 in createKmerDict_reads([str(target_line)], k) - ] ##changed k to k1, just want to avoid the mixes of this "k" (kmer) to the "k" above (kmer length) - else: - pass - return set(target_mers) - - -def target_read_kmerizer(file, k, kmerDict): - i = 1 - n_reads = 0 - total_coverage = 0 - target_mers = [] - if file.endswith(".gz"): - file_content = io.BufferedReader(gzip.open(file)) - else: - file_content = open(file, "r").readlines() - for line in file_content: - start = int((len(line) - k) // 2) - if i % 4 == 2: - if file.endswith(".gz"): - s1 = line[start:k + start].decode() - line = line.decode() - else: - s1 = line[start:k + start] - if s1 in kmerDict: #detect it is a potential read or not (use the middle part) - n_reads += 1 - total_coverage += len(line) - target_mers += [ - k1 for k1 in createKmerDict_reads([str(line)], k) - ] #changed k to k1, just want to avoid the mixes of this "k" (kmer) to the "k" above (kmer length) - i += 1 - if total_coverage >= 4000000: - break - return set(target_mers) - - -def minion_fasta_kmerizer(file, k, kmerDict): - i = 1 - n_reads = 0 - total_coverage = 0 - target_mers = {} - for line in open(file): - if i % 2 == 0: - for kmer, rc_kmer in kmers(line.strip().upper(), k): - if (kmer in kmerDict) or (rc_kmer in kmerDict): - if kmer in target_mers: - target_mers[kmer] += 1 - else: - target_mers[kmer] = 1 - if rc_kmer in target_mers: - target_mers[rc_kmer] += 1 - else: - target_mers[rc_kmer] = 1 - i += 1 - return set([h for h in target_mers]) - - -def minion_fastq_kmerizer(file, k, kmerDict): - i = 1 - n_reads = 0 - total_coverage = 0 - target_mers = {} - for line in open(file): - if i % 4 == 2: - for kmer, rc_kmer in kmers(line.strip().upper(), k): - if (kmer in kmerDict) or (rc_kmer in kmerDict): - if kmer in target_mers: - target_mers[kmer] += 1 - else: - target_mers[kmer] = 1 - if rc_kmer in target_mers: - target_mers[rc_kmer] += 1 - else: - target_mers[rc_kmer] = 1 - i += 1 - return set([h for h in target_mers]) - - -def multifasta_single_string2(multifasta): - single_string = '' - with open(multifasta, 'r') as f: - for line in f: - if line.strip()[0] == '>': - pass - else: - single_string += line.strip() - return single_string - - -def kmers(seq, k): - rev_comp = reverse_complement(seq) - for start in range(1, len(seq) - k + 1): - yield seq[start:start + k], rev_comp[-(start + k):-start] - - -def multifasta_to_kmers_dict(multifasta,k_size):#used to create database kmer set - multi_seq_dict = multifasta_dict(multifasta) - lib_dict = {} - for h in multi_seq_dict: - lib_dict[h] = set( - [k for k in createKmerDict_reads([multi_seq_dict[h]], k_size)]) - return lib_dict - - -def Combine(b, c): - fliC_combinations = [] - fliC_combinations.append(",".join(c)) - temp_combinations = [] - for i in range(len(b)): - for x in itertools.combinations(b, i + 1): - temp_combinations.append(",".join(x)) - for x in temp_combinations: - temp = [] - for y in c: - temp.append(y) - temp.append(x) - temp = ",".join(temp) - temp = temp.split(",") - temp.sort() - temp = ",".join(temp) - fliC_combinations.append(temp) - return fliC_combinations - - -def seqsero_from_formula_to_serotypes(Otype, fliC, fljB, special_gene_list,subspecies): - #like test_output_06012017.txt - #can add more varialbles like sdf-type, sub-species-type in future (we can conclude it into a special-gene-list) - from Initial_Conditions import phase1,phase2,phaseO,sero,subs,remove_list,rename_dict - rename_dict_not_anymore=[rename_dict[x] for x in rename_dict] - rename_dict_all=rename_dict_not_anymore+list(rename_dict) #used for decide whether to - seronames = [] - seronames_none_subspecies=[] - for i in range(len(phase1)): - fliC_combine = [] - fljB_combine = [] - if phaseO[i] == Otype: # no VII in KW, but it's there - ### for fliC, detect every possible combinations to avoid the effect of "[" - if phase1[i].count("[") == 0: - fliC_combine.append(phase1[i]) - elif phase1[i].count("[") >= 1: - c = [] - b = [] - if phase1[i][0] == "[" and phase1[i][-1] == "]" and phase1[i].count( - "[") == 1: - content = phase1[i].replace("[", "").replace("]", "") - fliC_combine.append(content) - fliC_combine.append("-") - else: - for x in phase1[i].split(","): - if "[" in x: - b.append(x.replace("[", "").replace("]", "")) - else: - c.append(x) - fliC_combine = Combine( - b, c - ) #Combine will offer every possible combinations of the formula, like f,[g],t: f,t f,g,t - ### end of fliC "[" detect - ### for fljB, detect every possible combinations to avoid the effect of "[" - if phase2[i].count("[") == 0: - fljB_combine.append(phase2[i]) - elif phase2[i].count("[") >= 1: - d = [] - e = [] - if phase2[i][0] == "[" and phase2[i][-1] == "]" and phase2[i].count( - "[") == 1: - content = phase2[i].replace("[", "").replace("]", "") - fljB_combine.append(content) - fljB_combine.append("-") - else: - for x in phase2[i].split(","): - if "[" in x: - d.append(x.replace("[", "").replace("]", "")) - else: - e.append(x) - fljB_combine = Combine(d, e) - ### end of fljB "[" detect - new_fliC = fliC.split( - "," - ) #because some antigen like r,[i] not follow alphabetical order, so use this one to judge and can avoid missings - new_fliC.sort() - new_fliC = ",".join(new_fliC) - new_fljB = fljB.split(",") - new_fljB.sort() - new_fljB = ",".join(new_fljB) - if (new_fliC in fliC_combine - or fliC in fliC_combine) and (new_fljB in fljB_combine - or fljB in fljB_combine): - ######start, remove_list,rename_dict, added on 11/11/2018 - if sero[i] not in remove_list: - temp_sero=sero[i] - if temp_sero in rename_dict: - temp_sero=rename_dict[temp_sero] #rename if in the rename list - if temp_sero not in seronames:#the new sero may already included, if yes, then not consider - if subs[i] == subspecies: - seronames.append(temp_sero) - seronames_none_subspecies.append(temp_sero) - else: - pass - else: - pass - ######end, added on 11/11/2018 - #analyze seronames - subspecies_pointer="" - if len(seronames) == 0 and len(seronames_none_subspecies)!=0: - seronames=seronames_none_subspecies - subspecies_pointer="1" - if len(seronames) == 0: - seronames = [ - "N/A (The predicted antigenic profile does not exist in the White-Kauffmann-Le Minor scheme)" - ] - star = "" - star_line = "" - if len(seronames) > 1: #there are two possible predictions for serotypes - star = "*" - #changed 04072019 - #star_line = "The predicted serotypes share the same general formula:\t" + Otype + ":" + fliC + ":" + fljB + "\n" - if subspecies_pointer=="1" and len(seronames_none_subspecies)!=0: - star="*" - star_line=" The predicted O and H antigens correspond to serotype '"+(" or ").join(seronames)+"' in the Kauffmann-White scheme. The predicted subspecies by SalmID (github.com/hcdenbakker/SalmID) may not be consistent with subspecies designation in the Kauffmann-White scheme." + star_line - #star_line="The formula with this subspieces prediction can't get a serotype in KW manual, and the serotyping prediction was made without considering it."+star_line - if Otype=="": - Otype="-" - predict_form = Otype + ":" + fliC + ":" + fljB - predict_sero = (" or ").join(seronames) - ###special test for Enteritidis - if predict_form == "9:g,m:-": - sdf = "-" - for x in special_gene_list: - if x.startswith("sdf"): - sdf = "+" - #star_line="Detected sdf gene, a marker to differentiate Gallinarum and Enteritidis" - star_line=" sdf gene detected." # ed_SL_04152019: new output format - #predict_form = predict_form + " Sdf prediction:" + sdf - predict_form = predict_form #changed 04072019 - if sdf == "-": - star = "*" - #star_line="Didn't detected sdf gene, a marker to differentiate Gallinarum and Enteritidis" - star_line=" sdf gene not detected." # ed_SL_04152019: new output format - #changed in 04072019, for new output - #star_line = "Additional characterization is necessary to assign a serotype to this strain. Commonly circulating strains of serotype Enteritidis are sdf+, although sdf- strains of serotype Enteritidis are known to exist. Serotype Gallinarum is typically sdf- but should be quite rare. Sdf- strains of serotype Enteritidis and serotype Gallinarum can be differentiated by phenotypic profile or genetic criteria.\n" - #predict_sero = "Gallinarum/Enteritidis" #04132019, for new output requirement - predict_sero = "Gallinarum or Enteritidis" # ed_SL_04152019: new output format - ###end of special test for Enteritidis - elif predict_form == "4:i:-": - predict_sero = "I 4,[5],12:i:-" # ed_SL_09242019: change serotype name - elif predict_form == "4:r:-": - predict_sero = "4:r:-" - elif predict_form == "4:b:-": # ed_SL_09272019: change for new output format - predict_sero = "N/A (4:b:-)" - #elif predict_form == "8:e,h:1,2": #removed after official merge of newport and bardo - #predict_sero = "Newport" - #star = "*" - #star_line = "Serotype Bardo shares the same antigenic profile with Newport, but Bardo is exceedingly rare." - claim = " The serotype(s) is/are the only serotype(s) with the indicated antigenic profile currently recognized in the Kauffmann White Scheme. New serotypes can emerge and the possibility exists that this antigenic profile may emerge in a different subspecies. Identification of strains to the subspecies level should accompany serotype determination; the same antigenic profile in different subspecies is considered different serotypes.\n" - if "N/A" in predict_sero: - claim = "" - #special test for Typhimurium - if "Typhimurium" in predict_sero or predict_form == "4:i:-": - normal = 0 - mutation = 0 - for x in special_gene_list: - if "oafA-O-4_full" in x: - normal = float(special_gene_list[x]) - elif "oafA-O-4_5-" in x: - mutation = float(special_gene_list[x]) - if normal > mutation: - pass - elif normal < mutation: - #predict_sero = predict_sero.strip() + "(O5-)" - predict_sero = predict_sero.strip() #diable special sero for new output requirement, 04132019 - star = "*" - #star_line = "Detected the deletion of O5-." - star_line = " Detected a deletion that causes O5- variant of Typhimurium." # ed_SL_04152019: new output format - else: - pass - #special test for Paratyphi B - if "Paratyphi B" in predict_sero or predict_form == "4:b:-": - normal = 0 - mutation = 0 - for x in special_gene_list: - if "gntR-family-regulatory-protein_dt-positive" in x: - normal = float(special_gene_list[x]) - elif "gntR-family-regulatory-protein_dt-negative" in x: - mutation = float(special_gene_list[x]) - #print(normal,mutation) - if normal > mutation: - #predict_sero = predict_sero.strip() + "(dt+)" #diable special sero for new output requirement, 04132019 - predict_sero = predict_sero.strip()+' var. L(+) tartrate+' if "Paratyphi B" in predict_sero else predict_sero.strip() # ed_SL_04152019: new output format - star = "*" - #star_line = "Didn't detect the SNP for dt- which means this isolate is a Paratyphi B variant L(+) tartrate(+)." - star_line = " The SNP that causes d-Tartrate nonfermentating phenotype of Paratyphi B was not detected. " # ed_SL_04152019: new output format - elif normal < mutation: - #predict_sero = predict_sero.strip() + "(dt-)" #diable special sero for new output requirement, 04132019 - predict_sero = predict_sero.strip() - star = "*" - #star_line = "Detected the SNP for dt- which means this isolate is a systemic pathovar of Paratyphi B." - star_line = " Detected the SNP for d-Tartrate nonfermenting phenotype of Paratyphi B." # ed_SL_04152019: new output format - else: - star = "*" - #star_line = " Failed to detect the SNP for dt-, can't decide it's a Paratyphi B variant L(+) tartrate(+) or not." - star_line = " " ## ed_SL_05152019: do not report this situation. - #special test for O13,22 and O13,23 - if Otype=="13": - #ex_dir = os.path.dirname(os.path.realpath(__file__)) - ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019 - f = open(ex_dir + '/special.pickle', 'rb') - special = pickle.load(f) - O22_O23=special['O22_O23'] - if predict_sero.split(" or ")[0] in O22_O23[-1] and predict_sero.split(" or ")[0] not in rename_dict_all:#if in rename_dict_all, then it means already merged, no need to analyze - O22_score=0 - O23_score=0 - for x in special_gene_list: - if "O:22" in x: - O22_score = O22_score+float(special_gene_list[x]) - elif "O:23" in x: - O23_score = O23_score+float(special_gene_list[x]) - #print(O22_score,O23_score) - for z in O22_O23[0]: - if predict_sero.split(" or ")[0] in z: - if O22_score > O23_score: - star = "*" - #star_line = "Detected O22 specific genes to further differenciate '"+predict_sero+"'." #diabled for new output requirement, 04132019 - predict_sero = z[0] - elif O22_score < O23_score: - star = "*" - #star_line = "Detected O23 specific genes to further differenciate '"+predict_sero+"'." #diabled for new output requirement, 04132019 - predict_sero = z[1] - else: - star = "*" - #star_line = "Fail to detect O22 and O23 differences." #diabled for new output requirement, 04132019 - if " or " in predict_sero: - star_line = star_line + " The predicted serotypes share the same general formula:\t" + Otype + ":" + fliC + ":" + fljB + "\n" - #special test for O6,8 - #merge_O68_list=["Blockley","Bovismorbificans","Hadar","Litchfield","Manhattan","Muenchen"] #remove 11/11/2018, because already in merge list - #for x in merge_O68_list: - # if x in predict_sero: - # predict_sero=x - # star="" - # star_line="" - #special test for Montevideo; most of them are monophasic - #if "Montevideo" in predict_sero and "1,2,7" in predict_form: #remove 11/11/2018, because already in merge list - #star="*" - #star_line="Montevideo is almost always monophasic, having an antigen called for the fljB position may be a result of Salmonella-Salmonella contamination." - return predict_form, predict_sero, star, star_line, claim -### End of SeqSero Kmer part - -### Begin of SeqSero2 allele prediction and output -def xml_parse_score_comparision_seqsero(xmlfile): - #used to do seqsero xml analysis - from Bio.Blast import NCBIXML - handle=open(xmlfile) - handle=NCBIXML.parse(handle) - handle=list(handle) - List=[] - List_score=[] - List_ids=[] - List_query_region=[] - for i in range(len(handle)): - if len(handle[i].alignments)>0: - for j in range(len(handle[i].alignments)): - score=0 - ids=0 - cover_region=set() #fixed problem that repeated calculation leading percentage > 1 - List.append(handle[i].query.strip()+"___"+handle[i].alignments[j].hit_def) - for z in range(len(handle[i].alignments[j].hsps)): - hsp=handle[i].alignments[j].hsps[z] - temp=set(range(hsp.query_start,hsp.query_end)) - est_bit=(handle[i].ka_params[0]*hsp.score-math.log(handle[i].ka_params[1]))/(math.log(2)) - if len(cover_region)==0: - cover_region=cover_region|temp - fraction=1 - else: - fraction=1-len(cover_region&temp)/float(len(temp)) - cover_region=cover_region|temp - if "last" in handle[i].query or "first" in handle[i].query: - #score+=hsp.bits*fraction - score+=est_bit*fraction - ids+=float(hsp.identities)/handle[i].query_length*fraction - else: - #score+=hsp.bits*fraction - score+=est_bit*fraction - ids+=float(hsp.identities)/handle[i].query_length*fraction - List_score.append(score) - List_ids.append(ids) - List_query_region.append(cover_region) - temp=zip(List,List_score,List_ids,List_query_region) - Final_list=sorted(temp, key=lambda d:d[1], reverse = True) - return Final_list - - -def Uniq(L,sort_on_fre="none"): #return the uniq list and the count number - Old=L - L.sort() - L = [L[i] for i in range(len(L)) if L[i] not in L[:i]] - count=[] - for j in range(len(L)): - y=0 - for x in Old: - if L[j]==x: - y+=1 - count.append(y) - if sort_on_fre!="none": - d=zip(*sorted(zip(count, L))) - L=d[1] - count=d[0] - return (L,count) - -def judge_fliC_or_fljB_from_head_tail_for_one_contig(nodes_vs_score_list): - #used to predict it's fliC or fljB for one contig, based on tail and head score, but output the score difference,if it is very small, then not reliable, use blast score for whole contig to test - #this is mainly used for - a=nodes_vs_score_list - fliC_score=0 - fljB_score=0 - for z in a: - if "fliC" in z[0]: - fliC_score+=z[1] - elif "fljB" in z[0]: - fljB_score+=z[1] - if fliC_score>=fljB_score: - role="fliC" - else: - role="fljB" - return (role,abs(fliC_score-fljB_score)) - -def judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(node_name,Final_list,Final_list_passed): - #used to predict contig is fliC or fljB, if the differnce score value on above head_and_tail is less than 10 (quite small) - #also used when no head or tail got blasted score for the contig - role="" - for z in Final_list_passed: - if node_name in z[0]: - role=z[0].split("_")[0] - break - return role - -def fliC_or_fljB_judge_from_head_tail_sequence(nodes_list,tail_head_list,Final_list,Final_list_passed): - #nodes_list is the c created by c,d=Uniq(nodes) in below function - first_target="" - role_list=[] - for x in nodes_list: - a=[] - role="" - for y in tail_head_list: - if x in y[0]: - a.append(y) - if len(a)==4: - role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) - if diff<20: - role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) - elif len(a)==3: - ###however, if the one with highest score is the fewer one, compare their accumulation score - role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) - if diff<20: - role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) - ###end of above score comparison - elif len(a)==2: - #must on same node, if not, then decide with unit blast score, blast-score/length_of_special_sequence(30 or 37) - temp=[] - for z in a: - temp.append(z[0].split("_")[0]) - m,n=Uniq(temp)#should only have one choice, but weird situation might occur too - if len(m)==1: - pass - else: - pass - role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) - if diff<20: - role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) - ###need to desgin a algorithm to guess most possible situation for nodes_list, See the situations of test evaluation - elif len(a)==1: - #that one - role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) - if diff<20: - role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) - #need to evaluate, in future, may set up a cut-off, if not met, then just find Final_list_passed best match,like when "a==0" - else:#a==0 - #use Final_list_passed best match - for z in Final_list_passed: - if x in z[0]: - role=z[0].split("_")[0] - break - #print x,role,len(a) - role_list.append((role,x)) - if len(role_list)==2: - if role_list[0][0]==role_list[1][0]:#this is the most cocmmon error, two antigen were assigned to same phase - #just use score to do a final test - role_list=[] - for x in nodes_list: - role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) - role_list.append((role,x)) - return role_list - -def decide_contig_roles_for_H_antigen(Final_list,Final_list_passed): - #used to decide which contig is FliC and which one is fljB - contigs=[] - nodes=[] - for x in Final_list_passed: - if x[0].startswith("fl") and "last" not in x[0] and "first" not in x[0]: - nodes.append(x[0].split("___")[1].strip()) - c,d=Uniq(nodes)#c is node_list - #print c - tail_head_list=[x for x in Final_list if ("last" in x[0] or "first" in x[0])] - roles=fliC_or_fljB_judge_from_head_tail_sequence(c,tail_head_list,Final_list,Final_list_passed) - return roles - -def decide_O_type_and_get_special_genes(Final_list,Final_list_passed): - #decide O based on Final_list - O_choice="?" - O_list=[] - special_genes={} - nodes=[] - for x in Final_list_passed: - if x[0].startswith("O-"): - nodes.append(x[0].split("___")[1].strip()) - elif not x[0].startswith("fl"): - special_genes[x[0]]=x[2]#08172018, x[2] changed from x[-1] - #print "special_genes:",special_genes - c,d=Uniq(nodes) - #print "potential O antigen contig",c - final_O=[] - O_nodes_list=[] - for x in c:#c is the list for contigs - temp=0 - for y in Final_list_passed: - if x in y[0] and y[0].startswith("O-"): - final_O.append(y) - break - ### O contig has the problem of two genes on same contig, so do additional test - potenial_new_gene="" - for x in final_O: - pointer=0 #for genes merged or not - #not consider O-1,3,19_not_in_3,10, too short compared with others - if "O-1,3,19_not_in_3,10" not in x[0] and int(x[0].split("__")[1].split("___")[0])*x[2]+850 <= int(x[0].split("length_")[1].split("_")[0]):#gene length << contig length; for now give 300*2 (for secureity can use 400*2) as flank region - pointer=x[0].split("___")[1].strip()#store the contig name - print(pointer) - if pointer!=0:#it has potential merge event - for y in Final_list: - if pointer in y[0] and y not in final_O and (y[1]>=int(y[0].split("__")[1].split("___")[0])*1.5 or (y[1]>=int(y[0].split("__")[1].split("___")[0])*y[2] and y[1]>=400)):#that's a realtively strict filter now; if passed, it has merge event and add one more to final_O - potenial_new_gene=y - #print(potenial_new_gene) - break - if potenial_new_gene!="": - print("two differnt genes in same contig, fix it for O antigen") - print(potenial_new_gene[:3]) - pointer=0 - for y in final_O: - if y[0].split("___")[-1]==potenial_new_gene[0].split("___")[-1]: - pointer=1 - if pointer!=0: #changed to consider two genes in same contig - final_O.append(potenial_new_gene) - ### end of the two genes on same contig test - final_O=sorted(final_O,key=lambda x: x[2], reverse=True)#sorted - if len(final_O)==0 or (len(final_O)==1 and "O-1,3,19_not_in_3,10" in final_O[0][0]): - #print "$$$No Otype, due to no hit"#may need to be changed - O_choice="-" - else: - highest_O_coverage=max([float(x[0].split("_cov_")[-1].split("_")[0]) for x in final_O if "O-1,3,19_not_in_3,10" not in x[0]]) - O_list=[] - O_list_less_contamination=[] - for x in final_O: - if not "O-1,3,19_not_in_3,10__130" in x[0]:#O-1,3,19_not_in_3,10 is too small, which may affect further analysis; to avoid contamination affect, use 0.15 of highest coverage as cut-off - O_list.append(x[0].split("__")[0]) - O_nodes_list.append(x[0].split("___")[1]) - if float(x[0].split("_cov_")[-1].split("_")[0])>highest_O_coverage*0.15: - O_list_less_contamination.append(x[0].split("__")[0]) - ### special test for O9,46 and O3,10 family - if ("O-9,46_wbaV" in O_list or "O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254" in O_list) and O_list_less_contamination[0].startswith("O-9,"):#not sure should use and float(O9_wbaV)/float(num_1) > 0.1 - if "O-9,46_wzy" in O_list:#and float(O946_wzy)/float(num_1) > 0.1 - O_choice="O-9,46" - #print "$$$Most possilble Otype: O-9,46" - elif "O-9,46,27_partial_wzy" in O_list:#and float(O94627)/float(num_1) > 0.1 - O_choice="O-9,46,27" - #print "$$$Most possilble Otype: O-9,46,27" - else: - O_choice="O-9"#next, detect O9 vs O2? - O2=0 - O9=0 - for z in special_genes: - if "tyr-O-9" in z: - O9=special_genes[z] - elif "tyr-O-2" in z: - O2=special_genes[z] - if O2>O9: - O_choice="O-2" - elif O2 0.1 and float(O946_wzy)/float(num_1) > 0.1 - if "O-3,10_not_in_1,3,19" in O_list:#and float(O310_no_1319)/float(num_1) > 0.1 - O_choice="O-3,10" - #print "$$$Most possilble Otype: O-3,10 (contain O-3,10_not_in_1,3,19)" - else: - O_choice="O-1,3,19" - #print "$$$Most possilble Otype: O-1,3,19 (not contain O-3,10_not_in_1,3,19)" - ### end of special test for O9,46 and O3,10 family - else: - try: - max_score=0 - for x in final_O: - if x[2]>=max_score and float(x[0].split("_cov_")[-1].split("_")[0])>highest_O_coverage*0.15:#use x[2],08172018, the "coverage identity = cover_length * identity"; also meet coverage threshold - max_score=x[2]#change from x[-1] to x[2],08172018 - O_choice=x[0].split("_")[0] - if O_choice=="O-1,3,19": - O_choice=final_O[1][0].split("_")[0] - #print "$$$Most possilble Otype: ",O_choice - except: - pass - #print "$$$No suitable Otype, or failure of mapping (please check the quality of raw reads)" - #print "O:",O_choice,O_nodes_list - Otypes=[] - for x in O_list: - if x!="O-1,3,19_not_in_3,10": - if "O-9,46_" not in x: - Otypes.append(x.split("_")[0]) - else: - Otypes.append(x.split("-from")[0])#O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254 - #Otypes=[x.split("_")[0] for x in O_list if x!="O-1,3,19_not_in_3,10"] - Otypes_uniq,Otypes_fre=Uniq(Otypes) - contamination_O="" - if O_choice=="O-9,46,27" or O_choice=="O-3,10" or O_choice=="O-1,3,19": - if len(Otypes_uniq)>2: - contamination_O="potential contamination from O antigen signals" - else: - if len(Otypes_uniq)>1: - if O_choice=="O-4" and len(Otypes_uniq)==2 and "O-9,46,27" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund - contamination_O="" - elif O_choice=="O-9,46" and len(Otypes_uniq)==2 and "O-9,46_wbaV" in Otypes_uniq and "O-9,46_wzy" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund - contamination_O="" - else: - contamination_O="potential contamination from O antigen signals" - return O_choice,O_nodes_list,special_genes,final_O,contamination_O,Otypes_uniq -### End of SeqSero2 allele prediction and output - -def get_input_files(make_dir,input_file,data_type,dirpath): - #tell input files from datatype - #": '1'(pair-end reads, interleaved),'2'(pair-end reads, seperated),'3'(single-end reads), '4'(assembly),'5'(nanopore fasta),'6'(nanopore fastq)" - for_fq="" - rev_fq="" - os.chdir(make_dir) - if data_type=="1": - input_file=input_file[0].split("/")[-1] - if input_file.endswith(".sra"): - subprocess.check_call("fastq-dump --split-files "+input_file,shell=True) - for_fq=input_file.replace(".sra","_1.fastq") - rev_fq=input_file.replace(".sra","_2.fastq") - else: - core_id=input_file.split(".fastq")[0].split(".fq")[0] - for_fq=core_id+"_1.fastq" - rev_fq=core_id+"_2.fastq" - if input_file.endswith(".gz"): - subprocess.check_call("gzip -dc "+input_file+" | "+dirpath+"/deinterleave_fastq.sh "+for_fq+" "+rev_fq,shell=True) - else: - subprocess.check_call("cat "+input_file+" | "+dirpath+"/deinterleave_fastq.sh "+for_fq+" "+rev_fq,shell=True) - elif data_type=="2": - for_fq=input_file[0].split("/")[-1] - rev_fq=input_file[1].split("/")[-1] - elif data_type=="3": - input_file=input_file[0].split("/")[-1] - if input_file.endswith(".sra"): - subprocess.check_call("fastq-dump --split-files "+input_file,shell=True) - for_fq=input_file.replace(".sra","_1.fastq") - else: - for_fq=input_file - elif data_type in ["4","5","6"]: - for_fq=input_file[0].split("/")[-1] - os.chdir("..") - return for_fq,rev_fq - -def predict_O_and_H_types(Final_list,Final_list_passed,new_fasta): - #get O and H types from Final_list from blast parsing; allele mode - from Bio import SeqIO - fliC_choice="-" - fljB_choice="-" - fliC_contig="NA" - fljB_contig="NA" - fliC_region=set([0]) - fljB_region=set([0,]) - fliC_length=0 #can be changed to coverage in future; in 03292019, changed to ailgned length - fljB_length=0 #can be changed to coverage in future; in 03292019, changed to ailgned length - O_choice="-"#no need to decide O contig for now, should be only one - O_choice,O_nodes,special_gene_list,O_nodes_roles,contamination_O,Otypes_uniq=decide_O_type_and_get_special_genes(Final_list,Final_list_passed)#decide the O antigen type and also return special-gene-list for further identification - O_choice=O_choice.split("-")[-1].strip() - if (O_choice=="1,3,19" and len(O_nodes_roles)==1 and "1,3,19" in O_nodes_roles[0][0]) or O_choice=="": - O_choice="-" - H_contig_roles=decide_contig_roles_for_H_antigen(Final_list,Final_list_passed)#decide the H antigen contig is fliC or fljB - #add alignment locations, used for further selection, 03312019 - for i in range(len(H_contig_roles)): - x=H_contig_roles[i] - for y in Final_list_passed: - if x[1] in y[0] and y[0].startswith(x[0]): - H_contig_roles[i]+=H_contig_roles[i]+(y[-1],) - break - log_file=open("SeqSero_log.txt","a") - extract_file=open("Extracted_antigen_alleles.fasta","a") - handle_fasta=list(SeqIO.parse(new_fasta,"fasta")) - - #print("O_contigs:") - log_file.write("O_contigs:\n") - extract_file.write("#Sequences with antigen signals (if the micro-assembled contig only covers the flanking region, it will not be used for contamination analysis)\n") - extract_file.write("#O_contigs:\n") - for x in O_nodes_roles: - if "O-1,3,19_not_in_3,10" not in x[0]:#O-1,3,19_not_in_3,10 is just a small size marker - #print(x[0].split("___")[-1],x[0].split("__")[0],"blast score:",x[1],"identity%:",str(round(x[2]*100,2))+"%",str(min(x[-1]))+" to "+str(max(x[-1]))) - log_file.write(x[0].split("___")[-1]+" "+x[0].split("__")[0]+"; "+"blast score: "+str(x[1])+" identity%: "+str(round(x[2]*100,2))+"%; alignment from "+str(min(x[-1]))+" to "+str(max(x[-1]))+" of antigen\n") - title=">"+x[0].split("___")[-1]+" "+x[0].split("__")[0]+"; "+"blast score: "+str(x[1])+" identity%: "+str(round(x[2]*100,2))+"%; alignment from "+str(min(x[-1]))+" to "+str(max(x[-1]))+" of antigen\n" - seqs="" - for z in handle_fasta: - if x[0].split("___")[-1]==z.description: - seqs=str(z.seq) - extract_file.write(title+seqs+"\n") - if len(H_contig_roles)!=0: - highest_H_coverage=max([float(x[1].split("_cov_")[-1].split("_")[0]) for x in H_contig_roles]) #less than highest*0.1 would be regarded as contamination and noises, they will still be considered in contamination detection and logs, but not used as final serotype output - else: - highest_H_coverage=0 - for x in H_contig_roles: - #if multiple choices, temporately select the one with longest length for now, will revise in further change - if "fliC" == x[0] and len(x[-1])>=fliC_length and x[1] not in O_nodes and float(x[1].split("_cov_")[-1].split("_")[0])>highest_H_coverage*0.13:#remember to avoid the effect of O-type contig, so should not in O_node list - fliC_contig=x[1] - fliC_length=len(x[-1]) - elif "fljB" == x[0] and len(x[-1])>=fljB_length and x[1] not in O_nodes and float(x[1].split("_cov_")[-1].split("_")[0])>highest_H_coverage*0.13: - fljB_contig=x[1] - fljB_length=len(x[-1]) - for x in Final_list_passed: - if fliC_choice=="-" and "fliC_" in x[0] and fliC_contig in x[0]: - fliC_choice=x[0].split("_")[1] - elif fljB_choice=="-" and "fljB_" in x[0] and fljB_contig in x[0]: - fljB_choice=x[0].split("_")[1] - elif fliC_choice!="-" and fljB_choice!="-": - break - #now remove contigs not in middle core part - first_allele="NA" - first_allele_percentage=0 - for x in Final_list: - if x[0].startswith("fliC") or x[0].startswith("fljB"): - first_allele=x[0].split("__")[0] #used to filter those un-middle contigs - first_allele_percentage=x[2] - break - additional_contigs=[] - for x in Final_list: - if first_allele in x[0]: - if (fliC_contig == x[0].split("___")[-1]): - fliC_region=x[3] - elif fljB_contig!="NA" and (fljB_contig == x[0].split("___")[-1]): - fljB_region=x[3] - else: - if x[1]*1.1>int(x[0].split("___")[1].split("_")[3]):#loose threshold by multiplying 1.1 - additional_contigs.append(x) - #else: - #print x[:3] - #we can just use the fljB region (or fliC depends on size), no matter set() or contain a large locations (without middle part); however, if none of them is fully assembled, use 500 and 1200 as conservative cut-off - if first_allele_percentage>0.9: - if len(fliC_region)>len(fljB_region) and (max(fljB_region)-min(fljB_region))>1000: - target_region=fljB_region|(fliC_region-set(range(min(fljB_region),max(fljB_region)))) #fljB_region|(fliC_region-set(range(min(fljB_region),max(fljB_region)))) - elif len(fliC_region)1000: - target_region=fliC_region|(fljB_region-set(range(min(fliC_region),max(fliC_region)))) #fljB_region|(fliC_region-set(range(min(fljB_region),max(fljB_region)))) - else: - target_region=set()#doesn't do anything - else: - target_region=set()#doesn't do anything - #print(target_region) - #print(additional_contigs) - target_region2=set(list(range(0,525))+list(range(1200,1700)))#I found to use 500 to 1200 as special region would be best - target_region=target_region2|target_region - for x in additional_contigs: - removal=0 - contig_length=int(x[0].split("___")[1].split("length_")[-1].split("_")[0]) - if fljB_contig not in x[0] and fliC_contig not in x[0] and len(target_region&x[3])/float(len(x[3]))>0.65 and contig_length*0.5 0.9 and float(x[0].split("__")[1].split("___")[0])*x[2]/len(x[-1])>0.96:#if high similiarity with middle part of first allele (first allele >0.9, already cover middle part) - removal=1 - else: - pass - if removal==1: - for y in H_contig_roles: - if y[1] in x[0]: - H_contig_roles.remove(y) - else: - pass - #print(x[:3],contig_length,len(target_region&x[3])/float(len(x[3])),contig_length*0.5,len(x[3]),contig_length*1.5) - #end of removing none-middle contigs - #print("H_contigs:") - log_file.write("H_contigs:\n") - extract_file.write("#H_contigs:\n") - H_contig_stat=[] - H1_cont_stat={} - H2_cont_stat={} - for i in range(len(H_contig_roles)): - x=H_contig_roles[i] - a=0 - for y in Final_list_passed: - if x[1] in y[0] and y[0].startswith(x[0]): - if "first" in y[0] or "last" in y[0]: #this is the final filter to decide it's fliC or fljB, if can't pass, then can't decide - for y in Final_list_passed: #it's impossible to has the "first" and "last" allele as prediction, so re-do it - if x[1] in y[0]:#it's very possible to be third phase allele, so no need to make it must be fliC or fljB - #print(x[1],"can't_decide_fliC_or_fljB",y[0].split("_")[1],"blast_score:",y[1],"identity%:",str(round(y[2]*100,2))+"%",str(min(y[-1]))+" to "+str(max(y[-1]))) - log_file.write(x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antigen\n") - H_contig_roles[i]="can't decide fliC or fljB, may be third phase" - title=">"+x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antiten\n" - seqs="" - for z in handle_fasta: - if x[1]==z.description: - seqs=str(z.seq) - extract_file.write(title+seqs+"\n") - break - else: - #print(x[1],x[0],y[0].split("_")[1],"blast_score:",y[1],"identity%:",str(round(y[2]*100,2))+"%",str(min(y[-1]))+" to "+str(max(y[-1]))) - log_file.write(x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antigen\n") - title=">"+x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antigen\n" - seqs="" - for z in handle_fasta: - if x[1]==z.description: - seqs=str(z.seq) - extract_file.write(title+seqs+"\n") - if x[0]=="fliC": - if y[0].split("_")[1] not in H1_cont_stat: - H1_cont_stat[y[0].split("_")[1]]=y[2] - else: - H1_cont_stat[y[0].split("_")[1]]+=y[2] - if x[0]=="fljB": - if y[0].split("_")[1] not in H2_cont_stat: - H2_cont_stat[y[0].split("_")[1]]=y[2] - else: - H2_cont_stat[y[0].split("_")[1]]+=y[2] - break - #detect contaminations - #print(H1_cont_stat) - #print(H2_cont_stat) - H1_cont_stat_list=[x for x in H1_cont_stat if H1_cont_stat[x]>0.2] - H2_cont_stat_list=[x for x in H2_cont_stat if H2_cont_stat[x]>0.2] - contamination_H="" - if len(H1_cont_stat_list)>1 or len(H2_cont_stat_list)>1: - contamination_H="potential contamination from H antigen signals" - elif len(H2_cont_stat_list)==1 and fljB_contig=="NA": - contamination_H="potential contamination from H antigen signals, uncommon weak fljB signals detected" - #get additional antigens - """ - if ("O-9,46_wbaV" in O_list or "O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254" in O_list) and O_list_less_contamination[0].startswith("O-9,"):#not sure should use and float(O9_wbaV)/float(num_1) > 0.1 - if "O-9,46_wzy" in O_list:#and float(O946_wzy)/float(num_1) > 0.1 - O_choice="O-9,46" - #print "$$$Most possilble Otype: O-9,46" - elif "O-9,46,27_partial_wzy" in O_list:#and float(O94627)/float(num_1) > 0.1 - O_choice="O-9,46,27" - #print "$$$Most possilble Otype: O-9,46,27" - elif ("O-3,10_wzx" in O_list) and ("O-9,46_wzy" in O_list) and (O_list[0].startswith("O-3,10") or O_list_less_contamination[0].startswith("O-9,46_wzy")):#and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1 - if "O-3,10_not_in_1,3,19" in O_list:#and float(O310_no_1319)/float(num_1) > 0.1 - O_choice="O-3,10" - #print "$$$Most possilble Otype: O-3,10 (contain O-3,10_not_in_1,3,19)" - else: - O_choice="O-1,3,19" - #print "$$$Most possilble Otype: O-1,3,19 (not contain O-3,10_not_in_1,3,19)" - ### end of special test for O9,46 and O3,10 family - - if O_choice=="O-9,46,27" or O_choice=="O-3,10" or O_choice=="O-1,3,19": - if len(Otypes_uniq)>2: - contamination_O="potential contamination from O antigen signals" - else: - if len(Otypes_uniq)>1: - if O_choice=="O-4" and len(Otypes_uniq)==2 and "O-9,46,27" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund - contamination_O="" - elif O_choice=="O-9,46" and len(Otypes_uniq)==2 and "O-9,46_wbaV" in Otypes_uniq and "O-9,46_wzy" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund - contamination_O="" - """ - additonal_antigents=[] - #print(contamination_O) - #print(contamination_H) - log_file.write(contamination_O+"\n") - log_file.write(contamination_H+"\n") - log_file.close() - return O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H,Otypes_uniq,H1_cont_stat_list,H2_cont_stat_list - -def get_input_K(input_file,lib_dict,data_type,k_size): - #kmer mode; get input_Ks from dict and data_type - kmers = [] - for h in lib_dict: - kmers += lib_dict[h] - if data_type == '4': - input_Ks = target_multifasta_kmerizer(input_file, k_size, set(kmers)) - elif data_type == '1' or data_type == '2' or data_type == '3':#set it for now, will change later - input_Ks = target_read_kmerizer(input_file, k_size, set(kmers)) - elif data_type == '5':#minion_2d_fasta - input_Ks = minion_fasta_kmerizer(input_file, k_size, set(kmers)) - if data_type == '6':#minion_2d_fastq - input_Ks = minion_fastq_kmerizer(input_file, k_size, set(kmers)) - return input_Ks - -def get_kmer_dict(lib_dict,input_Ks): - #kmer mode; get predicted types - O_dict = {} - H_dict = {} - Special_dict = {} - for h in lib_dict: - score = (len(lib_dict[h] & input_Ks) / len(lib_dict[h])) * 100 - if score > 1: # Arbitrary cut-off for similarity score very low but seems necessary to detect O-3,10 in some cases - if h.startswith('O-') and score > 25: - O_dict[h] = score - if h.startswith('fl') and score > 40: - H_dict[h] = score - if (h[:2] != 'fl') and (h[:2] != 'O-'): - Special_dict[h] = score - return O_dict,H_dict,Special_dict - -def call_O_and_H_type(O_dict,H_dict,Special_dict,make_dir): - log_file=open("SeqSero_log.txt","a") - log_file.write("O_scores:\n") - #call O: - highest_O = '-' - if len(O_dict) == 0: - pass - else: - for x in O_dict: - log_file.write(x+"\t"+str(O_dict[x])+"\n") - if ('O-9,46_wbaV__1002' in O_dict and O_dict['O-9,46_wbaV__1002']>70) or ("O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002" in O_dict and O_dict['O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002']>70): # not sure should use and float(O9_wbaV)/float(num_1) > 0.1 - if 'O-9,46_wzy__1191' in O_dict: # and float(O946_wzy)/float(num_1) > 0.1 - highest_O = "O-9,46" - elif "O-9,46,27_partial_wzy__1019" in O_dict: # and float(O94627)/float(num_1) > 0.1 - highest_O = "O-9,46,27" - else: - highest_O = "O-9" # next, detect O9 vs O2? - O2 = 0 - O9 = 0 - for z in Special_dict: - if "tyr-O-9" in z: - O9 = float(Special_dict[z]) - if "tyr-O-2" in z: - O2 = float(Special_dict[z]) - if O2 > O9: - highest_O = "O-2" - elif ("O-3,10_wzx__1539" in O_dict) and ( - "O-9,46_wzy__1191" in O_dict - ): # and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1 - if "O-3,10_not_in_1,3,19__1519" in O_dict: # and float(O310_no_1319)/float(num_1) > 0.1 - highest_O = "O-3,10" - else: - highest_O = "O-1,3,19" - ### end of special test for O9,46 and O3,10 family - else: - try: - max_score = 0 - for x in O_dict: - if float(O_dict[x]) >= max_score: - max_score = float(O_dict[x]) - highest_O = x.split("_")[0] - if highest_O == "O-1,3,19": - highest_O = '-' - max_score = 0 - for x in O_dict: - if x == 'O-1,3,19_not_in_3,10__130': - pass - else: - if float(O_dict[x]) >= max_score: - max_score = float(O_dict[x]) - highest_O = x.split("_")[0] - except: - pass - #call_fliC: - if len(H_dict)!=0: - highest_H_score_both_BC=H_dict[max(H_dict.keys(), key=(lambda k: H_dict[k]))] #used to detect whether fljB existed or not - else: - highest_H_score_both_BC=0 - highest_fliC = '-' - highest_fliC_raw = '-' - highest_Score = 0 - log_file.write("\nH_scores:\n") - for s in H_dict: - log_file.write(s+"\t"+str(H_dict[s])+"\n") - if s.startswith('fliC'): - if float(H_dict[s]) > highest_Score: - highest_fliC = s.split('_')[1] - highest_fliC_raw = s - highest_Score = float(H_dict[s]) - #call_fljB - highest_fljB = '-' - highest_fljB_raw = '-' - highest_Score = 0 - for s in H_dict: - if s.startswith('fljB'): - if float(H_dict[s]) > highest_Score and float(H_dict[s]) > highest_H_score_both_BC * 0.65: #fljB is special, so use highest_H_score_both_BC to give a general estimate of coverage, currently 0.65 seems pretty good; the reason use a high (0.65) is some fliC and fljB shared with each other - highest_fljB = s.split('_')[1] - highest_fljB_raw = s - highest_Score = float(H_dict[s]) - log_file.write("\nSpecial_scores:\n") - for s in Special_dict: - log_file.write(s+"\t"+str(Special_dict[s])+"\n") - log_file.close() - return highest_O,highest_fliC,highest_fljB - -def get_temp_file_names(for_fq,rev_fq): - #seqsero2 -a; get temp file names - sam=for_fq+".sam" - bam=for_fq+".bam" - sorted_bam=for_fq+"_sorted.bam" - mapped_fq1=for_fq+"_mapped.fq" - mapped_fq2=rev_fq+"_mapped.fq" - combined_fq=for_fq+"_combined.fq" - for_sai=for_fq+".sai" - rev_sai=rev_fq+".sai" - return sam,bam,sorted_bam,mapped_fq1,mapped_fq2,combined_fq,for_sai,rev_sai - -def map_and_sort(threads,database,fnameA,fnameB,sam,bam,for_sai,rev_sai,sorted_bam,mapping_mode): - #seqsero2 -a; do mapping and sort - print("building database...") - subprocess.check_call("bwa index "+database+ " 2>> data_log.txt",shell=True) - print("mapping...") - if mapping_mode=="mem": - subprocess.check_call("bwa mem -k 17 -t "+threads+" "+database+" "+fnameA+" "+fnameB+" > "+sam+ " 2>> data_log.txt",shell=True) - elif mapping_mode=="sam": - if fnameB!="": - subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameA+" > "+for_sai+ " 2>> data_log.txt",shell=True) - subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameB+" > "+rev_sai+ " 2>> data_log.txt",shell=True) - subprocess.check_call("bwa sampe "+database+" "+for_sai+" "+ rev_sai+" "+fnameA+" "+fnameB+" > "+sam+ " 2>> data_log.txt",shell=True) - else: - subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameA+" > "+for_sai+ " 2>> data_log.txt",shell=True) - subprocess.check_call("bwa samse "+database+" "+for_sai+" "+for_fq+" > "+sam) - subprocess.check_call("samtools view -@ "+threads+" -F 4 -Sh "+sam+" > "+bam,shell=True) - ### check the version of samtools then use differnt commands - samtools_version=subprocess.Popen(["samtools"],stdout=subprocess.PIPE,stderr=subprocess.PIPE) - out, err = samtools_version.communicate() - version = str(err).split("ersion:")[1].strip().split(" ")[0].strip() - print("check samtools version:",version) - ### end of samtools version check and its analysis - if LooseVersion(version)<=LooseVersion("1.2"): - subprocess.check_call("samtools sort -@ "+threads+" -n "+bam+" "+fnameA+"_sorted",shell=True) - else: - subprocess.check_call("samtools sort -@ "+threads+" -n "+bam+" >"+sorted_bam,shell=True) - -def extract_mapped_reads_and_do_assembly_and_blast(current_time,sorted_bam,combined_fq,mapped_fq1,mapped_fq2,threads,fnameA,fnameB,database,mapping_mode): - #seqsero2 -a; extract, assembly and blast - subprocess.check_call("bamToFastq -i "+sorted_bam+" -fq "+combined_fq,shell=True) - #print("fnameA:",fnameA) - #print("fnameB:",fnameB) - if fnameB!="": - subprocess.check_call("bamToFastq -i "+sorted_bam+" -fq "+mapped_fq1+" -fq2 "+mapped_fq2 + " 2>> data_log.txt",shell=True)#2> /dev/null if want no output - else: - pass - outdir=current_time+"_temp" - print("assembling...") - if int(threads)>4: - t="4" - else: - t=threads - if os.path.getsize(combined_fq)>100 and (fnameB=="" or os.path.getsize(mapped_fq1)>100):#if not, then it's "-:-:-" - if fnameB!="": - subprocess.check_call("spades.py --careful --pe1-s "+combined_fq+" --pe1-1 "+mapped_fq1+" --pe1-2 "+mapped_fq2+" -t "+t+" -o "+outdir+ " >> data_log.txt 2>&1",shell=True) - else: - subprocess.check_call("spades.py --careful --pe1-s "+combined_fq+" -t "+t+" -o "+outdir+ " >> data_log.txt 2>&1",shell=True) - #new_fasta=fnameA+"_"+database+"_"+mapping_mode+".fasta" - new_fasta=fnameA+"_"+database.split('/')[-1]+"_"+mapping_mode+".fasta" # ed_SL_09152019: change path to databse for packaging - subprocess.check_call("mv "+outdir+"/contigs.fasta "+new_fasta+ " 2> /dev/null",shell=True) - #os.system("mv "+outdir+"/scaffolds.fasta "+new_fasta+ " 2> /dev/null") contigs.fasta - subprocess.check_call("rm -rf "+outdir+ " 2> /dev/null",shell=True) - print("blasting...","\n") - xmlfile="blasted_output.xml"#fnameA+"-extracted_vs_"+database+"_"+mapping_mode+".xml" - subprocess.check_call('makeblastdb -in '+new_fasta+' -out '+new_fasta+'_db '+'-dbtype nucl >> data_log.txt 2>&1',shell=True) #temp.txt is to forbid the blast result interrupt the output of our program###1/27/2015 - subprocess.check_call("blastn -query "+database+" -db "+new_fasta+"_db -out "+xmlfile+" -outfmt 5 >> data_log.txt 2>&1",shell=True)###1/27/2015; 08272018, remove "-word_size 10" - else: - xmlfile="NA" - return xmlfile,new_fasta - -def judge_subspecies(fnameA,dirpath): - #seqsero2 -a; judge subspecies on just forward raw reads fastq - salmID_output=subprocess.Popen("python " + dirpath + "/SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - out, err = salmID_output.communicate() - out=out.decode("utf-8") - file=open("data_log.txt","a") - file.write(out) - file.close() - salm_species_scores=out.split("\n")[1].split("\t")[6:] - salm_species_results=out.split("\n")[0].split("\t")[6:] - max_score=0 - max_score_index=1 #default is 1, means "I" - for i in range(len(salm_species_scores)): - if max_score float(out.split("\n")[1].split("\t")[5]): #bongori and enterica compare - prediction="bongori" #if not, the prediction would always be enterica, since they are located in the later part - if max_score<10: - prediction="-" - return prediction - -def judge_subspecies_Kmer(Special_dict): - #seqsero2 -k; - max_score=0 - prediction="-" #default should be I - for x in Special_dict: - if "mer" in x: - if max_score95:#if bongori already, then no need to test enterica - prediction="bongori" - break - return prediction - -def main(): - #combine SeqSeroK and SeqSero2, also with SalmID - args = parse_args() - input_file = args.i - data_type = args.t - analysis_mode = args.m - mapping_mode=args.b - threads=args.p - make_dir=args.d - clean_mode=args.c - k_size=27 #will change for bug fixing - #database="H_and_O_and_specific_genes.fasta" - dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__))) - ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019: add ex_dir for packaging - #database=ex_dir+"/seqsero2_db/H_and_O_and_specific_genes.fasta" # ed_SL_09152019: change path to database for packaging - database="H_and_O_and_specific_genes.fasta" - note="Note:" - NA_note=" This predicted serotype is not in the Kauffman-White scheme." # ed_SL_09272019: add for new output format - if len(sys.argv)==1: - subprocess.check_call(dirpath+"/SeqSero2_package.py -h",shell=True)#change name of python file - else: - request_id = time.strftime("%m_%d_%Y_%H_%M_%S", time.localtime()) - request_id += str(random.randint(1, 10000000)) - if make_dir is None: - make_dir="SeqSero_result_"+request_id - if os.path.isdir(make_dir): - pass - else: - subprocess.check_call(["mkdir",make_dir]) - #subprocess.check_call("cp "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) - #subprocess.check_call("ln -sr "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) - #subprocess.check_call("ln -f -s "+database+" "+" ".join(input_file)+" "+make_dir,shell=True) # ed_SL_09152019: change path to database for packaging - subprocess.check_call("ln -f -s "+dirpath+"/seqsero2_db/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) ### ed_SL_05282019: use -f option to force the replacement of links, remove -r and use absolute path instead to avoid link issue (use 'type=os.path.abspath' in -i argument). - ############################begin the real analysis - if analysis_mode=="a": - if data_type in ["1","2","3"]:#use allele mode - for_fq,rev_fq=get_input_files(make_dir,input_file,data_type,dirpath) - os.chdir(make_dir) - ###add a function to tell input files - fnameA=for_fq.split("/")[-1] - fnameB=rev_fq.split("/")[-1] - current_time=time.strftime("%Y_%m_%d_%H_%M_%S", time.localtime()) - sam,bam,sorted_bam,mapped_fq1,mapped_fq2,combined_fq,for_sai,rev_sai=get_temp_file_names(fnameA,fnameB) #get temp files id - map_and_sort(threads,database,fnameA,fnameB,sam,bam,for_sai,rev_sai,sorted_bam,mapping_mode) #do mapping and sort - xmlfile,new_fasta=extract_mapped_reads_and_do_assembly_and_blast(current_time,sorted_bam,combined_fq,mapped_fq1,mapped_fq2,threads,fnameA,fnameB,database,mapping_mode) #extract the mapped reads and do micro assembly and blast - if xmlfile=="NA": - O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H=("-","-","-",[],"","") - else: - Final_list=xml_parse_score_comparision_seqsero(xmlfile) #analyze xml and get parsed results - file=open("data_log.txt","a") - for x in Final_list: - file.write("\t".join(str(y) for y in x)+"\n") - file.close() - Final_list_passed=[x for x in Final_list if float(x[0].split("_cov_")[1].split("_")[0])>=0.9 and (x[1]>=int(x[0].split("__")[1]) or x[1]>=int(x[0].split("___")[1].split("_")[3]) or x[1]>1000)] - O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H,Otypes_uniq,H1_cont_stat_list,H2_cont_stat_list=predict_O_and_H_types(Final_list,Final_list_passed,new_fasta) #predict O, fliC and fljB - subspecies=judge_subspecies(fnameA,dirpath) #predict subspecies - ###output - predict_form,predict_sero,star,star_line,claim=seqsero_from_formula_to_serotypes(O_choice,fliC_choice,fljB_choice,special_gene_list,subspecies) - claim="" #04132019, disable claim for new report requirement - contamination_report="" - H_list=["fliC_"+x for x in H1_cont_stat_list if len(x)>0]+["fljB_"+x for x in H2_cont_stat_list if len(x)>0] - if contamination_O!="" and contamination_H=="": - contamination_report="#Potential inter-serotype contamination detected from O antigen signals. All O-antigens detected:"+"\t".join(Otypes_uniq)+"." - elif contamination_O=="" and contamination_H!="": - contamination_report="#Potential inter-serotype contamination detected or potential thrid H phase from H antigen signals. All H-antigens detected:"+"\t".join(H_list)+"." - elif contamination_O!="" and contamination_H!="": - contamination_report="#Potential inter-serotype contamination detected from both O and H antigen signals.All O-antigens detected:"+"\t".join(Otypes_uniq)+". All H-antigens detected:"+"\t".join(H_list)+"." - if contamination_report!="": - #contamination_report="potential inter-serotype contamination detected (please refer below antigen signal report for details)." #above contamination_reports are for back-up and bug fixing #web-based mode need to be re-used, 04132019 - contamination_report=" Co-existence of multiple serotypes detected, indicating potential inter-serotype contamination. See 'Extracted_antigen_alleles.fasta' for detected serotype determinant alleles." - #claim="\n"+open("Extracted_antigen_alleles.fasta","r").read()#used to store H and O antigen sequeences #04132019, need to change if using web-version - ## ed_SL_09272019: change for new output format - #if contamination_report+star_line+claim=="": #0413, new output style - # note="" - #else: - # note="Note:" - if clean_mode: - subprocess.check_call("rm -rf ../"+make_dir,shell=True) - make_dir="none-output-directory due to '-c' flag" - else: - new_file=open("SeqSero_result.txt","w") - if O_choice=="": - O_choice="-" - if "N/A" not in predict_sero: - new_file.write("Output_directory:\t"+make_dir+"\n"+ - "Input files:\t"+"\t".join(input_file)+"\n"+ - "O antigen prediction:\t"+O_choice+"\n"+ - "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ - "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ - "Predicted subspecies:\t"+subspecies+"\n"+ - "Predicted antigenic profile:\t"+predict_form+"\n"+ - "Predicted serotype:\t"+predict_sero+"\n"+ # ed_SL_04152019: change serotype(s) to serotype - note+contamination_report+star_line+claim+"\n")#+## - else: - #star_line=star_line.strip()+"\tNone such antigenic formula in KW.\n" - star_line="" #04132019, for new output requirement, diable star_line if "NA" in output - new_file.write("Output_directory:\t"+make_dir+"\n"+ - "Input files:\t"+"\t".join(input_file)+"\n"+ - "O antigen prediction:\t"+O_choice+"\n"+ - "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ - "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ - "Predicted subspecies:\t"+subspecies+"\n"+ - "Predicted antigenic profile:\t"+predict_form+"\n"+ - "Predicted serotype:\t"+predict_form+"\n"+ # ed_SL_09242019: add serotype output for "N/A" prediction - note+NA_note+contamination_report+star_line+claim+"\n")#+## - new_file.close() - print("\n") - #subprocess.check_call("cat Seqsero_result.txt",shell=True) - #subprocess.call("rm H_and_O_and_specific_genes.fasta* *.sra *.bam *.sam *.fastq *.gz *.fq temp.txt *.xml "+fnameA+"*_db* 2> /dev/null",shell=True) - subprocess.call("rm H_and_O_and_specific_genes.fasta* *.sra *.bam *.sam *.fastq *.gz *.fq temp.txt "+fnameA+"*_db* 2> /dev/null",shell=True) - if "N/A" not in predict_sero: - #print("Output_directory:"+make_dir+"\nInput files:\t"+for_fq+" "+rev_fq+"\n"+"O antigen prediction:\t"+O_choice+"\n"+"H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+"H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+"Predicted antigenic profile:\t"+predict_form+"\n"+"Predicted subspecies:\t"+subspecies+"\n"+"Predicted serotype(s):\t"+predict_sero+star+"\nNote:"+contamination_report+star+star_line+claim+"\n")#+## - print("Output_directory:\t"+make_dir+"\n"+ - "Input files:\t"+"\t".join(input_file)+"\n"+ - "O antigen prediction:\t"+O_choice+"\n"+ - "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ - "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ - "Predicted subspecies:\t"+subspecies+"\n"+ - "Predicted antigenic profile:\t"+predict_form+"\n"+ - "Predicted serotype:\t"+predict_sero+"\n"+ # ed_SL_04152019: change serotype(s) to serotype - note+contamination_report+star_line+claim+"\n")#+## - else: - print("Output_directory:\t"+make_dir+"\n"+ - "Input files:\t"+"\t".join(input_file)+"\n"+ - "O antigen prediction:\t"+O_choice+"\n"+ - "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ - "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ - "Predicted subspecies:\t"+subspecies+"\n"+ - "Predicted antigenic profile:\t"+predict_form+"\n"+ - "Predicted serotype:\t"+predict_form+"\n"+ # ed_SL_09242019: add serotype output for "N/A" prediction - note+NA_note+contamination_report+star_line+claim+"\n") - else: - print("Allele modes only support raw reads datatype, i.e. '-t 1 or 2 or 3'; please use '-m k'") - elif analysis_mode=="k": - #ex_dir = os.path.dirname(os.path.realpath(__file__)) - ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019: change ex_dir for packaging - #output_mode = args.mode - for_fq,rev_fq=get_input_files(make_dir,input_file,data_type,dirpath) - input_file = for_fq #-k will just use forward because not all reads were used - os.chdir(make_dir) - f = open(dirpath + '/seqsero2_db/antigens.pickle', 'rb') - lib_dict = pickle.load(f) - f.close - input_Ks=get_input_K(input_file,lib_dict,data_type,k_size) - O_dict,H_dict,Special_dict=get_kmer_dict(lib_dict,input_Ks) - highest_O,highest_fliC,highest_fljB=call_O_and_H_type(O_dict,H_dict,Special_dict,make_dir) - subspecies=judge_subspecies_Kmer(Special_dict) - if subspecies=="IIb" or subspecies=="IIa": - subspecies="II" - predict_form,predict_sero,star,star_line,claim = seqsero_from_formula_to_serotypes( - highest_O.split('-')[1], highest_fliC, highest_fljB, Special_dict,subspecies) - claim="" #no claim any more based on new output requirement - ## ed_SL_09272019: change for new output format - #if star_line+claim=="": #0413, new output style - # note="" - #else: - # note="Note:" - if clean_mode: - subprocess.check_call("rm -rf ../"+make_dir,shell=True) - make_dir="none-output-directory due to '-c' flag" - ### ed_SL_05282019, fix the assignment issue of variable 'O_choice' using "-m k -c" - if highest_O.split('-')[-1]=="": - O_choice="-" - else: - O_choice=highest_O.split('-')[-1] - ### - else: - if highest_O.split('-')[-1]=="": - O_choice="-" - else: - O_choice=highest_O.split('-')[-1] - #print("Output_directory:"+make_dir+"\tInput_file:"+input_file+"\tPredicted subpecies:"+subspecies + '\tPredicted antigenic profile:' + predict_form + '\tPredicted serotype(s):' + predict_sero) - new_file=open("SeqSero_result.txt","w") - #new_file.write("Output_directory:"+make_dir+"\nInput files:\t"+input_file+"\n"+"O antigen prediction:\t"+O_choice+"\n"+"H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+"H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+"Predicted antigenic profile:\t"+predict_form+"\n"+"Predicted subspecies:\t"+subspecies+"\n"+"Predicted serotype(s):\t"+predict_sero+star+"\n"+star+star_line+claim+"\n")#+## - if "N/A" not in predict_sero: - new_file.write("Output_directory:\t"+make_dir+"\n"+ - "Input files:\t"+input_file+"\n"+ - "O antigen prediction:\t"+O_choice+"\n"+ - "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ - "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ - "Predicted subspecies:\t"+subspecies+"\n"+ - "Predicted antigenic profile:\t"+predict_form+"\n"+ - "Predicted serotype:\t"+predict_sero+"\n"+ # ed_SL_04152019: change serotype(s) to serotype - note+star_line+claim+"\n")#+## - else: - #star_line=star_line.strip()+"\tNone such antigenic formula in KW.\n" - star_line = "" #changed for new output requirement, 04132019 - new_file.write("Output_directory:\t"+make_dir+"\n"+ - "Input files:\t"+input_file+"\n"+ - "O antigen prediction:\t"+O_choice+"\n"+ - "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ - "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ - "Predicted subspecies:\t"+subspecies+"\n"+ - "Predicted antigenic profile:\t"+predict_form+"\n"+ - "Predicted serotype:\t"+predict_form+"\n"+ # ed_SL_09242019: add serotype output for "N/A" prediction - note+NA_note+star_line+claim+"\n")#+## - new_file.close() - subprocess.call("rm *.fasta* *.fastq *.gz *.fq temp.txt *.sra 2> /dev/null",shell=True) - if "N/A" not in predict_sero: - print("Output_directory:\t"+make_dir+"\n"+ - "Input files:\t"+input_file+"\n"+ - "O antigen prediction:\t"+O_choice+"\n"+ - "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ - "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ - "Predicted subspecies:\t"+subspecies+"\n"+ - "Predicted antigenic profile:\t"+predict_form+"\n"+ - "Predicted serotype:\t"+predict_sero+"\n"+ # ed_SL_04152019: change serotype(s) to serotype - note+star_line+claim+"\n")#+## - else: - print("Output_directory:\t"+make_dir+"\n"+ - "Input files:\t"+input_file+"\n"+ - "O antigen prediction:\t"+O_choice+"\n"+ - "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ - "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ - "Predicted subspecies:\t"+subspecies+"\n"+ - "Predicted antigenic profile:\t"+predict_form+"\n"+ - "Predicted serotype:\t"+predict_form+"\n"+ # ed_SL_09242019: add serotype output for "N/A" prediction - note+NA_note+star_line+claim+"\n")#+## - -if __name__ == '__main__': - main() diff -r 43f6b7f6ebb3 -r e6437d423693 SeqSero2_update_kmer_database.py --- a/SeqSero2_update_kmer_database.py Thu Apr 30 21:47:42 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,113 +0,0 @@ -#!/usr/bin/env python3 - -import argparse -import os,subprocess -import pickle - -### SeqSero Kmer -def parse_args(): - "Parse the input arguments, use '-h' for help." - parser = argparse.ArgumentParser(usage='Just type "SeqSero2_update_kmer_database.py", it will update kmer database automatically') - return parser.parse_args() - -def reverse_complement(sequence): - complement = { - 'A': 'T', - 'C': 'G', - 'G': 'C', - 'T': 'A', - 'N': 'N', - 'M': 'K', - 'R': 'Y', - 'W': 'W', - 'S': 'S', - 'Y': 'R', - 'K': 'M', - 'V': 'B', - 'H': 'D', - 'D': 'H', - 'B': 'V' - } - return "".join(complement[base] for base in reversed(sequence)) - -def multifasta_dict(multifasta): - multifasta_list = [ - line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0 - ] - headers = [i for i in multifasta_list if i[0] == '>'] - multifasta_dict = {} - for h in headers: - start = multifasta_list.index(h) - for element in multifasta_list[start + 1:]: - if element[0] == '>': - break - else: - if h[1:] in multifasta_dict: - multifasta_dict[h[1:]] += element - else: - multifasta_dict[h[1:]] = element - return multifasta_dict - -def createKmerDict_reads(list_of_strings, kmer): - kmer_table = {} - for string in list_of_strings: - sequence = string.strip('\n') - for i in range(len(sequence) - kmer + 1): - new_mer = sequence[i:i + kmer].upper() - new_mer_rc = reverse_complement(new_mer) - if new_mer in kmer_table: - kmer_table[new_mer.upper()] += 1 - else: - kmer_table[new_mer.upper()] = 1 - if new_mer_rc in kmer_table: - kmer_table[new_mer_rc.upper()] += 1 - else: - kmer_table[new_mer_rc.upper()] = 1 - return kmer_table - -def multifasta_to_kmers_dict(multifasta): - multi_seq_dict = multifasta_dict(multifasta) - lib_dict = {} - for h in multi_seq_dict: - lib_dict[h] = set( - [k for k in createKmerDict_reads([multi_seq_dict[h]], 27)]) - return lib_dict - -def get_salmid_invA_database(ex_dir): - # read invA kmer and return it - a = open(ex_dir + '/invA_mers_dict', 'rb') - invA_dict = pickle.load(a) - try: - del invA_dict['version'] - except: - pass - return invA_dict - -def get_salmid_rpoB_database(ex_dir): - # read invA kmer and return it - a = open(ex_dir + '/rpoB_mers_dict', 'rb') - rpoB_dict = pickle.load(a) - try: - del rpoB_dict['version'] - except: - pass - return rpoB_dict - -def main(): - args = parse_args() - ex_dir = os.path.dirname(os.path.realpath(__file__)) - lib_dict = multifasta_to_kmers_dict(ex_dir + '/H_and_O_and_specific_genes.fasta') - invA_dict=get_salmid_invA_database(ex_dir) - #rpoB_dict=get_salmid_rpoB_database(ex_dir) - lib_dict_new = lib_dict.copy() - #print(len(lib_dict_new)) - lib_dict_new.update(invA_dict) - #print(len(lib_dict_new)) - #lib_dict_new.update(rpoB_dict) - #print(len(lib_dict_new)) - f = open(ex_dir + '/antigens.pickle', "wb") - pickle.dump(lib_dict_new, f) - f.close() - -if __name__ == '__main__': - main() diff -r 43f6b7f6ebb3 -r e6437d423693 __init__.py diff -r 43f6b7f6ebb3 -r e6437d423693 __pycache__/version.cpython-36.pyc Binary file __pycache__/version.cpython-36.pyc has changed diff -r 43f6b7f6ebb3 -r e6437d423693 bin/Initial_Conditions.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bin/Initial_Conditions.py Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,109 @@ +#!/usr/bin/env python + +subs=['II', 'I', 'I', 'II', 'I', 'II', 'II', 'I', 'II', 'II', 'II', 'II', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 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+ +remove_list=['Schleissheim', 'Sendai', 'Blegdam', 'Naestved', 'Rostock', 'Moscow', 'Antarctica', 'Rosenberg', 'Chittagong', 'Bilu', 'Dessau', 'Cannonhill', 'Ilugun'] + +rename_dict={'Nitra': 'Enteritidis', + 'Kiel': 'Dublin', + 'Koessen': 'Panama', + 'Phaliron': 'Kalumburu', + 'Istanbul': 'Hadar', + 'Haardt': 'Blockley', + 'Ferruch': 'Kottbus', + 'Sanga': 'Eboko', + 'Pakistan': 'Litchfield', + 'Bellevue': 'Lezennes', + 'Sunnycove': 'Daarle', + 'Noya': 'Akanji', + 'Virginia': 'Muenchen', + 'Djelfa': 'Skansen', + 'Konstanz': 'Gatuni', + 'Bardo': 'Newport', + 'Houston': 'Panama', + 'Martonos': 'Finkenwerder', + 'Midway': 'Florida', + 'Lindern': 'Charity', + 'Bahrenfeld': 'Onderstepoort', + 'Schalkwijk': 'Moussoro', + 'Amberg': 'Boecker', + 'Madelia': 'Carrau', + 'Soahanina': 'Sundsvall', + 'Stafford': 'Poano', + 'Chichiri': 'Uzaramo', + 'II 16:g,[m],[s],t:[e,n,x]': 'II 16:g,[m],[s],t:[1,5]', + 'Hindmarsh':'Bovismorbificans', + 'Yovokome': 'Manhattan'} + + #potential merge for O22 and O23 + #'Ibadan': 'Mississippi', + #'Bracknell': 'Oudwijk', + #'Vaertan': 'Ullevi', + #'Bahati': 'Durham', + #'Wichita': 'Friedenau', + #'Diguel': 'Telelkebir', + #'II 13,22:l,z28:1,5': 'II 13,23:l,z28:1,5', + #'Washington': 'Kintambo', + #'II 13,23:m,t:z42': 'II 13,22:m,t:z42:z39', + #'Serenli': 'Winslow', + #'Farmsen': 'Poona', + #'Durance': 'Ivrysurseine', + #'Agoueve': 'Cubana', + #'II 13,23:z29:1,5': 'II 13,22:z29:1,5', + #'II 13,23:z29:e,n,x': 'II 13,22:z29:e,n,x', + #'Picpus': 'Mampong', + #'Anna': 'Nimes', + #'Fanti': 'Leiden', + #'Ried': 'Ajiobo', + + #potential O68 list + #'Djelfa': 'Skansen', + #'Korbol': 'Nagoya', + #'Sanga': 'Eboko', + #'Konstanz': 'Gatuni', + #'Presov': 'Shipley', + #'Heistopdenberg': 'Bukuru', + #'Tounouma': 'Banalia', + #'Gaillac': 'Utah', + #'Santiago': 'Belem', + #'Virginia': 'Muenchen', + #'Yovokome': 'Manhattan', + #'Portanigra': 'Dunkwa', + #'Bardo': 'Newport', + #'Ferruch': 'Kottbus', + #'Alminko': 'Nanergou', + #'Bargny': 'Takoradi', + #'Magherafelt': 'Cyprus', + #'Haardt': 'Blockley', + #'Pakistan': 'Litchfield', + #'Yokoe': 'Bassa', + #'Noya': 'Akanji', + #'Lamphun': 'Giza', + #'Tananarive': 'Brunei', + #'Inchpark': 'Alagbon', + #'Sunnycove': 'Daarle', + #'Sindelfingen': 'Benue', + #'Phaliron': 'Kalumburu', + #'Bazenheid': 'Zerifin', + #'Paris': 'Mapo', + #'Istanbul': 'Hadar', + #'Chomedey': 'Glostrup', + #'Wippra': 'Molade', + #'Uno': 'Tamale', + #'Kolda': 'Yarm', + #'Bellevue': 'Lezennes', + #'Albany':'Duesseldorf' diff -r 43f6b7f6ebb3 -r e6437d423693 bin/SeqSero2_package.py --- a/bin/SeqSero2_package.py Thu Apr 30 21:47:42 2020 -0400 +++ b/bin/SeqSero2_package.py Fri May 01 13:30:43 2020 -0400 @@ -1236,12 +1236,14 @@ def judge_subspecies(fnameA,dirpath): #seqsero2 -a; judge subspecies on just forward raw reads fastq samid_strcmd = "python " + dirpath + "/../SalmID.py -i "+fnameA - #subprocess.check_call(samid_strcmd + " > Salmidoutput.txt",shell=True) print(samid_strcmd) + #seqsero2 -a; judge subspecies on just forward raw reads fastq + #salmID_output=subprocess.Popen("SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE) salmID_output=subprocess.Popen(samid_strcmd,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE) out, err = salmID_output.communicate() - print("judge_subspecies -> err = salmID_output.communicate() " + err) out=out.decode("utf-8") + print(out) + print(err) file=open("data_log.txt","a") file.write(out) file.close() diff -r 43f6b7f6ebb3 -r e6437d423693 bin/__pycache__/Initial_Conditions.cpython-36.pyc Binary file bin/__pycache__/Initial_Conditions.cpython-36.pyc has changed diff -r 43f6b7f6ebb3 -r e6437d423693 build/lib/LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/LICENSE Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,339 @@ +GNU GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + Everyone is permitted to copy 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If this is what you want to do, use the GNU Lesser General +Public License instead of this License. diff -r 43f6b7f6ebb3 -r e6437d423693 build/lib/MANIFEST.in --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/MANIFEST.in Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,10 @@ +include LICENSE +include README.md +include MANIFEST.in +include version.py +include setup.py +include seqsero2_db/antigens.pickle +include seqsero2_db/H_and_O_and_specific_genes.fasta +include seqsero2_db/invA_mers_dict +include seqsero2_db/special.pickle +include bin/deinterleave_fastq.sh diff -r 43f6b7f6ebb3 -r e6437d423693 build/lib/README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/README.md Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,117 @@ +# SeqSero2 v1.1.1 +Salmonella serotype prediction from genome sequencing data. + +Online version: http://www.denglab.info/SeqSero2 + +# Introduction +SeqSero2 is a pipeline for Salmonella serotype prediction from raw sequencing reads or genome assemblies + +# Dependencies +SeqSero2 has three workflows: + +(A) Allele micro-assembly (default). This workflow takes raw reads as input and performs targeted assembly of serotype determinant alleles. Assembled alleles are used to predict serotype and flag potential inter-serotype contamination in sequencing data (i.e., presence of reads from multiple serotypes due to, for example, cross or carryover contamination during sequencing). + +Allele micro-assembly workflow depends on: + +1. Python 3; + +2. Biopython 1.73; + +3. [Burrows-Wheeler Aligner v0.7.12](http://sourceforge.net/projects/bio-bwa/files/); + +4. [Samtools v1.8](http://sourceforge.net/projects/samtools/files/samtools/); + +5. [NCBI BLAST v2.2.28+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download); + +6. [SRA Toolkit v2.8.0](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software); + +7. [SPAdes v3.9.0](http://bioinf.spbau.ru/spades); + +8. [Bedtools v2.17.0](http://bedtools.readthedocs.io/en/latest/); + +9. [SalmID v0.11](https://github.com/hcdenbakker/SalmID). + + +(B) Raw reads k-mer. This workflow takes raw reads as input and performs rapid serotype prediction based on unique k-mers of serotype determinants. + +Raw reads k-mer workflow (originally SeqSeroK) depends on: + +1. Python 3; +2. [SRA Toolkit](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software) (optional, just used to fastq-dump sra files); + + +(C) Genome assembly k-mer. This workflow takes genome assemblies as input and the rest of the workflow largely overlaps with the raw reads k-mer workflow + +# Installation +### Conda +To install the latest SeqSero2 Conda package (recommended): +``` +conda install -c bioconda seqsero2=1.1.1 +``` +### Git +To install the SeqSero2 git repository locally: +``` +git clone https://github.com/denglab/SeqSero2.git +cd SeqSero2 +python3 -m pip install --user . +``` +### Other options +Third party SeqSero2 installations (may not be the latest version of SeqSero2): \ +https://github.com/B-UMMI/docker-images/tree/master/seqsero2 \ +https://github.com/denglab/SeqSero2/issues/13 + + +# Executing the code +Make sure all SeqSero2 and its dependency executables are added to your path (e.g. to ~/.bashrc). Then type SeqSero2_package.py to get detailed instructions. + + Usage: SeqSero2_package.py + + -m (which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a) + + -t (input data type, '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore fasta, '6'for nanopore fastq) + + -i (/path/to/input/file) + + -p (number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1) + + -b (algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default "mem" mode) + + -d (output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number) + + -c (if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files) + + -n (optional, to specify a sample name in the report output) + + -s (if '-s' was flagged, SeqSero2 will not output header in SeqSero_result.tsv) + + --check (use '--check' flag to check the required dependencies) + + -v, --version (show program's version number and exit) + + +# Examples +Allele mode: + + # Allele workflow ("-m a", default), for separated paired-end raw reads ("-t 2"), use 10 threads in mapping and assembly ("-p 10") + SeqSero2_package.py -p 10 -t 2 -i R1.fastq.gz R2.fastq.gz + +K-mer mode: + + # Raw reads k-mer ("-m k"), for separated paired-end raw reads ("-t 2") + SeqSero2_package.py -m k -t 2 -i R1.fastq.gz R2.fastq.gz + + # Genome assembly k-mer ("-t 4", genome assemblies only predicted by the k-mer workflow, "-m k") + SeqSero2_package.py -m k -t 4 -i assembly.fasta + +# Output +Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode). + + +# Citation +Zhang S, Den-Bakker HC, Li S, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X. +SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data. +**Appl Environ Microbiology. 2019 Sep; 85(23):e01746-19.** [PMID: 31540993](https://aem.asm.org/content/early/2019/09/17/AEM.01746-19.long) + +Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X. +Salmonella serotype determination utilizing high-throughput genome sequencing data. +**J Clin Microbiol. 2015 May;53(5):1685-92.** [PMID: 25762776](http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15) diff -r 43f6b7f6ebb3 -r e6437d423693 build/lib/SeqSero2.egg-info/PKG-INFO --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/SeqSero2.egg-info/PKG-INFO Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,132 @@ +Metadata-Version: 1.1 +Name: SeqSero2 +Version: 1.1.1 +Summary: Salmonella serotyping +Home-page: https://github.com/denglab/SeqSero2/ +Author: Shaokang Zhang, Hendrik C Den-Bakker and Xiangyu Deng +Author-email: zskzsk@uga.edu, Hendrik.DenBakker@uga.edu, xdeng@uga.edu +License: GPLv2 +Description: # SeqSero2 v1.1.1 + Salmonella serotype prediction from genome sequencing data. + + Online version: http://www.denglab.info/SeqSero2 + + # Introduction + SeqSero2 is a pipeline for Salmonella serotype prediction from raw sequencing reads or genome assemblies + + # Dependencies + SeqSero2 has three workflows: + + (A) Allele micro-assembly (default). This workflow takes raw reads as input and performs targeted assembly of serotype determinant alleles. Assembled alleles are used to predict serotype and flag potential inter-serotype contamination in sequencing data (i.e., presence of reads from multiple serotypes due to, for example, cross or carryover contamination during sequencing). + + Allele micro-assembly workflow depends on: + + 1. Python 3; + + 2. Biopython 1.73; + + 3. [Burrows-Wheeler Aligner v0.7.12](http://sourceforge.net/projects/bio-bwa/files/); + + 4. [Samtools v1.8](http://sourceforge.net/projects/samtools/files/samtools/); + + 5. [NCBI BLAST v2.2.28+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download); + + 6. [SRA Toolkit v2.8.0](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software); + + 7. [SPAdes v3.9.0](http://bioinf.spbau.ru/spades); + + 8. [Bedtools v2.17.0](http://bedtools.readthedocs.io/en/latest/); + + 9. [SalmID v0.11](https://github.com/hcdenbakker/SalmID). + + + (B) Raw reads k-mer. This workflow takes raw reads as input and performs rapid serotype prediction based on unique k-mers of serotype determinants. + + Raw reads k-mer workflow (originally SeqSeroK) depends on: + + 1. Python 3; + 2. [SRA Toolkit](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software) (optional, just used to fastq-dump sra files); + + + (C) Genome assembly k-mer. This workflow takes genome assemblies as input and the rest of the workflow largely overlaps with the raw reads k-mer workflow + + # Installation + ### Conda + To install the latest SeqSero2 Conda package (recommended): + ``` + conda install -c bioconda seqsero2=1.1.1 + ``` + ### Git + To install the SeqSero2 git repository locally: + ``` + git clone https://github.com/denglab/SeqSero2.git + cd SeqSero2 + python3 -m pip install --user . + ``` + ### Other options + Third party SeqSero2 installations (may not be the latest version of SeqSero2): \ + https://github.com/B-UMMI/docker-images/tree/master/seqsero2 \ + https://github.com/denglab/SeqSero2/issues/13 + + + # Executing the code + Make sure all SeqSero2 and its dependency executables are added to your path (e.g. to ~/.bashrc). Then type SeqSero2_package.py to get detailed instructions. + + Usage: SeqSero2_package.py + + -m (which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a) + + -t (input data type, '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore fasta, '6'for nanopore fastq) + + -i (/path/to/input/file) + + -p (number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1) + + -b (algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default "mem" mode) + + -d (output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number) + + -c (if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files) + + -n (optional, to specify a sample name in the report output) + + -s (if '-s' was flagged, SeqSero2 will not output header in SeqSero_result.tsv) + + --check (use '--check' flag to check the required dependencies) + + -v, --version (show program's version number and exit) + + + # Examples + Allele mode: + + # Allele workflow ("-m a", default), for separated paired-end raw reads ("-t 2"), use 10 threads in mapping and assembly ("-p 10") + SeqSero2_package.py -p 10 -t 2 -i R1.fastq.gz R2.fastq.gz + + K-mer mode: + + # Raw reads k-mer ("-m k"), for separated paired-end raw reads ("-t 2") + SeqSero2_package.py -m k -t 2 -i R1.fastq.gz R2.fastq.gz + + # Genome assembly k-mer ("-t 4", genome assemblies only predicted by the k-mer workflow, "-m k") + SeqSero2_package.py -m k -t 4 -i assembly.fasta + + # Output + Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode). + + + # Citation + Zhang S, Den-Bakker HC, Li S, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X. + SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data. + **Appl Environ Microbiology. 2019 Sep; 85(23):e01746-19.** [PMID: 31540993](https://aem.asm.org/content/early/2019/09/17/AEM.01746-19.long) + + Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X. + Salmonella serotype determination utilizing high-throughput genome sequencing data. + **J Clin Microbiol. 2015 May;53(5):1685-92.** [PMID: 25762776](http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15) + +Keywords: Salmonella serotyping bioinformatics WGS +Platform: UNKNOWN +Classifier: Development Status :: 3 - Alpha +Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2) +Classifier: Programming Language :: Python :: 3 +Classifier: Topic :: Text Processing :: Linguistic diff -r 43f6b7f6ebb3 -r e6437d423693 build/lib/SeqSero2.egg-info/SOURCES.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/SeqSero2.egg-info/SOURCES.txt Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,19 @@ +LICENSE +MANIFEST.in +README.md +setup.py +version.py +SeqSero2.egg-info/PKG-INFO +SeqSero2.egg-info/SOURCES.txt +SeqSero2.egg-info/dependency_links.txt +SeqSero2.egg-info/not-zip-safe +SeqSero2.egg-info/requires.txt +SeqSero2.egg-info/top_level.txt +bin/Initial_Conditions.py +bin/SeqSero2_package.py +bin/SeqSero2_update_kmer_database.py +bin/deinterleave_fastq.sh +seqsero2_db/H_and_O_and_specific_genes.fasta +seqsero2_db/antigens.pickle +seqsero2_db/invA_mers_dict +seqsero2_db/special.pickle \ No newline at end of file diff -r 43f6b7f6ebb3 -r e6437d423693 build/lib/SeqSero2.egg-info/dependency_links.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/SeqSero2.egg-info/dependency_links.txt Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,1 @@ + diff -r 43f6b7f6ebb3 -r e6437d423693 build/lib/SeqSero2.egg-info/not-zip-safe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/SeqSero2.egg-info/not-zip-safe Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,1 @@ + diff -r 43f6b7f6ebb3 -r e6437d423693 build/lib/SeqSero2.egg-info/requires.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/SeqSero2.egg-info/requires.txt Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,1 @@ +biopython==1.73 diff -r 43f6b7f6ebb3 -r e6437d423693 build/lib/SeqSero2.egg-info/top_level.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/SeqSero2.egg-info/top_level.txt Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,1 @@ + diff -r 43f6b7f6ebb3 -r e6437d423693 build/lib/bin/Initial_Conditions.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/bin/Initial_Conditions.py Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,109 @@ +#!/usr/bin/env python + +subs=['II', 'I', 'I', 'II', 'I', 'II', 'II', 'I', 'II', 'II', 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u'Fomeco', u'Erfurt', u'Yaba', u'Neudorf', u'Epicrates', u'Egusitoo', u'Sanktjohann', u'Stourbridge', u'Tripoli', u'Durham', u'II 6,8:b:1,5', u'Nagoya', u'VI 11:b:1,7', u'Maryland', u'Onarimon', u'Shipley', u'Presov', u'Frintrop', u'Kalina', u'Butantan', u'Bata', u'Allerton', u'Huvudsta', u'II 21:b:1,5', u'II [1],9,12:b:e,n,x', u'Konstanz', u'Batonrouge', u'Gatuni', u'Bukuru', u'Heistopdenberg', u'II [1],9,12:b:z6', u'Ghana', u'Tounouma', u'Benfica', u'Minnesota', u'II [1],9,12:b:z39', u'II 56:b:[1,5]', u'Banalia', u'Riverside', u'Chittagong', u'Mana', u'Westminster', u'Wien', u'II 60:b:-', u'Mississippi', u'Ndjamena', u'Wenatchee', u'II 47:b:1,5', u'II 47:b:e,n,x,z15', u'Sya', u'II 47:b:z6', u'Cochise', u'Djelfa', u'Wilmington', u'Oudwijk', u'II 3,10:b:z39', u'Louga', u'Aschersleben', u'Tempe', u'IV 51:b:-', u'Karaya', u'II 58:b:1,5', u'Urbana', u'II [1],13,22:b:z42', u'II 30:b:z6', u'II 42:b:z6', u'Fluntern', u'II [1],13,23:b:[1,5]', u'II 28:b:z6', u'Vaertan', u'Rottnest', u'II 28:b:e,n,x', u'Soumbedioune', u'Langford', u'Bracknell', u'Freefalls', u'Bokanjac', u'Bahati', u'Skansen', u'Flottbek', u'Molesey', u'Ullevi', u'Moero', u'Ashanti', u'II [1],40:c:z39', u'Antwerpen', u'Montreal', u'IIIb 41:c:e,n,x,z15', u'Bida', u'Kampala', u'IIIb 47:c:z35', u'IIIb 47:c:z', u'IIIb 47:c:e,n,x,z15', u'Eastglam', u'Madigan', u'Kassberg', u'Blijdorp', u'Minna', u'Haouaria', u'Luedinghausen', u'Ridge', u'Alabama', u'IIIb 47:c:1,5,7', u'Keurmassar', u'Madiago', u'Elokate', u'Ipeko', u'Deversoir', u'II 41:c:z6', u'Runby', u'Goeteborg', u'Quebec', u'Kodjovi', u'Lonestar', u'Chiredzi', u'Schwabach', u'II 21:c:e,n,x', u'Utah', u'IIIb 21:c:e,n,x,z15', u'Bronx', u'Belfast', u'Alexanderpolder', u'Santiago', u'Belem', u'Yolo', u'Tado', u'II 40:c:z6', u'Wingrove', u'II 53:c:1,5', u'Rhone', u'Brindisi', u'Hermannswerder', u'Eberswalde', u'Halle', u'II 52:c:k', u'Dresden', u'Wedding', u'Techimani', u'II 11:c:e,n,z15', u'Woodinville', u'Namibia', u'Cotonou', u'Kaduna', u'Rawash', u'Victoriaborg', u'II 17:c:z39', u'IIIb 65:c:z53', u'IIIb 65:c:z', u'IIIb 65:c:1,5,7', u'Okefoko', u'Anderlecht', u'Agege', u'Pramiso', u'IIIb 61:c:z35', u'IIIb 61:c:1,5,(7)', u'Ikayi', u'Gaillac', u'Asylanta', u'II 1,9,12,46,27:c:z39', u'IIIb 59:c:e,n,x,z15', u'Legon', u'Abortusovis', u'Altendorf', u'II 58:c:z6', u'Bissau', u'Jericho', u'Hallfold', u'IIIb 57:c:z', u'IIIb 57:c:e,n,x,z15', u'Bury', u'Hydra', u'Gbadago', u'Morningside', u'Gouloumbo', u'Itutaba', u'II 39:c:e,n,x', u'Vancouver', u'Gafsa', u'Paratyphi C', u'Choleraesuis', u'Typhisuis', u'II 30:c:z39', u'Hissar', u'Kidderminster', u'IIIb 48:c:z', u'Sheffield', u'Quiniela', u'Argenteuil', u'Hithergreen', u'Zaire', u'II 51:c:-', u'Birkenhead', u'Yoruba', u'II [1],40:c:e,n,x,z15', u'Shamba', u'Groenekan', u'Sculcoates', u'II 16:d:1,5', u'Usumbura', u'Sherbrooke', u'II 38:d:z39', u'II 38:d:[1,5]', u'Willamette', u'Oldenburg', u'Nieukerk', u'Orleans', u'Wil', u'Gaminara', u'Livingstone', u'II 6,7:d:z42', u'II 3,10:d:e,n,x', u'Driffield', u'Berlin', u'Karlshamn', u'Niamey', u'II 40:d:-', u'Logone', u'Maron', u'Weybridge', u'Stormont', u'Madjorio', u'Gombe', u'Souza', u'Onireke', u'Lekke', u'II 43:d:z42', u'II 43:d:z39', u'II 43:d:e,n,x,z15', u'Shangani', u'Barranquilla', u'Birmingham', u'Plymouth', u'Dembe', u'Midway', u'Florida', u'Lindern', u'Charity', u'Quentin', u'Typhi', u'II 9,12:d:z39', u'Jaffna', u'Finkenwerder', u'Olten', u'Martonos', u'Sontheim', u'Messina', u'Amoutive', u'Hatfield', u'Mundonobo', u'Mocamedes', u'Patience', u'Cullingworth', u'II 42:d:z6', u'Encino', u'Strasbourg', u'Eschberg', u'Nottingham', u'Caen', u'Barmbek', u'II 35:d:1,5', u'Teko', u'Tarshyne', u'Spartel', u'Magwa', u'Madison', u'Woodhull', u'Ndolo', u'II 16:d:e,n,x', u'II 41:d:z6', u'Bangui', u'Zega', u'Ontario', u'Amersfoort', u'Kambole', u'Kivu', u'Isangi', u'Kisii', u'Albuquerque', u'Egusi', u'Niloese', u'II 47:d:z39', u'II 47:d:e,n,x,z15', u'Stellingen', u'II 47:d:1,5', u'Liverpool', u'Tilburg', u'Wanatah', u'II 13,22:d:1,5', u'Ayinde', u'Friedenau', u'Wichita', u'Grumpensis', u'II [1],9,12:d:e,n,x', u'Diguel', u'II 48:d:1,2', u'Telelkebir', u'Putten', u'Ati', u'Gustavia', u'Warmsen', u'Karachi', u'Dugbe', u'Isuge', u'Chandans', u'Findorff', u'Hemingford', u'IV 50:d:-', u'II 13,23:d:e,n,x', u'Stanley', u'Brezany', u'Schwarzengrund', u'Ahmadi', u'II 4,12:d:e,n,x', u'Sarajane', u'Duisburg', u'Mons', u'II 53:d:z42', u'II [1],53:d:z39', u'II 53:d:1,5', u'Eppendorf', u'II 56:d:-', u'Buckeye', u'Umbadah', u'II 48:d:z6', u'II 57:d:1,5', u'Virginia', u'Muenchen', u'II 58:d:z6', u'II 52:d:z39', u'II 52:d:e,n,x,z15', u'Utrecht', u'Yovokome', u'Manhattan', u'Portanigra', u'Dunkwa', u'Sterrenbos', u'Mishmarhaemek', u'Chennai', u'Palamaner', u'Handen', u'II 6,8:d:z6', u'Fischerstrasse', u'Kermel', u'Gokul', u'Bobo', u'Labadi', u'Herston', u'Newlands', u'Kaapstad', u'Korkeasaari', u'Kpeme', u'Gozo', u'Israel', u'Westafrica', u'Eastbourne', u'Chester', u'Eko', u'Redhill', u'Bahrenfeld', u'Nyborg', u'Anatum', u'Muenster', u'Vejle', u'Hayindogo', u'Kottbus', u'Cremieu', u'Fitzroy', u'Meleagridis', u'Vilvoorde', u'Winnipeg', u'Jubilee', u'Sekondi', u'Saintpaul', u'Weston', u'Beaudesert', u'Guerin', u'Waedenswil', u'Derkle', u'Butare', u'Bergedorf', u'Newport', u'Reading', u'Magumeri', u'Larochelle', u'Lomita', u'Norwich', u'Nola', u'Tilene', u'Onderstepoort', u'Lamberhurst', u'Ferruch', u'Atakpame', u'Bardo', u'Tschangu', u'Braenderup', u'Saboya', u'Rechovot', u'Chingola', u'Chartres', u'Vridi', u'Torhout', u'Livulu', u'Astridplein', u'Sao', u'Bournemouth', u'Calabar', u'Gassi', u'Fillmore', u'Tshiongwe', u'Willemstad', u'Meskin', u'Rhydyfelin', u'Moabit', u'Sanktmarx', u'Adamstua', u'Bruebach', u'Mara', u'Kasenyi', u'Thiaroye', u'Sandiego', u'Malakal', u'Rossleben', u'II 50:e,n,x:1,7', u'II 6,7:e,n,x:1,6', u'II 16:e,n,x:1,6', u'II 3,10:e,n,x:1,7', u'II [1],4,12,[27]:e,n,x:1,[5],7', u'II [1],40:e,n,x:1,[5],7', u'II 56:e,n,x:1,7', u'II 16:e,n,x:1,(5),7', u'II [1],13,23:e,n,x:1,[5],7', u'II 4,12:e,n,x:1,2,7', u'II 9,46:e,n,x:1,5,7', u'II [1],44:e,n,x:1,6', u'II 9,12:e,n,x:1,[5],7', u'II 39:e,n,x:1,7', u'II 28:e,n,x:1,7', u'II 9,12:e,n,x:1,6', u'II 42:e,n,x:1,6', u'II 48:e,n,x,z15:z6', u'II [1],40:e,n,x,z15:1,6', u'II 47:e,n,x,z15:1,6', u'II 17:e,n,x,z15:1,6', u'II 43:e,n,x,z15:1,(5),7', u'II 43:e,n,x,z15:1,6', u'II 17:e,n,x,z15:1,[5],7', u'II 28:e,n,z15:z87', u'6,14:e,n,z15:-', u'Kastrup', u'Wernigerode', u'Derby', u'Raus', u'Vleuten', u'Sljeme', u'Good', u'Friedrichsfelde', u'Rissen', u'Alfort', u'Suelldorf', u'Sandow', u'Rideau', u'Tees', u'Adelaide', u'Havana', u'Regent', u'Milwaukee', u'II 6,8:f,g,m,t:[e,n,x]', u'Borreze', u'Agona', u'II [1],4,[5],12:f,g,t:z6', u'Eingedi', u'Afula', u'Bilu', u'Petahtikve', u'Maiduguri', u'II 28:g,(m),[s],t:1,5', u'Riggil', u'II [1],40:g,[m],[s],[t]:e,n,x', u'II 21:g,[m],[s],t:-', u'II [1],40:g,[m],[s],t:[1,5]', u'II 9,46:g,[m],[s],t:[e,n,x]', u'II 16:g,[m],[s],t:[e,n,x]', u'II [1],40:g,[m],[s],t:z42', u'II 16:g,[m],[s],t:[1,5]', u'II [1],4,12,[27]:g,[m],[s],t:e,n,x', u'II 6,7:g,[m],s,t:[z42]', u'II 11:g,[m],s,t:z39', u'II 50:g,[m],s,t:[1,5]', u'II 57:g,[m],s,t:z42', u'II [1],4,12,[27]:g,[m],t:[1,5]', u'Senftenberg', u'II [1],13,23:g,[s],t:z42', u'Okatie', u'Enteritidis', u'Luke', u'Abadina', u'Yardley', u'Warragul', u'Bijlmer', u'Abuja', u'Bron', u'Essen', u'Hillingdon', u'Nitra', u'Suberu', u'Pontypridd', u'Montevideo', u'Korovi', u'Chincol', u'Gamaba', u'Tornow', u'Agbeni', u'II 6,7:g,m,[s],t:e,n,x', u'II [1],9,12:g,m,[s],t:[1,5,7]', u'II [1],13,23:g,m,[s],t:[e,n,x]', u'II 43:g,m,[s],t:[z42]', u'Godesberg', u'Othmarschen', u'Adeoyo', u'Kouka', u'Blegdam', u'Hato', u'Gueuletapee', u'Amsterdam', u'Nikolaifleet', u'Macclesfield', u'IIIb 13,22:g,m,s:z', u'Giessen', u'Ealing', u'Caracas', u'II 30:g,m,s:e,n,x', u'Croft', u'Athens', u'Emek', u'II [1],13,23:g,m,s,t:1,5', u'II 3,{10}{15}:g,m,s,t:[1,5]', u'II [1],9,12:g,m,s,t:e,n,x', u'II 45:g,m,s,t:1,5', u'II 17:g,m,s,t:-', u'II 6,7:g,m,s,t:z39', u'II 45:g,m,s,t:e,n,x', u'II [1],13,23:g,m,s,t:z42', u'II 41:g,m,s,t:z6', u'II 35:g,m,s,t:-', u'II 28:g,m,t:z39', u'II 28:g,m,t:e,n,x', u'II 60:g,m,t:z6', u'Reubeuss', u'II 6,8:g,m,t:1,7', u'II 45:g,m,t:e,n,x,z15', u'California', u'II 4,12:g,m,t:z39', u'Ebrie', u'II [1],13,22:g,m,t:[1,5]', u'II 48:g,m,t:-', u'Sylvania', u'Kiel', u'Dublin', u'Naestved', u'Rostock', u'Moscow', u'Menston', u'Plumaugat', u'Gateshead', u'Missouri', u'Catanzaro', u'Newyork', u'Sternschanze', u'Binningen', u'Anecho', u'II 9,12:g,s,t:e,n,x', u'Alminko', u'Nanergou', u'Cardoner', u'Ona', u'II 51:g,s,t:e,n,x', u'Lowestoft', u'Dessau', u'II 28:g,s,t:e,n,x', u'Splott', u'Kingston', u'Eaubonne', u'Uccle', u'Westhampton', u'II [1],13,22:g,t:[1,5]', u'IIIb [1],44:g,t:1,5', u'II 44:g,t:z42', u'IIIb 43:g,t:-', u'II 30:g,t:-', u'II 38:g,t:-', u'II 41:g,t:-', u'II 43:g,t:[1,5]', u'II 13,22:g,t:z6', u'II [1],13,23:g,t:1,5', u'Saintemarie', u'IV [1],40:g,t:-', u'II 17:g,t:[e,n,x,z15]', u'II 42:g,t:-', u'II 17:g,t:z39', u'II 65:g,t:-', u'Budapest', u'II 3,10:g,t:-', u'II 9,12,46,27:g,t:e,n,x', u'II [1],40:g,t:e,n,x,z15', u'II 57:g,t:-', u'Bloomsbury', u'II 13,23:g,t:e,n,x', u'II 52:g,t:-', u'II 35:g,t:1,5', u'II 35:g,t:z42', u'Agodi', u'II 40:g,t:z39', u'II 6,7:g,t:[e,n,x]', u'IIIa 50:g,z51:-', u'IIIa 51:g,z51:-', u'IV 48:g,z51:-', u'Larose', u'IV 21:g,z51:-', u'IIIa 21:g,z51:-', u'IIIa 63:g,z51:-', u'IIIa 62:g,z51:-', u'IV [1],53:g,z51:-', u'IV 43:g,z51:-', u'IV 11:g,z51:-', u'IV 6,7:g,z51:-', u'IIIa 35:g,z51:-', u'Wayne', u'IIIa 43:g,z51:-', u'Carswell', u'IV 44:g,z51:-', u'IIIa [1],13,23:g,z51:-', u'IIIa 53:g,z51:-', u'IIIa 47:g,z51:-', u'Newmexico', u'IIIa 18:g,z51:-', u'IV 18:g,z51:-', u'IV 45:g,z51:-', u'IV [1],40:g,z51:-', u'IV 50:g,z51:-', u'IIIa 45:g,z51:-', u'Alamo', u'IIIa 41:g,z51:-', u'IV [1],42:g,z51:-', u'IIIa 48:g,z51:-', u'IIIa 42:g,z51:-', u'IIIb 40:g,z51:e,n,x,z15', u'IV 38:g,z51:-', u'IIIa 38:g,z51:-', u'Tennyson', u'IIIa 40:g,z51:-', u'Travis', u'Maricopa', u'II 50:g,z62:e,n,x', u'II [1],9,12:g,z62:[e,n,x]', u'II 43:g,z62:e,n,x', u'II 9,46:g,z62:-', u'II 4,12:g,z62:-', u'Antarctica', u'Rosenberg', u'IIIb 60:i:[z]', u'Volkmarsdorf', u'Ouagadougou', u'Dieuppeul', u'Stratford', u'Chichester', u'IIIb 60:i:[e,n,x,z15]', u'Cotham', u'IIIb 53:i:z', u'Doorn', u'Machaga', u'IIIb 59:i:z35', u'Warnemuende', u'IIIb 65:i:z', u'Falkensee', u'Avonmouth', u'Zuilen', u'IIIb 17:i:z35', u'Ahanou', u'IIIb 50:i:e,n,x,z15', u'Diourbel', u'IIIb 21:i:1,5,7', u'IIIb 21:i:e,n,x,z15', u'IIIb 65:i:e,n,x,z15', u'Wisbech', u'IIIb 61:i:e,n,x,z15', u'Abobo', u'Pisa', u'IIIb 61:i:z53', u'IIIb 61:i:z35', u'Truro', u'Frankfurt', u'IIIb 59:i:z', u'Potto', u'Mathura', u'Agbara', u'Kabete', u'Amina', u'IIIb 58:i:z53', u'IIIb 61:i:z', u'Mjordan', u'Poeseldorf', u'Kuessel', u'Douala', u'IIIb 60:i:[z35]', u'Cuckmere', u'Amounderness', u'IIIb 58:i:e,n,x,z15', u'Bessi', u'IIIb 59:i:e,n,x,z15', u'Morehead', u'Landau', u'IIIb 16:i:z35', u'IIIb 57:i:e,n,x,z15', u'IIIb 57:i:z', u'Soerenga', u'Tibati', u'Magherafelt', u'Takoradi', u'Bergen', u'IIIb 47:i:e,n,x,z15', u'Kaneshie', u'Borromea', u'Middlesbrough', u'Warnow', u'Malmoe', u'IIIb 38:i:z53', u'Aba', u'IIIb 47:i:z35', u'Cyprus', u'Hoboken', u'Taksony', u'Yeerongpilly', u'IIIb 40:i:1,5,7', u'[1],13,22:i:-', u'Idikan', u'Typhimurium', u'Maritzburg', u'Bonariensis', u'Tumodi', u'48:i:-', u'IIIb 48:i:z61', u'Hofit', u'Cumberland', u'Alma', u'Samaru', u'Lindenburg', u'Verona', u'IIIb 48:i:z53', u'Bargny', u'IIIb 48:i:z', u'IIIb 47:i:z', u'II 4,12,27:i:z35', u'Gloucester', u'Tsevie', u'Farsta', u'Agama', u'Lagos', u'Seremban', u'IIIb 47:i:z53', u'Myrria', u'IIIb 48:i:z35', u'Heerlen', u'Veneziana', u'Norton', u'IIIb 35:i:z', u'Kentucky', u'IIIb 50:i:z53', u'Jukestown', u'Lika', u'IIIb 35:i:e,n,x,z15', u'Athinai', u'Brijbhumi', u'Gambia', u'IIIb 35:i:z53', u'Bandia', u'IIIb 35:i:z35', u'Evry', u'Aberdeen', u'IIIb 50:i:1,5,7', u'Kedougou', u'Mampeza', u'Buzu', u'IIIb 38:i:z', u'Lansing', u'Mgulani', u'Stuttgart', u'Mbao', u'Garoli', 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+ +remove_list=['Schleissheim', 'Sendai', 'Blegdam', 'Naestved', 'Rostock', 'Moscow', 'Antarctica', 'Rosenberg', 'Chittagong', 'Bilu', 'Dessau', 'Cannonhill', 'Ilugun'] + +rename_dict={'Nitra': 'Enteritidis', + 'Kiel': 'Dublin', + 'Koessen': 'Panama', + 'Phaliron': 'Kalumburu', + 'Istanbul': 'Hadar', + 'Haardt': 'Blockley', + 'Ferruch': 'Kottbus', + 'Sanga': 'Eboko', + 'Pakistan': 'Litchfield', + 'Bellevue': 'Lezennes', + 'Sunnycove': 'Daarle', + 'Noya': 'Akanji', + 'Virginia': 'Muenchen', + 'Djelfa': 'Skansen', + 'Konstanz': 'Gatuni', + 'Bardo': 'Newport', + 'Houston': 'Panama', + 'Martonos': 'Finkenwerder', + 'Midway': 'Florida', + 'Lindern': 'Charity', + 'Bahrenfeld': 'Onderstepoort', + 'Schalkwijk': 'Moussoro', + 'Amberg': 'Boecker', + 'Madelia': 'Carrau', + 'Soahanina': 'Sundsvall', + 'Stafford': 'Poano', + 'Chichiri': 'Uzaramo', + 'II 16:g,[m],[s],t:[e,n,x]': 'II 16:g,[m],[s],t:[1,5]', + 'Hindmarsh':'Bovismorbificans', + 'Yovokome': 'Manhattan'} + + #potential merge for O22 and O23 + #'Ibadan': 'Mississippi', + #'Bracknell': 'Oudwijk', + #'Vaertan': 'Ullevi', + #'Bahati': 'Durham', + #'Wichita': 'Friedenau', + #'Diguel': 'Telelkebir', + #'II 13,22:l,z28:1,5': 'II 13,23:l,z28:1,5', + #'Washington': 'Kintambo', + #'II 13,23:m,t:z42': 'II 13,22:m,t:z42:z39', + #'Serenli': 'Winslow', + #'Farmsen': 'Poona', + #'Durance': 'Ivrysurseine', + #'Agoueve': 'Cubana', + #'II 13,23:z29:1,5': 'II 13,22:z29:1,5', + #'II 13,23:z29:e,n,x': 'II 13,22:z29:e,n,x', + #'Picpus': 'Mampong', + #'Anna': 'Nimes', + #'Fanti': 'Leiden', + #'Ried': 'Ajiobo', + + #potential O68 list + #'Djelfa': 'Skansen', + #'Korbol': 'Nagoya', + #'Sanga': 'Eboko', + #'Konstanz': 'Gatuni', + #'Presov': 'Shipley', + #'Heistopdenberg': 'Bukuru', + #'Tounouma': 'Banalia', + #'Gaillac': 'Utah', + #'Santiago': 'Belem', + #'Virginia': 'Muenchen', + #'Yovokome': 'Manhattan', + #'Portanigra': 'Dunkwa', + #'Bardo': 'Newport', + #'Ferruch': 'Kottbus', + #'Alminko': 'Nanergou', + #'Bargny': 'Takoradi', + #'Magherafelt': 'Cyprus', + #'Haardt': 'Blockley', + #'Pakistan': 'Litchfield', + #'Yokoe': 'Bassa', + #'Noya': 'Akanji', + #'Lamphun': 'Giza', + #'Tananarive': 'Brunei', + #'Inchpark': 'Alagbon', + #'Sunnycove': 'Daarle', + #'Sindelfingen': 'Benue', + #'Phaliron': 'Kalumburu', + #'Bazenheid': 'Zerifin', + #'Paris': 'Mapo', + #'Istanbul': 'Hadar', + #'Chomedey': 'Glostrup', + #'Wippra': 'Molade', + #'Uno': 'Tamale', + #'Kolda': 'Yarm', + #'Bellevue': 'Lezennes', + #'Albany':'Duesseldorf' diff -r 43f6b7f6ebb3 -r e6437d423693 build/lib/bin/SeqSero2_package.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/bin/SeqSero2_package.py Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,1576 @@ +#!/usr/bin/env python3 + +import sys +import time +import random +import os +import subprocess +import gzip +import io +import pickle +import argparse +import itertools +from distutils.version import LooseVersion +from distutils.spawn import find_executable +sys.path.insert(1,sys.path[0]+'/..') + +try: + from .version import SeqSero2_version +except Exception: #ImportError + from version import SeqSero2_version + +### SeqSero Kmer +def parse_args(): + "Parse the input arguments, use '-h' for help." + parser = argparse.ArgumentParser(usage='SeqSero2_package.py -t -m -i [-d ] [-p ] [-b ]\n\nDevelopper: Shaokang Zhang (zskzsk@uga.edu), Hendrik C Den-Bakker (Hendrik.DenBakker@uga.edu) and Xiangyu Deng (xdeng@uga.edu)\n\nContact email:seqsero@gmail.com\n\nVersion: v1.1.1')#add "-m " in future + parser.add_argument("-i",nargs="+",help=": path/to/input_data",type=os.path.abspath) ### add 'type=os.path.abspath' to generate absolute path of input data. + parser.add_argument("-t",choices=['1','2','3','4','5','6'],help=": '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore fasta, '6' for nanopore fastq") + parser.add_argument("-b",choices=['sam','mem'],default="mem",help=": algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default 'mem' mode") + parser.add_argument("-p",default="1",help=": number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1") + parser.add_argument("-m",choices=['k','a'],default="a",help=": which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a") + parser.add_argument("-n",help=": optional, to specify a sample name in the report output") + parser.add_argument("-d",help=": optional, to specify an output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number") + parser.add_argument("-c",action="store_true",help=": if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files") + parser.add_argument("-s",action="store_true",help=": if '-s' was flagged, SeqSero2 will not output header in SeqSero_result.tsv") + parser.add_argument("--check",action="store_true",help=": use '--check' flag to check the required dependencies") + parser.add_argument('-v', '--version', action='version', version='%(prog)s ' + SeqSero2_version) + return parser.parse_args() + +### check paths of dependencies +check_dependencies = parse_args().check +dependencies = ['bwa','samtools','blastn','fastq-dump','spades.py','bedtools','SalmID.py'] +if check_dependencies: + for item in dependencies: + ext_path = find_executable(item) + if ext_path is not None: + print ("Using "+item+" - "+ext_path) + else: + print ("ERROR: can not find "+item+" in PATH") + sys.exit() +### end of --check + +def reverse_complement(sequence): + complement = { + 'A': 'T', + 'C': 'G', + 'G': 'C', + 'T': 'A', + 'N': 'N', + 'M': 'K', + 'R': 'Y', + 'W': 'W', + 'S': 'S', + 'Y': 'R', + 'K': 'M', + 'V': 'B', + 'H': 'D', + 'D': 'H', + 'B': 'V' + } + return "".join(complement[base] for base in reversed(sequence)) + + +def createKmerDict_reads(list_of_strings, kmer): + kmer_table = {} + for string in list_of_strings: + sequence = string.strip('\n') + for i in range(len(sequence) - kmer + 1): + new_mer = sequence[i:i + kmer].upper() + new_mer_rc = reverse_complement(new_mer) + if new_mer in kmer_table: + kmer_table[new_mer.upper()] += 1 + else: + kmer_table[new_mer.upper()] = 1 + if new_mer_rc in kmer_table: + kmer_table[new_mer_rc.upper()] += 1 + else: + kmer_table[new_mer_rc.upper()] = 1 + return kmer_table + + +def multifasta_dict(multifasta): + multifasta_list = [ + line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0 + ] + headers = [i for i in multifasta_list if i[0] == '>'] + multifasta_dict = {} + for h in headers: + start = multifasta_list.index(h) + for element in multifasta_list[start + 1:]: + if element[0] == '>': + break + else: + if h[1:] in multifasta_dict: + multifasta_dict[h[1:]] += element + else: + multifasta_dict[h[1:]] = element + return multifasta_dict + + +def multifasta_single_string(multifasta): + multifasta_list = [ + line.strip() for line in open(multifasta, 'r') + if (len(line.strip()) > 0) and (line.strip()[0] != '>') + ] + return ''.join(multifasta_list) + + +def chunk_a_long_sequence(long_sequence, chunk_size=60): + chunk_list = [] + steps = len(long_sequence) // 60 #how many chunks + for i in range(steps): + chunk_list.append(long_sequence[i * chunk_size:(i + 1) * chunk_size]) + chunk_list.append(long_sequence[steps * chunk_size:len(long_sequence)]) + return chunk_list + + +def target_multifasta_kmerizer(multifasta, k, kmerDict): + forward_length = 300 #if find the target, put forward 300 bases + reverse_length = 2200 #if find the target, put backward 2200 bases + chunk_size = 60 #it will firstly chunk the single long sequence to multiple smaller sequences, it controls the size of those smaller sequences + target_mers = [] + long_single_string = multifasta_single_string(multifasta) + multifasta_list = chunk_a_long_sequence(long_single_string, chunk_size) + unit_length = len(multifasta_list[0]) + forward_lines = int(forward_length / unit_length) + 1 + reverse_lines = int(forward_length / unit_length) + 1 + start_num = 0 + end_num = 0 + for i in range(len(multifasta_list)): + if i not in range(start_num, end_num): #avoid computational repetition + line = multifasta_list[i] + start = int((len(line) - k) // 2) + s1 = line[start:k + start] + if s1 in kmerDict: #detect it is a potential read or not (use the middle part) + if i - forward_lines >= 0: + start_num = i - forward_lines + else: + start_num = 0 + if i + reverse_lines <= len(multifasta_list) - 1: + end_num = i + reverse_lines + else: + end_num = len(multifasta_list) - 1 + target_list = [ + x.strip() for x in multifasta_list[start_num:end_num] + ] + target_line = "".join(target_list) + target_mers += [ + k1 for k1 in createKmerDict_reads([str(target_line)], k) + ] ##changed k to k1, just want to avoid the mixes of this "k" (kmer) to the "k" above (kmer length) + else: + pass + return set(target_mers) + + +def target_read_kmerizer(file, k, kmerDict): + i = 1 + n_reads = 0 + total_coverage = 0 + target_mers = [] + if file.endswith(".gz"): + file_content = io.BufferedReader(gzip.open(file)) + else: + file_content = open(file, "r").readlines() + for line in file_content: + start = int((len(line) - k) // 2) + if i % 4 == 2: + if file.endswith(".gz"): + s1 = line[start:k + start].decode() + line = line.decode() + else: + s1 = line[start:k + start] + if s1 in kmerDict: #detect it is a potential read or not (use the middle part) + n_reads += 1 + total_coverage += len(line) + target_mers += [ + k1 for k1 in createKmerDict_reads([str(line)], k) + ] #changed k to k1, just want to avoid the mixes of this "k" (kmer) to the "k" above (kmer length) + i += 1 + if total_coverage >= 4000000: + break + return set(target_mers) + + +def minion_fasta_kmerizer(file, k, kmerDict): + i = 1 + n_reads = 0 + total_coverage = 0 + target_mers = {} + for line in open(file): + if i % 2 == 0: + for kmer, rc_kmer in kmers(line.strip().upper(), k): + if (kmer in kmerDict) or (rc_kmer in kmerDict): + if kmer in target_mers: + target_mers[kmer] += 1 + else: + target_mers[kmer] = 1 + if rc_kmer in target_mers: + target_mers[rc_kmer] += 1 + else: + target_mers[rc_kmer] = 1 + i += 1 + return set([h for h in target_mers]) + + +def minion_fastq_kmerizer(file, k, kmerDict): + i = 1 + n_reads = 0 + total_coverage = 0 + target_mers = {} + for line in open(file): + if i % 4 == 2: + for kmer, rc_kmer in kmers(line.strip().upper(), k): + if (kmer in kmerDict) or (rc_kmer in kmerDict): + if kmer in target_mers: + target_mers[kmer] += 1 + else: + target_mers[kmer] = 1 + if rc_kmer in target_mers: + target_mers[rc_kmer] += 1 + else: + target_mers[rc_kmer] = 1 + i += 1 + return set([h for h in target_mers]) + + +def multifasta_single_string2(multifasta): + single_string = '' + with open(multifasta, 'r') as f: + for line in f: + if line.strip()[0] == '>': + pass + else: + single_string += line.strip() + return single_string + + +def kmers(seq, k): + rev_comp = reverse_complement(seq) + for start in range(1, len(seq) - k + 1): + yield seq[start:start + k], rev_comp[-(start + k):-start] + + +def multifasta_to_kmers_dict(multifasta,k_size):#used to create database kmer set + multi_seq_dict = multifasta_dict(multifasta) + lib_dict = {} + for h in multi_seq_dict: + lib_dict[h] = set( + [k for k in createKmerDict_reads([multi_seq_dict[h]], k_size)]) + return lib_dict + + +def Combine(b, c): + fliC_combinations = [] + fliC_combinations.append(",".join(c)) + temp_combinations = [] + for i in range(len(b)): + for x in itertools.combinations(b, i + 1): + temp_combinations.append(",".join(x)) + for x in temp_combinations: + temp = [] + for y in c: + temp.append(y) + temp.append(x) + temp = ",".join(temp) + temp = temp.split(",") + temp.sort() + temp = ",".join(temp) + fliC_combinations.append(temp) + return fliC_combinations + + +def seqsero_from_formula_to_serotypes(Otype, fliC, fljB, special_gene_list,subspecies): + #like test_output_06012017.txt + #can add more varialbles like sdf-type, sub-species-type in future (we can conclude it into a special-gene-list) + from Initial_Conditions import phase1,phase2,phaseO,sero,subs,remove_list,rename_dict + rename_dict_not_anymore=[rename_dict[x] for x in rename_dict] + rename_dict_all=rename_dict_not_anymore+list(rename_dict) #used for decide whether to + seronames = [] + seronames_none_subspecies=[] + for i in range(len(phase1)): + fliC_combine = [] + fljB_combine = [] + if phaseO[i] == Otype: # no VII in KW, but it's there + ### for fliC, detect every possible combinations to avoid the effect of "[" + if phase1[i].count("[") == 0: + fliC_combine.append(phase1[i]) + elif phase1[i].count("[") >= 1: + c = [] + b = [] + if phase1[i][0] == "[" and phase1[i][-1] == "]" and phase1[i].count( + "[") == 1: + content = phase1[i].replace("[", "").replace("]", "") + fliC_combine.append(content) + fliC_combine.append("-") + else: + for x in phase1[i].split(","): + if "[" in x: + b.append(x.replace("[", "").replace("]", "")) + else: + c.append(x) + fliC_combine = Combine( + b, c + ) #Combine will offer every possible combinations of the formula, like f,[g],t: f,t f,g,t + ### end of fliC "[" detect + ### for fljB, detect every possible combinations to avoid the effect of "[" + if phase2[i].count("[") == 0: + fljB_combine.append(phase2[i]) + elif phase2[i].count("[") >= 1: + d = [] + e = [] + if phase2[i][0] == "[" and phase2[i][-1] == "]" and phase2[i].count( + "[") == 1: + content = phase2[i].replace("[", "").replace("]", "") + fljB_combine.append(content) + fljB_combine.append("-") + else: + for x in phase2[i].split(","): + if "[" in x: + d.append(x.replace("[", "").replace("]", "")) + else: + e.append(x) + fljB_combine = Combine(d, e) + ### end of fljB "[" detect + new_fliC = fliC.split( + "," + ) #because some antigen like r,[i] not follow alphabetical order, so use this one to judge and can avoid missings + new_fliC.sort() + new_fliC = ",".join(new_fliC) + new_fljB = fljB.split(",") + new_fljB.sort() + new_fljB = ",".join(new_fljB) + if (new_fliC in fliC_combine + or fliC in fliC_combine) and (new_fljB in fljB_combine + or fljB in fljB_combine): + ######start, remove_list,rename_dict, added on 11/11/2018 + if sero[i] not in remove_list: + temp_sero=sero[i] + if temp_sero in rename_dict: + temp_sero=rename_dict[temp_sero] #rename if in the rename list + if temp_sero not in seronames:#the new sero may already included, if yes, then not consider + if subs[i] == subspecies: + seronames.append(temp_sero) + seronames_none_subspecies.append(temp_sero) + else: + pass + else: + pass + ######end, added on 11/11/2018 + #analyze seronames + subspecies_pointer="" + if len(seronames) == 0 and len(seronames_none_subspecies)!=0: + # ed_SL_12182019: modified to fix the subspecies output problem + #seronames=seronames_none_subspecies + seronames=["N/A"] + #subspecies_pointer="1" + subspecies_pointer="0" + if len(seronames) == 0: + seronames = [ + "N/A (The predicted antigenic profile does not exist in the White-Kauffmann-Le Minor scheme)" + ] + star = "" + star_line = "" + if len(seronames) > 1: #there are two possible predictions for serotypes + star = "*" + #changed 04072019 + #star_line = "The predicted serotypes share the same general formula:\t" + Otype + ":" + fliC + ":" + fljB + "\n" + if subspecies_pointer=="1" and len(seronames_none_subspecies)!=0: + star="*" + star_line="The predicted O and H antigens correspond to serotype '"+(" or ").join(seronames)+"' in the Kauffmann-White scheme. The predicted subspecies by SalmID (github.com/hcdenbakker/SalmID) may not be consistent with subspecies designation in the Kauffmann-White scheme. " + star_line + #star_line="The formula with this subspieces prediction can't get a serotype in KW manual, and the serotyping prediction was made without considering it."+star_line + if Otype=="": + Otype="-" + predict_form = Otype + ":" + fliC + ":" + fljB + predict_sero = (" or ").join(seronames) + ###special test for Enteritidis + if predict_form == "9:g,m:-": + sdf = "-" + for x in special_gene_list: + if x.startswith("sdf"): + sdf = "+" + #star_line="Detected sdf gene, a marker to differentiate Gallinarum and Enteritidis" + star_line="sdf gene detected. " + #predict_form = predict_form + " Sdf prediction:" + sdf + predict_form = predict_form #changed 04072019 + if sdf == "-": + star = "*" + #star_line="Didn't detected sdf gene, a marker to differentiate Gallinarum and Enteritidis" + star_line="sdf gene not detected. " + #changed in 04072019, for new output + #star_line = "Additional characterization is necessary to assign a serotype to this strain. Commonly circulating strains of serotype Enteritidis are sdf+, although sdf- strains of serotype Enteritidis are known to exist. Serotype Gallinarum is typically sdf- but should be quite rare. Sdf- strains of serotype Enteritidis and serotype Gallinarum can be differentiated by phenotypic profile or genetic criteria.\n" + #predict_sero = "Gallinarum/Enteritidis" #04132019, for new output requirement + predict_sero = "Gallinarum or Enteritidis" + ###end of special test for Enteritidis + elif predict_form == "4:i:-": + predict_sero = "I 4,[5],12:i:-" # change serotype name + elif predict_form == "4:r:-": + predict_sero = "N/A (4:r:-)" + elif predict_form == "4:b:-": + predict_sero = "N/A (4:b:-)" + #elif predict_form == "8:e,h:1,2": #removed after official merge of newport and bardo + #predict_sero = "Newport" + #star = "*" + #star_line = "Serotype Bardo shares the same antigenic profile with Newport, but Bardo is exceedingly rare." + claim = "The serotype(s) is/are the only serotype(s) with the indicated antigenic profile currently recognized in the Kauffmann White Scheme. New serotypes can emerge and the possibility exists that this antigenic profile may emerge in a different subspecies. Identification of strains to the subspecies level should accompany serotype determination; the same antigenic profile in different subspecies is considered different serotypes.\n" + if "N/A" in predict_sero: + claim = "" + #special test for Typhimurium + if "Typhimurium" in predict_sero or predict_form == "4:i:-": + normal = 0 + mutation = 0 + for x in special_gene_list: + if "oafA-O-4_full" in x: + normal = float(special_gene_list[x]) + elif "oafA-O-4_5-" in x: + mutation = float(special_gene_list[x]) + if normal > mutation: + pass + elif normal < mutation: + #predict_sero = predict_sero.strip() + "(O5-)" + predict_sero = predict_sero.strip() #diable special sero for new output requirement, 04132019 + star = "*" + #star_line = "Detected the deletion of O5-." + star_line = "Detected a deletion that causes O5- variant of Typhimurium. " + else: + pass + #special test for Paratyphi B + if "Paratyphi B" in predict_sero or predict_form == "4:b:-": + normal = 0 + mutation = 0 + for x in special_gene_list: + if "gntR-family-regulatory-protein_dt-positive" in x: + normal = float(special_gene_list[x]) + elif "gntR-family-regulatory-protein_dt-negative" in x: + mutation = float(special_gene_list[x]) + #print(normal,mutation) + if normal > mutation: + #predict_sero = predict_sero.strip() + "(dt+)" #diable special sero for new output requirement, 04132019 + predict_sero = predict_sero.strip()+' var. L(+) tartrate+' if "Paratyphi B" in predict_sero else predict_sero.strip() + star = "*" + #star_line = "Didn't detect the SNP for dt- which means this isolate is a Paratyphi B variant L(+) tartrate(+)." + star_line = "The SNP that causes d-Tartrate nonfermentating phenotype of Paratyphi B was not detected. " + elif normal < mutation: + #predict_sero = predict_sero.strip() + "(dt-)" #diable special sero for new output requirement, 04132019 + predict_sero = predict_sero.strip() + star = "*" + #star_line = "Detected the SNP for dt- which means this isolate is a systemic pathovar of Paratyphi B." + star_line = "Detected the SNP for d-Tartrate nonfermenting phenotype of Paratyphi B. " + else: + star = "*" + #star_line = " Failed to detect the SNP for dt-, can't decide it's a Paratyphi B variant L(+) tartrate(+) or not." + star_line = " " ## ed_SL_05152019: do not report this situation. + #special test for O13,22 and O13,23 + if Otype=="13": + #ex_dir = os.path.dirname(os.path.realpath(__file__)) + ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019 + f = open(ex_dir + '/special.pickle', 'rb') + special = pickle.load(f) + O22_O23=special['O22_O23'] + if predict_sero.split(" or ")[0] in O22_O23[-1] and predict_sero.split(" or ")[0] not in rename_dict_all:#if in rename_dict_all, then it means already merged, no need to analyze + O22_score=0 + O23_score=0 + for x in special_gene_list: + if "O:22" in x: + O22_score = O22_score+float(special_gene_list[x]) + elif "O:23" in x: + O23_score = O23_score+float(special_gene_list[x]) + #print(O22_score,O23_score) + for z in O22_O23[0]: + if predict_sero.split(" or ")[0] in z: + if O22_score > O23_score: + star = "*" + #star_line = "Detected O22 specific genes to further differenciate '"+predict_sero+"'." #diabled for new output requirement, 04132019 + predict_sero = z[0] + elif O22_score < O23_score: + star = "*" + #star_line = "Detected O23 specific genes to further differenciate '"+predict_sero+"'." #diabled for new output requirement, 04132019 + predict_sero = z[1] + else: + star = "*" + #star_line = "Fail to detect O22 and O23 differences." #diabled for new output requirement, 04132019 + if " or " in predict_sero: + star_line = star_line + "The predicted serotypes share the same general formula: " + Otype + ":" + fliC + ":" + fljB + "." + #special test for O6,8 + #merge_O68_list=["Blockley","Bovismorbificans","Hadar","Litchfield","Manhattan","Muenchen"] #remove 11/11/2018, because already in merge list + #for x in merge_O68_list: + # if x in predict_sero: + # predict_sero=x + # star="" + # star_line="" + #special test for Montevideo; most of them are monophasic + #if "Montevideo" in predict_sero and "1,2,7" in predict_form: #remove 11/11/2018, because already in merge list + #star="*" + #star_line="Montevideo is almost always monophasic, having an antigen called for the fljB position may be a result of Salmonella-Salmonella contamination." + return predict_form, predict_sero, star, star_line, claim +### End of SeqSero Kmer part + +### Begin of SeqSero2 allele prediction and output +def xml_parse_score_comparision_seqsero(xmlfile): + #used to do seqsero xml analysis + from Bio.Blast import NCBIXML + handle=open(xmlfile) + handle=NCBIXML.parse(handle) + handle=list(handle) + List=[] + List_score=[] + List_ids=[] + List_query_region=[] + for i in range(len(handle)): + if len(handle[i].alignments)>0: + for j in range(len(handle[i].alignments)): + score=0 + ids=0 + cover_region=set() #fixed problem that repeated calculation leading percentage > 1 + List.append(handle[i].query.strip()+"___"+handle[i].alignments[j].hit_def) + for z in range(len(handle[i].alignments[j].hsps)): + hsp=handle[i].alignments[j].hsps[z] + temp=set(range(hsp.query_start,hsp.query_end)) + if len(cover_region)==0: + cover_region=cover_region|temp + fraction=1 + else: + fraction=1-len(cover_region&temp)/float(len(temp)) + cover_region=cover_region|temp + if "last" in handle[i].query or "first" in handle[i].query: + score+=hsp.bits*fraction + ids+=float(hsp.identities)/handle[i].query_length*fraction + else: + score+=hsp.bits*fraction + ids+=float(hsp.identities)/handle[i].query_length*fraction + List_score.append(score) + List_ids.append(ids) + List_query_region.append(cover_region) + temp=zip(List,List_score,List_ids,List_query_region) + Final_list=sorted(temp, key=lambda d:d[1], reverse = True) + return Final_list + + +def Uniq(L,sort_on_fre="none"): #return the uniq list and the count number + Old=L + L.sort() + L = [L[i] for i in range(len(L)) if L[i] not in L[:i]] + count=[] + for j in range(len(L)): + y=0 + for x in Old: + if L[j]==x: + y+=1 + count.append(y) + if sort_on_fre!="none": + d=zip(*sorted(zip(count, L))) + L=d[1] + count=d[0] + return (L,count) + +def judge_fliC_or_fljB_from_head_tail_for_one_contig(nodes_vs_score_list): + #used to predict it's fliC or fljB for one contig, based on tail and head score, but output the score difference,if it is very small, then not reliable, use blast score for whole contig to test + #this is mainly used for + a=nodes_vs_score_list + fliC_score=0 + fljB_score=0 + for z in a: + if "fliC" in z[0]: + fliC_score+=z[1] + elif "fljB" in z[0]: + fljB_score+=z[1] + if fliC_score>=fljB_score: + role="fliC" + else: + role="fljB" + return (role,abs(fliC_score-fljB_score)) + +def judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(node_name,Final_list,Final_list_passed): + #used to predict contig is fliC or fljB, if the differnce score value on above head_and_tail is less than 10 (quite small) + #also used when no head or tail got blasted score for the contig + role="" + for z in Final_list_passed: + if node_name in z[0]: + role=z[0].split("_")[0] + break + return role + +def fliC_or_fljB_judge_from_head_tail_sequence(nodes_list,tail_head_list,Final_list,Final_list_passed): + #nodes_list is the c created by c,d=Uniq(nodes) in below function + first_target="" + role_list=[] + for x in nodes_list: + a=[] + role="" + for y in tail_head_list: + if x in y[0]: + a.append(y) + if len(a)==4: + role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) + if diff<20: + role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) + elif len(a)==3: + ###however, if the one with highest score is the fewer one, compare their accumulation score + role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) + if diff<20: + role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) + ###end of above score comparison + elif len(a)==2: + #must on same node, if not, then decide with unit blast score, blast-score/length_of_special_sequence(30 or 37) + temp=[] + for z in a: + temp.append(z[0].split("_")[0]) + m,n=Uniq(temp)#should only have one choice, but weird situation might occur too + if len(m)==1: + pass + else: + pass + role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) + if diff<20: + role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) + ###need to desgin a algorithm to guess most possible situation for nodes_list, See the situations of test evaluation + elif len(a)==1: + #that one + role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) + if diff<20: + role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) + #need to evaluate, in future, may set up a cut-off, if not met, then just find Final_list_passed best match,like when "a==0" + else:#a==0 + #use Final_list_passed best match + for z in Final_list_passed: + if x in z[0]: + role=z[0].split("_")[0] + break + #print x,role,len(a) + role_list.append((role,x)) + if len(role_list)==2: + if role_list[0][0]==role_list[1][0]:#this is the most cocmmon error, two antigen were assigned to same phase + #just use score to do a final test + role_list=[] + for x in nodes_list: + role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) + role_list.append((role,x)) + return role_list + +def decide_contig_roles_for_H_antigen(Final_list,Final_list_passed): + #used to decide which contig is FliC and which one is fljB + contigs=[] + nodes=[] + for x in Final_list_passed: + if x[0].startswith("fl") and "last" not in x[0] and "first" not in x[0]: + nodes.append(x[0].split("___")[1].strip()) + c,d=Uniq(nodes)#c is node_list + #print c + tail_head_list=[x for x in Final_list if ("last" in x[0] or "first" in x[0])] + roles=fliC_or_fljB_judge_from_head_tail_sequence(c,tail_head_list,Final_list,Final_list_passed) + return roles + +def decide_O_type_and_get_special_genes(Final_list,Final_list_passed): + #decide O based on Final_list + O_choice="?" + O_list=[] + special_genes={} + nodes=[] + for x in Final_list_passed: + if x[0].startswith("O-"): + nodes.append(x[0].split("___")[1].strip()) + elif not x[0].startswith("fl"): + special_genes[x[0]]=x[2]#08172018, x[2] changed from x[-1] + #print "special_genes:",special_genes + c,d=Uniq(nodes) + #print "potential O antigen contig",c + final_O=[] + O_nodes_list=[] + for x in c:#c is the list for contigs + temp=0 + for y in Final_list_passed: + if x in y[0] and y[0].startswith("O-"): + final_O.append(y) + break + ### O contig has the problem of two genes on same contig, so do additional test + potenial_new_gene="" + for x in final_O: + pointer=0 #for genes merged or not + #not consider O-1,3,19_not_in_3,10, too short compared with others + if "O-1,3,19_not_in_3,10" not in x[0] and int(x[0].split("__")[1].split("___")[0])*x[2]+850 <= int(x[0].split("length_")[1].split("_")[0]):#gene length << contig length; for now give 300*2 (for secureity can use 400*2) as flank region + pointer=x[0].split("___")[1].strip()#store the contig name + print(pointer) + if pointer!=0:#it has potential merge event + for y in Final_list: + if pointer in y[0] and y not in final_O and (y[1]>=int(y[0].split("__")[1].split("___")[0])*1.5 or (y[1]>=int(y[0].split("__")[1].split("___")[0])*y[2] and y[1]>=400)):#that's a realtively strict filter now; if passed, it has merge event and add one more to final_O + potenial_new_gene=y + #print(potenial_new_gene) + break + if potenial_new_gene!="": + print("two differnt genes in same contig, fix it for O antigen") + print(potenial_new_gene[:3]) + pointer=0 + for y in final_O: + if y[0].split("___")[-1]==potenial_new_gene[0].split("___")[-1]: + pointer=1 + if pointer!=0: #changed to consider two genes in same contig + final_O.append(potenial_new_gene) + ### end of the two genes on same contig test + final_O=sorted(final_O,key=lambda x: x[2], reverse=True)#sorted + if len(final_O)==0 or (len(final_O)==1 and "O-1,3,19_not_in_3,10" in final_O[0][0]): + #print "$$$No Otype, due to no hit"#may need to be changed + O_choice="-" + else: + highest_O_coverage=max([float(x[0].split("_cov_")[-1].split("_")[0]) for x in final_O if "O-1,3,19_not_in_3,10" not in x[0]]) + O_list=[] + O_list_less_contamination=[] + for x in final_O: + if not "O-1,3,19_not_in_3,10__130" in x[0]:#O-1,3,19_not_in_3,10 is too small, which may affect further analysis; to avoid contamination affect, use 0.15 of highest coverage as cut-off + O_list.append(x[0].split("__")[0]) + O_nodes_list.append(x[0].split("___")[1]) + if float(x[0].split("_cov_")[-1].split("_")[0])>highest_O_coverage*0.15: + O_list_less_contamination.append(x[0].split("__")[0]) + ### special test for O9,46 and O3,10 family + if ("O-9,46_wbaV" in O_list or "O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254" in O_list) and O_list_less_contamination[0].startswith("O-9,"):#not sure should use and float(O9_wbaV)/float(num_1) > 0.1 + if "O-9,46_wzy" in O_list or "O-9,46_wzy_partial" in O_list:#and float(O946_wzy)/float(num_1) > 0.1 + O_choice="O-9,46" + #print "$$$Most possilble Otype: O-9,46" + elif "O-9,46,27_partial_wzy" in O_list:#and float(O94627)/float(num_1) > 0.1 + O_choice="O-9,46,27" + #print "$$$Most possilble Otype: O-9,46,27" + else: + O_choice="O-9"#next, detect O9 vs O2? + O2=0 + O9=0 + for z in special_genes: + if "tyr-O-9" in z: + O9=special_genes[z] + elif "tyr-O-2" in z: + O2=special_genes[z] + if O2>O9: + O_choice="O-2" + elif O2 0.1 and float(O946_wzy)/float(num_1) > 0.1 + if "O-3,10_not_in_1,3,19" in O_list:#and float(O310_no_1319)/float(num_1) > 0.1 + O_choice="O-3,10" + #print "$$$Most possilble Otype: O-3,10 (contain O-3,10_not_in_1,3,19)" + else: + O_choice="O-1,3,19" + #print "$$$Most possilble Otype: O-1,3,19 (not contain O-3,10_not_in_1,3,19)" + ### end of special test for O9,46 and O3,10 family + else: + try: + max_score=0 + for x in final_O: + if x[2]>=max_score and float(x[0].split("_cov_")[-1].split("_")[0])>highest_O_coverage*0.15:#use x[2],08172018, the "coverage identity = cover_length * identity"; also meet coverage threshold + max_score=x[2]#change from x[-1] to x[2],08172018 + O_choice=x[0].split("_")[0] + if O_choice=="O-1,3,19": + O_choice=final_O[1][0].split("_")[0] + #print "$$$Most possilble Otype: ",O_choice + except: + pass + #print "$$$No suitable Otype, or failure of mapping (please check the quality of raw reads)" + if O_choice=="O-9,46,27" and len(O_list)==2 and "O-4_wzx" in O_list: #special for very low chance sitatuion between O4 and O9,27,46, this is for serotypes like Bredeney and Schwarzengrund (normallly O-4 will have higher score, but sometimes sequencing quality may affect the prediction) + O_choice="O-4" + #print "O:",O_choice,O_nodes_list + Otypes=[] + for x in O_list: + if x!="O-1,3,19_not_in_3,10": + if "O-9,46_" not in x: + Otypes.append(x.split("_")[0]) + else: + Otypes.append(x.split("-from")[0])#O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254 + #Otypes=[x.split("_")[0] for x in O_list if x!="O-1,3,19_not_in_3,10"] + Otypes_uniq,Otypes_fre=Uniq(Otypes) + contamination_O="" + if O_choice=="O-9,46,27" or O_choice=="O-3,10" or O_choice=="O-1,3,19": + if len(Otypes_uniq)>2: + contamination_O="potential contamination from O antigen signals" + else: + if len(Otypes_uniq)>1: + if O_choice=="O-4" and len(Otypes_uniq)==2 and "O-9,46,27" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund + contamination_O="" + elif O_choice=="O-9,46" and len(Otypes_uniq)==2 and "O-9,46_wbaV" in Otypes_uniq and "O-9,46_wzy" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund + contamination_O="" + else: + contamination_O="potential contamination from O antigen signals" + return O_choice,O_nodes_list,special_genes,final_O,contamination_O,Otypes_uniq +### End of SeqSero2 allele prediction and output + +def get_input_files(make_dir,input_file,data_type,dirpath): + #tell input files from datatype + #": '1'(pair-end reads, interleaved),'2'(pair-end reads, seperated),'3'(single-end reads), '4'(assembly),'5'(nanopore fasta),'6'(nanopore fastq)" + for_fq="" + rev_fq="" + os.chdir(make_dir) + if data_type=="1": + input_file=input_file[0].split("/")[-1] + if input_file.endswith(".sra"): + subprocess.check_call("fastq-dump --split-files "+input_file,shell=True) + for_fq=input_file.replace(".sra","_1.fastq") + rev_fq=input_file.replace(".sra","_2.fastq") + else: + core_id=input_file.split(".fastq")[0].split(".fq")[0] + for_fq=core_id+"_1.fastq" + rev_fq=core_id+"_2.fastq" + if input_file.endswith(".gz"): + subprocess.check_call("gzip -dc "+input_file+" | "+dirpath+"/deinterleave_fastq.sh "+for_fq+" "+rev_fq,shell=True) + else: + subprocess.check_call("cat "+input_file+" | "+dirpath+"/deinterleave_fastq.sh "+for_fq+" "+rev_fq,shell=True) + elif data_type=="2": + for_fq=input_file[0].split("/")[-1] + rev_fq=input_file[1].split("/")[-1] + elif data_type=="3": + input_file=input_file[0].split("/")[-1] + if input_file.endswith(".sra"): + subprocess.check_call("fastq-dump --split-files "+input_file,shell=True) + for_fq=input_file.replace(".sra","_1.fastq") + else: + for_fq=input_file + elif data_type in ["4","5","6"]: + for_fq=input_file[0].split("/")[-1] + os.chdir("..") + return for_fq,rev_fq + +def predict_O_and_H_types(Final_list,Final_list_passed,new_fasta): + #get O and H types from Final_list from blast parsing; allele mode + from Bio import SeqIO + fliC_choice="-" + fljB_choice="-" + fliC_contig="NA" + fljB_contig="NA" + fliC_region=set([0]) + fljB_region=set([0,]) + fliC_length=0 #can be changed to coverage in future; in 03292019, changed to ailgned length + fljB_length=0 #can be changed to coverage in future; in 03292019, changed to ailgned length + O_choice="-"#no need to decide O contig for now, should be only one + O_choice,O_nodes,special_gene_list,O_nodes_roles,contamination_O,Otypes_uniq=decide_O_type_and_get_special_genes(Final_list,Final_list_passed)#decide the O antigen type and also return special-gene-list for further identification + O_choice=O_choice.split("-")[-1].strip() + if (O_choice=="1,3,19" and len(O_nodes_roles)==1 and "1,3,19" in O_nodes_roles[0][0]) or O_choice=="": + O_choice="-" + H_contig_roles=decide_contig_roles_for_H_antigen(Final_list,Final_list_passed)#decide the H antigen contig is fliC or fljB + #add alignment locations, used for further selection, 03312019 + for i in range(len(H_contig_roles)): + x=H_contig_roles[i] + for y in Final_list_passed: + if x[1] in y[0] and y[0].startswith(x[0]): + H_contig_roles[i]+=H_contig_roles[i]+(y[-1],) + break + log_file=open("SeqSero_log.txt","a") + extract_file=open("Extracted_antigen_alleles.fasta","a") + handle_fasta=list(SeqIO.parse(new_fasta,"fasta")) + + #print("O_contigs:") + log_file.write("O_contigs:\n") + extract_file.write("#Sequences with antigen signals (if the micro-assembled contig only covers the flanking region, it will not be used for contamination analysis)\n") + extract_file.write("#O_contigs:\n") + for x in O_nodes_roles: + if "O-1,3,19_not_in_3,10" not in x[0]:#O-1,3,19_not_in_3,10 is just a small size marker + #print(x[0].split("___")[-1],x[0].split("__")[0],"blast score:",x[1],"identity%:",str(round(x[2]*100,2))+"%",str(min(x[-1]))+" to "+str(max(x[-1]))) + log_file.write(x[0].split("___")[-1]+" "+x[0].split("__")[0]+"; "+"blast score: "+str(x[1])+" identity%: "+str(round(x[2]*100,2))+"%; alignment from "+str(min(x[-1]))+" to "+str(max(x[-1]))+" of antigen\n") + title=">"+x[0].split("___")[-1]+" "+x[0].split("__")[0]+"; "+"blast score: "+str(x[1])+" identity%: "+str(round(x[2]*100,2))+"%; alignment from "+str(min(x[-1]))+" to "+str(max(x[-1]))+" of antigen\n" + seqs="" + for z in handle_fasta: + if x[0].split("___")[-1]==z.description: + seqs=str(z.seq) + extract_file.write(title+seqs+"\n") + if len(H_contig_roles)!=0: + highest_H_coverage=max([float(x[1].split("_cov_")[-1].split("_")[0]) for x in H_contig_roles]) #less than highest*0.1 would be regarded as contamination and noises, they will still be considered in contamination detection and logs, but not used as final serotype output + else: + highest_H_coverage=0 + for x in H_contig_roles: + #if multiple choices, temporately select the one with longest length for now, will revise in further change + if "fliC" == x[0] and len(x[-1])>=fliC_length and x[1] not in O_nodes and float(x[1].split("_cov_")[-1].split("_")[0])>highest_H_coverage*0.13:#remember to avoid the effect of O-type contig, so should not in O_node list + fliC_contig=x[1] + fliC_length=len(x[-1]) + elif "fljB" == x[0] and len(x[-1])>=fljB_length and x[1] not in O_nodes and float(x[1].split("_cov_")[-1].split("_")[0])>highest_H_coverage*0.13: + fljB_contig=x[1] + fljB_length=len(x[-1]) + for x in Final_list_passed: + if fliC_choice=="-" and "fliC_" in x[0] and fliC_contig in x[0]: + fliC_choice=x[0].split("_")[1] + elif fljB_choice=="-" and "fljB_" in x[0] and fljB_contig in x[0]: + fljB_choice=x[0].split("_")[1] + elif fliC_choice!="-" and fljB_choice!="-": + break + #now remove contigs not in middle core part + first_allele="NA" + first_allele_percentage=0 + for x in Final_list: + if x[0].startswith("fliC") or x[0].startswith("fljB"): + first_allele=x[0].split("__")[0] #used to filter those un-middle contigs + first_allele_percentage=x[2] + break + additional_contigs=[] + for x in Final_list: + if first_allele in x[0]: + if (fliC_contig == x[0].split("___")[-1]): + fliC_region=x[3] + elif fljB_contig!="NA" and (fljB_contig == x[0].split("___")[-1]): + fljB_region=x[3] + else: + if x[1]*1.1>int(x[0].split("___")[1].split("_")[3]):#loose threshold by multiplying 1.1 + additional_contigs.append(x) + #else: + #print x[:3] + #we can just use the fljB region (or fliC depends on size), no matter set() or contain a large locations (without middle part); however, if none of them is fully assembled, use 500 and 1200 as conservative cut-off + if first_allele_percentage>0.9: + if len(fliC_region)>len(fljB_region) and (max(fljB_region)-min(fljB_region))>1000: + target_region=fljB_region|(fliC_region-set(range(min(fljB_region),max(fljB_region)))) #fljB_region|(fliC_region-set(range(min(fljB_region),max(fljB_region)))) + elif len(fliC_region)1000: + target_region=fliC_region|(fljB_region-set(range(min(fliC_region),max(fliC_region)))) #fljB_region|(fliC_region-set(range(min(fljB_region),max(fljB_region)))) + else: + target_region=set()#doesn't do anything + else: + target_region=set()#doesn't do anything + #print(target_region) + #print(additional_contigs) + target_region2=set(list(range(0,525))+list(range(1200,1700)))#I found to use 500 to 1200 as special region would be best + target_region=target_region2|target_region + for x in additional_contigs: + removal=0 + contig_length=int(x[0].split("___")[1].split("length_")[-1].split("_")[0]) + if fljB_contig not in x[0] and fliC_contig not in x[0] and len(target_region&x[3])/float(len(x[3]))>0.65 and contig_length*0.5 0.9 and float(x[0].split("__")[1].split("___")[0])*x[2]/len(x[-1])>0.96:#if high similiarity with middle part of first allele (first allele >0.9, already cover middle part) + removal=1 + else: + pass + if removal==1: + for y in H_contig_roles: + if y[1] in x[0]: + H_contig_roles.remove(y) + else: + pass + #print(x[:3],contig_length,len(target_region&x[3])/float(len(x[3])),contig_length*0.5,len(x[3]),contig_length*1.5) + #end of removing none-middle contigs + #print("H_contigs:") + log_file.write("H_contigs:\n") + extract_file.write("#H_contigs:\n") + H_contig_stat=[] + H1_cont_stat={} + H2_cont_stat={} + for i in range(len(H_contig_roles)): + x=H_contig_roles[i] + a=0 + for y in Final_list_passed: + if x[1] in y[0] and y[0].startswith(x[0]): + if "first" in y[0] or "last" in y[0]: #this is the final filter to decide it's fliC or fljB, if can't pass, then can't decide + for y in Final_list_passed: #it's impossible to has the "first" and "last" allele as prediction, so re-do it + if x[1] in y[0]:#it's very possible to be third phase allele, so no need to make it must be fliC or fljB + #print(x[1],"can't_decide_fliC_or_fljB",y[0].split("_")[1],"blast_score:",y[1],"identity%:",str(round(y[2]*100,2))+"%",str(min(y[-1]))+" to "+str(max(y[-1]))) + log_file.write(x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antigen\n") + H_contig_roles[i]="can't decide fliC or fljB, may be third phase" + title=">"+x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antiten\n" + seqs="" + for z in handle_fasta: + if x[1]==z.description: + seqs=str(z.seq) + extract_file.write(title+seqs+"\n") + break + else: + #print(x[1],x[0],y[0].split("_")[1],"blast_score:",y[1],"identity%:",str(round(y[2]*100,2))+"%",str(min(y[-1]))+" to "+str(max(y[-1]))) + log_file.write(x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antigen\n") + title=">"+x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antigen\n" + seqs="" + for z in handle_fasta: + if x[1]==z.description: + seqs=str(z.seq) + extract_file.write(title+seqs+"\n") + if x[0]=="fliC": + if y[0].split("_")[1] not in H1_cont_stat: + H1_cont_stat[y[0].split("_")[1]]=y[2] + else: + H1_cont_stat[y[0].split("_")[1]]+=y[2] + if x[0]=="fljB": + if y[0].split("_")[1] not in H2_cont_stat: + H2_cont_stat[y[0].split("_")[1]]=y[2] + else: + H2_cont_stat[y[0].split("_")[1]]+=y[2] + break + #detect contaminations + #print(H1_cont_stat) + #print(H2_cont_stat) + H1_cont_stat_list=[x for x in H1_cont_stat if H1_cont_stat[x]>0.2] + H2_cont_stat_list=[x for x in H2_cont_stat if H2_cont_stat[x]>0.2] + contamination_H="" + if len(H1_cont_stat_list)>1 or len(H2_cont_stat_list)>1: + contamination_H="potential contamination from H antigen signals" + elif len(H2_cont_stat_list)==1 and fljB_contig=="NA": + contamination_H="potential contamination from H antigen signals, uncommon weak fljB signals detected" + #get additional antigens + """ + if ("O-9,46_wbaV" in O_list or "O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254" in O_list) and O_list_less_contamination[0].startswith("O-9,"):#not sure should use and float(O9_wbaV)/float(num_1) > 0.1 + if "O-9,46_wzy" in O_list:#and float(O946_wzy)/float(num_1) > 0.1 + O_choice="O-9,46" + #print "$$$Most possilble Otype: O-9,46" + elif "O-9,46,27_partial_wzy" in O_list:#and float(O94627)/float(num_1) > 0.1 + O_choice="O-9,46,27" + #print "$$$Most possilble Otype: O-9,46,27" + elif ("O-3,10_wzx" in O_list) and ("O-9,46_wzy" in O_list) and (O_list[0].startswith("O-3,10") or O_list_less_contamination[0].startswith("O-9,46_wzy")):#and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1 + if "O-3,10_not_in_1,3,19" in O_list:#and float(O310_no_1319)/float(num_1) > 0.1 + O_choice="O-3,10" + #print "$$$Most possilble Otype: O-3,10 (contain O-3,10_not_in_1,3,19)" + else: + O_choice="O-1,3,19" + #print "$$$Most possilble Otype: O-1,3,19 (not contain O-3,10_not_in_1,3,19)" + ### end of special test for O9,46 and O3,10 family + + if O_choice=="O-9,46,27" or O_choice=="O-3,10" or O_choice=="O-1,3,19": + if len(Otypes_uniq)>2: + contamination_O="potential contamination from O antigen signals" + else: + if len(Otypes_uniq)>1: + if O_choice=="O-4" and len(Otypes_uniq)==2 and "O-9,46,27" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund + contamination_O="" + elif O_choice=="O-9,46" and len(Otypes_uniq)==2 and "O-9,46_wbaV" in Otypes_uniq and "O-9,46_wzy" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund + contamination_O="" + """ + additonal_antigents=[] + #print(contamination_O) + #print(contamination_H) + log_file.write(contamination_O+"\n") + log_file.write(contamination_H+"\n") + log_file.close() + return O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H,Otypes_uniq,H1_cont_stat_list,H2_cont_stat_list + +def get_input_K(input_file,lib_dict,data_type,k_size): + #kmer mode; get input_Ks from dict and data_type + kmers = [] + for h in lib_dict: + kmers += lib_dict[h] + if data_type == '4': + input_Ks = target_multifasta_kmerizer(input_file, k_size, set(kmers)) + elif data_type == '1' or data_type == '2' or data_type == '3':#set it for now, will change later + input_Ks = target_read_kmerizer(input_file, k_size, set(kmers)) + elif data_type == '5':#minion_2d_fasta + input_Ks = minion_fasta_kmerizer(input_file, k_size, set(kmers)) + if data_type == '6':#minion_2d_fastq + input_Ks = minion_fastq_kmerizer(input_file, k_size, set(kmers)) + return input_Ks + +def get_kmer_dict(lib_dict,input_Ks): + #kmer mode; get predicted types + O_dict = {} + H_dict = {} + Special_dict = {} + for h in lib_dict: + score = (len(lib_dict[h] & input_Ks) / len(lib_dict[h])) * 100 + if score > 1: # Arbitrary cut-off for similarity score very low but seems necessary to detect O-3,10 in some cases + if h.startswith('O-') and score > 25: + O_dict[h] = score + if h.startswith('fl') and score > 40: + H_dict[h] = score + if (h[:2] != 'fl') and (h[:2] != 'O-'): + Special_dict[h] = score + return O_dict,H_dict,Special_dict + +def call_O_and_H_type(O_dict,H_dict,Special_dict,make_dir): + log_file=open("SeqSero_log.txt","a") + log_file.write("O_scores:\n") + #call O: + highest_O = '-' + if len(O_dict) == 0: + pass + else: + for x in O_dict: + log_file.write(x+"\t"+str(O_dict[x])+"\n") + if ('O-9,46_wbaV__1002' in O_dict and O_dict['O-9,46_wbaV__1002']>70) or ("O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002" in O_dict and O_dict['O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002']>70): # not sure should use and float(O9_wbaV)/float(num_1) > 0.1 + #if 'O-9,46_wzy__1191' in O_dict or "O-9,46_wzy_partial__216" in O_dict: # and float(O946_wzy)/float(num_1) > 0.1 + #modified to fix miscall of O-9,46 + if ('O-9,46_wzy__1191' in O_dict and O_dict['O-9,46_wzy__1191']>40) or ("O-9,46_wzy_partial__216" in O_dict and O_dict["O-9,46_wzy_partial__216"]>40): # and float(O946_wzy)/float(num_1) > 0.1 + highest_O = "O-9,46" + elif "O-9,46,27_partial_wzy__1019" in O_dict: # and float(O94627)/float(num_1) > 0.1 + highest_O = "O-9,46,27" + else: + highest_O = "O-9" # next, detect O9 vs O2? + O2 = 0 + O9 = 0 + for z in Special_dict: + if "tyr-O-9" in z: + O9 = float(Special_dict[z]) + if "tyr-O-2" in z: + O2 = float(Special_dict[z]) + if O2 > O9: + highest_O = "O-2" + elif ("O-3,10_wzx__1539" in O_dict) and ( + "O-9,46_wzy__1191" in O_dict + ): # and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1 + if "O-3,10_not_in_1,3,19__1519" in O_dict: # and float(O310_no_1319)/float(num_1) > 0.1 + highest_O = "O-3,10" + else: + highest_O = "O-1,3,19" + ### end of special test for O9,46 and O3,10 family + else: + try: + max_score = 0 + for x in O_dict: + if float(O_dict[x]) >= max_score: + max_score = float(O_dict[x]) + #highest_O = x.split("_")[0] + # ed_SL_12182019: modified to fix the O-9,46 error example1 + if (x == 'O-9,46_wbaV__1002' or x == 'O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002') and ('O-9,46_wzy__1191' not in O_dict and 'O-9,46_wzy_partial__216' not in O_dict): + highest_O = "O-9" + else: + highest_O = x.split("_")[0] + if highest_O == "O-1,3,19": + highest_O = '-' + max_score = 0 + for x in O_dict: + if x == 'O-1,3,19_not_in_3,10__130': + pass + else: + if float(O_dict[x]) >= max_score: + max_score = float(O_dict[x]) + #highest_O = x.split("_")[0] + # ed_SL_12182019: modified to fix the O-9,46 error example1 + if (x == 'O-9,46_wbaV__1002' or x == 'O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002') and ('O-9,46_wzy__1191' not in O_dict and 'O-9,46_wzy_partial__216' not in O_dict): + highest_O = "O-9" + else: + highest_O = x.split("_")[0] + except: + pass + #call_fliC: + if len(H_dict)!=0: + highest_H_score_both_BC=H_dict[max(H_dict.keys(), key=(lambda k: H_dict[k]))] #used to detect whether fljB existed or not + else: + highest_H_score_both_BC=0 + highest_fliC = '-' + highest_fliC_raw = '-' + highest_Score = 0 + log_file.write("\nH_scores:\n") + for s in H_dict: + log_file.write(s+"\t"+str(H_dict[s])+"\n") + if s.startswith('fliC'): + if float(H_dict[s]) > highest_Score: + highest_fliC = s.split('_')[1] + highest_fliC_raw = s + highest_Score = float(H_dict[s]) + #call_fljB + highest_fljB = '-' + highest_fljB_raw = '-' + highest_Score = 0 + for s in H_dict: + if s.startswith('fljB'): + if float(H_dict[s]) > highest_Score and float(H_dict[s]) > highest_H_score_both_BC * 0.65: #fljB is special, so use highest_H_score_both_BC to give a general estimate of coverage, currently 0.65 seems pretty good; the reason use a high (0.65) is some fliC and fljB shared with each other + #highest_fljB = s.split('_')[1] + #highest_fljB_raw = s + #highest_Score = float(H_dict[s]) + if s.split('_')[1]!=highest_fliC: + highest_fljB = s.split('_')[1] + highest_fljB_raw = s + highest_Score = float(H_dict[s]) + log_file.write("\nSpecial_scores:\n") + for s in Special_dict: + log_file.write(s+"\t"+str(Special_dict[s])+"\n") + log_file.close() + return highest_O,highest_fliC,highest_fljB + +def get_temp_file_names(for_fq,rev_fq): + #seqsero2 -a; get temp file names + sam=for_fq+".sam" + bam=for_fq+".bam" + sorted_bam=for_fq+"_sorted.bam" + mapped_fq1=for_fq+"_mapped.fq" + mapped_fq2=rev_fq+"_mapped.fq" + combined_fq=for_fq+"_combined.fq" + for_sai=for_fq+".sai" + rev_sai=rev_fq+".sai" + return sam,bam,sorted_bam,mapped_fq1,mapped_fq2,combined_fq,for_sai,rev_sai + +def map_and_sort(threads,database,fnameA,fnameB,sam,bam,for_sai,rev_sai,sorted_bam,mapping_mode): + #seqsero2 -a; do mapping and sort + print("building database...") + subprocess.check_call("bwa index "+database+ " 2>> data_log.txt",shell=True) + print("mapping...") + if mapping_mode=="mem": + subprocess.check_call("bwa mem -k 17 -t "+threads+" "+database+" "+fnameA+" "+fnameB+" > "+sam+ " 2>> data_log.txt",shell=True) + elif mapping_mode=="sam": + if fnameB!="": + subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameA+" > "+for_sai+ " 2>> data_log.txt",shell=True) + subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameB+" > "+rev_sai+ " 2>> data_log.txt",shell=True) + subprocess.check_call("bwa sampe "+database+" "+for_sai+" "+ rev_sai+" "+fnameA+" "+fnameB+" > "+sam+ " 2>> data_log.txt",shell=True) + else: + subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameA+" > "+for_sai+ " 2>> data_log.txt",shell=True) + subprocess.check_call("bwa samse "+database+" "+for_sai+" "+for_fq+" > "+sam) + subprocess.check_call("samtools view -@ "+threads+" -F 4 -Sh "+sam+" > "+bam,shell=True) + ### check the version of samtools then use differnt commands + samtools_version=subprocess.Popen(["samtools"],stdout=subprocess.PIPE,stderr=subprocess.PIPE) + out, err = samtools_version.communicate() + version = str(err).split("ersion:")[1].strip().split(" ")[0].strip() + print("check samtools version:",version) + ### end of samtools version check and its analysis + if LooseVersion(version)<=LooseVersion("1.2"): + subprocess.check_call("samtools sort -@ "+threads+" -n "+bam+" "+fnameA+"_sorted",shell=True) + else: + subprocess.check_call("samtools sort -@ "+threads+" -n "+bam+" >"+sorted_bam,shell=True) + +def extract_mapped_reads_and_do_assembly_and_blast(current_time,sorted_bam,combined_fq,mapped_fq1,mapped_fq2,threads,fnameA,fnameB,database,mapping_mode): + #seqsero2 -a; extract, assembly and blast + subprocess.check_call("bamToFastq -i "+sorted_bam+" -fq "+combined_fq,shell=True) + #print("fnameA:",fnameA) + #print("fnameB:",fnameB) + if fnameB!="": + subprocess.check_call("bamToFastq -i "+sorted_bam+" -fq "+mapped_fq1+" -fq2 "+mapped_fq2 + " 2>> data_log.txt",shell=True)#2> /dev/null if want no output + else: + pass + outdir=current_time+"_temp" + print("assembling...") + if int(threads)>4: + t="4" + else: + t=threads + if os.path.getsize(combined_fq)>100 and (fnameB=="" or os.path.getsize(mapped_fq1)>100):#if not, then it's "-:-:-" + if fnameB!="": + subprocess.check_call("spades.py --careful --pe1-s "+combined_fq+" --pe1-1 "+mapped_fq1+" --pe1-2 "+mapped_fq2+" -t "+t+" -o "+outdir+ " >> data_log.txt 2>&1",shell=True) + else: + subprocess.check_call("spades.py --careful --pe1-s "+combined_fq+" -t "+t+" -o "+outdir+ " >> data_log.txt 2>&1",shell=True) + new_fasta=fnameA+"_"+database+"_"+mapping_mode+".fasta" + #new_fasta=fnameA+"_"+database.split('/')[-1]+"_"+mapping_mode+".fasta" # change path to databse for packaging + subprocess.check_call("mv "+outdir+"/contigs.fasta "+new_fasta+ " 2> /dev/null",shell=True) + #os.system("mv "+outdir+"/scaffolds.fasta "+new_fasta+ " 2> /dev/null") contigs.fasta + subprocess.check_call("rm -rf "+outdir+ " 2> /dev/null",shell=True) + print("blasting...","\n") + xmlfile="blasted_output.xml"#fnameA+"-extracted_vs_"+database+"_"+mapping_mode+".xml" + subprocess.check_call('makeblastdb -in '+new_fasta+' -out '+new_fasta+'_db '+'-dbtype nucl >> data_log.txt 2>&1',shell=True) #temp.txt is to forbid the blast result interrupt the output of our program###1/27/2015 + subprocess.check_call("blastn -query "+database+" -db "+new_fasta+"_db -out "+xmlfile+" -outfmt 5 >> data_log.txt 2>&1",shell=True)###1/27/2015; 08272018, remove "-word_size 10" + else: + xmlfile="NA" + return xmlfile,new_fasta + +def judge_subspecies(fnameA): + #seqsero2 -a; judge subspecies on just forward raw reads fastq + salmID_output=subprocess.Popen("SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE) + out, err = salmID_output.communicate() + out=out.decode("utf-8") + file=open("data_log.txt","a") + file.write(out) + file.close() + salm_species_scores=out.split("\n")[1].split("\t")[6:] + salm_species_results=out.split("\n")[0].split("\t")[6:] + max_score=0 + max_score_index=1 #default is 1, means "I" + for i in range(len(salm_species_scores)): + if max_score float(out.split("\n")[1].split("\t")[5]): #bongori and enterica compare + if float(out.split("\n")[1].split("\t")[4]) > 10 and float(out.split("\n")[1].split("\t")[4]) > float(out.split("\n")[1].split("\t")[5]): ## ed_SL_0318: change SalmID_ssp_threshold + prediction="bongori" #if not, the prediction would always be enterica, since they are located in the later part + #if max_score<10: ## ed_SL_0318: change SalmID_ssp_threshold + if max_score<60: + prediction="-" + return prediction + +def judge_subspecies_Kmer(Special_dict): + #seqsero2 -k; + max_score=0 + prediction="-" #default should be I + for x in Special_dict: + #if "mer" in x: ## ed_SL_0318: change ssp_threshold + if "mer" in x and float(Special_dict[x]) > 60: + if max_score95:#if bongori already, then no need to test enterica + prediction="bongori" + break + return prediction + +## ed_SL_11232019: add notes for missing antigen +def check_antigens(ssp,O_antigen,H1_antigen,H2_antigen,NA_note): + antigen_note = '' + if ssp != '-': + if O_antigen != '-' and H1_antigen == '-' and H2_antigen == '-': # O:-:- + antigen_note = 'H antigens were not detected. This is an atypical result that should be further investigated. Most Salmonella strains have at least fliC, encoding the Phase 1 H antigen, even if it is not expressed. ' + NA_note = '' + elif O_antigen != '-' and H1_antigen == '-' and H2_antigen != '-': # O:-:H2 + antigen_note = 'fliC was not detected. This is an atypical result that should be further investigated. Most Salmonella strains have fliC, encoding the Phase 1 H antigen, even if it is not expressed. ' + NA_note = '' + elif O_antigen == '-' and H1_antigen != '-': # -:H1:X + antigen_note = 'O antigen was not detected. This result may be due to a rough strain that has deleted the rfb region. For raw reads input, the k-mer workflow is sometimes more sensitive than the microassembly workflow in detecting O antigen. Caution should be used with this approach because the k-mer result may be due to low levels of contamination. ' + NA_note = '' + elif O_antigen == '-' and H1_antigen == '-' and H2_antigen == '-': # -:-:- + antigen_note = 'No serotype antigens were detected. This is an atypical result that should be further investigated. ' + NA_note = '' + else: + antigen_note = 'The input genome cannot be identified as Salmonella. Check the input for taxonomic ID, contamination, or sequencing quality. ' + NA_note = '' +# if [O_antigen, H1_antigen, H2_antigen].count('-') >= 2: +# antigen_note = 'No subspecies marker was detected and less than 2 serotype antigens were detected; further, this genome was not identified as Salmonella. This is an atypical result that should be further investigated. ' +# else: +# antigen_note = 'No subspecies marker was detected. This genome may not be Salmonella. This is an atypical result that should be further investigated. ' + return (antigen_note,NA_note) + +def main(): + #combine SeqSeroK and SeqSero2, also with SalmID + args = parse_args() + input_file = args.i + data_type = args.t + analysis_mode = args.m + mapping_mode=args.b + threads=args.p + make_dir=args.d + clean_mode=args.c + sample_name=args.n + ingore_header=args.s + k_size=27 #will change for bug fixing + dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__))) + ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019: add ex_dir for packaging + seqsero2_db=ex_dir+"/H_and_O_and_specific_genes.fasta" # ed_SL_11092019: change path to database for packaging + database="H_and_O_and_specific_genes.fasta" + note="Note: " + NA_note="This predicted serotype is not in the Kauffman-White scheme. " # ed_SL_09272019: add for new output format + if len(sys.argv)==1: + subprocess.check_call(dirpath+"/SeqSero2_package.py -h",shell=True)#change name of python file + else: + request_id = time.strftime("%m_%d_%Y_%H_%M_%S", time.localtime()) + request_id += str(random.randint(1, 10000000)) + if make_dir is None: + make_dir="SeqSero_result_"+request_id + make_dir=os.path.abspath(make_dir) + if os.path.isdir(make_dir): + pass + else: + subprocess.check_call("mkdir -p "+make_dir,shell=True) + #subprocess.check_call("cp "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) + #subprocess.check_call("ln -sr "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) + subprocess.check_call("ln -f -s "+seqsero2_db+" "+" ".join(input_file)+" "+make_dir,shell=True) # ed_SL_11092019: change path to database for packaging + #subprocess.check_call("ln -f -s "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) ### use -f option to force the replacement of links, remove -r and use absolute path instead to avoid link issue (use 'type=os.path.abspath' in -i argument). + ############################begin the real analysis + if analysis_mode=="a": + if data_type in ["1","2","3"]:#use allele mode + for_fq,rev_fq=get_input_files(make_dir,input_file,data_type,dirpath) + os.chdir(make_dir) + ###add a function to tell input files + fnameA=for_fq.split("/")[-1] + fnameB=rev_fq.split("/")[-1] + current_time=time.strftime("%Y_%m_%d_%H_%M_%S", time.localtime()) + sam,bam,sorted_bam,mapped_fq1,mapped_fq2,combined_fq,for_sai,rev_sai=get_temp_file_names(fnameA,fnameB) #get temp files id + map_and_sort(threads,database,fnameA,fnameB,sam,bam,for_sai,rev_sai,sorted_bam,mapping_mode) #do mapping and sort + ### avoid error out when micro assembly fails. ed_SL_03172020 + try: + xmlfile,new_fasta=extract_mapped_reads_and_do_assembly_and_blast(current_time,sorted_bam,combined_fq,mapped_fq1,mapped_fq2,threads,fnameA,fnameB,database,mapping_mode) #extract the mapped reads and do micro assembly and blast + except (UnboundLocalError, subprocess.CalledProcessError): + xmlfile="NA" + H1_cont_stat_list=[] + H2_cont_stat_list=[] + ### + if xmlfile=="NA": + O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H=("-","-","-",[],"","") + else: + Final_list=xml_parse_score_comparision_seqsero(xmlfile) #analyze xml and get parsed results + file=open("data_log.txt","a") + for x in Final_list: + file.write("\t".join(str(y) for y in x)+"\n") + file.close() + Final_list_passed=[x for x in Final_list if float(x[0].split("_cov_")[1].split("_")[0])>=0.9 and (x[1]>=int(x[0].split("__")[1]) or x[1]>=int(x[0].split("___")[1].split("_")[3]) or x[1]>1000)] + O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H,Otypes_uniq,H1_cont_stat_list,H2_cont_stat_list=predict_O_and_H_types(Final_list,Final_list_passed,new_fasta) #predict O, fliC and fljB + subspecies=judge_subspecies(fnameA) #predict subspecies + ###output + predict_form,predict_sero,star,star_line,claim=seqsero_from_formula_to_serotypes(O_choice,fliC_choice,fljB_choice,special_gene_list,subspecies) + claim="" #04132019, disable claim for new report requirement + contamination_report="" + H_list=["fliC_"+x for x in H1_cont_stat_list if len(x)>0]+["fljB_"+x for x in H2_cont_stat_list if len(x)>0] + if contamination_O!="" and contamination_H=="": + contamination_report="#Potential inter-serotype contamination detected from O antigen signals. All O-antigens detected:"+"\t".join(Otypes_uniq)+"." + elif contamination_O=="" and contamination_H!="": + contamination_report="#Potential inter-serotype contamination detected or potential thrid H phase from H antigen signals. All H-antigens detected:"+"\t".join(H_list)+"." + elif contamination_O!="" and contamination_H!="": + contamination_report="#Potential inter-serotype contamination detected from both O and H antigen signals.All O-antigens detected:"+"\t".join(Otypes_uniq)+". All H-antigens detected:"+"\t".join(H_list)+"." + if contamination_report!="": + #contamination_report="potential inter-serotype contamination detected (please refer below antigen signal report for details)." #above contamination_reports are for back-up and bug fixing #web-based mode need to be re-used, 04132019 + contamination_report="Co-existence of multiple serotypes detected, indicating potential inter-serotype contamination. See 'Extracted_antigen_alleles.fasta' for detected serotype determinant alleles. " + #claim="\n"+open("Extracted_antigen_alleles.fasta","r").read()#used to store H and O antigen sequeences #04132019, need to change if using web-version + #if contamination_report+star_line+claim=="": #0413, new output style + # note="" + #else: + # note="Note:" + + ### ed_SL_11232019: add notes for missing antigen + if O_choice=="": + O_choice="-" + antigen_note,NA_note=check_antigens(subspecies,O_choice,fliC_choice,fljB_choice,NA_note) + if sample_name: + print ("Sample name:\t"+sample_name) + ### + + if clean_mode: + subprocess.check_call("rm -rf ../"+make_dir,shell=True) + make_dir="none-output-directory due to '-c' flag" + else: + new_file=open("SeqSero_result.txt","w") + ### ed_SL_01152020: add new output + conta_note="yes" if "inter-serotype contamination" in contamination_report else "no" + tsv_file=open("SeqSero_result.tsv","w") + if ingore_header: + pass + else: + tsv_file.write("Sample name\tOutput directory\tInput files\tO antigen prediction\tH1 antigen prediction(fliC)\tH2 antigen prediction(fljB)\tPredicted subspecies\tPredicted antigenic profile\tPredicted serotype\tPotential inter-serotype contamination\tNote\n") + if sample_name: + new_file.write("Sample name:\t"+sample_name+"\n") + tsv_file.write(sample_name+'\t') + else: + tsv_file.write(input_file[0].split('/')[-1]+'\t') + ### + if "N/A" not in predict_sero: + new_file.write("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+"\t".join(input_file)+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ + "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+predict_sero+"\n"+ + note+contamination_report+star_line+claim+antigen_note+"\n")#+## + tsv_file.write(make_dir+"\t"+" ".join(input_file)+"\t"+O_choice+"\t"+fliC_choice+"\t"+fljB_choice+"\t"+subspecies+"\t"+predict_form+"\t"+predict_sero+"\t"+conta_note+"\t"+contamination_report+star_line+claim+antigen_note+"\n") + else: + #star_line=star_line.strip()+"\tNone such antigenic formula in KW.\n" + star_line="" #04132019, for new output requirement, diable star_line if "NA" in output + new_file.write("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+"\t".join(input_file)+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ + "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, add subspecies + note+NA_note+contamination_report+star_line+claim+antigen_note+"\n")#+## + tsv_file.write(make_dir+"\t"+" ".join(input_file)+"\t"+O_choice+"\t"+fliC_choice+"\t"+fljB_choice+"\t"+subspecies+"\t"+predict_form+"\t"+subspecies+' '+predict_form+"\t"+conta_note+"\t"+NA_note+contamination_report+star_line+claim+antigen_note+"\n") + new_file.close() + tsv_file.close() + #subprocess.check_call("cat Seqsero_result.txt",shell=True) + #subprocess.call("rm H_and_O_and_specific_genes.fasta* *.sra *.bam *.sam *.fastq *.gz *.fq temp.txt *.xml "+fnameA+"*_db* 2> /dev/null",shell=True) + subprocess.call("rm H_and_O_and_specific_genes.fasta* *.sra *.bam *.sam *.fastq *.gz *.fq temp.txt "+fnameA+"*_db* 2> /dev/null",shell=True) + if "N/A" not in predict_sero: + #print("Output_directory:"+make_dir+"\nInput files:\t"+for_fq+" "+rev_fq+"\n"+"O antigen prediction:\t"+O_choice+"\n"+"H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+"H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+"Predicted antigenic profile:\t"+predict_form+"\n"+"Predicted subspecies:\t"+subspecies+"\n"+"Predicted serotype(s):\t"+predict_sero+star+"\nNote:"+contamination_report+star+star_line+claim+"\n")#+## + print("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+"\t".join(input_file)+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ + "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+predict_sero+"\n"+ + note+contamination_report+star_line+claim+antigen_note+"\n")#+## + else: + print("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+"\t".join(input_file)+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ + "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, subspecies + note+NA_note+contamination_report+star_line+claim+antigen_note+"\n") + else: + print("Allele modes only support raw reads datatype, i.e. '-t 1 or 2 or 3'; please use '-m k'") + elif analysis_mode=="k": + #ex_dir = os.path.dirname(os.path.realpath(__file__)) + ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019: change ex_dir for packaging + #output_mode = args.mode + for_fq,rev_fq=get_input_files(make_dir,input_file,data_type,dirpath) + input_file = for_fq #-k will just use forward because not all reads were used + os.chdir(make_dir) + f = open(ex_dir + '/antigens.pickle', 'rb') + lib_dict = pickle.load(f) + f.close + input_Ks=get_input_K(input_file,lib_dict,data_type,k_size) + O_dict,H_dict,Special_dict=get_kmer_dict(lib_dict,input_Ks) + highest_O,highest_fliC,highest_fljB=call_O_and_H_type(O_dict,H_dict,Special_dict,make_dir) + subspecies=judge_subspecies_Kmer(Special_dict) + if subspecies=="IIb" or subspecies=="IIa": + subspecies="II" + predict_form,predict_sero,star,star_line,claim = seqsero_from_formula_to_serotypes( + highest_O.split('-')[1], highest_fliC, highest_fljB, Special_dict,subspecies) + claim="" #no claim any more based on new output requirement + #if star_line+claim=="": #0413, new output style + # note="" + #else: + # note="Note:" + + ### ed_SL_11232019: add notes for missing antigen + if highest_O.split('-')[-1]=="": + O_choice="-" + else: + O_choice=highest_O.split('-')[-1] + antigen_note,NA_note=check_antigens(subspecies,O_choice,highest_fliC,highest_fljB,NA_note) + if sample_name: + print ("Sample name:\t"+sample_name) + ### + + if clean_mode: + subprocess.check_call("rm -rf ../"+make_dir,shell=True) + make_dir="none-output-directory due to '-c' flag" + # ### ed_SL_05282019, fix the assignment issue of variable 'O_choice' using "-m k -c" + # if highest_O.split('-')[-1]=="": + # O_choice="-" + # else: + # O_choice=highest_O.split('-')[-1] + # ### + else: + # if highest_O.split('-')[-1]=="": + # O_choice="-" + # else: + # O_choice=highest_O.split('-')[-1] + #print("Output_directory:"+make_dir+"\tInput_file:"+input_file+"\tPredicted subpecies:"+subspecies + '\tPredicted antigenic profile:' + predict_form + '\tPredicted serotype(s):' + predict_sero) + new_file=open("SeqSero_result.txt","w") + #new_file.write("Output_directory:"+make_dir+"\nInput files:\t"+input_file+"\n"+"O antigen prediction:\t"+O_choice+"\n"+"H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+"H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+"Predicted antigenic profile:\t"+predict_form+"\n"+"Predicted subspecies:\t"+subspecies+"\n"+"Predicted serotype(s):\t"+predict_sero+star+"\n"+star+star_line+claim+"\n")#+## + ### ed_SL_01152020: add new output + tsv_file=open("SeqSero_result.tsv","w") + if ingore_header: + pass + else: + tsv_file.write("Sample name\tOutput directory\tInput files\tO antigen prediction\tH1 antigen prediction(fliC)\tH2 antigen prediction(fljB)\tPredicted subspecies\tPredicted antigenic profile\tPredicted serotype\tNote\n") + if sample_name: + new_file.write("Sample name:\t"+sample_name+"\n") + tsv_file.write(sample_name+'\t') + else: + tsv_file.write(input_file.split('/')[-1]+'\t') + ### + if "N/A" not in predict_sero: + new_file.write("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+input_file+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ + "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+predict_sero+"\n"+ + note+star_line+claim+antigen_note+"\n")#+## + tsv_file.write(make_dir+"\t"+input_file+"\t"+O_choice+"\t"+highest_fliC+"\t"+highest_fljB+"\t"+subspecies+"\t"+predict_form+"\t"+predict_sero+"\t"+star_line+claim+antigen_note+"\n") + else: + #star_line=star_line.strip()+"\tNone such antigenic formula in KW.\n" + star_line = "" #changed for new output requirement, 04132019 + new_file.write("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+input_file+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ + "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, subspecies + note+NA_note+star_line+claim+antigen_note+"\n")#+## + tsv_file.write(make_dir+"\t"+input_file+"\t"+O_choice+"\t"+highest_fliC+"\t"+highest_fljB+"\t"+subspecies+"\t"+predict_form+"\t"+subspecies+' '+predict_form+"\t"+NA_note+star_line+claim+antigen_note+"\n") + new_file.close() + tsv_file.close() + subprocess.call("rm *.fasta* *.fastq *.gz *.fq temp.txt *.sra 2> /dev/null",shell=True) + if "N/A" not in predict_sero: + print("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+input_file+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ + "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+predict_sero+"\n"+ + note+star_line+claim+antigen_note+"\n")#+## + else: + print("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+input_file+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ + "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, subspecies + note+NA_note+star_line+claim+antigen_note+"\n")#+## + +if __name__ == '__main__': + main() diff -r 43f6b7f6ebb3 -r e6437d423693 build/lib/bin/SeqSero2_update_kmer_database.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/bin/SeqSero2_update_kmer_database.py Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,113 @@ +#!/usr/bin/env python3 + +import argparse +import os,subprocess +import pickle + +### SeqSero Kmer +def parse_args(): + "Parse the input arguments, use '-h' for help." + parser = argparse.ArgumentParser(usage='Just type "SeqSero2_update_kmer_database.py", it will update kmer database automatically') + return parser.parse_args() + +def reverse_complement(sequence): + complement = { + 'A': 'T', + 'C': 'G', + 'G': 'C', + 'T': 'A', + 'N': 'N', + 'M': 'K', + 'R': 'Y', + 'W': 'W', + 'S': 'S', + 'Y': 'R', + 'K': 'M', + 'V': 'B', + 'H': 'D', + 'D': 'H', + 'B': 'V' + } + return "".join(complement[base] for base in reversed(sequence)) + +def multifasta_dict(multifasta): + multifasta_list = [ + line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0 + ] + headers = [i for i in multifasta_list if i[0] == '>'] + multifasta_dict = {} + for h in headers: + start = multifasta_list.index(h) + for element in multifasta_list[start + 1:]: + if element[0] == '>': + break + else: + if h[1:] in multifasta_dict: + multifasta_dict[h[1:]] += element + else: + multifasta_dict[h[1:]] = element + return multifasta_dict + +def createKmerDict_reads(list_of_strings, kmer): + kmer_table = {} + for string in list_of_strings: + sequence = string.strip('\n') + for i in range(len(sequence) - kmer + 1): + new_mer = sequence[i:i + kmer].upper() + new_mer_rc = reverse_complement(new_mer) + if new_mer in kmer_table: + kmer_table[new_mer.upper()] += 1 + else: + kmer_table[new_mer.upper()] = 1 + if new_mer_rc in kmer_table: + kmer_table[new_mer_rc.upper()] += 1 + else: + kmer_table[new_mer_rc.upper()] = 1 + return kmer_table + +def multifasta_to_kmers_dict(multifasta): + multi_seq_dict = multifasta_dict(multifasta) + lib_dict = {} + for h in multi_seq_dict: + lib_dict[h] = set( + [k for k in createKmerDict_reads([multi_seq_dict[h]], 27)]) + return lib_dict + +def get_salmid_invA_database(ex_dir): + # read invA kmer and return it + a = open(ex_dir + '/invA_mers_dict', 'rb') + invA_dict = pickle.load(a) + try: + del invA_dict['version'] + except: + pass + return invA_dict + +def get_salmid_rpoB_database(ex_dir): + # read invA kmer and return it + a = open(ex_dir + '/rpoB_mers_dict', 'rb') + rpoB_dict = pickle.load(a) + try: + del rpoB_dict['version'] + except: + pass + return rpoB_dict + +def main(): + args = parse_args() + ex_dir = os.path.dirname(os.path.realpath(__file__)) + lib_dict = multifasta_to_kmers_dict(ex_dir + '/H_and_O_and_specific_genes.fasta') + invA_dict=get_salmid_invA_database(ex_dir) + #rpoB_dict=get_salmid_rpoB_database(ex_dir) + lib_dict_new = lib_dict.copy() + #print(len(lib_dict_new)) + lib_dict_new.update(invA_dict) + #print(len(lib_dict_new)) + #lib_dict_new.update(rpoB_dict) + #print(len(lib_dict_new)) + f = open(ex_dir + '/antigens.pickle', "wb") + pickle.dump(lib_dict_new, f) + f.close() + +if __name__ == '__main__': + main() diff -r 43f6b7f6ebb3 -r e6437d423693 build/lib/bin/deinterleave_fastq.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/bin/deinterleave_fastq.sh Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,30 @@ +#!/bin/bash +# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress] +# +# Deinterleaves a FASTQ file of paired reads into two FASTQ +# files specified on the command line. Optionally GZip compresses the output +# FASTQ files using pigz if the 3rd command line argument is the word "compress" +# +# Can deinterleave 100 million paired reads (200 million total +# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s) +# +# Latest code: https://gist.github.com/3521724 +# Also see my interleaving script: https://gist.github.com/4544979 +# +# Inspired by Torsten Seemann's blog post: +# http://thegenomefactory.blogspot.com.au/2012/05/cool-use-of-unix-paste-with-ngs.html + +# Set up some defaults +GZIP_OUTPUT=0 +PIGZ_COMPRESSION_THREADS=10 + +# If the third argument is the word "compress" then we'll compress the output using pigz +if [[ $3 == "compress" ]]; then + GZIP_OUTPUT=1 +fi + +if [[ ${GZIP_OUTPUT} == 0 ]]; then + paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" > $1) | cut -f 5-8 | tr "\t" "\n" > $2 +else + paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $1) | cut -f 5-8 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $2 +fi diff -r 43f6b7f6ebb3 -r e6437d423693 build/lib/seqsero2_db/H_and_O_and_specific_genes.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/seqsero2_db/H_and_O_and_specific_genes.fasta Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,7094 @@ +>fliC_g,m_Enteritidisstr_AKFY01000033_g,m__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_g,m,s_Montevideostr_AESV01000018_g,m__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTATGACACCTATGCAGCGGGTGCCAATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAATGGTCAGTTGACAACTGACGATGCGGAA +AATAACACTGCGGTTAACCTATTCAAGACGACTAAATCTGCTGCTGGTACCGATGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fljB_1,2_Salmonella.enterica_Stanley_AY353267_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATTACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fljB_1,2_Saintpaulstr_AYDS01000021_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAATCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fliC_z4,z23_Cerrostr_AYVH01000420_z4,z23__1257 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +TGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACTGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +CTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAACAACTGGTGGTCCGGCTGCGGATAAAT +TATCTCTGACAAAAGATGATACAGGTAATTACTTTGTCAAAGATGTTACTGCGACGGCTAAATACTATGCAGCTACCGTA +GATATGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGACTCCGCCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGTACTGCCGTAGACTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_i_4,[5],12_i_-str_ABAO01000026_r,i__1476 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_d_Typhistr_AJGK01000049_b,d,j__1509 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +TGCTATCGAGCGTTTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGACAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCGAATGGTACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATTGATTTA +AAAGAAATCAGCTCTAAAACACTGGGACTTGATAAGCTTAATGTCCAAGATGCCTACACCCCGAAAGAAACTGCTGTAAC +CGTTGATAAAACTACCTATAAAAATGGTACAGATCCTATTACAGCCCAGAGCAATACTGATATCCAAACTGCAATTGGCG +GTGGTGCAACGGGGGTTACTGGGGCTGATATCAAATTTAAAGATGGTCAATACTATTTAGATGTTAAAGGCGGTGCTTCT +GCTGGTGTTTATAAAGCCACTTATGATGAAACTACAAAGAAAGTTAATATTGATACGACTGATAAAACTCCGTTGGCAAC +TGCGGAAGCTACAGCTATTCGGGGAACGGCCACTATAACCCACAACCAAATTGCTGAAGTAACAAAAGAGGGTGTTGATA +CGACCACAGTTGCGGCTCAACTTGCTGCAGCAGGGGTTACTGGCGCCGATAAGGACAATACTAGCCTTGTAAAACTATCG +TTTGAGGATAAAAACGGTAAGGTTATTGATGGTGGCTATGCAGTGAAAATGGGCGACGATTTCTATGCCGCTACATATGA +TGAGAAAACAGGTGCAATTACTGCTAAAACCACTACTTATACAGATGGTACTGGCGTTGCTCAAACTGGAGCTGTGAAAT +TTGGTGGCGCAAATGGTAAATCTGAAGTTGTTACTGCTACCGATGGTAAGACTTACTTAGCAAGCGACCTTGACAAACAT +AACTTCAGAACAGGCGGTGAGCTTAAAGAGGTTAATACAGATAAGACTGAAAACCCACTGCAGAAAATTGATGCTGCCTT +GGCACAGGTTGATACACTTCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCAACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_i_Salmonella.enterica_Kentucky_AY353427_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_r_Heidelbergstr_AJGW01000023_r,i__1470 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTCACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTC +CTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGAT +GGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTT +CCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAG +CAGCGGGTGTTGCAGCGGCCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGT +GGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATACTACGAA +ATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTA +TTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCTGCT +ACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGT +ACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCGAAG +ATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAG +GCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fljB_1,2_Heidelbergstr_AMMX01000009_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGTAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAATCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fljB_z6_Kentuckystr_AYDR01000034_k,z__1493 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TTACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGATCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGTAAGGCTGTGAC +AGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTG +CAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCT +GATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGA +GGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCA +AAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTTGTCAAAATGTCTTACACCGATAAA +AATGGTAAGACGATTGATGGCGGTTACGCTGTAAAGGTGGGCGATAATTACTATGCCGCTACCCAGAAAAAAGATGGTAG +CTTCAGTGTTAACACCACGTCTTACACCGCAGCTGACGGTACTACCAAAACTGCCCTGAACCAACTGGGTGGCGCAGACG +GTAAAACTGAAGTCGTTTCTATTGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAGCCA +GAGCTGGCGGAAGCAGCTGCTAAAACCACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCT +GCGTTCTGACCTGGGTGCGGTTCAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAATAACCTGTCTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCC +GGTACCTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fliC_g,s,t_Senftenbergstr_AOYU01000052_g,m__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTGACAACTGACGATGCGGAG +AACAACACTGCGGTTAACCTATTCAAGACGACTAAATCTACTGCTGGTACCGATGAAGCCAAAGCGATAGCTAGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATACAAAAGCTGGTGATGACGGTA +ATGGTACGGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCAGCGAATGTT +AATGATGCCACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_d_Manhattanstr_CBKW010000019_b,d,j__1509 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACGGTACTAACTCCCAGTC +TGACCTTGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATTGATATTGATTTA +AAAGAAATTAGCTCTAAAACACTGGGACTTGATAAGCTTAATGTCCAGGATGCCTACACCCCGAAAGAAACTGCTGTAAC +CGTTGATAAAACTACCTATAAAAATGGTACAGATACTATTACAGCCCAGAGCAATACTGATATCCAAACTGCAATTGGCG +GTGGTGCAACGGGGGTTACTGGGGCTGATATCAAATTTAAAGATGGTCAATACTATTTAGATGTTAAAGGCGGTGCTTCT +GCTGGTGTTTATAAAGCCACTTATGATGAAACTACAAAGAAAGTTAATATTGATACGACTGATAAAACTCCGTTAGCAAC +TGCGGAAGCTACAGCTATTCGGGGAACGGCCACTATAACCCACAACCAAATTGCTGAAGTAACAAAAGAGGGTGTTGATA +CGACCACAGTTGCGGCTCAACTTGCTGCTGCAGGGGTTACTGGTGCCGATAAGGACAATACTAGCCTTGTAAAACTATCG +TTTGAGGATAAAAACGGTAAGGTTATTGATGGTGGCTATGCAGTGAAAATGGGCGACGATTTCTATGCCGCTACATATGA +TGAGAAAACAGGTACAATTACTGCTAAAACAACCACTTATACAGATGGTGCTGGCGTTGCTCAAACTGGAGCTGTGAAAT +TTGGTGGCGCAAATGGTAAATCTGAAGTTGTTACTGCTACCGATGGTAAAACTTACTTAGCAAGCGACCTTGACAAACAT +AACTTCAGAACAGGCGGTGAGCTTAAAGAGGTTAATACAGATAAGACTGAAAACCCACTGCAGAAAATTGATGCTGCCTT +GGCACAGGTTGATACACTTCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_e,h_Salmonella.enterica_Saintpaul_AY353377_e__1509 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTATCAGCAACTGCTGCAAT +GGATCCGAAATCATTTACTGACGGTACTAAAAATCTTACAGCGCCTGATGCTACTGCTATCAAAGCCGCGTTGGGAAATC +CCGCGGCAACAGGCGATTCCTTGTCTGCTACGCTTTCGTTTAAAGATGGTAAGTATTACGCCACTGTTGCAGGGTATACG +AATGCTGCCGATACCAGTAAGAATGGTAAATATGAAGTGAATGTTGATAGTGCGACAGGTGCGGTAACTTTCAATGCAGC +ACCAACTAAAGCCACAGTAACTGGGGATACAACAGTAACCAAAGTACAGGTTAATGCTCCTGTTGCAGTCAGTACTGATG +TTAAAAAAGCGCTAGAAGATGGTGGCGTTTCAAATGCGGACGCTACCGCAGCTAAATTAGTAAAAATGTCTTATACCGAT +AAAAATGGAAAATCTATTGACGGTGGTTATGCGCTTGAAGCCGGTGGCAAGTACTATGCTGCAACCTATGACGAAGGTAC +AGGTAAAATCACAGCTAATGTAACCACTTATACTGATTCCACGGGAGCCACAAAAACTGCGGCTAACCAACTTGGTGGCG +TAGACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCTAGTAAAGCCGCTGGTCACGATTTCAAAGCG +CAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGA +TGCGTTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACT +TGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCTGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_1,5,7_Salmonella.enterica_IIIb.6,7:l,v:1,5,7_AY353273_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGTTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTGAAAGATACAGCAGCAAC +AACGAAAGCTTATGCTGATAATGGTACTACACTGGATGTATCAGGTCTTGATGATGCAGCGATTAAAGCGGCTACGGGTG +GTACGACTGGTGCGCCTACTGTAACGGGCGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGGTGATGCTGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTAACACTTGCGAC +TGGTGCAACTAAAACCACAATGCCTGCAGGTGCTACAACCAAAACAGAAGTACAGGAATTAAAAGATACACCGGCAGTTG +TATCAGCTGATGCTAAAAATGCTTTAATTGCTGCTGGCGTTGATACTACAGATGCAAATGCCGCGACATTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAATATTACGCTGCTGATTA +CAATGAAACTACAGGAGCTATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACTAAAACGGCGGCTAACC +AACTTGGTGGCGCAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCAT +GATTTCAAAGCACAGCCAGATCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCT +GGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACA +CCGTAAACAACCTGACTTCTGCACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCGGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTA +A +>fliC_g,p_Dublinstr_ATFR01000073_g,m__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGTAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCATTGGCGCGGCGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fljB_1,2_Salmonella.enterica_Muenchen_AY353269_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAATAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATTACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fliC_g,m_Salmonella.enterica_Enteritidis_AY353386_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_i_Typhimuriumstr_AUQT01000018_r,i__1476 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTAAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_z10_Hadarstr_ALPP01000007_other.z10__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTTGATAGCACTGGCGTTAC +TCAATCTCTTGATTTAAAAACTGCTGGAATTACTGGTGCTACATTAAAAGCTGGTATTACTGGTACAACGACAGAAACCG +GTAGCGTTAAAGATGGTAAAGTCTACTATGATGCAGATAGCAAAAATTACTATGTAGAGGTTGATTTTACTGATACTACG +GATAAAGCAGCGCATGCTGGTTTCTACAAAGCTGACGTCGATGCTGACGGTAATGTTTCTTTAGCAACTGGTGCGACTAA +AGAAGCAAAACCAACGAATGCAGTTGAAGTTGAAAAAACTATTGATGAAAAACCGCTGAAAGCATCAAGTAGTGTTCAGG +ATGCCTTAAAAGCGAGTGGTATTGCTGATGCGGTTGCAGAAGCTGCGACGGTAGTGAAAATGTCGTACACTGATAAGAAT +GGTAAAACTATTGATGGTGGATACGGTATTAAAGTAGGTGATGACTACTATGCTGCAACTAAAGAAAAAGACGGCAGCTA +TAGTATTAATAGTACTTCTTATACCGATAAAGACGGCAACACTAAAACTGCACTAAACCAACTGGGTGGCGCAGACGGTA +AAACTGAAGTTGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCACAACTTCAAAGCACAGCCTGAT +CTGGCGGAAGCGGCTGCTACAACTACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCTGCG +TTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTG +CCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGT +ACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_z29_Salmonella.enterica_Tennessee_AY353474_other.z29__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAGGGT +GCGCTGAATGAAATTAACAACAACCTGCAGCGTGTACGTGAGTTGACTGTTCAGGCAACTAATGGGACAAACTCTGACAG +CGACCTGACCTCTATTCAAAATGAAATCACACAACGTTTGAGTGAAATTGATCGTGTCTCTGGTCAAACTCAATTTAACG +GCGTGAAAGTGCTGGCCCAAGACAATACGCTGAAAATTCAAGTAGGAGCCAACGACGGCGAAACCATTTCTATTGATCTT +AAGAAAATTGACTCAAAAAGCCTTGGAATGGATGGTTTTAACGTTAATGGCGCGCACAAAGCAACAGGAAGTGATTTAAT +TTCTCAATTTGGTGCTACAGGTACTGATAATTATAACGTTACCAAAGGGGCTACTACCACTACTTATTCGGTAGACATTA +AATCTGGCGCTGTTACTACTGGTACACCAGCTGAAGCTGTCTTTGTTAACGCGGCTGATGGTAGCTTGACAACTGATGCT +ACTACCAAAAACACTGAAATTAAAGGTAACGATGACTTTACAAAGGGACTTGCAGACGCAGCAAAAGGCGCTGTTAAAGA +TTCTACATTTACCTACAGTGGCATCGAATTTACTGCTAAGACTGCTGGTACAGCAGATGGTAATGGTACTTTTGAAGCGA +AAATTGATGGTGCAGTGTTTTCCTTTGTAATTACTGGTGGTACAACACCTTCCTCTGCAGTAACTGGAGCTGGTGGTGCA +AAAGCTTATGTTTCTAAAATTGATGGTAGTATTACGACAACAGCTGAAGTCGATAACCGTGCTGCGAAAATGTCCGATTT +GGATTTAAACAACGCGGTTAAAATAGGTAGTACATTAAATGTTAACGGTGCTACCTATAATGTTAATGCTAAAGGTGATG +AAGTTACTGGTAAGTTTGATGATGGTGCAGGCGGACTGGTTGATAAACAAGTATTCTTGGGAAAAACCGCTGGCGGAGCT +GCAACATTAATTAATGAGGATGCTGCTAAATCCCAACAATCTACCGTAGATCCGTTGAAAACTATTGATGATGCACTTGC +TCAGGTTGATGCGCTTCGCTCCGATTTGGGCGCAGTACAGAACCGCTTTGATTCTGCCATTACCAACCTTGGCAATACGG +TAAATAACTTATCTTCTGCCCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAAGCTGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_1,5_Infantisstr_ASRF01000034_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGACAGCTTATGCCGATAATGGTACTACACTGGATGTATCGGGTCTTACTGATGCAGCTATTAAAACGGCTACGGGTG +GTACGACTGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGTGACAACTAAAACAGAAGTACAGGAGTTAACAACTACACCGGTAGTTG +CTTCAGCAGATGCTAAGAATGCCTTAATCGCTGGCGGCGTTGACACTGCCGATGCTAATGCCGCGACATTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCAGCGTT +GGCGCAGGTGGATGCGCTGCGCTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fliC_i_Salmonella.enterica_Typhimurium_AY353420_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,m,p,s_Montevideostr_AETD01000005_g,m__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTATGACACCTATGCAGCGGGTGCCAATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAATGGTCAGTTGACAACTGACGATGCGGAA +AAAAACACTGCGGTTAACCTATTCAAGACGACTAAATCTGCTGCTGGTACCGATGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fljB_1,6_Anatumstr_AOZZ01000116_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATTACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +CACGAAAACTTATGCCGATAATGGTACTACACTGGATGCCTCAGGCCTTGATGATACAGCTATCAAAGCGGCTATAGGTG +GTACGCTTGGCACGGCTTCTGTAACCGGTGGTACAGTTAAATTTGACGCAGATAATAATAAGTACTTTGTTACTATTGGT +GGCTATACTGGTGCTGATGCCACCAAAAATGGCGATTATGAAGTTAACGTCGCTACTGACGGTAAAGTAACCCTTGCGCC +TGGCGCAACTAAAACCACAATACCGGCAGGTGCTACAACCAAAACAGAAGTACAGGAGTTAAAAGATACACCGACAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGATGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACTGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fliC_k_Salmonella.enterica_IIIb.38:k:z35_AY353439_k,z__1485 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACCATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCTTGGGTCTGGATGCGCTGAATGTGCAGAAAGCGTATGATGTAGATAGCAAACCAACAAG +TATGAAGTTGGATACTAGCGGTATAACAGCGGAGGCAATTAAAAACGGTGTAACTGGCGCAACGACAGATGGTGCACTTA +AAGACGGCAAGATTTATTCCGATGGTACTAACTACTACGTAGAAGTTAGCTTTGCTGCTACCGCAGACACAAGTAAAGGC +GGTTTTCTTAAAGTGGATGTTGATTCCTCTAATGGTAAAGTGTCTATTCCTACCACTGCTGCATCTGCTGTCGCGGCAAA +ACCAGCTGGAGTAAAAGAAGTTTCTGAAGTTCAAGGGAAAATTGCTGCATCAACAGATGTTAAAAATCAATTGACAGCAG +GCGGTATTGATGCTGGTGTTGCCGCCAATGCAGAAATGGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATTGAT +GGCGGTTATGCTGTAAAAGTAGGCAATGACTACTACGCCGCTACTCAGAAAAAAGATGGTAGCTTTAGTGTTAACACTAC +GTCTTACACTGCAGATGACGGTACATCCAAAACTGCACTAAACCAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTT +CTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCT +ACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGC +GGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCG +AAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTGGCG +CAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_z6_Sloterdijkstr_AOXT01000012_k,z__1493 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TTACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGATCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGTAAGGCTGTGAC +AGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTG +CAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCT +GATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGA +GGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCA +AAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTTGTCAAAATGTCTTACACCGATAAA +AATGGTAAGACGATTGATGGCGGTTACGCTGTAAAGGTGGGCGATAATTACTATGCCGCTACCCAGAAAAAAGATGGTAG +CTTCAGTGTTAACACCACGTCTTACACCGCAGCTGACGGTACTACCAAAACTGCCCTGAACCAACTGGGTGGCGCAGACG +GTAAAACTGAAGTCGTTTCTATTGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAGCCA +GAGCTGGCGGAAGCAGCCGCTAAAACCACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCT +GCGTTCTGACCTGGGTGCGGTTCAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTACGCTACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCC +GGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAGAACGTGCTGTCTCT +>fljB_1,7_Salmonella.enterica_Bredeney_AY353296_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCCTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGATGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTGCACCTAGTGTAACAGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATCTCGACAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCCGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACCGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCAT +GATTTTAAAGCACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATCCTGCAGCAGGCCGGTACTTCCGTTCTGGCACAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fljB_e,n,x_Minnesotastr_AOYO01000082_e__1496 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCCTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACTCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fliC_z4,z32_Salmonella.enterica_Tallahassee_AY353507_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATTTCCATTGCGCAGACGACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCAAACGGCTCGAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACTGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGTTCTGGAGC +CTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACAACGGGTGGTCCGGCTGCAGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGTTACTGCGACGGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGGCTCCGTCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGGGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCAGGGACTTCTGTTCTGGCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_1,2_Typhimuriumstr_AHVA01000007_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACTACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAATCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fljB_1,5_Salmonella.enterica_Thompson_AY353285_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCGATAATGGTACTACACTGGATGCCTCAGGCCTTGATGATGCGGCCATCAAAGCGGCCATTGGTG +GTACGACTGGTACGGCTGCTGTAACGGGTGGTACAGTTAAATTTGACGCAGATAATAATAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTTACACTTGCTGC +GGGTGCAACTAAAACCACAATGCCTGCTGGTGCGGCAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCAGCAGTTG +TTTCAGCAGATGCTAAGAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATCTTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fljB_1,2_Salmonella.enterica_Typhimurium_AY353264_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAATCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fljB_1,7_Pomonastr_AHIA01000072_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCGCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTGCACCTAGTGTAACAGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATCTCGACAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCAGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATCGCTGGCGGCGTTGACACTGCCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATATTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATCCTGCAGCAGGCCGGTACTTCCGTTCTGGCACAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fliC_k_Salmonella.enterica_IIIb.65:k:z_AY353438_k,z__1485 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACCATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCTTGGGTCTGGATGCGCTGAATGTGCAGAAAGCGTATGATGTAGATAGCAAACCAACAAG +TATGAAGTTGGATACTAGCGGTATAACAGCGGAGGCAATTAAAAACGGTGTAACTGGCGCAACGACAGATGGTGCACTTA +AAGACGGCAAGATTTATTCCGATGGTACTAACTACTACGTAGAAGTTAGCTTTGCTGCTACCGCAGACACAAGTAAAGGC +GGTTTTCTTAAAGTGGATGTTGATTCCTCTAATGGTAAAGTGTCTATTCCTACCACTGCTGCATCTGCTGTCGCGGCAAA +ACCAGCTGGAGTAAAAGAAGTTTCTGAAGTTCAAGGGAAAATTGCTGCATCAACAGATGTTAAAAATCAATTGACAGCAG +GCGGTATTGATGCTGGTGTTGCCGCCAATGCAGAAATGGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATTGAT +GGCGGTTATGCTGTAAAAGTAGGCAATGACTACTACGCCGCTACTCAGAAAAAAGATGGTAGCTTTAGTGTTAACACTAC +GTCTTACACTGCAGATGACGGTACATCCAAAACTGCACTAAACCAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTT +CTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCT +ACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGC +GGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCG +AAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTGGCG +CAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_j_Salmonella.enterica_Typhi.var.j+_AY353433_b,d,j__1260 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +TGCTATCGAGCGTTTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGACAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCGAATGGTACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATTGATTTA +AAAGAAATCAGCTCTAAAACACTGGGACTTGATAAGCTTAATGTCCAAGATGCCTACACCCCGAAAGAAACTGCTGTAAC +CGTTGATAAAACTACCTATAAAAATGGTACAGATCCTATTACAGCCCAGAGCAATACTGATATCCAAACTGCAATTGGCG +GTGGTGCAACGGGGGTTACTGGCGCCGATAAGGACAATACTAGCCTTGTAAAACTATCGTTTGAGGATAAAAACGGTAAG +GTTATTGATGGTGGCTATGCAGTGAAAATGGGCGACGATTTCTATGCCGCTACATATGATGAGAAAACAGGTGCAATTAC +TGCTAAAACCACTACTTATACAGATGGTACTGGCGTTGCTCAAACTGGAGCTGTGAAATTTGGTGGCGCAAATGGTAAAT +CTGAAGTTGTTACTGCTACCGATGGTAAGACTTACTTAGCAAGCGACCTTGACAAACATAACTTCAGAACAGGCGGTGAG +CTTAAAGAGGTTAATACAGATAAGACTGAAAACCCACTGCAGAAAATTGATGCTGCCTTGGCACAGGTTGATACACTTCG +TTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTG +CCCGTAGCCGTATCGAAGATTCCGACTACGCAACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGT +ACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_e,h_Anatumstr_AOZZ01000009_e__1497 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCACAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTATCAGCAACTGCTGCAAT +GGATCCGAAATCATTTACTGACGGTACTAAAAATCTTACAGCGCCTGATGCTACTGCTATCAAAGCCGCGTTGGGAAATC +CCACGGCAACAGGCGATTCCTTGTCTGCTACGCTTTCGTTTAAAGATGGTAAGTATTACGCCACTGTTGCAGGGTATACG +AATGCTGCCGATACCAGTAAGAATGGTAAATATGAAGTGAATGTTGATAGTGCGACAGGTGCGGTAACTTTCAATGCAGC +ACCAACTAAAGCCACAGTAACTGGGGATACAACAGTAACCAAAGTACAGGTTAATGCTCCTGTTGCAGTCAGTACTGATG +TTAAAAAAGCGCTAGAAGATGGTGGCGTTTCAAATGCGGACGCTACCGCAGCTAAATTAGTAAAAATGTCTTATACCGAT +AAAAATGGAAAATCTATTGACGGTGGTTATGCGCTTGAAGCCGGTGGCAAGTACTATGCTGCAACCTATGACGAAGGTAC +AGGTAAAATCACAGCTAATGTAACCACTTATACTGATTCCACGGGAGCCACAAAAACTGCGGCTAACCAACTTGGTGGCG +TAGACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCTAGTAAAGCCGCTGGTCACGATTTCAAAGCG +CAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGA +TGCGTTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACT +TGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fljB_1,6_Salmonella.enterica_Poona_AY353295_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCGCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAACTTATGCCGATAATGGTACTACACTGGATGCCTCAGGCCTTGATGATACAGCTATCAAAGCGGCTATAGGTG +GTACGCTTGGCACGGCTTCTGTAACCGGTGGTACAGTTAAATTTGACGCAGATAATAATAAGTACTTTGTTACTATTGGT +GGCTATACTGGTGCTGATGCCACCAAAAATGGCGATTATGAAGTTAACGTCGCTACTGACGGTAAAGTAACCCTTGCGCC +TGGCGCAACTAAAACCACAATACCGGCAGGTGCTACAACCAAAACAGAAGTACAGGAGTTAAAAGATACACCGACAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGATGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACCATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGTT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTTAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCACAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fliC_f,g,t_Salmonella.enterica_Berta_AY353532_g,m__1527 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTGCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATCCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +GTCCAGCTTCAAGAATGTTACGGGGTATGATACCTATGCTGTTGGTGCCAATAAATATCGCGTGGATGTCAACTCAGGGG +CGGTAGTAACTGACACCACTGCTCCAACTGTTCCTGATAAAGTATACGTAAACGCTGCAAACGGTCAGTTAACAACTGAC +GATGCGGAAAATAACACTGCGGTTGACCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGC +TGGTGCCATTAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGCA +ATGACGGTAATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCG +GCGAATGTTGATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGA +TAAAACCAAAAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAA +ATGGGGCTGAATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCT +TCTGGCGTTAGTACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTC +TGCATTGTCAAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTG +GCAATACGGTAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCT +AAAGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACT +GCGTTAA +>fliC_d_Schwarzengrundstr_ABEJ01000027_b,d,j__1509 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGA +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACGGTACTAACTCCCAGTC +TGACCTTGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATTGATATTGATTTA +AAAGAAATTAGCTCTAAAACACTGGGACTTGATAAGCTTAATGTCCAAGATGCCTACACCCCGAAAGAAACTGCTGTAAC +CGTTGATAAAACTACCTATAAAAATGGTACAGATACTGTTACAGCCCAGAGCAATACTGATATCGAAACTGCAATTGGCG +GTGGTGCAACGGGGGTTACTGGGGCTGATATCAAATTTAAAGATGGTCAATACTATTTAGATGTTAAAGGCGGTGCTTCT +GCTGGTGTTTATAAAGCCACTTATGATGAAACTACAAAGAAAGTTAATATTGATACGACTGATAAAACTCCGTTAGCAAC +TGCGGAAGCTACAGCTATTCGGGGAACGGCCACTATAACCCACAACCAAATTGCTGAAGTAACAAAAGAGGGTGTTGATA +CGACCACAGTTGCGGCTCAACTTGCTGCTGCAGGGGTTACTGGTGCCGATAAGGACAATACTAGCCTTGTAAAACTATCG +TTTGAGGATAAAAACGGTAAGGTTATTGATGGTGGCTATGCAGTGAAAATGGGCGACGATTTCTATGCCGCTACATATGA +TGAGAAAACAGGTACAATTACTGCTAAAACAACCACTTATACAGATGGTGCTGGCGTTGCTCAAACTGGAGCTGTGAAAT +TTGGTGGCGCAAATGGTAAATCTGAAGTTGTTACTGCTACCGATGGTAAAACTTACTTAGCAAGCGACCTTGACAAACAT +AACTTCAGAACAGGCGGTGAGCTTAAAGAGGTTAATACAGATAAGACTGAAAACCCACTGCAGAAAATTGATGCTGCCTT +GGCACAGGTTGATACACTTCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_k_Thompsonstr_AMSN01000007_k,z__1476 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTTCAAGCTACAGTTGAAAA +CAGTGTCAAACTGGATACTAGTGCTCTTACTGCCGATGCAATTAAAGGTGGCGTAACAGGTGCGACAACAGCTGGTGCCC +TCAAGGACGGTAAAGTTTACTCTAATGGTACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGACTCAGGTAAA +AATGGTTTCCTTAAAGTTGACGTTAATACAACTACTGGAGCGGTTACAGTTCCTGCAGCAGCAGCAAATACTGTAGCAGC +AAAACCAGCAGGTGTGTCTGAAGTTACTGAAGTTCAGGGACTAAATACACCGAGTTCGGCTGTACAAGATCAGTTAACAG +CTGCAGGTGTAAGTGCCGCTGATGCTGCTAAATCTGAAGTTGTGAAAATGTCTTACACGGATAAAAACGGTAAGACGATT +GATGGCGGCTTCGGTGTTAAAGTTGGAGACGATATTTATGCTGCAACTAAAAATAAAGATGGATCGATCAGCATTAACGC +CACTGAATATACCGATAAAGACGGCAACACAAAAACTGCACTGAACCAACTGGGTGGCGTAGACGGTAAAACCGAAGTTG +TTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAGCTGGCGGAAGCG +GCTGCTACAACCACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCTGCGTTCTGACCTGGG +TGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_z4,z23_Salmonella.enterica_IIIa.43:z4,z23:-_AY353495_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACGACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCAAACGGCTCGAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACTGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +CTCGGTAGTTGGTGATGTAAAAATTGCGGCCGCTGATTTCGATAACGCAAAAGCAACGGGTGGTCCGGCTGCAGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGGGGCGGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATTAGTTTTGATTCAGATAAAGATGCAACTGCAACTGCGGGGACTCCGCCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCAGGGACTTCTGTTCTGGCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z39_Salmonella.enterica_Grancanaria_AY353489_other.z39__1500 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGCAC +CGCTATCGAGCGTCTGTCCTCCGGTCTGCGTATCAACAGCGCGAAGGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAATGACGGTATTTCTATTGCGCAGACTACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGTCTGGATACGCTGAATGTTCAGAAAGCGTATGATGTGAATAGTGAAGTTGTTAC +TGATGGTAGTGGTGGTAAGGCACTAAATATTAGCGGTCTTGATGATGCTGCGATTAAAACCGCGGTTGGGGGGACACCAA +CTGGTACTGGTGAAATTAAAGATAACAAAGTTTATCACAACAGTACTGATGGTAAATATTATGTTGAAGTTGCTGGTTAT +ACCTCAGGGGAGAACGGTTTCTATGAAGTAGAGGCAAACCCTACTGATGGTACAGTTACATTTGCTACCGGTGCTACTAA +AATAACGGCTAAACCAGCTGGTGTTGAAGAAGTTACAACTGTCCAATCAAAACCCGTAGCTCTCAGTGCTGATGTTAAAA +CTCAATTAACTAATAGTGGAGTTAGTACTGCAGACGCTGATAAAGGTCAGTTAGTCACTATGTCTTATACGGATAAAAAC +GGTAAGACGATTGATGGCGGCTTCGGTGTTAAAGTTGGAGACGATATTTATGCTGCAACTAAGAATAAAGATGGTTCTTT +TAGTATCAACACCACGAAATATACCGATAAAGACGGTAATACCCAAACTGCATTGAACAAACTTGGTGGTGTAGACGGTA +AAACTGAAGTTGTTTCGATTGAAGGTAAAACCTACACTGCAGCGAAAGCAAAAGATCACGATTTCAAAGCACAGCCAGAA +CTGGCGGAAGCGGCTACTACAACCACCGAAAACCCGCTGCAGAAAATCGATGCTGCGCTGGCACAGGTGGATGCACTGCG +TTCTGACCTGGGCGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGTCTGAAG +CGCGTAGCCGTATCGAAGATTCCGACTATGCGACTGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGG +ACCTCCGTTCTGGCACAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_e,n,x_Chesterstr_AOZI01000020_e__1496 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCCGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fliC_r_Infantisstr_ASRF01000003_r,i__1470 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCTTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTCACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTC +CTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGAT +GGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTT +CCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAG +CAGCGGGTGTTGCAGCGGCCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGT +GGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATACTACGAA +ATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTA +TTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCTGCT +ACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGT +ACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCGAAG +ATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAG +GCGAACCAGGTTCCGCAAAACGTCCTCTCT +>sdf-I_AF370707__333 +GATCTATCCTAATGAAAATAAATGTGTTTTATCTGATGCAAGAGGGGGAGGGAGGAGCTTTAGCCAAAAGAAAACCGCCG +GGAGAGGCGGTTTGATGTGGTTGGTTCGTCACTGATTTTTTAGGCGCTTTTGTGCAGCGAGCATGTTCTGGAAAGCCTCT +TTATATAGCTCATTCTGACCTCTAAGCCGGTCAATGAGTTTTTCTTTCTCAGATTCAGGGAGTATATCAAAAAGGTTTAG +TAAATCAGCCTGTTGTCTGCTCACCATTCGCCAGCCACCACCTTCGAAGTTGTCATCGTAAGTACCAGAAGAACGAACGT +AGTTCATTAGATC +>fljB_z35_Salmonella.enterica_III.b.65:z52:z35_AY353342_other.z35__1488 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTTTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTAGATAGCAAAGCTGTGAC +ACCTCCGGCAAAACTTGATATTGCAGGATTAACTGGAACTGCAATTAAAACGGGCGTTGATAGCGCTACGGTTGATACTG +GCTCCATTAAAGATGGCAAAGTTTATTATAATAGTACCTCTAAGAACTATTACGTAGAGGTTGATTTTGGTACATCAGCC +GATGCTGCTAAGAGTGGTTACTATAAAGTCAATGTTGCTGATGATGGTACAGTCTCAATGACAGCTTCTACCACTAAAGA +GGCTACAACTCCTACTGGTATTACTGAAGTTACTCAGGTTCAAAAACCTGTAGCCGCTCCAGCCGCTATTCAGGCTCAGT +TGACAGCTGCCCATGTGACCGGAGCTGATACTGCTGAAATGGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATT +GATGGCGGTTACGCTGTAAAAGTGGGTGATGACTACTACGCCGCTACCCAGAAAAAAGATGGTAGCTTTAGTATTAACAC +CACGTCTTACACCGCAGCGGACGGTACATCCAAAACTGCCCTGAACCAACTTGGTGGCGCAGACGGTAAAACCGAAGTCG +TTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAGCTGGCTGAAGCA +GCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>fliC_r_Infantisstr_AFYI01000002_r,i__1470 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTC +CTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGAT +GGTGTTTATGAAGTAACAGTTGCAGCTGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTT +CCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAG +CAGCGGGTGTTGCAGCGGCTGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGT +GGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATACTACGAA +ATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTA +TTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCTGCT +ACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGT +ACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCGAAG +ATTCCGACTACGCGACCGAGGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAG +GCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fljB_k_Salmonella.enterica_II.52:c:k_AY353328_k,z__1488 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGTAC +CGCTATCGAGCGGCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGACAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCACAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACTCTGACCATTCAGGTTGGCGCCAACGACGGTGAAACCATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTGATAGCAAAGCTGCGCA +AAGCGTTAAACTGGATACCAGTGCTCTTACTGCCGCTGCAATCAAAGGCGGTGTAACAGGTGCAACAACAGATGGTGCCC +TCAAAGACGGTAAAGTTTACTCTAATGGCACAGACTATTATGTAGAAGTAAGCTTTGCTGATGCAACGGACTCTGCTAAA +GGTGGTTTCCTTAAAGTAGATGTTGATTCCACTACTGGTAAAGTTACCGTACCGGGTACGGCAGCAGCAGCTTCTTCAAC +TAAACCTGTTGGTGTGAACGAGGTTACAGAAGTACAAGGTAAAATCCCTGCATCTACTGCTATCCAGGACCAATTGAAAG +CTGGTGGTGTGAGTAACGCAGATGCTGCTACTGCTGAGGTTGTCAAAATGTCTTATACCGATAAAAATGGTAAGACGATT +GATGGCGGTTACGCTGTAAAAGTAGGTGATGACTACTATGCCGCTACCCAGAAAAAAGATGGTAGCTTTAGTGTTAACAC +CACGTCTTACACCGATAAAGACGGCAACACTAAATCCGCACTGAACCAACTGGGTGGCGCAGACGGTAAAACCGAAGTCG +TTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAACCAGAGCTGGCTGAAGCA +GCCGCTAAAACCACCGAAAATCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCCGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fliC_k_Salmonella.enterica_Inverness_AY353441_k,z__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTTCAAGCTACAGTTGAAAA +CAGTGTCAAACTGGATACTAGTGCTCTTACTGCCGATGCAATTAAAGGTGGCGTAACAGGTGCGACAACAGCTGGTGCCC +TCAAGGACGGTAAAGTTTACTCTAATGGTACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGACTCAGGTAAA +AATGGTTTCCTTAAAGTTGACGTTAATACAACTACTGGAGCGGTTACAGTTCCTGCAGCAGCAGCAAATACTGTAGCAGC +AAAACCAGCAGGTGTGTCTGAAGTTACTGAAGTTCAGGGACTAAATACACCGAGTTCGGCTGTACAAGATCAGTTAACAG +CTGCAGGTGTAAGTGCCGCTGATGCTGCTAAATCTGAAGTTGTGAAAATGTCTTACACGGATAAAAACGGTAAGACGATT +GATGGCGGCTTCGGTGTTAAAGTTGGAGACGATATTTATGCTGCAACTAAAAATAAAGATGGATCGATCAGCATTAACGC +CACTGAATATACCGATAAAGACGGCAACACAAAGACTGCACTGAACCAACTGGGTGGCGCAGACGGTAAAACTGAAGTTG +TTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAGCTGGCGGAAGCG +GCTGCTACAACCACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCTGCGTTCTGACCTGGG +TGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_e,n,x_Hadarstr_ARYR01000012_e__1496 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATTACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGTGTAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAGAACGTGCTGTCTCT +>fliC_g,m,q_Salmonella.enterica_Blegdam_AY353393_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGGCGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_1,2,7_Salmonella.enterica_Kambole_AY353275_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAAACTACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGATGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTGCACCTAGTGTAACTGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTTACACTTGCTAC +GGGGGCAACTAAAACCACAATGCCTGCTGGTGCGGCAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCAGCAGTTG +TTTCAACAGATGCTAAGAATGCCTTAATCGCTGGCGGCGTGGACGCTACCAATGCTAATGGCGCCGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fliC_m,t_Salmonella.enterica_Oranienburg_AY353411_g,m__1527 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGGTATGATACCTATGCTGTTGGTGCCAATAAATATCGCGTGGATGTCAACTCAGGGG +CGGTAGTAACTGACACCACTGCTCCAACTGTTCCTGATAAAGTATACGTAAACGCTGCAAACGGTCAGTTGACAACTGCC +GATGCGCAAAATAACACCGCGGTTGATTTGTTTAAATCTACTAAATCTGCTGCAGGTACTGACGATGCCAAGGCTATCGC +AACTTCTATCAAAGGCGGAAAAGTTGGTGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATACAAAAGCTGGTG +ATGACGGTAATGGTACGGTTTCTACTACCATCAATGGTGAAAAAGTTACATTAACAATTAGTGATATTGGCGCGAGTGCA +ACAGACGTAAATAGCGCGAAGATTCAATCAAGTAAAGATGTTTATACTTCCGTTGTAAGCGGTCAGTTTACTTTTGCTGA +TAAAACCAAAAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAA +ATGGGGCTGAATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCT +TCTGGCGTAAGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTC +TGCATTGTCAAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTG +GCAATACGGTAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCC +AAAGCGCAGATCCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACT +GCGTTAA +>fliC_g,p_Salmonella.enterica_Dublin_AY353399_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGTAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCATTGGCGCGGCGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_i_Salmonella.enterica_Augustenborg_AY353418_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGTACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCTCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_f,g,s_Salmonella.enterica_Agona_AY353383_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTGACAACTGACGATGCGGAG +AACAACACTGCGGTTAACCTATTCAAGACGACTAAATCTACTGCTGGTACCGATGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTAATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGGTGGTGCGGCGAATGTT +GATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAAGGCGAAAGTAAAATTACAGTAAACGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGGTCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_1,5_Muensterstr_AOYX01000059_1__1511 +ATGGCACAAGTAATCAACACTAAcagtctgtcgctgctgacccagaataacctgaacaaatcccagtccgcactgggcac +cgctatcgagcgtctgtcttctggtctgcgtatcaacagcgcgaaagacgatgcggcaggtcaggcgattgctaaccgtt +ttaccgcgaacatcaaaggtctgactcaggcttcccgtaacgctaacgacggtatctccattgcgcagaccactgaaggc +gcgctgaacgaaatcaacaacaacctgcagcgtgtgcgtgaactggcggttcagtctgctaacagcaccaactcccagtc +tgacctcgactccatccaggctgaaatcacccagcgcctgaacgaaatcgaccgtgtatccggtcagactcagttcaacg +gcgtgaaagtcctggcgcaggacaacaccctgaccatccaggttggtgccaacgacggtgaaactatcgatatcgatctg +aagcagatcaactctcagaccctgggcctggattcactgaacgtgcagaaagcgtatgatgtgaaagatacagcagtaac +cacgaaaacttatgccaataatggtactacactggatgtatcgggtcttgatgatgcagccatcaaagcggccataggtg +gtacgactggtacgcctgctgtaacgggcggtacagttaaatttgacgcagataataataagtattttgtttctattggt +ggctatactggtgctgatgcatccaaaaatggcgattatgaagttaacgttgctgctgacggtaaagttacacttgctac +aggtgcaactaaaaccacaataccggcaggtgcgacaactaaaacagaagtacaggagttaaaagatacaccaacagttg +tttcagcagatgcgaaaaatgccttaatcgctggcggcgtggatgctaccgatgctaatggcgctgagttggtcaaaatg +tcttataccgataaaaatggtaagacaattgaaggcggttatgcgcttaaagctggcgataagtattacgccgcagatta +cgatgaagcgacaggagcaattaaagctaaaaccacaagttataccgctgctgacggcgctaccaaaacagcggctaacc +aactgggtggcgtagacggtaaaaccgaagtcgttactatcgacggtaaaacctacaatgccagcaaagccgctggtcat +gatttcaaagcacaaccagagctggctgaagcagccgctaaaaccaccgaaaacccgctgcagaaaattgatgccgcgct +ggcgcaggtggatgcgctgcgttctgacctgggtgcggtacagaaccgttttaactccgctatcaccaacctgggcaata +ccgtaaacaacctgtctgaagcgcgtagccgtatcgaagattctgactatgcgaccgaagtttccaacatgtctcgcgcg +cagatcctgcagcaggccggtacttccgttctggcacaggctaaccaggtcccgcagaaCGTGCTGTCTcT +>fliC_z_Indianastr_AOZC01000051_k,z__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAATAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTGAC +TGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGCGCGAATATTAAAACTGGCGTTGATGGAGCTACCACTACGAGTG +GCTCCATTAAAGATGGCAAAGTATACTATGATGGTGCTACTAAAAATTATTATGTTGAAGTAGACTTTTCTGATGCCGCT +GATACTGCTAAAAATGGCTACTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCCTCGACTACTAAAGA +ACCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCGTCTGCTGAGGTGAAAG +CTGCTTTGACTGCTGGTGGCGTCGATGCTGCTGATGCAGCTACGGCAGAAATGGTCAAAATGTCTTATACCGATAAAAAC +GGTAAGACGATTGATGGTGGTTATGCTGTAAAAGTAGGCGATAGCTACTATGCCGCTACCCAGAAAAAAGACGGTAGTTT +CAGTGTTAATACTACTTCTTACACTGATAAAGACGGCAACACTAAATCTGCACTGAACCAACTGGGTGGCGTAGACGGTA +AAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAG +CTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCG +TTCTGACCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACTTGGGCAATACCGTAAACAACCTGTCTGAAG +CGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGT +ACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_b_Salmonella.enterica_Paratyphi.B_AY353358_b,d,j__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACTTTAAGTGTACAGGATGCCTATACGCCAAAAGGTACCGCTGTTAC +CAGAGATGTTACCACCTATAAAAATGGTGGTACTACTCTTACAGCACCTAACGCAGCAGCAATTGATACCGCTTTAGGTA +CGACTGGTGCGGCGGGTACTGCGGCTGTGAAATTTAAAGACGGTAACTACTTCGTTGAGGTGACCGGTACAACTAAAGAT +GGTCTGTATGAAGCGACAGTTGATGCAGCTGGCGCGGTGACAATGACCGCAAATAAAGCAACAGTAACTGGGGCTAGTAC +AGTTACTGAAAACCAAATTGTAGACGCTGTTACACCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATG +CAGGTGTGACAGGTGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCG +GGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAAACTGGTGAGATAAAAGCTAAAACTGT +AAATTATACTGACGCTACTGGTGCGACAAAAACCGGTGCTGTGAAATTTGGCGGTGCGAATGGTAAAACTGAAGTTGTGA +CCACCGTTGATGGTAATACTTATCAGGCTAGTGATGTAAAAGGGCATAATTTCCAGAGTGGTGGCGCTTTAAGCGAGGCT +GTAACCACTAAAACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAAGTTGATGCGCTGCGTTCTGACTTGGG +TGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCCCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_e,h_Salmonella.enterica_Sandiego.var.d+_AY353378_e__1509 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTATCAGCAACTGATGCAAT +GGATCCGAAATCATTTACTGACGGTACTAAAAATCTTACAGCGCCTGATGCTACTGCTATCAAAGCCGCGTTGGGAAATC +CCACGGCAACAGGCGATTCCTTGTCTGCTACGCTTTCGTTTAAAGATGGTAAGTATTACGCCACTGTTGCAGGGTATACG +AATGCTGCCGATACCAGTAAGAATGGTAAATATGAAGTGAATGTTGATAGTGCGACAGGTGCGGTAACTTTCAATGCAGC +ACCAACTAAAGCCACAGTAACTGGGGATACAACAGTAACCAAAGTACAGGTTAATGCTCCTGTTGCAGTCAGTACTGATG +TTAAAAAAGCGCTAGAAGATGGTGGCGTTTCAAATGCGGACGCTACCGCAGCTAAATTAGTAAAAATGTCTTATACCGAT +AAAAATGGAAAATCTATTGACGGTGGTTATGCGCTTGAAGCCGGTGGCAAGTACTATGCTGCAACCTATGACGAAGGTAC +AGGTAAAATCACAGCTAATGTAACCACTTATACTGATTCCACGGGAGCCACAAAAACTGCGGCTAACCAACTTGGTGGCG +TAGACGGTAAAACCGAGGTTGTTACTATCGACGGTAAAACCTACAATGCTAGTAAAGCCGCTGGTCACGATTTCAAAGCG +CAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGA +TGCGCTGCGTTCTGACCTGGGTGCGGTCCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACC +TGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_e,n,z15_Braenderupstr_AOZM01000055_e__1496 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAGGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTATCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGTGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAGTTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fliC_l,v_Litchfieldstr_APAN01000015_l,v__1503 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTTTCTGGCCAGACCCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTCGGCGCTAACGACGGTGAAACCATCGATATCGATCTG +AAACAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAATACCACTGGTCTTAATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAACG +GTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGACAACCACGAA +AGTGACAGGAGGCATGCCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAGTTA +AAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGATAAA +AACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGGATC +GTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAGACG +GTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCACAACTTCAAAGCACAGCCA +GAGCTGGCTGAAGCGGCTGCTACAACCACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCT +GCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCC +GGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTATTGCGTTAA +>O-9,46,27_partial_wzy__1019 +ATGTTACCGCATACATTTATGTTCCTGATTTTTAATATAGTATATATGTTACCAGTAGCCTATGTACATTTTTTTGGGTT +CTCCCTTGGAGGGGTTGAAGAGATTCTCAACGGTGATCCCAGTATGCTTGCAGATATGATGGTCTTTTACGTCGCTGTCT +GGTTCTTTTATCTTGCCGGTTCGGCATTATTAGGATTTGGTATAAAAAATAAAAATATACAATGGATTATAGCATTCGAA +CTTCCAATTATTGTAAAGATTTTATTCAGTTTAGTTTTATTTTTTATAGTACTATCAAAAGTATTGCTTTATCCTGAAGG +GGTTTACTCATCTTATGCCTTTGATTCTGGCGCTATGGCAAGTCGTGTCTGGAATATCTCGATGGGATTATCAGAACTAG +GTATAATAATTTTTACATTTTGTTTAGTTACAAAGAATATAAAGTTTGCAGTTGTTACCTTTCTTATAGTCTCATTAAAT +CTACTACATGGGACTAGAATATTTACATTGATATTACTTTTAATGATCATATTTTATATAATTTTTATTAATAAAAAAAT +ATCAAAGCTGAAATTATTTATTATTTTGAGCCTTTTTTTTGGCGCAATAGTGATATCATTTTTGATAATATTCATTATCC +GTTCTAATGTTTCAATTGAAAATATAAATATAGACCTAATTCTAAGTCCAATAGTATATGAGTCTTTATTTAATCAAATA +TCTTTTATGCGGATGCTGGATTGGCTACATCAAGGGGCAGTTCCGTTTGCACCACAAATGCTTTTTTCTGATTCAGCTAT +ATTTACGTTACCGACTTTTCTTTTTGATGAAAAATCATCTTTAATGTATATAAATAAATTTGGAGAACTTAGCCCTTTAG +GTGGGCTTTCCGGTTATGCTAGTGCAGTAATATATTTTTCGTATTATTATTTCCTGTGGTATTTTATTCTCGGTATTACA +TCAAGCTTATTATTAAGGTTTACATCGAGTGTAAACTTTGTAATATTGTCGAGAGTTAT +>fliC_z69_Salmonella.enterica_Pietersburg_AY353520_k,z__1503 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGTAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACCGCAAACATCAAAGGTCTGAGCCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCGAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCGGAAATCACGCAGCGTCTGAACGAAATCGACCGCGTATCCGGTCAGACCCAGTTCAACG +GCGTGAAAGTTCTGGCACAGGACAACACTCTGACCATCCAGGTTGGCGCTAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAATTCGCAGACCCTGGGTCTGGATACGCTGAATGTACAGAAAGCGTATGATGTTGATAGTAAAGCTGTAAC +AGTAGCTGCTGATTTAGATATTACCGCTCTTAATACCGATGCAGCTCTTAAAGCAGGAACGGGAGCTACAACAGGTACTC +CATCAATAAAAGATGACAAAGTTTATTATGATAGTGCCAGCAAAAACTACTACGTTGAAGTTACCGGATTAACCGCCCCT +GATGATGCTAAGAATGGCTTCTATAAAGTAAATGTTGCTGATGACGGTACAGTATCCATGGCCGCTAATACAGCTATAGA +GGCGGGTAAACCAGCCGGTGCAGTAGAAGTAACAAAAACTCAAGAAGAAAAAAACCCATTACCATTATCAGCAGATCTCA +AAACTTCTCTTAAATCTGGCGAGATTACAGATCCAGACATTGCTACCGCCCAAGTTGTCAAAATGTCTTATACCGATAAA +AACGGTAAGACGATTGATGGCGGTTATGCTGTAAAAGTAGGGAATGATTACTATGCTGCCACTCAGAAAAAAGACGGTAG +CTTTAGCGTTAATACCACTTCTTATACCGATAAAGATGGCAATACTAAATCTGCACTGAATCAACTTGGCGGCGTAGACG +GTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAACGCCAGCAAAGCCGCTGGTCACGATTTCAAAGCGCAGCCA +GAGCTGGCTGAAGCCGCTACTGCAACCACCGAAAACCCGCTGCAGAAAATCGATGCCGCGCTGGCGCAGGTTGATGCGCT +GCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGTCTG +AAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCA +GGGACTTCCGTCCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23_Salmonella.enterica_IIIa.62:z4,z23:-_AY353545_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGGGC +TTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAGCAACTGGTGGTCCGGCTGCGGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGCTGCAGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAAC +CCTATCACGCGAAGTGAAATTTGATGGAGCAGATTTAAAAGCCGATCAATCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACTTTGGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAA +ACTACGGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACGGTAAATAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>O-9,46_wzy__1191 +ATGAGATGTGCTATGGTATTTTTAGCGTGGTTTATTGCTATTGGGATATATATAATATGTGGTATTTTTTATCTTCAATT +TCCTCAATTATCACCACTAGGGGCTCTTGCATATACTGATACAGTGGGCGATGTAATCATTGTCGTATCCACGGGGATAG +TGGGAGTTTTTCTCGGCTATTTTGCATTTTCTAAAATCAAGTTAGTAGGAATAAAAGATTTTAATAATTCGTGTTTTATA +AATTTTTGTTCAGTATGCTTTATTATTTCAGCGTTTCTAATTTTCGCCTTAGGCGTCGCTGCATATGGTGGTTACATAGC +ATTTCTACATACGCCTTATATAGCAATCTATGAAGGTAGTGCAGAAAATCAAACCAGAGATATCCTCATATCTTCATCGG +GATTGCTTGCTAACTATGCACTATTAACTAGCATTCGTGTCAACTTTAAAGAAATATCAATAACTAATAAAGTTGTCATA +GCAGTATCGCTATTAATACTTGTTTCTATATTTATTCAGGGACGAAGAGAAAATTTAATTTTGCTAATATTATGTTTCGT +GTCATTCTATATGCTAAATTATAAAATTAATTTTAAACGTATTATCAAAGTAAGCATTATTTGTATAATAATGTTTTTCA +TTGCTGGATTAGGTTTATATTTGCGTGAAAGCACTTCAACTTCAGGAGGAAGTATTTTTACAGCTATACCTTTTGCCGTG +ATGTATGAAACACATTTTTCTTTAGCGACTTTGGCTAATGAAGTGAGAACGCATTTATATAATAATTTACCTTATGGGGG +AGTATTAGATTTATTTTCTCCCATATTATTTATTATCCCTGCTTTTATATATGGGATTTTTGGTTTAGATAAACAATCTT +TGTTCGAGAATAATGAGATGCGTTTTTATGAGGATAAAGGCGGCCAGTTTATATTCACAGAGGCTTTTCATTCACTTGGT +TATGTCGGAGTATTCCTGCATGGTTTAATCTTGGGTGTAATGCTAATAGTATTTTATCGTGTAGCCAAGAAAAGCAGGCT +CATAATTTATCATTTTCCAATTATTTCCCTCATATTTGTTGCAATGAGAAAAGACCTTACCTATGGTGTTAAATATATTT +CTCTTTTGTTCATATTTATGATGATTTTTTATTTCATCTATAAGTTACTCCCACTTAAAAATAATGGTTGA +>fliC_f,g_Havanastr_APAH01000011_g,m__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +GTCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGAATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGACCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTAATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGGTGGTGCGGCGAATGTT +GATGCTGCTACCTTACAATCAAGCAAAAATGTTTTTACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAAGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGGTCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCTAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>O-45_wzy__1164 +ATGTCGTACAAAAGTAATAATTTCTATAGAAATATACTTTTATTGAGTTTTTTCTTTTCTGGCTTTAGCTTGTATACTGT +TTTTATACCGTTACTATTTTTGACTATTCTTCTTTCTTTGCACAAAAATAAGGCACTGTATTTTGGAAGGCTAGCAGCAA +GCGCTAATATATTATTTATTATTTTATTTATTTTATTTGTTTTTTTTATAGGGGAAGATAGGCTATTATTAGAAAAACCA +TTTAAATATGCAGCATATATTATATTTATGATTTTTTGTTTGACATTATTACTATTGAATAATATAGAATATGCACAGAA +AGCAATACTATTTTTTATTTTTGGAATATTTTTACGAGCAGAGATTATTGTTATATATAGTTTCCTTGACCCATCAGGAG +TCTATGGATATGGTAAATTATTAGATCCTTTTAACCATGAAGAAATTAACTCACCAGGTATCAGTAATTCACTGGCTATG +GTTTTTGTATTTTTATTAGTTGTTTTCGAACCGAAGACATTAGCCAGAAAAATTTTTCTTATACTAGTTTACCCGTTACT +TTTATTATCCTCTATATTTTTAGGAGGGCGAGCATTTTTTATAATTGCAATTCTTGGGTTGGTTTATCAATACAAAAATA +ATACAAATATAAAGGCGATTATTTTTTTATTATTTTCTGCTCTTGGATGCTTAGTGCTATTTTTTATTATGTTTAAGGAC +GCTCCAGTTTTCGAAAAATATTTTAATTTAATTTTTGAGCGTTTTGGAAGTGAAGGATTAAAATCAGCACGCTTTGAACT +AATACAGGACGGGATTAGTAAATTCTTTATGTATCCGTTTGGAGGGTTTACTCCATATGCAAGTGAATACTCAGGTAGTT +GGTATCATAATATATACTTGGATAGTGCCAGAGTTGCAGGTTTTTTACCTTTGATAATGTTTCTTATATCAAATATTATT +TTATTTTCATGCTATTTCAAGTGTAAAAAGCGTAATCACAAAAATAAATATTTTTTCTTGTCAGTTATTACCTTAATTAT +AATGTGCCAGGACGTTATTCTCGAAGGAAATATGATGTTGCTGATTTGTTATGCATTATTCACAACAATGCAACTTCAAA +CGGGAGGGAGAAGTAAAAATGAAATTATATTACAGAGTAAATGA +>fljB_1,7_Indianastr_AOZC01000015_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCACAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTGCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTGCACCTAGTGTAACAGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATCTTGACAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGTGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTACGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCG +CAGATCCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fljB_z6_Kentuckystr_AOYY01000105_k,z__1493 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATTACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGTAAGGCTGTGAC +AGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTG +CAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCT +GATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGA +GGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCA +AAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTTGTCAAAATGTCTTACACCGATAAA +AATGGTAAGACGATTGATGGCGGTTACGCTGTAAAGGTGGGCGATAATTACTATGCCGCTACCCAGAAAAAAGATGGTAG +CTTCAGTGTTAACACCACGTCTTACACCGCAGCTGACGGTACTACCAAAACTGCCCTGAACCAACTGGGTGGCGCAGACG +GTAAAACTGAAGTCGTTTCTATTGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAGCCA +GAGCTGGCGGAAGCAGCTGCTAAAACCACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCT +GCGTTCTGACCTGGGTGCGGTTCAAAACCGTTTCAACTCCGCTATCACCAACTTGGGCAATACCGTAAATAACCTGTCTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCC +GGTACCTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fljB_1,5_Bareillystr_AOZP01000315_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGTGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCGATAATGGTACTACACTGGATGCCTCAGGCCTTGATGATGCGGCCATCAAAGCGGCCATTGGTG +GTACGACTGGTACGGCTGCTGTAACGGGTGGTACAGTTAAATTTGACGCAGATAATAATAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTTACACTTGCTAC +GGGTGCAACTAAAACCACAATGCCTGCTGGTGCGGCAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCAGCAGTTG +TTTCAGCAGATGCTAAGAATGCCTTAATCGCTGGCGGCGTTGACACTGCCGATGCTAATGCCGCGACATTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACATACAATGCCAGCAAAGCCGCTGGTCAT +GATTTTAAAGCACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATCCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAGAACGTGCTGTCTCT +>fljB_z39_Salmonella.enterica_II.6,7:z39:1,5,7_AY353349_other.z39__1500 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAATCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTACGTATCAATAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACGCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAATAACCTGCAGCGTGTACGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATACAGGTTGGCGCGAACGACGGTGAAACTATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTAAC +TGATGGTAGTGGTGGTAAGACATTAAATATTAGTGGTCTTGATGCTGCTGCAATTAAAACCGCTGTTGGAGGGACACCAA +CTGGTACTGGCGAAATTAAGGATAATAAGGTTTATCACAATAGTACTGATGGTAAATATTATGTTGAAGTTGCTGGTTAT +ACCTCAGGGGAGAATGGCTTCTATGAGGTAGATGCAAATCCTGCTGATGGTACAGTTACATTTGCTACCGGTGCTACGAA +AATAACGGCTAAACCTGCTGATGTTGAAGAGGTTACAACTGTCCAATCAAAACCTATAGCTCTCAGTGCTGAGGTTAAAA +CACAATTAACTGCTAATGGAGTTAGCACAGCGGCCGCTGATAAAGGCCAATTGGTCACAATGTCTTATACAGATAAAAAT +GGTAAGACTATTGATGGTGGCTTCGGTGTTAAAGTTGGCGCTGATATTTATGCTGCAACTAAGAATAAAGATGGCTCTTT +TAGTATCAATACCACGAAATATACTGATAAAGACGGTAATACCCAAACTACACTGAATAAACTTGGTGGCGTTGATGGTA +AAACTGAAGTTGTTTCGATTGAAGGTAAAACCTACACCGCAGCGAAAGCAAAAGATCATAATTTCAAAGCCGATCCTGAT +CTAGCGGAAGCAGCCGTTAAAACCACCGAAAACCCGTTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCG +TTCCGATCTGGGTGCGGTACAGAACCGTTTCAATTCCGCTATCACCAACCTGGGCAATACCGTAAACAACTTGTCTGAAG +CGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATCCTGCAGCAGGCCGGT +ACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_z39_Salmonella.enterica_II.51:l,z28:z39_AY353348_other.z39__1500 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGCCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAATAACCTGCAGCGTGTACGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTAAC +TGATGGTAGTGGTGGTAAGACATTAAATATTAGTGGTCTTGATGCTGCTGCAATTAAAACCGCTGTTGGAGGGACACCAA +CTGGTACTGGCGAAATTAAGGATAATAAGGTTTATCACAATAGTACTGATGGTAAATATTATGTTGAAGTTGCTGGTTAT +ACCTCAGGGGAGAATGGCTTCTATGAGGTAGATGCAAATCCTGCTGATGGTACAGTTACATTTGCTACCGGTGCTACGAA +AATAACGGCTAAACCTGCTGATGTTGAAGAGGTTACAACTGTCCAATCAAAACCTATAGCTCTCAGTGCTGAGGTTAAAA +CACAATTAACTGCTAATGGAGTTAGCACAGCGGCCGCTGATAAAGGCCAATTGGTCACAATGTCTTATACAGATAAAAAT +GGTAAGACTATTGATGGTGGCTTCGGTGTTAAAGTTGGCGCTGATATTTATGCTGCAACTAAGAATAAAGATGGCTCTTT +TAGTATCAATACCACGAAATATACTGATAAAGACGGTAATACCCAAACTACACTGAATAAACTTGGTGGCGTTGATGGTA +AAACTGAAGTTGTTTCGATTGAAGGTAAAACCTACACCGCAGCGAAAGCAAAAGATCATAATTTCAAAGCCGATCCTGAT +CTAGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCG +TTCCGATCTGGGTGCGGTACAGAACCGTTTCAATTCCGCTATCACCAACCTGGGCAATACCGTAAACAACTTGTCTGAAG +CGCGTAGTCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATCCTGCAGCAGGCCGGT +ACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_1,5_Manhattanstr_CBKW010000016_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCGATAATGGTACTACACTGGATGCCTCAGGCCTTGATGATGCGGCCATCAAAGCGGCCATTGGTG +GTACGACTGGTACGGCTGCTGTAACGGGTGGTACAGTTAAATTTGACGCAGATAATAATAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTTACACTTGCTAC +GGGTGCAACTAAAACCACAATGCCTGCTGGTGCGGCAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCAGCAGTTG +TTTCAGCAGATGCTAAGAATGCCTTAATCGCTGGCGGCGTTGACACTGCCGATGCTAATGCCGCGACATTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACATACAATGCCAGCAAAGCCGCTGGTCAT +GATTTTAAAGCACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATCCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAGAACGTGCTGTCTCT +>fljB_1,5_Idikan_SRR1272896__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACGACACTGGATGTATCGGGTCTTGATGATACAGCTATCAAAGCGGCTATAGGTG +GTACGACTGGTACGGCTGCTGTAACCGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGATGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>O-44_wzy__1134 +ATGATAATAAATAATATATTATTAATGGCATTATTAGCTGTATGTACTATAGACCTACCTTCCTTTATAGTAGTTTATGG +CTTGCAATTGTATATTCTGCCGTGTATTGTACTAATGTGTCTAATAAGAGGGGGAGTGTTTCCATTAAAATTTTTTTTCG +TAGCATCTTTTCTATCATTAATAATAATTATTATTACCGTAATCCAGGAGACTTATACTCCCTATCCTGATTTACTATGG +AGTTATACTGCTAGATTAATTTATTGGATTATGGTTTTTACACTGCTTATTCCATTTATACAAAAAATACCACTGATAGA +TTTAATAAAAATAATAAGAAGATGGATATTGTTATATTCTACATTCTTATTTATACAGTTTATAGCATTTTATCTATTTC +ATATTATAGTTGATTACTCATTAATTATTGGTGGTCAGGAATCAAGAATACTAAACGAAGTAGGTTTAAGAGCTTCCGGC +TTGACTGCTGAACCCTCAATTTATTCCGGGATAATGATTTCACTATTGATACTATTGTATCTCATGACTGGGAAAAATAA +TATAATAACATACATAGGGTTAATAAGTATATTATGTACTTTATCTACTTTAGGAATTTTTTTGGTTATTATTTATTTAG +CTATAACAAATTTATATCGAATTAAAATTTCTAGAATAGTCTTTTTTATATCCCTTTCAATTGCAATTATTTTTATTTTA +TGGGATTTTATTTTAAAAAGAATAGAACTTTTTCTGCAGGGCGGGGATGTTAGTAATAATATAAAAATCATGGTCATTGA +TAATCTGTTTAATAATGAGTCTTTATTTTTGCTTGGATATGGGTTGGTTGGTTATAGTGATAAAGCTCCCCCATATTATC +AGGCTCTTTATGACCTAACTTTATTTGGGAATTTATGTGTTATCTTTGGTATTCCTATTGGTCTTATGTTATCTATAACT +GTTTTTTTATTTACGTTGAATATGAGGATTTGTTTCGAGAAGAAAATACTGATAATTCTTTCTTTTATAAAAATCACTAT +CCCAAACTATATATTTTTTTATTTTTTCTTGGTTTTACTATATGTCATAACTAATAAAATATCGGTAAGATATCACAATA +GAAGAGAAGTATGA +>fljB_1,2_Saintpaulstr_AOXF01000050_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fljB_1,2_Newportstr_AJMO01000050_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fliC_e,h_Meleagridisstr_AOYN01000134_e__1497 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGTGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTATCAGCAACTGATGCAAT +GGATCCGAAATCATTTACTGACGGTACTAAAAATCTTACAGCGCCTGATGCTACTGCTATCAAAGCCGCGTTGGGAAATC +CCACGGCAACAGGCGATTCCTTGTCTGCTACGCTTTCGTTTAAAGATGGTAAGTATTACGCCACTGTTGCAGGGTATACG +AATGCTGCCGATACCAGTAAGAATGGTAAATATGAAGTGAATGTTGATAGTGCGACAGGTGCGGTAACTTTCAATGCAGC +ACCAACTAAAGCCACAGTAACTGGGGATACAACAGTAACCAAAGTACAGGTTAATGCTCCTGTTGCAGTCAGTACTGATG +TTAAAAAAGCGCTAGAAGATGGTGGCGTTTCAAATGCGGACGCTACCGCAGCTAAATTAGTAAAAATGTCTTATACCGAT +AAAAATGGAAAATCTATTGACGGTGGTTATGCGCTTGAAGCCGGTGGCAAGTACTATGCTGCAACCTATGACGAAGGTAC +AGGTAAAATCACAGCTAATGTAACCACTTATACTGATTCCACGGGAGCCACAAAAACTGCGGCTAACCAACTTGGTGGCG +TAGACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCTAGTAAAGCCGCTGGTCACGATTTCAAAGCG +CAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGA +TGCGTTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACTTGGGCAACACCGTAAACAACT +TGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_z10_Salmonella.enterica_Istanbul_AY353471_other.z10__1500 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTTGATAGCACTGGCGTTAC +TCAATCTCTTGATTTAAAAACTGCTGGAATTACTGGTGCTACATTAAAAGCTGGTATTACTGGTACAACGACAGAAACCG +GTAGCGTTAAAGATGGTAAAGTCTACTATGATGCAGATAGCAAAAATTACTATGTAGAGGTTGATTTTACTGATACTACG +GATAAAGCAGCGCATGCTGGTTTCTACAAAGCTGGCGTCGATGCTGACGGTAATGTTTCTTTAGCAACTGGTGCGACTAA +AGAAGCAAAACCAACGAATGCAGTTGAAGTTGAAAAAACTATTGATGAAAAACCGCTGAAAGCATCAAGTAGTGTTCAGG +ATGCCTTAAAAGCGAGTGGTATTGCTGATGCGGTTGCAGAAGCTGCGACGGTAGTGAAAATGTCGTACACTGATAAGAAT +GGTAAAACTATTGATGGTGGATACGGTATTAAAGTAGGTGATGACTACTATGCTGCAACTAAAGAAAAAGACGGCAGCTA +TAGTATTAATAGTACTTCTTATACCGATAAAGACGGCAACACTAAAACTGCACTAAACCAACTGGGTGGCGCAGACGGTA +AAACTGAAGTTGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCACAACTTCAAAGCACAGCCTGAT +CTGGCGGAAGCGGCTGCTACAACTACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCTGCG +TTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTG +CCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGT +ACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z35_Salmonella.enterica_Tema_AY353480_other.z35__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAATGACGGTATTTCTATTGCACAGACCACGGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAATC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCCGTCAC +GCCTCCGGCAAAACTTGATATTACAGGATTAACTGGAGCTGATATTAAAACTGGCGTTGATGGCGCTACGGTTGATACTG +GCTCAATTAAAGATGGCAAAGTTTATTATAATAGTACTTCTAAGGACTATTACGTACAGGTTGATTTTGGTACATCAGCT +GATGCTGCTAAGAGTGGTTACTATAAGGTCAATGTTAATGATGATGGTACAGTCTCAATGACGGCTGATACCACCAAAGA +GGCTACAACTCCTACAGGTATTACTGAAGTTACTCAAGTTCAAAAACCTGTAGCTGCTCCAGCCGCTATCCAGGACCAGT +TGACTGCCGCTCATGTCACCGGGGCTGATACAGCTGAAATGGTCAAGATGTCTTACACGGATAAAAACGGTAAGACTATT +GATGGCGGTTTCGGTGTTAAAGTTGGGGCTGATATTTATGCTGCAACAAAAAATAAAGATGGATCGTTCAGCATTAACAC +CACTGAATATACCGATAAAGACGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAGACGGTAAAACTGAAGTCG +TTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCACGATTTCAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_l,v_Salmonella.enterica_Brandenburg_AY353444_l,v__1503 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCGGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAATACCACTGGTCTTAATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAACG +GTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGACAACCACGAA +AGTGACAGGAGGCATGCCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAGTTA +AAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGCCAATTAGTTACGATGTCTTATACGGATAAA +AACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGGATC +GTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAGACG +GTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCACAACTTCAAAGCACAGCCA +GAGCTGGCTGAAGCGGCTGCTACAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCT +GCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATCCTGCAGCAGGCC +GGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_r,i_Salmonella.enterica_Bovismorbificans_AY353463_r,i__1476 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTC +CTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGAT +GGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTT +CCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAG +CAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTA +GCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATACTACGAAATACAC +TGCAGAAGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTATTGGTG +GTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCTGCTACAACC +ACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGTACAGAA +CCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCGAAGATTCCG +ACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCGAAC +CAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z6_Salmonella.enterica_II.48:e,n,x,z15:z6_AY353519_k,z__1503 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAGGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCACAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTAAC +AGTAGCTGCTAATTTAGATATTACTGATCTTAATAAAGATGCGGCCCTTAAAGCAGGGACTGGTGCTACAACAGGTACTG +CAGCAATAAAAGATGACAAAGTTTATTATGATAGTGCTAGCAAAAACTACTACGTTGAAGTTACCGGTCTGACTACCCCT +GATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTATCTATGGCCGCTGGTACGGCTATGGA +GGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAGAAAAATCCATTACCGTTATCAGCAGATCTCA +AGACTTCTCTTAAATCTGGCGGGGTTACAGATCCAGAAATTGCTGCTGCCCAAGTTGTCAAAATGTCTTATACCGATAAA +AACGGTAAGACGATTGATGGCGGTTACGCTGTAAAAGTGGGTGATGACTACTACGCCGCTACCCAGAAAAAAGATGGTAG +CTTTAGTATTAACACCACGTCTTACACCGCAGCTGACGGTACATCCAAAACTGCACTGAACCAACTGGGTGGCGCAGACG +GCAAAACCGAAGTTGTTTCTATTGGTGGTAAAACCTACAATGCCAGCAAAGCCGAAGGTCACAACTTCAAAGCACAGCCT +GATCTGGCGGAAGCGGCTGCTACAACCACCGAAAATCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTT +ACGTTCTGACTTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCA +GGGACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_y_Bareillystr_ALPN01000010_other.y__1509 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTTGATAACACGGTTGTCAC +GAACCCTAATTATGTTGATGGTGCAGCGTTAAGCACTACGATGCCTACTGCGGCTGAGATTAAAACGGCTATTGGCACTG +GTGCGGGAACTCCGGCAGTTAAAGGTAATGAAGTTCAATTTGATAAGAGCACTGGGAAGTATTACGTTGAAATTGAAGGA +TATTCAGCTCCTGATGCAGCTAAAAACGGCATTTATGAAGCCAAAGTTGCTGATGATGGCACAATATCTTTGGAGACTGG +GACCAAAAAAATTGGCACCGCAATGCCTGCTGGTGCTGAAGTTATTACTCACGTGCAGAAAAAAGATCAACCAGTTGTTG +TTGATGCCAGCGTTAAAGATGCTCTAAAAGCTGGTGGGGTAGATGATGCAGTTGCAGATACCGCGCAATTAGTCAAAATG +TCTTACACTGATAAGAATGGTAAAACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGCAAAACCGAAGTTGTTACTATCGATGGTAAAACCTATAATGCCAGCAAAGCTGAAGGTCAC +AACTTTAAAGCACAGCCTGATCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCTGCTTT +GGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_i_Kentuckystr_AYDR01000065_r,i__1476 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCTATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGGTGGCTATTATGAAGTTTCCGTTAATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_z4,z23_Salmonella.enterica_IIIa.18:z4,z23:-_AY353546_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGAAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGGGC +TTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAGCAACTGGTGGTCCGGCTGCGGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGCTGCAGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAAC +CCTATCACGCGAAGTGAAATTTGATGGAGCAGATTTAAAAGCCGATCAATCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACTTTGGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAA +ACTACGGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACGGTAAATAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z24_Albanystr_AOZW01000055_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +TGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTAAACGAAATTAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAAGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +CTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACAACGGGTGGTCCCGCAGCAGATAAAT +TATCTTTGGTAAAAGATGATAAAGGAAATTACCTTGTTAAAGATGTTACTGTCACTGCTACTCCTAAATATTATGCCGCT +ACCGTAGATAATAGTACTGGGGAAATTAGCTTTGATTCGGCTAAAGAAGTTACTTTAGCTGGTGGTGCACCAGCTCCGAG +TACGGTTGATACTTTGTCGCGTGAAGTGAAATTTGATGGAGCAAATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAG +ATGATAAGGGTAAAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCC +GCGGACGGTAAAACAACAGAGGGTACTACCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCT +TAAAACCGTTGACGCTTTCCGTAGCCAATTGGGGGCGGTGCAGAACCGTTTTGAATCTGCTATCACTAACCTGGGCAACA +CCGTCAACAACCTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_i_Salmonella.enterica_Agama_AY353430_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>O-44_wzy2__1247 +AATACGCTCTGTACCACCTGAATTACTTAGATCGTTTATAAAAAAACAAATAGTTTTCATAGTTCTCTTCTATTATGATA +ATTTTACCGATATTTTATTAGTTATAGCGTATAGCAAAACCAAGAAGAAATAAAAAAATATATAGTTTGGAATAGTAATC +TTTAGAAAAGAAAGAATTATCAGCATTTTCTTTTCAAAACAAATTTTCATATTTAGCACAAATGCAAAAACGATTATAGT +TAATATAAGACCAATAGGGACACCAAAGATAACACATAAATTCCCAAATAGCGTTAGATCATAAAGGGCCTGATAATATG +GGGGAGCTTTATCACTATAACCAACCAGCCCATAACCAAGCAGAAATAAAGATTCATTATTAAATAGGTTATCAATAACC +ATAATTTTAATATTATTACTAACATCTCCCCCCTGCAGAAAAAGCTCTACTCTTTTTAAAATAAAATCCCATAATACAAA +AACAATTATAATTGAAAGAGATATAAAAAAAATTATTTTAGAGGGTTTGAGTCTATATAAATTTGTTATAGCCAAATATA +GAATAACCAGAAAAATCCCTAATGTAGATAAGGTACATAATATACTTGTCAGACCTATGTATGTTATTATATTATTTTCC +CCGGTCATAAGGTATAACAATATTAACAAAGAAATCATTATGCCAGAATAAATTGAAGGTTCAGCAGTCAAACCTGAGGC +TCTTAAGCCTACTTCATTTAATATTCTTGATTCTTGGCCACCAATAATTAATGAGTAATCAACGGTAATATGAAATAGAT +AAAATGCTATAAACTGTATAAATAAAAATGCAGAATATATTACTATCCATTTTTTTATTACTTTTATTAAAATTTTCGGT +GGTATTTTTTTTATAAATGGAACAAGCATTGTAAAAAGCATAATCCAATAAATTAACCTAGCAGTATAACTCCATAGTAA +ATCAGGATAAGGTGTATAGGTCTTTTGGATTAAAGTAATAATTATTATTATGAATGATAAAGAGAAGGTGACGAAAAATA +GTTTTACTGGGAAAACCTTTCCTCTAATTAAACACATTAGTACTATGCATGGTAAAATATACAATTGCAAACCATAAACT +ACTATAGAAGCTGGCAAATCTATAGTACATATAGCTAATAATGCCATTAATAATGTATTATTTATTAACATATTAATATC +TTATTTATTTCTTATAAAAATATAATATAAACATTGAAAATATCGTA +>O-51_wzy__1026 +ATGCTTATCTATAATACAGTGTTCTTATTTTTGGTATTATGTGCATTGCTGGATTTAGCTGACAAGAAAAATTTTTTTTT +GTTTACATTGTCATTTATAGTATTACTTATATTAATGGGATTTCGTGGAAATGGTGGTGATGATTTTTTGGTTTATCAAC +AATACTTTAATTCACTACCAATAATATTGTATGATTATGGTGTTGGCTATTTTTATCTGAATTCTTTTGCTAAATATTTT +GGCAATTATGAATTTTTTATTTTTGTGTCTTCTTTATTATGTCTCTCGCTGCAATCATTTTTTATTTATAGCGAAACAGA +AAAACCATGTCTTGTCTTGCTGCTATTTTATTCAACTAGTTTTTTATGGCTTGACTTTATTCTTATAAGGCAGTCTATTG +CCGTAGGATTTTTTGTAGTTGCAATAAGTTTATATAAGAATAGCAGGAATAAATTGAGTTTTTTATTTTTTGTTTTTTCT +GCATTGTTCCACGAAACAGCATTTTTTGCTGCAGCTTTATTTTACATTTTTAGTAAACTAGAGAAAAAGGGGATTCTCAT +TGCCATTTTGATATTACTCATTTTATCTCCTTTTCTTTCAGATATTTTAGTTATCATCAATAATATTACTATAAAAAACA +AAAATGTAGAGTTATATCTCGGAGAGCATGCTTTACCAAGTATAGCTAATATAGCTGAGTTTTTGATGGCAGTATTAGCT +TTTATTATAATTAAAAAAGATGATATATTTAGAAATAGTAAAGAATATAGATTGTATAAAGTTATAATTATAGCATCCTT +TTGTATATTAGTGTTATCCTATACTGTTCCTACCTTGGCTCGCTTTCTTGAATACTATCGATTATTTTATTTCTTATTGC +TAACTCGTATGTTCATGTATTTTAATTTAAGAAGCCGATATATGATATTTATTGCTCTTACAGTATATGGTTTTGTCCGT +ATGAATAGTTTTATATATCAGTTCGATTCTGGATTTGATTATATATTTAATGGGAGTTCTATATGA +>O-3,10_wzx__1539 +ATGTTTAGAAATAAAGTTGCTCTTGGGTCTCAGATAGGATTGTTTACTTCAGTTCTTATATTAATAACAAACTTTTTTTT +AAGAAGTTACTTTGTTAAAGTATATGGTGCTGATTTAACCGGGTATTATTTATTAGTAGTACAGTTGATGGGAGTATTAA +ATCTTGCTGAGCTAGGTATAAGTACAGCCTTAACATATATCCTATTTAAACCACTGCATAGAAAAGAAAATAGTGAGTTA +AGACAATTATATTTTATAATAAAGAAAATATACCATTTTATAGCATTGGGCATATTAGTTATTGGACTACTTTTCTTTTT +GTTATTAAATTCTATAGTAAATGCAAGTATATCCCCTGAAAATCTATATATAACATGGGGGGTGTTTGTTATAAGTACAT +CATTATCATATTTATACTCTGCTCAATCTGTCATTTTAACAGCAGACCAGAATGTCTATTTGGTTAAATTAATTACTGGG +TTAACTAGAAGTTTAGCGTATATATTGCAAATATTTCTAATGATTTGCGGCGTCTCCTTTTGGATTGTGTGCGCTATTGA +ATTACTTTCTAATGTAATACAACTTATTCTTTTTAACAAACTAACATTAAAAAAATATCCGCAATTAGTAAAGTTGGATA +TTACTGATACTATCAATAAAGAAAATATAATAAGTGTAAAATCTAAAATAAAAAGAGAGATAAAATATACGTTTGTACAT +AAAATTGCCGGTGTTGTTGTATTTAATACAGATTATTTAATTATATCTGTCTTTCTAGGTATAACGGTTATCACATCTTT +TTCTTCCTATATGATGTTAATTCAAGCATTGGCTTTTCTGATATCAGCAATAGCTTCCCCACTGGGTGCCTATATAGGAG +CAAAACTATATTCTGATAGTAAGGAAAAAGTTATCAGGATTATATCACTTTATAATTCACTTTTTTTTATGCTAGGTATT +TTTTGCGCGTATATGTTTTATATATCTTCAAGTACATTTGTATCCTTATGGATGGGAAAAGAAATTGTACTTAGCCAACA +ATTAGTTTTGTTACTTTCTGTTAATTGCTTCGTATTGATTGCAAGGATCTCTTTTGATGTTGCAAAAGTAGGCCTTGGTT +ATATGTCAGATATTGAATTACCCCTACTGGAAGCCATAATTAATATTATCGTTTCATTAGTTTTAGTACATTATTTAGGT +TTAAATGGGATAGTTATTGGAACTATCGTTAGTAATATCATCGTTGTCATGATCTTGAAACCAGTATTTTTATACAAAAA +TGCCCTTAAATCGGATAATGCATTTATTATTCATGAGCTTATAAGGTCATGGTTCTTTATAAGCATATTCTTGCTTTCCA +TCTTTTTTATTACAAGGGCAAAAGTTATAGTCAGCAACGAATGGCTAGATTTCTTTATACAAGTGTGTATGAGTAGCATT +ACTCCTTTATTGTTATTGATAATGATATACAGCGTCTTTGATAGCAACGTTCGGAAATTCATGTTTGTTATGTTTAAAAA +AAAGTATAGGGAAAATTGA +>O-13_wzx__1236 +ATGGAAAAGCGTATTTATATAAATACCATTGCTAATTTATGTGGGGTTTTTTGGCAGGGAGCTATAATTCTTTTAATGGC +TCCTTTTTACCTGAAGTTATTAGGGAAAGAACAATGGGGTATGGTGGCTGCATGTTTATCCTTACAAGGGATATTATTAC +TGCTTGATGCAGGAATGTCACAAGTTATGCCAAGGGACTTTGCACAAAAAAAACAGAATATTAAAGAGATATATTCAAAC +TATATAGCTTTATATTTTTTGATTGCGCTTTGTGCTGTGTTTTTCTTGTATTTTTCTGCAGAGGCTATTGCTGAAAAATG +GTTTAGATTGGATGCTTTTTCTGCAAAGCAACTTGAACTCGCTATAAAAATTTTTGCAGGGCAGTTTTTTTTCCAGTTTT +GCAATAACGTTAATTTGGCATATTGGAATGGGAATGAAGAGCAAGTAAAAGCAAACTTATCGCAATGTATATTCATTTCT +TTGAAAAATATTACAGCAGTAATTTTAATTCTAAACGTTAGCCGACAAACATATATTTATGTATTATCTTTCTTCCTAAT +TGCTATGATTGAGTTTATCTGTAATTTTTCTTTTATCGTATCAAGGATAGGAGCGTGTAAACCGTCATGGGGAAAAATCA +AAAGAATTATTATTACTAACTATAAAATATCCTTAGGGATTCTGTTAGGCGTTTTTTCTTCACAATTAGATAGAATATTT +ATGTCAAGGTTTTTAAGCATTCAAAACTTTGGCTTGTATGTTATGACTATGCAATTTGGACTTGCGTTATTGCAGTTACA +GTATCCAATGGTTAAAGCAATATTACCTCATATCGCAAAAATTGGCGATACAACTAAGTTGGGATTATATAAAACAATAG +CTTTTTTTTGTGTCTTAATGCCATCTTGCATATTATTTTTTTGGGCAAAAGACATACTTTGGTTATGGAGTCATAATATT +GAAGTTGTAGAGTATGGAGTTATTATTGTCAAAATTTTGAGCGTTGCTGTGCTGATAAACTTTTTTTATAACTTTATTCA +CGTTAAGTTAATTGTTGAAAATAGAGGTGGGGTGATATTTATTTCGCAACTTTTGATTATTATTATTAACTCTATTTTCC +TAATATTCTTTTCCCCAAGAATTCATGAGGTGGCTGGAGCATTATCATGGATGATTAATTTTAGCATAGTCTTATTATGT +GGTTTGTTTTTTCTCCATAAAGGAAAAAAAAGATAA +>fliC_z81_Salmonella.bongori_40:z81:-_AY353261_other.z81__1485 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGCAC +TGCTATCGAACGTCTGTCTTCCGGTCTGCGTATCAACAGCGCAAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGTT +TTACCGCCAACATCAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCTGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCACAGGACAACACCCTGACCATCCAGGTCGGCGCTAACGACGGTGAAACCATCGATATTGATCTG +AAACAGATCAACTCGCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAAAATATGATGTGAAGAGCGAGGTTGCCAC +GCCAACAGCAAAACTGGATATTTCAGGCTTGGATGGCGCTGCGCTAAAAACGGGGACGGGTTCTACTGGTGATACTGGTT +CTATCAAAGATGGCAAAGTTTATTATGATGGAACAGATTATTACGCAGAAATTACTTTCACCGATACTGCTGATCAAACA +GCGAAAGGTGGTTATTACAAAGTCAACGTTGATGATGCAACCGGTGCTGTTACTATGACAGCATCAACAACTAAAGAAAC +GACAACCCCAACAGGTATTACTGCAGTGGCTCAGGTTCAGAAGCCTGTAGCAGCGCCATCAGCTATCCAGGATCAGTTGA +CAGCGGCAAGTGTTGCTAATGCTGACAAAGCAGAAATGGTCAAAATGTCTTATACCGATAAAAATGGTAAGACTATTGAT +GGCGGTTACGCTGTAAAAGTGGGGGACGATTACTACGCTGCTACTCAGAAAAAAGACGGTAGCTTTACCATTAACACCAC +TTCTTACACGGATAAAGACGGTAATACCCAAACTGCATTGAACAAACTTGGTGGTGTAGACGGTAAAACTGAAGTTGTTT +CGATTGAAGGTAAAACCTACACTGCAGCGAAAGCAAAAGATCACGATTTCAAAGCGCAGCCAGAGCTGGCGGAAGCGGCT +ACTGCAACCACCGAAAACCCGCTGCAGAAAATCGATGCTGCGCTGGCACAGGTTGATGCGCTGCGTTCTGACCTGGGTGC +GGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCG +AAGATTCCGACTATGCGACTGAAGTTTCCAACATGTCTCGCGCGCAGATCCTGCAGCAGGCAGGGACCTCCGTTCTGGCA +CAGGCGAACCAGGTACCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,t_Salmonella.enterica_Agodi_AY353407_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTGACAACTGACGATGCGGAG +AACAACACTGCGGTTAACCTATTCAAGACGACTAAATCTACTGCTGGTACCGATGAAGCCAAAGCGATAGCTAGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATACAAAAGCTGGTAATGACGGTA +ATGGTACGGTTTCTACTACTATTAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCAGCGAATGTT +AATGATGCCACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_i_Salmonella.enterica_IIIb.48:i:z_AY353419_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATAACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCAATACTGCGATTGCTTTAAACAATGGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACAG +ACCAGCAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TGCAGGTGGATTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCCAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGCTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCGAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCCGATCTGGCGGAAGCG +GCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTATGCGACCGAAGTCTCTAACATGTCTCGTGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_d_Salmonella.enterica_Isangi_AY353376_b,d,j__1521 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACGGTACTAACTCCCAGTC +TGACCTTGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATTGATATTGATTTA +AAAGAAATTAGCTCTAAAACACTGGGACTTGATAAGCTTAATGTCCAAGATGCCTACACCCCGAAAGAAACTGCTGTAAC +CGTTGATAAAACTACCTATAAAAATGGTACAGATACTATTACAGCCCAGAGCAATACTGATATCCAAACTGCAATTGGCG +GTGGTGCAACGGGGGTTACTGGGGCTGATATCAAATTTAAAGATGGTCAATACTATTTAGATGTTAAAGGCGGTGCTTCT +GCTGGTGTTTATAAAGCCACTTATGATGAAACTACAAAGAAAGTTAATATTGATACGACTGATAAAACTCCGTTAGCAAC +TGCGGAAGCTACAGCTATTCGGGGAACGGCCACTATAACCCACAACCAAATTGCTGAAGTAACAAAAGAGGGTGTTGATA +CGACCACAGTTGCGGCTCAACTTGCTGCTGCAGGGGTTACTGGTGCCGATAAGGACAATACTAGCCTTGTAAAACTATCG +TTTGAGGATAAAAACGGTAAGGTTATTGATGGTGGCTATGCACTGAAAATGGGCGACGATTTCTATGCCGCTACATATGA +TGAGAAAACAGGTACAATTACTGCTAAAACAACCACTTATACAGATGGTGCTGGCGTTGCTCAAACTGGAGCTGTGAAAT +TTGGTGGCGCAAATGGTAAATCTGAAGTTGTTACTGCTACCGATGGTAAAACTTACTTAGCAAGCGACCTTGACAAACAT +AACTTCAGAACAGGCGGTGAGCTTAAAGAGGTTAATACAGATAAGACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTT +GGCGCAGGTTGATGCGCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTA +A +>fliC_g,p,u_Salmonella.enterica_Rostock_AY353402_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGTAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGGCATTGGCGCGGCGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_1,2_Salmonella.enterica_Heidelberg_AY353265_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGTAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACACCACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAACCTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAATCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fliC_g,z62_Salmonella.enterica_II.9,46:g,z62:-_AY353415_g,m__1515 +ATGGCACAAGTCATTAACACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCTCAGTCCTCACTGAGTTC +CGCTATCGAGCGTCTGTCCTCTGGTCTGCGTATCAATAGTGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAGTTCAACG +GCGTTAAAGTCCTGTCACAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGATTCAATGTTAACGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGTTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTGCTGCTGGTACCGCTGACGCCAAAGCGATAGCTAATGTCAT +TAAGGGTGGTAAAGAGGGAGATACCTTTGATTATAAAGGCGTATCTTTTACTATTGATACAAAAACTGGTAATGATGGTA +ATGGTACGGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGGTGGTGGTAGTGTTAAT +GATGCTACCTTACAATCAAGCAGAAATGTTTATACATCTGCAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAAAAA +TGAGAGTGCGAAACTTTCTGATTTGGAAGCAAATAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTGAAT +ATACTGCTAACGCCGCGGGTGATAAGATCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTTAGT +ACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAATCCACTGGCTGCAATTGATTCTGCATTGTCAAA +AGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGGTAA +CCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAGATT +CTGCAGCAGGCCGGTACCTCTGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_i_Salmonella.enterica_IIIb.61:i:z_AY353417_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATAACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCAATACTGCGATTGCTTTAAACAATGGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACAG +ACCAGCAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TGCAGGTGGATTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCCAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCCTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGCTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCGAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCCGATCTGGCGGAAGCG +GCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTATGCGACCGAAGTCTCTAACATGTCTCGTGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_c_Salmonella.enterica_IIIb.57:c:z:z60_AY353366_other.c__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAGCGATACTGCTGTAGC +TGCTTCCTATTCCGACTCGAAACAGAATATTGCTGTTCCTGATAAAGCAGCTATTACTGCAAAAATTGGTGCAGCAACCA +GTGGTGGTGCTGGTATAAAAGCAGATATTAGCTTTAAAGATGGCAAGTATTACGCGACTGTCAGTGGATACGATGATGCC +GCAGATACAGATAAAAATGGAACCTATGAAGTCACTGTTGCCGCAGATACAGGAGCAGTTACTTTTGCGACTACACCAAC +AGTGGTTGACTTACCAACGGATGCAAAAGCAGTTTCAAAAGTTCAACAGAATGATACTGAAATAGCAGCAACAAATGCGA +AAGCTGCATTAAAAGCTGCAGGAGTTGCAGATGCAGAAGCTGATACAGCTACTTTAGTGAAAATGTCTTATACAGATAAT +AACGGCAAAGTTATTGATGGTGGGTTCGCATTTAAGACCTCCGGTGGTTATTATGCAGCATCTGTTGATAAATCTGGCGC +AGCTAGCTTGAAAGTTACTAGCTACGTTGACGCTACCACTGGTACCGAAAAAACTGCTGCGAATAAATTAGGTGGCGCAG +ACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGAAGGTCACAACTTTAAAGCACAG +CCTGATCTGGCGGAAGCGGCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACAC +GTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGA +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,s,t_Salmonella.enterica_Missouri_AY353405_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTGACAACTGACGATGCGGAG +AACAACACTGCGGTTAACCTATTCAAGACGACTAAATCTACTGCTGGTACCGATGAAGCCAAGGCGATAGCTAGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATACAAAAGCTGGTAATGACGGTA +ATGGTACGGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCAGCGAATGTT +AATGATGCCACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCCCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAAGCTGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_i_Salmonella.enterica_Gloucester_AY353429_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23,z32_Salmonella.enterica_IIIa.44:z4,z23,z32:-_AY353502_z4,z23__1266 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGTTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATTGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +TTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCAAAGATGCAAAAACCGGCGGTCCGGCTGCGGATAAATTAT +CTCTGACACAAGATGATAAAGGCAATTACTTTGTCAAAGATGATACTGCTGCAGCTAAATACTATGCAGCTACCGTAGAT +ACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAACCCT +ATCACGCGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGACCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAG +ATCTCTATGCTATCCAAACGTTAGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAAACT +ACGGAGGGCGCTGCCGTAGCCTTAGCTGCAAACGTCGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACTGTTGACGC +ATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATAACTAACCTGGGCAACACGGTAAATAACCTGT +CTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCACAGATTCTGCAGCAG +GCCGGCACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAGCGTCCTCTCTTTACTGCGTTAA +>fliC_z52_Salmonella.enterica_IIIb.50:z52:z35_AY353516_l,v__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGTACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGTTGTTAC +TGATGGTAGTGGTGGTAAGGCATTTGATCTCACCGCGCTTAATGATACTAACCTTAAGGCTGCAGTTGGTGGGACTCCTG +CTCCGACAGGAACCGCTGTAGTAAAAGATGATAAAGTATATTATAACAGCGCTGACGATAAATATTTCGTCGAGATTGAT +GGGCTAAGTAGTGGTAATGGCTTCTATGAAGTTAGCGCAAATGCAACAACTGGTGCTCTTACAATTGGTGCAGGGTTAAC +AACGGCTGGCGCAACGGTACCGGCGGGTGCTGAAGAAGTTACATCTGTGCAGTCAAAACCCGTAGCTCTCAGTGCTGATG +TTAAAAAACAATTGACTGATAGTGGCGTTAGCGTAGCGGACGCTGGTAAAGGCCGATTAGTCACAATGTCTTATACTGAT +AAAAACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCAGATATTTATGCTGCAACAAAAAATAAAGATGG +ATCGATCAGCATTAACACCACTAAATATACCGATAAAGACGGCAATACTAAATCCGCACTAAACCAACTGGGTGGCGCAG +ACGGCAAAACCGAAGTTGTTTCTATTGGTGGTAAAACTTACGCTGCGAGTAAAGCCGAAGGTCACAACTTTAAAGCACAG +CCCGATCTGGCGGAAGCGGCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACAC +GTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGA +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCTAACATGTCTCGTGCGCAGATTCTGCAGCAG +GCAGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_z53_IIIb.60:(k):z53_HM142067_other.z53__1497 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTTTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTAGATAGCAAAGCTGTAAC +TGATGCTAAGACTATTGATCTCTCCGCCTTAAACGAAGCCGCGCTCAAAGCTGGTACTACTGGTACAACAGGTGCTCCGG +TCGTTAAAGATGATAAAATTTATTATGACGAAGCCAGTAAAAACTACTATGTTGAGGTTGATGGTTTCACTACTGGTGAT +GTAGGTAAAAACGGTTTTTATAAAGTTACTGTTGATGCTGATGGTAAAGCGACTATGGCTGCCTCTACTACGATGGAGGC +TGCGAAACCAGCTGGCGCTGTCGAAGTGACTAAGACTCAAACAGAAACACCAGTTAAACTAAGCGCAGCACTTAAAAAAT +CGTTGACTGATGGTGGTGTTGACACTGCTGCTGCAGGTACTGCCCAAATTGTCAAAATGTCTTATACCGATAAAAACGGT +AAGACGATTGATGGCGGTTACGCTGTAAAAGTGGGCGATAACTACTATGCCGCTACCCAGAAAAAAGATGGTAGCTTTAG +TGTTAACACCACGTCTTACACCGCAGCGGACGGTACATCCAAAACTGCCCTGAACCAACTTGGTGGCGCAGACGGTAAAA +CCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAGCTG +GCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTC +TGACTTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCAC +GTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGGACT +TCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>fliC_l,v_Salmonella.enterica_IIIb.38:l,v:z54_AY353445_l,v__1503 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACCATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGTGAGGCTGTTAA +AAGCGGCGGTGGGGCAACACTAAGTACCACTGGTCTTAATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAGCG +GTACTGCTGCCATTAAAGATAATAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACC +GCTGGCGACGCTGCTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGTACTGTTACAATGCCGGCAACCACGAA +AGTGGCAGGTGGTATGCCAGCAACGGCGGCGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACTGAAGTTA +AAGCTCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTCACAATGTCTTATACTGATAAA +AACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTGATATTTATGCTGCAACAAAAAATAAAGATGGATC +GATCAGCATTAACACCACTAAATATACCGATAAAGACGGCAATACTAAATCCGCACTAAACCAACTGGGTGGCGCAGACG +GCAAAACCGAAGTTGTTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCT +GATCTGGCGGAAGCGGCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCACTGGCACAGGTTGACACGTT +ACGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCA +GGGACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_c_Salmonella.enterica_Choleraesuis_AY353365_other.c__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACTCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTAGATACGCTGAATGTGCAGAAAAAATATGATGTGAGCGATACTGCTGTAGC +TGCTTCCTATTCCGACTCGAAACAGAATATTGCTGTTCCTGATAAAACAGCTATTACTGCAAAAATTGGTGCAGCAACCA +GTGGTGGTGCTGGTATAAAAGCAGATATTAGCTTTAAAGATGGCAAGTATTACGCGACTGTCAGTGGATACGATGATGCC +GCAGATACAGATAAAAATGGAACCTATGAAGTCACTGTTGCCGCAGATACAGGAGCAGTTACTTTTGCGACTACACCAAC +AGTGGTTGACTTACCAACTGATGCAAAAGCAGTTTCAAAAGTTCAACAGAATGATACTGAAATAGCAGCAACAAATGCGA +AAGCTGCATTAAAAGCTGCAGGAGTTGCAGATGCAGAAGCTGATACAGCTACTTTAGTGAAAATGTCTTATACAGATAAT +AATGGCAAAGTTATTGATGGTGGGTTCGCATTTAAGACCTCCGGTGGTTATTATGCAGCATCTGTTGATAAATCTGGCGC +AGCTAGCTTGAAAGTTACTAGCTACGTTGACGCTACCACTGGTACCGAAAAAACTGCTGCGAATAAATTAGGTGGCGCAG +ACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGGCACAACTTCAAAGCACAG +CCAGAGCTGGCGGAAGCGGCTGCTACAACCACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGC +GCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGT +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_f,g_Salmonella.enterica_Adelaide_SRR1068324__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTGCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATCCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +GTCCAGCTTCAAGAATGTTACGGGGTATGATACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGAATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGACCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGCAATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCGGCGAATGTT +GATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_z39_Salmonella.enterica_IIIb.40:z39:1,6_AY353350_other.z39__1500 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGCAC +CGCTATCGAGCGCCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACGCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTAAC +TGATGGTAGTGGTGGTAAGACATTAAATATTAGTGGTCTTGATGCTGCTGCAATTAAAACCGCTGTTGGAGGGACACCAA +CTGGTACTGGCGAAATTAAGGATAATAAGGTTTATCACAATAGTACTGATGGTAAATATTATGTTGAAGTTGCTGGTTAT +ACCTCAGGGGAGAATGGCTTCTATGAGGTAGATGCAAATCCTGCTGATGGTACAGTTACATTTGCTACCGGTGCTACGAA +AATAACGGCTAAACCTGCTGATGTTGAAGAGGTTACAACTGTCCAATCAAAACCTATAGCTCTCAGTGCTGAGGTTAAAA +CACAATTAACTGCTAATGGAGTTAGCACAGCGGCCGCTGATAAAGGCCAATTGGTCACAATGTCTTATACAGATAAAAAT +GGTAAGACTATTGATGGTGGCTTCGGTGTTAAAGTTGGCGCTGATATTTATGCTGCAACTAAGAATAAAGATGGCTCTTT +TAGTATCAATACCACGAAATATACTGATAAAGACGGTAATACCCAAACTACACTGAATAAACTTGGTGGCGTTGATGGTA +AAACTGAAGTTGTTTCGATTGAAGGTAAAACCTACACCGCAGCGAAAGCAAAAGATCATAATTTCAAAGCCGATCCTGAT +CTAGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCG +TTCCGATCTGGGTGCGGTACAGAACCGTTTCAATTCCGCTATCACCAACCTGGGCAATACCGTAAACAACTTGTCTGAAG +CGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATCCTGCAGCAGGCCGGT +ACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_l,w_Salmonella.enterica_Gloucester_AY353332_l,v__1503 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAAAATATGATGTGAAGAGCGAAGCAGTTAA +AAGCGGCGGTGGGGCAACCCTCAATACTGCTGGTCTTAATGATACAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAACG +GTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCACGAA +AGTGGCAGGAGGCATGCCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAGTTA +AAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGATAAA +AACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGGATC +GTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAGACG +GTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGGCACAACTTCAAAGCACAGCCA +GAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCT +GCGCTCTGACCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTG +AAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCC +GGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_l,z13,z28_Salmonella.enterica_Poano_AY353333_l,v__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAAACTACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTTTCTGGCCAGACCCAGTTCAACG +GCGTGAAAGTTCTGGCACAGGACAACACCCTGACCATCCAGGTCGGCGCTAACGACGGTGAAACCATTGATATCGATCTG +AAACAGATCAACTCGCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAGGCAGTTAA +AAGCGGCGGTGGGACAACACTCAGTACCACTGGTCTTGATGATGCAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCG +GTACCGCTGCAATTAAAGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCGCTGC +GAAAGTGACAGGTGGCATACCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAG +TTAAAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGAT +AAAAACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGG +ATCGTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAG +ACGGTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCACAACTTCAAAGCACAG +CCAGAGCTGGCGGAAGCGGCTGCTACAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGC +GCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGT +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_1,5_Bareilly_CFSAN000189__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCTATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACTTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCGATAATGGTACTACACTGGATGTATCGGGTCTTACTGATGCAGCTATTAAAACGGCTACGGGTG +GTACGACTGGTACGGCTGCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>O:22-gene2__1023 +TTCCTTATGACAAATGTTGCATTCATTATCACAAAATCTGAAATCGGCGGTGCTCAAACTTGGGTAAATGAGATAGCTAA +ACTTATAGAACAGGATTGCAAAGTATTTCTCATAACATCCGAGTATGGATGGTTAACTCAATGTAGTGTTTTTTCTGAGG +TTTATATAATTCCAGGGATAAAAAAATATTTTGATGTTATTGCATATATAAAATTAATTAAGTTTATAAAAAAAAATAAC +ATTAAATCTATAGTGGCTAGTTCTGCAAATGCGGGGGTTTATTCTAGACTTGCCAGATTAACGTGCTCTTTTAAATGTAT +TTACGTTTCACATGGGTGGTCATGCTTATATAATGGTGGTCGGCTAAAAAGTATATTTTGCAAAATAGAAAAATACCTTT +CCAAATTAACGGATGTCATCTGGTGTATTTCTGAAAGTGATAGAGAAAAAGCTATAAAAAAAATAGGAATTGATGAGGGT +AAGATTATTACAGCTACGAATGCTGTTCCACCCATGCCTGCTCGTTTAAAAGAGTGTTTGGAATATAAAATTTTGTTTGT +TGGTAGATTGACACATCCTAAGCGCCCATGTTTATTGGCCCAAGTGATATCAAAAAAACCGCAATATAAGCTGGATATTG +TTGGAGGGGGAGAACAGTTAGAATCTCTCAAAGCCCAGTTCAAGGATTTTAAAAATATTCGTTTTTTAGGTGAAATAAAA +GGTTTTTCTGCTTATAAAGATTATGATATTTTTGCTCTTATATCCGATAGTGAGGGTTTGCCCATGTCGGGAATTGAGGC +TCATACTGCAGGTGTTCCCCTCCTTCTCAGTGATGTTGGAGGATGCCATGAGTTAATCGAGAAGAATGGAGTTTTGGTAG +AAAATATTGAAAGAGACATTGAGCTTAGTATAGATAGAATTTTTGAAAGATATGATTTTTTCCATACGCAAGCTGTCCTT +TCTGCTGATAGGTTTGTTATTGATAATTATATTCAATTATATAAAGAAATTATTTTGAATTAA +>fliC_b_Salmonella.enterica_Urbana_No-upload-yet_b,d,j__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGACAGGCAATTGCTAACCGTT +TTACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACTTTAAGTGTACAGGATGCCTATACGCCAAAAGGTACCGCTGTTAC +CAGAGATGTTACTACCTATAAAGATGGTGGTACTACTCTTGCAGCACCTGACGCAGCAGCAATTGATGCCGCCTTAGGTA +CGACTGGTGCGTCGGGTACTGCGGCTGTGAAATTTAAAGACGGTAACTACTTCGTTGAGGTGACCGGTACAACTAAAAAT +GGTCTGTATGAAGCGACAGTTGATGCAGCTGGCGCGGTGACCATGACCGCAAATAAAGCAACAGTAACTGGTGCCGGCAC +AGTTACCAAAAACCAAGTTGTAGACGCTGTTACTCCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATG +CAGGTGTGACAGGGGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCA +GGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAAACTGGTGAGATAAAAGCTAAAACTGT +AAATTATACTGACGCTACTGGTGCGGCAAAAACCGGTGCTGTGAAATTTGGCGGTGCGAATGGTAAAACTGAAGTTGTGA +CCACCGTTGATGGTAATACTTATCAGGCTAGTGATGTAAAAGGACATAATTTCCAGAGTGGTGGCGCTTTAAGCGAGGCT +GTAACTACTAAAACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGACTTGGG +TGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z81_Salmonella.bongori_66:z81:-_AY353260_other.z81__1485 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGCAC +TGCTATCGAACGTCTGTCTTCCGGTCTGCGTATCAACAGCGCAAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGTT +TTACCGCCAACATCAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCGGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTTTCCGGCCAGACCCAGTTCAACG +GCGTGAAAGTTCTGGCACAGGACAACACCCTGACCATCCAGGTCGGCGCTAACGACGGTGAAACCATCGATATCGATCTG +AAACAGATCAACTCGCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAAAATATGATGTGAAGAGCGAGGTTGCCAC +GCCAACAGCAAAACTGGATATTTCAGGCTTGGATGGCGCTGCGCTAAAAACGGGGACGGGTTCTACTGGTGATACTGGTT +CTATCAAAGATGGCAAAGTTTATTATGATGGAACAGATTATTACGCAGAAATTACTTTCACCGATACTGCTGATCAAACA +GCGAAAGGTGGTTATTACAAAGTCAACGTTGATGATGCAACCGGTGCTGTTACTATGACAGCATCAACAACTAAAGAAAC +GACAACCCCAACAGGTATTACTGCAGTGGCTCAGGTTCAGAAGCCTGTAGCAGCGCCATCAGCTATCCAGGATCAGTTGA +CAGCGGCAAGTGTTGCTAATGCTGACAAAGCAGAAATGGTCAAAATGTCTTATACCGATAAAAATGGTAAGACTATTGAT +GGCGGTTACGCTGTAAAAGTGGGGGACGATTACTACGCTGCTACTCAGAAAAAAGACGGTAGCTTTACCATTAACACCAC +TTCTTACACGGATAAAGATGGTAATACGCAAACTGCACTCAATAAATTAGGCGGCGTTGACGGAAAAACTGAAGTTGTTT +CGATTGAAGGTAAAACCTACACCGCAGCTAAAGCAAAAGATCATAATTTCAAAGCTGATCCTGATCTGGCGGAAGCGGCT +ACTACAACCACCGAAAACCCGCTGCAGAAAATCGATGCTGCGCTGGCACAGGTGGATGCGCTGCGTTCTGACCTGGGTGC +GGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCG +AAGATTCCGACTATGCGACTGAAGTTTCCAACATGTCTCGCGCGCAGATCCTGCAGCAGGCAGGGACCTCCGTTCTGGCA +CAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_b_Salmonella.enterica_IIIb.6,14:b:e,n,x,z15_AY353362_b,d,j__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAGGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCACAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACTTTAAGTGTACAGGATGCCTATACGCCAAAAGGTACCGCTGTTAC +CAGAGATGTTACCACCTATAAAAATGGTGGTACTACTCTTACAGCACCTAACGCAGCAGCAATTGATACCGCTTTAGGTA +CGACTGGTGCGGCGGGTACTGCGGCAGTGAAATTTAAAGACGGTAACTACTTCGTTGAGGTGACCGGTACAGCTAAAGAT +GGTCTGTATGAAGCGACAGTTGATACAGCTGGCGCGGTGACAATGACCGCAAATAAAGCAACAGTAACTGGGGCTAGCAC +AGTTACCGAAAACCAAATTGTAGACGCTGTTACACCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATG +CAGGTGTGACAGGTGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCG +GGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAAACTGGTGAGATAAAAGCTAAAACTGT +TAATTATACTGACGCTACTGGTGCAGCAAAAACTGGTGCTGTGAAATTTGGTGGTGCGAATGGTAAGACTGAAGTTGTGA +CCACAGTTGATGGTAATACTTATCAAGCTAGTGATGTTAAAGGACATAATTTCCAGAGTGGCGGCGCTTTAAGCGAGGCT +GTAACTACTAAAACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGACTTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTA +TCGAAGATTCTGATTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_l,z13,z28_Salmonella.enterica_Lutetia_AY353334_l,v__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATTGATATCGATCTG +AAACAGATCAACTCGCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAGGCAGTTAA +AAGCGGCGGTGGGACAACACTCAGTACCACTGGTCTTGATGATGCAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCG +GTACCGCTGCAATTAAAGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCGCTGC +GAAAGTGACAGGTGGCATACCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAG +TTAAAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGAT +AAAAACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGG +ATCGTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAG +ACGGTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCACAACTTCAAAGCACAG +CCAGAGCTGGCGGAAGCGGCTGCTACAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGC +GCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGT +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_z35_Salmonella.enterica_Kolar_AY353341_other.z35__1488 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTTTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGACAGACCCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAATACCCTGACCATCCAGGTTGGTGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCATATGATGTGAAGAGTGAAGCTGTCAC +GCCTCCGGCAAAACTTGATATTTCAGGATTAACTGGAACTGCAATTAAAACTGGTGTTGATGGTGCTACGGTTGATACAG +GCTCCATTAAAGATGGCAAAGTTTATTATAATAGTACCTCTAAGGACTATTACGTAGAAGTTGATTTTGGTACATCAGCC +GATGCTGCTAAGAGTGGTTACTATAAAGTCAACGTTGCTGATGATGGTACAGTCTCAATGGCAGCTTCTACCACTAAAGA +GGGTACAACTCCTACTGGTATTACTGAAGTTACTCAGGTTCAAAAACCTGTAGCTGCTCCAGCCGCTATTCAGGCTCAGT +TGACAGCTGCTCATGTGACTGGAGCTGATACTGCTGAAATGGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATT +GATGGCGGTTACGCTGTAAAAGTGGGGGATGACTACTACGCCGCTACCCAGAAAAAAGACGGTAGTTTCAGTGTAAATAC +TACTTCTTACACTGATAAAGACGGCAATACTAAAACCGCACTGAACCAACTTGGCGGCGTAGACGGAAAAACCGAAGTCG +TTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCGGGTCATGATTTCAAAGCACAGCCAGAGCTGGCGGAAGCA +GCCGCTAAAACCACCGAAAACCCACTGCAAAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGATCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTA +TCGAAGATTCCGACTATGCGACTGAAGTTTCTAACATGTCTCGCGCGCAGATTCTGCAACAGGCCGGTACTTCCGTTCTG +GCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,x_Salmonella.enterica_II.56:e,n,x:1,7_AY353314_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +TGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACGCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATTGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACGGATATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACAGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACTCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTACCACGA +AAAAAGCTTTACAAGATGGAGGCGTTTCATCTGCGGATGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACGGTGGCTAACCAACTGGGGGGCGTAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCATGATTTTAAAGCACAG +CCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGTTCCGATCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACTTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATCCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_1,5_Choleraesuis_CP007639_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCACAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATACAGCTATCAAAGCGGCTATAGGTG +GTACGACTGGTACGGCTGCTGTAACCGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCAGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fljB_e,n,x,z15_Salmonella.enterica_Verity_AY353311_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAATCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTACGTATCAATAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACGCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAATAACCTGCAGCGTGTACGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATACAGGTTGGCGCGAACGACGGTGAAACTATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTAAAGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACCGTAGGTGGTTATACCGAT +ACGGGGGATGCTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACTCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTACCACGA +AGAAAGCCTTACAAGATGGAGGCGTCTCATCTACAGATGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAACGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAG +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATACCGTAAACAACTTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGGACTTCCGTTCTGGCGCAGGCAAACCAGGTCCCGCAGAACGTGCTGTCTTTGTTACGTTAA +>O-48_wzy__1194 +GTGATTATAAAGAAGAATAAATTTGTTTATTCGGTACTTAAAGTCTGGTTAATAGTCTCTTCATTGTATTATTTAAATGC +TATTTTTTCCGGTGTTGATGCGTTAAAATATAATGAAGATTTGACGCAAAAGTTCATCAAATATGCAATATGTTTTATAA +TAAGTTTTTTTATTCTGTTCAATAGTAAACGAGTCAAATTTTTGGGGGCTTCGTTATTTTTCATAATCCTTTCGGTAGCT +TCAGTAGTTATTGGTAATGTAGTAACGGTATATGCTACCGCGATGCTGATAATTGCTACCATGGTTGGTTTCAGCCAAAT +TATTCTTTATTTTTCTAATGATATGTCGAAGATTAATATGGTTTTATTATGGACTGGAATTATAATAGGCGCCATTTCTG +TATTAGAATTAACAGTATTCTACGATTATATGGTCTCATATTGGGTTTCGACTGGTGGAGTCCGATCAATATCTTCTCTT +CTTAATCCTACAAATAGCGGGGCTTATTCAGCGATTATAATTTTAATTGCTTTAGGGACTAATATAAGGAGTAAATTTAA +GAGAACTTTATTTGCTTTAATGCCAATGATTACTTTAATCAGCAGCGGATCACGTACAGCATGGTTATCATTAGCATTAA +CATTATTATTGACGGTATTATTAAATGATAAGGCTAGTATACGATTACGGAAAAAAATATTAGCTATTGCAGGTATTGGA +GCTATTTGTGGTGTGTTATATGTAGCATTTTATATGAGTAGTATCTCTGGTATTCAATCCCAACATCGAGGGCTTGATAC +ATATACCGCATCAATTCGAGTTGAAAACTTTATAACATATATGAATTCAATTGATTTTGATATGTTATTACCTGATTTCC +TTGATAAAAATATTAACCTTATATCAGATAATTTTTATCTAGTGTTATTAAATTATTTTGGAATTATTGGGGGTTATATT +GTTTTTTTTATTTCAGTATTATTATTCTATTATAATATGCAAACAAAGGATTTTGATAAAAATATAGATGAAAGTATTTC +TGTTTGGAGAGTGATATTCATCTATTTTCTGATATCTGGACTTTCAAACTCATTCATAAATTCTTTTCCTGTAAACCAAC +TATTTTTTATCTCATGCGGGTATTATGTGTATAAATATAACTTAATAAAGAAAAATGCTGGAAAGCAAATATGA +>O-48_wzy-from-2013K-0909__1194 +TCATATTTACTTTCCAGCATTTTTCTTTATTAGTTTATATTTATATACATAATACCCACATGATATAAAAAATAGTTGGT +TTACAGGAAAAGAACTTATGAATGAGTTTGAAAGACCAGATATCAAAAAATAGATAAATATCACTCTCCAAATAGCAATA +TCTTCATCTATAACTTCACTAAAATATTTTATTTGTGCATTATAATAGAACAGTAACATTGAGATTAAAAAGAAAATATA +AAACCCAATAATCCCAAAATAATTCACTAATACCAGATAAAAATTATCTGATATAAGGTTAATATTTTTATCAAGAAAAT +CAGGAAATAACATACCAAGGTCAATTGAGTTTATATATGTCATAAAGTTCTCAACTCGAATTGACGCGGTATATGTATCA +AGCCCTCGATATTGTGATTGTATATTAGAGATACTACTCATATAAAATACTGCATATAGCACACCACAAATAGCTCCAAC +ACCTGCAATAGCTAATATTTTTTTCCGTAATCGCATGCTAGCCTTATCATTTAAGAGAACCGTCAGTAATAATGTTAGCG +CCAATGATAACCATGCTGTGCGTGATCCACTACTGATTAAAGTAATCATTGGCATTAAAACAAACAAAGTTTTCTTAAAT +TTATTCCTTATATTAGTTGCTAAAGCAATTAATATTATGATTGCTGAATAAGCCCCGCTATTTGTAGGATTAAGAAGAGA +AGATATTGATCGTATTCCACCAGTCGAAGTCCAATATGAGACCATATAATCGTAGAACACCGTCAATTCTAACACGGAAA +TTGTGCCTACAATAACTCCCGTCCATAATAAAACCATATTAATCTTCGACATATCATTGGAAAGATAAACAATAATTTGG +CTAAAACCAAGCATGGTAGCAATTATCAGCATCGTGGTTGCATATACCGTCACTACATTACTAATAATTACTGAAGATAC +TGAAAGGAGTATGAAAAATAACGAAGCCCACAGATATTTGACTCTTCTATTATTGAACAGAACAAGAAAACTTATTATAA +AACAAATTGCATACTTGATGAACTTTTGCGTTAAATCTTCATTATATTTTAATGCATCCACACCGGAAAAAATAGCATTA +AGATAATATAATGAAGAGACTATTAACCAGACTTTAAGTAACGAATAAACAAATTTATTCTTCTTTATAATCAC +>O-1,3,19_not_in_3,10__130 +acgagaagtactgaataataattgtatcaaatagcctgcgtaaaatctgaacgcatcaatcgctaccttaatatcatacc +tttgagttaacatactattcacctttaacctgccatgaccgtttgtggca +>fliC_d_from-II-48:d:z6_SRR1168371__1521 +TTAACGCAGTAAAGAGAGGACGTTTTGCGGAACCTGGTTAGCCTGCGCCAGAACGGAGGTACCGGCCTGCTGCAGAATCT +GCGCGCGAGACATGTTGGAGACTTCGGTCGCGTAGTCGGAATCTTCGATACGGCTACGGGCAGAAGACAGGTTGTTTACA +GTATTGCCCAGGTTGGTGATAGCGGAGTTGAAACGGTTCTGTACCGCACCCAGATCGGAACGTAATGTGTCAACCTGCGC +CAGCGCAGCATCAATTTTCTGCAGCGGGTTTTCGGTCTTATCTGTATTCACCTCTTTAAGATCGCCGCCTGTCCTGAAAT +TATGTTTATCAAGATCACTTGCCAGGTAAGTTTTACCATCGGTAGCAGTAACCACTTCAGATTTACCATTTGCGCCACCA +AATTTCACAGCTCCAGTTTGAGCAGCGCCAGTACTATCTGTATAAGAAGCAGTTTTAGCAGTAATTGTACCTGTTTTCTC +ATCATAGGTAGCGGCATAGAAATCGTCGCCCATTTTCACTGCATAGCCACCATCAATAACCTTACCGTTTTTATCCTCAA +ACGATAGTTTTACAAGGCTGGTATTGTCCTTATCGGCACCAGTTACACCCGCAGCAGCAAGTTGAGCCGCAACTGCGGTT +GTATCAGCATCACCTTTTGTTATTTCAGCAACCTGGTTATTAGTTATGGTAGCTGTTGCCTGAATATCTGTAGCAGCCGC +ACCTGTTAACGGAGTTGTATCAGTTGTATCTATACTAACTTTCTTGGTAGCTTCATCATAAGTCGCTTTATAAACGCCAG +CAGAAGCACCACCTTTAACATCTAAATAGTATTGACCATCTTTAAATTTGATATCAGCCCCAGTGACACCCGTCGCACCA +CCACCAATCGCAGTTTGGATATCCGTATTGCTCTGGGCTGTGATAGTATCTGTACCATTTTTATAGGTAGTCCTATCAAC +TGTTACAGCAGTTTCTTTAGGTGTGTAAGCATCCTGTACATTAAGTTTATCAAGTCCCAGCGTTTTAGAGCTAATTTCTT +TTAGATCAATATCAATAGTTTCACCATCGTTGGCGCCAACCTGGATGGTCAGGGTGTTGTCCTGCGCCAGAACTTTCACG +CCGTTGAACTGAGTCTGGCCGGATACACGGTCGATTTCGTTCAGACGCTGGGTGATTTCAGCCTGGATGGAGTCAAGGTC +AGACTGGGAGTTGGTACCGTTAGCAGACTGAACCGCCAGTTCACGCACACGCTGCAGGTTGTTGTTGATTTCGTTCAGCG +CGCCTTCAGTGGTCTGCGCAATAGAAATACCGTCGTTAGCGTTACGGGAAGCCTGCGTCAGACCTTTAATGTTCGCGGTG +AAACGGTTAGCAATCGCCTGACCTGCCGCATCGTCTTTCGCGCTGTTGATACGCAGACCGGAAGACAGACGCTCGATAGC +GGTGCCCAGTGCGGACTGGGATTTGTTCAGGTTATTCTGGGTCAACAGCGACAGGCTGTTTGTATTAATGACTTGTGCCA +T +>O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002 +ATGAAGGTGTCATTTTGTATCCCAACGTATAATCGAGTAAAATTCATTGAAGAGCTTCTTGAAAGTATTAATAATCAGTC +CTCTCACTCCTTAACGGTAGAAGTATGCATTTCAGATAATGCATCAACTGATGGAACTGAAGAATCAATAAATATCTGGA +GAGGTAGATTTAATTTTCCAATATTGTATCAAAGGCATAACGAGAATATTGGGCCGGATAGGAATTATTTATCTGCAGTT +AATATGGGGACTGGGGATTATTGTTGGATTTTCGGAAGTGATGATATTCTTACAAAAAACTCCCTCGTATTGATGGAAGA +TAAATTGGCTAACGAAAGTGACATTTATTTATGTGACAGACGAGAATTAGATATTTCAATGACGAGGATATGTAATCCAC +ATCGGCGATGGTTAAGCGGTGGTAGTAGATTATTTTCTTTTAGCAATGAAGCCGATTTGATAGAGTACTTTAGTAAATGT +AACTCAGTTGGCGGACTTTTTAGCTATTTAAGCTCTATTATAGTGAAAAGGGATAAATGGTCTGACGTCATATTTGACGA +ATCCTACATTGGTACAGCTTATGCGCATGTATATATTTTATTAAGAATAATTAACAATATGAATTCGACCCTACAATACA +TATCACTGCCGCTGGTTGATTGCAGAGGCGATAACGATACATTCGAAACTAATGGGAAGGCTCGTCGAATAAAAATAGAT +TTCATCGGCTATTTAAAACTAAGGGAGGATTTTTATGATAAAAATACAAAAATATATAGCTCATTTGGGCGGGTTCTTAC +AAAAGAGCGCCCTTGGTTTTATACTTCTTTAGCTATGGCATGTTATGGTGATTCCACAGACAGAGCTGAACTTGCATCCT +TTTATAAGAGGTTGGGCTATCCGGAAATAGCCACTAATTTTATATTTCGTCTTAAAGGACTGGCTAGCTACGCTAAAAGA +ATTAAATTAGCTAAAATGGTAATAAAAAAAATATTTTCATAG +>fliC_z_Salmonella.enterica_Poona_AY353467_k,z__1500 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACTACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTGAC +TGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGCACGGATATTAAAACTGGCGTTGATGGAGCTACCACTACGAGTG +GCTCCATTAAAGATGGCAAAGTATACTATGATGGTGCTACTAAAAATTATTATGTTGAAGTAGACTTTTCTGATGCCGCT +GATACTGCTAAAAATGGCTACTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCCTCGACTACTAAAGA +ACCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCGTCTGCTGAGGTGAAAG +CTGCTTTGACTGCTGGTGGTGTCGATGCTGCTGATGTAGCTACGGCAGAAATGGTCAAAATGTCTTATACCGATAAAAAC +GGTAAGACGATTGATGGTGGTTATGCTGTAAAAGTAGGCGATAGCTACTATGCCGCTACCCAGAAAAAAGACGGTAGTTT +CAGTGTTAATACTACTTCTTACACTGATAAAGACGGCAACACTAAATCTGCACTGAACCAACTGGGTGGCGTAGACGGTA +AAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAG +CTGGCTGAAGCAGCCGCTAAAACCACCGAAAATCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCG +TTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAG +CGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCTGGT +ACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z36_Salmonella.enterica_Potosi_AY353482_z36,z38__1266 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCAAACTCTGACTC +TGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATTGCTACAACAGTTAAAGAAGGTAC +GAAGCTCACTGCCGATTTTGCAGTTAAGGTCGCAGATTTTGATGATCAAGCAACAACTGGTAAATTAACTGCAGACTTAG +AATTGAAGCAGGATAAATCCGGAAACTACTTTGCCTTCGATAAAGCAAACAGTAAATATTACGACGCAACTGTGGATGCT +GCTACAGGTAAAATAGAATTTACTTCTGGGACAGGTAAAGAGACAACGAAAGATACATCTAAACTTACGGATGTTACTTC +TTTGTCCAAAGAAGTAACGATAGATAGTGGGCTCACGGATGATAAATTATTAGTAAAATACAAAGGGGATGATGGTAAAG +AACAGTATGCCGTTCAAACTCTTGATAATAAAGGTAATGCGACCTATAAGACTGCCGTTATAGCGCGTGACGGCAAAGTG +ACAGAGGGTACTGCCGTAGCCTTAGCTGCAAACGTCGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGACGC +TTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAGTCTGCCATAACTAACCTGGGCAACACGGTAAATAACCTGT +CTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGCACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAGCGTCCTCTCTTTACTGCGTTAA +>fliC_r_Salmonella.enterica_Rubislaw_AY353458_r,i__1482 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTC +CTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGAT +GGTGTTTATGAAGTAACAGTTGCAGCTGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTT +CCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAG +CAGCGGGTGTTGCAGCGGCTGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGT +GGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATACTACGAA +ATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTA +TTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCTGCT +ACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGT +ACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCGAAG +ATTCCGACTACGCGACCGAGGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAG +GCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_f,g_Salmonella.enterica_Derby_AY353381_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAGGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCTACAGTGGGTGATCTGAA +GTCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGTAGCACCGAATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGACCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTAATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGGTGGTGCGGCGAATGTT +GATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAAGGCGAAAGTAAAATTACAGTAAACGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGGTCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCTAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,m,s,t_Salmonella.enterica_II.43:g,m,s,t:z42_AY353397_g,m__1515 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCTCAGTCCTCACTGAGTTC +CGCTATCGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAGTTCAACG +GCGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGATTCAATGTTAACGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGGTACGATACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCTGCAAACGGTCAGTTGACAACTGATGATGCGCAA +AATAACACTGCAGTTGATCTATTCAAGACCACTAAATCTACTGCTGGTACCGATGATGCCAAAGCGATAGCTAATGTCAT +TAAGGGTGGTAAAGAGGGAGATACCTTTGATTATAAAGGCGTATCTTTTACTATTGATACAAAAACTGGTAATGATGGTA +ATGGTACGGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGGCGGTGGTGGTAGTGTTAAT +GATGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAAAAA +TGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGTGAAAGTAAGATTACAGTAAATGGGGCTGAAT +ATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTTAGT +ACATTAATCAATGAAGACGCTGCCGCTGCTAAGAAAAGTACCGCTAATCCACTGGCTGCAATTGATTCTGCATTGTCAAA +AGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGGTAA +CCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAGATT +CTGCAGCAGGCTGGTACCTCTGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_1,5_from-cdc_Stk2184_1__1521 +TTAACGTAACAGCGACAGCACGTTTTGCGGGACCTGGTTAGCCTGCGCCAGAACGGAAGTACCGGCCTGTTGCAGAATCT +GCGCGCGAGACATGTTGGAAACTTCAGTCGCATAGTCGGAATCTTCGATACGGCTACGCGCTTCAGACAGGTTGTTTACA +GTATTGCCCAGGTTGGTGATAGCGGAGTTGAAACGGTTCTGTACCGCACCCAGATCAGAACGCAGCGCATCCACCTGCGC +CAGCGCGGCATCAATTTTCTGCAGTGGGTTTTCGGTGGTTTTAGCGGCTGCTTCCGCCAGCTCTGGCTGTGCTTTGAAAT +CATGACCCGCGGCTTTGCTGGCATTATAGGTTTTACCGTCGATAGTAACGACTTCGGTTTTTCCGTCTACGCCGCCAAGT +TGGTTAGCCGCAGTTTTGGTAGTACCGTCAGCAGCAGTATAACTTGTGGTTTTAGCTTTAATGGCTCCTGTCGCTTCATC +GTAATCTGCGGCGTAATACTTATCACCAGCTTTAAGCGCATAACCGCCTTCAATTGTCTTACCATTTTTATCGGTATAAG +ACATTTTGACCAACTCAGCGCCATTAGCATCGGTAGCGTCAACGCCGCCAGCGATTAAGGCATTTTTAGCATCGGCTGAT +ACAACTGCCGGTGTATCTTTTAATTCCTGCACTTCTGTTTTGGTTGCAGCACCAGCAGGCATTGTGGTTTTAGTTGCGCC +AGCCGCAAGGGTTACTGTACCGTCAGTAGCAACGTTAACTTCATAATCGCCATTTTTGGCGGCATCAGCACCAGTAAAGC +CACCAATAGTAACAAAGTACTTGTTATTATCTGCGTCAAATTTAACCGCACCACCGGTTACAGCAGCCGTACCAGTCGTA +CCACCCGTAGCCGTTTTAATAGCTGCATCAGTAAGACCCGATACATCCAGTGTAGTACCATTATCGGCATAAGCTTTCGT +TGTTACTGCTGTATCTTTCACATCATACGCTTTCTGCACGTTCAGTGAATCCAGACCCAGGGTCTGAGAGTTGATCTGCT +TCAGATCGATATCGATAGTTTCACCGTCGTTGGCACCAACCTGGATGGTCAGGGTGTTGTCCTGCGCCAGGACTTTCACG +CCGTTGAACTGGGTCTGGCCGGATACACGGTCGATTTCGTTCAGACGCTGGGTGATTTCAGCCTGGATGGAGTCAAGGTC +AGACTGGGAGTTGGTGCTGTTAGCAGACTGAACTGCCAGTTCACGCACGCGCTGCAGGTTGTTGTTGATTTCGTTCAGCG +CGCCTTCAGTGGTCTGCGCAATAGAAATACCGTCGTTAGCGTTACGGGAAGCCTGAGTCAGACCTTTAATGTTCGCGGTG +AAACGGTTAGCAATCGCCTGACCTGCCGCATCGTCTTTCGCGCTGTTGATACGCAGACCAGAAGACAGACGCTCGATAGC +GGTGCCCAGTGCGGACTGGGATTTGTTCAGGTTATTCTGAGTCAGCAGCGACAGACTGTTAGTGTTGATTACTTGTGCCA +T +>fljB_1,2,7_Salmonella.enterica_Eingedi_AY353276_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAAACTACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGATGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTGCACCTAGTGTAACTGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTTACACTTGCTAC +GGGTGCAACTAAAACCACAATGCCTGCTGGTGCGGCAACTAAAACAGAAGTACAGGAGTTAAAATATACACCAGCAGTTG +TTTCAACAGATGCTAAGAATGCCTTAATCGCTGGCGGCGTGGACGCTACCAATGCTAATGGCGCCGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fliC_k_Salmonella.enterica_IIIb.50:k:z_AY353538_k,z__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATGCGCTGAATGTGCAGAAAGCTTATGATGTAGATAGCAAACCAGCGCA +GAGCATTAAACTGGATACCAGTGCTCTTACTGCTACTGCAATTAAAGATGGTGTAACTGGTGCATCGACAGATGGTGCCC +TAAAAGACGGTAAAGTTTACTCTAATGGCACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGATTCTGCTAAA +AGTGGTTTCCTTAAAGTAGATGTTGATTCCGCTACTGGTGCAGTTACCGTTCCGGGTACGGCAGCAACAGCAGCTGCAAC +TAAACCTGCCGGTGTGAAAGAGGTTACAGAAGTACAAGGTAAAATCCCAGCATCTACTGCTATTCAAGACCAATTGAAAG +CAGGCGGTGTGACTACTGCAGATGCAGCTACTGCTGAAGTTGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATT +GATGGCGGTTATGCTGTAAAAGTAGGCAATGACTACTACGCCGCTACTCAGAAAAAAGATGGTAGCTTTAGTGTTAACAC +TACGTCTTACACTGCAGATGACGGTACATCCAAAACTGCACTGAACCAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCGAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCCGATCTGGCGGAAGCG +GCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z39_Salmonella.enterica_IIIb.6,7:z39:1,2_AY353491_other.z39__1500 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAGGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCACAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTGGATAATGAGGTTGTTAC +TGATGGTAGTGGTGGTAAGGCACTAAATATTAGTGGTCTTGATGATGCTACGATTAAAACCGCCGTCGGGGGGACACCAA +CTGGTACTGGTGTAATTAAAGATAACAAGGTTTATCACAATAGCACTGATGGTAAATATTATGTTGAAGTTGCTGGTTAT +ACCTCAGGGGAGAATGGTTTCTATGAGGTAGATGCAAATCCTACTGATGGTACAGTTACATTTGCTGCCGGTGCTACGAA +AATAACGGCTAAACCAGCTGGTGTTGAAGAAGTTACAACCGTACAATCAAAACCTGTAGCTCTCAGCGCTGATGTTAAAA +CACAATTAACTAATAATGGTGTTAGCACAGCGGACGCTGATAAAGGCCAATTAGTCACAATGTCTTACACTGATAAAAAC +GGTAAGACTATTGATGGCGGTTTAGGTGTTAAAGTTGGAGCCGATATTTATGCTGCAACAAAAAATAAAGATGGCTCTAT +CAGTATTAACACCACAAAATATACAGATAAAGACGGTAATACTCAAACTGCACTGAATAAACTTGGTGGGGTTGATGGTA +AAACTGAAGTGGTTACTATTGATAGTAAAACCTATGCAGCTGCTAAAGCTAAAGATCATAACTTCAAAGCTGATCCTGAC +CTAGCGTTGGTAGCTACTGATACCACTGAAAACCCGCTGCAGAAAATCGATGCCGCGCTGGCGCAGGTTGATGCGCTGCG +TTCCGACTTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTGAACAACCTGTCTGAAG +CGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGG +ACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,m,t_Salmonella.enterica_II.6,8:g,m,t:1,7_AY353537_g,m__1515 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCTCAGTCCTCACTGAGTTC +CGCTATCGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAGTTCAACG +GCGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTGGGTGCTAACGATGGTGAATCTATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGATTCAATGTTAACGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTGACGGGGTACGATACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGCAGCAGCCCCGGATAAAGTATATGTAAATGCTGCAAACGGTCAGTTGACAACTGATGATGCGCAA +AATAACACTGCAGTTGATCTATTCAAGACCACTAAATCTACTGCTGGTACCGATGACGCCAAAGCGATAGCTAATGTCAT +TAAGGGTGGTAAAGAGGGAGATACCTTTGATTATAAAGGCGTATCTTTTACTATTGATACAAAAGCTGGTAATGATGGTA +ATGGTACGGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGGCGGTGGTGGTAGTGTTAAT +GATGCTACCTTACAATCAAGCAGAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAAAAA +TGAGAGTGCGAAACTTTCTGATTTGGAAGCAAATAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTGAAT +ATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTTAGT +ACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAATCCACTGGCTGCAATTGATTCTGCATTGTCAAA +AGTGGACGCAGTTCGTTCTTCGCTGGGGGCAATTCAGAACCGCTTTGATTCTGCCATTACCAACCTTGGTAATACGGTAA +ATAACTTATCTTCTGCCCGTAGTCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAGATT +CTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>O-54_wbbF__1380 +ATGAATGATTATATAATTGACATAGTGGAATATGTTTTATATGTGCTTGTAACTGCCATGACATGGTATTTGTTTGCCCT +GTCTTCCTATTCCATTTTTTTGAGTGTATTTGGGTTTGCTAAAAATAAAAAAGACTATCCTGACTGTCCTCCTGAAGCCC +GCTTTCTAATTCTTGTGGCTGCGCATAATGAAGAGGCTGTGATTGGCTCAACACTTATTAATCTTAAGAATATTCAATAT +GATAAAAAACTCTTTGATATAGTAGTGGTTAATGATAATTCCACTGATCGGACAGGACTTATCTGTGATAGTCATGAAGT +AAAGCATGTGGATACTATAGAAGGCGAGTTTGAACGTGAAGGTGTGGGCAAACCAGCTGGTATTCAGTACGCTCTGCGCA +AGCTTGGATTTGAAACTGTTAAAGAAAATTATGATTTGGTCATGGTGTTGGATGCCGACAATTTTGTTGATGCGAATATC +CTTACTGAGCTTAATTCTCAATGGATATCAAAGGACAAGCCGGAAGCTATACAGGCGTATCTGGATTGTAAAAACTCAAC +ATCTCTTCTCTCTTTTGGCTACTGTACATCATACTGGATGATGAATCGATTTTTCCAATTATCAAAATATCGCTTAGGTC +TACCTAATGCAATTGGCGGAACAGGATTTGTAGTGTCCAGTAACTTTCTGATAAATACTGGAGGATTTTGTTTTAAATCT +CTGACCGAGGACATTGAACTGGAAATTGAAATTGTGCGCAAGCGTGGTCGTGTACTATGGAATCACAATGTACGAGTCTA +TGATGAAAAGCCAGACAATCTAAGAATAAGCCTCAAACAACGCTATCGCTGGTCAAAGGGACACTGGTATGTGGCTTTTA +CTAACTTTTTTAACTTGTTCAAGTTGACCTTTGTTGAGCGTAAGTGGAAATATGTAGATCAATTGTTATATCTGTTCTCT +ATGGGCCGTGCTTTCGAGGTTTGTATTATTTTCATCAATATCTTTCTATTAAGTCTTCTTAAAGAAAATTACCATCCAGA +GATTGGAAATATTTCTACGGCGATAAAAGATCTTACTGTGACCAATATGAGTTTTGCCGACAGCGTGAGTGCGCAGTTTA +GCTCAATAAATTGGATTAGAGTTATTACTAATATTAATATCGTCACATTAATATCCATCTGTTATGGTATGCTGATTTTA +CCTATTTATGGTGCATGGATGGATAAAGGTATTTTCCTTAATCCATTCAGGGTATTTTTTTCCGGTCTTTATTTTGGATT +GTCGTTTGTGTTTGTTCAGTTTTTGGCTCTTTTTCGTTGGAAAAAACAGCATAAATGGGTAGTTACGCCGCATAATAAAA +TAAAGGAAGAGCACAAATGA +>fljB_1,2_Salmonella.enterica_1,4,5,12:i:1,2,7_AY353272_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTTCGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAATCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fljB_1,5_Salmonella.enterica_Bovismorbificans_AY353283_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAAACTACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGACAGCTTATGCCGATAATGGTACTACACTGGATGTATCGGGTCTTACTGATGCAGCTATTAAAACGGCTACGGGTG +GTACGACTGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGG +GGCTTTAGTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGTAACAACTAAAACAGAAGTACAGGAGTTAACAACTACACCGGTAGTTG +CTTCAGCAGATGCTAAAAATGCCTTAATCGCTGGCGGCGTTGACACTGCCGATGCTAATGCCGCTACATTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCAT +GATTTTAAAGCACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fljB_z35_Salmonella.enterica_IIIb.38:k:z35_AY353262_other.z35__1488 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTTTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTAGATAGCAAAGCTGTGAC +ACCTCCGGCAAAACTTGATATTGCAGGATTAACTGGAACTGCAATTAAAACGGGCGTTGATAGCGCTACGGTTGATACTG +GCTCCATTAAAGATGGCAAAGTTTATTATAATAGTACCTCTAAGAACTATTACGTAGAGGTTGATTTTGGTACATCAGCC +GATGCTGCTAAGAGTGGTTACTATAAAGTCAATGTTGCTGATGATGGTACAGTCTCAATGACAGCTTCTACCACTAAAGA +GGCTACAACTCCTACTGGTATTACTGAAGTTACTCAGGTTCAAAAACCTGTAGCCGCTCCAGCCGCTATTCAGGCTCAGT +TGACAGCTGCCCATGTGACCGGAGCTGATACTGCTGAAATGGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATT +GATGGCGGTTACGCTGTAAAAGTGGGTGATGACTACTACGCCGCTACCCAGAAAAAAGATGGTAGCTTTAGTATTAACAC +CACGTCTTACACCGCAGCGGACGGTACATCCAAAACTGCCCTGAACCAACTTGGTGGCGCAGACGGTAAAACCGAAGTCG +TTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAGCTGGCTGAAGCA +GCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCACGTAGCCGTA +TCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>fliC_g,m,t_Salmonella.enterica_II.28:g,m,t:e,n,x_AY353536_g,m__1515 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCTCAGTCCTCACTGAGTTC +CGCTATCGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAGTTCAACG +GCGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTGGGTGCTAACGATGGTGAATCTATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGATTCAATGTTAACGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGGTACGATACCTATGCAGCTGGTGCCGATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGCAGCAGCCCCGGATAAAGTATATGTAAATGCTGCAAACGGTCAGTTGACAACTGATGATGCGCAA +AATAACACTGCAGTTGATCTATTCAAGACCACTAAATCTACTGCTGGTACCGATGACGCCAAAGCGATAGCTAATGTCAT +TAAGGGTGGTAAAGAGGGAGATACCTTTGATTATAAAGGCGTATCTTTTACTATTGATACAAAAAATGGTAATGATGGTA +ATGGTACTGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCGGTGGTGGTAGTGTTAAT +GATGCTACCTTACAATCAAGCAGAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAAAAA +TGAGAGTGCGAAACTTTCTGATTTGGAAGCAAATAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTGAAT +ATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTTAGT +ACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAATCCACTGGCTGCAATTGATTCTGCATTGTCAAA +AGTGGACGCAGTTCGTTCTTCGCTGGGGGCAATTCAGAACCGCTTTGATTCTGCCATTACCAACCTTGGTAATACGGTAA +ATAACTTATCTTCTGCCCGTAGTCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAGATT +CTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_d_Muenchenstr_AOYT01000015_b,d,j__1509 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACGGTACTAACTCCCAGTC +TGACCTTGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATTGATATTGATTTA +AAAGAAATTAGCTCTAAAACACTGGGACTTGATAAGCTTAATGTCCAAGATGCCTACACCCCGAAAGAAACTGCTGTAAC +CGTTGATAAAACTACCTATAAAAATGGTACAGATACTATTACAGCCCAGAGCAATACTGATATCCAAACTGCAATTGGCG +GTGGTGCAACGGGGGTTACTGGGGCTGATATCAAATTTAAAGATGGTCAATACTATTTAGATGTTAAAGGCGGTGCTTCT +GCTGGTGTTTATAAAGCCACTTATGATGAAACTACAAAGAAAGTTAATATTGATACGACTGATAAAACTCCGTTAGCAAC +TGCGGAAGCTACAGCTATTCGGGGAACGGCCACTATAACCCACAACCAAATTGCTGAAGTAACAAAAGAGGGTGTTGATA +CGACCACAGTTGCGGCTCAACTTGCTGCTGCAGGGGTTACTGGTGCCGATAAGGACAATACTAGCCTTGTAAAACTATCG +TTTGAGGATAAAAACGGTAAGGTTATTGATGGTGGCTATGCACTGAAAATGGGCGACGATTTCTATGCCGCTACATATGA +TGAGAAAACAGGTACAATTACTGCTAAAACAACCACTTATACAGATGGTGCTGGCGTTGCTCAAACTGGAGCTGTGAAAT +TTGGTGGCGCAAATGGTAAATCTGAAGTTGTTACTGCTACCGATGGTAAAACTTACTTAGCAAGCGACCTTGACAAACAT +AACTTCAGAACAGGCGGTGAGCTTAAAGAGGTTAATACAGATAAGACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTT +GGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>oafA-O-4_full__332 +TCATCATCAGAGTTCAACTTTTTGCTTCACACCTGGTCACTATCAGTTGAGTGGCAATTTTATATTTTATATCCTTTATT +AGTCATTATAGTTAAAAAATTACGGTTTCCTGTTGGACTCTCATTATCTGTAATTTTAGCCATGTCACTTGCAATTACAC +TTATGCGAGTGACTGGAACCAAAGAAGATATTTTCTATCTTATCCCTACCAGGGCATGGGAAATGCTGGCTGGCGGCCTT +GTATACATAGCATCTGTACGTTACAAAATGCCAGAATGGATAAAGCATTGTGAGGTTTATGGGATAGTCCTCATTGTTGT +TGCTGTTGTTAT +>fljB_z6_from-II-48:d:z6_SRR1168371__1503 +TTAACGTAACAGAGACAGCACGTTCTGCGGGACCTGGTTAGCCTGCGCCAGAACGGAAGTACCGGCCTGCTGCAGGATCT +GCGCACGAGACATGTTGGAAACTTCGGTCGCATAGTCAGAATCTTCGATACGGCTACGCGCTTCAGACAAGTTGTTTACG +GTATTGCCCAGGTTGGTGATAGCGGAGTTGAAACGGTTCTGTACCGCACCCAGATCGGAACGCAGCGCATCCACCTGCGC +CAGCGCGGCATCAATTTTCTGCAGCGGGTTTTCGGTGGTTTTAGCGGCTGCTTCAGCCAGCTCTGGCTGTGCTTTGAAAT +CATGACCAGCGGCTTTGCTGGCATTGTAGGTTTTACCGTCGATAGTAACGACTTCGGTTTTACCGTCTACGCCACCCAGT +TGGTTCAGGGCAGTTTTGGTAGAACCATCAGCTGCAGTGTAAGACGTGGTGTTAACACTAAAGCTACCATCTTTGTTCTG +GGTAGCGGCATAATAGTTATCGCCCACTTTTACAGCGTAACCGCCATCAATCGTCTTACCGTTTTTATCGGTATAAGACA +TTTTAACAACTTGGGCAGCAGCAATTTCTGGATCTGTAACCCCGCCAGATTTGAGAGAAGTTTTGAGATCTGCTGATAAC +GGTAATGGATTTTTTTCTTCCTGAGTTTTTGTTACTTCTACCGCACCAGCTGGTTTACCCGTCTCCATAGCCGTACCAGC +GGTCATAGATACCTTACCATCATCGGCGACATTTACTTTATAGAAACCATTTTTACCATCATCAGGGGTAGTCAGGCCAG +TAACTTCAACGTAGTAGTTTTTGCTAGCACTATCATAATAAACTTTGCCATCTTTTATTGCTGCAGTACCTGTTGTAGCA +CCAGTCCCTGTTTTAAGGGCCGCGTCTTTATTAAGATCAGTAATATCTAAATTAGCAGCTACTGTCATAGCTTTGCTATC +TACATCATACGCTTTCTGCACGTTCAGTGAATCCAGGCCCAGGGTCTGAGAGTTAATCTGCTTCAGATCGATATCGATAG +TTTCACCGTCGTTCGCGCCAACCTGAATGGTCAGGGTGTTGTCCTGCGCCAGGACTTTCACGCCGTTGAACTGAGTCTGG +CCGGATACACGGTCGATTTCGTTCAGACGCTGGGTGATTTCAGCCTGGATGGAGTCGAGGTCAGACTGGGAGTTGGTGCT +GTTAGCAGACTGAACCGCCAGTTCACGCACACGCTGCAGGTTATTGTTGATTTCGTTCAGCGCGCCTTCAGTGGTCTGCG +CAATAGAAATACCGTCGTTAGCGTTACGGGAAGCCTGAGTCAGGCCTTTGATGTTCGCGGTGAAACGGTTAGCAATCGCC +TGACCTGCCGCATCGTCTTTCGCGCTGTTGATACGCAGACCGGAAGACAGACGCTCGATAGCGGTGCCCAGTGCGGACTG +GGATTTGTTCAGGTTATTCTGGGTCAGCAGCGACAGACTGTTAGTGTTGATTACTTGTGCCAT +>fljB_z39_Salmonella.enterica_II.52:z39:1,5,7_AY353347_other.z39__1500 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGCCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAATAACCTGCAGCGTGTACGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTAAC +TGATGGTAGTGGTGGTAAGACATTAAATATTAGTGGTCTTGATGCTGCTGCAATTAAAACCGCTGTTGGAGGGACACCAA +CTGGTACTGGCGAAATTAAGGATAATAAGGTTTATCACAATAGTACTGATGGTAAATATTATGTTGAAGTTGCTGGTTAT +ACCTCAGGGGAGAATGGCTTCTATGAGGTAGATGCAAATCCTGCTGATGGTACAGTTACATTTGCTACCGGTGCTACGAA +AATAACGGCTAAACCTGCTGATGTTGAAGAGGTTACAACTGTCCAATCAAAACCTATAGCTCTCAGTGCTGAGGTTAAAA +CACAATTAACTGCTAATGGAGTTAGCACAGCGGCCGCTGATAAAGGCCAATTGGTCACAATGTCTTATACAGATAAAAAT +GGTAAGACTATTGATGGTGGCTTCGGTGTTAAAGTTGGCGCTGATATTTATGCTGCAACTAAGAATAAAGATGGCTCTTT +TAGTATCAATACCACGAAATATACTGATAAAGACGGTAATACCCAAACTACACTGAATAAACTTGGTGGCATTGATGGTA +AAACTGAAGTTGTTTCGATTGAAGGTAAAACCTACACCGCAGCGAAAGCAAAAGATCATAATTTCAAAGCCGATCCTGAT +CTAGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCG +TTCCGATCTGGGTGCGGTACAGAACCGTTTCAATTCCGCTATCACCAACCTGGGCAATACCGTAAACAACTTGTCTGAAG +CGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATCCTGCAGCAGGCCGGT +ACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,x_Salmonella.enterica_II.9,46:e,n,x:1,5,7_AY353316_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACGCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATTCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGATGGTGAAACTATTGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACGGATATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACAGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACTCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTACCACGA +AAAAAGCTTTACAAGATGGAGGCGTTTCATCTGCGGATGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACGGTGGCTAACCAACTGGGGGGCGTAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCATGATTTTAAAGCACAG +CCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGTTCCGATCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACTTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATCCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,x_Salmonella.enterica_II.9,12:lw:enx_AY353320_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +TGCTATCGAGCGTTTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACGCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGATGGTGAAACTATTGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACGGATATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACAGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACTCC +AACTAAATCTACGGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCGGCAGATGCTACCACGA +AAAAAGCCTTACAAGATGGAGGTGTTTCATCTGCGGATGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACGGTGGCTAACCAACTGGGGGGCGTAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCATGATTTTAAAGCACAG +CCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGTTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACTTGGGCAATACCGTAAACAACTTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATCCTGCAGCAG +GCCGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fliC_g,m,s,t_Salmonella.enterica_II.50:.g,m,s,t:1,5_AY353396_g,m__1515 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCTCAGTCCTCACTGAGTTC +CGCTATCGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAGTTCAACG +GCGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGATTCAATGTTAACGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGGTACGATACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTGACAACTGATGATGCGCAA +AATAACACTGCAGTTGATCTATTCAAGACCACTAAATCTGCTGCTGGTACCGATGACGCCAAAGCGATAGCTAATGTCAT +TAAGGGTGGTAAAGAGGGAGATACCTTTGATTATAAAGGCGTATCTTTTACTATTGATACAAAAACTGGTAATGATGGTA +ATGGTACGGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCGGTGGTGGTAGTGTTAAT +GATGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAAAAA +TGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTGAAT +ATACTGCTAACGCCACGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTTAGT +ACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAATCCACTGGCTGCAATTGATTCTGCATTGTCAAA +AGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGGTAA +CCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAGATT +CTGCAGCAGGCTGGTACCTCTGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,m_Salmonella.enterica_Enteritidis_AY353398_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTAATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCGCTAGCGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,m,s_Salmonella.enterica_Montevideo_AY353392_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTATGACACCTATGCAGCGGGTGCCAATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAATGGTCAGTTGACAACTGACGATGCGGAA +AATAACACTGCGGTTAACCTATTCAAGACGACTAAATCTGCTGCTGGTACCGATGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCATTGGCGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>O-58_wzy__1263 +GTGTATTTAACAAATAATTATTGTAATTTCCTTTTTCGCACTCGTATTGTTAGGCGCATATTTTTACTAGTTTACTTGGT +TTCTAATGTTTATGCTTATATGGTGCTTACTGATACAGGGTTATTGATTGGCGATTATCAAGGAATACTCATTAAGTATA +AAGAACAAGTTGCATATTTGTTAACGCTAACTATATTATCATATTATATTGTCTGTGGACCAGTGTTTTCCTGTATAGCA +AAGATAAAAGTTAAGTTGTCTACAATTAAAGGCTTAAATTCTTTTGCTTATTTATTGCTTTTTTTTCAGGTGTTATTTTT +TGCTTTTAATATTTCAACAGGTTCCAACACTGCGGGTACTGATTTCCAAACTGGTGGGTTTATAAGACTATTATGGCTTT +TTTTACCTGTCGATTATTTATTCTATATATATTATTTTGTTGGAAGAGAGACTAAAGTAAATAAAATATATCTGGTCAAT +GTAATCGTTTTTATTCTGTCGATGTTAAGTCGGGGGTGGCTCGGCTGGACTTTAGTTTTGCTTTATGCAGAGCTTTGTTT +CTTTTTTTGTTCGCAAAAATCCATCAAAAATAAAAAAATTAACTATTTGATCTTATTGTGTTTCTTTCTTATTGTTGCGC +CATTGGTATTTAGTCTGAAAGTGCAACTCCGTGCTGATTTGTATTTCAGTGGTATTGGTGGGGTGGTATCAACTTTAAGT +AATATTGATTACATTCAATCTTATAATAATTTTATCGCTAGTTTTTTATCCCGAATACAGCAGCTATCAAATGTTGTTTT +CTTTTATGACCATAAACAAGAATTGTATAAATTTGTTTCTTCGGAAATTGTATCAACCTATGCTTGGGAAGGCTTACCTC +AACAAACAGTAGCAAAATTGTTAGGATTAGCTCCAGGTGTTGACATGCATGTTTTTCTTTACAGTCATTACATTTCTTCA +TCTGCTGAAGCTGTAACTACATTGCAAGTTGGCTTCATTTCATGGTTCTTTTTAGATACACTATCATCTGTATTTTATCC +GTTGTACGTTCTGATTATCATTGGATTATCTTTATTTTTATCCAAAAAAATCGGTGGAGAAAAACTATGTGCGCTTACAT +GGATTATGATTTTTCTTTCTGTCATGTGCGGGTGGTACAATGCTTATCTGGTTTATCTGCAGGCATTAATTACGTTTTAC +TTTATCATGGGGTTATTGACTTTAATTACTCAAGAAAAAGCAAAGGGTAATCATAATGGGTAA +>O-61_wzy__1326 +GTGACTATTTATTATATTAAATGCTATTTAGGGGGATGTGTGATTTATCGGTTTGCTATTTTAATAGTCATTGTTATATT +AGGTATTATTTCTATTGCAACAGCTTATGCCATTGGCGCACCAACTTCTATATTTTTTTATATTTTTTATATTGTATTGT +TTATTTTTTATCCCCCTAAATATGTAATATCACCACTCACGATCCTTTATGTTTACTATGGCTTATGGTTCTTATTAGCT +CCACTTTTTGCTCAGCGTTATGTGGGTATTAACAACGAGTTATCTTATTCATATTCTTTTATTTTGCTTTCGGTTACTTT +TGGTATTGGCGTAATATTTCTTTATGATAAAAAAGATTTTAGACATTTTTCAGATTCTACAATTAGCAGTAAAAATGTTC +GGATACCATCCAAAAAAACACTGTTACTCTTATTTTTAATATCAACCTTATTTGTTATATTGATTGTGGCAAATTCTGGC +GGAATTGATAAATGGATTCATTCGCCCGGTGATGCTTTTCTGAATCGCAGCGGTTCAGGGGTATATGTTGTTGGTAGTCA +TTTTTCATCATTAGCATTAGCTGCACTCTGTGGCTACCATGCTTTCGTTACCCGTCAAAAAAAGATCTTGTGCTTATTTT +TATTATGGTTGTTGCTGACATCCCCTGTGCATGGAAGTAAGTTTCAAATTTCGCTTTTATTAATTATGTCGTTACTTCCA +TGGTTAAAGGAATTACGTTTCTATAGTAGGGGAACTTTGATCTTAGGGATAGCTCTTCTCGGGATCCTGTTTCTTGGGCT +TTATTTTCGCAATATATCTTGGATGACATGGCATGATCTAGTTCCCTACACTCTAAATTACTTTGACACGCTTGATAACT +TAGCGCTGTCTTTGAAGGAATTATCTCCTGCATTAAATAAAACATTTTTTATGCCTTTTAATAAATTGCTTACTCCTTTC +GGAAATGATGGCGGTATCATATTTTACGATATGAGTCAGTGGCTAACTTCGATCTACGATCCTGACGCATGGAAAATAAG +AGCAACAATACAGTTTCCTGTTGAAACTGACATGTATCTTAATTTTTATTTTTATCTTGGAATTCCTATATTAATGTCTT +TTTTCTTTTTTATTGCAAGGATATATTCAGCAGCTCATAGTAAACAACATTTGGGTGCATGGTTTGCGGCAATGCTAATG +ACATTATTTATGATTTCACATTTGCGGGGTAGCATTTATAACCATACTGATTTTTATATGTATCCCTATATTGCAGTGAT +GTTCTTCCTTTTCAGGAAGTATAAATTTCCATCGAAACGGATGTGA +>fliC_z4,z23,z32_Salmonella.enterica_IIIa.13,23:z4,z23,z32:-_AY353500_z4,z23__1266 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATTGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +TTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCAAAGATGCAAAAACCGGCGGTCCGGCTGCGGATAAATTAT +CTCTGACACAAGATGATAAAGGCAATTACTTTGTCAAAGATGATACTGCTGCAGCTAAATACTATGCAGCTACCGTAGAT +ACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAACCCT +ATCACGCGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGACCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAG +ATCTCTATGCTATCCAAACGTTAGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAAACT +ACGGAGGGCGCTGCCGTAGCCTTAGCTGCAAACGTCGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACTGTTGACGC +ATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATAACTAACCTGGGCAACACGGTAAATAACCTGT +CTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCACAGATTCTGCAGCAG +GCCGGCACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAGCGTCCTCTCTTTACTGCGTTAA +>fliC_z52_Salmonella.enterica_IIIb.65:z52:z35_AY353517_l,v__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGTTGTTAC +TGATGGTAGTGGTGGTAAGGCATTTGATCTCACCGCGCTTAATGATACTAACCTTAAGGCTGCAGTTGGTGGGACTCCTG +CTCCGACAGGAACCGCTGTAGTAAAAGATGATAAAGTATATTATAACAGCGCTGACGATAAATATTTCGTCGAGATTGAT +GGGCTAAGTAGTGGTAATGGCTTCTATGAAGTTAGCGCAAATGCAACAACTGGTGCTCTTACAATTGGTGCAGGGTTAAC +AACGGCTGGCGCAACGGTACCGGCGGGTGCTGAAGAAGTTACATCTGTGCAGTCAAAACCCGTAGCTCTCAGTGCTGATG +TTAAAAAACAATTGACTGATAGTGGCGTTAGCGTAGCGGACGCTGGTAAAGGCCGATTAGTCACAATGTCTTATACTGAT +AAAAACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTGATATTTATGCTGCAACAAAAAATAAAGATGG +ATCGATCAGCATTAACACCACTAAATATACCGATAAAGACGGCAATACTAAATCTGCACTAAACAAACTGGGTGGCGCAG +ACGGCAAAACCGAAGTTGTTTCTATTGGTGGTAAAACTTACGCTGCGAGTAAAGCCGAAGGTCACAACTTTAAAGCACAG +CCCGATCTGGCGGAAGCGGCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACAC +GTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGA +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCAGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_l,z28_Salmonella.enterica_Javiana_AY353454_l,v__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTTTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAGGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAGTACCACTGGTCTTGATGATACAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCG +GTACCGCTGCAATTAAAGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAATTGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGTACTGTTACAATGCCGGCAACCGCCGC +GAAAGTGACAGGTGGCATACCAGCCACGGCGACTGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAG +TTAAAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGAT +AAAAACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGG +ATCGTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTAAACCAACTGGGTGGCGCAG +ACGGTAAAACTGAAGTTGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCACAACTTTAAAGCACAG +CCAGAGCTGGCTGAAGCGGCTGCTGCAACCACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGC +GCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGT +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATCCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCACAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_i_Salmonella.enterica_IIIb.21:i:e,n,x,z15_AY353431_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCAATACTGCGATTGCTTTAAACAATGGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACAG +ACCAGCAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TGCAGGTGGATTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCCAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGCTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCGAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCCGATCTGGCGGAAGCG +GCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTATGCGACCGAAGTCTCTAACATGTCTCGTGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTG +GCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_l,z13_Salmonella.enterica_Kenya_AY353449_l,v__1503 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAGTACCACTGGTCTTGATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAGCG +GTACCGCTGCAATTAAGGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTCATTGAAGTTGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACTACGAA +AGTGGCAGGAGGCATGCCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAGTTA +AAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGATAAA +AACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACGAAAAATAAAGATGGTTC +GTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCTCTGAACCAACTGGGTGGCGCAGACG +GTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCTGCTGGTCACAACTTTAAAGCACAGCCT +GATCTGGCGGAAGCGGCTGCTACAACTACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTT +GCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACTGTAAACAACCTGACTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCC +GGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23_Salmonella.enterica_I.8,20:z4,z23:-_AY353544_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +TGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTAAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACTGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +CTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAACAACTGGTGGTCCGGCTGCGGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGTTACTGCGACGGCTAAATACTATGCAGCTACCGTA +GATATGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAGCTGCGGGGACTCCGTCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTGAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGTACTGCCGTAGACTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCCGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23_Salmonella.enterica_IIIa.41:z4,z23:-_AY353547_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTCAATAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGGGC +TTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAGCAACTGGTGGTCCGGCTGCGGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGCTGCAGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAAC +CCTATCACGCGAAGTGAAATTTGATGGAGCAGATTTAAAAGCCGATCAATCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACTTTGGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAA +ACTACGGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACGGTAAATAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z41_Salmonella.enterica_Ottawa_AY353510_k,z__1491 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTTTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACCCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCGAACGACGGTGAAACCATCGATATTGATCTG +AAGCAGATCAACTCGCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTCGATAGCAAAGCTGTTAC +TGCAACTCTTGATCTGGATGTGACAGATCTTGATACTAATGCTTTGAAAACCGCAACTGGGATCAGTGCAGGTAATCCTG +CTGTTAAAGACGATAAAGTTTATTATGACAGCGCAAATAATAATTATTATGTAGAGGTTGAGGGCTTTACTGATAATACG +AAAGATGGTTTCTACAAAGTTCAGGTTGGTGATGATGGCAAAGTGTCAATGGCCACAACTACCAATAAAGAAACAGCTAC +TCCTCCCGGAATTGTTGAAGTAAGTAAAACTCATGATGAGAAAGCTCTTAAAGCTTCTGCAGAGGTTAAAGCAGCTCTGA +TTGCTGGAGATATTGATACTGCTGATGCAGATGCTGCTGAAATGGTCAAAATGTCTTATACCGATAAAAATGGTAAGACG +ATTGATGGTGGTTATGCTGTAAAAGTAGGCGATAACTACTATGCCGCTACCCAGAAAAAAGACGGTAGTTTCAGTGTTAA +TACTACTTCTTACACTGATAAAGACGGCAATACTAAATCCGCACTGAACCAACTGGGTGGTGCAGACGGTAAAACCGAAG +TCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCACAACTTCAAAGCACAGCCTGATCTGGCGGAA +GCGGCTACTGCAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAAGTTGATGCGCTGCGTTCTGACCT +GGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGTCTGAAGCGCGTAGCC +GTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTT +CTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z24_Salmonella.enterica_Romanby_AY353503_z4,z23__1281 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +TGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAAGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +CTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACAACGGGTGGCCCCGCAGCAGATAAAT +TATCTTTGGTAAAAGATGATAAAGGAAATTACCTTGTTAAAGATGTTACTGTCACTGCTACTCCTAAATATTATGCCGCT +ACCGTAGATAATAGTACTGGGGAAATTAGCTTTGATTCGGCTAAAGAAGTTACTTTAGCTGGTGGTGCACCAGCTCCGAG +TACGGTTGATACTTTGTCGCGTGAAGTGAAATTTGATGGAGCAAATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAG +ATGATAAGGGTAAAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCC +GCGGACGGTAAAACAACAGAGGGTACTACCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCT +TAAAACCGTTGACGCTTTCCGTAGCCAATTGGGGGCGGTGCAGAACCGTTTTGAATCTGCTATCACTAACCTGGGCAACA +CCGTCAACAACCTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTA +A +>fliC_z4,z32_Salmonella.enterica_IV.44:z4z32:-_AY353506_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCAAACGACGGTATTTCCATTGCGCAGACGACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCAAACGGCTCGAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACTGATTTTAACG +GTAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGTTCTGGAGC +CTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACAACGGGTGGCCCCGCAGCAGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGTTACTGCGACGGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGTCTCCGTCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCAGGGACTTCTGTTCTGGCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_e,n,z15_from-Chailey_SRR1049702_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAGGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGTTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,x_Salmonella.enterica_Tiergarten_AY353315_e__1506 +ATGGCACAAGTAATCAACACTAACAGTTTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACTACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACGGATATTAAAGCTGCATTAGGCAACCCGA +CGGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAGAATGGTAAATATGAAGTTACCGTTGATAGTACTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCAGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTATCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAGGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACTTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fliC_d_Muenchenstr_ARYX01000110_b,d,j__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACGGTACTAACTCCCAGTC +TGACCTTGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTAAAGTCCTGGCGCAGG +ACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATTGATATTGATTTAAAAGAAATTAGCTCTAAAACA +CTGGGACTTGATAAGCTTAATGTCCAGGATGCCTACACCCCGAAAGAAACTGCTGTAACCGTTGATAAAACTACCTATAA +AAATGGTACAGATACTATTACAGCCCAGAGCAATACTGATATCCAAACTGCAATTGGCGGTGGTGCAACGGGGGTTACTG +GGGCTGATATCAAATTTAAAGATGGTCAATACTATTTAGATGTTAAAGGCGGTGCTTCTGCTGGTGTTTATAAAGCCACT +TATGATGAAACTACAAAGAAAGTTAATATTGATACGACTGATAAAACTCCGTTAGCAACTGCGGAAGCTACAGCTATTCG +GGGAACGGCCACTATAACCCACAACCAAATTGCTGAAGTAACAAAAGAGGGTGTTGATACGACCACAGTTGCGGCTCAAC +TTGCTGCTGCAGGGGTTACTGGTGCCGATAAGGACAATACTAGCCTTGTAAAACTATCGTTTGAGGATAAAAACGGTAAG +GTTATTGATGGTGGCTATGCAGTGAAAATGGGCGACGATTTCTATGCCGCTACATATGATGAGAAAACAGGTACAATTAC +TGCTAAAACAACCACTTATACAGATGGTGCTGGCGTTGCTCAAACTGGAGCTGTGAAATTTGGTGGCGCAAATGGTAAAT +CTGAAGTTGTTACTGCTACCGATGGTAAAACTTACTTAGCAAGCGACCTTGACAAACATAACTTCAGAACAGGCGGTGAG +CTTAAAGAGGTTAATACAGATAAGACTGAAAACCCACTGCAGAAAATTGATGCTGCCTTGGCACAGGTTGATACACTTCG +TTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTG +CCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGT +ACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_i_Kentuckystr_AOYZ01000062_r,i__1476 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCTATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGAAACT +GGTAAAAATGGCTATTATGAAGTTTCCGTTAATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_z10_Mbandakastr_AOYR01000081_other.z10__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTTGATAGCACTGGCGTTAC +TCAATCTCTTGATTTAAAAACTGCTGGAATTACTGGTGCTACATTAAAAGCTGGTATTACTGGTACAACGACAGAAACCG +GTAGCGTTAAAGATGGTAAAGTCTACTATGATGCAGATAGCAAAAATTACTATGTAGAGGTTGATTTTACTGATACTACG +GATAAAGCAGCGCATGCTGGTTTCTACAAAGCTGACGTCGATGCTGACGGTAATGTTTCTTTAGCAACTGGTGCGACTAA +AGAAGCAAAACCAACGAATGCAGTTGAAGTTGAAAAAACTATTGATGAAAAACCGCTGAAAGCATCAAGTAGTGTTCAGG +ATGCCTTAAAAGCGAGTGGTATTGCTGATGCGGTTGCAGAAGCTGCGACGGTAGTGAAAATGTCGTACACTGATAAGAAT +GGTAAAACTATTGATGGTGGATACGGTATTAAAGTAGGTGATGACTACTATGCTGCAACTAAAGAAAAAGACGGCAGCTA +TAGTATTAATAGTACTTCTTATACCGATAAAGACGGCAACACTAAAACTGCACTAAACCAACTGGGTGGCGCAGACGGTA +AAACTGAAGTTGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCACAACTTCAAAGCACAGCCTGAT +CTGGCGGAAGCGGCTGCTACAACTACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCTGCG +TTCTGACCTGGGGGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTG +CCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGT +ACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_l,z13,z28_Salmonella.enterica_Fallowfield_AY353453_l,v__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAGGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAGTACCACTGGTCTTGATGATGCAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCG +GTACCGCTGCAATTAAAGATGGTAAGGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCGCCGC +GAAAGTGACAGGTGGCATACCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAG +TTAAAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGAT +AAAAACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGG +ATCGTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAG +ACGGTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCACAACTTCAAAGCACAG +CCAGAGCTGGCTGAAGCTGCTGCTACAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGC +GCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGT +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z29_Salmonella.enterica_IIIa.41:z29:-_AY353478_other.z29__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAGGGT +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTACGTGAGTTGACTGTTCAGGCAACTAATGGGACAAACTCTGATAG +CGACCTGACCTCTATTCAAAATGAAATCACACAACGTTTGAGTGAAATTGATCGTGTCTCTGGTCAAACTCAATTTAACG +GCGTGAAAGTGCTGGCCCAAGACAATACGCTGAAAATTCAAGTAGGAGCCAACGACGGCGAAACCATTTCTATTGATCTT +AAGAAAATTGACTCAAAAAGTCTTGGAATGGATGGCTTTAACGTCAATGGCGCACACAAAGCAACAGGAAGTGATTTAAT +TTCTCAATTTGGTGCTACAGGTACTGATAATTATAACGTTACCAAAGGGGCTACTACCACTACTTATTCGGTAGACATTA +AATCTGGCGCTGTTACTACTGGTACACCAGCTGAAGCTGTCTTTGTTAACGCGGCTGATGGTAGCTTGACAACTGATGCT +ACTACCAAAAACACTGAAATTAATGGTAACGATGACTTTACAAAGGGACTTGCAGACGCAGCAAAAGGCGCTGTTAAAGA +TTCTACATTTACCTACAGTGGCATCGAATTTACTGCTAAGACTGCTGGTACAGCAGATGGTAATGGTACTTTTGAAGCGA +AAATTGATGGTACAGTAATTTCCTTTGAAATTACTGGTGGTACAACACCTTCCTCCGCAGTAACTGGAGCTGGTGGTGCA +AAAGCTTATGTTTCTAAAATTGATGGTAGTATTACGACAACAGCTGAAGTCGATAACCGTGCTGCGAAAATGTCCGATTT +GGATTTAAACAACGCGGTTAAAATAGGTAGTACATTAAATGTTAACGGTGCTACCTATAATGTTAATGCTAAAGGTGATG +AAGTTACTGGTAAGTTTGATAATGGTGCAGGCGGACTGGTTGATAAACAAGTATTCTTGGGAAAAACCGCTGGCGGAGCT +GCAACATTAATTAATGAGGATGCTGCTAAATCCCAACAATCTACCGTAGATCCGTTGAAAACTATTGATGATGCACTTGC +TCAGGTTGATGCGCTTCGCTCCGATTTGGGCGCAGTACAGAACCGCTTTGATTCTGCCATTACCAACCTTGGTAATACGG +TAAATAACTTATCTTCTGCCCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCCGGCACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAGCGTCCTCTCTTTACTGCGTTAA +>fliC_k_Salmonella.enterica_IIIb.50:k:z53_AY353440_k,z__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGMTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACCATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATGCGCTGAATGTGCAGAAAGCTTATGATGTAGATAGCAAACCAGCGCA +GAGCATTAAACTGGATACCAGTGCTCTTACTGCTACTGCAATTAAAGATGGTGTAACTGGTGCATCGACAGATGGTGCCC +TAAAAGACGGTAAAGTTTACTCTAATGGCACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGATACTGCTAAA +GGTGGTTTCCTTAAAGTAGATGTTGATTCCGCTACTGGTGCAGTTACCGTTCCGGGTACGGCAGCAACAGCAGCTGCAAC +TAAACCTGCCGGTGTGAAAGAGGTTACAGAAGTACAAGGTAAAATCCCAGCATCTACTGCTATTCAAGACCAATTGAAAG +CAGGCGGTGTGACTACTGCAGATGCAGCTACTGCTGAAGTTGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATT +GATGGCGGTTATGCTGTAAAAGTAGGCAATGACTACTACGCCGCTACTCAGAAAAAAGATGGTAGCTTTAGTGTTAACAC +TACGTCTTACACTGCAGATGACGGTACATCCAAAACTGCACTAAACCAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,p,s_Salmonella.enterica_Naestved_AY353401_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGTAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTGCTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCATTGGCGCGGCGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,z51_Salmonella.enterica_IIIa.45:g,z51:-_AY353414_g,m__1515 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCTCACTGAGTTC +CGCTATCGAGCGTTTGTCCTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATCAAAGGACTGACTCAGGCTTCCCGTAATGCGAACGACGGTATCTCCATTGCGCAGACCACCGAAGGG +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATTCAGGATGAAATTCAGCAGCGCTTATCGGAAATTGACCGTGTTTCTAACCAGACTCAGTTTAACG +GTGTTAAAGTCCTGTCTCAGGATAATCAGATGAAAATTCAGGTGGGCGCTAACGATGGCGAGACTATTACCATTGATCTA +CAAAAAATTGATGTGAAAAGTCTTGGTCTGGATGGGTTCAACGTGAATGGGCCTAAACAAGCAACCGCTGGGGATTTGAA +ATCTAATTTCAAAAACGTTACTGGTTATGATACGTATGCTGTTGGTGCTGATAGTTATCGTGTAGATATTAATTCTGGAG +CAGTAACTGATGATGCTGGTACCGATAAGATTTACGTAAACGCAGCAAACGGTAAACTCACAACTGATGATGCACAGAAT +AACACCGCAGTTGATCTATTTAAGACAACAAAATCATCAGCCGGTACAGCTGAATCTAAAGCAATTGCTACCGCTATTAA +AGGTGGTAAAGAAGGAGATACTTTTGATTATAAAGGTGTTTCTTTTACCATTGATACAAAGAATGGCACTGACGGTAATG +GTACAGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTGACTGTCGCTGACATTACCACGGGTGCGGCAGACGTTAAT +GCGGCAACCTTACAATCAAGTAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACCTTTGATGATAAAACGAAAAA +CGAAGGTGCGAAATTATCTGATTTAGAAGCAAATAATGCTGTTAAAGGTGAAAGTAAAATCACGGTAAACGGTGCTGAAT +ATACAGCTAACGCTGAGGGTGATAAAATTACCTTAGCAGGTAAAACCATGTTTATTGATAAGACAGCCTCTGGCGTTAGC +ACATTAATTAATGAAGATGCTGCTGCAGCTAAGAAGAGTACCGCTAATCCACTCGCTTCAATTGATTCTGCATTGTCAAA +AGTGGATGCTGTACGTTCTTCATTGGGGGCTATTCAGAACCGTTTTGATTCTGCCATTACCAACTTGGGTAATACGGTAA +ATAATCTGACTTCCGCACGTAGCCGTATCGAAGATGCTGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATT +CTGCAGCAGGCAGGGACTTCTGTTCTGGCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23_Salmonella.enterica_Gera_AY353498_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +CTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAGCAACTGGTGGTCCGGCTGCGGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGCGGCGGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGACTCCGCCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGTACTGCCGTAGACTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACTTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23,z32_Salmonella.enterica_IIIa.56:z4,z23,z32:-_AY353501_z4,z23__1266 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATTGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +TTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCAAAGATGCAAAAACCGGCGGTCCGGCTGCGGATAAATTAT +CTCTGACACAAGATGATAAAGGCAATTACTTTGTCAAAGATGATACTGCTGCAGCTAAATACTATGCAGCTACCGTAGAT +ACGACACCGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAACCCT +ATCACGCGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGACCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAG +ATCTCTATGCTATCCAAACGTTAGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAAACT +ACGGAGGGCGCTGCCGTAGCCTTAGCTGCAAACGTCGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACTGTTGACGC +ATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATAACTAACCTGGGCAACACGGTAAATAACCTGT +CTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCACAGATTCTGCAGCAG +GCCGGCACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAGCGTCCTCTCTTTACTGCGTTAA +>fliC_z36,z38_Salmonella.enterica_IV.43:z36,z38:-_AY353486_z36,z38__1266 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCAAACGACGGTATTTCCATTGCGCAGACGACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCAAACGGCTCAAACTCTGACTC +TGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATTACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATTGCTACAACAGTTAAAGAAGGTAC +GAAGCTCACTGCCGATTTTGCAGTTAAGGTCGCAGATTTTGATGATAAAGCAACAACTGGTAAATTAACTGCAAACTTAG +AATTGAAGCAGGATAAATCCGGAAATTATTTTGCCTACGATAAAACAGCCAGTAAATACTATGATGCGACTGTAGATACT +GCTACAGGTAAAATAGAATTTACTTCTGGGGCAGGTAAAGAGACAACGAAAGATACATCTAAACTTACGGATGTTACTTC +TTTGTCCAAAGAAGTAACGATAGATAGTGGGCTCACGGATGATAAATCATTAGTAAAATACAAAGGGGATGATGGTAAAG +AACAGTATGCCGTTCAAACTCTTGATAATAAAGGTAATGCGACCTATAAGACTGCCGTTATAGCGCGTGACGGCAAAGTG +ACAGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGACGC +TTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACCTGT +CTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCAGGGACTTCTGTTCTGGCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z29_Salmonella.enterica_IIIa.62:z29:-_AY353479_other.z29__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAGGGT +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTACGTGAGTTGACTGTTCAGGCAACTAATGGGACAAACTCTGATAG +CGACCTGACCTCTATTCAAAATGAAATCACACAACGTTTGAGTGAAATTGATCGTGTCTCTGGTCAAACTCAATTTAACG +GCGTGAAAGTGCTGGCCCAAGACAATACGCTGAAAATTCAAGTAGGAGCCAACGACGGCGAAACCATTTCTATTGATCTT +AAGAAAATTGACTCAAAAAGTCTTGGAATGGATGGCTTTAACGTCAATGGCGCACACAAAGCAACAGGAAGTGATTTAAT +TTCTCAATTTGGTGCTACAGGTACTGATAATTATAACGTTACCAAAGGGGCTACTACCACTACTTATTCGGTAGACATTA +AATCTGGCGCTGTTACTACTGGTACACCAGCTGAAGCTGTCTTTGTTAACGCGGCTGATGGTAGCTTGACAACTGATGCT +ACTACCAAAAACACTGAAATTAATGGTAACGATGACTTTACAAAGGGACTTGCAGACGCAGCAAAAGGCGCTGTTAAAGA +TTCTACATTTACCTACAGTGGCATCGAATTTACTGCTAAGACTGCTGGTACAGCAGATGGTAATGGTACTTTTGAAGCGA +AAATTGATGGTACAGTAATTTCCTTTGAAATTACTGGTGGTACAACACCTTCCTCCGCAGTAACTGGAGCTGGTGGTGCA +AAAGCTTATGTTTCTAAAATTGATGGTAGTATTACGACAACAGCTGAAGTCGATAACCGTGCTGCGAAAATGTCCGATTT +GGATTTAAACAACGCGGTTAAAATAGGTAGTACATTAAATGTTAACGGTGCTACCTATAATGTTAATGCTAAAGGTGATG +AAGTTACTGGTAAGTTTGATAATGGTGCAGGCGGACTGGTTGATAAACAAGTATTCTTGGGAAAAACCGCTGGCGGAGCT +GCAACATTAATTAATGAGGATGCTGCTAAATCCCAACAATCTACCGTAGATCCGTTGAAAACTATTGATGATGCACTTGC +TCAGGTTGATGCGCTTCGCTCCGATTTGGGCGCAGTACAGAACCGCTTTGATTCTGCCATTACCAACCTTGGTAATACGG +TAAATAACTTATCTTCTGCCCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTATAAAGCGCAG +ATTCTGCAGCAGGCCGGCACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAGCGTCCTCTCTTTACTGCGTTAA +>fliC_z36_Salmonella.enterica_IIIa.43:z36:-_AY353484_z36,z38__1266 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAGTTGTCTGTTCAGGCAGCAAACGGCTCAAACTCTGACTC +TGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAACTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACAAAAGGAATTGCTACAACGGTTAAAGAAGGTAC +GAAGCTCACTGCCGATTTTGCAGTTAAGGTCGCAGATTTTGATGATCAAGCAACAACTGGTAAATTAACTGCAGACTTAG +AATTGAAGCAGGATAAATCCGGAAACTACTTTGCCTTCGATACAGCAAACAGTAAATATTACGACGCAACTGTAGATGCT +GCTACAGGTAAAATAGAATTTACTTCTGGGGCAGGTAAAGAGACAACGAAAGATACATCTAAACTTACGGATGTTACTTC +TTTGTCCAAAGAAGTAACGATAGATAGTGGGCTCACGGATGATAAATCATTAGTAAAATACAAAGGGGATGATGGTAAAG +AACAGTATGCCGTTCAAACTCTTGATAATAAAGGTAATGCGACCTATAAGACTGCCGTTATAGCGCGTGACGGCAAAGTG +ACAGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGACGC +ATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACGGTAAATAACCTGT +CTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_e,n,z15_Salmonella.enterica_Brandenburg_AY353323_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTAACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGTTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAGGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATCCTGCAGCAG +GCCGGTACTTCCGTTCTGGCACAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>O-7_wzy__1080 +ATGATATATTATATTTTTATTGTAATTTTTCCGTTCTTTTCATTTGTTAAGAATAAAAATATAAAAATTTACGCCTTGAT +GCTAAGTTTTTTATTTCTTGTCTCGTTTTGTTCTTTACGTTGGCAGACTGGTACTGATTGGCTCCCCTATTACGATGATT +TCATGAGTCCAGGGAATCGACATGACTTTGAAATCGGGTATGTATTATACGTCAAATTAATAAGATATTTGACAGATAAT +TATACATTGTTTCTATTCACTACATCAATTATTCCTATCGCGTTAATATTCTGGGGATGCCTGAAAACACAAAAAAATAT +ATCATTAACTATTCTGTCTGTTTGTGTTTTTTATAGTTATTATTATCTGGGGTCTTTTTTTGGGGCCGAAAGAAGAATTA +TTGCAATTGGGTTATCTTTTTTCGCTTTAATCCAATATAAAAGTAATAAAAAGGTGCAATCGCTTATTCTTATTCTATGT +GCGTCGACATTTCATATCTCGTCTTTAGTTACCTTATCTGTTTTTTTAATCAATAAGTTATCTTTAAACTTATATAAAAT +ATTACTTGTGCTTGGTGCCATTCTATCATTGCCTTTGTCACATTATTTATCAGATATAATTTCTTCCGTTATTAGTCTAA +TTCCTGTCGAAATTGTTCGCTATAAACTCACTGTTTATACTCAAAATGCACAAGAATATGGGTCCATAAGTATATCTGGA +ATTTTAAAAAGGGTGGTAATTTCTGCTATTTTTATTTACACATTATCTTTTGATATAAAAAATAATAAGGCAAATTTATT +TTTGGTAAAAACATATTTATTTGGAACTATCATATATTTATTTTTATCTCCGATCTCAGCCATGTTCTCAGTAATTAGTA +TATATTTTACTATAGTCGAAATATTGTTGATTCCTGCAGTATTAGTGCGTGTAGGAATTTTTACACGGATTCCTGCTCTG +ATTTTTATAGTGATTTTTTATTTTGGCTATCAAGTTTACTCTATACTAGGGTCTTATCCTGAACTTTTCTATCCTTACAT +ATCGGTATTTTCAGAAATTCAGCGTCAAGGTATTTACTAA +>fliC_z65_Salmonella.bongori_V.66:z65:-_AY353259_other.z65__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGCAC +TGCTATCGAACGTCTGTCTTCCGGTCTGCGTATCAACAGCGCAAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGTT +TTACCGCCAACATCAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCACTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCGAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCGGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTTTCCGGCCAGACCCAGTTCAACG +GCGTGAAAGTTCTGGCACAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAACAGATCAACTCGCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAGGATGAAGCTGTTAC +TGCTGGTACTTTCAGTGTAGATAGTGGTGTGGCAATTAAATCTGCAACGGTTGACGTTAAAACAGCTTTAAGCACGACTG +GTAATGACGGTACTGTAAGTAAAATTGAACTTGATAAGGCAACAGGTAAATATTACGCAACTGTATCAGGGCTTACAGAT +TCTGCAGATACAAGTAAAAATGGCACTTATGAAGTTAATGTTAGTTCTACTGGCGATATTACTTTTGTTGATACAACCAA +AGACACTGTCACTGCTGGCTCGGTAGAAGTACAAAATGTTCATACGAAAGCTGCTGGTGCACTTCCTGATTTAGCCGACG +CAAAAGCAGCTTTAACCAAAGCCAATGTTGCTAATGCAGACACTGCTTCTTTAGTGAAAATGTCTTATACGGATAAGAAC +GGTAAGGTCATTGACGGCGGTTATGCATTAAAAACAGATGATACCAAATATTATGTTGCATCATATAACGAAACTACTGG +AAAAGTCGAAGCTGCGGTTACAAAATATACCGATTCAAATGGATTTTCTAAAACAGCTGCTAATCAATTAGGTGGTGTAG +ATCGCAAAACAGAAGTTGTGGAAATTGGTGGTAAAACTTACACAGCAGCCAAAGCTAAAGACCATAACTTTAAAGCTGAT +CCAGATCTGGCAGTTGTTGCAGCTGCAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCACAGGTTGATGC +GCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACTGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCAGGGACCTCCGTTCTGGCACAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>O-67_wzt__741 +ATGGAACCAGTAATAAACTTTAGTCACGTTACGAAAGAGTATCCTCTTTACCACCATATTGGCTCAGGAATTAAGGATCT +CGTATTTCACCCTAAAAGAGCTTTTCAGCTGTTAAAAGGGCGTAAATATCTTGCGATCGAAGACATTACCTTCACCGTGG +GTAAAGGCGAGGCCGTAGCGCTGATTGGTCGTAACGGCGCAGGGAAAAGTACCTCCCTCGGGCTGGTGGCCGGCGTCATT +AAGCCTACAAAAGGCACTGTTACAACCCAGGGGCGCGTTGCCTCAATGCTTGAGCTAGGCGGCGGTTTTCACCCTGAATT +AACCGGGCGAGAAAATATTTATCTCAATGCGACCCTGCTTGGGCTACGCCGCAAAGAGGTTCAGCAACGGATGGATCGGA +TAATTGAGTTCTCCGAGCTGGGTGATTTCATTGACGAACCTATTCGCGTGTACTCAAGTGGTATGCTTGCGAAGCTTGGA +TTCTCTGTCATCAGCCAGGTAGAACCCGATATACTTATTATCGATGAGGTACTTGCTGTCGGTGACATTTCGTTCCAGGC +CAAATGTATACAAACAATACGAGACTTCAAAAATAAGGGTGTAACGATATTATTCGTTAGCCACAATATGAGTGATGTTG +AAAAAATCTGTGACAGAGTTGTTTGGATCGAAAACCATAAACTCCGCGAAATTGGCTCAGCAGAGAGAATCATTGAACTT +TACAAGCAAGCAATGGCTTAA +>O-40_wzy__1368 +ATGTTTCAGATTAAAACCAGAAAAAAACCATTGTTAATATTATATTTAACTTTGTTATTAAGTATTTTGATGTCGTTAAT +TATCGATGATGGTATAAATCGATCCTTATACATACTTTGTATATCCACACTAAGTGTTTTTTTTATATGCTATTGTTGTA +ATAAAATAACCTCCCCTGCAAGTTTATTAATTATTTCTTCCTTTGTTTTCCTTGGTTGTAGGCCATTTCTCTCATTATTC +ACAAGTTTCGATTATAGAAATGCCGATTGGTTTATAACTGGTTATTTAGATGAGAATGTTATCTATACTAATTATGCTGT +TTCTTTTATGTATTTTGGATATAGTGTTGCATTGATATTAAGTAATAATAATTCAGCACATAGAGAATGTTACAATCTAA +ATAAAATAAAACCTAATATTATATTTTTGTCTATGCTTTTTCTTTTTGGCTCATTAGGACAAATCCTTAAAGGTTTTTAT +TTTTATTCCTTCATTGAGTCGAATAGTTATGTTGGAATTTATCAAGATAAAGTAAATTTACCCATGGGATATAATTTTTT +ATCATATCTGTTTTATTGTTCATTTTTCCTCATCTGTGCATTTTATGACAAATTCCGAGTTAATAAATCATTTTTATTAA +TATCAATATTGATTGCTGCTTTTAGTGCCATGAAAGGTAGTCGAGGGGAGTTTGTTACATTCTTGCTTACAGTTTTTTGT +ATTTATTATAATGAGAAGAAAGTAAGCAATATTAGCTTATTATTGAAAATGTTTTTAATATTTATTGCTGTTTTTATTAT +AAGTGAATTTGTTTCAATGTGGCGGTCAGGCGGTAGCTTTATTGCTCTTATTGAAGGCGATAATCCACTCATGCAATTTA +TATATGGAATGGGAGTATCATATATTACACTTTACCAATCGGTTAAAATAAGTTTGATCTCGGGAGTGTTTGAGTTTCAT +TATTTAATCAGTCAACTATTAATTACTATATTTTCAGTGTTAGGAGTTCAGGTATATTTACCTGGAATTAGTTACAGCCA +TTTGGCATCTAAAACTGCGAACCCACAATTATATGAACAAGGGTTTGGATTAGGAGGAAGCTATCTTGGTGAATCATATA +TAGCTATGGGACTAATAGGATGCTTTATTATTCCATTTATAGTTTTATTTCTTATTAATAAGCTAGAAGTATTTACCAGA +TATAATAAAACTTTTTATTTTGTATATTATAGCTCTCTACCATCTGTTTTATTTATACCCAGAGAAACCTTGTTCTATTT +TTTCCCTTATGCAGTTAAAGGCATTATTGTGGTATTTATATTTACATTTTACGCGAATATTAAAATGAGAAGATTTAATA +ATGGTTGA +>O-56_wzy__1179 +ATGGAATTGAAAAAAAACAATACCAGGATTCTTGTCTTTTTTTTATACCTTACCGTTAATATTATAGCATTTATATTATC +TTGTGTTCAGGGGTACATATTAGTCGAAAATTATAGTTTTAGCTTTAACGTTGATAACGGAGCGCTGGGTTTTGCATATG +TGATATTTTCGTTACTATTCATAACTCTATTGTATATTTTTTTTACTTTCCTGTTGAGGCCATATAATGAGCATATAAAT +ATTACAAGATTTTATGAAAATAAAAAAATCAGTATTTCTATTTTTAGTATACAAACTTTATTTATAGTCTTTAATTTATA +TTATGGACTAAATGTCGCCGGTGCTGGTGAAGACGTTAATATTGCACCATCATTGCTACGTTATTTTTTTGTGATATTTA +ATCCAGATATTTTGTTTTTAATATATGCATGCACGAACATTAACAATCAGCTTTATAAAGTTAATTGTTGTGCTTATTTT +GTATCGACTCTAATAAGAGGCTGGAGTGGTGGTGTTCTGTTCTTGTTATTTATTTTTTTATGCCGCAGTGATAAAATTAA +TTTAAAATTAATTTTACTTTTTATCATATGTCTCTTATTCGCACCATTTATTATGGAAATAAAATGGCTAATTAGAAGTA +ATACATTTGATTATAATAATATAATATCTGAGTTTGATTATGGTAAAAGTTTAGGGCAGTTCTTAGAGTATTTAGTGTAT +CGATTACAGCAGGTCACTAATGTTATCTATCTTATCGACCGGGTAGAGCACATTTCTATTTTATATCAAGATAATACTTT +AGTTCCATATTGGGGGGAATTTATCGGATTAAAAAACTTATATCAGCTTTATTATCCACAGGCAATTCCTTTGGGGCAGT +GGCTCGGAAGCAGTATTGAAAACTCACTAGTTTCATGGAATTCTAATCCTGGGCTTGCAGGATGGTTTATAATACTTACA +AATTACTCACTATTTTATGGTGGGCTTTTTATATTAATTACAGTAACTGCAATTTTTTTTAATGTGTATTTTTCTATTAT +AATTGGAAGAGGGTGTATAACTGGTTTTTCTTATATTTTATGTATTCTTTATCTTTTTCCGGGATGGATGGGAATGTATT +TTAATTTGATATTTTATCTAATTATTTGGTGTGTTGTAATTAAAATCTTAAAGGTATAA +>fliC_b_Salmonella.enterica_Niederoderwitz_AY353360_b,d,j__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCAGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGCTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACTTTAAGTGTACAGGATGCCTATACGCCAAAAGGTACCGCTGTTAC +CAGAGATGTTACCACCTATAAAAATGGTGGTACTACTCTTACAGCACCTGACGCAGCAGCAATTGATACCGCTTTAGGTA +CGACTGGTGCGGCGGGTACTGCGGCTGTGAAATTTAAAGACGGTAACTACTTCGTTGAGGTGACCGGTACAACTAAAGAT +GGTCTGTATGAAGCGACAGTTGATGCAGCTGGCGCGGTGACAATGACCGCAAATAAAGCAACAGTAACTGGGGCTAGTAC +AGTTACTGAAAACCAAATTGTAGACGCTGTTACACCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATG +CAGGTGTGACAGGTGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCG +GGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAAACTGGTGAGATAAAAGCTAAAACTGT +AAATTATACTGACGCTACTGGTGCGACAAAAACCGGTGCTGTGAAATTTGGCGGTGCGAATGGTAAAACTGAAGTTGTGA +CCACCGTTGATGGTAATACTTATCAGGCTAGTGATGTAAAAGGGCATAATTTCCAGAGTGGTGGCGCTTTAAGCGAGGCT +GTACCACTAAAACTGGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAAGTTGATGCGCTGCGTTCTGACCTGGG +TGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_b_Salmonella.enterica_IIIa.47:b:-_AY353363_b,d,j__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCAGCAGGTCAGGCCATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGCTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACTATCCAGGTTGGCGCCAACGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACTTTAAGTGTACAGGACGCCTATACGCCAAAAGGTACCGCTGTTAC +CAAGGATGTTACCACTTATAAAGATGGTGGTACTACTCTTACAGCACCTACCGCAGCAGCAATTGATACCGCCTTAGGTA +CGACTGGTGCGTCGGGTACTGCGGCTGTGAAATTTAAAGACGGTAACTATTTCGTTGAGGTGACCGGTACAACTAAAAAT +GGTCTGTATGAAGCGACAGTTGATGCAGCTGGCGCGGTGACAATGACCGCAAATAAATCAACAGTAACTGGGGCCGGCAC +AGTTACCAAAAACCAAATTGTAGACGCTGTTACTCCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATG +CAGGTGTGGCAGGGGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCA +GGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAGACTGGTGAGATAAAAGCTAAGACTGT +AAATTATACTGACGCTACTGGTGCAACAAAAACTGGTGCTGTGAAATTTGGCGGCGCGAATGGTAAAACTGAAGTTGTGA +CTACAGTTGATGGTAATACTTATCAGGCTAGTGATGTGAAAGGGCATAATTTCCAGAGTGGTGGCGCTTTAAGCGAGGCT +GTGACTACTAAAACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGACCTGGG +TGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAATCTGGGCAATACTGTAAACAACTTGTCTGAAGCGCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGTGCGCAGATTCTGCAGCAGGCCGGTACTTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_a_Salmonella.enterica_from-cdc-Stk2184_other.a__1488 +TTAACGCAGTAAAGAGAGGACGTTTTGCGGAACCTGGTTAGCCTGCGCCAGAACGGAAGTACCGGCCTGTTGCAGAATCT +GCGCGCGAGACATGTTGGAAACTTCAGTCGCATAGTCGGAATCTTCGATACGGCTACGCGCTTCAGACAGGTTGTTTACG +GTATTGCCCAGGTTGGTGATAGCGGAGTTGAAACGGTTTTGTACCGCACCCAGATCAGAACGCAGCGCATCAACCTGCGC +CAGCGCGGCATCAATTTTCTGCAGCGGGTTTTCGGTGGTTTTAGCGGCTGCTTCAGCCAGCTCTGGCTGTGCTTTGAAAT +CATGACCAGCAGCTTTGCTGGCATTATAGGTTTTACCGTCGATAGTAACGACTTCGGTTTTACCATCTACGCCGCCAAGT +TGGTTCAGTGCGGTTTTAGTATTGCCGTCTTTATCGGTATATTTAGTGGTGTTAATGCTGAACGATCCATCTTTATTTTT +TGTTGCCGCATAAATATCAGCCCCAACTTTAACACCAAAACCGCCATCAATCGTCTTACCGTTTTTATCGGTATAGGACA +TTTTGACCATTTCAGCAGTATCAGCTCCGGCCACATGGGCAGCTGTCAACTGAGCCTGAATAGCTGCTGGAGCAGCTACA +GGTTTTTGAACCTGAGTAACTTCAGTAATACCAGTAGGAGTTGTACCCTCTTTAGTGGTAGCCGCAGTCATTGTGACTGC +ACCATCATCAGCAACATTAACTTTATAGAATCCGCCTTTGTTAGTTTGATCGGTCGCATCGGTAAATTCTACTTCAACAT +AATAATCTTTAGAGGTGCTATTATAGTAAACCTTACCATCCTTAATTGAACCAGTGTCAGTTGTAGAACCGGTTCCGGTT +TTGAGGCCAGCACCATCAAGTGCAGTTGTGCTTAACGTAGCCGGAGGCGTGACAGCTTCACTCTTCACATCATACGCTTT +CTGCACATTCAGCGTATCCAGACCCAGGGTCTGAGAGTTGATCTGCTTCAGATCGATATCGATAGTTTCACCGTCATTGG +CGCCAACCTGGATGGTCAGGGTGTTGTCCTGCGCCAGGACTTTCACGCCGTTGAACTGGGTCTGGCCGGATACACGGTCG +ATTTCGTTCAGACGCTGGGTGATTTCAGCCTGGATGGAGTCAAGGTCAGACTGGGAGTTGGTGCTGTTAGCAGACTGAAC +TGCCAGTTCACGCACGCGCTGCAAGTTGTTGTTGATTTCGTTCAGCGCGCCTTCAGTGGTCTGCGCAATAGAAATACCGT +CGTTAGCGTTACGGGAAGCCTGAGTCAGACCTTTAATGTTCGCGGTGAAACGGTTAGCAATCGCCTGACCTGCCGCATCG +TCTTTCGCGCTGTTGATACGCAGACCGGAAGACAAACGCTCGATAGCGGTGCCCAGTGCGGACTGGGATTTGTTCAGGTT +ATTCTGGGTCAACAGCGACAGGCTGTTTGTATTAATGACTTGTGCCAT +>fliC_a_Salmonella.enterica_Paratyphi.A_AY353356_other.a__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATTGATATCGATCTG +AAACAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCGGTCAC +GCCTTCGGCTACATTAAGCACTACTGCACTTGATGGTGCTGGCCTCAAAACCGGAACCGGTTCTACAACTGATACTGGTT +CAATTAAGGATGGTAAGGTTTACTATAACAGCACCTCTAAAAATTATTATGTTGAAGTAGAATTTACCGATGCGACCGAT +CAAACCAACAAAGGCGGATTCTATAAAGTTAATGTTGCTGATGATGGTGCAGTCACAATGACTGCGGCTACCACCAAAGA +GGCTACAACTCCTACAGGTATTACTGAAGTTACTCAAGTCCAAAAACCTGTGGCTGCTCCAGCTGCTATCCAGGCTCAGT +TGACTGCTGCCCATGTGACCGGCGCTGATACTGCTGAAATGGTTAAGATGTCTTATACGGATAAAAACGGTAAGACTATT +GATGGCGGTTTCGGTGTTAAAGTTGGGGCTGATATTTATGCTGCAACAAAAAATAAAGATGGATCGTTCAGCATTAACAC +CACTGAATATACCGATAAAGACGGCAACACTAAAACTGCACTAAACCAACTGGGTGGCGCAGACGGTAAAACTGAAGTTG +TTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCACAACTTTAAAGCACAGCCAGAGCTGGCTGAAGCG +GCTGCTGCAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGACTTGGG +TGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATCCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_a_Salmonella.enterica_Paratyphi.A_AY353357_other.a__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATTGATATCGATCTG +AAACAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCGGTCAC +GCCTTCGGCTACATTAAGCACTACTGCACTTGATGGTGCTGGCCTCAAAACCGGAACCGGTTCTACAACTGATACTGGTT +CAATTAAGGATGGTAAGGTTTACTATAACAGCACCTCTAAAAATTATTATGTTGAAGTAGAATTTACCGATGCGACCGAT +CAAACCAACAAAGGCGGATTCTATAAAGTTAATGTTGCTGATGATGGTGCAGTCACAATGACTGCGGCTACCACCAAAGA +GCCTACAACTCCTACAGGTATTACTGAAGTTACTCAAGTCCAAAAACCTGTGGCTGCTCCAGCTGCTATCCAGGCTCAGT +TGACTGCTGCCCATGTGACCGGCGCTGATACTGCTGAAATGGTTAAGATGTCTTATACGGATAAAAACGGTAAGACTATT +GATGGCGGTTTCGGTGTTAAAGTTGGGGCTGATATTTATGCTGCAACAAAAAATAAAGATGGATCGTTCAGCATTAACAC +CACTGAATATACCGATAAAGACGGCAACACTAAAACTGCACTAAACCAACTGGGTGGCGCAGACGGTAAAACTGAAGTTG +TTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCACAACTTTAAAGCACAGCCAGAGCTGGCTGAAGCG +GCTGCTGCAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGACTTGGG +TGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATCCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_1,5_Panamastr_AOYJ01000008_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAATACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGGCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGACAGCTTATGCCGATAATGGTACTACGCTGGATGTATCGGGTCTTACTGATGCAGCTATTAAAACGGCTACGGGTG +GTACGACTGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGG +GGCTTTAGTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGTAACAACTAAAACAGAAGTACAGGAGTTAACAACTACACCGGTAGTTG +CTTCAGCAGATGCTAAAAATGCCTTAATCGCTGGCGGCGTTGACACTGCCGATGCTAATGCCGCTACATTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCAT +GATTTTAAAGCACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCACAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>oafA-O-4_5-__325 +TCATCATCAGAGTTCAACTTTTTGCTTCACACCTGGTCACTATCAGTTGAGTGGCAATTTTATATCCTTTATTAGTCATT +ATAGTTAAAAAATTACGGTTTCCTGTTGGACTCTCATTATCTGTAATTTTAGCCATGTCACTTGCAATTACACTTATGCG +AGTGACTGGAACCAAAGAAGATATTTTCTATCTTATCCCTACCAGGGCATGGGAAATGCTGGCTGGCGGCCTTGTATACA +TAGCATCTGTACGTTACAAAATGCCAGAATGGATAAAGCATTGTGAGGTTTATGGGATAGTCCTCATTGTTGTTGCTGTT +GTTAT +>fljB_e,n,z15_Mbandakastr_AMRS01000032_e__1496 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TTACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAGGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTATCATCTGCGGATGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ACGGTAAAACCGAAGTCGTTACTATAGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fljB_e,n,z15_Salmonella.enterica_Uno_AY353325_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAGGTGGTTATACCGAT +GCGGGGGATACTGCTAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCTACGA +AAAAAGCCTTACAAGATGGGGGCGTATCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCAGCTAACCAACTGGGTGGCGTAG +ATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_z_Salmonella.enterica_IIIb.48:i:z_AY353336_k,z__1500 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTTTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTAGATAGCAAAGCTGTAAC +TGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGTACAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACAACTG +GTTCCATTAAAGATGACAAAGTATATTATGATAGTGCTACTAAAAATTATTATGCTGAAGTGAACTTTACAGATGCCGCT +GATACCGCTAAAAATGGTTTCTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCTTCGACTACTAAAGA +AGCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCATCCGCAGATGTGAAAG +CTGCTCTGACTGCTGGAGGTATTGATACTGCTGATGCAGCTACGGCAGAAATGGTCAAAATGTCTTACACCGATAAAAAC +GGTAAGACGATTGATGGCGGTTACGCTGTAAAAGTGGGCGATAACTACTATGCCGCTACCCAGAAAAAAGATGGTAGCTT +TAGTGTTAACACCACGTCTTACACCGCAGCGGACGGTACATCCAAAACTGCCTTGAACCAACTTGGTGGCGCAGACGGTA +AAACCGAAGTCGTTACTATCAACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGCCATGATTTCAAAGCACAGCCAGAG +CTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACG +TTCTGACCTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTG +CACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGG +ACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>O-28_wzy-another-lineage__1296 +ATGGAATATTTAATTATTTTGATTTTCTTTACTCTCTTATTTTTTACGACTAAAAGTACATGGCCTTTTGGTGGAGTGAA +TGCTCATCCTATATATTTTGTATTTCTTACTCAAATTTTTATATTAACGCTCCCCGGTGTTCTTATTTTAACATTTTTCA +GGAACTGTGTTGGATCTATTACATGTGAAATTGTCACTAATGCCACTAAAATAAATGTGATGCTTGATTATTTTACAATT +CTTAGTTCTATCGTTTTGGCAATATTATTTTCCTACTTATTAATGCGAGGGCGTAAAGATTTTACTCCTTCTGCGTTGTC +TCAAAAACGTTTTCTTAATTTTTGTTTTTTTATAACAATTCTAATTATTATAATTAAAATTATCTTTGTGAAGCATGTTC +CTCTCTTTATGGTTTTATTTGGCAACAAAGAGGCTGCAGAAATTCAAAAGGCAGCTATTTTACGTGGTGAGGATGGGTTT +TCTTTTCCTGTTCTCAATTTTCTTATTAAGTATTTTCCTCTCTATTTTTATTACTCAGTATTAATAACTTTTTTTAAGCG +CAAAATTAGCTTTTTTTATTTAATAATAGCTTTTGCTACAACATGTTTAGCAATGCTTTATGATTTACAAAAAGCACCGG +TAGTCATTATGATTATAGGTTCATTTTGGCTATACTGGGCTTTTTTTGGTAAATCTAAAATGATTATCATTGGGGCATTA +CTAAGCTTAGGATTGGTTAGTTTATTATTTTATATCTCGTATGATTTTGGTGGAAATACAAATTATTTTATTGACGCTAT +TCTCAATAGGACTTTTGTTGCGCAAGATGATGGTATGTACTGGGTATATCAATATTATGATTCATTGCCTAATAAAGAAC +TATACGCCTATTGGGGTATACCTTTTGCTCAACAGTTTGGTTTACCACAGATAGATCCTTTAAGTGATATTATCGGTGTG +GTATTTCCAAATGCTAGTGATAATTGGGTTAATACAACAACATTTCTTCTGGGGGAGGCTAAAGCAATATTCGGAAGTTA +TAGTTTGATTCTTGCTACTTTTGTAGTATTCATTAATGTGATTATTATAATGATAGTTTCATCAGTATTGGTTAGAATAT +CAAAAGACCTTTTTTATCCAGCTATATTTGTTATGTTGCAAACAATTCCATTTGCTAATAATATCACGGATTTGATTTAT +GGCCGATTTATATTTGGTTTTCTGACGTTTATGCTATTTCCGACACTTTTTTGTTTGCTATGTAACGGCAAGATGAGTAA +ATACGATGCGAAGTGA +>O-35_wzy__1065 +ATGTCTATTGATTTTCTTTTTTCAATTACTGAGATTGCAGTTGTTTTTTCTTGTGCTATTTATATATTTGTTCAATGCTT +GTTAATGCACAAGATTTATTTAGATAAAGTTGTTTTAATTCTATTGTGTTTACTCCTTTGCTTGGTCATTATTCAACTTC +CCGAACTTAATGAGCAAGGTTTGATAGATGCTGTAAAGCTATTATTACCTTTACTAATAGTATTTATCGCTTTTCAAAAA +CCGAAATTATGCTTGTGGATCATTATTGCATTATTGTTCTTCAATTCCACGCTAAATTTCTGGCACTTCAAAGTTTTTGA +TAAATTTAGCTCATTTCCTTTTACATTTTTTATATTATTATATTTTTTGTACAAATTGGTCAATGATCAACCTCCAAGGC +AGAGGAATAAAAAATTTTACGTTGTAATTTTCATATTTATATTAATTGATGTAACACAATCATTATTAATAAGTTACAGA +GGACAGATTCTATACTCTTTAATATGTGTTATAATGCTTGTATTGAGGATTAATTTAAGGAAAACAATCCCATATATTTT +TCTAACTTTACCGTTTATATATGTTTTTATAATGACTTTTATTGGTTTTAATTACTTTAATAAAGACGTGGTTTTTTTTG +AACCTACGGCAAGTAATATTGAACGTACGGGGATGATATATTATTTGGTTATCCATGCAAATGATTATATATTTCACGGT +ATGGGGACGTTACATTTCTTAAATGAGGGGGGGCAATATAAAATGTTATATGGATTTCCTTCTCTAATACCAAATGATCC +TCATGATTTTTTATTAAGATTCTTTATAAGTATTGGTATGATGGGGGCGTTGATCTATCATTGTATATTTTTTGTTTTTT +TTAAAAATATATCTTCGTTATTGCGTCAAAAAAACAGTTATTTTGTCATAGTAAGTTGTTTATTATTATTACAAGTTGTG +TTGTTTTATACACTAAACCCTTTTAATGCATTTAATCGATTAATTTGCGGGCTTACAATCGGAGTCATTTATGGATTTTC +AAAGAGTAGACAGATATATATGTAG +>O-11_wzy-new-from-CP019192__1080 +ATGAATATATTATTTTTTTTGCTTCTAAGTGTTGGGCTATTATTTTCCCTCGCATATACTAATAAAAATAAAAATATAAA +TGATAGTATCATGTTTATGCTTGTCGTCCTGATGATATTAATGTCAGGACTTAGAGTTAATGATAGTGATTATCTTGAGT +ATAATAAAATGTATAATGAAGTTCCTTCATTATACAATTTTACGTTATCTGCGATAAAAGATATTCATGGAGAGATTGGC +TATCTTTTCCTTTCATCTTTTTTTAAAACATTTGATCTACCGTTTCAGTTTTTTTTATTCTTTATAGCATCGTTATCTTT +GATGCTTACTTATTTTTCTTTTAAAAAAGCAAGTATTATACCAATATTGTCTCTAGTTTTTTATTTAAGTCATGCTTTTA +TTGTTAGGGATATGATACAAATAAGAGCTGGATTAGCTGTGAGTATGTCTCTATACACAATTGTGACATATAAGAAGAAT +CGAAATGTGATCGCAGGGATACTGCTTGCATCGCTGATTCATTCTGGAGCAATTATAATTGCTATTTGCTACCCATTTAT +AAGAAAAAGATATTTATCGTTAAGAAAAATATTTTCTCTTTTTCTGGTTGCCTTAATATTTTCTTATTTACATGGGCTCG +ACTTTATATTAAATACCCTTATTCATTATAATCTTCTGCCAGATGCTGTTGCAAATTATATTGGGTGGGAAGAATATGAT +TATAGAATTAATATTTTCACTAATCCAGTGTTTATTAAAGGGGTGATGATAGTTTTTTTAATGAAAAAATATATTAAAAT +AAATATAAATAATGAAAAGGATAAGGTGGTTATATTATATAATTTATATGTTTTAGGTGTTTTAGCAATGGTTGGATTAA +GTGAGATGGCTATTCTTTCAGGACGTCTCTCATCATTTTTAACACTAGGTGAAAGCATATTAATAGTATATGGTCTTTTT +TATAAAAGAAATATCTCGGTAGGTTTTGTTTTCTTTTTGTTATTAACTTTCATACAGATGGGATATGATCTGTTAATTTC +AAACGTACATCCGAAGCTCTCTCTTTTTATATTTGGATAA +>gntR-family-regulatory-protein_dt-negative__291 +AATATGCTGACCCGCTATGTTGGTGACCCTTCTGCCTGATCTTTTCGCCTGCGTGAGCATCGCAGGCGCTTCAACCAATT +CTTCAATTCTATTAATCACGTCCAGTAACGATCTAACCACGATCTTGATGTAGATCCCACTCCTGCATCTTTCCTGAGAA +ACGATTTGACTTAGTTTTTGTATGGGAATAATTTCTCCCTGTCAACATTGGATACAATATCATATATCATTGATTGGATA +ATTATAAATATAGAACCCATTACCCTTACCTTATGTTTATTGGTGTTCGCT +>O:22-gene1__1071 +GCCAGGGGCGGTAGCGTATATAAAAATAATTTTTGTTTATTAATAGGAGATATGAGTATGTTAGTTTTAATCACTGGCGG +TGCAGGCTATATAGGTTCACATACTATTATACCCCTATTAGAAAATAATCATGATGTAATTGTACTTGATAATTTGTGTA +ATTCATCAATTGAATCTATAAAACGAGTCGAATATCTTACTAAGAAACAAGTAACTTTATATATAGGTGATGTTCGTGAT +CGGGATTTATTGAATAAAATATTTATGTCTCATCAAATTGATGCAGTTATGCACTTTGCTGCTTTAAAGTCAGTGGGAGA +GTCAAATAATATTCCGCTAACTTATTATTCTAATAATATTACAGGCACGCTTAACTTACTTGAAAGCATGCAGCGATATA +ACGTAAAAAAATTAATATTTAGTTCTTCTGCAACCGTCTATACTGCCGGGAATAAGATGCCAAATACAGAAAGTGATAAA +ACTGGAATAGCTAAAAATCCTTATGGCACATCGAAGTTTATTATGGAAACTATACTGAAAGATATTAGTAAAAGTGATCC +GAGTTTCTCCATTATTTCTTTAAGATATTTTAACCCTACAGGAGCTCACCCTTCAGGTATGATTGGAGAGAACCCTAACG +GCATACCTAATAATCTTATCCCTTACGTTGCAAAAGTTGCACAGAATACACTCCCCGTTTTACATATTTATGGCAACGAT +TACCCAACGAAGGATGGCACCGGTGTAAGAGACTATATACATGTAATGGATTTAGCTTTGGGACATGTAAAAGCTTTGGA +TTATATCTTTCTAAATAAGATTAATTATGAGGTTTTTAATTTAGGAACTGGACGCGGGTATTCAGTGCTCGATGTTGTTT +ATCTGTTCGAAAAAGTTTCACAAAAAAAAATATCATATGTCTTCTGTGATAAAAGAGAAGGGGACGTTGCAGTTTCATGG +GCATGCCCTCAACTAGCTAATGAAAAATTAAAATGGCAGGCAACTAAAGATTTAGAGGAAATGTTGAAAGACGTCTGGCA +TTGGCAAACAAAAAATCCGAATGGTTATTAA +>fljB_z39_Salmonella.enterica_II.43:d:z39_AY353345_other.z39__1500 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACGCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAATAACCTGCAGCGTGTACGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTAAC +TGATGGTAGTGGTGGTAAGACATTAAATATTAGTGGTCTTGATGCTGCTGCAATTAAAACCGCTGTTGGAGGGACACCAA +CTGGTACTGGCGAAATTAAGGATAATAAGGTTTATCACAATAGTACTGATGGTAAATATTATGTTGAAGTTGCTGGTTAT +ACCTCAGGGGAGAATGGCTTCTATGAGGTAGATGCAAATCCTGCTGACGGTACAGTTACATTTGCTACCGGTGCTACGAA +AATAACGGCTAAACCTGCTGATGTTGAAGAGGTTACAACTGTCCAATCAAAACCTATAGCTCTCAGTGCTGAGGTTAAAA +CACAATTAACTGCTAATGGAGTTAGCACAGCGGCCGCTGATAAAGGCCAATTGCTCACAATGTCTTATACAGATAAAAAT +GGTAAGACTATTGATGGTGGCTTCGGTGTTAAAGTTGGCGCTGATATTTATGCTGCAACTAAGAATAAAGATGGCTCTTT +TAGTATCAATACCACGAAATATACTGATAAAGACGGTAATACCCAAACTACACTGAATAAACTTGGTGGCGTTGATGGTA +AAACTGAAGTTGTTTCGATTGAAGGTAAAACCTACACCGCAGCGAAAGCAAAAGATCATAATTTCAAAGCCGATCCTGAT +CTAGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCG +TTCCGATCTGGGTGCGGTACAGAACCGTTTCAATTCCGCTATCACCAACCTGGGCAATACCGTAAACAACTTGTCTGAAG +CGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATCCTGCAGCAGGCCGGT +ACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_z39_Salmonella.enterica_II.4,12:g,m,t:z39_AY353346_other.z39__1500 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTACAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATTGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTGAC +TGATGGTAGTGGTGGTAAGACATTAAATATTAGTGGTCTTGATGCTGCTGCAATTAAAACCGCTGTTGGAGGGACACCAA +CTGGTACTGGCGAAATTAAGGATAATAAGGTTTATCACAATAGTACTGATGGTAAATATTATGTTGAAGTTGCTGGTTAT +ACCTCAGGGGAGAATGGCTTCTATGAGGTAGATGCAAATCCTGCTGATGGTACAGTTACATTTGCTACCGGTGCTACGAA +AATAACGGCTAAACCTGCTGATGTTGAAGAGGTTACAACTGTCCAATCAAAACCTATAGCTCTCAGTGCTGATGTTAAAA +CACAATTAACTGCTAATGGAGTTAGCACAGCGGCCGCTGATAAAGGCCAATTGGTCACAATGTCTTATACAGATAAAAAT +GGTAAGACTATTGATGGTGGCTTCGGTGTTAAAGTTGGCGCTGATATTTATGCTGCAACTAAGAATAAAGATGGCTCTTT +TAGTATCAATACCACGAAATATACTGATAAAGACGGTAATACCCAAACTACACTGAATAAACTTGGTGGCGTTGATGGTA +AAACTGAAGTTGTTTCGATTGAAGGTAAAACCTACACCGCAGCGAAAGCAAAAGATCATAATTTCAAAGCCGATCCTGAT +CTAGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCG +TTCCGATCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACTTGTCTGAAG +CACGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATCCTGCAGCAGGCCGGT +ACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_z_Salmonella.enterica_IIIb.53:z:1,5,7_AY353338_k,z__1500 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGTTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGTAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTAGATAGCAAAGCTGTGAC +TGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGTACAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACAACTG +GTTCCATTAAAGATGACAAAGTATATTATGATAGTGCTACTAAAAATTATTATGCTGAAGTGAACTTTACAGATGCCGCT +GATACCGCTAAAAATGGTTTCTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCTTCGACTACTAAAGA +AGCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCATCTGCAGATGTGAAAG +CTGCTCTGACTGCTGGAGGTATTGATACTGCTGATGCAGCTACGGCAGAAATGGTCAAAATGTCTTACACCGATAAAAAC +GGTAAGACGATTGATGGCGGTTACGCTGTAAAAGTGGGCGATAACTACTATGCCGCTACCCAGAAAAAAGATGGTAGCTT +TAGTGTTAACACCACGTCTTACACCGCAGCGGACGGTACATCCAAAACTGCCCTGAACCAACTTGGTGGCGCAGACGGTA +AAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAG +CTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACG +TTCTGACTTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTG +CACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGG +ACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>fljB_1,2_from-Brazzaville_SRR2058145_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTTTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGACAGACCCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAATGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +CACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCAGGCCTTGATGATGCAGCTATTAAAGCGGCTACAGGTG +GTACGGCTGGTACGGCTTCTGTAACAGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATCGGT +GGTTTTACTGGCGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTAACCCTTGCGAC +TGGCGCAACTAAAACTACAATGCCTGCAGGTGCTGCAACCAAAACAGAAGTGCAGGAATTAAAAGATACACCGGCAGTTG +TATCAGCCGATGCTAAAAATGCCTTAATCGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAACGACAGGAGCCATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACCAAAACTGCGGCTAATC +AACTTGGCGGCGTAGACGGAAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCGGGTCAT +GATTTCAAAGCACAGCCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAAAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACTTGTCTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATCCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAGAACGTGCTGTCTCTGTTACGTTA +A +>fljB_z_Salmonella.enterica_IIIb.50:k:z_AY353337_k,z__1500 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTTTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTAGATAGCAAAGCTGTAAC +TGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGTACAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACAACTG +GTTCCATTAAAGATGACAAAGTATATTATGATAGTGCTACTAAAAATTATTATGCTGAAGTGAACTTTACAGATGCCGCT +GATACCGCTAAAAATGGTTTCTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCTTCGACTACTAAAGA +AGCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCATCTGCAGATGTGAAAG +CTGCTCTGACTGCTGGAGGTATTGATACTGCTGATGCAGCTACGGCAGAAATGGTCAAAATGTCTTACACCGATAAAAAC +GGTAAGACGATTGATGGCGGTTACGCTGTAAAAGTGGGCGATAACTACTACGCCGCTACCCAGAAAAAAGATGGTAGCTT +TAGTGTTAACACCACGTCTTACACCGCAGCGGACGGTACATCCAAAACTGCCCTGAACCAACTTGGTGGCGCAGACGGTA +AAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAG +CTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACG +TTCTGACCTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTG +CACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGG +ACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>O:22-gene3__411 +GCAGAAAAACCTTTTATTTCACCTAAAAAACGAATATTTTTAAAATCCTTGAACTGGGCTTTGAGAGATTCTAACTGTTC +TCCCCCTCCAACAATATCCAGCTTATATTGCGGTTTTTTTGATATCACTTGGGCCAATAAACATGGGCGCTTAGGATGTG +TCAATCTACCAACAAACAAAATTTTATATTCCAAACACTCTTTTAAACGAGCAGGCATGGGTGGAACAGCATTCGTAGCT +GTAATAATCTTACCCTCATCAATTCCTATTTTTTTTATAGCTTTTTCTCTATCACTTTCAGAAATACACCAGATGACATC +CGTTAATTTGGAAAGGTATTTTTCTATTTTGCAAAATATACTTTTTAGCCGACCACCATTATATAAGCATGACCACCCAT +GTGAAACGTAA +>fliC_d_Salmonella.enterica_Livingstone_SRR1299429__1521 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACGGTACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATTGATATTGATTTA +AAAGAAATTAGCTCTAAAACGCTGGGACTTGATAAACTTAATGTACAGGATGCTTACACACCTAAAGAAACTGCTGTAAT +AGTTGATAGGACTACCTATAAAGATGGTACAGATACTATCTCAGCCCAGAGCAATGCGGATATCCAAACTGCAATTGGCG +GTGGTGCGACGGGTGTTACTGGGGCTGATATCAAATTTAAAGATGGTCAATACTATTTAGATGTTAAAGGTGGTGCTGCT +GCTGGCATTTATAAAGCAACTTATGATGAAACTACCAAGAAAGTTAGTATAGATACAACTGATAAAACTCCGTTAACAGG +TACGGCTGCTGCAGATATTCAGGCAACAACTGCCATAACTAAGAACCAAGTTGCTGAAGTAACAAAAGGTAATGCTGATA +CAACCACAGTTGCGGCTCAACTTGCTGCAGCAGGGGTTACTGGTGCCGATAAGGACAATACTAGCCTTGTAAAACTATCG +TTTGAGGATAAAAACGGTAAGGTTATTGATGGTGGCTATGCAGTGAAAATGGGCGACGATTTCTATGCCGCTACATATGA +TGAGAAAACAGGTACAATTACTGCTAAAACAACTACTTATACAGATGGTGCTGGCGTTGCTCAAACTGGAGCTGTGAAAT +TTGGTGGCGCAAATGGTAAATCTGAAGTTGTTACTGCTACCGATGGTAAAACTTACTTAGCAAGCGACCTTGACAAACAT +AACTTCAGAACAGGCGGTGAGCTTAAAGAGGTTAATACAGATAAGACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTT +GGCGCAGGTTGATGCGCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACTTGGGCAATA +CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTA +A +>O:23-gene3__454 +CCAATGAGAAACATCATTCACATATCCTACATAGTTAATTATTTCTTCTTTAATAATTGTATCAAGTTCATTTTGTTTTA +GACTACCAGGGTTTGCTGGATCAATATTACCCAGCACATTAAACGTCACCCCTTCAAATCTTTCTTTTATATTTTTAGCA +GCAGCGATAAATTCATAAATCCCCTTTTCTCTGAGCAATCGGCCAATGAAAATAAAAGAAATTGGTTCAAGTGGTGCTGG +TGAATACTTGTAATGCTCTAAATTTATTCCAATACCCCCCAATACATATACTTTTCTATCTTCTATACAACCAGCGTTAA +GTAAATCATTCCTATCATCTTCATTAAGTACAATAAGTGTATTAATTTTCTTAAAAGCTATTCTATAGAGCAGAATCTGT +ATTCTTTTTAGGATTTTTGTCTTTTGGGGAATCCCAGATGGTTGTTCGGTAAAT +>fljB_e,n,x_Hadarstr_AOZE01000017_e__1496 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATTACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGTGTAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>gntR-family-regulatory-protein_dt-positive__291 +AATATGCTGACCCGCTATGTTGGTGACCCTTCTGCCTGATCTTTTCGCCTGCGTGAGCATCGCAGGCGCTTCAACCAATT +CTTCAATTCTATTAATCACGTCCAGTAACGATCTAACCACGATCTTGATGTAGATCCCACTCCTGCATCTTTCCTGAGAA +ACGATTTGACTTAGTTTTTGTATGGGAATAATTTCTCCCTGTCAACATTGGATACAATATCATATATCATTGATTGGATA +ATTATAAATATGGAACCCATTACCCTTACCTTATGTTTATTGGTGTTCGCT +>fliC_z4,z23_Namurstr_AWGG01000011_z4,z23__1257 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +TGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTAAACGAAATTAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGCGC +CTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAGCAACTGGTGGTCCGGCTGCGGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGCGGCGGCTAAATACTATGCAGCTACCGTA +GATATGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGACTCCACCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGAGCAAATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGTACTGCCGTAGACTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_g,s,t_Salmonella.enterica_Senftenberg_AY353406_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATTCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTGACAACTGACGATGCGGAG +AACAACACTGCGGTTAACCTATTCAAGACGACTAAATCTACTGCTGGTACCGATGAAGCCAAAGCGATAGCTAGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATACAAAAGCTGGTAATGACGGTA +ATGGTACGGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCAGCGAATGTT +AATGATGCCACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_l,z13,z28_Salmonella.enterica_Connecticut_AY353452_l,v__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAATC +TGACCTCGACTCCATCCAGGCGGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTTTCTGGCCAGACCCAGTTCAACG +GCGTGAAAGTTCTGGCACAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAGGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAGTACCACTGGTCTTGATGATGCAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCG +GTACCGCTGCAATTAAAGATGGTAAGGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCGCCGC +GAAAGTGACAGGTGGCATACCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAG +TTAAAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGAT +AAAAACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGG +ATCGTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAG +ACGGTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCACAACTTCAAAGCACAG +CCAGAGCTGGCTGAAGCGGCTGCTACAACCACTGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAAGTTGATGC +GCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGT +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,q_Salmonella.enterica_Moscow_AY353403_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGGCGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGAATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_f,g,m,t_Salmonella.enterica_II.6,8:f,g,m,t:.e,n,x_AY353382_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCTCAGTCCTCACTGAGTTC +CGCTATCGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGATGGTATCTCCATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATTAACAACAACCTGCAGCGTGTACGTGAGTTGTCTGTTCAGGCAACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAGTTCAACG +GCGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATTCAGGTTGGTGCTAACGATGGTGAATCTATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGATTCAATGTTAACGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTGACGGGGTACGATACCTATGCAGCTGGTGCCGATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGCAGCAGCCCCGGATAAAGTATATGTAAATGCTGCAAACGGTCAGTTGACAACTGATGATGCGCAA +AATAACACTGCAGTTGCTCTATTCAATACCACTAAATCTACTGCTGGTACCGATGACGCCAAAGCGATAGCTAATGTCAT +TAAGGGTGGTAAAGAGGGAGATACCTTTGATTATAAAGGCGTATCTTTTACTATTGATACAAAAACTGGTAATGATGGTA +ATGGTACGGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGGTGGTGCGGCGAATGTT +AATGATGCTACCTTACAATCAAGCAGAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAATGAGAGTGCGAAACTTTCTGATTTGGAAGCAAATAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCAGCTAAGAAAAGTACCGCTAATCCACTGGCTGCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCGCTGGGGGCAATTCAGAACCGCTTTGATTCTGCCATTACCAACCTTGGTAATACGG +TAAATAACTTATCTTCTGCCCGTAGTCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,m,s_Salmonella.enterica_Amsterdam.var.O15+_AY353394_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTGCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTATGACACCTATGCAGCGGGTGCCAATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAATGGTCAGTTGACAACTGACGATGCGGAA +AATAACACTGCGGTTAACCTATTCAAGACGACTAAATCTGCTGCTGGTACCGATGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z44_Salmonella.enterica_Quinhon_AY353513_k,z__1491 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACTACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTGAC +TGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGCACGGATATTAAAACTGGCGTTGATGGAGCTACCACTACGAGTG +ACTCCATTAAAGATGGCAAAGTATACTATGATGGTGCTGCTAAAAATTATTATGTTGAAGTAGACTTTTCTGATACTGCT +AAAAATGGCTACTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCCTCGACTACTAAAGAACCTGCGAA +ACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGACGTCTGCTGAGGTGAAAGCTGCTTTGA +CTGCTGGTGGTGTCGATACTGCTGATGTAGCTACGGCAGAAATGGTCAAAATGTCTTATACCGATAAAAACGGTAAGACG +ATTGATGGTGGTTATGCTGTAAAAGTAGGCGATAGCTACTATGCCGCTACCCAGAAAAAAGACGGTAGTTTCAGTGTTAA +TACTACTTCTTACACTGATAAAGACGGCAACACTAAATCTGCACTGAACCAACTGGGTGGCGTAGACGGTAAAACCGAAG +TTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAGCTGGCTGAA +GCAGCCGCTAAAACCACCGAAAATCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGACCT +GGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCGCGTAGCC +GTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTT +CTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z10_Mbandakastr_AMRS01000012_other.z10__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTTGATAGCACTGGCGTTAC +TCAATCTCTTGATTTAAAAACTGCTGGAATTACTGGTGCTACATTAAAAGCTGGTATTACTGGTACAACGACAGAAACCG +GTAGCGTTAAAGATGGTAAAGTCTACTATGATGCAGATAGCAAAAATTACTATGTAGAGGTTGATTTTACTGATACTACG +GATAAAGCAGCGCATGCTGGTTTCTACAAAGCTGACGTCGATGCTGACGGTAATGTTTCTTTAGCAACTGGTGCGACTAA +AGAAGCAAAACCAACGAATGCAGTTGAAGTTGAAAAAACTATTGATGAAAAACCGCTGAAAGCATCAAGTAGTGTTCAGG +ATGCCTTAAAAGCGAGTGGTATTGCTGATGCGGTTGCAGAAGCTGCGACGGTAGTGAAAATGTCGTACACTGATAAGAAT +GGTAAAACTATTGATGGTGGATACGGTATTAAAGTAGGTGATGACTACTATGCTGCAACTAAAGAAAAAGACGGCAGCTA +TAGTATTAATAGTACTTCTTATACCGATAAAGACGGCAACACTAAAACTGCACTAAACCAACTGGGTGGCGCAGACGGTA +AAACTGAAGTTGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCACAACTTCAAAGCACAGCCTGAT +CTGGCGGAAGCGGCTGCTACAACTACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCTGCG +TTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTTCTG +CCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCTGGT +ACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_z4,z32_Salmonella.enterica_IIIa.41:z4,z32:-_AY353509_z4,z23__1266 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTATCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATTGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +TTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCAAAGATGCAAAAACCGGCGGTCCGGCTGCGGATAAATTAT +CTCTGACACAAGATGATAAAGGCAATTACTTTGTCAAAGATGATACTGCTGCAGCTAAATACTATGCAGCTACCGTAGAT +ACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAACCCT +ATCACGCGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGACCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAG +ATCTCTATGCTATCCAAACGTTAGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAAACT +ACGGAGGGCGCTGCCGTAGCCTTAGCTGCAAACGTCGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACTGTTGACGC +ATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATAACTAACCTGGGCAACACGGTAAATAACCTGT +CTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCACAGATTCTGCAGCAG +GCCGGCACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAGCGTCCTCTCTTTACTGCGTTAA +>fliC_z10_Salmonella.enterica_IIIb.28:z10:z57_AY353473_other.z10__1500 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATAACCCAGCGTCTGAACGAAATCGATCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACACCACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATGCGCTGAATGTGCAGAAAAAATATGATGTTGATAGTACCGGTGTTAC +TCAATCTCTTGATTTAAAAACTGCTGGAATTACTGGTGCTACATTAAAAACAAGCATTACTGGTACTACGACAGAAACTG +GTAGTGTTAAAGATGGTAAAGTTTACTACGATAAAGATAGTAAAAATTACTATGTAGAAGTTGATTTTACTGATACTACG +GATAAAACAGCGCATGCTGGCTTCTATAAAGCTGACGTTGATGCTGACGGCAATGTTGTTTTGGCGGCTGGTGCTACTAA +AGAAACAAAACCAACGAATGCAGTTGAAGTTAAGAAAACTATTGATGAAAAACCACTGAAAGCATCAAGTGATGTTCAGG +ATGCCTTAAAAGCGAGTGGTATTGCTGATGCAGTTGCAGAAGCGGCGACAGTAGTGAAGATGTCGTACACTGATAAAAAT +GGTAAAACCATTGATGGTGGATATGGTATTAAAGTAGGTAATGATTACTATGCTGCAACCAAAGAAAAAGACGGCAGCTA +TAGTATTAATACTACTTCTTACACTGATAAAGACGGCAATACTAAATCCGCACTGAACCAACTGGGTGGTGCAGACGGTA +AAACTGAAGTCGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGAT +CTGGCGGAAGCGGCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACG +TTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTG +CCCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGG +ACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z24_Salmonella.enterica_IIIa.53:z4,z24:-_AY353505_z4,z23__1281 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTAGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +TTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACAACGGGTGGCCCCGCAGCAGATAAAT +TATCTTTGGTAAAAGATGATAAAGGAAACTATCTTGTTAAAGATGTTACTGTCACTGCTACTCCTAAATATTATGCCGCT +ACCGTAGATAATAGTACTGGGGAAATTAGCTTTGATTCGGCTAAAGAAGTCACTTTAGCTGGTGGTGCTTCAACCCCAAG +TGCGGTTGATACTTTATCACGCGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGACCAGTCTTTAGTGAAATATAAAG +ATGATAAGGGTAAAGATCTCTATGCTATCCAAACTTTGGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCC +TCTGACGGTAAAACTACGGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCT +TAAAACCGTTGACGCATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACA +CGGTAAATAACCTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCTAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTA +A +>fliC_z38_Salmonella.enterica_Fresno_AY353487_z36,z38__1266 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +TGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTGAATGAAATCAACAACAACCTGCAGCGCGTGCGCGAACTGTCCGTCCAGGCAGCAAACGGCTCGAACTCTGATTC +TGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAGCAAACCGATTTTAACG +GGAAAAAAGTCTTAAGCCAGGATGGACAGTTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGTTTAGATAAATTAGATGTGACTAAAGGGATTGCCACAACCGTTAAAGAAGGTAC +GAAGCTTACAGCCGATTTTGCAGTTAAGGATGCCGATTTTGATGATAAATCAACTGGTACAAAAGTAACTGCAAACTTAG +AATTAAAGCAGGATAAATCCGGAAATTATTTTGCCTACGATAAAACAGCCAGTAAATACTATGATGCGACTGTAGATACT +GCTACAGGTAAAATAGAATTTACTTCTGGGACAGGTAAAGAGACAACGAAAGATACATCTAAACTTACGGATGTTACTTC +TTTGTCCAAAGAAGTAACGATAGATAGTGGACTTACGGATGATAAATCATTAGTAAAATACAAAGGGGATGATGGTAAAG +AACAGTATGCCGTTCAAACTCTTGATAATAAAGGTAATGCGACCTATAAGACTGCCGTTATAGCGCGTGACGGCAAAGTA +ACAGAGGGCACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGACGC +TTTCCGTAGCCAGTTGGGGGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACTTGGGCAACACCGTCAACAACCTGT +CTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATTCTGCAGCAG +GCAGGGACGTCCGTACTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23_Salmonella.enterica_Ajiobo_AY353493_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +CTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAGCAACTGGTGGTCCGGCTGCGGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGCGGCGGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGACTCCGCCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGTACTGCCGTAGACTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGGGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATTCTGCAG +CAGGCAGGGACGTCCGTACTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z_Salmonella.enterica_II.40:z:z42_AY353470_k,z__1500 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGATGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACTATCCAGGTTGGCGCCAACGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTGAC +CGGTGTTTCTACTTTGGATACTGCAGGACTTACTGGCGCAGCTATTAAAACTGGCGTTGATGGAGCTACCACTACGAGTG +GTTCCATTAAAGATGGCAAAGTATACTTTGATGATGCTACTAAAAATTATTATGTTGAAGTAGAGTTTTCTGATGCCGCT +GATACTGCTAAAAATGGCTACTATAAAGTCAATGTTGCTGATGATGGTACTGTTACAATGGGGGCTTCGACTACTAAAGA +AGCCGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCGTCTGTTGATGTGAAAG +CTGCTCTGACTGCTGGTGGCGTTGATACTGCTGATGCAGCTACGGCAGAAATGGTCAAAATGTCTTACACCGATAAAAAT +GGTAAGACGATTGACGGAGGTTATGCTGTAAAAGTGGGTGATAACTACTATGCTGCGACCCAGAAAAAAGATGGTAGCTT +TAGTGTTAATACCACGTCTTACATCGCAACTGACGGTACTACCAAAACAGCACTGAACCAACTGGGTGGCGCAGACGGTA +AAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAGCCAGAG +CTGGCTGAAGTAGCTACTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCGCAGGTTGACACATTACG +TTCTGACCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTG +CCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGT +ACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_l,z28_Salmonella.enterica_Javiana_AY353455_l,v__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACAAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAGGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAGTACCACTGGTCTTGATGATACAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCG +GTACCGCTGCAATTAAAGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAATTGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGTACTGTTACAATGCCGGCAACCGCCGC +GAAAGTGACAGGTGGCATACCAGCCACGGCGACTGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAG +TTAAAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGAT +AAAAACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGG +ATCGTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTAAACCAACTGGGTGGCGCAG +ACGGTAAAACTGAAGTTGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCACAACTTTAAAGCACAG +CCAGAGCTGGCTGAAGCGGCTGCTGCAACCACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGC +GCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGT +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATCCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCACAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_r,i_Salmonella.enterica_Hidalgo_AY353464_r,i__1476 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGACAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTCACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTC +CTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGAT +GGTGTTTATGAAGTAACAGTTGCAGCTGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTT +CCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCTAAAGCCGCATTGACAG +CAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTA +GCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATACTACGAAATACAC +TGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTATTGGTG +GTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCTGCTACAACC +ACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGTACAGAA +CCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCGAAGATTCCG +ACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATCCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCGAAC +CAGGTTCCACAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_k_Salmonella.enterica_IIIb.61:k:1,5_AY353539_k,z__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATGCGCTGAATGTGCAGAAAGCTTATGATGTAGATAGCAAACCAGCGCA +GAGCATTAAACTGGATACCAGTGCTCTTACTGCTACTGCAATTAAAAATGGTGTAACTGGTGCATCGACAGATGGTGCCC +TAAAAGACGGTAAAGTTTACTCTAATGGCACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGATACTGCTAAA +GGTGGTTTCCTTAAAGTAGATGTTGATTCCGCTACTGGTGCAGTTACCGTTCCGGGTACGGCAGCAACAGCAGCTGCAAC +TAAACCTGCCGGTGTGAAAGAGGTTACAGAAGTACAAGGTAAAATCCCAGCATCTACTGCTATTCAAGACCAATTGAAAG +CAGGCGGTGTGACTACTGCAGATGCAGCTACTGCTGAAGTTGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATT +GATGGCGGTTATGCTGTAAAAGTAGGCAATGACTACTACGCCGCTACTCAGAAAAAAGATGGTAGCTTTAGTGTTAACAC +TACGTCTTACACCGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCGAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCCGATCTGGCGGAAGCG +GCTACCACAACAACCGAAAACCCGCTGCAGAAAATTGATGCTGCGTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACTTGGGCAACACCGTAAWCAACYTGACTTCTGCCCGTAGCYGTA +TCGAAGATTCCGACTATGCGWCCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTG +GCGCAGGCTAACCAAGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23_Salmonella.enterica_I.47:z4,z23:-_AY353549_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +TGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTAAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACTGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +CTCTGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAACAACTGGTGGTCCGGCTGCGGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGTTACTGCGACGGCTAAATACTATGCAGCTACCGTA +GATATGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAGCTGCGGGGACTCCGTCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGTACTGCCGTAGACTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCCGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_f,g,t_Salmonella.enterica_II.1,40:f,g,t:z42_AY353535_g,m__1518 +ATGGCACAAGTCATTAACACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCTCAGTCCACACTGAGTTC +CGCCATCGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGTGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATTGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCCCCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATACAAAAGCTGGTAATGACGGTA +ATGGTACGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCGGCAGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAATGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGTGAAAGTAAGATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCTAAGAAAAGTACCGCTAATCCACTGGCTGCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCGCTGGGGGCAATTCAGAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCCGGTACCTCTGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23_Salmonella.enterica_IIIa.40:z4,z23:-_AY353496_z4,z23__1242 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGTGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATTGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +TTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAGCAACTGGTGGTCCTGCTGCGGATAAAT +TATCTCTGACAAAAGATGATACTGCTGCAGCTAAATACTATGCAGCTACCGTAGATACGACAACGGGTAAAATCAGTTTT +GATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAACCCTATCACGCGAAGTGAAATTTGATGG +AGCAGATCTAAAAGCCGACCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACGTTAG +ATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAAACTACGGAGGGCGCTGCCGTAGCCTTA +GCTGCAAACGTCGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACTGTTGACGCATTCCGTAGCCAGTTGGGTGCGGT +GCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACGGTAAATAACCTGTCTTCTGCACGTAGCCGTATCGAAG +ATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGCACTTCCGTTCTGGCGCAG +GCTAACCAGGTTCCGCAAAGCGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z24_Salmonella.enterica_II.1,9,12,46,27:z4,z24:1,5_AY353504_z4,z23__1281 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +TGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGTTGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAAGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +CTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACAACGGGTGGTCCCGCAGCAGATAAAT +TATCTTTGATAAAAGATGATAAAGGAAATTACCTTGTTAAAGATGTTACTGTCACTGCTACTCCTAAATATTATGCCGCT +ACCGTAGATAATAGTACTGGGGAAATTAGCTTTGATTCGGCTAAAGAAGTTACTTTAGCTGGTGGTGCACCAGCTCCGAG +TACGGTTGATACTTTGTCGCGTGAAGTGAAATTTGATGGAGCAAATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAG +ATGATAAGGGTAAAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCC +GCGGACGGTAAAACAACAGAGGGTACTACCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCT +TAAAACCGTTGACGCTTTCCGTAGCCAGTTGGGGGCGGTGCAGAACCGTTTTGAATCTGCTATCACTAACTTGGGCAACA +CCGTCAACAACCTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTA +A +>fliC_l,v_Salmonella.enterica_Give_AY353443_l,v__1503 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAATACCACTGGTCTTAATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAACG +GTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGACAACCACGAA +AGTGACAGGAGGCATGCCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAGTTA +AAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGCCAATTAGTTACGATGTCTTATACGGATAAA +AACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGGATC +GTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAGACG +GTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCACAACTTCAAAGCACAGCCA +GAGCTGGCTGAAGCGGCTGCTACAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCT +GCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATCCTGCAGCAGGCC +GGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>O-48_unknown-from-serveral-cdc-new-genomes__4477 +CTGCAGCAAGCTCCTGAAGCTTATCCCCACCTTGAGCACCAAATTTCCAATTTTGTAAAATGTTACTCTTAAAGTTGCTA +CAATAATCACACTCTCCACTATTATCAAAAACTATGTTAGGATCAGATGTATCCATAATACAATGGCTACAAACTTTATA +ACTTTGATTTTCCATGTTCCCCCCTATTTAAAATGACTTTCATAACAATTTCATTAATTTCTTCTGTTTGTACTACATGT +AATCCATGAAATAACACTAGTGTTCCCATTTCTTCATATTTATATGCAAGAGTTGATGGATATGAGATAACTACATCAAC +CTTAGGAAAAAAGTTATCGTCTATAATAAAATTGAATTTAAATTGCCTGACTTTTGAGGAAGCTCTTGCCTTAGGATGCT +CTTTATAATAAATAGAACAATTTTCAATTTGTTGATTAATTAGAGAGCAAATTTTTAGCTGACCTTTCTCACACAATGAA +TGCCCAATAACTAACAATGTTAGCTGGTTCGATGATACTTGAGTAAGGGACAACATAGGTTTACTATATTCCACCTTTAT +AATTTCGGCCAAATTATAATCCAGTATGTTGTTTATAAACAATTGAAATTCAACTTCATCGAAAACAATTATTTTATCCA +AATGCTTTAATTTATATGGTATCTTAAAAAGTAAATAGGCACTTGAATCAAGGGCTCTCAAAGATCCATGCTGGATAAGA +GTATATTGAATTCCTTTTTCTCCTAACATTGAATCAATCAGGACCGCCCAACGATCATAATGTTCACTACTTATAACCTT +TCCTTGTATTCTATTCATCACTAATGCGACAAGGAACCAAGATGGAGCTGTGTATATTTGCAGGCACCATTTGATAGTAT +GCTTCGATTTAAAAAAATAGAAAAACGCAAATATGCTTAGCAACATGCTTTTGAAAATATCTAAATACGAAGCCATCTCA +TAAATTGAAATAACTGTAGCATCACTTCTATCATTACACGATGATAATTTAATAACATTTAACTTTTTTCCATCCGAAAT +TTTACTATTATAATAATTAATTGCTTGCTCCGTACCTATTTCAGCGAATGAAAAATAGTAAAAGTCGCTTCTATCAATCA +ATTTATTTTTATCTGTAATTATTTTTTTGTATAATGCAACTATACATTTTAATATAGGATAAAATATAAACCCCCCTAAT +ATGAAGAAAATCATAAGAGAGATATATCCCCCCCACAATTTATGCCTCCCATATGCCCATTTGCTGATCCGAGGTAATGG +TGGTATTCTACCTTTCATGCCAGCGATCAACAATTTATCAATAGAGATTTCATTTTCCGTAGCTAACATATAGTAGCGTA +AATATGTTTTATAAGAAATTCTCATCCGACATGCCCGTCATTAATAATATGTAGACGCTCTAATTAATAATCAATTATTG +ACTTTTTTAGAGATATTTGTAACTAGTTAACATGAAAAATTCATATAAAAATGCTAAGTCATCTTCTTATTTATATTTTT +CTTGTTGACTAAATAAATTATCGATATAAAAATCATAACTGCTGACGGTGTAAAATACCCAGAACCTCTTAGCAAAAAAT +ATATTATGCTCATTATTAAAACTATACTAAAAAACTTTATTTTTTTGTCATTGCATTTAAACCGCATGACACCTAAAAAT +AATGTATAAAGAAAAAAAATGCCCCCTAAGATACCAAATTCAACAATCAATTTAGAAATAAATAGTCCACCATCATATAA +GTTAGAATCTGTATTCCCTCCCCTTAACCGCCCAATGATTGATACAAACTCTCCTCTTTCATTTGCATATCCCATATTTT +GTAAACCATAACCAAGGCCATAGCTATCTCGCAACGCTAGATATGCTTGTTCATATCCAGATAATAAAGTTAATGTTGAT +GTATTTTTCGATTCTTGGCTTATATCTAATCGTTGCGAATAATAACTTAGTTTATCAATAGGTAAGATTCCAGCAATCAG +CATACACGATGAAGATACGCAAATCATAATAATGAACATTGATTTAACTCTCATATAGTTTATAGCTATCGCTACAACAA +TACCTATAATCAATGTTAAATTCTGGACAATAAGAGCCGTAAATAAAAGAGGAATTCCATAGAGCAAATTTAATTTTTTC +TGAGATATCTTATAGCAATAAAAGATTGTAACTATTAGTGCATAATGAGAGGGCTCAGTAAAAAACAACATTTCCTTTGA +AGTGCTACTGCTTGATAATATAAAAAGAGATGACAATACCCCCAAAGCTATTAGTAATTTAAATAATTTTGATACTATTC +TATCAAACTCCTGGTGAGTAATATTATCAATTGCCACCGATGAAAAATAACATGCGAGTAAAATATAAAATAAGAATAAC +AATGATGTAATATTCTTAGTGAAAGTAGTATTACCATTCTGAAATAGTAGACTACTTAACCCAAAATGAAACAATATTAG +AAAAAAACTAATAACACTAAAAATTAAAAATGAATAACTTATAGTTAATTTATTAAAGCCAGAAATAACCACTAAAAATA +ATATTATAGTTGATATAAAGAAAATACCAATGAAATTCGAACCAACTTTATCATTTAACACCATTAACAGGCCTGGAACC +AGCACCATTCCATAAAAAAATATTGAGGTCAGAACTTTATTAGTATTAAATTGCATTATAGTTAAACCTTATTATTCCTT +TTAATTACAATAAAAAATTATATAGCATAAGTATTTTAATTTAAAACAATTAAACTTTTCGTACTTTTCGTAGTTCATGC +TTTTAATAATAAACTATGTATCTCACCGAGAAATTCGCTATAACAAACGTAACACTATGCATTTTATATCTATATAAAAT +ACAATAGGTAAGATATCATCTATTAGAATAAAATAAACTCTCGCCGGCAGATCGTCTAATTATAACCAAGAGTTTTATAA +ACATAGCCAGCTTTAAAAATAATAAAACTGAAAAAGAAATAATCATACCATAAGCAATGTAATTAATATTCGCGACCTTA +AGTGCAATATAAAGAAAAGATGAAAACAGTAAAAAAGTTAAACACTGGCTCCAGACTATCATTTTATCTTTTCTTAGTGC +ATACAGACCCAGATGTGGTATAAGGCTTAAACAATATATAAACGTCGCCACAATTAGCAACTGAAATAGTGGAAGTAATT +CCCAATATTCGATCTTTCCAATCCACTGAATGAGGATATAACCGGTAAAAAAACAACAAATACATAACAGAAGCGACACT +GCTATTAATTTGAATGCGAATGACTTCATTCCAGCGATGAATCCAATGTAGTCCTTTCGATAACACAATTTTGCCAATTT +TGGGAATGAAAAAGATATTAGGATCGTATCGAGGAAAGATTGTATAGCCGCCGTCATACTAATAAACAAAGTATATACAC +CAAGGATCTTTAGTCCAGCAATATGTTCAACGGCAAACCTATCAAATGTAAAAAAACCTCTGAGCGCCAAAGCGGCAATT +AGCATTGGTGCGGAAAGGATAATTCCTCTCATTATCCAGCGCCAGCTAAATGGCGATGTAAACTTCCGTTTATTATTTTT +TAGAATATAAAAAAAGCCCATTGCACTAGCACAGAATGTACCAAATAGCCATAATGTAAATACAATAAATAGATTTCTTG +ACGTAGGAAATAATAGCATAATGGCTATCACGAGCCAGCACCAAAGTCCTTGTCGTATAAACAACACAAGACTTGCGAAA +GCTTGATTCTCGAGAGTTATTAATATTCTATTAATTTCTTGAGCTATATGTTCAAAAAAGAGAATAGCAAGAAACCAGTA +CTCACTTCCGTGGGGAAGAAAGGAATAATGTTGGATAACAATAAAAATGGGGATATAAAATATATATGATAATACATAAA +AAAATGACTGATTTTTTAAAATAAAAAAAAGATCGTCACTTTTTGAGTTTATTATCTCTCTAGTACTATAAGTATAAAAT +TCAAATCCAATAGCAAAAATTGCGTAGCCCACAGCGGCGCTTATAAGACCATAGACTCCCAAATCTGATGATTGCAACAA +TTTTGCTAATAAAATTATAAACACAAACTTGCTTATCAAAGTAAAGCCACGTATACCTATACTTAAATAATATATAAAAA +GAGATTTTTTCATTTGAATAAGCCAATAATGCTTAAAAATATCGTTAACATAATATTAAAAATAGGCCATATACTAATAG +ATAGCTTTTTAGAAGTTTACAGATCATAGAATGCTTTGAAGCCTAGATTAGCAGGATCATTTGATAAAAATGCTTTAATT +ATATCCACAATTCTATCTTTTACATTTTCCATAAAATATGGGTTTTTAGAGCTTTCTAGCTTAGAAATAAAAACTTTATC +AGTCACACTCGAAATAGCTTCACGTATAGCATTTTTTTCACAAATAGTATCGACAACGCTTTCACCACGAATGCGCC +>O-4_wzx__1293 +GTGAAAGTTCAATTGTTAAAAATTCCGAGTCATTTAATTGTTGCAGGTTCATCATGGTTATCCAAAATAATAATTGCCGG +GGTGCAGTTAGCAAGTATTTCATATCTTATTTCTATGCTAGGTGAAGAGAAATATGCAATCTTTAGTTTGTTAACTGGTT +TATTAGTATGGTGTAGCGCTGTTGATTTTGGCATAGGTACAGGACTGCAAAATTATATATCAGAATGCAGAGCCAAAAAC +AAAAGTTATGATGCATATATTAAATCAGCATTACATCTAAGCTTTATAGCTATTATTTTTTTTATTGCTTTATTTTATAT +TTTTTCTGGGGTAATTTCCGCTAAATATCTTTCTTCTTTTCATGAGGTATTACAGGACAAAACCAGAATGCTCTTTTTTA +CCTCATGTCTGGTTTTCAGTTCTATTGGAATCGGAGCTATTGCTTATAAAATACTTTTTGCCGAATTGGTCGGGTGGAAA +GCTAATCTATTAAACGCATTATCTTATATGATAGGTATGCTCGGCTTGCTATATATATACTATAGGGGGATCTCAGTTGA +CATAAAATTATCACTAATAGTCCTGTATCTTCCAGTGGGTATGATTTCATTGTGCTATATTGTATATAGATACATAAAGC +TTTATCATGTTAAAACAACAAAATCTCATTATATAGCAATTTTACGTAGATCTTCAGGGTTTTTTCTTTTTACTTTATTA +TCGATAGTGGTGCTTCAAACAGATTATATGGTCATTTCTCAAAGGCTAACTCCTGCTGATATTGTTCAATATACAGTAAC +GATGAAAATTTTTGGTTTAGTCTTTTTTATTTATACTGCTATTTTGCAAGCATTATGGCCTATATGTGCTGAATTGAGAG +TCAAACAGCAATGGAAAAAACTTAACAAAATGATAGGTGTCAATATTTTGCTTGGCTCACTATATGTTGTTGGATGTACA +ATATTTATTTATTTATTTAAAGAACAGATATTTTCAGTAATAGCCAAAGATATTAATTATCAAGTTTCTATTTTATCTTT +TATGTTAATTGGCATATATTTCTGTATTCGCGTTTGGTGTGACACTTATGCAATGTTATTGCAAAGTATGAATTATTTAA +AAATACTTTGGATATTAGTACCACTACAAGCAATAATTGGTGGAATAGCACAATGGTATTTTTCTAGTACGCTTGGAATC +AGTGGAGTGCTGCTTGGCTTGATTATATCTTTTGCTTTAACTGTTTTTTGGGGGCTTCCACTAACTTACTTAATTAAGGC +AAATAAGGGATAA +>O-41_wzy__1221 +GTGTCGAAAAGTAATAGAATTTTAATCATTGCATTTTTGTTGTTATATATTATATCTGCGTTAATATCAATGTTTCAGAC +TTTAACGCAAAATAACTATCCAGGCGAATTAGAAGAGTTCACAAGGTCTATCTCTACTGTTGAAGTTATCCTGTTGAGCA +TGTTAAACATTATCTCATTCATACTTTGCTATTTTGTGTTTCTCGTGCTTTCTAGTTTTAGGCTTAAGCTTAATAAAAAT +ATCAACGTGATTTTTAATAAGACAAAAATTAATAAATTATTCTTTTTCTTATTAATTGCACAAATATTTTTTTTAGTAAC +AACGGGAGTAGGAAAAGTAACTACTAGTGCTAATGAAATTGCAACTTCCATTTACAGTCCTTTATTTTCTTTTCTGAAAC +CTGAGCCGTTTATATATTTATTTTTTCTGTATTTTAGAATGGATAAGAATTTCTCTTATAAAGGTAATATTCTGTTTACA +ATAAACATTGTATTATTTATTTTCTTTAAAATACTTCAAGGATGGACAAGTTTTCTTCTTATACTGTTTTTTTTAGAGAT +GTACGCGCGATACCGCCTAAAAAATAAAAAAATTATTTTATTGCTACCCCTGTTTATTATTTTTTTTGGTGGCTGGGTAT +ATCAGTATGCCTTTGTATTAAAAAATGAAATTCGTGGGAATGATGTGGCTCCTTTGAGTTATTACCAAGGGGTTGAACAG +TTAACATCTAGGCTATCAATGAATCCTGTTTCATTAGGTGCTTATGAAAATTACGATACTGTAGTACATCTATATCAAAA +AGAAAATAGAGTTTTTAAAGAATCTGGATCTTTATTGAGGCCAATACTACCTGCAGGTTTTATAAATAAAGATTTTAGAA +TACTCAATAATAATGTTATGACATCATTTTATCCAGACTTAAATCCATATACGAGCTCTGATTTTGGTGTTGTAATGTAT +TACAGCATATTGTTTAATTCTAGCCTACCTGGTTTTATACTGTTAACTATACTTACTATCCTGTTGTTTATTATAGCAAA +AATATATTTTGATTCTATGTCGTCTTATAATGGGCAATATGATATCTTACTTTTTTTTATTATTTTTTATTCATTTTATA +CAGTAAGTATAGAAAACGTATTTGGACAAGGGTTCTTTCCATACATATTTAGTACTTTATTTTTTTTCTTAACTGGTTGT +ATCAAATTTAGCCGAAGGTAA +>O-41_wzy-from-Waycross-SRR1233896__1221 +CTATCTTCGGTTAAATTTGATCCCACCAGTTGCGTAAAAAAATATAGTACTAAATATGTATGGAAAGAATCCTTGTCCAA +ATACGTTTTCTATACTTACTGTATAAAATGAATAAAAAACAATAAAAAAAAGTAAGATATCATATTGTCCATCATAAGAG +GACATAGAATCAAAATATACTTTATCTATCAAAAACAACATTATAGTAAGTATTGTTAACAGTATAAAGTCAGGCAAACT +GGAATTAAACAATATACTGTAATACATAACAATACCAAAATCAGAACTCGTATATGGGTTTAAATCCGGATAAAATGATG +CCATGACATTATTATTAAGTATTCTAAAATCTTTATTTATAAAACCTCCAGGTAGTATTGGTCTCAATAAAGATTCCGAT +TCTTTAAAAACTCTATTTTCTTTTTGATATAGATGCACAACCACATCGTAATTTTCATATGCACCTAAAGAAACAGGATT +CATTGATAGCCTGGATGTTAGCTGCTCAACTCCCTGGTAATAACTCAAAGGAGCAACATCATTCCCACGAATTTCGTTTT +TTAATACAAAGGCATACTGATATACCCAGCCACCAAAAAAAATAATAAACAGGGGTAATAATAAAATGATTTTTTTATTT +TTTAGCCGATATCGAGCGTACATTTCTAAAAAAAATAGTATAAGAAGGAAGCTTGTCCACCCCTGAAGTATTTTAAAAAA +AACAAACAATAGTATATTTGTTGTAAATAGAATATCGCCTTTGTAAGAGAAATTTTTATTCATTCGGAAATATAGAAAAA +ATAAATATATAAAAGGCTCTGGTTTTAGAAAAGAAAATAAAGGACTGTAAATCGAAGTTGTAATTTCGTTAGCATTAGTA +GTTACTTTTCCTACTCCCGTTGTTACTAAAAAAAATATTTGCGCTATTAATAAAAACAAAAATATCTTATTGATTCTTCT +CTTATTAAAAATCACACTGATATTTTTATTAAATTTAAGTCTAAAGCTTGAAAGCACGAGAAACACGAAGTAGCAAACTA +TGAACGAGATAATGTTTAACATGCTCAATAGAATAACTTCAACAGTAGATATAGATCGTGTGAATTCTTCTAATTCTCCC +GGATAGTTATTTTGCGTTAAGGTCTGAAACATTGATATTAACGCAGATATGATATACAACAGCAAAAAGGAAATGATTAA +AGTTCTATTACTTTTCGACAC +>O-16_wzy__1233 +ATGAATAACCAAGATTTAAAAATTGGTACTGCATTTATTTCAATGATTTATTTTCCCTTGGGATTTTTGGTATCACTTAT +TGAAGTAATTAATGGATATAGGTGGGGAAACTTTCTATTCGCATTTATCTTGGGTCTATTAGCATTCTCACTAATACCGT +ATAGTGATTGGGATCTAACAAGACATTATGAAACCTATTTAAGTTATAATAATACCTCTTTTAGTGAAGTATGGGAACAA +AGTGATAATCGATATTTAGTAATAAATACTATAATTTATCTATTTAATACTTTCGCTATCAAAAAGGAGTTTTTACCGTT +CTTTGCTGTTTTTATATCTTATTTGTTTTACTTAAATGTATTTTCGAAATTTATTAGAGAAAAAAAGCCTAATATTTTAA +TCCGAAGCATCTATTTATATATTTTATTAACGGTAATACCTTTTTTTGCTATAGCTAGTTCACTACGACAATATTTAGCC +TTCAGTATTATATTATATATAATAATTACCTACTGTAGTAAGCAAGATAGACGTACTTTCCTTATATCTTTCCCACTAGT +TGTTATGGCAATAGGAATACATCCAAGCGTAATTCTGTTAATAGCACTGTTTCTATTTAGCAGATTTATACGCCTAAATC +GAATAGTTGTGCTTCTTATTTTTTTCATATTAGTTCTAAATTTTAATGGTTATATTTCAATACAATTATTCAAGCTATTT +AAACCATTATTAATGAATACAGGTTTTTATTATCCGGAATATATGGATGCAGAGGTTATTCATATGAATAACCAACTATT +AAGCACGAATGAATTTATACTTAATAAATTGATTTTACCCAGTATATTTTATTTGTTAATCCCAGTCTTTTTGATTTTCT +ATAAAAAATCAAACAGTAAACAGGAAAAGCAACTAAAAAACTATTGCGCACTACTCCTTTTGACTATATGCCTGTTATCT +TTATCACCTGATCTTTTTTATCGATTTTCAATATTTTGGACATTATTCTATAGCTATATATATTTCACTTATGATAGTGA +GAGAATGAGTTTGCCTGCCAAACAGTGCTATCTTGTAATTATAATTGTTGCATCATGTGTCATAAACTTAGCTCAAGCTA +ATATGGGCAAGAAAATCATATATAATTCATGGGGATCATTTTTTTACCAACCTTCACTATTCGTGTTTGTTAAAGAAATC +AAAACGACTGACTATATAAATGTGAGCCAATAA +>fliC_m,p,t,u_Salmonella.enterica_Haelsingborg_AY353409_g,m__1527 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGGTATGATACCTATGCTGTTGGTGCCAATAAATATCGCGTGGATGTCAACTCAGGGG +CGGTAGTAACTGACACCACTGCTCCAACTGTTCCTGATAAAGTATACGTAAACGCTGCAAACGGTCAGTTGACAACTGCC +GATGCGCAAAATAACACCGCGGTTGATTTGTTTAAATCTACTAAATCTGTTGCAGGTACTGACGATGCCAAGGCTATCGC +AACTTCTATCAAAGGCGGAAAAGTTGGTGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATATAAAAGCTGGTG +ATGACGGTAATGGTACGGTTTCTACTACCATCAATGGTGAAAAAGTTACATTAACAATTAGTGATATTAGCGTGGGTGCA +GCAGACGTAAATAGCGCGAAGATTCAATCAAGTAAAGATGTTTATACTTCCGTTGTAAGCGGTCAGTTTACTTTTGCTGA +TAAAACCAAAAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAA +ATGGGGCTGAATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCT +TCTGGCGTAAGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTC +TGCATTGTCAAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTG +GCAATACGGTAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCC +AAAGCGCAGATCCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACT +GCGTTAA +>fliC_k_Salmonella.enterica_IIIb.17:k:z_AY353437_k,z__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACTATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACCATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATGCGCTGAATGTGCAGAAAGCTTATGATGTAGATAGCAAACCAGCGCA +GAGCATTAAACTGGATACCAGTGCTCTTACTGCTACTGCAATTAAAGATGGTGTAACTGGTGCATCGACAGATGGTGCCC +TAAAAGACGGTAAAGTTTACTCTAATGGCACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGATACTGCTAAA +GGTGGTTTCCTTAAAGTAGATGTTGATTCCGCTACTGGTGCAGTTACCGTTCCGGGTACGGCAGCAACAGCAGCTGCAAC +TAAACCTGCCGGTGTGAAAGAGGTTACAGAAGTACAAGGTAAAATCCCAGCATCTACTGCTATTCAAGACCAATTGAAAG +CAGGCGGTGTGACTACTGCAGATGCAGCTACTGCTGAAGTTGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATT +GATGGCGGTTATGCTGTAAAAGTAGGCAATGACTACTACGCCGCTACTCAGAAAAAAGATGGTAGCTTTAGTGTTAACAC +TACGTCTTACACTGCAGATGACGGTACATCCAAAACTGCACTAAACCAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_e,h_Salmonella.enterica_Newport_AY353379_e__1509 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTATCAGCAACTGCTGCAAT +GGATCCGAAATCATTTACTGACGGTACTAAAAATCTTACAGCGCCTGATGCTACTGCTATCAAAGCCGCGTTGGGAAATC +CCGCGGCAACAGGCGATTCCTTGTCTGCTACGCTTTCGTTTAAAGATGGTAAGTATTACGCCACTGTTGCAGGGTATACG +AATGCTGCCGATACCAGTAAGAATGGTAAATATGAAGTGAATGTTGATAGTGCGACAGGTGCGGTAACTTTCAATGCAGC +ACCAACTAAAGCCACAGTAACTGGGGATACAACAGTAACCAAAGTACAGGTTAATGCTCCTGTTGCAGTCAGTACTGATG +TTAAAAAAGCGCTAGAAGATGGTGGCGTTTCAAATGCGGACGCTACCGCAGCTAAATTAGTAAAAATGTCTTATACCGAT +AAAAATGGAAAATCTATTGACGGTGGTTATGCGCTTGAAGCCGGTGGCAAGTACTATGCTGCAACCTATGACGAAGGTAC +AGGTAAAATCACAGCTAATGTAACCACTTATACTGATTCCACGGGAGTCACAAAAACTGCGGCTAACCAACTTGGTGGCG +TAGACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCTAGTAAAGCCGCTGGTCACGATTTCAAAGCG +CAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGA +TGCGTTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACT +TGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATCCTGCAG +CAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>O-63_wzy__945 +ATGATAAACAAAAATCGATATAAAGGCTATTATTTAATTCTTTCGTTTTTTCTGACATTAATTTTTGCACTTCGGTTTTT +TTATTTTTCCCATTATGAGATATTATTGGTCAGTGATACCTTAGAGTATTATAATAATTTTTCTGATATCGAAAATGATT +TATTCCCATATGGCTTAGAAATATTGATGCCAATTTTAATGTTTTTTATAAAAGCGATAGGGGGAAATTTTTATGACTTT +TTATTCTTTGTTTTAACACTATGGCTCCCGTTGATTTTTATTATTATTTATAGAAGTTGCTATAACCCATTATTTTTCAT +AATAGTTTTTATTTCTTCGTTCTTTTATATGAACGCTGTATTAATTATTAGGCAATATATTTCTGGGGTTTTTTTTATTT +ATTGTATGCTTTTTGCGTATCAACATAAAAAGATATCCTTATTTTTAGCATTTTTATCAATCTTATCTCATTCCTATGCA +ATAGTATGGTTAATAGTTGTCGGACGTTGGTTTAGAAATTTTATCACCAATAAAATTATTTTAAGTGTTATTATACCAAT +ATCATTATTTGCTGTAAGCTTCTCATTTTCTTCTTATCAATTGCAGTCAGTTTCTTCCTTTCTCCTCCAATACAATATGC +CAGGTTTGTTACAAAGGAAAATACAATATTATAATAATAATAATGATCCTGTAGAGTCAGTTTCAAATATAAGTTTGATT +CTTGTTGATATTATATTTATATTAAGTATAATAAACCTTTTGAAACAAAAAAATGAATTTGTTTTAAAGTTATCATCTCT +CCTAATTTTTAATTCCTTTTGTTTCATTATGCTTGGTTCAAATATTGTTTCAGCGAGTCGTTTTGGCTTTTGGTCATACT +ATTTTTCAATACCTTCATTAGTAATACTATTGTATTATTGTCTTAATCTTGTTAAAGATAAATAA +>O-9,46_wbaV__1002 +ATGAAGGTATCATTTTGTATCCCAACGTATAATCGAGTAAAATTCATTGAAGACCTTCTTGAAAGTATTAATAATCAATC +TTCTCACTCCTTAATTGTAGAAGTATGTATTTCAGATAATGCATCAACTGATGGAACTGAAGAGTCAATAAATATCTGGA +GAGATAGATTTAATTTTCCAATTTTGTATCAAAGGCATAACGAAAATATTGGGCCAGATAGGAATTATTTATCTGCAGTT +AATATGGGGACTGGAGATTATTGTTGGATTTTCGGAAGTGATGATATTCTTACAAAAAATTCCCTTGCATTGATGGAAGA +TAAATTGGCTGCCGGAAGTGGCATTTATTTATGTGACAGACGAGAATTAGATATTTCAATGACGAAAATATCTAATCCAC +ATCGGCGATGGTTAAATGGTGGCAGTAGATTATTTTCTTTTAGCAATGAAGCTGATTTGATAGAGTACTTTAGTAAATGT +AACTCAGTCGGCGGACTTTTTAGCTACTTAAGCTCTATTATAGTGAAAAGGAATAAATGGTCTGACGTCATATTTGACGA +GTCATACATTGGTACAGCTTATGCGCATGTATATATTTTATTAAGAATAATTAACAATATGAATTCGACCCTGCAGTACA +TATCACTGCCACTGGTTGATTGCAGAGGAAATAACGATACATTCGAAAGTAATGGGAAGGCTCGTCGAATAAAAATTGAT +TTCATCGGTTATTTAAAACTGAGGGAGGATTTTTATAATAACAATACAAAAATATATATCTCATTTGGACGGGTTCTTAC +AAAAGAGCGTCCTTGGTTTTATACTTCTTTAGCTATGGCATGTTATGGTGATTCCACCGATAGGGCTGAACTTGCATCAT +TTTATAAGAAGTTGGGATATCCGAAAATAGCCACCAATTTAATATTTCGTCTTAAAGGGCTGGCTAGCTACACTAAAAAA +ATAAAATTAGCAAAAATGGTAATAAAAAAAATATTTTCATAG +>O-65_wzy__1125 +ATGGTAATCTATCTGGTTCTTCTTATTTTTATTTTTTCTTTCTCTATAGTGATGATGTTAAATCCTTCGAAAAGGACTGC +TAACAAATTTTTAGGCATATATGTATTGTTGCTATCACTATTTGCAGGTTTAAGATTTCATACTGGTTGGGATTGGGAAG +CGTATGATTATTTTTTTAATCTATTAAATCAAGCTAACATTTATGATTTTTTTAGTTACAATATATTTAACTATGAACCC +GGTTTTGTATTACTTTCATATATATCAATATTATTAAATATTCCACCTTTTCTGCTTTTTGCTATAATAACTGTATCTCT +CATCGTATCCTCTGCTCATAAATACTTAGGTAAATTTGTCCCCTATATATTTTGTTTGATTTATCTGTATTATGGTTATT +TTCATAACTTTTCAATAGTACGACAAGGAATAGCAGCTGCTTTATTTGCTTACTCTATTCGTTTTCTTATTGTTAGGAGT +TACAAATTTTATTTTGTCATAATTTTTGCTTCGTTATTCCATATATCAGCAGCCATGTTACTAGCTATACCGTTACTCCT +TGTGATAGCTAATCGGGTTCCGTTTTTTTTACTACTGCTATTATCTATATGTATGGTTCTTTTGCCTTTAAGTGATATGC +TGGGCTTAAAATCATTAATGTCTAAAATACCGGCATTAAATATTTACCTAAATAATAGCACGTTAAGTTACAAAGTCGGA +TTTTCATTAAAATACCTAGAGTTGCTAATTGTATTTTATTGTTATTATGAAAGAAAGTTTTTTTTGCCACTTATAAATAA +TTTTGGAATAAGACAGTTTTGGATCTTTAAAGGGCTCATTATAATTGAGCTGATGATTTATTCTATTTTTAATGATTATA +GTATCATTTATGAAAGATTGAGTGTATATTTTGAATTTTCACACGCTATCGCAATAGCAATGATCGTTTCAACTTTTAAA +TATAAAAGAATACAATTTTTTCTAATGCTTATATTGCTTTTTTTTGTATTTGCAAGATACTATCAATTAGTTTATTCCCC +TGTCCGAGTGCCAGGCGAAATGTCACATCTTGAACGATTCGAAAATTATTGTTCTATTTTTAACGAAAGAGAATGCCAAA +GGTAA +>fliC_i_Salmonella.enterica_IIIb.57:i:e,n,x,z15_AY353432_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCAATACTGCGATTGCTTTAAACAATGGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACAG +ACCAGCAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TGCAGGTGGATTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCCAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGCTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCCAGCAAAGCCGAAGGTCACAACTTTAAAGCACAGCCCGATCTGGCGGAAGCG +GCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_l,w_Salmonella.enterica_Ayton_AY353446_l,v__1503 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCACAGGACAACACCCTGACCATCCAGGTCGGCGCGAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAATACCGCTGGTCTTAATGATACAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAACG +GTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCACTAA +AGTGGCAGGAGGCATGCCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAGTTA +AAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGATAAA +AACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGGATC +GTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAGACG +GTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCACAACTTCAAAGCACAGCCA +GAGCTGGCTGAAGCGGCTGCTGCAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCT +GCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCC +GGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_m,p,t,u_Salmonella.enterica_Haelsingborg_AY353410_g,m__1527 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGGTATGATACCTATGCTGTTGGTGCCAATAAATATCGCGTGGATGTCAACTCAGGGG +CGGTAGTAACTGACACCACTGCTCCAACTGTTCCTGATAAAGTATACGTAAACGCTGCAAACGGTCAGTTGACAACTGCC +GATGCGCAAAATAACACCGCGGTTGATTTGTTTAAATCTACTAAATCTGTTGCAGGTACTGACGATGCCAAGGCTATCGC +AACTTCTATCAAAGGCGGAAAAGTTGGTGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATATAAAAGCTGGTG +ATGACGGTAATGGTACGGTTTCTACTACCATCAATGGTGAAAAAGTTACATTAACAATTAGTGATATTGGCGTGGGTGCA +GCAGACGTAAATAGCGCGAAGATTCAATCAAGTAAAGATGTTTATACTTCCGTTGTAAGCGGTCAGTTTACTTTTGCTGA +TAAAACCAAAAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAA +ATGGGGCTGAATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCT +TCTGGCGTAAGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTC +TGCATTGTCAAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTG +GCAATACGGTAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCC +AAAGCGCAGATCCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACT +GCGTTAA +>fliC_b_Salmonella.enterica_I.6,7:b:z33_AY353361_b,d,j__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCAGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGCTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACTTTAAGTGTACAGGATGCCTATACGCCAAAAGGTACCGCTGTTAC +CAGAGATGTTACCACCTATAAAAATGGTGGTACTACTCTTACAGCACCTAACGCAGCAGCAATTGATACCGCTTTAGGTA +CGACTGGTGCGGCGGGTACTGCGGCTGTGAAATTTAAAGACGGTAACTACTTCGTTGAGGTGACCGGTACAACTAAAGAT +GGTCTGTATGAAGCGACAGTTGATGCAGCTGGCGCGGTGACAATGACCGCAAATAAAGCAACAGTAACTGGGGCTAGTAC +AGTTACTGAAAACCAAATTGTAGACGCTGTTACACCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATG +CAGGTGTGACAGGTGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCG +GGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAAACTGGTGAGATAAAAGCTAAAACTGT +AAATTATACTGACGCTACTGGTGCGACAAAAACCGGTGCTGTGAAATTTGGCGGTGCGAATGGTAAAACTGAAGTTGTGA +CCACCGTTGATGGTAATACTTATCAGGCTAGTGATGTAAAAGGGCATAATTTCCAGAGTGGTGGCGCTTTAAGCGAGGCT +GTAACCACTAAAACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAAGTTGATGCGCTGCGTTCTGACCTGGG +TGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACTTGGGCAATACCGTAAACAACCTGTCTGAAGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCCCGCGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_c_Salmonella.enterica_Choleraesuis_AY353364_other.c__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACTCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTAGATACGCTGAATGTGCAGAAAAAATATGATGTGAGCGATACTGCTGTAGC +TGCTTCCTATTCCGACTCGAAACAGAATATTGCTGTTCCTGATAAAACAGCTATTACTGCAAAAATTGGTGCAGCAACCA +GTGGTGGTGCTGGTATAAAAGCAGATATTAGCTTTAAAGATGGCAAGTATTACGCGACTGTCAGTGGATACGATGATGCC +GCAGATACAGATAAAAATGGAACCTATGAAGTCACTGTTGCCGCAGATACAGGAGCAGTTACTTTTGCGACTAGACCAAC +AGTGGTTGACTTACCAACTGATGCAAAAGCAGTTTCAAAAGTTCAACAGAATGATACTGAAATAGCAGCAACAAATGCGA +AAGCTGCATTAAAAGCTGCAGGAGTTGCAGATGCAGAAGCTGATACAGCTACTTTAGTGAAAATGTCTTATACAGATAAT +AATGGCAAAGTTATTGATGGTGGGTTCGCATTTAAGACCTCCGGTGGTTATTATGCAGCATCTGTTGATAAATCTGGCGC +AGCTAGCTTGAAAGTTACTAGCTACGTTGACGCTACCACTGGTACCGAAAAAACTGCTGCGAATAAATTAGGTGGCGCAG +ACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGGCACAACTTCAAAGCACAG +CCAGAGCTGGCGGAAGCGGCTGCTACAACCACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGC +GCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGT +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z36_Salmonella.enterica_Weslaco_AY353483_z36,z38__1266 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCAAACTCTGACTC +TGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATTGCTACAACAGTTAAAGAAGGTAC +GAAGCTCACTGCCGATTTTGCAGTTAAGGTCGCAGATTTTGATGATCAAGCAACAACTGGTAAATTAACTGCAGACTTAG +AATTGAAGCAGGATAAATCCGGAAACTACTTTGCCTTCGATAAAGCAAACAGTAAATATTACGACGCAACTGTGGATGCT +GCTACAGGTAAAATAGAATTTACTTCTGGGACAGGTAAAGAGACAACGAAAGATACATCTAAACTTACGGATGTTACTTC +TTTGTCCAAAGAAGTAACGATAGATAGTGGGCTCACGGATGATAAATTATTAGTAAAATACAAAGGGGATGATGGTAAAG +AACAGTATGCCGTTCAAACTCTTGATAATAAAGGTAATGCGACCTATAAGACTGCCGTTATAGCGCGTGACGGCAAAGTG +ACAGAGGGTACTGCCGTAGCCTTAGCTGCAAACGTCGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGACGC +TTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAGTCTGCCATAACTAACCTGGGCAACACGGTAAATAACCTGT +CTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGCACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAGCGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23_Salmonella.enterica_IIIa.44:z4,z23:-_AY353497_z4,z23__1275 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +TTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAACAACTGGTGGTCCGGCTGCGGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTACTACTGGGGCGGCTAAATACTATGCAGCT +ACCGTAGATACGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGACTCCGCCAGCAGT +AACTACCTTATCACGCGAAGTGAAATTTGATGGAGCAGATTTAAAAGCCGATCAATCTTTAGTGAAATATAAAGATGATA +AGGGTAAAGATCTCTATGCTATCCAAACTTTGGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGAC +GGTAAAACTACGGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAAC +CGTTGACGCATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACGGTAA +ATAACCTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATT +CTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z_Salmonella.enterica_II.16:z:z42_AY353469_k,z__1500 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACGCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTGAC +CGGTGTTTCTAATTTGGATACTACAGGTCTTACTGGCGCAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACGAGTG +GTTCCATTAAAAATGACAAAGTATACTATGATGATGCTACTAAAAATTATTATGTTGAAGTAGACTTTTCTGATGCCGCT +GATACTGCTAAAAATGGCTACTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCCTCGACTGCTAAAGA +AGCCGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCGTCTGCTGATGTGAAAG +CTGCTCTGACTGCTGGTGGCGTTGATACTGCTGATGCAGCTACGGCAGAAATGGTCAAAATGTCTTACACCGATAAAAAT +GGTAAGACGATTGACGGAGGTTATGCTGTAAAAGTGGGTGATAACTACTATGCTGCGACCCAGAAAAAAGATGGTAGCTT +TAGTGTTAATACCACGTCTTACATCGCAACTGACGGTACTACCAAAACAGCACTGAACCAACTGGGTGGCGCAGACGGTA +AAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAGCCAGAG +CTGGCTGAAGTAGCTACTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCGCAGGTTGACACATTACG +TTCTGACCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTG +CCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGT +ACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_l,w_Salmonella.enterica_Glidji_AY353447_l,v__1503 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATATCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAATACCGCTGGTCTTAATGATACAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAACG +GTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCACGAA +AGTGACAGGAGGCATGCCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAGTTA +AAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGATAAA +AACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGGATC +GTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAGACG +GTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCACAACTTCAAAGCACAGCCA +GAGCTGGCTGAAGCGGCTGCTACAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCT +GCGTTCTGACTTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCC +GGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_y_Salmonella.enterica_Freetown_AY353466_other.y__1521 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGACAGGCAATTGCTAACCGTT +TTACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTTGATAACACGGCTGTCAC +GAACCCTAATTATGTTGATGGTGCAGCGTTAAGCACTACGATGCCTACTGCGGCTGAGATTAAAACGGCTATTGGCACTG +GTGCGGGAACTCCGGCAGTTAAAGGTAATGAAGTTCAATTTGATAAGAGCACTGGGAAGTATTACGTTGAAATTGAAGGA +TATTCAGCTCCTGATGCAGCTAAAAACGGCATTTATGAAGCCAAAGTTGCTGATGATGGCACAATATCTTTGGAGACTGG +GACCAAAAAAATTGGCACCGCAATGCCTGCTGGTGCTGAAGTTATTACTCACGTGCAGAAAAAAGATCAACCAGTTGTTG +TTGATGCCAGCGTTAAAGATGCTCTAAAAGCTGGTGGGGTAGATGATGCAGTTGCAGATACCGCGCAATTAGTCAAAATG +TCTTACACTGATAAGAATGGTAAAACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGCAAAACCGAAGTTGTTACTATCGATGGTAAAACCTATAATGCCAGCAAAGCTGAAGGTCAC +AACTTTAAAGCACAGCCTGAACTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCT +GGCGCAGGTTGATGCGCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTA +A +>fliC_b_Salmonella.enterica_from-cdc_Stk1415_b,d,j__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTTTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGCGTGCGTGAACTGGCAGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACCCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACTTTAAGTGTGCAGGATGCCTATACGCCAAAAGGTACCGCTGTTAC +CAATGATGTTACCACCTATAAAAATGGTGGTACTACTCTCACAGCTCCTAACGCAGCAGCAATTGATACCGCTTTAGGTA +CGACTGGTGCGGCGGGTTCTGCGGCTGTGAAATTTAAAGACGGTAACTACTTCGTTGAGGTGACTGGTACAGCTAAAGAT +GGTCTGTATGAAGCGACAGTTGATGCAGCTGGCGCAGTGACAATGACCGCAAATAAATCGACAGTAACTGGGGCTAGCAC +AGTTACCGAAAACCAAATTGTAGACGCTGTTACTCCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATG +CAGGTGTGACAGGGGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCA +GGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAAACTGGTGAGATAAAAGCTAAGACTGT +AAATTATACTGACGCTACTGGTGCGACAAAAACTGGCGCTGTGAAATTTGGCGGTGCGAATGGTAAAACTGAAGTTGTGA +CCACAGTTGATGGTAATACTTATCAGGCTAGTGATGTAAAAGGGCATAATTTCCAGAGTGGTGGTGCTTTAAGCGAGGCT +GTGACTACTAAAACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTA +TCGAAGATTCCGACTATGCGACTGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAACAGGCCGGTACTTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>O-42_wzy__1017 +ATGCCAGTAAAAACTAACAACTTTCTTTATTTCATAATGGTCATAAGTGCTACCATTTTTGCTGTTAAAATAGTGCCTTA +TTCGAATGACTATCAGGCATATATTGATTTATTCAAATATACAATTCAAGATCCTTCTTACGAGAGAATGGAAATTGGCT +TTAAAAACCTTATTGGTTTTTCAAAATTTCTTGATTTGAATTTTGATGTATTATGGTTTTTAGTTGCTTTTATTTCTTTG +TCGCTAAAATGTTATGTATTAAAATCCTATGATTCAGATATCCTTGTATTATTTTTGTTGTACTTTTTGTACGCTATATC +ATTATTAGCTTTACACGAAACCACACAGATACGAGCGGCTATTGCAATTGCTTTAGGTATAGCAGGCTTTCGATGTACGA +ATAAATTTGTTGGTATCTGTTTAATCCTTTCTTCTGTATTATTTCACTATTCAGCAATTTTATTTATTATTTTGTATACT +TTGAGCTTTATAGTTAAACCGTATAAGTTCACATGGTTAATAGTTGTTGTTACTATGGCGATACTAATACCCTTGCTTCT +GGAACAATACTCAGATCCATTAATTAGTATTAATCCATTATTTTCATTATATTTAGAAAACTCTGATAATGCCAAGGTAA +ATAAATTTTCTTTTACTTTAATTCTTGCTACAATATTTTTTGTAATAAATTTTTTTATTGGAAGAAAAATTAACTATTAT +AGCAATAATAATTTCATATTTAAGCAATATAATCTTTTTTCTTTTCTTTATCTTTCTAGCGTAGTACTTTTATCTGCGTT +GTCTTTTTCGCCAGTCATTTCAATAAGATTATATGAGTTATTTTCGTTAAGCCCTTTTATTATTATCGCATGCCTTTATT +CTAAAAGTATGAAATACGTTTTTTATTCTAATATAAATTTGCGCTTGCTAAGAAGAGTTTTGCTTTTAACATTATGGCTA +ATCTCAGTGCATCGCTTTATTGCTTATTACTTTGTTAATCCAATCATTAAATTTTAA +>O-47_wzy__1095 +ATGATTGAAGGATATGTAGTATATAATAGTATTTTTCTTCTTGCCTTACTATTTGGCTTTATGAAGAATTACTGTCTTCG +GAAATATTTTTTATTATGCTTATTCCTTGTCTTATGGGTTCCACTTGCCACTCGTTATGGCATTGGTCGTGACTATTTTA +GCTATGTTGATATTTATAAAAATGTGTTAGTTACCAGAGATGGTATTGAAGTAGGTTTTTATTATCTAAATTATCTGTTG +GCATATTTTGGTTTCCATTATCAATCTATATTTATATTGACATCTTTTATTACTGTCTATTTAAGTGTTAAAAGTTTTGA +TAGAGAATATACAATAGTATCAATTATATTATTTGGGGTTTTGGTTTACTTACAGGCGTTTAGTATTGTTAGGCAAATGC +TTGCTGTAGCCTTATGTCTTTATAGCTGTTCGTTATGGAATAAAGGTGTTAAGGTTAAAGCAATTATTTTTCTTATGCTG +GCACCTTTGTTTCATTATTCTGCTGTAATAATATTTATATTGGCAATAATTAGCAGATGTGTTAAAATCGATACGTTTAA +ATGTCTTGCTATGTTAGGGCTTAGCCTTATTTTTGTTTTTGTATTTAATGGGATCGATTTTATATTTTCAAATCCTATAC +TATTAAATAGTAAGTATGGATATTATGTAACATCAGCCTTTAACAGACCGACTGAAATAGGTTCAGGCATTGGAGTGGCA +ATAGCATTATTTCTTCCATTCTTGATTTTTATGAAAGCATCAAAAATATATAAACATAATAAAAATTATAATCTGATGCT +ATTAATAAACCTTGTATATGTTGTTTCATTTGTTTTATCTTTGAAAATATATATATTCGCCAGATTCACTGATGCGCTAT +CCTTTGTCCTGATATTACTTATCCCTGCTGCTCTTAAAATATCAAATACTAGAGGCCTATATTATAACTGTATGTTATCT +GTTGTTATTCTTCACATTATGCTATTTGAAGTAAATCTTAAAGCAAATACAATTGCAGCTGGAGATATGTCTAATAGCGG +GCTTGGAATCATGCCGTATAGCAACATAATAAACGCACATATGCTAAAATACTAG +>O-39_wzy__1341 +ATGCCTATAGCTGTACATTTGATTGAGCTAGCATATGTATTAATAATAATATCATTTATTATCTTGTTTTACATGAAAAA +TGTCCCATTATTAGAGGGAGGGTTTTTATTACTTATTATTTGTTCACCTTACTCTATTTCAATTATACCATTTAGACAAG +ATACAATAGAACTCTATGGATTGTATAGTAATAGCGGGCTTCTTAATTTATTTAATTTTTACAAAGTAGCCGGCTTATCT +ATTTTAGATCTAATAGCATTACTAGTTATAGTGAAAAACTTTAAATTAGCATTGAAGATGCCAATCTTTTTTAAGTTTTT +TTATATACTAATAAGTTTTTTTTCAATAATAGCTTATGCAATATCAGCTTATTTAATATGGTCTCCTGAACTAGATAATG +TAATTCGCGCTTTATCTGTCTTCAAATCAATTATATATATAATAAGTATTTATTGTGTTATTGAGAAAATTTGTTCACGT +ATTGGTTTTAAATTATTTCTCAAAATACTTATGAATATAATACTAACATATTGTATTATTAATTGTGTACTACTAAGTTT +TCTCCCCAGCTGGTATACGTGGGTGAAATATTCATTCAATTATTTATTTCTTGACCAAACAGATCAATTCCTTGTTTTTT +TATTTTGTCTGTTAACTTTTTGGGGGCCATTAAGTAAGCTATATCGTTATAAGCTGTATGCTTTTTTATTATGTATTATG +CTTTTTCTTAGTGGAGGAAAGGCTGGAGTCTATTCAATAATGATATTAGCAATGGGATGGCTATATCAAAAAAGTAATAT +TAAAGGCTCTAATCTTGGAGTAATTTTCCTCTGTGCTATGATATTTTCATGGCTATTATCATATTTTATTGGAGTATATG +AACTAGATATATCAATATACAGTCGTTATTTTCAAGTACAGCAATTATTTCTTAATTACTCTAATAATATTCTTTTGGTA +TTTTTTGGTATTGGACCCTCAAAAGCTTATATTTTTTATGATTTTCCAACTATATTCGATCCCGGAGCCTATACATCAGA +AGAGTTAAGCTCCAGTTTTAGATTGGGTTTTCAAATGCCGTATTTATCATGGATTAAAAACTTTGGTCTGTCTGGAGTTA +TATTGCTATTATTGGCACTTAATTATATTATTAAAGTCGCATGGTCATTTAAGAAAGACGATATATTTTTTTCTGGGGCA +GTATATTCTTTAGGCTTATATTTTATTCTAATTGGATTCATGGATTTTCCTGCTTTTGGTTTAAAGACAATTATCCCAAT +AAGTTTATATATATATATAATAAATAATAAGCTAACATATAAAAAACAGGAGATTATATGA +>O-17_wzx__1221 +ATGAAATTTTCCCATAATACTGTATTTTTTTATTTGTTAACTATCGTAAATGGTTTGGTTCCGTTAATAACAATTTCATT +TATATCAAGGATAGTAACAAGTGAGCAGCTAGGTATCTATTTATTATCATTTACGATAATGAATGTTTTAGGCTTAGTTA +TAGATTGGGGCTTTACAATATCTGGCATTAGATTTTTAAAAAATAGTAATAAAAAAATGCCTGAAACAATATTCGTTTCA +ACTACTTTTTTTATTAAAATTACTATATCTTGTGTGGTTTTTATTTCATACTTCTTTTTTTATATATTTTACTCGCATGA +TGAAGTGTCTTTTTTTTTAATAACTATAATAGGAGCCTTTGTTACGGGGTTAGATAGCATTTGGATTTTACAGGCAAATA +ACCGATTAATGAAAGTTATAAAAAGGAGTTTATACTCAAATTTAATATATGTTATAAGCGTTTTACCTGTAATTATCTTT +TATAAAAATATCTACTACATATTATGGTTGTTTATTATATATAAATCTTACATGTTTCTGATATCTTTCCATGAGGTGAG +GGCTATATATGCTATTACTTGGCGAAATATCCACAAGGAAGAAGTTATTACTGTTTTTAAAAGTACATGCGGCGTAGCTA +TATTTAGAATATTTGCGCTGTCCTATACATCCGCAAATGGTATTTTTCTTAATTATTTGACTAATAAATATCAAGTGGCC +TTGTTTTTAGCTTTTGAAAAAATAAATAAAGCCATATTGTTTATTGCAACGCCAATTAGTCAGGCTTTGCTACCTTATTT +TTCGGAAAAGTCTAATAAGAAAAAACTTACGCAATATATTCTTATTATATTTTGTTTTTGCAGTCTAGGACTAATTATTG +GTAATATGTTTTCTCGGGATATAGTCGGAATTTTTATGGGGTATCCTTATCTAAGTGACAATACTGGCGAGTTATTTTTC +TTTATGACAATTATAACGCCATTTATTTTAGTCAGTAATGCAATTGGCATGCTCTATATTATTCCTCAAAAACTTGATAA +AGTATTAAATATAATTATTATTAGCGCTGCAGTGATAAATACATTACTTGTTTTTAATTTTGTTCATTCATCTACCGATG +GTGCATTGCAAATGGCGAAAGTAATAGCATTTAGTGAGTTCTTTGTTATGTCTTTAATGATAATAGTAATGTTTATTCAT +GGGAGGAAAAGTGGCGAATAG +>O-38_wzy__1083 +ATGATATATATTATAATAAATACTCTCACGACTATATTTTTATACTTATATAGTAGTTATAAGTATACCCCCTTAAGTCG +ACTGTTTATTGGTGGCATGTGTATTTTTTTAATAGCACTGTTGCCCGCATTCCAGTATGGTGTCGGTACTGATTATTTTA +GCTATCAAAATATATATAATAATGCCAATGTGCTAGATACTTTTTATCAAAATAAAGAATACTTATTCTATGCATATGTG +AAATTTTTTCAATTTTTAGGGGGGGGATTTAAAACTTTTGTTATCTATACGTCTTTATTGCAATCATTATTAATATTTAT +TATTATTACTCAGATGTGTAAAAATTATGGTCAATCGATTATCATAATATTTTTCCTTTTCTGGACTGTGACAAATTTAT +TACACACTCAGATGAATATAATAAGGGCTTCGTTTGCTATATATATATTTATAATATCCATGCTTTTTAAGTTTAGAGGT +AAAATAATTATTTGTTTTGCCTTAATGATTATTGCAATTGGATTTCATCGTTCAGCATTATTAGGGTTGTGTTTTGCATT +AATTCCCTTAAAAACATATTACTTTGCATATAATCATGTTGTTAAATTTTATTTTTTATCTTTTTTGTTATTTGTTACCC +CATTTTTACATCAGGTGGTGTTTTATATTGTTCAGGAGTTGTTTCCATATTATACACATTATCTATTTTCATTTGATGAA +AATGCAGTGAGCTTTTGGAATGTGGCTACAAAAATATACTGGCTTCCGTTTGGGTTATTTTTTATATATTTAATTAAATG +TAATGCTATTTTTATTAAGGGTTGTGAGCGTGGTTTGATTGGTTTGTGGATATTAACTGGGAATGTTTATTTATTAATTC +TTAATTTTGATTTTGTTTCCAGAGTTAATTTTTATTTTGTGTTTTTCTATGTAATTCCTATTGCATATGTTTTTCGTTAC +TTTATTAGAAATAAGAATGTTATTTTATTATATATTAGTGTGCTATATTGTTTTATACCGTATTTATTAAAAGTTACTTT +GTTTCCTATAGCTGAATTTTATTATAAAACTTATCTTTTTTAA +>O-60_wzy__1050 +ATGGAATTCTATTTCATTATATTATTCTTTCTAAGCACTTTGGGACTGTTATCCTTAGCAAATAAAGAAAAAAATAATTT +TTCGTTTTTTGCATGTTTTATAATATGCTTTTTTTTCATAGTGTTGTCTTCAATCAGATGGGATAGAGGTACTGACTGGT +CCGCATATTATGAGATCTATCAGGCGACGAACATTATCGGCGTATGCTTGAAGATATATTGCATAGGTGTCGAACCCGGA +TTTTATTTTATTAATTGGCTATTCTCCTCTTTTTATTCTTATAGCTTTTTTTTGTTTTTTTTAGCCTGCGTTATAATTCC +ATTAAAAACGTTGTTTTTCTTTAAGAAAAGTGAATATCCATTTATTGCTTTATTATTATATTTTAGCATTTTAGTGTTTG +ACATTTTTCCTGTTAGGCAAAGTTTATCTAGCTCTTTATGTCTTTTATTTTACTTGATCTATAAGAACCATAAAAAAAGT +TCATTTTTAGTTGCTCTATTGGCATTAATGGTACATTATTCGGCAATAATATTTTTTATTGGTTTATTAGTCTGCTCAAC +GAAAAAAATTCATAAGGGAAAAGTAGTAATTTTTTCAATTTTTATATTAGTTTTATTTTTTATAGTTGTTAAATACCCAC +CTGAAATCCTTTCTAGTAGGATAAATGATTATATTATTAACCAAAAGGTTTACTCAGACGACATCACACCGTTGAGGAAT +TTATTAAAATGCCTAGATCAAATATTTATTATGTTTCTATGTTGGCGCTTAATGTTAGTTGGTTGTGTCGATAAGATTAT +TTTAAGATTATCAATATTTGGCTCATTTTTATTTATATCAGCTACGCTTCTTGCTCCTCAACTTGCTCGACTTGGGTTAT +TCTTTGTTCCCTTTCAAATAATTACTTTATCTTCACTTATATTACTCTTCTCTAAAAATTCAAGACTTCTTGCTTATTTG +ATTTTAGTAGTTTATGCGGCTATTAAATTGAATTTAATAATACGGCCTTTTTATGATTTATTTGTGCCATTCAAAACGTT +TTTTATGTGA +>O-8_wzy__1200 +ATGCTGCCATTTCCACCAGGAGCAATCCTAAGGGATGTACTCAATGTATTTTTTGTGGCGTTAGTGCTAGTTCGATTTGT +CATTGATAGGAAAAAAACTTATTTCCCGTTGGTTTTTACTATTTTTTCATGGTCGGCGGTAATACTATGGGTAATAGCGT +TAACTATATTCTCACCGGATAAAATTCAAGCAATTATGGGGGGGCGGAGTTATATTTTATTCCCGGCAGTTTTCATAGCA +TTAGTGATTTTAAAAGTATCATACCCGCAATCCTTAAATATTGAAAAAATAGTTTGCTACATAATTTTTCTAATGTTTAT +GGTTGCGACAATATCTATTATTGATGTACTAATGAATGGAGAGTTCATTAAATTGCTCGGATATGATGAGCATTATGCAG +GAGAACAATTAAACTTAATTAATAGCTATGATGGGATGGTCCGGGCTACAGGCGGTTTTAGTGATGCTCTCAATTTTGGA +TATATGCTCACATTAGGTGTTTTGTTATGTATGGAGTGTTTTTCCCAAGGATATAAAAGATTATTGATGCTTATTATTAG +TTTTGTGCTATTTATAGCGATCTGCATGAGTCTTACTAGAGGAGCAATACTTGTTGCTGCGCTTATTTACGCACTTTATA +TAATTTCAAATCGGAAGATGCTTTTTTGTGGAATAACTTTATTTGTAATAATTATACCCGTTTTAGCAATTTCTACTAAT +ATTTTTGACAACTATACAGAAATTTTGATCGGCAGGTTTACAGATTCGTCTCAGGCATCGCGTGGATCTACACAGGGGCG +GATAGATATGGCAATTAATTCATTAAACTTCCTGTCAGAACATCCATCAGGTATAGGTCTGGGTACTCAAGGTTCAGGAA +ACATGCTTTCGGTAAAAGATAATAGGTTAAATACGGATAATTATTTTTTCTGGATCGCCCTTGAGACTGGTATTATTGGC +TTAATCATAAATATTATTTATCTGGCAAGTCAATTTTATTCTTCAACTTTACTAAATAGAATATATGGCAGTCATTGTAG +CAATATGCACTATAGATTATATTTTCTCTTTGGAAGTATATATTTTATAAGTGCAGCGTTAAGTTCAGCACCTTCGTCAT +CAACTTTTTCTATATATTATTGGACAGTTTTAGCTTTGATTCCATTTTTAAAATTAACAAATAGACGGTGCACGCGATAA +>O-59_wzy__1236 +ATGCTGTTATTTTATTGGTTCTTATATGTTTTTTCGTTATCAATTCCTATTTTTTATCATTCAGCGTTTCTGGTTGGATT +CGTATCAGCCATCCATTACCTATTGATTTACAAAAGGAATTTATTAGTTTTAAGCAGATATCAAATATTTTATTTTTCTT +CGTTTTTGCTTGGGTATATCATTGTCGGGTTAATAATTATTTTAAATGAGACATATGATATTAGCTTCTTTAAAACATAT +ACTAACTCTTTTTTATCAGCAATAAGTGGCGTACCACTTGTTTTAATATTTTTAGAACGATTTGGGAAAAACGCCCCAGC +TTATGTAATGAAATATACGTTTTATATTTTTATTATACAAAGCATAATTATAATATTGGTTCTGTTTGTACCTGCATTAA +AACCTTTCGTTATGTATTTTCAGAGAAATGCTGAGTTAGCTAGCGAATTAGACCTTTTTTCTAATGGCTTAAGAACAAAT +GCTCTGTCAGGAGGGTTATTTTATGGATTGAGCTTAAGCTTTAGTATGGCTATAATATTATATCTATATTATATTCTTGT +TTATAAATTTCAACTTAAACTGAGATATGTTTTTCTTTTTACTTTGGTCAATATTGGCCTTATATGTACAGGTAGGTTTG +GTTTTATATATGTTATATGTATAATCCCTATAATATGTACAATAAAAATCACAAGGAAGATTAAGCTTATACTCTTTTCG +CTTTGCATGATAGTTTTGCTTTGTATATTGTTCTTCACACTATATGAGTTATTCCCACAAGTAAAAAAAATATATAATGA +AACTATTTACCCCTATGCTTTTGAGTTTTTATCAAATTATCAAAAAAGTGGTGATTTCGATACAAGTTCAACAAACGAAT +TGGCCTCAATGTATAATGTAACAATAACGGATAATACATGGTTTTTTGGGGATGGACTATACACAGGAAATGATGGCCTT +TATTATCAACATACAGATGTAGGATATTTGAGGTTATTGTTGCTTGGTGGCGTTGGACTAAATATATACTTCATTTCCTT +TACGGTTTTAATGCTAATACCAATATTAAAATCTACCTTGCCTAATAATAAATCATTATATTTTTCATTGCTCTTACTTT +TTTTACTGTCACAGTTTAAAGGTGAGGCTATGATAACATTAGTGCAGTTAAATAATATGTGCTTTATATTATGCAGTACA +ATCAGTTTTCTTTACAGAAAGGACGTGAATGAGTAA +>O-50_wzy__978 +ATGTTCAAAAAGAAAAGTATATTTGTTTTTTTAGGGCTTCTTAGCTCTATACTTCTTGCGTTACCTTTAGCTATGCAAGG +CGGTTTTGATGATTCCTTAGTTTACTATTCACAAGCTGATTATATATGGAGTTACGGTTTATATGATGGACTAAGAGCTA +TTTATATCCAAACAAATAAATTTGAGCCCGCTATGGGGCTACTATTTTTTATAGAAGGGTTTATTGTTACCGAAAAATTC +TATTTTTTATTACTTAATTTAACACTAGTGAATTTTATTACAGTTTTGATATATATAAAAATTAATGAACAATCAAATAC +AAGTATAAGTTTTATATATGCAATACTATTGCTCTCTACATATTATATTTTTTCTAATAATATTTACGTGTGGAGGACTA +TCATTTCTTTATACTTTTTTATTTTGTTTGTTTTTTCTAAATCAAAGAGTTGCAAGGTTATTTTTTTCTCATTGGGGTTT +TTGTTTCATTACTCATTTTTACTATTTTATTTTTGTTATATAATATGTAAATTTAATAAGTCAAGTTTGAAATTTTTTTT +GATATATGCATTTTTATTTTCTTTATTTATTTCTAATGTATTAAATTTTTTAAGTTATTTTTCTTTTTTTGTTTCAGGGG +GGGAACTAACGATCTTCTTGGATAAAAGTAGTGATAGTATTAAGAGGATTATTATTGGAGTATCATTCCTTATTATATTG +ATTATGGTTAAGGTTGATAAGAAAAGTTATAGTTGGAGTCTTTATAAATTATCCTTGTTTTTCTGTATATTATCGATTGC +GCTTTATCAAAACTGGCAGTTATCCTGGAGGGTATTTGTTCCCGCAGCTACTTTAGGGAGTGCTATAGTTTTAGCGAATA +TAAGAAAGGATAATATAATCCCTTTTTTGGGGGTGGTTTTATCAACTATCCCCACAATGAGAATAATTTATAATTTATTA +TATCTAGGACATCCATAA +>O-52_wzy__1065 +ATGAAAGGCGGTCTTATTGTTATTCTGTGGTATTCAGGCTTTTTATTTATTGCAGCAACAGGTTTAACCGGGCTTCAGGA +GTTAAGTTCAAAATCTATACTAATGTATATTGCTTTTTTGTTTTGCTTCCTTTTAGGGATGGTACTATCTGGTGTATCCC +TTTATGAACCGAAAAAGGAAATGCATCAGCAGATTCTCAAAAGAAAACATAACTTAGTGATAGTGAGTATATTCTATCTA +TTTATAATATATTGTTTTTTAGTTGCATTAAATATTTATTTTTTCAATAAAGTTGATCTTTCGTCTTATAGGCAGGCATT +CTTTGATGGCTCAAGAGATAATGTAAAGTTCTTTTTTGGTTCATTTGGATTTTATTTTTATTATTTCTTAAGTTTAATCA +TTTATGCGTTAGTTCCATTTGTTGTTATAATGAATAATAAAAAAGTGTTATTCCTATGCTTTCTGTCATTATTGCTATAT +GATATAATTTTTCTTTCGAGAACCGGAGTTTATTACTATATATTGTCATATATAGTGGCATGTATCATCCAGAAAAAGCA +ATTAAAAAAAATAATTATTTTTATCGTGATTGCATTGCTGTTTTCTTTTGTAATAAGCTATACTCGCGATATGCAAAGTA +ACATAATTAATTCAATTTTTAGCTCAATTATTAATTATCACGTAGCCCCTTTTATTCTATTAGATAACAACATAATTTCA +AAAAATGTAATAACATACCATGGTGTTGGTTTAGCATCACTTGGTATATATAATATTATTTTCTTTCCTATAGATGTAAC +AATAATGCAAACTATAAACGACTTTAGAACTCAGTTAAATATGTTCTATGATCTAGGATTAAAAGAATATTTACCATATA +ATGCTTACTACACATCACTAGGGGGAGTATACATAGATAGTGGTTTTTTGGGATGCATGATAGTTACCTTTTTTTTCGGT +TTTATTATCGTAGCAATAGAAAAAAAAGCTTATAAATCAAGAAAATACTTAGCGTCAACTGTGTTTTTTACAACATTATG +CTTAGAGTCAATTTTGCTCCAATAA +>O:23-gene1__1029 +AAGGTGCGGATGATGATATTAGTCACTGGTGGAGCTGGTTATATAGGATCGCATACTTGTTTAGCGCTTATTGCCAAAGG +GCACGACATTATTGTTATTGATAATTTAAGTAATTCCTCTTATGAGTCGATTAGGCGTGTTGAGAATTTAACCAATAAAA +AAATAAAATTTATAAAAAGTGATATAAAAGAACGACATTGCCTGGATGAAGTGTTTAATAATTATTCGATAGAAGCAGTA +ATACATTTTGCAGCATTAAAATCAGTAAGTGAGTCTGTTGAAAAACCATTGGTTTATTATGATAATAATATCACAGGTAC +CTTGACTCTACTGGCTGCAATGCAAAGTGCAAATGTAAATAATTTGATTTTTAGTTCGTCTGCTACCGTATATGGTTGTT +CTTCGATTGTTCCAAATAAAGAGAACGATACAATTGGGGGGACTACAAATCCCTATGGAACATCAAAATATTTTAGTGAG +ATTATTCTGCAGGATTTTTGTAAGTCTAATGAGTTATTTTCCGCAGTAAGTCTTCGTTATTTTAATCCTACTGGTGCTCA +TAAATCAGGTATGATTGGGGAAGATCCTAATGGAATACCAAATAACCTCATTCCATATATATCACAAGTTGCCACTGGAA +AACTTAAATATTTAAATGTATATGGTGGTGATTATGACACAATTGATGGCACTGGCATGCGAGATTATATACATGTAGAT +GATTTAGCTGAAGGACATGTCAAGACATTAGAATACATGTTATCAACAAAAGTAGGTTATGATGTTTTTAATTTGGGGTC +AGGTCGAGCATATAGTGTTTTGCAAATCATTAAAGCTTTTGAGCTCGTCACTAAAAAAGAGATTCCCTATAATATTGTCG +CACGAAGAAATGGTGATTTAGACAAATCTTGGGCTGATACTGAAAAAGCCAGAAACCTCCTGGGGTGGGAGGCAAAATAT +GGAATAGAGGATATGTTGCAAGATGTTTGGAACTGGCAATCACACAATCCAAATGGTTATAGAGTTTAA +>O-11_wzy__1080 +ATGAATATATTATTTTTTTTGCTTCTAAGTGTTGGGTTATTATTTTCCCTCGCATATAAAAATAAAAATAAAAATATAAA +TGATAGTATCATGTTTATGCTTGTCGTCCTGATGATATTAATGTCAGGCCTTAGAGTTAATGATAGTGATTATCTTGAGT +ATAATAAAATGTATAATGAAGTTCCTTCATTATACAATTTTACGTTATCTGCGATAAAAGATATTCATGGAGAGATTGGC +TATCTTTTCCTTTCATCTTTTTTTAAAACATTTGATTTACCGTTTCAGTTTTTTTTATTCTTTATAGCATCGTTATCTTT +GATGCTTACTTATTTTTCTTTTAAAAAAGCAAGTATTATACCAATATTATCTCTAGTTTTTTATTTAAGTCATGCTTTTA +TTGTTAGGGATATGATACAAATAAGAGCTGGATTAGCGGTGAGTATGTCTCTATACACAATTGTGACATATAAGAAAAAT +CGAAATGTGATCACAGGGATACTGCTTGCATCGCTGATTCATTCTGGAGCAATTATAATTGCTATTTGCTACCCATTTAT +AAGAAAAAGATATTTATCGTTAAAAAAAATATTTTCTCTTTTCTTGGTTGCCTTAATATTTTCTTATTTACATGGGCTCG +ACTTTATATTAAACACCCTTATTCATTATAATCTTCTGCCAGATGCTGTTGCAAATTATATTGGGTGGGAAGAATATGAT +TATAGAATTAATATTTTCACTAATCCAGTATTTATTAAAGGGATAATGATAGTTTTTTTAATGAGAAAATATATTAAAAC +AAATATAAATAATGAAAATGATAAGGTGGTTATATTATATAATTTATATGTTTTAGGTGTTTTAGCAATGGTTGGGTTAA +GTGAGATGGCTATACTTTCAGGACGTCTTTCATCGTTTTTAACACTAGGTGAAAGCATATTAATAGTATATAGTGTTTTT +TATAAAAGAAATATCTCGGTAGGTTTTGTTTTCTTTTTGTTATTAACTTTCATACAGATGGGATATGATCTGTTAATTTC +AAACGTACATCCGAAGCTCTCTCTTTTTATATTTGGATAA +>fljB_1,2_Newportstr_AYDZ01000021_1__1510 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATTACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAACCTACAATGCCAGCAAAGCCGCTGGTCATG +ATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTG +GCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATAC +CGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGC +AGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fljB_z35_Salmonella.enterica_IIIb.35:z52:z35_AY353343_other.z35__1488 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTAGATAGCAAAGCTGTGAC +ACCTCCGGCAAAACTTGATATTGCAGGATTAACTGGAACTGCAATTAAAACGGGCGTTGATAGCGCTACGGTTGATACTG +GCTCCATTAAAGATGGCAAAGTTTATTATAATAGTACCTCTAAGAACTATTACGTAGAGGTTGATTTTGGTACATCAGCC +GATGCTGCTAAGAGTGGTTACTATAAAGTCAATGTTGCTGATGATGGTACAGTCTCAATGACAGCTTCTACCACTAAAGA +GGCTACAACTCCTACTGGTATTACTGAAGTTACTCAGGTTCAAAAACCTGTAGCCGCTCCAGCCGCTATTCAGGCTCAGT +TGACAGCTGCCCATGTGACCGGAGCTGATACTGCTGAAATGGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATT +GATGGCGGTTACGCTGTAAAAGTGGGTGATGACTACTACGCCGCTACCCAGAAAAAAGATGGTAGCTTTAGTATTAACAC +CACGTCTTACACCGCAGCGGACGGTACATCCAAAACTGCCCTGAACCAACTTGGTGGCGCAGACGGTAAAACCGAAGTCG +TTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAGCTGGCTGAAGCA +GCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>fljB_1,5_Infantisstr_AFYI01000002_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAATGACGGTATTTCTATTGCGCAAACTACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCACAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGACAGCTTATGCCGATAATGGTACTACACTGGATGTATCGGGTCTTACTGATGCAGCTATTAAAACGGCTACGGGTG +GTACGACTGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGG +GGCTTTAGTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGCGTAACAACTAAAACAGAAGTACAGGAGTTAACAACTACACCGGTAGTTG +CTTCAGCAGATGCTAAAAATGCCTTAATCGCTGGCGGCGTTGACACTGCCGATGCTAATGCCGCTACATTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTTAAAGCACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>O-6,14_wzy__1344 +ATGAATAAAGAATATTATTTACTGCCTTCGAATAAATTAAGATTTAAACACTTGATTATATATCTTGTGGTATGCCTGTG +CCTTTTTTCTGGCTTTCTTATCAATGATGCAAAGACTCAGATAGCTCAAGAAATTACTGATATATTAGCAATAATATCCA +GCGCGTTGCTAATTGTGCTAATTCTGTATTATTATATATATCGGGTGCGCTTTTTTTCTCTGACGCTACTATTTTCTTTT +GTTTTTTCACTAATAATTGGTTTGCCTTCGATATATCTCTTTTATTTTAAAAACACAGATAATGACTTTGGGATTATTTG +TATATGGGCAATGCTAATTAATGTTGCTCTCTATCTACTTTCAACAAAAACTTTTTATAAAAAAGAAGAAAGGCGTTTAT +CCAACCTCTTTTATGCGATATTTTTTATTGCAGCATTTTGCCAGATCTATAAGGTTATGATTTATTTTCTTTTTATTCTT +AATTCTGGTGCCGGGCATCTCGCAATATATACAGAAAGCGAAGAGTTATTATCCCAAGTGCCCTTTGTTATACGTGCTAT +AAGTGGTTTTACAGTAACTATGGCATTGGCTGTTTTTTATTTTAAAAGTCCAAGTATAATAAAATTTATTGCATTTATCC +TGCTAGCTTCAGATTTAATTATAGGGATACGTAATAAATTCTTTTTTTCAATGATATGCATATTTATACTATATTTATAT +TCAAATGAGATTAGAGTAAAGCATATTTTCAAAAAAATCTCAAAACCTACTGTTCTTCTGGTTGGTTTTATATTATTTTC +TTTGGTTTCATATTTTAGAGAAGGCTACCAGATTAATTTTGTAAATTATATTGGTATTGTATTAGATTCTTTGTCGTCTA +CTCTTGGTGGTATGCAGAATTTATTTAGTGGACAAATAGGGAGTTGGGATAAGTTAAGTCCTGAAGTCGTATTCACACAG +ATATTGCCGTTAAGTGGTTTAGGTTTTATTAACAACCATCAAATTGCAAAGGATTTTTCTATCATTGTACTAGGCGATGT +TTCATCAGGTATTGCATTGTCATCCTCCGGATTATTAGAGTCGACAATATTAAGCCTACACTTTGGATCTGTATTTTATT +TAATCTATCTAATAGGCTTTATTTCATTAATAACACGCGCATTGAATAGTCAAAAAGTATTAATAAACTTCATTGCTATT +TCAATGATTTCCGGTTTCTTCTATGCAGTGCGGGGAGAGTTGATATTACCTTTAGCTTTCTTATTAAAGTCTCTGCCTAT +CGTTATAATATCCCCCTTGCTTGTAAAAGGGCATTTTAGGGCTTTGTCAGTAGAATCAAAATGA +>O-6,14_wzy-from-Stk2184__1344 +ATGAATAAAGAATATTATTTGCTGCCTTCGAATAAATTAAGATTTAAACACTTGATTATATATCTTGTAGTATGCCTGTG +TCTTTTTTCTGGTTTTCTTATCGATAATGCAAAGACTCAGATAGCTCAAAAGATTACTGATATATTAGCAATAATATCCA +GCGCGTTATTAATTGTGCTCATTCTGTATTATTATATATATCGAGTGCGCTTTTTTTCTCTAACGCTACTATTTTCTTTT +GTTTTTTCACTAATAATCGGTTTGCCTTCGGTATATCTATTTTATTTTAAAAACACAGATAATGACTTTGGGATTATTTG +TATATGGGCAATGCTAATTAATATTGTTCTCTATCTGCTTTCAACAAAAACTTTTTATAAAAAAGAAGAAAGATGTTTAT +CTAGCCTTTTTTATGCGATATTTTTTATTGCGGCATTTTGCCAGATCTATAAGATTATAATTTATTTTATTTTTATTCTG +AATTCTGGCGCTGGGCATCTCGCAATATATACAGAAAGCGAAGAGTTATTATCCCAAGTTCCCTTTGTTATACGTGCTAT +AAGTGGTTTTACAGTAACTATGGCATTGGCTGTTTTTTATTTTAAAAGCCCAAGTATAATAAAATTTATTGCATTTATCT +TGCTGGCTTCAGATTTAGTTATAGGAATACGTAATAAATTCTTTTTTTCAATGATATGCATATTTGTACTATATTTATAT +TCAAATGAGATTAGAGTAAAGCATATTTTCAAAAAAATCTCAAAACCTACTGTACTTCTAGTTGGTTTTATATTGTTTTC +TTTGGTCTCATATTTTAGAGAAGGCTATCAGATTAATTTTATAAATTATATTGGTATTGTATTAGACTCTTTGTCGTCTA +CTCTTGGTGGTATGCAGAATCTATTTAGTGGACAAATAGGGTATTGGGATAAGTTAAGCCCTGAAGTCGTATTCACACAG +ATATTACCGTTAAGTGGTTTAAGTTTTATTAACGACCACCAAATTGCAAAGGATTTTTCTATCATTGTACTAGGCGATGT +TTCATCAGGTATTGCATTGTCATCCTCCGGGTTATTAGAGTCGACGATATTAAGCTTACATTTTGGATCTGTATTTTATT +TAATCTATCTAGTGGGCTTTATTTCATTAATAACACGTGCATTGAATAGTCAAAAAGTATTAATAAACTTCATTGCTATC +TCAATGATTTCCGGTTTCTTCTATGCAGTGCGTGGAGAGTTGATATTACCTTTAGCTTTCTTATTAAAGTCTCTGCCAAT +CGTTATAATATCCCCCTTGCTTGTAAAAGGGCGTTTTGGGGCTTTATCAGTAGAATCAAAATGA +>O-55_wzy__1128 +ATGTTTGTTTTAATAAATGTATTTATCTTGTTGTTTTTTTCTTGTTTTTGGGGACGTTTTGATTTTAAGAGTAAAGTCAT +TCTTAGGTTTCTAATATGGTCAGGGTTAGTATTCTCTTTTTCTTCATTTTATATCAATGGTGTTGATTGGACTGTTTATT +TCAGCAAATTTAGTTATGAGGATAATTATTATTTATTTTTGTCATTTGAACCTGGTTTTGTCATCTTTTTAAAAGCATTG +CTGTTCTTGACTTATGGTAATTTTGGGGGGGCTATTTTTTGTTTTTTCATGATTACATTTGGTTTTCTAATGTACTCATT +AGAAAAATATAAAATTAATGAACCGCTGTTTCTTGCTGGATTAATATTGGCATGTGGATATACACTGATACTTGAGCAGC +TTAGGCAATTTATAGCATGTCTTATTGTTTTTGTTTTTCTTATTAATTATAATAAAAATAAATCTTTAGTTAGATTAATT +TTTGGTGTGACAATTGCTTCATTTTTTCATATTTCTGCACTTGTGGTAATTCCTGCCGTTATTCTATGTAATATTAAAAA +TCGATTTGTATTTATTGTTACAACAATTATTTTTGGTATTCTGTTTGTTTTATTTTTATTTTTCGGTTTATATATACTGG +AGCAAATTCCACAATTTGCTTTTGTAGTCCGGAAAATTAATTTTTATCTGGAACAAAACCCAACGATCTTACAACTGGGA +TGGTTGAATTTATTCGTGCTTATTTATACGGTAGCTTATGTTTTTTTTAGCTATTCTATAGAAAGAAACTCGAATGCTAA +TTTATTGAATCGTTTTATTTTTGTTGGTTCTATAATTTTTATTTTTAGTGGAACATTCCCTTTTTTGGGGCGGATGACGC +TTTATTTCATATTTATCGCTCTTTATATAATCTCAGATCCTAAAAAGAATTGGCGAATTGGTAATGCGATAGTAGTAAAC +GGATATTTTTCTATTTTCTTGGTGTTGAATTTTTCTTCATATTTTCGTAATGATTTAGCACCCGTAGACTTTGATAATTT +AAATTATTGTTTTTTAAATTTGTTTGATAATAACTATATGCAGAAAATAGCGACTGAAAATTTACCTGAAATGTTAGTTG +GAGAATAA +>O-3,10_not_in_1,3,19__1519 +TTTTATATTATATTTGGCAGAGTGTTAGTATAATTGTCATGTTCAGTTTGAGGTAATTTATGTACTAATTATCTTATATT +GTAAATCATGTGCAATTATTTTCATATTTTTATATGAAAAACGTCCAGTATATATATTGAGAAACATTATTGTTATGGAG +ACATCATCGGAGTTATGATGGAAAAAAACTCTTTTCCCATAAGCCACGAACATTCCTTAACTATGGATTATGTTAAAGCT +TTTGGTATGATTTTCGTATTGGTTGGGCATATAAATAATGACATATTTAATGTTTATTATGCCTATCTTTTCCATATGCC +ATTATTTTTCTTTATTGGTGGGGTTTTATATAAAGATACACGGTGTATAACAAATTTTACAGCGCATGTTATAAAAAAAC +AGTTACCTTATCTTATAGTAACTTATTTGATTATTGGTTCTATTGCATTATTAATTAATGTACGTTATGGAATACACACA +GGTGATGCTTTTTCGACAGGACTATATGAAACGGTTAAACTTGCTATAAAATCAAATTTTCATAACAATAAAATGTTTCT +AACAGGTTGGTTTCTGTTTGCTTATATATTTGTGAGCATTTTGTCGGTGATTATAATAAAAAGCATAAAACGGGTCGTTG +TTAGCAATGCTTTATTATTATCGGTATTGGTGGCGATTAGTGTATTATTAATAACTGTCTCAATAACATATTTATCCCCT +CAATATATTCTGGTAAAAGACTATAAGCTGAATTTTATATGCCAAGTGTTAACCGGTATGTCGTTTTATATTTTTGGATA +CGTGATCAGAAATCAGATATATAACTTATTAAATTTTTATGTTTTTATTTTATTAACTGTAATATTATATGTTTCGAAAA +GTTATGGTTTCTCTACGCAGACAATTATGTCATGGAGTTATTATCCGGATGGGTTAATAATGTCTGTTATTAACGCGCTG +ATAGGTATTTATGCTGTGTTTTTTATCTCTCTATTAATTACAAGGGGAATGAAAGAAATTAAGCTGCTAAAAATGATAGG +TCAGAATTCAAGAGCTATCATGGCATATCATTTACTTGTATATGTAATTTTAGATATAATTGCTTCAATTTTAGGTGATT +ATAGCCTATCGGGAACAGATGTATATGATAATCACTTTATCACTAAATGGTCCGTTCCTGTCTACATTGCATTAGGTTTG +CTACTGCCTCTAATTTTTAGTATTCTGAAACAGAAAGTAATAGGGAAGATAAAATTTAAGCGGGATTTTAGAATCAATTA +AAAGCTAATTTTAGCTTTAATGCAGCCTAATGTTTAAGTATTAATTTTTGGATAAATATCACATAATAGGTTACTCAGGA +GATTTTTATTTAGTCTACCGACGCGTTCCCAGATAAGGATTCCGGTGTGTCGTAGGTAGAAATAGGTAATTAATGATTGT +TTCTTCGGGCTTTAAGTCTGGGTTATCATATTATTCACTTTATCTCATTGGATATAGTTCCTATGAGTAACCACACCTG +>O-48_wzy-from-blake-2014K-0232__1194 +GTGATAATAAAAAAGTACAAAATTTTTTATTCAGCACTTAAAGTCTGGTTAATAGCCTCTTCATTGTATTATTTAAATGC +TATTTTTTTAGGTGTTGATGCTTTAAAATATAATGAAGATTTGACGCAAAAGTTCATCAAATATGCAGTTTGTTTCATCA +TAAGCATCTATATTCTGATCAATAATAAACGAGTCAAATATCTGTGGGCTTCATTTTTTTTCATAATTCTTTCTGTAGCT +TCAGTAGTTATTGATAGTGTTGTAACGGTATATGCAACCACGATGTTGATAATTGCTACCATGCTTGGTTTTAGCCAAAT +CATTGTTTATTTATCCAATGATATGTCGAGAATTAATATTGTTTTATTATGGACAGGTGTTATTGTAGGCACAATTTCTG +TGTTAGAGCTGACTGTGTTCTACGATTATATGGTTTCATATTGGATTTCGACTGGCGGAATTCGATCAATATCTTCCCTT +CTGAATCCTACAAATAGTGGAGCTTACTCAGCGATCATAATTTTAATTGCTTTAGCGACTAATATAAAGAATAAGTTTAG +GAAAAGTTTATTTGTTTTAATGCCAATGATTACTTTAATCAGTAGTGGATCACGCACCGCATGGTTATCATTAGCATTAA +CATTGTTATTGACAGTATTGTTAAATGATAAGGCTAGCATACGATTACGGAAAAAAATATTAGCTGTTGCAGGTATTGGA +GCTATTTGTGGTCTATTATATGTAGTATTTTATATGAATGCTACCTCTAGCATTCAATCTCAATATCGAGGACTTGATAC +ATATACCGCATCAATTCGGATTGAAAACTTTATATCGTATATAAATTCAATTGATCTTTGCATGTTATTTCCTGATTTTT +TTGACAAAAATATTATTCTTATATCAGATAATTTTTACCTTGTTTTATTAAATTATTTTGGGATTATTGGTTTTTATATT +ATTCTCTTAATGTCAATGTTGCTATTCTATTGTAATGTACAGATAAAGGATTTTAATGATATTATAAATGAAGATATTGC +TATTTGGAGAGTAATCTTTATCTATTTTTTGATATCTGGTTTTTCAAACTCATTTATAAGTTCTTTTCCTGTAAACCAGC +TATTCTTTATCTCATGCGGGTATTATGTGTATAAATATAAGTTAATAAAAGAAAATGTTGGAAAGTAAATATGA +>fliC_l,z13,z28_Salmonella.enterica_Hiduddify_DTU-unknown_l,v__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAGGCAGTTAA +AAGCGGCGGTGGGACAACACTCAGTACCACTGGTCTTGATGATGCAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCG +GTACCGCTGCAATTAAAGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCGCTGC +GAAAGTGACAGGTGGCATACCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAG +TTAAAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGAT +AAAAACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGG +ATCGTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAG +ACGGTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCACAACTTTAAAGCACAG +CCTGATCTGGCGGAAGCGGCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACAC +GTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGA +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_b_ParatyphiBstr_AOXH01000168_b,d,j__1476 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACTTTAAGTGTACAGGATGCCTATACGCCAAAAGGTACCGCTGTTAC +CAGAGATGTTACCACCTATAAAAATGGTGGTACTACTCTTACAGCACCTAACGCAGCAGCAATTGATACCGCTTTAGGTA +CGACTGGTGCGGCGGGTACTGCGGCTGTGAAATTTAAAGACGGTAACTACTTCGTTGAGGTGACCGGTACAACTAAAGAT +GGTCTGTATGAAGCGACAGTTGATGCAGCTGGCGCGGTGACAATGACCGCAAATAAAGCAACAGTAACTGGGGCTAGTAC +AGTTACTGAAAACCAAATTGTAGACGCTGTTACACCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATG +CAGGTGTGACAGGTGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCG +GGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAAACTGGTGAGATAAAAGCTAAAACTGT +AAATTATACTGACGCTACTGGTGCGACAAAAACCGGTGCTGTGAAATTTGGCGGTGCGAATGGTAAAACTGAAGTTGTGA +CCACCGTTGATGGTAATACTTATCAGGCTAGTGATGTAAAAGGGCATAATTTCCAGAGTGGTGGCGCTTTAAGCGAGGCT +GTAACCACTAAAACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAAGTTGATGCGCTGCGTTCTGACCTGGG +TGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCCCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_f,g_Rissenstr_AHUI01000019_g,m__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGTT +TCACGTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAACGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +GTCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGAATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGACCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTAATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGGTGGTGCGGCGAATGTT +GATGCTGCTACCTTACAATCAAGCAAAAATGTTTTTACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAAGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCTAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_g,m_Enteritidisstr_ALHY01000185_g,m__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGTT +TCACGTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTAGCGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_z41_Salmonella.enterica_Maska_AY353511_k,z__1491 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAGAAAGCGTATGATGTCGATAGCAAAGCTGTTAC +TGCAACTCTTGATCTGGATGTGACAGATCTTGATACTAATGCTTTGAAAACCGCAACTGGTATCAGTGCAGGTAATCCTG +CTGTTAAAGACGATAAAGTTTATTATGACAGCGCAAATAATAATTATTATGTAGAGGTTGAGGGCTTTACTGATAATACG +AAAGATGGTTTCTACAAAGTTCAGGTTGGTGATGATGGCAAAGTGTCAATGGCCACAACTACCAATAAAGAAACAGCTAC +TCCTCCCGGAATTGTTGAAGTAAGTAAAACTCATGATGAGAAAGCTCTTAAAGCTTCTGCAGAGGTTAAAGCAGCTCTGA +TGGCTGGAAATATTGATACTGCTGATGCAGATGCTGCTGAAATGGTCAAAATGTCTTATACCGATAAAAACGGTAAGACG +ATTGATGGTGGTTATGCTGTAAAAGTAGGCGATAACTACTATGCCGCTACCCAGAAAAAAGACGGTAGTTTCAGTGTTAA +TACTACTTCTTACACTGATAAAGACGGCAACACTAAATCTGCACTGAACCAACTTGGCGGCGTAGACGGCAAAACCGAAG +TTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCTGAAGGTCACAACTTTAAAGCACAGCCAGAACTGGCGGAA +GCGGCTACTGCAACCACCGAAAACCCGCTGCAGAAAATCGATGCTGCGCTGGCACAGGTTGATGCGCTGCGTTCTGACCT +GGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGTCTGAAGCGCGTAGCC +GTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTT +CTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z32_Salmonella.enterica_IV.48:z4,z32:-_AY353548_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCAAACGACGGTATTTCCATTGCGCAGACGACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCAAACGGCTCGAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACTGATTTTAACG +GTAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGTTCTGGAGC +CTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACAACGGGTGGCCCCGCAGCAGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGTTACTGCGACGGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGTCTCCGTCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGATTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCAGGGACTTCTGTTCTGGCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_e,n,x_Salmonella.enterica_Kokomlemle_AY353319_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCTATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCGCGGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGTGTAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCTACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAGAATGTGCTGTCTCTGTTACGTTAA +>fljB_k_Salmonella.enterica_II.13,23:k:z41_AY353329_k,z__1488 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGTAC +CGCTATCGAGCGGCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCACAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTGATAGCAAGGCTGCGCA +AAGCGTTAAACTGGATACCAGTGCTCTTACTGCCGCTGCAATCAAAGGCGGCGTAACAGGTGCAACAACAGATGGTGCCC +TCAAAGACGGTAAAGTTTACTCTAATGGCACAGACTATTATGTAGAAGTAAGCTTTGCTGATGCAACGGACTCTGCTAAA +GGTGGTTTCCTTAAAGTAGATGTTGATTCCACTACTGGTAAAGTTACCGTACCGGGTACGGCAGCAGCAGCTTCTTCAAC +TAAACCTGTTGGTGTGAACGAGGTTACAGAAGTACAAGGTAAAATCCCTGCATCTACTGCTATCCAGGACCAATTGAAAG +CTGGTGGTGTGAGTAACGCAGATGCTGCTACTGCTGAGGTTGTCAAAATGTCTTATACCGATAAAAATGGTAAGACGATT +GATGGCGGTTACGCTGTAAAAGTAGGTGATGACTACTATGCCGCTACCCAGAAAAAAGATGGTAGCTTTAGTGTTAACAC +CACGTCTTACACCGATAAAGACGGCAACACTAAATCCGCACTGAACCAACTGGGTGGCGCAGACGGTAAAACCGAAGTCG +TTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAGCTGGCTGAAGCA +GCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATCGATGCCGCGCTGGCACAGGTTGACACGTTACGTTCCGACCTGGG +TGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAATAACCTGACTTCTGCACGTAGTCGTA +TCGAAGATTCTGACTATGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,z15_Salmonella.enterica_Sandiego.var.d+_AY353303_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATTAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAATGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACGGTACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATTGATATTGATTTA +AAACAAATTAGCTCTAAAACACTGGGACTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGTTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAGGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATCCTGCAGCAG +GCCGGTACTTCCGTTCTGGCACAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fliC_z35_Sloterdijkstr_AOXT01000110_other.z35__1476 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTGCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAGAAAAAATATGATGTGAAGAGTGAAGCCGTCAC +GCCTCCGGCAAAACTTGATATTACAGGATTAACTGGAGCTGATATTAAAACTGGCGTTGATGGCGCTACGGTTGATACTG +GCTCAATTAAAGATGGCAAAGTTTATTATAATAGTACTTCTAAGGACTATTACGTACAGGTTGATTTTGGTACATCAGCT +GATGCTGCTAAGAGCGGTTACTATAAGGTCAATGTTAATGATGATGGTACAGTCTCAATGACGGCTGATACCACCAAAGA +AGCTACAACTCCTACTGATATTACTGAAGTTACTCAAGTTCAAAAACCTGTAGCTGCTCCAGCCGCTATCCAGGACCAGT +TGACTGCCGCTCATGTCACCGGGGCTGATACAGCTGAAATGGTCAAGATGTCTTATACGGATAAAAACGGTAAGACGATT +GATGGCGGCTTCGGTGTTAAAGTTGGAGACGATATTTATGCTGCAACTAAGAATAAAGATGGTTCTTTTAGTATCAACAC +CACGAAATATACCGATAAAGACGGTAATACCCAAACTGCATTGAACAAACTTGGTGGTGTAGACGGTAAAACTGAAGTTG +TTTCGATTGAAGGTAAAACCTACACTGCAGCGAAAGCAAAAGATCACGATTTCAAAGCGCAGCCAGAGCTGGCAGAAGCG +GCTACTGCAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTAGCACAGGTTGATGCGCTGCGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fljB_1,5_Salmonella.enterica_I.43:e,h:1,5_AY353284_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGTAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAATGACGGTATTTCTATTGCGCAAACTACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACTCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAACTTATGCCGATAATGGTATTACACTGGATGCCTCAGGCCTTGATGATGCAGCCATCAAAGCGGCCATTGGTG +GTACGACTGGTACGGCTGCTGTTACGGGTGGTACAGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGG +GGCTTTAGTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTCGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACCAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGTGGTTATGCGCTTAAAGCCGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAAGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fliC_f,g_Salmonella.enterica_Derby_AY353380_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGTT +TCACGTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAGGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +GTCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGTAGCACCGAATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGACCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTAATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGGTGGTGCGGCGAATGTT +GATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAAGGCGAAAGTAAAATTACAGTAAACGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGGTCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCTAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,m,s_Salmonella.enterica_Amsterdam_AY353395_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTGCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTATGACACCTATGCAGCGGGTGCCAATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAATGGTCAGTTGACAACTGACGATGCGGAA +AATAACACTGCGGTTAACCTATTCAAGACGACTAAATCTGCTGCTGGTACCGATGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_c_Salmonella.enterica_IIIb.57:c:e,n,x,z15_AY353370_other.c__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCACACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAGCGATACTGCTGTAGC +TGCTTCCTATTCCGACTCGAAACAGAATATTGCTGTTCCTGATAAAGCAGCTATTACTGCAAAAATTGGTGCAGCAACCA +GTGGTGGTGCTGGTATAAAAGCAGATATTAGCTTTAAAGATGGCAAGTATTACGCGACTGTCAGTGGATACGATGATGCC +GCAGATACAGATAAAAATGGAACCTATGAAGTCACTGTTGCCGCAGATACAGGAGCAGTTACTTTTGCGACTACACCAAC +AGTGGTTGACTTACCAACGGATGCAAAAGCAGTTTCAAAAGTTCAACAGAATGATACTGAAATAGCAGCAACAAATGCGA +AAGCTGCATTAAAAGCTGCAGGAGTTGCAGATGCAGAAGCTGATACAGCTACTTTAGTGAAAATGTCTTATACAGATAAT +AACGGCAAAGTTATTGATGGTGGGTTCGCATTTAAGACCTCCGGTGGTTATTATGCAGCATCTGTTGATAAATCTGGCGC +AGCTAGCTTGAAAGTTACTAGCTACGTTGACGCTACCACTGGTACCGAAAAAACTGCTGCGAATAAATTAGGTGGCGCAG +ACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGAAGGTCACAACTTTAAAGCACAG +CCTGATCTGGCGGAAGCGGCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACAC +GTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGA +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>O-62_wzy__1023 +ATGAATGGAGTAGCCAAACCCATTATAATTTTTTTGTTCGCCTGTTGTACTCTTGTGACTTTTCTTTCATGTAATTTAAA +TTTATTTCCTGATTATTATTCATATCTAAATTGGTATGAGTTATCAGCATCCACAAATATGAATAATGATTGGGTCTTTT +TTAAAGATCCTGGATTTTATCTGTTGTCAGTTATATCAAATAATTTTGGCTTTGGTGTCATTGGAGTGATTTTTTCGCTT +TTTATAATATCACTTTCGTCTAAGATTTTTTTTTGTATTAAGTTACTTAATAGAGAAACTCTATTCTGGGTGCTACTTTT +ATATCTGTCTAGGCTCTTTATTGTTCATGATCTTGTTCAATATCGAGCCGGTGCGTCAATTGGTTTGTCAGCATTATTTT +TGTATTTTTATTTAGAGAAAAAAAAGTTTAAGTCTTTTTTTTTCTTATGCCTCGCACTTTCTATCCATCTTTCTAGTTTG +CTGATTGTGTCAGTTATCCCTATAGTGTGGTATCTTAATAGGAATATAGGTAACAATATATTCAACCAGATAATAATAAT +AAGTTTACTATTGTCTGTGATTTTACTTTTTGACCCTTACATTAATTTGCTAAGGTTGGTCGCAGAGTTTCCTATGATGC +ATGAAAGAATTGCTCCATATTTGGATGGTTCATATGCTGTTAATAATGCACCAATGTTTAATAGCTTTGTAGTAATTAAA +ATTATATCATATGTAATTTTTTTTATATGGATCTATAAAAATAAAAAAGTTGGTTTAACCATAGAAAACTACTTAATTTA +TCTATGTTTCTTTCTGTCTATTGTAGGATTGTTTCTTTTTTGGTGTTTCAGAAGTAATGACTCGCTATCCATTAGATTTT +CTGACTTTTTCGCCATATACGATATTATTTTTTTTGCTCTATTATTAAATGTTTTTGATGTGTTTGGGAAATTTATCTAT +AGATACTATCTTTTAGTTATGATGATTGCTTTTTTTATATCTTCATTTAAGTTGATAAATTAG +>O-66_wzx__1257 +ATGCATAGTAAATTAAAAATGAAAAAATTATTAGACAATGCTATTGTTAAGAATATCTTGTGGCTTATAAGTGAGAAGCT +ATATTTCGTTATTCTTATTTTTTTTGGCGAGGGGCTTATAAGTCGTACACTTGGAGTGAATGATTATGGTAAGTGGATTT +ATTCCTTGAACATAATAATTATTATATCCTCAGTTGCACTAATTGCTGGAAGTGAGGTCATGGTGCCGGCTTTGAGCAAG +AATAAAAAATTAGCAGGGGAATTAATAACTTCAGCTTTCATAATTAGATTCTCAGGCGCATTACTATCATTTTTGGTTTT +GAATATATACTCTCTTGTGTTAGTAAATGATTTAGTGATACAACATATGCTTCTTTCTCTTTCGTTAGTGCTTTTATTCA +ATGAGCCTTTCGGTGCGATAACTAACTATTTTCAAGCAAAAATAGACATGAAAAAAGTAGTTCTGGCTCGCTGCTTATCA +CTAGCATTGCGTACAATATTTGTTTTGGTCGCATTTAAAATTTTCGAAAGTAATCTCATTTATTTTTCAAGAGCCAGTGA +ATCTATTCTTTTGGCTCTAATACTATCATTGCTTTTATATAAAAGTAAAATAAGGCTGAATTTTTCAAAAAAAGTATTTT +TAATAGTATTAAAAAGAGGGTGTTTATTATGGGTCCCTCTAATTAGTATGATGATTTATCTTAGAATTGACAGGTTTTTT +GTTGAAAAGTACTTCTCTTATGAGACGTTAGCTATGTATGGCGTTGCTGTTCAGTTTATTGAACAGGCATTTTTATTATT +AGTTATAGTGATTCAGACAATTTCCCCAAAATATATTTTTCAATCAATGCCAAAAAAAACAATGTTGAAAAATATAAAGC +TTATATCTTTATTGCTCATTATGCTTGTTTTTATGATGCAGGTCTTTTGCTTGTTTTTTTTGAAAAGTATTATTACCATA +GTATATGGGGATTCATATATTCAAGCAGCTACGTTGGCTATCTCGTTATTACCTTCATTATTATTTTATGCAGTAGATAC +CATTCTTATGCAGGTGTTTTACAAGTATAGGAATAATAAAGCGATACTAACTAAATGGATTTCAATGATGTTTTTCTCCT +GTGCGATGTATTACATTTGGTTCGACTTGCTTTCAAAATCTAATGTAACTATGGTTTTTAATATTAATTATTTGACTATG +TCAGTAATTACATTTGTTTTATTTAGACGTGGATTAAAAGATTGCAAAAATGATTAA +>fliC_i_Salmonella.enterica_Lindenburg_AY353428_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTTTCTGGCCAGACCCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACTTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_k_Salmonella.enterica_IIIb.42:k:e,n,x,z15_AY353436_k,z__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATGCGCTGAATGTGCAGAAAGCTTATGATGTAGATAGCAAACCAGCGCA +GAGCATTAAACTGGATACCAGTGCTCTTACTGCTACTGCAATTAAAAATGGTGTAACTGGTGCATCGACAGATGGTGCCC +TAAAAGACGGTAAAGTTTACTCTAATGGCACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGATACTGCTAAA +GGTGGTTTCCTTAAAGTAGATGTTGATTCCGCTACTGGTGCAGTTACCGTTCCGGGTACGGCAGCAACAGCAGCTGCAAC +TAAACCTGCCGGTGTGAAAGAGGTTACAGAAGTACAAGGTAAAATCCCAGCATCTACTGCTATTCAAGACCAATTGAAAG +CAGGCGGTGTGACTACTGCAGATGCAGCTACTGCTGAAGTTGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATT +GATGGCGGTTATGCTGTAAAAGTAGGCAATGACTACTACGCCGCTACTCAGAAAAAAGATGGTAGCTTTAGTGTTAACAC +TACGTCTTACACCGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCGAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_i_Salmonella.enterica_II.4,12,27:i:z35_AY353425_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTTTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAATGACGGCATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCAATACTGCGATTGCTTTAAACAATGGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACAG +ACCAGCAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TGCAGGTGGATTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCCAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGCTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCGAGCAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCAGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACTGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,t_Salmonella.enterica_II.16:g,t:1,5_AY353408_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCTCAGTCCTCACTGAGTTC +CGCTATCGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATTGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATACAAAAGCTGGTAATGACGGTA +ATGGTACGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCGGCAGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAATGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGTGAAAGTAAGATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCTAAGAAAAGTACCGCTAATCCACTGGCTGCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCGCTGGGGGCAATTCAGAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCCGGTACCTCTGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,z62_Salmonella.enterica_II.50:g,z62:e,n,x_AY353416_g,m__1515 +ATGGCACAAGTCATTAACACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCTCAGTCCTCACTGAGTTC +CGCTATCGAGCGTCTGTCCTCTGGTCTGCGTATCAATAGTGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAGTTCAACG +GCGTTAAAGTCCTGTCACAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGATTCAATGTTAACGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGTTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTGCTGCTGGTACCGCTGACGCCAAAGCGATAGCTAATGTCAT +TAAGGGTGGTAAAGAGGGAGATACCTTTGATTATAAAGGCGTATCTTTTACTATTGATACAAAAACTGGTAATGATGGTA +ATGGTACGGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGGTGGTGGTAGTGTTAAT +GATGCTACCTTACAATCAAGCAGAAATGTTTATACATCTGCAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAAAAA +TGAGAGTGCGAAACTTTCTGATTTGGAAGCAAATAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTGAAT +ATACTGCTAACGCCGCGGGTGATAAGATCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTTAGT +ACATTAATCAATGAAGACGCTGCCGCTGCTAAGAAAAGTACCGCTAATCCACTGGCTGCAATTGATTCTGCATTGTCAAA +AGTGGACGCAGTTCGTTCTTCGCTGGGGGCAATTCAGAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGGTAA +CCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAGATT +CTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>O-57_wzy__1038 +ATGATACCATATATAATTGTATTTCTTATTTTTGCAACTATTGCTTTACTTAATTATGATAGGTGTAAACTATTTTACTC +CTCCATGATTTTTTTGGGTTTTGCCTGTGTAATGAGAGGAAGTGACGTAGATAGGGATTACGAGACATATGTAAATATTT +ATAATTATATAATTCATGGTTATAGTTATACAATTGAACCAACTTTTTTTATAATCTCAAAAATTTCTTATTTAGTGGCT +GGGACCCCTTTTTTTATTTTTATTCTCTATGGCTTGCTGGCGATTTACTTTAAGGCTAAGTTTATAATCGATTGGTCTCC +CTATCCTCTACTTTCTGTTATAGTTTACTTTTCAAATGTTTATCTCTTACATGAGATGACTCAAATAAGAATAGGTTTAG +CCAGTGCGATTGGATTCTATAGCCTAAAATATCTTATTACTAATGAAAAAAGAAAATATTTTATATGTATCTTTGTTGCA +ACCCTTTTTCATTATTCAATGGTTATTTTTTTGTTTCTTCCATTATTCAATGTAAGAAAAATATCGTCACAGTATAAATT +ATTTTATTTTATTCTTATTGTATTATTATATTTTTTGTATCTGTTTAATATAGATTTATCACTTTTAATAAAATATATTG +ATATAGGATTAATACAATCGAAATACAATATATATAAGGAACAGGTTATAGATAATGGTACTAATGTAAATGTCTTTTCA +GTAATGCAAATATTAAATTTACTTATTATTTTTTTTGCTATGTCATATTCTTCGCATTTTAAAGAAAATAGAAAATTAAT +TTTAATAGTAAAGGTTTTTTCATTAGGCCCTATCTCATTAATATTTTTCTCTGCAATTCCTGGATTTGCGTTAAGATTAA +GTGAATTATTTACTGTAGGACAAATAGTATTACTTCCTATGCTTGTGAAGCAGATACGACAAGTAAAACTGGCTTATTTA +GGTGTTATACTTTTATCGTTTATCATACTATTGAATAATTTATATTATCTGTCACTTGTTAAGGCATATTCTATTTAA +>fljB_l,w_Salmonella.enterica_Ohio_AY353331_l,v__1503 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGTGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCACAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAATACTGCTGGTCTTAATGATACAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAACG +GTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCACGAA +AGTGGCAGGAGGCATGCCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAGTTA +AAGATCAATTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGATAAA +AACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGGATC +GTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAGACG +GTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGGCACAACTTCAAAGCACAGCCA +GAGCTGGCGGAAGCGGCTGCTACAACCACTGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCT +GCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGTGCGCAGATTCTGCAGCAGGCC +GGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_z_Salmonella.enterica_IIIb.61:i:z_AY353335_k,z__1500 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTTTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTAGATAGCAAAGCTGTAAC +TGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGTACAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACAACTG +GTTCCATTAAAGATGACAAAGTATATTATGATAGTGCTACTAAAAATTATTATGCTGAAGTGAACTTTACAGATGCCGCT +GATACCGCTAAAAATGGTTTCTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCTTCGACTACTAAAGA +AGCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCATCCGCAGATGTGAAAG +CTGCTCTGACTGCTGGAGGTATTGATACTGCTGATGCAGCTACGGCAGAAATGGTCAAAATGTCTTACACCGATAAAAAC +GGTAAGACGATTGATGGCGGTTACGCTGTAAAAGTGGGCGATAACTACTATGCCGCTACCCAGAAAAAAGATGGTAGCTT +TAGTGTTAACACCACGTCTTACACCGCAGCGGACGGTACATCCAAAACTGCCTTGAACCAACTTGGTGGCGCAGACGGTA +AAACCGAAGTCGTTACTATCAACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGCCATGATTTCAAAGCACAGCCAGAG +CTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACG +TTCTGACCTGGGTGCAGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTG +CACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGG +ACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,x_Salmonella.enterica_Chester_AY353321_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCGCAGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCCGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,x,z15_Salmonella.enterica_IIIb.42:k:e,n,x,z15_AY353309_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATTCACTGAATGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +TAGCTCTACCTATAGTGATGGTACTAAGGCTCTTACGGCACCAACTGCAACTGATATTAAAACTGCATTAGGCAACCCGA +CGGTAACTGGTGATACATTAACTGCCACCGTATCCTTTAAGGATGGTAAATATTACGCCACCGTAGGTGGTTATACCGAT +GCGGGGGATGTTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACTCC +GACTAAAGCTACAGTAACTGGGGATACAACCGTAACTAAAGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGAGGCGTCTCATCTGCGGACGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAATATTACGCTGCTGATTACAATGAAACTACAGG +AGCTATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACTAAAACGGCGGCTAACCAACTTGGTGGCGCAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAG +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACAC +GTTACGTTCTGACTTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGA +CTTCTGCACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCGGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,x,z15_Salmonella.enterica_IIIb.57:i:e,n,x,z15_AY353312_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTTTCTGCGACAGACGTTAT +TAGCTCTACCTATAGTGATGGTACTAAGGCTCTTACGGCACCAACTGCAACTGATATTAAAACTGCATTAGGCAACCCGA +CGGTAACTGGTGATACATTAACTGCCACCGTATCCTTCAAGGATGGTAAATATTACGCCACCGTAGGTGGTTATACCGAT +ACGGGGGATGCTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACTCC +GACTAAAGCTACAGTAACTGGGGATACAACCGTAACTAAAGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGAGGCGTCTCATCTGCGGACGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAATATTACGCTGCTGATTACAATGAAACTACAGG +AGCTATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACTAAAACGGCGGCTAACCAACTTGGTGGCGCAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAG +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACAC +GTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGA +CTTCTGCACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCGGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>O-43_wzy__1344 +ATGCAAATATTAAAAGCTAAAGAAAGTAATAAACAATCTGTTCTATTTATTTGCATGCTTGTTTTTTTTTACTTACTTAC +TTTTGTTTTGTTTCTTTTAGATGAAGGTTTATTTAGTTTTCTTTTTTTTATTGAAGCTTTGCTGGTATTATTATGTTGCT +TGTTTGTTGTGTTTTCAGAAAAGAAAAATGGTTTTTTAAATCCTTTATCTTTTTTTATTATATCAACATTTTTTTTTATA +ATAGTTAGACCTATTTTCTATTCACTGAGTATAGCTGAAAATGTGAATGAGGTTATCACTGCTGGTTATTCTATAGATAA +GAATTATTTATTTTATTCTTTATTTGTAGTGAATATTTGTTCAGCTTTGACGATACTTAGCTGTTTATTGCTAAGGCCAT +TATGTAAATCTATTACTGTCAATATATATGACTTATATTTTTATAATGGAAATGTATCTCGTCTTTTTATGTTATCAGGA +GTAATTTTTACAGGTGTTTTTTTAATAAAATCATATTCTAAATTTATCCTGTTAGGTGATGTTTCGGTTTTTGAGGTAGA +TAAATATGGTTTACATGACGACCTTTACTGGTTCACATTTGCGAAATATTCATATATTGTGTCTTTGTTGTTTGCTAAAC +GTAAAGATTTTATTTTTTACTCCCTTCTAATCTTTCTTGCATCTATAGGCTATATTATGGTAGGTCTAAGAGGGTATACT +ATATCTTATGCTTTTCTATTGTTATTCTTTTTAGATCTTAGATATAAATTAAAGTTTAGGTATTTACTAGTTTTTGCTAT +TCTGGTAGCTATAGTTTCATCTCTTATTCTTAATTACAGGATAGGTATCGAGGTAAATCGTGGCTTTTGGGAAATGATAT +TTAATCCCTTATTACAGCAAGGGGCCTCTTTTGAAACCGTATATGGAGTTTTAAAATATCATAGTAGCGTACTTAATTGT +ATTTCTTATTATGACTATTTTTTTTCAATTAAGGATATTGGCAGTTGTATTGATAGCGCGCGTGGTATATATTTTGCTGA +AGGTGGAAGTTTTGCAACAAGCTTTTATAGTGAGTTGATATACTTTGGTTGGTTTATTGGAGGCATAGCCTTGCTTCTGT +TTTCTTTCTCATTATCCTTTATTCAGTCCTGTTATGATTGTATTGTAAAAAACAAAAGAATATCAGAAAATTACACATAT +AAATTAATTTTATTCCTATTATTACCAAACCTTATATACTTTGCTCGTTCTTCTCTATTTGATTTTAGTATTAAGCTGGT +TTTTGTATTGTTTTTTATTATTCTTTTGTGGTTTATGAAAAAAACATTAGTGAATGTTAAATAA +>O-53_wzy__1119 +ATGTCTTATTTATATCTATTGTTTTCCGGTATCTCCTTAACCAGTAAATTGGGGGTCATAGTATTTTGGTTATCAATTCC +TGTGATTTTTTTTTACTGTTTTGGAGTATCATTGCTTTATAATAGAAAAGTGCATAAAAAATACTTCATTATAGTTATTT +GGAGTGTTTTTTTTATTCTTATGGCTGGTTTAAGCGGGTATTTTCTTGATGATTTTAATTCAAGGGTTATCAGTAATGTC +TATTTATCTCTAGTTGGTCTATTTATGGCATTAGTGTTTTATAATAGGGGAAATAGCTCTAATGATAAATCCTTTCTTAC +AGCGATAAAGATCACTATTTCTATAAATTTATGTGCTTTCTATATACAATTCGTTTCGTTCTATCTCTTTCATTACATCA +TTGATTATAATTTATTAAGTGGAGGGCTGGGGGGACGTTTTTACTGGGGCGATCTTTTTCGGGCAGCAGGATTTTTTGAC +GAGCCTGCTGTATATTCATTACATATGGTTGCTTTGACAGTAATGCTATATATGCAGGAGAGAAAATTTTCAATTCTAAT +TATTGTTACATTGCTCAGTCTATTGCTATCTTTTTCGTTTATTGCTATTTTTCAAGCAATGATTTTGAGCTTGCTTTTTA +TTAAAAATAAACGAGGCCTGCTTGTGCCTCTCGTAGTGTGTTTGGTTGTTGCATTACTATTTAAAGATAATATTTATGAG +CGTTATTTACAATTCGTTAGTGGAGGTGATGGTAGCAACAATACTAAGTTAGATACTATTTATAACTTATTTCAGGGAGT +AAAGTGGCTTTATGGCTATGGTCTTGTAGGATATTCACAATCATTCCCACTATACTATCAAGGTTTGTATGATTTAACAT +TTTGGGGAGCAAATATAAGTTTATATGGGATAGTTTTAGGCTTAATTATAAATGTAACTGTATTATTCTTTCTGCTTAAA +TTTACTATGAGGGACTTTTTATTAATAAACGTTGTCCTGTTGAAATTATCAACTCCCACATATGGAATATATTTTTGTTT +TCTTTTTTTTCTACTATGGTATAAACAGAATATGGTAATTCGAGATGCCAAAAATATCAGTTTTAATGGCGATAAATAA +>O-30_wzx__1392 +ATGATTAAAGAAAAAATCAAAATATTATTTAAATATTGCACGTTAAGAAAATATAACACTACAACTGACTATGGTAGACA +GCAAGAAAGATATAGGATTATTTCATTATCTATCATATCGAATTTTATTAGTAAACTATTAGCGCTACTTTCGCTTATTT +TAACTGTTAGTCTGACTTTACCATATTTGGGGCAAGATCGTTTTGGAATATGGATGACAATCGCAAGCTTTAGTGCAGCT +TTAACTTTTTTAGACTTAGGTATTGGAAATGCATTAACAAACAGGATTGCACATTCATTTGCGCGTGGCAAAAAAATTAG +AATGATTAGACAGATTAGTGGAGGGTTGACTCTCCTCGCTATATTAGCATTCATCATTATTGCTATTTTCTTAACCATTG +CTAATTTTGTCAACTGGGGAAGCTTGCTTAAAGGAATTAACGATAACACACATGATGAAGTACAGTTTGCTATAAAACTG +TTCGCCATTATATTTGGTATTGGTATATTCTCGAATGGTGTTCAAAGAATTTATATGGGAATGCAAAAAGCATATATTAG +TTATATATCTAATGCCTTCTTTATTTTAATATCTATAATATCTCTTTTTATTTCATCTAGGCTTCATGCAGGAATACCGA +TGCTAATCCTTTCGACAATTGGTGTTCAATATCTTTCAGGCCTAAGCTTAACTATACTTCTAATTTATAAAAAACTTATA +ACTCTTAATAAAATAAGAATAAATGTAAAAAAGGAAACGCCCTATTTAATCTCTAATGGTTTCTTCTTTTTCATTTTGCA +GATGGGGACATTAGCAACTTGGAGTGGGGATAACTTTATAATATCTACAACATTAGGGGTGACATATGTATCAATATTGA +GTATAACTCAGAGGCTTTTTCAAATTTCTACAGTACCTTTAACTATCTACAATGCACCGTTATGGGCAGCCTATGCTGAT +GCGCATGCTCGCCATGATGTTGATTTTATAAGAAAAACTCTTTTAGGCTCACTTAAAATTGTTGGGATCTCTTCTACTAC +TTTGGCATTAATATTAGTAATATTTGGTCAATCCATCATAGCAATATGGACTGGGGAAGAATTAAGAGTTCCGCAATCGC +TTATTGTTGCTTACGCAGTCTGGTCTATTATTGATGCTTATTCAAATACATTATCAAGTTTTTTAAATGGCTTAAATATT +ATTAAACAACAAGTTTTTGCAGTAGTTACTTTGATATTGATTTCAATTCCATCAAAATACTTTATCGTTAGTCACTTTGG +ATTAACGGCTATGCTAAGTTGTTTTATTATTTTGTATGTAACTAATTATCTAATATGGTATAAATGTTCTTTTAAAAAGA +GTATTCATTTACAGTTAAATATAAGAGGGTGA +>O-21_wzy__1089 +ATGAGAATAGCTATAGAGAATAGCGCTGTCTTTTTATTAACTGCGTTTTCTGGTATTTATTTACGTAGTACAATGATTAA +GCCGGGGTATATAGCAGTTATTATATCAATGTTATTAATGGTAATTTTTATTGTTTATAGAAAAACTGTAATATCGGCCT +TATTATGTTTTTTTATTCTTTTTTTTGTTGGTTATATATGGGGAACCCAGCCTTTTTTACAGGGGGAGTATGCAACGCTA +ATTTTTACAAGCTCGATTATAATGTTGATTTTTCTGCCACAGATGATTAGAAAGAGTACATTTAATATAAATATAGCTTT +TATAGTGATAATTATATTTTATTCTCTTGAGAGTTACATAAGGATAAAAAACCCCGATTATGATTTTGAGCCAAAAGAGA +TTTCTAATAGCATTTTAGATACTTTTTATATTTATAAAGTAAATAGCATTGCGTTTGAAGATTCAAATTTTGTAGCTATG +ATTTTAACATGCTATTATATTCTATGTAGGGTGTTGGGGAAAGAAAATGTATATGGCAAGACCAATGTTATTTATTCATT +ATTATTTCTTGCTCTCATAGTATTGACATTTTCAAGATCTGCCTACATAGGGGTGATAGTTTTTGAGTCGCTAATGTTTT +ATCAGTACTCCAAACGATATAGAGTCTTGTCTATCTTTTCTATAGTGATAGCAGTGATAGTGTTTTTATATTTTCTGCTT +GATAAAATTCAATCAGACGGCAGTTTTCAAAGTAAGTTTTATATATTTGATTTGTTTTTAAACTATATCAAAGTTGCACC +ACTATTTGATGTGTTAACGGGAGTTGGTTTCGGTAATACATTTTCATACATTGGTATTGGACCTCATAATATATATATAG +CCTTATTTATTGAGACAGGATTAATCGGACTGATCTTATACTTATTAATTTTTATCTATATCTATATTAAATACAAGTTT +TCTAGGCTAATTATTTTACCAATTATGATCATGGGATTATCGTTTTCGCCAATTGCGTTACCATATTTTTATGTTGCTCT +ATCTTGGTTAATGTATTTAGAGAGAAAAAATGGATATTTTGAAAGGTAA +>O-28_wzy__1317 +ATGGAGTTTACTATAAATTTACTCATAATTTTATTGAGTTTTATTCCCGGTTACTACTTGGGGGTCTTTTATTTTAAACG +ACTTAATTATTATTGCGTCCTTTTTTGGACTATGTTCTTATTTTGTGTTGTGGGATCGTTTATAATATATTCTGGCATAA +TGGACAATTCATTTTTTGTCGAACCGATTGCGAATAATACAAAAGCAAAGAACCTTGGCCTTTTTATTACCACTATTTCT +TTTTTTATATTTTTTCTTGCTGCTTTTATTGTTGAGATTTTTTATTCATTCTACACAAAAAATACCACTAGCAAAGTGAA +TTGGGATAGGTACTACTCACGTTTGATACTTAATAGTAATAGCCTACTCATGTTAGTCTTATTTTTACTGTCGTGTATGC +TGATTTTATATTATATAGTATCAATATACCCTGCCCCACTATTTATGGTACTCAAAGGAGCTTCTGCGGAAGAAATTGCC +ATTCGAAGATTAGAAGTGACAAAAGATTATTCAGGAATCGGTTATTTCAAAACATTGGCTGGAATATTACCAACAATTTT +TTCATATTATTGTTTTATTTCATATTTAAAATTCAAGAAACACTTTTTTATTTTTATCATTACTTTATTTCTCTCTATGT +TAACATTAATTATAAATGGAGAGAAAGCACCGCTAGTTTTTTATTTTTTGGGGCTTTTAGTGTCATATTCATCTGTAAAA +GACATTAGTAAAAAGATTTACTTTTTTGCGCTGTTATTAATATTTTCTTTGATTTTTTTGATGTATATTATTCTTTTTCA +GTTTGATAGCTCAGATTATCTTCTGTATATACTTATTGAGAGATTATTTATTGCTCAGGAAGCCGCTGTATTCTATGCGG +CAGATTACTTTTCAAGCCATAATGTTTTGGGTCTATCCAGTATGGATACGATTTTTAATAAATTATTGAATATTACTCCA +GCACCTAGAGCATCAGAGATTTTCATGTACCAATATCTGCCAACAATGGTTGAAAATGGTGGTTGGAATGTGAATGGATT +TTTTGCTCACGAAACTTTCTCCAATTTTGGTTACATAGGGGTTGTTTTTGGAAGTTTTTATGGTGGCATAGTAAATAGTT +TGTTGTGTATATTTTTCCGGACAAGAAAAAAGACATTATTAACAATGAGTTTTTATAGCTTTTTCATCGTTTCCGTAACT +ACGGTTATCAGTAATTTTAATGCGATGTTATTTAATACACAATTAATATTAATATTTATTATTTATATTTTATTGTCTTT +TCTCGATAGGGGAGGTAAATATCATGTATCAAAGTGA +>fljB_e,n,x_Salmonella.enterica_Singapore_AY353305_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAAACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,x_Salmonella.enterica_Bessi_AY353317_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAATGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACTCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_1,6_Salmonella.enterica_Agama_AY353294_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATTACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +CACGAAAACTTATGCCGATAATGGTACTACACTGGATGCCTCAGGCCTTGATGATACAGCTATCAAAGCGGCTATAGGTG +GTACGCTTGGCACGGCTTCTGTAACCGGTGGTACAGTTAAATTTGACGCAGATAATAATAAGTACTTTGTTACTATTGGT +GGCTATACTGGTGCTGATGCCACCAAAAATGGCGATTATGAAGTTAACGTCGCTACTGACGGTAAAGTAACCCTTGCGCC +TGGCGCAACTAAAACCACAATACCGGCAGGTGCTACAACCAAAACAGAAGTACAGGAGTTAAAAGATACACCGACAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGATGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fljB_1,5_Salmonella.enterica_Rough:r:1,5_AY353281_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGTTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATACAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTGAAAGATACAGCAGCAAC +AACGAAAGCTTATGCTGATAATGGTACTACACTGGATGTATCAGGTCTTGATGATGCAGCGATTAAAGCGGCTACGGGTG +GTACGACTGGTGCGCCTACTGTAACGGGCGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGGTGATGCTGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTAACACTTGCGAC +TGGTGCAACTAAAACCACAATGCCTGCAGGTGCTACAACCAAAACAGAAGTACAGGAATTAAAAGATACACCGGCAGTTG +TATCAGCTGATGCTAAAAATGCTTTAATTGCTGCTGGCGTTGATACTACAGATGCAAATGCCGCGACATTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAATATTACGCTGCTGATTA +CAATGAAACTACAGGAGCTATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACTAAAACGGCGGCTAACC +AACTTGGTGGCGCAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCAT +GATTTCAAAGCACAGCCAGATCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCT +GGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACA +CCGTAAACAACCTGACTTCTGCACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCGGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTA +A +>fljB_1,5,7_Salmonella.enterica_Hisingen_AY353289_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGCCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCCAACATAAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGATGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCTGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAATGTGCAGAAAGCGTATGATGTGAAAGACACAGCAGCAAC +AACGAAAGCTTATGCTGATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCCATTAAAGCAGCTACGGGGG +GGACGGCTGGTGCGCCTACTGTAACGGGCGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGTTGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGATGGTAAAGTAACACTTGCGAC +TGGCGCAACTAAAACCACAATGCCTGCAGGTGCGACAACCAAAACAGAAGTACAGGAGTTGAAAGATACACCGGCAGTTG +TATCAGCTGATGCTAAAAATGCTTTAATTGCTGGCGGTGTTGATACTACAGATGCAAATGCTGCGACACTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACTACAAGTTATACTGCTGCTGACGGCACTACCAAGACGGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGGCAT +GATTTTAAAGCACAGCCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAATCCGTTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGTTGCGCTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAATAACCTGTCTGAAGCACGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATCCTGCAGCAGGCCGGTACTTCCGTTCTGGCACAGGCTAACCAGGTCCCGCAAAACGTGCTGTCTCTGCTACGTTA +A +>fljB_z6_Salmonella.enterica_Bere_AY353352_k,z__1503 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAAACTACTGAAGGT +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGTAAGGCTGTGAC +AGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTG +CAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCT +GATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGA +GGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCA +AAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTTGTCAAAATGTCTTACACCGATAAA +AATGGTAAGACGATTGATGGCGGTTACGCTGTAAAGGTGGGCGATAATTACTATGCCGCTACCCAGAAAAAAGATGGTAG +CTTCAGTGTTAACACCACGTCTTACACCGCAGCTGACGGTACTACCAAAACTGCCCTGAACCAACTGGGTGGCGCAGACG +GTAAAACTGAAGTCGTTTCTATTGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAGCCA +GAGCTGGCGGAAGCAGCCGCTAAAACCACTGAAAATCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCT +GCGTTCTGACCTGGGTGCGGTTCAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTG +AAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCC +GGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_1,7_Gaminarastr_AOZF01000073_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCACAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTGCACCTAGTGTAACAGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATCTCGACAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCAGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATCGCTGGCGGCGTTGACACTGCCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGTT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTTAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fljB_z35_Salmonella.enterica_Tamilnadu_AY353340_other.z35__1488 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTTTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGCGTGCGTGAACTGGCAGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACCCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCATATGATGTGAAGAGTGAAGCTGTCAC +GCCTCCGGCAAAACTTGATATTTCAGGATTAACTGGAACTGCAATTAAAACTGGTGTTGATGGTGCTACGGTTGATACAG +GCTCCATTAAAGATGGCAAAGTTTATTATAATAGTACCTCTAAGGACTATTACGTAGAAGTTGATTTTGGTACATCAGCC +GATGCTGCTAAGAGTGGTTACTATAAAGTCAACGTTGCTGATGATGGTACAGTCTCAATGGCAGCTTCTACCACTAAAGA +GGGTACAACTCCTACTGGTATTACTGAAGTTACTCAGGTTCAAAAACCTGTAGCTGCTCCAGCCGCTATTCAGGCTCAGT +TGACAGCTGCTCATGTGACTGGAGCTGATACTGCTGAAATGGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATT +GATGGCGGTTACGCTGTAAAAGTGGGGGATGACTACTACGCCGCTACCCAGAAAAAAGACGGTAGTTTCAGTGTAAATAC +TACTTCTTACACTGATAAAGACGGCAATACTAAAACCGCACTGAACCAACTTGGCGGCGTAGACGGAAAAACCGAAGTCG +TTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCGGGTCATGATTTCAAAGCACAGCCAGAGCTGGCGGAAGCA +GCCGCTAAAACCACCGAAAACCCACTGCAGAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGATCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTA +TCGAAGATTCCGACTATGCGACTGAAGTTTCTAACATGTCTCGCGCGCAGATTCTGCAACAGGCCGGTACTTCCGTTCTG +GCGCAGGCTAACCAGGTCCCACAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,x_Salmonella.enterica_Gatuni_AY353322_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCCGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,z15_Salmonella.enterica_Sanktgeorg_AY353326_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCAGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACAGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCTACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAGGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCATGATTTTAAAGCACAG +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATCCTGCAGCAG +GCCGGTACTTCCGTTCTGGCACAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fliC_y_Bareillystr_AOZP01000027_other.y__1508 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTTGATAACACGGTTGTCAC +GAACCCTAATTATGTTGATGGTGCAGCGTTAAGCACTACGATGCCTACTGCGGCTGAGATTAAAACGGCTATTGGCACTG +GTGCGGGAACTCCGGCAGTTAAAGGTAATGAAGTTCAATTTGATAAGAGCACTGGGAAGTATTACGTTGAAATTGAAGGA +TATTCAGCTCCTGATGCAGCTAAAAACGGCATTTATGAAGCCAAAGTTGCTGATGATGGCACAATATCTTTGGAGACTGG +GACCAAAAAATTGGCACCGCAATGCCTGCTGGTGCTGAAGTTATTACTCACGTGCAGAAAAAAGATCAACCAGTTGTTGT +TGATGCCAGCGTTAAAGATGCTCTAAAAGCTGGTGGGGTAGATGATGCAGTTGCAGATACCGCGCAATTAGTCAAAATGT +CTTACACTGATAAGAATGGTAAAACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTAC +GATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCA +ACTGGGTGGCGTAGACGGCAAAACCGAAGTTGTTACTATCGATGGTAAAACCTATAATGCCAGCAAAGCTGAAGGTCACA +ACTTTAAAGCACAGCCTGATCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCTGCTTTG +GCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATAC +CGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGC +AGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_r_Salmonella.enterica_IIIb.35:r:z61_AY353460_r,i__1482 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTCACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTGCCTTAGGTGGTACTC +CTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGAT +GGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGGTGGCTT +CCCTTCAACTGCAACAAAAGATGTTAAACAAACCCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAG +CAGCGGGTGTTGCAGCGGCCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGT +GGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGCTCCATAAGTATTAATACTACGAA +ATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTA +TTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCTACC +ACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGT +ACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCGAAG +ATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTGGCGCAG +GCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z10_Salmonella.enterica_Harrisonburg_AY353472_other.z10__1500 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTTGATAGCACTGGCGTTAC +TCAATCTCTTGATTTAAAAACTGCTGGAATTACCGGTGCTACATTAAAAACCAGTATTACTGGTACAACAACAGAAACCG +GTAGCGTTAAAGATGGTAAAGTCTACTATGATGCAGATAGCAAAAATTACTATGTAGAGGTTGACTTTACTGATACTACG +GATAAAGCAGCGCATGCTGGTTTCTACAAAGCTGACGTCGATGCTGACGGTAATGTTTCTTTAGCAACTGGTGCGACTAA +AGAAGCAAAACCAACGAATGCAGTTGAAGTTGAAAAAACTATTGATGAAAAACCGCTGAAAGCATCAAGTAGTGTTCAGG +ATGCCTTAAAAGCGAGTGGTATTGCTGATGCGGTTGCAGAAGCTGCGACGGTAGTGAAAATGTCGTACACTGATAAGAAT +GGTAAAACTATTGATGGTGGATACGGTATTAAAGTAGGTGATGACTACTATGCTGCAACTAAAGAAAAAGACGGCAGCTA +TACTATTAATAGTACTTCTTATACCGATAAAGACGGCAACACTAAAACTGCACTAAACCAATTGGGTGGCGCAGACGGTA +AAACTGAAGTTGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCACAACTTCAAAGCACAGCCTGAT +CTGGCGGAAGCGGCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCG +TTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTG +CCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGT +ACCTCCGTTCTGGCGCAAGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_l,z13,z28_Salmonella.enterica_from-CDC_2011K-0215_l,v__1506 +TTAACGCAGTAAAGAGAGGACGTTTTGCGGAACCTGGTTAGCCTGCGCCAGGACGGAAGTCCCTGCCTGCTGCAGAATCT +GCGCGCGAGACATGTTGGAGACTTCGGTCGCGTAGTCGGAATCTTCGATACGGCTACGGGCAGAAGTCAGGTTGTTTACG +GTGTTGCCCAGGTTGGTGATAGCGGAGTTGAAACGGTTTTGTACCGCACCCAGGTCAGAACGTAACGTGTCAACCTGTGC +CAAAGCAGCATCAATTTTCTGCAGCGGGTTTTCGGTGGTTGCGGTAGCCGCTTCCGCCAGATCAGGCTGTGCTTTAAAGT +TGTGACCTTCGGCTTTGCTGGCATTGTAGGTTTTACCGTCGATAGAAACGACTTCAGTTTTACCGTCTGCGCCACCCAGT +TGGTTCAGTGCGGATTTAGTGTTGCCATCTTTATCGGTGTATTTCGTGGTGTTAATGCTGAACGAGCCATCTTTATTTTT +TGTTGCAGCATAAATATCAGCCCCAACTTTAACACCGAAACCGCCATCAATAGTCTTACCGTTTTTATCCGTATAAGACA +TCGTAACTAATTGACCTTTTGCAGCATCAGCAGTACTAATACCGCTGTCAGTCAACTGAGCTTTAACTTCAGTACTGAGA +GCTACAGGTTTTGGCTGCGTTTCGGTTACTGCCGTCGCCGTTGCTGGCATACCACCTGTCACTTTCGTGGTGGTTGCCGG +CATTGTAACAGTACCATCATCTGCAACATTAACTTCATAAACACCATTTTTACCAGCGTCGCCAACGGTTAAACCTTCTA +CTTCAATAAAATATTTATTATCAGTTGCATCGAAGAAGACTTTACCATCCTTAATTGCAGCGGTACCGCTTGTTGCACCA +CCAATACCTGCTTTAAGAGCTGCATCATCAAGACCTGTGGTATTGAGTGTTGCCCCACCGCCGCTTTTAACTGCCTCACT +CTTCACATCATATTTTTTCTGCACATTCAGCGTATCCAGACCCAGGGTCTGAGAGTTGATCTGCTTCAGATCGATATCAA +TAGTTTCACCGTCGTTGGCGCCAACCTGGATGGTCAGGGTGTTGTCCTGCGCCAGGACTTTCACGCCGTTGAACTGAGTC +TGGCCGGATACACGGTCGATTTCGTTCAGGCGCTGGGTGATTTCAGCCTGGATAGAGTCGAGGTCAGACTGGGAGTTGGT +GCTGTTAGCAGACTGAACCGCCAGTTCACGCACACGCTGCAGGTTGTTGTTGATTTCGTTCAGCGCGCCTTCAGTGGTCT +GCGCAATAGAAATACCGTCGTTAGCGTTACGGGAAGCCTGAGTCAGGCCTTTGATGTTCGCGGTGAAACGGTTAGCAATC +GCCTGACCTGCCGCATCGTCTTTCGCGCTGTTGATACGCAGACCGGAAGACAGACGCTCGATAGCGGTGCCCAGTGCGGA +CTGGGATTTGTTCAGGTTATTCTGGGTCAACAGCGACAGGCTGTTTGTATTAATGACTTGTGCCAT +>fliC_k_Salmonella.enterica_Blockley_AY353442_k,z__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCACAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTTCAAGCTACAGTTGAAAA +CAGTGTCAAACTGGATACTAGTGCTCTTACTGCCGATGCAATTAAAGGTGGCGTAACAGGTGCGACAACAGCTGGTGCCC +TCAAGGACGGTAAAGTTTACTCTAATGGTACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGACTCAGGTAAA +AATGGTTTCCTTAAAGTTGACGTTAATACAACTACTGGAGCGGTTACAGTTCCTGCAGCAGCAGCAAATACTGTAGCAGC +AAAACCAGCAGGTGTGTCTGAAGTTACTGAAGTTCAGGGACTAAATACACCGAGTTCGGCTGTACAAGATCAGTTAACAG +CTGCAGGTGTAAGTGCCGCTGATGCTGCTAAATCTGAAGTTGTGAAAATGTCTTACACGGATAAAAACGGTAAGACGATT +GATGGCGGCTTCGGTGTTAAAGTTGGAGACGATATTTATGCTGCAACTAAAAATAAAGATGGATCGATCAGCATTAACGC +CACTGAATATACCGATAAAGACGGCAACACAAAAACTGCACTGAACCAACTGGGTGGCGTAGACGGTAAAACCGAAGTTG +TTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAGCTGGCGGAAGCG +GCTGCTACAACCACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCTGCGTTCTGACCTGGG +TGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_l,z13_Salmonella.enterica_Westerstede_AY353450_l,v__1503 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAGTACCACTGGTCTTGATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAGCG +GTACCGCTGCAATTAAGGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCACGAA +AGTGGCAGGAGGCATGCCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAGTTA +AAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGATAAA +AACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACGAAAAATAAAGATGGATC +GTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCTCTGAACCAACTGGGTGGCGCAGACG +GTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCTGCTGGTCACAACTTTAAAGCACAGCCA +GAGCTGGCGGAAGCGGCTGCTGCAACCACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCT +GCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCC +GGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z47_Salmonella.enterica_IIIb.38:z47:z53_AY353514_l,v__1500 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACCATTGATATCGATCTG +AAAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGGCAGAAAAAATATGATGTGAAGAGTGAGGCTGTTAAAAG +CGGCGGTGGGGCAACACTAAGTACCACTGGTCTTAATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAGCGGTA +CTGCTGCCATTAAAGATAATAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACCGCT +GGCGACGCTGCTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGTACTGTTACAATGCCGGCAACCACGAAAGT +GGCAGGTGGTATGCCAGCAACGGCGGCGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACTGAAGTTAAAG +CTCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTCACAATGTCTTATACTGATAAAAAC +GGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTGATATTTATGCTGCAACAAAAAATAAAGATGGATCGAT +CAGCATTAACACCACTAAATATACCGATAAAGACGGCAATACTAAATCCGCACTAAACCACTGGGTGGCGCAAGACGGCA +AAACCGAAGTTGTTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGAT +CTGGCGGAAGCGGCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACG +TTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTG +CCCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGG +ACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_f,g,t_Salmonella.enterica_II.17:f,g,t:e,n,x,z15_AY353534_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCTCAGTCCTCACTGAGTTC +CGCTATCGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAGTTCAACG +GCGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTGGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATACAAAAGCTGGTAATGACGGTA +ATGGTACGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCGGCAGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAATGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGTGAAAGTAAGATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCTAAGAAAAGTACCGCTAATCCACTGGCTGCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCGCTGGGGGCAATTCAGAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z32_Salmonella.enterica_IIIa.63:z4,z32:-_AY353508_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TAACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +TTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACCGGCGGTCCGGCTGCGGATAAATTAT +CTCTGACACAAGATGATAAAGGCAATTACTTTGTCAAAGATGATACTGCTGCTGCAGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAAC +CCTATCACGCGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGACCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTGGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAA +ACTACGGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACGGTAAATAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23_Salmonella.enterica_IV.1,40:z4,z23:-_AY353492_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCAAACGACGGTATTTCCATTGCGCAGACGACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCAAACGGCTCGAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACTGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +CTCGGTAGTTGGTGATGTAAAAATTGCGGCCGCTGATTTCGATAACGCAAAAGCAACTGGTGGTCCGGCTGCAGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGGGGCGGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATTAGTTTTGATTCAGATAAAGATGCAACTGCAACTGCGGGGACTCCGCCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCAGGGACTTCTGTTCTGGCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23_Salmonella.enterica_Ekotedo_AY353494_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACTGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +CTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAACAACTGGTGGTCCGGCTGCAGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGTTACTGCGACGGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAGCTGCGGGGACTCCGTCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGCACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGGGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATTCTGCAG +CAGGCAGGGACGTCCGTACTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_e,n,x_Salmonella.enterica_from-CDC_Stk0811_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACTCAGAATAACCTGAACAAATCCCAGTCTGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGCGTGCGTGAACTGGCAGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACCCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAATGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAACCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCACTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAACGACAGG +AGCCATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACCAAAACTGCGGCTAACCAACTTGGCGGCGTAG +ACGGAAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCGGGTCATGATTTCAAAGCACAG +CCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCACTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGTTCTGATCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACTGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACTGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAACAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAAAACGTGCTGTCGCTGTTACGTTAA +>O-18_wzy__1323 +ATGACTCTATTATCTGAACGGCAAACATCAGTTAAAAACTTTTCAAGATATATTCCACTGTACTTTTGTTTATGCTTAGC +TATCGCATTGTTATTGTGTGAGAGTATATTCACTCAAGCATTATACGAGGTGATACTTAAGGTGGTTTCATCATCATTGT +CAGCTTTATTAATTGTTATTATTGCTTACTTTTATATTAAGAGAGCTTATTTTTTTTCATTGCAGTTAATGTATGCATAC +GCCTTTTCTTTAATAATAGGAATACCTTCCGTATACTTACTCAATTTTGGCGAAGCAAAGGGAGGTTTTGAATTAGTATG +CTTATGGTGTATATTATTAAATATTATATTATATTTTTCTGCATGCTCTAGTAAAGTAATAGAACAAAAAAAAACGGTTA +ATAAAATATTTGTTGTGATATTTTTCGTTGTCGGTTTTTGTCAGTTAGTTAAAACGTTGCTCTATTTTAGATTTATTATT +GACTCAGGCTTAGGTCATTTGGCTATTTATACTGAAGGCGAAATTTTAACCGCCCAAGTGCCCTTTGTTATTAGAGCCAT +TAGCGGCCTTTCATTAATCATGTCACTAGCGACGTTTTATTTTAAGGCACCAAGATATTTAAGGTGGATAGGGTTTATAT +TATTAGCATCTGAACTTTTGATTGGGATAAGAAGTAAATTCTTTTTCTCATTGATTTGTATTATTGCTTTATCCTTATAT +AGTAATAGACACTTAATTCAATCAAAATTCGTAAAACTTTCCAAGATACAATATTTATTAATTGGATTCATATTATTCTC +CTTAATTTCTTATTTTAGGGAGGGTTACGAAATTAATTTCATTAACTATTTAGTCATAGTATTAGACTCACTCTCTTCGA +CGCTAGCAGGTTTACAAGATGTATTTCTTTTACCGACAGCGCAGGGTTGGGATAAAATAGATGCACATGTTATATTAACG +CAAATATTACCAATAAGCGGTTTTGGATTTATAAGCGATTCTCAAATTTATAAGCAATTTTCTATCATAGTGCTCGGAGA +TATTTCAAGTGGTATTGCACTATCATCTTCTGGAATTCTAGAAGCAACAGTTTTAAATATAAAGTTTGGTTTTTTTATTT +ATTTATTTTATCTTTTAATTATGCTTGCATTGATCCAGAAATGTCTAAATAGCTCGCTTAATTTGTTGAATTTTATTGCT +ATCGCGATGTTGCCCGGATTATTATATTCAATTCGGGGAGAGTTGGTTTTACCTTTTGCATATATAATAAAATCACTACC +CATTATATTTCTATCTCCTTTTTTAACTTCAACAAATAAATAA +>O-40_wzy-from-blake-2014K-0489__1368 +ATGTTTCAGATTAAAACCAGAAAAAAACCATTGTTGATATTATATTTAACTTTGCTATTAAGTGTTTTAGTGTCATTGAT +TATCGATGATGGTACAAATCGATCCTTATACATACTTTTTATATCCACACTAAGTGTTTTTTTTATCTGCTATTCTTGTA +ATAAAATAACTTCTCCTGCAAGTTTGTTAATTATATCTTCATTTGTTTTTCTTGGTTGTAGACCATTTCTCTCATTATTT +ACAAGTTTCGATTATAGAAATGGCGATTGGTTTATAACTGGTTATTTAGATAAGGATGTTATCTATGCTAATTATGCTAT +TTCTTTTATGTATTTTGGGTATAGTGTTGCATTAATACTAAGTAATAATAATTCAACACGTAGAGAATGTTACAGTTTAA +ATCAAATAAATCCTAATATTAGATTTTTGTTTGTACTCTTTCTTTTTGGCTCTTTAGGCCAAATCCTTAAAGGTTTGTAT +TTTTATTCTTTCATTGAGTCGAATAGTTATGTTGGAATTTATCAAGATAAAGTAAATTTACCAATGGGATATGATTTTTT +ATCATATCTATTTTATTGCTCCTTTTTCCTCATATGCGCATTTTATGATAAACTTCGTGTTAATAAATTATTTTTATTGA +TATCTATATTGATTGCCGCTTTTAGTGCCATGAAAGGCAGTCGAGGGGAGTTTATTACATTTCTGCTTACGGTTTTTTGT +ATTTATTATAATGAGAGAAAAGTAAGTAACATTAGATTGCTATTAAAAATGTTTTTAATATTTATTGCTATTTTCACTGT +TAGTGAATTTGTTTCGATGTGGCGGTCAGGCGGCAGCTTTATTGCTCTTATTGAAGGCGATAATCCACTTTTGCAATTTA +TATATGGAATGGGAGTGTCATATATTGCAATTTACCAATCGGTTAAAATAACTTTAATTTCTGGAGTGTTTGATTTTCAT +TATTTAATCAGTCAACTATTAATTACTATATCTTCTGTGTTAGGGGTTCAGGTGTATTTACCTGACATTAGTTATAGCCA +TTTGGTGTCTAAGACTGCTAACCCACAATTATACCAACAAGGGTTTGGATTAGGAGGAAGCTATCTTGGTGAATCATTTT +TAGCTATGGGGCTAATAGGGTGTTTTATCATTCCATTTATAGTTTTGTTTCTTATTAATAATTTAGAGCGATTTACTAAA +TATAATAAAACTTTTTATTTTTTATATTATAGCTCTCTGCCATCTGTTTTATTTATACCCAGAGAAACTTTGCTCTATTT +TTTCCCTTATGTAATTAAAGGTATTGTTGTGGCATTTTTGTTTATATGCTATTCAAATATTAAAATGAGAAGATTTAATA +ATGGTTGA +>fliC_l,v_from-Nchanga_SRR1153349__1503 +TTAACGCAGTAAAGAGAGGACGTTTTGCGGAACCTGGTTCGCCTGCGCCAGAACGGAAGTACCAGCCTGCTGCAGAATCT +GCGCGCGAGACATGTTGGAGACTTCGGTCGCGTAGTCGGAATCTTCGATACGGCTACGGGCAGAAGACAGGTTATTTACG +GTATTGCCCAGGTTGGTGATAGCGGAGTTGAAACGGTTCTGAACCGCACCCAGGTCAGAACGCAGCGCATCCACCTGCGC +CAAAGCAGCATCAATTTTCTGCAGCGGGTTTTCAGTGGTTGTAGCAGCCGCTTCCGCCAGCTCTGGCTGTGCTTTGAAGT +TGTGCCCAGCGGCTTTGCTGGCATTGTAGGTTTTACCGTCGATAGAAACGACTTCAGTTTTACCGTCTGCGCCACCCAGT +TGGTTCAGTGCAGTTTTAGTGTTGCCGCCTTTATCGGTATATTCAGTGGTGTTAATGCTGAACGATCCATCTTTATTTTT +TGTTGCAGCATAAATATTAGCCCCAACTTTAACACCGAAACCGCCATCAATAGTCTTACCGTTTTTATCCGTATAAGACA +TCGTAACTAATTGACCTTTTGCAGCATCAGCAGCACTAATACCACTGTCGGTCAACTGATCTTTAACTGCTGTACTGAGA +GCTACAGGTTTTGGCTGCGTTTCGGTTACTGCCGTCGCCGTGGCTGGCATGCCTCCTGTCACTTTCGTGGTTGCCGGCAT +TGTAACAGTGCCATCATCTGCAACACTAACTTCATAAACACCATTTTTAGTAGCGTCGCCAGCGGTTAAACCTTCTACTT +CAATAAAATATTTATTATCAGTTGCATCGAAGAAGACTTTACCATCCTTAATTGCAGCAGTACCGTTTGTTGCACCACCA +ACACCCGTTTTAAGAGCTGCATCATTAAGACCAGTGGTATTGAGTGTTGCCCCACCGCCGCTTTTAACTGCTTCGCTCTT +CACATCATATTTTTTCTGCACATTCAGCGTATCCAGACCCAGGGTCTGAGAGTTGATCTGCTTCAGATCGATATCGATGG +TTTCACCGTCGTTGGCACCAACCTGGATGGTCAGGGTGTTGTCCTGCGCCAGGACTTTCACGCCGTTGAACTGAGTCTGG +CCGGATACACGGTCGATTTCGTTCAGGCGCTGGGTGATTTCAGCCTGGATGGAGTCAAGGTCAGACTGGGAGTTGGTGCT +GTTAGCAGACTGAACCGCCAGTTCACGCACACGCTGCAGGTTGTTGTTGATTTCGTTCAGCGCGCCTTCAGTGGTCTGCG +CAATGGAGATACCGTCGTTAGCGTTACGGGAAGCCTGAGTCAGACCTTTGATGTTCGCGGTGAAACGGTTAGCAATTGCC +TGACCTGCCGCATCGTCTTTCGCGCTGTTGATACGCAGACCGGAAGACAGACGCTCGATAGCGGTACCCAGAGCAGACTG +GGATTTGTTCAGGTTATTCTGGGTCAACAGCGACAGGCTGTTTGTATTAATGACTTGTGCCAT +>tyr-O-9__609 +ATGAAGCTTTTAATTACCGGTGGATGTGGCTTCCTTGGGAGTAATCTTGCCTCCTTTGCTTTAAGTCAAGGGATTGATTTAATTGTATTCGATAATCTATCACGTAAAGGTGCAACAGATAATTTACATTGGTTATCCTCCTTAGGAAACTTTGAGTTTGTACATGGTGATATTCGCAACAAAAATGATGTTACAAGATTAATAACTAAGTATATGCCTGATAGCTGTTTTCATCTTGCAGGTCAAGTGGCAATGACTACATCTATTGACAATCCTTGTATGGATTTTGAAATTAATGTAGGTGGAACTTTAAATTTACTTGAGGCAGTACGGCAGTATAATTCAAATTGTAATATAATTTATTCATCAACAAATAAAGTATACGGCGATCTTGAGCAATATAAATACAATGAAACAGAAACTAGATACACTTGTGTAGATAAGCCTAATGGATATGATGAGAGCACACAATTAGATTTCCACTCACCATATGGTTGTTCAAAAGGTGCTGCAGACCAATACATGCTTGATTATGCAAGGATTTTTGGTTTGAATACAGTGGTGTTCAGGCATTCATCAATGTATGGTGGGAGACAGTTTGCTACTTAT +>O:23-gene2__1146 +CCGGAATTTTATAAAAAGAATATGAAAATATTAATGATTGGTACTACGGTGCAATCTTTATTAGGATTCAGATATGAATT +ACTTAAAGATTTAGTTAGCGCAGGACATGAAGTATATGCGTTATCTGTTGATTATGATTACAAATCGAAGCAGACATTGA +TTGATATCGGTGTCGTACCGATAGATTATACAATAAGTCGCTCAGGAATTAATCCCTTCAAGGATTTTGTTAATTTTATT +TTTTTATATAAGCTAATAAAAAAAATAACACCAGACATCGTTTTTTCTTATTTTACTAAGCCTTGTATTTGGGGATCGCT +TGCCGCATATTATGCTGGTGTTCATAAGATTATCGCGATGCTTGAAGGGTTAGGTTTTTTATTTACCGAACAACCATCTG +GGATTCCCCAAAAGACAAAAATCCTAAAAAGAATACAGATTCTGCTCTATAGAATAGCTTTTAAGAAAATTAATACACTT +ATTGTACTTAATGAAGATGATAGGAATGATTTACTTAACGCTGGTTGTATAGAAGATAGAAAAGTATATGTATTGGGGGG +TATTGGAATAAATTTAGAGCATTACAAGTATTCACCAGCACCACTTGAACCAATTTCTTTTATTTTCATTGGCCGATTGC +TCAGAGAAAAGGGGATTTATGAATTTATCGCTGCTGCTAAAAATATAAAAGAAAGATTTGAAGGGGTGACGTTTAATGTG +CTGGGTAATATTGATCCAGCAAACCCTGGTAGTCTAAAACAAAATGAACTTGATACAATTATTAAAGAAGAAATAATTAA +CTATGTAGGATATGTGAATGATGTTTCTCATTGGTTAAGTAAGAGCAGTGTTTTCGTTTTACCTTCTTATAGAGAAGGAT +TTCCTCGAAGTACACAGGAGGCTATGGCTATAGGAAGAGCTGTAATAACTACCGATGTTCCTGGATGTAGAGATACTGTT +GTTAATAATTCTAATGGTTTTTTAATACAACGGTGGTCTAGCGATGCTCTTGCAGAGGCGATGGAAAAATTTATTTTATC +TAAAGAATTGATTCGCGACTGTGGTAAAGAAAGTGCCAGGATAGCTAAAGAAAAATTTGACACCCGAATTACCAATAAGA +AAATAATTACTATATTATTGTCTTAA +>fliC_f,g,s_Salmonella.enterica_DTU-genomes_unknown_g,m__1518 +atggcacaagtcattaatacaaacagcctgtcgctgttgacccagaataacctgaacaaatctcagtcctcactgagttc +cgctattgagcgtctgtcctctggtctgcgtatcaacagcgcgaaagacgatgcggcaggccaggcgattgctaaccgct +tcacttctaatatcaaaggtctgactcaggcttcccgtaacgctaacgacggcatttctattgcgcagaccactgaaggt +gcgctgaatgaaattaacaacaacctgcagcgtgtgcgtgagttgtctgtgcaggccactaacgggactaactctgattc +cgatctgaaatctatccaggatgaaattcagcaacgtctggaagaaatcgatcgcgtttctaatcagactcaatttaacg +gtgttaaagtcctgtctcaggacaaccagatgaaaatccaggttggtgctaacgatggtgaaaccattaccatcgatctg +caaaaaattgatgtgaaaagccttggccttgatgggttcaatgttaatgggccaaaagaagcgacagtgggtgatctgaa +atccagcttcaagaatgttacgggttatgacacctatgcagcgggtgccaataaatatcgtgtagatattaattcaggtg +ctgtagtaactgatgatgcagcaccggataaagtatatgtaaatgcagcaaatggtcagttgacaactgacgatgcggaa +aataacactgcggttaacctattcaagacgactaaatctgctgctggtaccgatgaagccaaagcgatagctggtgccat +taagggtggtaaggaaggagatacctttgattataaaggcgtgacttttactattgatacaaaaactggtaatgacggta +atggtaaggtttctactaccatcaatggtgaaaaagttacgttaactgtcgctgatattaccggtggtgcggcgaatgtt +gatgctgctaccttacaatcaagcaaaaatgtttttacatctgtagtgaacggtcagtttacttttgatgataaaaccaa +aaacgagagtgcgaaactttctgatttggaagcaaacaatgctgttaaaggcgaaagtaaaattacagtaaatggggctg +aatatactgctaacgccacgggtgataaggtcaccttagcaggcaaaaccatgtttattgacaaaacagcttctggcgtt +agtacattaatcaatgaagacgctgccgctgctaagaaaagtaccgctaacccactggcttcaattgattctgcattgtc +aaaagtggacgcagttcgttcttctctgggggcaattcaaaaccgttttgattcagccattaccaaccttggcaatacgg +taaccaatctgaactccgcgcgtagccgtatcgaagatgctgactatgcaacggaagtttctaatatgtctaaagcgcag +attctgcagcaggctggtacttccgttctggcgcaggctaaccaggttccgcaaaacgtcctctctttactgcgttaa +>fliC_g,z51_Salmonella.enterica_Travis_AY353413_g,m__1515 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGACGCAGGCTTCCCGTAACGCTAACGACGGTATCTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAATGGTACTAACTCTGATTC +CGATTTGAAATCCATTCAGGATGAAATCCAGCAGCGCTTATCGGAAATCGACCGTGTTTCTAACCAGACTCAGTTTAACG +GTGTTAAAGTCCTGTCTCAGGATAATCAGATGAAAATTCAGGTGGGCGCTAACGATGGCGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGTCTGGATGGATTCAATGTTAACGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGATACGTATACTGCTGGTGCTAATACTTATCGCGTAGATATTAATTCTGGAG +CAGTAACTGATGATGCTGGTACCGATAAGATTTACGTAAATGCAGCAAACGGTCAGCTCACAACTGATGATGCACAGAAT +AACACTGCAGTTGATCTATTTAAGACAGCAAAATCATCAGCAGGTACAGCTGAATCTAAAGCAATAGCTGGCGCTATTAA +AGGTGGTAAAGAAGGAGATACTTTTGATTATAAAGGTGTTTCTTTCACCATTGATACAAAGAATGGCGCTGACGGTAATG +GTACTGTTTCCACTATGATCAATGGTGAAAAAGTTACGTTGACTGTTGCTGATATTACCACTGGTGCGGCGGACGTTAAT +GCGGCTACCTTACAATCAAGTAAAAATGTTTATACATCTGTAGTAAACGGCCAGTTTACTTTTGATGATAAAACCAAAAA +CGAGAGTGCGAAACTTTCTGATTTAGAAGCAAATAATGCTGTTAAAGGTGAAAGTAAAATCACGGTAAACGGCGCTGAGT +ATACAGCTAACGCTGAAGGTGATAAAGTTACCTTAGCAGGTAAAACCATGTTTATTGATAAGACCGCTTCTGGCGTTAGC +ACATTAATCAATGAAGATGCTGCTGCTGCTAAGAAGAGTACAGCTAATCCACTGGCTTCAATTGATTCTGCATTGTCAAA +AGTGGATGCTGTACGTTCTTCACTGGGGGCGATCCAGAATCGCTTTGATTCTGCCATCACTAACCTGGGCAACACGGTAA +ATAACCTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATT +CTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAGCGTCCTCTCTTTACTGCGTTAA +>fliC_c_Salmonella.enterica_IIIb.41:c:e,n,x,z15_AY353369_other.c__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGTACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAGCGATACTGCTGTAGC +TGCTTCCTATTCCGACTCGAAACAGAATATTGCTGTTCCTGATAAAGCAGCTATTACTGCAAAAATTGGTGCAGCAACCA +GTGGTGGTGCTGGTATAAAAGCAGATATTAGCTTTAAAGATGGCAAGTATTACGCGACTGTCAGTGGATACGATGATGCC +GCAGATACAGATAAAAATGGAACCTATGAAGTCACTGTTGCCGCAGATACAGGAGCAGTTACTTTTGCGACTACACCAAC +AGTGGTTGACTTACCAACGGATGCAAAAGCAGTTTCAAAAGTTCAACAGAATGATACTGAAATAGCAGCAACAAATGCGA +AAGCTGCATTAAAAGCTGCAGGAGTTGCAGATGCAGAAGCTGATACAGCTACTTTAGTGAAAATGTCTTATACAGATAAT +AACGGCAAAGTTATTGATGGTGGGTTCGCATTTAAGACCTCCGGTGGTTATTATGCAGCATCTGTTGATAAATCTGGCGC +AGCTAGCTTGAAAGTTACTAGCTACGTTGACGCTACCACTGGTACCGAAAAAACTGCTGCGAATAAATTAGGTGGCGCAG +ACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGAAGGTCACAACTTTAAAGCACAG +CCTGATCTGGCGGAAGCGGCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACAC +GTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGA +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_c_Salmonella.enterica_Jericho_AY353367_other.c__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAACAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAGCGATACTGCTGTAGC +TGCTTCCTATTCCGACTCGAAACAGAATATTGCTGTTCCTGATAAAACAGCTATTACTGCAAAAATTGGTGCAGCAACCA +CTGGTGGTGCTGGTATAAAAGCAGATATTAGCTTTAAAGATGGCAAGTATTACGCGACTGTCAGTGGATACGATGATGCC +GCAGATACAGATAAAAATGGAACCTATGAAGTCACTGTTGCCGCAGATACAGGAGCAGTTACTTTTGCGACTACACCAAC +AGTGGTTGACTTACCAACGGATGCAAAAGCAGTTTCAAAAGTTCAACAGAATGATACTGAAATAGCAGCAACAAATGCGA +AAGCTGCATTAAAGGCTGCAGGAGTTGCAGATGCAGAAGCTGATACAGCTACTTTAGTGAAAATGTCTTATACAGATAAT +AACGGCAAAGTTATTGATGGTGGGTTCGCATTTAAGACCTCCGGTGGTTATTATGCAGCATCTGTTGATAAATCTGGCGC +AGCTAGCTTGAAAGTTACTAGCTACGTTGACGCTACCACTGGTACCGAAAAAACTGCTGCGAATAAATTAGGTGGCGCAG +ACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGGCACAACTTCAAAGCACAG +CCAGAGCTGGCGGAAGCGGCTGCTACAACCACTGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAAGTTGATGC +GCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAATAACCTGT +CTTCTGCTCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACCTCCGTTTTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_c_Salmonella.enterica_Goeteborg_AY353368_other.c__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGGATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAGCGATACTGCTGTAGC +TGCTTCCTATTCCGACTCGAAACAGAATATTGCTGTTCCTGATAAAGCAGCTATTACTGCAAAAATTGGTGCAGCAACCA +GTGGTGGTGCTGGTATAAAAGCAGATATTAGCTTTAAAGATGGCAAGTATTACGCGACTGTCAGTGGATACGATGATGCC +GCAGATACAGATAAAAATGGAACCTATGAAGTCACTGTTGCCGCAGATACAGGAGCAGTTACTTTTGCGACTACACCAAC +AGTGGTTGACTTACCAACTGATGCAAAAGCAGTTTCAAAAGTTCAACAGAATGATACTGAAATAGCAGCAACAAATGCGA +AAGCTGCATTAAAAGCTGCAGGAGTTGCAGATGCAGAAGCTGATACAGCTACTTTAGTGAAAATGTCTTATACAGATAAT +AATGGCAAAGTTATTGATGGTGGGTTCGCATTTAAGACCTCCGGTGGTTATTATGCAGCATCTGTTGATAAATCTGGCGC +AGCTAGCTTGAAAGTTACTAGCTACGTTGACGCTACCACTGGTACCGAAAAAACTGCTGCGAATAAATTAGGTGGCGCAG +ACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGGCACAACTTCAAAGCACAG +CCAGAGCTGGCGGAAGCGGCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGATGC +GCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGT +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>tyr-O-2__608 +ATGAAGCTTTAATTACCGGTGGATGTGGCTTCCTTGGGAGTAATCTTGCCTCCTTTGCTTTAAGTCAAGGGATTGATTTAATTGTATTCGATAATCTATCACGTAAAGGTGCAACAGATAATTTACATTGGTTATCCTCCTTAGGAAACTTTGAGTTTGTACATGGTGATATTCGCAACAAAAATGATGTTACAAGATTAATAACTAAGTATATGCCTGATAGCTGTTTTCATCTTGCAGGTCAAGTGGCAATGACTACATCTATTGACAATCCTTGTATGGATTTTGAAATTAATGTAGGTGGAACTTTAAATTTACTTGAGGCAGTACGGCAGTATAATTCAAATTGTAATATAATTTATTCATCAACAAATAAAGTATACGGCGATCTTGAGCAATATAAATACAATGAAACAGAAACTAGATACACTTGTGTAGATAAGCCTAATGGATATGATGAGAGCACACAATTAGATTTCCACTCACCATATGGTTGTTCAAAAGGTGCTGCAGACCAATACATGCTTGATTATGCAAGGATTTTTGGTTTGAATACAGTGGTGTTCAGGCATTCATCAATGTATGGTGGGAGACAGTTTGCTACTTAT +>fliC_y_Pomonastr_AHIA01000046_other.y__1509 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGACAGGCAATTGCTAACCGTT +TTACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTTGATAACACGGCTGTCAC +GAACCCTAATTATGTTGATGGTGCAGCGTTAAGCACTACGATGCCTACTGCGGCTGAGATTAAAACGGCTATTGGCACTG +GTGCGGGAACTCCGGCAGTTAAAGGTAATGAAGTTCAATTTGATAAGAGCACTGGGAAGTATTACGTTGAAATTGAAGGA +TATTCAGCTCCTGATGCAGCTAAAAACGGCATTTATGAAGCCAAAGTTGCTGATGATGGCACAATATCTTTGGAGACTGG +GACCAAAAAAATTGGCACCGCAATGCCTGCTGGTGCTGAAGTTATTACTCACGTGCAGAAAAAAGATCAACCAGTTGTTG +TTGATGCCAGCGTTAAAGATGCTCTAAAAGCTGGTGGGGTAGATGATGCAGTTGCAGATACCGCGCAATTAGTCAAAATG +TCTTACACTGATAAGAATGGTAAAACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGCAAAACCGAAGTTGTTACTATCGATGGTAAAACCTATAATGCCAGCAAAGCTGAAGGTCAC +AACTTTAAAGCACAGCCTGAACTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCT +GGCGCAGGTTGATGCGCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_r_Weltevredenstr_ABFF01000030_r,i__1470 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTC +CTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGAT +GGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTT +CCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAG +CAGCGGGTGTTGCAGCGGCTGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGT +GGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATACTACGAA +ATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTA +TTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCTGCT +ACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGT +TCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAG +ATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAG +GCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_y_Hartfordstr_ALPO01000014_other.y__1509 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTTGATAACACGGTTGTCAC +GAACCCTAATTATGTTGATGGTGCAGCGTTAAGCACTACGATGCCTACTGCGGCTGAGATTAAAACGGCTATTGGCACTG +GTGCGGGAACTCCGGCAGTTAAAGGTAATGAAGTTCAATTTGATAAGAGCACTGGGAAGTATTACGTTGAAATTGAAGGA +TATTCAGCTCCTGATGCAGCTAAAAACGGCATTTATGAAGCCAAAGTTGCTGATGATGGCACAATATCTTTGGAGACTGG +GACCAAAAAAATTGGCACCGCAATGCCTGCTGGTGCTGAAGTTATTACTCACGTGCAGAAAAAAGATCAACCAGTTGTTG +TTGATGCCAGCGTTAAAGATGCTCTAAAAGCTGGTGGGGTAGATGATGCAGTTGCAGATACCGCGCAATTAGTCAAAATG +TCTTACACTGATAAGAATGGTAAAACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGTGTAGACGGCAAAACCGAAGTTGTTACTATCGATGGTAAAACCTATAATGCCAGCAAAGCTGAAGGTCAC +AACTTTAAAGCACAGCCTGATCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCTGCTTT +GGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_g,z51_50_g,z51_-str_AOXJ01000042_g,m__1503 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCTCACTGAGTTC +CGCTATCGAGCGTTTGTCCTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATCAAAGGCCTGACTCAGGCTTCCCGTAATGCGAACGACGGTATCTCCATTGCGCAGACCACCGAAGGG +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATTCAGGATGAAATTCAGCAGCGCTTATCGGAAATTGACCGTGTTTCTAACCAGACTCAGTTTAACG +GTGTTAAAGTCCTGTCTCAGGATAATCAGATGAAAATTCAGGTGGGCGCTAACGATGGCGAGACTATTACCATTGATCTA +CAAAAAATTGATGTGAAAAGTCTTGGTCTGGATGGGTTCAACGTGAATGGGCCTAAACAAGCAACCGCTGGGGATTTGAA +ATCTAATTTCAAAAACGTTACTGGTTATGATACGTATGCTGTTGGTGCTGATAGTTATCGTGTAGATATTAATTCTGGAG +CAGTAACTGATGATGCTGGTACCGATAAGATTTACGTAAACGCAGCAAACGGTAAACTCACAACTGATGATGCACAGAAT +AACACCCCAGTTGATCTATTTAAGACAACAAAATCATCAGCCGGTACAGCTGAATCTAAAGCAATTGCTACCGCTATTAA +AGGTGGTAAAGAAGGAGATACTTTTGATTATAAAGGTGTTTCTTTTACCATTGATACAAAGAATGGCACTGACGGTAATG +GTACAGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTGACTGTCGCTGACATTACCACGGGTGCGGCAGACGTTAAT +GCGGCAACCTTACAATCAAGTAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACCTTTGATGATAAAACGAAAAA +CGAAGGTGCGAAATTATCTGATTTAGAAGCAAATAATGCTGTTAAAGGTGAAAGTAAAATCACGGTAAACGGTGCTGAAT +ATACAGCTAACGCTGAGGGTGATAAAATTACCTTAGCAGGTAAAACCATGTTTATTGATAAGACAGCCTCTGGCGTTAGC +ACATTAATTAATGAAGATGCTGCTGCAGCTAAGAAGAGTACCGCTAATCCACTCGCTTCAATTGATTCTGCATTGTCAAA +AGTGGATGCTGTACGTTCTTCATTGGGGGCTATTCAGAACCGTTTTGATTCTGCCATTACCAACTTGGGTAATACGGTAA +ATAATCTGACTTCCGCACGTAGCCGTATCGAAGATGCTGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATT +CTGCAGCAGGCAGGGACTTCTGTTCTGGCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_g,m_Enteritidisstr_ALGW01000034_g,m__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGACGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fljB_z_Salmonella.enterica_IIIb.48:z:1,5,7_AY353339_k,z__1500 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGTTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTAGATAGCAAAGCTGTGAC +TGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGTACAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACAACTG +GTTCCATTAAAGATGACAAAGTATATTATGATAGTGCTACTAAAAATTATTATGCTGAAGTGAACTTTACAGATGCCGCT +GATACCGCTAAAAATGGTTTCTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCTTCGACTACTAAAGA +AGCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCATCTGCAGATGTGAAAG +CTGCTCTGACTGCTGGAGGTATTGATACTGCTGATGCAGCTACGGCAGAAATGGTCAAAATGTCTTATACCGATAAAAAC +GGTAAGACGATTGATGGCGGTTACGCTGTAAAAGTGGGCGATAACTACTATGCCGCTACCCAGAAAAAAGATGGTAGCTT +TAGTGTTAACACCACGTCTTACACCGCAGCGGACGGTACATCCAAAACTGCCCTGAACCAACTTGGTGGCGCAGACGGTA +AAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAG +CTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACG +TTCTGACTTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTG +CACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGG +ACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGCTACGTTAA +>oafA__1830 +ATGATCTACAAGAAATTCAGACTCGATATAAATGGGCTAAGAGCTTTTGCATTGATAAGTGTTGTGCTGTATCACTTCGG +TGTACCTTATGTGTCAGGTGGCTTTATAGGTGTAGATGTTTTCTTTGTAATTTCTGGTTTTCTTATGACTGGAATTGTCC +TTGAACGCGTAGACCACAAAGGAGTACTTGATTTTTATATTGCAAGATTCCTAAGAATTGTACCAGCTCTGGTATTTGCA +ATTCTCTTGTTGATGATTTTCGGTTTATTTACACTAAGTACAAATGAATACGAAGCACTTAGCAAGAACGCAATATCGTC +TTTACTTTTTTATTCAAATAATTATTACGCAATTCACTCTAGTTATTTCGACTCATCATCAGAGTTCAACTTTTTGCTTC +ACACCTGGTCACTATCAGTTGAGTGGCAATTTTATATTTTATATCCTTTATTAGTCATTATAGTTAAAAAATTACGGTTT +CCTGTTGGACTCTCATTATCTGTAATTTTAGCCATGTCACTTGCAATTACACTTATGCGAGTGACTGGAACCAAAGAAGA +TATTTTCTATCTTATCCCTACCAGGGCATGGGAAATGCTGGCTGGCGGCCTTGTATACATAGCATCTGTACGTTACAAAA +TGCCAGAATGGATAAAGCATTGTGAGGTTTATGGGATAGTCCTCATTGTTGTTCGTGTTGTTATACTCGACAGTAATGGT +TACTGGCCAAGCTATTCAGCACTCGCTCCCGTGCTGGGTGCTTCGATGGTTATTCTGGCTAACAAACAGAACTCTTTATT +CACATCAAACAGAATTGCACAGTGGGTGGGTAAGATTTCTTACTCAGTTTATTTATGGCACTGGCCTGTAATTGTAGCGA +TGAAACATTATGATATTGAGTTCAGCGCTATAAATATTTTCTTTGGTGTAATTGTGTCTTTTGCGCTTGGGGATATTTCA +GACAGAACAATTGAAAACACGCTCAGGAAACGAGTTAAGCTACAATTTAATATTGTATTATTTTCCTCTACTCTGGCTCT +ATGCTTGTTTGTCATGTTCACAAAAGGTGTTAGTTTTAGATTTTCAGACACCCTAAAGCAAGTCGTTGAGTATCGTATGG +ACAACTCTCCCTGGAGGCCTGATATTTGCTTCCTCAATCCAGATCAAGATTATTCAGCATTCTCAAAATGTCAGGATAAA +ATGACTGAAAAGTCTTTTGTTGTATGGGGTGACTCGCATGCCGCACATCTTATGCCAGGGCTGAAATCGGTATTTGGAAA +TTCACTTAACATTACGCAGAGAACTGCAAGCTTGTGCCCACCAATCATTGGGCTTCAAAAAGATGACAGGCCGTATTGCA +AAGACATCAATGATATGGTAGCCAAGGAAATTTCAGACAACAAGCCTACTACGGTATTAATGTCCGCGTTGTGGCCTGTC +TATCCTATGCGTGATTATCTGCCTGAGACTATTAAATTCCTGAAGGATAACAAAGTAAAAAACATCATCATTGTTGGCCC +GTTCCCGGTTTGGAAGAAAACGATGATTGATACTATTGAGGATATGGGGATTAATTCCGGAAGGACCGTTCCATGGAGCA +TGACGGATGAAACCCGTAATCTGAGAGATAATGACAAATATCTTAGAGAGCTGGCGAAAGAGCATTCCCTTACTTATATT +TCACCACTTGAGACTATGTGTACAGAAAGTTATTGCAAAGCAATAATAGGGAATAGAATTGCTTACCCTATACAATATGA +CAATGCGCACCTAACACCAGAAGGCTCAGGGTGGTTTATTGAGGAAGTGAGAAAGCAGATTTCAAAATAA +>fljB_e,n,x,z15_Salmonella.enterica_IIIb.47:i:e,n,x,z15_AY353313_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTTTCTGCGACAGACGTTAT +TAGCTCTACCTATAGTGATGGTACTAAGGCTCTTACGGCACCAACTGCAACTGATATTAAAACTGCATTAGGCAACCCGA +CGGTAACTGGTGATACATTAACTGCCACCGTATCCTTCAAGGATGGTAAATATTACGCCACCGTAGGTGGTTATACCGAT +ACGGGGGATGCTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACTCC +GACTAAAGCTACAGTAACTGGGGATACAACCGTAACTAAAGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGAGGCGTCTCATCTGCGGACGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAATATTACGCTGCTGATTACAATGAAACTACAGG +AGCTATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACTAAAATGGCGGCTAACCAACTTGGTGGCGCAG +ACGGTAAAACCGAAGTCGTTACTATCAACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGCCATGATTTCAAAGCACAG +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACAC +GTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGA +CTTCTGCACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCGGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>fljB_1,5_from-Ibadan-micro-assembly_SRR1753831_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCACAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCGATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCCATCAAAGCGGCCATAGGTG +GTACGACTGGTACGCCTGCTGTAACGGGCGGTACAGTTAAATTTGACGCAGATAATAATAAGTATTTTGTTTCTATTGGT +GGCTATACTGGTGCTGATGCATCCAAAAATGGCGATTATGAAGTTAACGTTGCTGCTGACGGTAAAGTTACACTTGCTAC +AGGTGCAACTAAAACCACAATACCGGCAGGTGCTACAACCAAAACAGAAGTACAGGAGTTAAAAGATACACCAGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATCGCTGGCGGCGTTGACACTGCTGATGCAAATGCCGCCGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACCATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGTT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTTAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fljB_1,5,7_Salmonella.enterica_IIIb.47:r:1,5,7_AY353291_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTTTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTGAAAGATACAGCAGCAAC +AACGAAAGCTTATGCTGATAATGGTACTACACTGGATGTATCAGGTCTTGATGATGCAGCGATTAAAGCGGCTACGGGTG +GTACGACTGGTGCGCCTACTGTAACGGGCGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGGTGATGCTGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTAACACTTGCGAC +TGGTGCAACTAAAACCACAATGCCTGCAGGTGCTACAACCAAAACAGAAGTACAGGAATTAAAAGATACACCGGCAGTTG +TATCAGCTGATGCTAAAAATGCTTTAATTGCTGCTGGCGTTGATACTACAGATGCAAATGCCGCGACATTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAATATTACGCTGCTGATTA +CAATGAAACTACAGGAGCTATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACTAAAACGGCGGCTAACC +AACTTGGTGGCGCAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCAT +GATTTCAAAGCACAGCCAGATCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCT +GGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACA +CCGTAAACAACCTGACTTCTGCACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCGGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTA +A +>fljB_1,5_from-Infantis-micro-assembly_SRR1106258_1__1521 +TTAACGTAACAGAGACAGCACGTTCTGCGGGACCTGGTTAGCCTGCGCCAGAACGGAAGTACCGGCCTGCTGCAGAATCT +GCGCGCGAGACATGTTGGAAACTTCGGTCGCGTAGTCGGAATCTTCGATACGGCTACGCGCTTCAGACAGGTTGTTTACG +GTATTGCCCAGGTTGGTGATAGCGGAGTTGAAACGGTTTTGTACCGCACCCAGATCAGAGCGCAGCGCATCCACCTGCGC +CAGCGCGGCATCAATTTTCTGCAGCGGGTTTTCGGTGGTTTTAGCGGCTGCTTCCGCCAGCTCTGGTTGTGCTTTGAAAT +CATGACCAGCGGCTTTGCTGGCATTGTAGGTTTTACCGTCGATAGTAACGACTTCGGTTTTACCGTCTACGCCACCCAGT +TGGTTAGCTGCTGTTTTGGTAGTGCCGTCAGCAGCAGTATAACTTGTGGTTTTAGCTTTAATTGCTCCTGTCGCTTCATC +GTAATCTGCGGCGTAATACTTATCGCCAGCTTTAAGCGCATAACCGCCTTCAATTGTCTTACCATTTTTATCGGTATAAG +ACATTTTGACCAACTCAGCGCCATTAGCATCGGTAGCGTCAACGCCGCCAGCAATTAAGGCATTTTTAGCATCTGCTGAA +ACAACTGCCGGTGTATCTTTTAACTCCTGTACTTCTGTTTTAGTTGTCGCACCAGCAGGCATTGTGGTTTTAGTTGCGCC +AGCCGCAAGGGTTACTGTACCGTCAGTAGCAACGTTAACTTCATAATCGCCATTTTTGGCGGCATCAGCACCAGTAAAGC +CACCAATAGTAACAAAGTACTTGTTATTATCTGCGTCAAATTTAACCGCACCACCGGTTACAGCAGCCGTACCAGTCGTA +CCACCCGTAGCCGTTTTAATAGCTGCATCAGTAAGACCCGATACATCCAGTGTAGTACCATTATCGGCATAAGCTTTCGT +TGTTACTGCTGTATCTTTCACATCATACGCTTTCTGCACGTTCAGTGAGTCCAGACCCAGGGTCTGAGAGTTGATCTGCT +TCAGATCGATATCGATAGTTTCACCGTCGTTGGCACCAACCTGGATGGTCAGGGTGTTGTCCTGCGCCAGGACTTTCACG +CCGTTGAACTGAGTCTGGCCGGATACACGGTCGATTTCGTTCAGGCGCTGGGTGATTTCAGCCTGGATGGAGTCGAGGTC +AGACTGGGAGTTGGTGCTGTTAGCAGACTGAACCGCCAGTTCACGCACACGCTGCAGGTTGTTGTTGATTTCGTTCAGCG +CGCCTTCAGTGGTCTGCGCAATGGAGATACCGTCGTTAGCGTTACGGGAAGCCTGAGTCAGACCTTTGATGTTCGCGGTA +AAACGGTTAGCAATCGCCTGACCTGCCGCATCGTCTTTCGCGCTGTTGATACGCAGACCAGAAGACAGACGCTCGATAGC +GGTGCCCAGTGCGGACTGGGATTTGTTCAGGTTATTCTGGGTCAGCAGCGACAGACTGTTAGTGTTGATTACTTGTGCCA +T +>fljB_1,5_Javiana_SAMN02902435_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCGATAATGGTACTACACTGGATGCCTCAGGCCTTGATGATGCGGCCATCAAAGCAGCCATTGGTG +GTACGACTGGTACGGCTGCTGTAACGGGTGGTACAGTTAAATTTGACGCAGATAATAATAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTTACACTTGCTAC +GGGTGCAACTAAAACCACAATGCCTGCTGGCGCGGCAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCAGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATCGCTGGCGGCGTTGACACTGCCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATATTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCAT +GATTTTAAAGCACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACTACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATCCTGCAGCAGGCCGGTACTTCCGTTCTGGCACAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fliC_r_Virchowstr_ABFH02000002_r,i__1470 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATTACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTC +CTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGAT +GGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTT +CCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAG +CAGCGGGTGTTGCAGCGGCTGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGT +GGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATACTACGAA +ATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTA +TTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCTGCT +ACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGT +ACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCGAAG +ATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAG +GCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_g,m_Enteritidisstr_ALGQ01000046_g,m__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGTTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTT +AATGCTGCTACCTTACGATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_d_Muenchenstr_ARYW01000085_b,d,j__1496 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACGGTACTAACTCCCAGTC +TGACCTTGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGTGATATTGATTTAAAAGAAATTAGCT +CTAAAACACTGGGACTTGATAAGCTTAATGTCCAGGATGCCTACACCCCGAAAGAAACTGCTGTAACCGTTGATAAAACT +ACCTATAAAAATGGTACAGATACTATTACAGCCCAGAGCAATACTGATATCCAAACTGCAATTGGCGGTGGTGCAACGGG +GGTTACTGGGGCTGATATCAAATTTAAAGATGGTCAATACTATTTAGATGTTAAAGGCGGTGCTTCTGCTGGTGTTTATA +AAGCCACTTATGATGAAACTACAAAGAAAGTTAATATTGATACGACTGATAAAACTCCGTTAGCAACTGCGGAAGCTACA +GCTATTCGGGGAACGGCCACTATAACCCACAACCAAATTGCTGAAGTAACAAAAGAGGGTGTTGATACGACCACAGTTGC +GGCTCAACTTGCTGCTGCAGGGGTTACTGGTGCCGATAAGGACAATACTAGCCTTGTAAAACTATCGTTTGAGGATAAAA +ACGGTAAGGTTATTGATGGTGGCTATGCAGTGAAAATGGGCGACGATTTCTATGCCGCTACATATGATGAGAAAATAGGT +ACAATTACTGCTAAAACAACCACTTATACAGATGGTGCTGGCGTTGCTCAAACTGGAGCTGTGAAATTTGGTGGCGCAAA +TGGTAAATCTGAAGTTGTTACTGCTACCGATGGTAAAACTTACTTAGCAAGCGACCTTGACAAACATAACTTCAGAACAG +GCGGTGAGCTTAAAGAGGTTAATACAGATAAGACTGAAAACCCACTGCAGAAAATTGATGCTGCCTTGGCACAGGTTGAT +ACACTTCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCT +GTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGC +AGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fljB_e,n,x,z15_Salmonella.enterica_16:z10:e,n,x,z15_AY353306_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATTCACTGAATGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +TAGCTCTACCTATAGTGATGGTACTAAGGCTCTTACGGCACCAACTGCAACTGATATTAAAACTGCATTAGGCAACCCGA +CGGTAACTGGTGATACATTAACTGCCACCGTATCCTTCAAGGATGGTAAATATTACGCCACCGTAGGTGGTTATACCGAT +ACGGGGGATGCTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACTCC +GACTAAAGCTACAGTAACTGGGGATACAACCGTAACTAAAGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGAGGCGTCTCATCTGCGGACGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAATATTACGCTGCTGATTACAATGAAACTACAGG +AGCTATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACTAAAACGGCGGCTAACCAACTTGGTGGCGCAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAG +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACAC +GTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGA +CTTCTGCACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCGGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,x_Salmonella.enterica_Bonn_AY353308_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_1,7_Salmonella.enterica_from-cdc_Stk1415_1__1521 +TTAACGTAACAGCGACAGCACGTTTTGCGGGACCTGGTTAGCCTGCGCCAGAACGGAAGTACCGGCCTGTTGCAGAATCT +GCGCGCGAGACATGTTGGAAACTTCAGTCGCATAGTCGGAATCTTCGATACGGCTACGCGCTTCAGACAGGTTGTTTACA +GTATTGCCCAGGTTGGTGATAGCGGAGTTGAAACGGTTCTGTACCGCACCCAGATCAGAACGCAGCGCATCAACCTGCGC +CAGCGCGGCATCAATTTTCTGCAGTGGGTTTTCGGTGGTTTTAGCGGCTGCTTCCGCCAGCTCTGGCTGTGCTTTGAAAT +CATGACCCGCGGCTTTGCTGGCATTATAGGTTTTACCGTCGATAGTAACGACTTCGGTTTTTCCGTCTACGCCGCCAAGT +TGGTTAGCCGCAGTTTTGGTAGTACCGTCAGCAGCAGTATAACTTGTGGTTTTAGCTTTAATGGCTCCTGTCGTTTCATC +GTAATCTGCGGCGTAATACTTATCGCCAGCTTTAAGCGCATAACCGCCTTCAATTGTCTTACCATTTTTATCGGTATAAG +ACATTTTGACCAATGTCGCAGCATTTGCATCTGTAGTATCAACGCCAGCAGAAATTAAAGCATTTTTAGCATCGGCTGAT +ACAACTGCCGGTGTATCTTTTAATTCCTGCACTTCTGTTTTGGTTGCAGCACCTGCAGGCATTGTGGTTTTAGTTGCACC +CGTAGCAAGTGTAACTTTACCGTCAGTAGCAACGTTAACTTCATAATCGCCATTTTTGGCGGCATCAGCGCCAGTAAAAC +CACCGATAGTAACAAAATACTTGTTATTATCTGCGTCAAATTTAACCGCACTACCTGTTACACTAGGTGCACCATTCGTA +CCACCCGTAGCCGCTTTAATAGCTGCATCATCAAGGCCTGATACATCCAGTGTAGTACCATTATTGGCATAAGCTTTCGT +GGTTACTGCTGTATCTTTCACATCATACGCTTTCTGCACATTCAGTGAATCCAGACCCAGGGTCTGAGAGTTGATCTGCT +TCAGATCGATGTCGATAGTTTCACCGTCATTGGCGCCAACCTGGATGGTCAGGGTGTTGTCCTGCGCCAGGACTTTCACG +CCGTTGAACTGGGTCTGGCCGGATACACGGTCGATTTCGTTCAGACGCTGGGTGATTTCAGCCTGGATGGAGTCGAGGTC +AGACTGGGAGTTGGTGCTGTTAGCAGACTGAACTGCCAGTTCACGCACGCGCTGCAGGTTGTTGTTGATTTCGTTCAGCG +CGCCTTCAGTGGTCTGCGCAATAGAAATACCGTCGTTAGCGTTACGGGAAGCCTGAGTCAGACCTTTAATGTTCGCGGTG +AAACGGTTAGCAATCGCCTGACCTGCCGCATCGTCTTTCGCGCTGTTGATACGCAGACCAGAAGACAGACGCTCGATAGC +GGTGCCCAGAGCAGACTGGGATTTGTTCAGGTTATTCTGAGTCAGCAGCGACAGACTGTTAGTGTTGATTACTTGTGCCA +T +>fljB_1,5_Muenster_DTU-unknown(tail&head may be fliC due to extract by mapping)_1__1521 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +CACGAAAACTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCCATCAAAGCGGCCATAGGTG +GTACGACTGGTACGCCTGCTGTAACGGGCGGTACAGTTAAATTTGACGCAGATAATAATAAGTATTTTGTTTCTATTGGT +GGCTATACTGGTGCTGATGCATCCAAAAATGGCGATTATGAAGTTAACGTTGCTGCTGACGGTAAAGTTACACTTGCTAC +AGGTGCAACTAAAACCACAATACCGGCAGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCAACAGTTG +TTTCAGCAGATGCGAAAAATGCCTTAATCGCTGGCGGCGTGGATGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACCGCTGCTGACGGCGCTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTA +A +>fljB_1,7_Salmonella.enterica_Nola_AY353298_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAAACTACTGAAGGT +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTGCACCTAGTGTAACAGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATCTCGACAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACCGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCAT +GATTTTAAAGCACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTTGATGCGCTGCGCTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fliC_g,m_Enteritidisstr_ALHD01000038_g,m__1507 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGACAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCA +AAAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCT +GAATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGT +AAGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGT +CAAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACG +GTAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCA +GATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_r_Salmonella.enterica_IIIb.38:r:e,n,x,z15_AY353462_r,i__1482 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTCACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTGCCTTAGGTGGTACTC +CTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGAT +GGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGGTGGCTT +CCCTTCAACTGCAACAAAAGATGTTAAACAAACCCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAG +CAGCGGGTGTTGCAGCGGCCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGT +GGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGCTCCATAAGTATTAATACTACGAA +ATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTA +TTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCCGATCTGGCGGAAGCGGCTACC +ACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGT +ACAGAAACCGTTTAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCGAAG +ATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTGGCGCAG +GCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_y_Salmonella.enterica_Giza_AY353465_other.y__1521 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTTGATAACACGGTTGTCAC +GAACCCTAATTATGTTGATGGTGCAGCGTTAAGCACTACGATGCCTACTGCGGCTGAGATTAAAACGGCTATTGGCACTG +GTGCGGGAACTCCGGCAGTTAAAGGTAATGAAGTTCAATTTGATAAGAGCACTGGGAAGTATTACGTTGAAATTGAAGGA +TATTCAGCTCCTGATGCAGCTAAAAACGGCATTTATGAAGCCAAAGTTGCTGATGATGGCACAATATCTTTGGAGACTGG +GACCAAAAAAATTGGCACCGCAATGCCTGCTGGTGCTGAAGTTATTACTCACGTGCAGAAAAAAGATCAACCAGTTGTTG +TTGATGCCAGCGTTAAAGATGCTCTAAAAGCTGGTGGGGTAGATGATGCAGTTGCAGATACCGCGCAATTAGTCAAAATG +TCTTACACTGATAAGAATGGTAAAACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGCAAAACCGAAGTTGTTACTATCGATGGTAAAACCTATAATGCCAGCAAAGCTGAAGGTCAC +AACTTTAAAGCACAGCCTGATCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCTGCTTT +GGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTA +A +>fliC_r_Salmonella.enterica_IIIb.58:r:z53:z47_AY353461_r,i__1482 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTCACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTGCCTTAGGTGGTACTC +CTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGAT +GGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGGTGGCTT +CCCTTCAACTGCAACAAAAGATGTTAAACAAACCCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAG +CAGCGGGTGTTGCAGCGGCCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGT +GGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGCTCCATAAGTATTAATACTACGAA +ATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTA +TTGGTGGTAAAACTTACGCTGCGAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCTACC +ACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGT +ACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCGAAG +ATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTGGCGCAG +GCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_i_Salmonella.enterica_Bandia_AY353421_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGATGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGATACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_i_Salmonella.enterica_Idikan_AY353422_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z32_Salmonella.enterica_IIIa.18:z4,z32:-_AY353543_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +TTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACCGGCGGTCCGGCTGCGGATAAATTAT +CTCTGACACAAGATGATAAAGGCAATTACTTTGTCAAAGATGATACTGCTGCTGCAGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAAC +CCTATCACGCGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGACCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACTTTGGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAA +ACTACGGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACGGTAAATAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_f,g_Derbystr_AOZH01000145_g,m__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGTT +TCACGTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAGGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +GTCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGTAGCACCGAATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGACCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTAATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCAGTGGTGCGGCGAATGTT +GATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAAGGCGAAAGTAAAATTACAGTAAACGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGGTCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCTAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_z38_Salmonella.enterica_Lille_AY353488_z36,z38__1266 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +TGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTGAATGAAATCAACAACAACCTGCAGCGCGTGCGCGAACTGTCCGTCCAGGCAGCAAACGGCTCGAACTCTGATTC +TGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAGCAAACCGATTTTAACG +GGAAAAAAGTCTTAAGCCAGGATGGACAGTTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGTTTAGATAAATTAGATGTGACTAAAGGGATTGCCACAACCGTTAAAGAAGGTAC +GAAGCTTACAGCCGATTTTGCAGTTAAGGATGCCGATTTTGATGATAAATCAACTGGTACAAAAGTAACTGCAAACTTAG +AATTAAAGCAGGATAAATCCGGAAATTATTTTGCCTACGATAAAACAGCCAGTAAATACTATGATGCGACTGTAGATACT +GCTACAGGTAAAATAGAATTTACTTCTGGGACAGGTAAAGAGACAACGAAAGATACATCTAAACTTACGGATGTTACTTC +TTTGTCCAAAGAAGTAACGATAGATAGTGGACTTACGGATGATAAATCATTAGTAAAATACAAAGGGGATAATGGTAAAG +AACAGTATGCCGTTCAAACTCTTGATAATAAAGGTAATGCGACCTATAAGACTGCCGTTATAGCGCGTGACGGCAAAGTA +ACAGAGGGCACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGACGC +TTTCCGTAGCCAGTTGGGGGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACCTGT +CTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATTCTGCAGCAG +GCAGGGACGTCCGTACTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z35_Salmonella.enterica_Tienba_AY353481_other.z35__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAAGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTGCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAGAAAAAATATGATGTGAAGAGTGAAGCCGTCAC +GCCTCCGGCAAAACTTGATATTACAGGATTAACTGGAGCTGATATTAAAACTGGCGTTGATGGCGCTACGGTTGATACTG +GCTCAATTAAAGATGGCAAAGTTTATTATAATAGTACTTCTAAGGACTATTACGTACAGGTTGATTTTGGTACATCAGCT +GATGCTGCTAAGAGCGGTTACTATAAGGTCAATGTTAATGATGATGGTACAGTCTCAATGACGGCTGATACCACCAAAGA +AGCTACAACTCCTACTGATATTACTGAAGTTACTCAAGTTCAAAAACCTGTAGCTGCTCCAGCCGCTATCCAGGACCAGT +TGACTGCCGCTCATGTCACCGGGGCTGATACAGCTGAAATGGTCAAGATGTCTTATACGGATAAAAACGGTAAGACGATT +GATGGCGGCTTCGGTGTTAAAGTTGGAGACGATATTTATGCTGCAACTAAGAATAAAGATGGTTCTTTTAGTATCAACAC +CACGAAATATACCGATAAAGACGGTAATACCCAAACTGCATTGAACAAACTTGGTGGTGTAGACGGTAAAACTGAAGTTG +TTTCGATTGAAGGTAAAACCTACACTGCAGCGAAAGCAAAAGATCACGATTTCAAAGCGCAGCCAGAGCTGGCAGAAGCG +GCTACTGCAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTAGCACAGGTTGATGCGCTGCGTTCTGACCTGGG 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+ATGACATTTTAACCAAGCTGGTATTACCTGTCGCACCTGTCACACCTGCATTGGTCAATGCAGTAGCTGC +TGCGACTGTATCAACTGGTGCCGGAGTAACAGCGTCTACAATTTGGTTTTTGGTAACTGTGCCGGCCCCA +GTTACTGTTGATTTATTTGCGGTCATTGTCACCGCGCCAGCTGCATCAACTGTCGCTTCATACAGACCAT +TTTTAGCAGTTGTACCGGTCACCTCAACGAAGTAGTTACCGTCTTTAAATTTCACAGCCGCAGTACCCGT +CGCACCAGTCAAACCTAAGGCGGTATCAATTTCTGCTGCGGTAGGTGCTGTAAGAGTAGTACCACCATCT +TTATAGGTGGTAACATCCCTGGTAACAGCGGTACCTTTTGGCGTATAGGCGTCCTGTACACTTAAAGTAT +CCAGACCCAGGGTCTGAGAGTTGATCTGCTTCAGATCGATATCAATAGTTTCACCATCGTTGGCGCCAAC +CTGGATGGTCAGGGTGTTGTCCTGCGCCAGGACTTTCACGCCGTTGAACTGAGTCTGGCCGGATACACGG +TCGATTTCGTTCAGACGCTGGGTGATTTCAGCCTGGATGGAGTCGAGGTCAGACTGGGAGTTGGTGCTGT +TAGCAGACTGAACCGCCAGTTCACGCACACGCTGCAGGTTGTTGTTGATTTCGTTCAGCGCGCCTTCAGT +GGTCTGCGCAATGGAGATACCGTCGTTAGCGTTACGGGAAGCCTGCGTCAGGCCTTTGATGTTCGCGGTG +AAACGGTTAGCAATCGCCTGACCTGCCGCATCGTCTTTCGCGCTGTTGATACGCAGACCAGAAGACAGAC +GCTCGATAGCGGTGCCCAGTGCGGACTGGGATTTGTTCAGGTTATTCTGGGTCAACAGCGACAGGCTGTT +TGTATTAATGACTTGTGCCAT + diff -r 43f6b7f6ebb3 -r e6437d423693 build/lib/seqsero2_db/antigens.pickle Binary file build/lib/seqsero2_db/antigens.pickle has changed diff -r 43f6b7f6ebb3 -r e6437d423693 build/lib/seqsero2_db/invA_mers_dict Binary file build/lib/seqsero2_db/invA_mers_dict has changed diff -r 43f6b7f6ebb3 -r e6437d423693 build/lib/seqsero2_db/special.pickle Binary file build/lib/seqsero2_db/special.pickle has changed diff -r 43f6b7f6ebb3 -r e6437d423693 build/lib/version.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/version.py Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,1 @@ +SeqSero2_version = '1.1.1' diff -r 43f6b7f6ebb3 -r e6437d423693 build/scripts-3.6/Initial_Conditions.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/scripts-3.6/Initial_Conditions.py Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,109 @@ +#!/Users/charles.strittmatter/miniconda3/bin/python + +subs=['II', 'I', 'I', 'II', 'I', 'II', 'II', 'I', 'II', 'II', 'II', 'II', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 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3,10:a:e,n,x', u'Galil', u'Solna', u'Toowong', u'Bakau', u'Aminatu', u'Meekatharra', u'VI 45:a:e,n,x', u'II 11:a:z6', u'Massilia', u'VI 11:a:1,5', u'Dakar', u'Luciana', u'Brazil', u'II [1],13,23:a:z42', u'Denver', u'Oslo', u'II 39:a:z39', u'Sanjuan', u'II 6,7,[14]:a:1,5', u'Heron', u'Fischerhuette', u'Togba', u'Damman', u'Amunigun', u'II 6,7:a:z6', u'Austin', u'Hannover', u'Umhlali', u'II 48:a:z39', u'II 48:a:z6', u'Hisingen', u'Shikmonah', u'Salinas', u'Greiz', u'II 40:a:z39', u'Nyeko', u'IV 44:a:-', u'Guarapiranga', u'Doulassame', u'II 30:a:z39', u'Tione', u'Windsheim', u'IV 51:a:-', u'Faji', u'II 58:a:z6', u'Marshall', u'Coleypark', u'II 13,22:a:e,n,x', u'Zehlendorf', u'Mim', u'II [1],13,23:a:1,5', u'Chagoua', u'Oran', u'IV 50:a:-', u'Burundi', u'Doba', u'Baildon', u'Detmold', u'II 6,7:a:z42', u'Wyldegreen', u'Miami', u'Lomalinda', u'Kinondoni', u'Saarbruecken', u'Jangwani', u'Graz', u'Berkeley', u'II 43:a:1,5', u'II 43:a:z6', u'Be', u'Os', u'II [1],4,[5],12,[27]:a:e,n,x', u'Bonames', u'Valdosta', u'II [1],9,12:a:e,n,x', u'Curacao', u'Niumi', u'Juba', u'Gwoza', u'Alkmaar', u'Sendai', u'Doncaster', u'Paratyphi A', u'Huettwilen', u'II 6,8:a:z39', u'II 6,8:a:z52', u'II [1],4,12,[27]:a:z39', u'Banjul', u'Nakuru', u'Tinda', u'Nordufer', u'Fulica', u'II 9,12:a:z39', u'Garba', u'VI [1],6,14:a:1,5', u'Niakhar', u'Tiergarten', u'Niarembe', u'Kisangani', u'II 9,12:a:1,5', u'Hessarek', u'Durban', u'Marseille', u'Gallen', u'Leith', u'II 6,8:a:e,n,x', u'Narashino', u'Arechavaleta', u'Brazos', u'Bispebjerg', u'VI [1],6,14,[25]:a:e,n,x', u'II 11:a:e,n,z15', u'Tchad', u'Abony', u'Uppsala', u'II 42:b:e,n,x,z15', u'Bamboye', u'Tomegbe', u'II 9,46:b:e,n,x', u'Linguere', u'Frederiksberg', u'Accra', u'Worb', u'Zadar', u'Cheltenham', u'Montaigu', u'Georgia', u'Lockleaze', u'Ibadan', u'Wagenia', u'Niederoderwitz', u'Ede', u'II 43:b:z42', u'Tambacounda', u'Kande', u'II 4,12:b:1,5', u'Broughton', u'Kolar', u'II 42:b:1,5', u'Canada', u'Kotte', u'Leopoldville', u'Ohio', u'II 6,7:b:[e,n,x]', u'Koumra', u'II [1],4,[5],12,[27]:b:[e,n,x]', u'Orbe', u'II 6,7:b:z39', u'Elbeuf', u'Vaugirard', u'Sedgwick', u'Wa', u'Melaka', u'Hull', u'Kirkee', u'Dahra', u'Mattenhof', u'II 17:b:e,n,x,z15', u'Wandsworth', u'II 17:b:z6', u'Glasgow', u'48:b:-', u'II 48:b:e,n,x,z15', u'II 48:b:z6', u'Shahalam', u'Riogrande', u'Saugus', u'Johannesburg', u'Duval', u'Benguella', u'II 40:b:-', u'Bignona', u'Paratyphi B', u'II 38:b:1,2', u'IV 50:b:-', u'II 50:b:z6', u'Rochdale', u'Rittersbach', u'Sica', u'Vietnam', u'Gnesta', u'VI 41:b:1,7', u'Abidjan', u'Limete', u'Adime', u'II 16:b:z42', u'II 16:b:z39', u'Malstatt', u'Visby', u'Edinburg', u'Brazzaville', u'Vegesack', u'Sangera', u'II 16:b:e,n,x', u'Hvittingfoss', u'II 41:b:1,5', u'Pharr', u'Eboko', u'Tonev', u'Sanga', u'Kuntair', u'Tucson', u'IIIb (6),14:b:e,n,x', u'Schleissheim (Schleissheim is extremely rare)', u'II 3,10:b:e,n,x', u'Atento', u'Leeuwarden', u'Wohlen', u'Korbol', u'VI 11:b:e,n,x', u'Fomeco', u'Erfurt', u'Yaba', u'Neudorf', u'Epicrates', u'Egusitoo', u'Sanktjohann', u'Stourbridge', u'Tripoli', u'Durham', u'II 6,8:b:1,5', u'Nagoya', u'VI 11:b:1,7', u'Maryland', u'Onarimon', u'Shipley', u'Presov', u'Frintrop', u'Kalina', u'Butantan', u'Bata', u'Allerton', u'Huvudsta', u'II 21:b:1,5', u'II [1],9,12:b:e,n,x', u'Konstanz', u'Batonrouge', u'Gatuni', u'Bukuru', u'Heistopdenberg', u'II [1],9,12:b:z6', u'Ghana', u'Tounouma', u'Benfica', u'Minnesota', u'II [1],9,12:b:z39', u'II 56:b:[1,5]', u'Banalia', u'Riverside', u'Chittagong', u'Mana', u'Westminster', u'Wien', u'II 60:b:-', u'Mississippi', u'Ndjamena', u'Wenatchee', u'II 47:b:1,5', u'II 47:b:e,n,x,z15', u'Sya', u'II 47:b:z6', u'Cochise', u'Djelfa', u'Wilmington', u'Oudwijk', u'II 3,10:b:z39', u'Louga', u'Aschersleben', u'Tempe', u'IV 51:b:-', u'Karaya', u'II 58:b:1,5', u'Urbana', u'II [1],13,22:b:z42', u'II 30:b:z6', u'II 42:b:z6', u'Fluntern', u'II [1],13,23:b:[1,5]', u'II 28:b:z6', u'Vaertan', u'Rottnest', u'II 28:b:e,n,x', u'Soumbedioune', u'Langford', u'Bracknell', u'Freefalls', u'Bokanjac', u'Bahati', u'Skansen', u'Flottbek', u'Molesey', u'Ullevi', u'Moero', u'Ashanti', u'II [1],40:c:z39', u'Antwerpen', u'Montreal', u'IIIb 41:c:e,n,x,z15', u'Bida', u'Kampala', u'IIIb 47:c:z35', u'IIIb 47:c:z', u'IIIb 47:c:e,n,x,z15', u'Eastglam', u'Madigan', u'Kassberg', u'Blijdorp', u'Minna', u'Haouaria', u'Luedinghausen', u'Ridge', u'Alabama', u'IIIb 47:c:1,5,7', u'Keurmassar', u'Madiago', u'Elokate', u'Ipeko', u'Deversoir', u'II 41:c:z6', u'Runby', u'Goeteborg', u'Quebec', u'Kodjovi', u'Lonestar', u'Chiredzi', u'Schwabach', u'II 21:c:e,n,x', u'Utah', u'IIIb 21:c:e,n,x,z15', u'Bronx', u'Belfast', u'Alexanderpolder', u'Santiago', u'Belem', u'Yolo', u'Tado', u'II 40:c:z6', u'Wingrove', u'II 53:c:1,5', u'Rhone', u'Brindisi', u'Hermannswerder', u'Eberswalde', u'Halle', u'II 52:c:k', u'Dresden', u'Wedding', u'Techimani', u'II 11:c:e,n,z15', u'Woodinville', u'Namibia', u'Cotonou', u'Kaduna', u'Rawash', u'Victoriaborg', u'II 17:c:z39', u'IIIb 65:c:z53', u'IIIb 65:c:z', u'IIIb 65:c:1,5,7', u'Okefoko', u'Anderlecht', u'Agege', u'Pramiso', u'IIIb 61:c:z35', u'IIIb 61:c:1,5,(7)', u'Ikayi', u'Gaillac', u'Asylanta', u'II 1,9,12,46,27:c:z39', u'IIIb 59:c:e,n,x,z15', u'Legon', u'Abortusovis', u'Altendorf', u'II 58:c:z6', u'Bissau', u'Jericho', u'Hallfold', u'IIIb 57:c:z', u'IIIb 57:c:e,n,x,z15', u'Bury', u'Hydra', u'Gbadago', u'Morningside', u'Gouloumbo', u'Itutaba', u'II 39:c:e,n,x', u'Vancouver', u'Gafsa', u'Paratyphi C', u'Choleraesuis', u'Typhisuis', u'II 30:c:z39', u'Hissar', u'Kidderminster', u'IIIb 48:c:z', u'Sheffield', u'Quiniela', u'Argenteuil', u'Hithergreen', u'Zaire', u'II 51:c:-', u'Birkenhead', u'Yoruba', u'II [1],40:c:e,n,x,z15', u'Shamba', u'Groenekan', u'Sculcoates', u'II 16:d:1,5', u'Usumbura', u'Sherbrooke', u'II 38:d:z39', u'II 38:d:[1,5]', u'Willamette', u'Oldenburg', u'Nieukerk', u'Orleans', u'Wil', u'Gaminara', u'Livingstone', u'II 6,7:d:z42', u'II 3,10:d:e,n,x', u'Driffield', u'Berlin', u'Karlshamn', u'Niamey', u'II 40:d:-', u'Logone', u'Maron', u'Weybridge', u'Stormont', u'Madjorio', u'Gombe', u'Souza', u'Onireke', u'Lekke', u'II 43:d:z42', u'II 43:d:z39', u'II 43:d:e,n,x,z15', u'Shangani', u'Barranquilla', u'Birmingham', u'Plymouth', u'Dembe', u'Midway', u'Florida', u'Lindern', u'Charity', u'Quentin', u'Typhi', u'II 9,12:d:z39', u'Jaffna', u'Finkenwerder', u'Olten', u'Martonos', u'Sontheim', u'Messina', u'Amoutive', u'Hatfield', u'Mundonobo', u'Mocamedes', u'Patience', u'Cullingworth', u'II 42:d:z6', u'Encino', u'Strasbourg', u'Eschberg', u'Nottingham', u'Caen', u'Barmbek', u'II 35:d:1,5', u'Teko', u'Tarshyne', u'Spartel', u'Magwa', u'Madison', u'Woodhull', u'Ndolo', u'II 16:d:e,n,x', u'II 41:d:z6', u'Bangui', u'Zega', u'Ontario', u'Amersfoort', u'Kambole', u'Kivu', u'Isangi', u'Kisii', u'Albuquerque', u'Egusi', u'Niloese', u'II 47:d:z39', u'II 47:d:e,n,x,z15', u'Stellingen', u'II 47:d:1,5', u'Liverpool', u'Tilburg', u'Wanatah', u'II 13,22:d:1,5', u'Ayinde', u'Friedenau', u'Wichita', u'Grumpensis', u'II [1],9,12:d:e,n,x', u'Diguel', u'II 48:d:1,2', u'Telelkebir', u'Putten', u'Ati', u'Gustavia', u'Warmsen', u'Karachi', u'Dugbe', u'Isuge', u'Chandans', u'Findorff', u'Hemingford', u'IV 50:d:-', u'II 13,23:d:e,n,x', u'Stanley', u'Brezany', u'Schwarzengrund', u'Ahmadi', u'II 4,12:d:e,n,x', u'Sarajane', u'Duisburg', u'Mons', u'II 53:d:z42', u'II [1],53:d:z39', u'II 53:d:1,5', u'Eppendorf', u'II 56:d:-', u'Buckeye', u'Umbadah', u'II 48:d:z6', u'II 57:d:1,5', u'Virginia', u'Muenchen', u'II 58:d:z6', u'II 52:d:z39', u'II 52:d:e,n,x,z15', u'Utrecht', u'Yovokome', u'Manhattan', u'Portanigra', u'Dunkwa', u'Sterrenbos', u'Mishmarhaemek', u'Chennai', u'Palamaner', u'Handen', u'II 6,8:d:z6', u'Fischerstrasse', u'Kermel', u'Gokul', u'Bobo', u'Labadi', u'Herston', u'Newlands', u'Kaapstad', u'Korkeasaari', u'Kpeme', u'Gozo', u'Israel', u'Westafrica', u'Eastbourne', u'Chester', u'Eko', u'Redhill', u'Bahrenfeld', u'Nyborg', u'Anatum', u'Muenster', u'Vejle', u'Hayindogo', u'Kottbus', u'Cremieu', u'Fitzroy', u'Meleagridis', u'Vilvoorde', u'Winnipeg', u'Jubilee', u'Sekondi', u'Saintpaul', u'Weston', u'Beaudesert', u'Guerin', u'Waedenswil', u'Derkle', u'Butare', u'Bergedorf', u'Newport', u'Reading', u'Magumeri', u'Larochelle', u'Lomita', u'Norwich', u'Nola', u'Tilene', u'Onderstepoort', u'Lamberhurst', u'Ferruch', u'Atakpame', u'Bardo', u'Tschangu', u'Braenderup', u'Saboya', u'Rechovot', u'Chingola', u'Chartres', u'Vridi', u'Torhout', u'Livulu', u'Astridplein', u'Sao', u'Bournemouth', u'Calabar', u'Gassi', u'Fillmore', u'Tshiongwe', u'Willemstad', u'Meskin', u'Rhydyfelin', u'Moabit', u'Sanktmarx', u'Adamstua', u'Bruebach', u'Mara', u'Kasenyi', u'Thiaroye', u'Sandiego', u'Malakal', u'Rossleben', u'II 50:e,n,x:1,7', u'II 6,7:e,n,x:1,6', u'II 16:e,n,x:1,6', u'II 3,10:e,n,x:1,7', u'II [1],4,12,[27]:e,n,x:1,[5],7', u'II [1],40:e,n,x:1,[5],7', u'II 56:e,n,x:1,7', u'II 16:e,n,x:1,(5),7', u'II [1],13,23:e,n,x:1,[5],7', u'II 4,12:e,n,x:1,2,7', u'II 9,46:e,n,x:1,5,7', u'II [1],44:e,n,x:1,6', u'II 9,12:e,n,x:1,[5],7', u'II 39:e,n,x:1,7', u'II 28:e,n,x:1,7', u'II 9,12:e,n,x:1,6', u'II 42:e,n,x:1,6', u'II 48:e,n,x,z15:z6', u'II [1],40:e,n,x,z15:1,6', u'II 47:e,n,x,z15:1,6', u'II 17:e,n,x,z15:1,6', u'II 43:e,n,x,z15:1,(5),7', u'II 43:e,n,x,z15:1,6', u'II 17:e,n,x,z15:1,[5],7', u'II 28:e,n,z15:z87', u'6,14:e,n,z15:-', u'Kastrup', u'Wernigerode', u'Derby', u'Raus', u'Vleuten', u'Sljeme', u'Good', u'Friedrichsfelde', u'Rissen', u'Alfort', u'Suelldorf', u'Sandow', u'Rideau', u'Tees', u'Adelaide', u'Havana', u'Regent', u'Milwaukee', u'II 6,8:f,g,m,t:[e,n,x]', u'Borreze', u'Agona', u'II [1],4,[5],12:f,g,t:z6', u'Eingedi', u'Afula', u'Bilu', u'Petahtikve', u'Maiduguri', u'II 28:g,(m),[s],t:1,5', u'Riggil', u'II [1],40:g,[m],[s],[t]:e,n,x', u'II 21:g,[m],[s],t:-', u'II [1],40:g,[m],[s],t:[1,5]', u'II 9,46:g,[m],[s],t:[e,n,x]', u'II 16:g,[m],[s],t:[e,n,x]', u'II [1],40:g,[m],[s],t:z42', u'II 16:g,[m],[s],t:[1,5]', u'II 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+ +remove_list=['Schleissheim', 'Sendai', 'Blegdam', 'Naestved', 'Rostock', 'Moscow', 'Antarctica', 'Rosenberg', 'Chittagong', 'Bilu', 'Dessau', 'Cannonhill', 'Ilugun'] + +rename_dict={'Nitra': 'Enteritidis', + 'Kiel': 'Dublin', + 'Koessen': 'Panama', + 'Phaliron': 'Kalumburu', + 'Istanbul': 'Hadar', + 'Haardt': 'Blockley', + 'Ferruch': 'Kottbus', + 'Sanga': 'Eboko', + 'Pakistan': 'Litchfield', + 'Bellevue': 'Lezennes', + 'Sunnycove': 'Daarle', + 'Noya': 'Akanji', + 'Virginia': 'Muenchen', + 'Djelfa': 'Skansen', + 'Konstanz': 'Gatuni', + 'Bardo': 'Newport', + 'Houston': 'Panama', + 'Martonos': 'Finkenwerder', + 'Midway': 'Florida', + 'Lindern': 'Charity', + 'Bahrenfeld': 'Onderstepoort', + 'Schalkwijk': 'Moussoro', + 'Amberg': 'Boecker', + 'Madelia': 'Carrau', + 'Soahanina': 'Sundsvall', + 'Stafford': 'Poano', + 'Chichiri': 'Uzaramo', + 'II 16:g,[m],[s],t:[e,n,x]': 'II 16:g,[m],[s],t:[1,5]', + 'Hindmarsh':'Bovismorbificans', + 'Yovokome': 'Manhattan'} + + #potential merge for O22 and O23 + #'Ibadan': 'Mississippi', + #'Bracknell': 'Oudwijk', + #'Vaertan': 'Ullevi', + #'Bahati': 'Durham', + #'Wichita': 'Friedenau', + #'Diguel': 'Telelkebir', + #'II 13,22:l,z28:1,5': 'II 13,23:l,z28:1,5', + #'Washington': 'Kintambo', + #'II 13,23:m,t:z42': 'II 13,22:m,t:z42:z39', + #'Serenli': 'Winslow', + #'Farmsen': 'Poona', + #'Durance': 'Ivrysurseine', + #'Agoueve': 'Cubana', + #'II 13,23:z29:1,5': 'II 13,22:z29:1,5', + #'II 13,23:z29:e,n,x': 'II 13,22:z29:e,n,x', + #'Picpus': 'Mampong', + #'Anna': 'Nimes', + #'Fanti': 'Leiden', + #'Ried': 'Ajiobo', + + #potential O68 list + #'Djelfa': 'Skansen', + #'Korbol': 'Nagoya', + #'Sanga': 'Eboko', + #'Konstanz': 'Gatuni', + #'Presov': 'Shipley', + #'Heistopdenberg': 'Bukuru', + #'Tounouma': 'Banalia', + #'Gaillac': 'Utah', + #'Santiago': 'Belem', + #'Virginia': 'Muenchen', + #'Yovokome': 'Manhattan', + #'Portanigra': 'Dunkwa', + #'Bardo': 'Newport', + #'Ferruch': 'Kottbus', + #'Alminko': 'Nanergou', + #'Bargny': 'Takoradi', + #'Magherafelt': 'Cyprus', + #'Haardt': 'Blockley', + #'Pakistan': 'Litchfield', + #'Yokoe': 'Bassa', + #'Noya': 'Akanji', + #'Lamphun': 'Giza', + #'Tananarive': 'Brunei', + #'Inchpark': 'Alagbon', + #'Sunnycove': 'Daarle', + #'Sindelfingen': 'Benue', + #'Phaliron': 'Kalumburu', + #'Bazenheid': 'Zerifin', + #'Paris': 'Mapo', + #'Istanbul': 'Hadar', + #'Chomedey': 'Glostrup', + #'Wippra': 'Molade', + #'Uno': 'Tamale', + #'Kolda': 'Yarm', + #'Bellevue': 'Lezennes', + #'Albany':'Duesseldorf' diff -r 43f6b7f6ebb3 -r e6437d423693 build/scripts-3.6/SeqSero2_package.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/scripts-3.6/SeqSero2_package.py Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,1576 @@ +#!/Users/charles.strittmatter/miniconda3/bin/python + +import sys +import time +import random +import os +import subprocess +import gzip +import io +import pickle +import argparse +import itertools +from distutils.version import LooseVersion +from distutils.spawn import find_executable +sys.path.insert(1,sys.path[0]+'/..') + +try: + from .version import SeqSero2_version +except Exception: #ImportError + from version import SeqSero2_version + +### SeqSero Kmer +def parse_args(): + "Parse the input arguments, use '-h' for help." + parser = argparse.ArgumentParser(usage='SeqSero2_package.py -t -m -i [-d ] [-p ] [-b ]\n\nDevelopper: Shaokang Zhang (zskzsk@uga.edu), Hendrik C Den-Bakker (Hendrik.DenBakker@uga.edu) and Xiangyu Deng (xdeng@uga.edu)\n\nContact email:seqsero@gmail.com\n\nVersion: v1.1.1')#add "-m " in future + parser.add_argument("-i",nargs="+",help=": path/to/input_data",type=os.path.abspath) ### add 'type=os.path.abspath' to generate absolute path of input data. + parser.add_argument("-t",choices=['1','2','3','4','5','6'],help=": '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore fasta, '6' for nanopore fastq") + parser.add_argument("-b",choices=['sam','mem'],default="mem",help=": algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default 'mem' mode") + parser.add_argument("-p",default="1",help=": number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1") + parser.add_argument("-m",choices=['k','a'],default="a",help=": which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a") + parser.add_argument("-n",help=": optional, to specify a sample name in the report output") + parser.add_argument("-d",help=": optional, to specify an output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number") + parser.add_argument("-c",action="store_true",help=": if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files") + parser.add_argument("-s",action="store_true",help=": if '-s' was flagged, SeqSero2 will not output header in SeqSero_result.tsv") + parser.add_argument("--check",action="store_true",help=": use '--check' flag to check the required dependencies") + parser.add_argument('-v', '--version', action='version', version='%(prog)s ' + SeqSero2_version) + return parser.parse_args() + +### check paths of dependencies +check_dependencies = parse_args().check +dependencies = ['bwa','samtools','blastn','fastq-dump','spades.py','bedtools','SalmID.py'] +if check_dependencies: + for item in dependencies: + ext_path = find_executable(item) + if ext_path is not None: + print ("Using "+item+" - "+ext_path) + else: + print ("ERROR: can not find "+item+" in PATH") + sys.exit() +### end of --check + +def reverse_complement(sequence): + complement = { + 'A': 'T', + 'C': 'G', + 'G': 'C', + 'T': 'A', + 'N': 'N', + 'M': 'K', + 'R': 'Y', + 'W': 'W', + 'S': 'S', + 'Y': 'R', + 'K': 'M', + 'V': 'B', + 'H': 'D', + 'D': 'H', + 'B': 'V' + } + return "".join(complement[base] for base in reversed(sequence)) + + +def createKmerDict_reads(list_of_strings, kmer): + kmer_table = {} + for string in list_of_strings: + sequence = string.strip('\n') + for i in range(len(sequence) - kmer + 1): + new_mer = sequence[i:i + kmer].upper() + new_mer_rc = reverse_complement(new_mer) + if new_mer in kmer_table: + kmer_table[new_mer.upper()] += 1 + else: + kmer_table[new_mer.upper()] = 1 + if new_mer_rc in kmer_table: + kmer_table[new_mer_rc.upper()] += 1 + else: + kmer_table[new_mer_rc.upper()] = 1 + return kmer_table + + +def multifasta_dict(multifasta): + multifasta_list = [ + line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0 + ] + headers = [i for i in multifasta_list if i[0] == '>'] + multifasta_dict = {} + for h in headers: + start = multifasta_list.index(h) + for element in multifasta_list[start + 1:]: + if element[0] == '>': + break + else: + if h[1:] in multifasta_dict: + multifasta_dict[h[1:]] += element + else: + multifasta_dict[h[1:]] = element + return multifasta_dict + + +def multifasta_single_string(multifasta): + multifasta_list = [ + line.strip() for line in open(multifasta, 'r') + if (len(line.strip()) > 0) and (line.strip()[0] != '>') + ] + return ''.join(multifasta_list) + + +def chunk_a_long_sequence(long_sequence, chunk_size=60): + chunk_list = [] + steps = len(long_sequence) // 60 #how many chunks + for i in range(steps): + chunk_list.append(long_sequence[i * chunk_size:(i + 1) * chunk_size]) + chunk_list.append(long_sequence[steps * chunk_size:len(long_sequence)]) + return chunk_list + + +def target_multifasta_kmerizer(multifasta, k, kmerDict): + forward_length = 300 #if find the target, put forward 300 bases + reverse_length = 2200 #if find the target, put backward 2200 bases + chunk_size = 60 #it will firstly chunk the single long sequence to multiple smaller sequences, it controls the size of those smaller sequences + target_mers = [] + long_single_string = multifasta_single_string(multifasta) + multifasta_list = chunk_a_long_sequence(long_single_string, chunk_size) + unit_length = len(multifasta_list[0]) + forward_lines = int(forward_length / unit_length) + 1 + reverse_lines = int(forward_length / unit_length) + 1 + start_num = 0 + end_num = 0 + for i in range(len(multifasta_list)): + if i not in range(start_num, end_num): #avoid computational repetition + line = multifasta_list[i] + start = int((len(line) - k) // 2) + s1 = line[start:k + start] + if s1 in kmerDict: #detect it is a potential read or not (use the middle part) + if i - forward_lines >= 0: + start_num = i - forward_lines + else: + start_num = 0 + if i + reverse_lines <= len(multifasta_list) - 1: + end_num = i + reverse_lines + else: + end_num = len(multifasta_list) - 1 + target_list = [ + x.strip() for x in multifasta_list[start_num:end_num] + ] + target_line = "".join(target_list) + target_mers += [ + k1 for k1 in createKmerDict_reads([str(target_line)], k) + ] ##changed k to k1, just want to avoid the mixes of this "k" (kmer) to the "k" above (kmer length) + else: + pass + return set(target_mers) + + +def target_read_kmerizer(file, k, kmerDict): + i = 1 + n_reads = 0 + total_coverage = 0 + target_mers = [] + if file.endswith(".gz"): + file_content = io.BufferedReader(gzip.open(file)) + else: + file_content = open(file, "r").readlines() + for line in file_content: + start = int((len(line) - k) // 2) + if i % 4 == 2: + if file.endswith(".gz"): + s1 = line[start:k + start].decode() + line = line.decode() + else: + s1 = line[start:k + start] + if s1 in kmerDict: #detect it is a potential read or not (use the middle part) + n_reads += 1 + total_coverage += len(line) + target_mers += [ + k1 for k1 in createKmerDict_reads([str(line)], k) + ] #changed k to k1, just want to avoid the mixes of this "k" (kmer) to the "k" above (kmer length) + i += 1 + if total_coverage >= 4000000: + break + return set(target_mers) + + +def minion_fasta_kmerizer(file, k, kmerDict): + i = 1 + n_reads = 0 + total_coverage = 0 + target_mers = {} + for line in open(file): + if i % 2 == 0: + for kmer, rc_kmer in kmers(line.strip().upper(), k): + if (kmer in kmerDict) or (rc_kmer in kmerDict): + if kmer in target_mers: + target_mers[kmer] += 1 + else: + target_mers[kmer] = 1 + if rc_kmer in target_mers: + target_mers[rc_kmer] += 1 + else: + target_mers[rc_kmer] = 1 + i += 1 + return set([h for h in target_mers]) + + +def minion_fastq_kmerizer(file, k, kmerDict): + i = 1 + n_reads = 0 + total_coverage = 0 + target_mers = {} + for line in open(file): + if i % 4 == 2: + for kmer, rc_kmer in kmers(line.strip().upper(), k): + if (kmer in kmerDict) or (rc_kmer in kmerDict): + if kmer in target_mers: + target_mers[kmer] += 1 + else: + target_mers[kmer] = 1 + if rc_kmer in target_mers: + target_mers[rc_kmer] += 1 + else: + target_mers[rc_kmer] = 1 + i += 1 + return set([h for h in target_mers]) + + +def multifasta_single_string2(multifasta): + single_string = '' + with open(multifasta, 'r') as f: + for line in f: + if line.strip()[0] == '>': + pass + else: + single_string += line.strip() + return single_string + + +def kmers(seq, k): + rev_comp = reverse_complement(seq) + for start in range(1, len(seq) - k + 1): + yield seq[start:start + k], rev_comp[-(start + k):-start] + + +def multifasta_to_kmers_dict(multifasta,k_size):#used to create database kmer set + multi_seq_dict = multifasta_dict(multifasta) + lib_dict = {} + for h in multi_seq_dict: + lib_dict[h] = set( + [k for k in createKmerDict_reads([multi_seq_dict[h]], k_size)]) + return lib_dict + + +def Combine(b, c): + fliC_combinations = [] + fliC_combinations.append(",".join(c)) + temp_combinations = [] + for i in range(len(b)): + for x in itertools.combinations(b, i + 1): + temp_combinations.append(",".join(x)) + for x in temp_combinations: + temp = [] + for y in c: + temp.append(y) + temp.append(x) + temp = ",".join(temp) + temp = temp.split(",") + temp.sort() + temp = ",".join(temp) + fliC_combinations.append(temp) + return fliC_combinations + + +def seqsero_from_formula_to_serotypes(Otype, fliC, fljB, special_gene_list,subspecies): + #like test_output_06012017.txt + #can add more varialbles like sdf-type, sub-species-type in future (we can conclude it into a special-gene-list) + from Initial_Conditions import phase1,phase2,phaseO,sero,subs,remove_list,rename_dict + rename_dict_not_anymore=[rename_dict[x] for x in rename_dict] + rename_dict_all=rename_dict_not_anymore+list(rename_dict) #used for decide whether to + seronames = [] + seronames_none_subspecies=[] + for i in range(len(phase1)): + fliC_combine = [] + fljB_combine = [] + if phaseO[i] == Otype: # no VII in KW, but it's there + ### for fliC, detect every possible combinations to avoid the effect of "[" + if phase1[i].count("[") == 0: + fliC_combine.append(phase1[i]) + elif phase1[i].count("[") >= 1: + c = [] + b = [] + if phase1[i][0] == "[" and phase1[i][-1] == "]" and phase1[i].count( + "[") == 1: + content = phase1[i].replace("[", "").replace("]", "") + fliC_combine.append(content) + fliC_combine.append("-") + else: + for x in phase1[i].split(","): + if "[" in x: + b.append(x.replace("[", "").replace("]", "")) + else: + c.append(x) + fliC_combine = Combine( + b, c + ) #Combine will offer every possible combinations of the formula, like f,[g],t: f,t f,g,t + ### end of fliC "[" detect + ### for fljB, detect every possible combinations to avoid the effect of "[" + if phase2[i].count("[") == 0: + fljB_combine.append(phase2[i]) + elif phase2[i].count("[") >= 1: + d = [] + e = [] + if phase2[i][0] == "[" and phase2[i][-1] == "]" and phase2[i].count( + "[") == 1: + content = phase2[i].replace("[", "").replace("]", "") + fljB_combine.append(content) + fljB_combine.append("-") + else: + for x in phase2[i].split(","): + if "[" in x: + d.append(x.replace("[", "").replace("]", "")) + else: + e.append(x) + fljB_combine = Combine(d, e) + ### end of fljB "[" detect + new_fliC = fliC.split( + "," + ) #because some antigen like r,[i] not follow alphabetical order, so use this one to judge and can avoid missings + new_fliC.sort() + new_fliC = ",".join(new_fliC) + new_fljB = fljB.split(",") + new_fljB.sort() + new_fljB = ",".join(new_fljB) + if (new_fliC in fliC_combine + or fliC in fliC_combine) and (new_fljB in fljB_combine + or fljB in fljB_combine): + ######start, remove_list,rename_dict, added on 11/11/2018 + if sero[i] not in remove_list: + temp_sero=sero[i] + if temp_sero in rename_dict: + temp_sero=rename_dict[temp_sero] #rename if in the rename list + if temp_sero not in seronames:#the new sero may already included, if yes, then not consider + if subs[i] == subspecies: + seronames.append(temp_sero) + seronames_none_subspecies.append(temp_sero) + else: + pass + else: + pass + ######end, added on 11/11/2018 + #analyze seronames + subspecies_pointer="" + if len(seronames) == 0 and len(seronames_none_subspecies)!=0: + # ed_SL_12182019: modified to fix the subspecies output problem + #seronames=seronames_none_subspecies + seronames=["N/A"] + #subspecies_pointer="1" + subspecies_pointer="0" + if len(seronames) == 0: + seronames = [ + "N/A (The predicted antigenic profile does not exist in the White-Kauffmann-Le Minor scheme)" + ] + star = "" + star_line = "" + if len(seronames) > 1: #there are two possible predictions for serotypes + star = "*" + #changed 04072019 + #star_line = "The predicted serotypes share the same general formula:\t" + Otype + ":" + fliC + ":" + fljB + "\n" + if subspecies_pointer=="1" and len(seronames_none_subspecies)!=0: + star="*" + star_line="The predicted O and H antigens correspond to serotype '"+(" or ").join(seronames)+"' in the Kauffmann-White scheme. The predicted subspecies by SalmID (github.com/hcdenbakker/SalmID) may not be consistent with subspecies designation in the Kauffmann-White scheme. " + star_line + #star_line="The formula with this subspieces prediction can't get a serotype in KW manual, and the serotyping prediction was made without considering it."+star_line + if Otype=="": + Otype="-" + predict_form = Otype + ":" + fliC + ":" + fljB + predict_sero = (" or ").join(seronames) + ###special test for Enteritidis + if predict_form == "9:g,m:-": + sdf = "-" + for x in special_gene_list: + if x.startswith("sdf"): + sdf = "+" + #star_line="Detected sdf gene, a marker to differentiate Gallinarum and Enteritidis" + star_line="sdf gene detected. " + #predict_form = predict_form + " Sdf prediction:" + sdf + predict_form = predict_form #changed 04072019 + if sdf == "-": + star = "*" + #star_line="Didn't detected sdf gene, a marker to differentiate Gallinarum and Enteritidis" + star_line="sdf gene not detected. " + #changed in 04072019, for new output + #star_line = "Additional characterization is necessary to assign a serotype to this strain. Commonly circulating strains of serotype Enteritidis are sdf+, although sdf- strains of serotype Enteritidis are known to exist. Serotype Gallinarum is typically sdf- but should be quite rare. Sdf- strains of serotype Enteritidis and serotype Gallinarum can be differentiated by phenotypic profile or genetic criteria.\n" + #predict_sero = "Gallinarum/Enteritidis" #04132019, for new output requirement + predict_sero = "Gallinarum or Enteritidis" + ###end of special test for Enteritidis + elif predict_form == "4:i:-": + predict_sero = "I 4,[5],12:i:-" # change serotype name + elif predict_form == "4:r:-": + predict_sero = "N/A (4:r:-)" + elif predict_form == "4:b:-": + predict_sero = "N/A (4:b:-)" + #elif predict_form == "8:e,h:1,2": #removed after official merge of newport and bardo + #predict_sero = "Newport" + #star = "*" + #star_line = "Serotype Bardo shares the same antigenic profile with Newport, but Bardo is exceedingly rare." + claim = "The serotype(s) is/are the only serotype(s) with the indicated antigenic profile currently recognized in the Kauffmann White Scheme. New serotypes can emerge and the possibility exists that this antigenic profile may emerge in a different subspecies. Identification of strains to the subspecies level should accompany serotype determination; the same antigenic profile in different subspecies is considered different serotypes.\n" + if "N/A" in predict_sero: + claim = "" + #special test for Typhimurium + if "Typhimurium" in predict_sero or predict_form == "4:i:-": + normal = 0 + mutation = 0 + for x in special_gene_list: + if "oafA-O-4_full" in x: + normal = float(special_gene_list[x]) + elif "oafA-O-4_5-" in x: + mutation = float(special_gene_list[x]) + if normal > mutation: + pass + elif normal < mutation: + #predict_sero = predict_sero.strip() + "(O5-)" + predict_sero = predict_sero.strip() #diable special sero for new output requirement, 04132019 + star = "*" + #star_line = "Detected the deletion of O5-." + star_line = "Detected a deletion that causes O5- variant of Typhimurium. " + else: + pass + #special test for Paratyphi B + if "Paratyphi B" in predict_sero or predict_form == "4:b:-": + normal = 0 + mutation = 0 + for x in special_gene_list: + if "gntR-family-regulatory-protein_dt-positive" in x: + normal = float(special_gene_list[x]) + elif "gntR-family-regulatory-protein_dt-negative" in x: + mutation = float(special_gene_list[x]) + #print(normal,mutation) + if normal > mutation: + #predict_sero = predict_sero.strip() + "(dt+)" #diable special sero for new output requirement, 04132019 + predict_sero = predict_sero.strip()+' var. L(+) tartrate+' if "Paratyphi B" in predict_sero else predict_sero.strip() + star = "*" + #star_line = "Didn't detect the SNP for dt- which means this isolate is a Paratyphi B variant L(+) tartrate(+)." + star_line = "The SNP that causes d-Tartrate nonfermentating phenotype of Paratyphi B was not detected. " + elif normal < mutation: + #predict_sero = predict_sero.strip() + "(dt-)" #diable special sero for new output requirement, 04132019 + predict_sero = predict_sero.strip() + star = "*" + #star_line = "Detected the SNP for dt- which means this isolate is a systemic pathovar of Paratyphi B." + star_line = "Detected the SNP for d-Tartrate nonfermenting phenotype of Paratyphi B. " + else: + star = "*" + #star_line = " Failed to detect the SNP for dt-, can't decide it's a Paratyphi B variant L(+) tartrate(+) or not." + star_line = " " ## ed_SL_05152019: do not report this situation. + #special test for O13,22 and O13,23 + if Otype=="13": + #ex_dir = os.path.dirname(os.path.realpath(__file__)) + ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019 + f = open(ex_dir + '/special.pickle', 'rb') + special = pickle.load(f) + O22_O23=special['O22_O23'] + if predict_sero.split(" or ")[0] in O22_O23[-1] and predict_sero.split(" or ")[0] not in rename_dict_all:#if in rename_dict_all, then it means already merged, no need to analyze + O22_score=0 + O23_score=0 + for x in special_gene_list: + if "O:22" in x: + O22_score = O22_score+float(special_gene_list[x]) + elif "O:23" in x: + O23_score = O23_score+float(special_gene_list[x]) + #print(O22_score,O23_score) + for z in O22_O23[0]: + if predict_sero.split(" or ")[0] in z: + if O22_score > O23_score: + star = "*" + #star_line = "Detected O22 specific genes to further differenciate '"+predict_sero+"'." #diabled for new output requirement, 04132019 + predict_sero = z[0] + elif O22_score < O23_score: + star = "*" + #star_line = "Detected O23 specific genes to further differenciate '"+predict_sero+"'." #diabled for new output requirement, 04132019 + predict_sero = z[1] + else: + star = "*" + #star_line = "Fail to detect O22 and O23 differences." #diabled for new output requirement, 04132019 + if " or " in predict_sero: + star_line = star_line + "The predicted serotypes share the same general formula: " + Otype + ":" + fliC + ":" + fljB + "." + #special test for O6,8 + #merge_O68_list=["Blockley","Bovismorbificans","Hadar","Litchfield","Manhattan","Muenchen"] #remove 11/11/2018, because already in merge list + #for x in merge_O68_list: + # if x in predict_sero: + # predict_sero=x + # star="" + # star_line="" + #special test for Montevideo; most of them are monophasic + #if "Montevideo" in predict_sero and "1,2,7" in predict_form: #remove 11/11/2018, because already in merge list + #star="*" + #star_line="Montevideo is almost always monophasic, having an antigen called for the fljB position may be a result of Salmonella-Salmonella contamination." + return predict_form, predict_sero, star, star_line, claim +### End of SeqSero Kmer part + +### Begin of SeqSero2 allele prediction and output +def xml_parse_score_comparision_seqsero(xmlfile): + #used to do seqsero xml analysis + from Bio.Blast import NCBIXML + handle=open(xmlfile) + handle=NCBIXML.parse(handle) + handle=list(handle) + List=[] + List_score=[] + List_ids=[] + List_query_region=[] + for i in range(len(handle)): + if len(handle[i].alignments)>0: + for j in range(len(handle[i].alignments)): + score=0 + ids=0 + cover_region=set() #fixed problem that repeated calculation leading percentage > 1 + List.append(handle[i].query.strip()+"___"+handle[i].alignments[j].hit_def) + for z in range(len(handle[i].alignments[j].hsps)): + hsp=handle[i].alignments[j].hsps[z] + temp=set(range(hsp.query_start,hsp.query_end)) + if len(cover_region)==0: + cover_region=cover_region|temp + fraction=1 + else: + fraction=1-len(cover_region&temp)/float(len(temp)) + cover_region=cover_region|temp + if "last" in handle[i].query or "first" in handle[i].query: + score+=hsp.bits*fraction + ids+=float(hsp.identities)/handle[i].query_length*fraction + else: + score+=hsp.bits*fraction + ids+=float(hsp.identities)/handle[i].query_length*fraction + List_score.append(score) + List_ids.append(ids) + List_query_region.append(cover_region) + temp=zip(List,List_score,List_ids,List_query_region) + Final_list=sorted(temp, key=lambda d:d[1], reverse = True) + return Final_list + + +def Uniq(L,sort_on_fre="none"): #return the uniq list and the count number + Old=L + L.sort() + L = [L[i] for i in range(len(L)) if L[i] not in L[:i]] + count=[] + for j in range(len(L)): + y=0 + for x in Old: + if L[j]==x: + y+=1 + count.append(y) + if sort_on_fre!="none": + d=zip(*sorted(zip(count, L))) + L=d[1] + count=d[0] + return (L,count) + +def judge_fliC_or_fljB_from_head_tail_for_one_contig(nodes_vs_score_list): + #used to predict it's fliC or fljB for one contig, based on tail and head score, but output the score difference,if it is very small, then not reliable, use blast score for whole contig to test + #this is mainly used for + a=nodes_vs_score_list + fliC_score=0 + fljB_score=0 + for z in a: + if "fliC" in z[0]: + fliC_score+=z[1] + elif "fljB" in z[0]: + fljB_score+=z[1] + if fliC_score>=fljB_score: + role="fliC" + else: + role="fljB" + return (role,abs(fliC_score-fljB_score)) + +def judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(node_name,Final_list,Final_list_passed): + #used to predict contig is fliC or fljB, if the differnce score value on above head_and_tail is less than 10 (quite small) + #also used when no head or tail got blasted score for the contig + role="" + for z in Final_list_passed: + if node_name in z[0]: + role=z[0].split("_")[0] + break + return role + +def fliC_or_fljB_judge_from_head_tail_sequence(nodes_list,tail_head_list,Final_list,Final_list_passed): + #nodes_list is the c created by c,d=Uniq(nodes) in below function + first_target="" + role_list=[] + for x in nodes_list: + a=[] + role="" + for y in tail_head_list: + if x in y[0]: + a.append(y) + if len(a)==4: + role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) + if diff<20: + role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) + elif len(a)==3: + ###however, if the one with highest score is the fewer one, compare their accumulation score + role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) + if diff<20: + role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) + ###end of above score comparison + elif len(a)==2: + #must on same node, if not, then decide with unit blast score, blast-score/length_of_special_sequence(30 or 37) + temp=[] + for z in a: + temp.append(z[0].split("_")[0]) + m,n=Uniq(temp)#should only have one choice, but weird situation might occur too + if len(m)==1: + pass + else: + pass + role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) + if diff<20: + role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) + ###need to desgin a algorithm to guess most possible situation for nodes_list, See the situations of test evaluation + elif len(a)==1: + #that one + role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) + if diff<20: + role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) + #need to evaluate, in future, may set up a cut-off, if not met, then just find Final_list_passed best match,like when "a==0" + else:#a==0 + #use Final_list_passed best match + for z in Final_list_passed: + if x in z[0]: + role=z[0].split("_")[0] + break + #print x,role,len(a) + role_list.append((role,x)) + if len(role_list)==2: + if role_list[0][0]==role_list[1][0]:#this is the most cocmmon error, two antigen were assigned to same phase + #just use score to do a final test + role_list=[] + for x in nodes_list: + role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) + role_list.append((role,x)) + return role_list + +def decide_contig_roles_for_H_antigen(Final_list,Final_list_passed): + #used to decide which contig is FliC and which one is fljB + contigs=[] + nodes=[] + for x in Final_list_passed: + if x[0].startswith("fl") and "last" not in x[0] and "first" not in x[0]: + nodes.append(x[0].split("___")[1].strip()) + c,d=Uniq(nodes)#c is node_list + #print c + tail_head_list=[x for x in Final_list if ("last" in x[0] or "first" in x[0])] + roles=fliC_or_fljB_judge_from_head_tail_sequence(c,tail_head_list,Final_list,Final_list_passed) + return roles + +def decide_O_type_and_get_special_genes(Final_list,Final_list_passed): + #decide O based on Final_list + O_choice="?" + O_list=[] + special_genes={} + nodes=[] + for x in Final_list_passed: + if x[0].startswith("O-"): + nodes.append(x[0].split("___")[1].strip()) + elif not x[0].startswith("fl"): + special_genes[x[0]]=x[2]#08172018, x[2] changed from x[-1] + #print "special_genes:",special_genes + c,d=Uniq(nodes) + #print "potential O antigen contig",c + final_O=[] + O_nodes_list=[] + for x in c:#c is the list for contigs + temp=0 + for y in Final_list_passed: + if x in y[0] and y[0].startswith("O-"): + final_O.append(y) + break + ### O contig has the problem of two genes on same contig, so do additional test + potenial_new_gene="" + for x in final_O: + pointer=0 #for genes merged or not + #not consider O-1,3,19_not_in_3,10, too short compared with others + if "O-1,3,19_not_in_3,10" not in x[0] and int(x[0].split("__")[1].split("___")[0])*x[2]+850 <= int(x[0].split("length_")[1].split("_")[0]):#gene length << contig length; for now give 300*2 (for secureity can use 400*2) as flank region + pointer=x[0].split("___")[1].strip()#store the contig name + print(pointer) + if pointer!=0:#it has potential merge event + for y in Final_list: + if pointer in y[0] and y not in final_O and (y[1]>=int(y[0].split("__")[1].split("___")[0])*1.5 or (y[1]>=int(y[0].split("__")[1].split("___")[0])*y[2] and y[1]>=400)):#that's a realtively strict filter now; if passed, it has merge event and add one more to final_O + potenial_new_gene=y + #print(potenial_new_gene) + break + if potenial_new_gene!="": + print("two differnt genes in same contig, fix it for O antigen") + print(potenial_new_gene[:3]) + pointer=0 + for y in final_O: + if y[0].split("___")[-1]==potenial_new_gene[0].split("___")[-1]: + pointer=1 + if pointer!=0: #changed to consider two genes in same contig + final_O.append(potenial_new_gene) + ### end of the two genes on same contig test + final_O=sorted(final_O,key=lambda x: x[2], reverse=True)#sorted + if len(final_O)==0 or (len(final_O)==1 and "O-1,3,19_not_in_3,10" in final_O[0][0]): + #print "$$$No Otype, due to no hit"#may need to be changed + O_choice="-" + else: + highest_O_coverage=max([float(x[0].split("_cov_")[-1].split("_")[0]) for x in final_O if "O-1,3,19_not_in_3,10" not in x[0]]) + O_list=[] + O_list_less_contamination=[] + for x in final_O: + if not "O-1,3,19_not_in_3,10__130" in x[0]:#O-1,3,19_not_in_3,10 is too small, which may affect further analysis; to avoid contamination affect, use 0.15 of highest coverage as cut-off + O_list.append(x[0].split("__")[0]) + O_nodes_list.append(x[0].split("___")[1]) + if float(x[0].split("_cov_")[-1].split("_")[0])>highest_O_coverage*0.15: + O_list_less_contamination.append(x[0].split("__")[0]) + ### special test for O9,46 and O3,10 family + if ("O-9,46_wbaV" in O_list or "O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254" in O_list) and O_list_less_contamination[0].startswith("O-9,"):#not sure should use and float(O9_wbaV)/float(num_1) > 0.1 + if "O-9,46_wzy" in O_list or "O-9,46_wzy_partial" in O_list:#and float(O946_wzy)/float(num_1) > 0.1 + O_choice="O-9,46" + #print "$$$Most possilble Otype: O-9,46" + elif "O-9,46,27_partial_wzy" in O_list:#and float(O94627)/float(num_1) > 0.1 + O_choice="O-9,46,27" + #print "$$$Most possilble Otype: O-9,46,27" + else: + O_choice="O-9"#next, detect O9 vs O2? + O2=0 + O9=0 + for z in special_genes: + if "tyr-O-9" in z: + O9=special_genes[z] + elif "tyr-O-2" in z: + O2=special_genes[z] + if O2>O9: + O_choice="O-2" + elif O2 0.1 and float(O946_wzy)/float(num_1) > 0.1 + if "O-3,10_not_in_1,3,19" in O_list:#and float(O310_no_1319)/float(num_1) > 0.1 + O_choice="O-3,10" + #print "$$$Most possilble Otype: O-3,10 (contain O-3,10_not_in_1,3,19)" + else: + O_choice="O-1,3,19" + #print "$$$Most possilble Otype: O-1,3,19 (not contain O-3,10_not_in_1,3,19)" + ### end of special test for O9,46 and O3,10 family + else: + try: + max_score=0 + for x in final_O: + if x[2]>=max_score and float(x[0].split("_cov_")[-1].split("_")[0])>highest_O_coverage*0.15:#use x[2],08172018, the "coverage identity = cover_length * identity"; also meet coverage threshold + max_score=x[2]#change from x[-1] to x[2],08172018 + O_choice=x[0].split("_")[0] + if O_choice=="O-1,3,19": + O_choice=final_O[1][0].split("_")[0] + #print "$$$Most possilble Otype: ",O_choice + except: + pass + #print "$$$No suitable Otype, or failure of mapping (please check the quality of raw reads)" + if O_choice=="O-9,46,27" and len(O_list)==2 and "O-4_wzx" in O_list: #special for very low chance sitatuion between O4 and O9,27,46, this is for serotypes like Bredeney and Schwarzengrund (normallly O-4 will have higher score, but sometimes sequencing quality may affect the prediction) + O_choice="O-4" + #print "O:",O_choice,O_nodes_list + Otypes=[] + for x in O_list: + if x!="O-1,3,19_not_in_3,10": + if "O-9,46_" not in x: + Otypes.append(x.split("_")[0]) + else: + Otypes.append(x.split("-from")[0])#O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254 + #Otypes=[x.split("_")[0] for x in O_list if x!="O-1,3,19_not_in_3,10"] + Otypes_uniq,Otypes_fre=Uniq(Otypes) + contamination_O="" + if O_choice=="O-9,46,27" or O_choice=="O-3,10" or O_choice=="O-1,3,19": + if len(Otypes_uniq)>2: + contamination_O="potential contamination from O antigen signals" + else: + if len(Otypes_uniq)>1: + if O_choice=="O-4" and len(Otypes_uniq)==2 and "O-9,46,27" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund + contamination_O="" + elif O_choice=="O-9,46" and len(Otypes_uniq)==2 and "O-9,46_wbaV" in Otypes_uniq and "O-9,46_wzy" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund + contamination_O="" + else: + contamination_O="potential contamination from O antigen signals" + return O_choice,O_nodes_list,special_genes,final_O,contamination_O,Otypes_uniq +### End of SeqSero2 allele prediction and output + +def get_input_files(make_dir,input_file,data_type,dirpath): + #tell input files from datatype + #": '1'(pair-end reads, interleaved),'2'(pair-end reads, seperated),'3'(single-end reads), '4'(assembly),'5'(nanopore fasta),'6'(nanopore fastq)" + for_fq="" + rev_fq="" + os.chdir(make_dir) + if data_type=="1": + input_file=input_file[0].split("/")[-1] + if input_file.endswith(".sra"): + subprocess.check_call("fastq-dump --split-files "+input_file,shell=True) + for_fq=input_file.replace(".sra","_1.fastq") + rev_fq=input_file.replace(".sra","_2.fastq") + else: + core_id=input_file.split(".fastq")[0].split(".fq")[0] + for_fq=core_id+"_1.fastq" + rev_fq=core_id+"_2.fastq" + if input_file.endswith(".gz"): + subprocess.check_call("gzip -dc "+input_file+" | "+dirpath+"/deinterleave_fastq.sh "+for_fq+" "+rev_fq,shell=True) + else: + subprocess.check_call("cat "+input_file+" | "+dirpath+"/deinterleave_fastq.sh "+for_fq+" "+rev_fq,shell=True) + elif data_type=="2": + for_fq=input_file[0].split("/")[-1] + rev_fq=input_file[1].split("/")[-1] + elif data_type=="3": + input_file=input_file[0].split("/")[-1] + if input_file.endswith(".sra"): + subprocess.check_call("fastq-dump --split-files "+input_file,shell=True) + for_fq=input_file.replace(".sra","_1.fastq") + else: + for_fq=input_file + elif data_type in ["4","5","6"]: + for_fq=input_file[0].split("/")[-1] + os.chdir("..") + return for_fq,rev_fq + +def predict_O_and_H_types(Final_list,Final_list_passed,new_fasta): + #get O and H types from Final_list from blast parsing; allele mode + from Bio import SeqIO + fliC_choice="-" + fljB_choice="-" + fliC_contig="NA" + fljB_contig="NA" + fliC_region=set([0]) + fljB_region=set([0,]) + fliC_length=0 #can be changed to coverage in future; in 03292019, changed to ailgned length + fljB_length=0 #can be changed to coverage in future; in 03292019, changed to ailgned length + O_choice="-"#no need to decide O contig for now, should be only one + O_choice,O_nodes,special_gene_list,O_nodes_roles,contamination_O,Otypes_uniq=decide_O_type_and_get_special_genes(Final_list,Final_list_passed)#decide the O antigen type and also return special-gene-list for further identification + O_choice=O_choice.split("-")[-1].strip() + if (O_choice=="1,3,19" and len(O_nodes_roles)==1 and "1,3,19" in O_nodes_roles[0][0]) or O_choice=="": + O_choice="-" + H_contig_roles=decide_contig_roles_for_H_antigen(Final_list,Final_list_passed)#decide the H antigen contig is fliC or fljB + #add alignment locations, used for further selection, 03312019 + for i in range(len(H_contig_roles)): + x=H_contig_roles[i] + for y in Final_list_passed: + if x[1] in y[0] and y[0].startswith(x[0]): + H_contig_roles[i]+=H_contig_roles[i]+(y[-1],) + break + log_file=open("SeqSero_log.txt","a") + extract_file=open("Extracted_antigen_alleles.fasta","a") + handle_fasta=list(SeqIO.parse(new_fasta,"fasta")) + + #print("O_contigs:") + log_file.write("O_contigs:\n") + extract_file.write("#Sequences with antigen signals (if the micro-assembled contig only covers the flanking region, it will not be used for contamination analysis)\n") + extract_file.write("#O_contigs:\n") + for x in O_nodes_roles: + if "O-1,3,19_not_in_3,10" not in x[0]:#O-1,3,19_not_in_3,10 is just a small size marker + #print(x[0].split("___")[-1],x[0].split("__")[0],"blast score:",x[1],"identity%:",str(round(x[2]*100,2))+"%",str(min(x[-1]))+" to "+str(max(x[-1]))) + log_file.write(x[0].split("___")[-1]+" "+x[0].split("__")[0]+"; "+"blast score: "+str(x[1])+" identity%: "+str(round(x[2]*100,2))+"%; alignment from "+str(min(x[-1]))+" to "+str(max(x[-1]))+" of antigen\n") + title=">"+x[0].split("___")[-1]+" "+x[0].split("__")[0]+"; "+"blast score: "+str(x[1])+" identity%: "+str(round(x[2]*100,2))+"%; alignment from "+str(min(x[-1]))+" to "+str(max(x[-1]))+" of antigen\n" + seqs="" + for z in handle_fasta: + if x[0].split("___")[-1]==z.description: + seqs=str(z.seq) + extract_file.write(title+seqs+"\n") + if len(H_contig_roles)!=0: + highest_H_coverage=max([float(x[1].split("_cov_")[-1].split("_")[0]) for x in H_contig_roles]) #less than highest*0.1 would be regarded as contamination and noises, they will still be considered in contamination detection and logs, but not used as final serotype output + else: + highest_H_coverage=0 + for x in H_contig_roles: + #if multiple choices, temporately select the one with longest length for now, will revise in further change + if "fliC" == x[0] and len(x[-1])>=fliC_length and x[1] not in O_nodes and float(x[1].split("_cov_")[-1].split("_")[0])>highest_H_coverage*0.13:#remember to avoid the effect of O-type contig, so should not in O_node list + fliC_contig=x[1] + fliC_length=len(x[-1]) + elif "fljB" == x[0] and len(x[-1])>=fljB_length and x[1] not in O_nodes and float(x[1].split("_cov_")[-1].split("_")[0])>highest_H_coverage*0.13: + fljB_contig=x[1] + fljB_length=len(x[-1]) + for x in Final_list_passed: + if fliC_choice=="-" and "fliC_" in x[0] and fliC_contig in x[0]: + fliC_choice=x[0].split("_")[1] + elif fljB_choice=="-" and "fljB_" in x[0] and fljB_contig in x[0]: + fljB_choice=x[0].split("_")[1] + elif fliC_choice!="-" and fljB_choice!="-": + break + #now remove contigs not in middle core part + first_allele="NA" + first_allele_percentage=0 + for x in Final_list: + if x[0].startswith("fliC") or x[0].startswith("fljB"): + first_allele=x[0].split("__")[0] #used to filter those un-middle contigs + first_allele_percentage=x[2] + break + additional_contigs=[] + for x in Final_list: + if first_allele in x[0]: + if (fliC_contig == x[0].split("___")[-1]): + fliC_region=x[3] + elif fljB_contig!="NA" and (fljB_contig == x[0].split("___")[-1]): + fljB_region=x[3] + else: + if x[1]*1.1>int(x[0].split("___")[1].split("_")[3]):#loose threshold by multiplying 1.1 + additional_contigs.append(x) + #else: + #print x[:3] + #we can just use the fljB region (or fliC depends on size), no matter set() or contain a large locations (without middle part); however, if none of them is fully assembled, use 500 and 1200 as conservative cut-off + if first_allele_percentage>0.9: + if len(fliC_region)>len(fljB_region) and (max(fljB_region)-min(fljB_region))>1000: + target_region=fljB_region|(fliC_region-set(range(min(fljB_region),max(fljB_region)))) #fljB_region|(fliC_region-set(range(min(fljB_region),max(fljB_region)))) + elif len(fliC_region)1000: + target_region=fliC_region|(fljB_region-set(range(min(fliC_region),max(fliC_region)))) #fljB_region|(fliC_region-set(range(min(fljB_region),max(fljB_region)))) + else: + target_region=set()#doesn't do anything + else: + target_region=set()#doesn't do anything + #print(target_region) + #print(additional_contigs) + target_region2=set(list(range(0,525))+list(range(1200,1700)))#I found to use 500 to 1200 as special region would be best + target_region=target_region2|target_region + for x in additional_contigs: + removal=0 + contig_length=int(x[0].split("___")[1].split("length_")[-1].split("_")[0]) + if fljB_contig not in x[0] and fliC_contig not in x[0] and len(target_region&x[3])/float(len(x[3]))>0.65 and contig_length*0.5 0.9 and float(x[0].split("__")[1].split("___")[0])*x[2]/len(x[-1])>0.96:#if high similiarity with middle part of first allele (first allele >0.9, already cover middle part) + removal=1 + else: + pass + if removal==1: + for y in H_contig_roles: + if y[1] in x[0]: + H_contig_roles.remove(y) + else: + pass + #print(x[:3],contig_length,len(target_region&x[3])/float(len(x[3])),contig_length*0.5,len(x[3]),contig_length*1.5) + #end of removing none-middle contigs + #print("H_contigs:") + log_file.write("H_contigs:\n") + extract_file.write("#H_contigs:\n") + H_contig_stat=[] + H1_cont_stat={} + H2_cont_stat={} + for i in range(len(H_contig_roles)): + x=H_contig_roles[i] + a=0 + for y in Final_list_passed: + if x[1] in y[0] and y[0].startswith(x[0]): + if "first" in y[0] or "last" in y[0]: #this is the final filter to decide it's fliC or fljB, if can't pass, then can't decide + for y in Final_list_passed: #it's impossible to has the "first" and "last" allele as prediction, so re-do it + if x[1] in y[0]:#it's very possible to be third phase allele, so no need to make it must be fliC or fljB + #print(x[1],"can't_decide_fliC_or_fljB",y[0].split("_")[1],"blast_score:",y[1],"identity%:",str(round(y[2]*100,2))+"%",str(min(y[-1]))+" to "+str(max(y[-1]))) + log_file.write(x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antigen\n") + H_contig_roles[i]="can't decide fliC or fljB, may be third phase" + title=">"+x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antiten\n" + seqs="" + for z in handle_fasta: + if x[1]==z.description: + seqs=str(z.seq) + extract_file.write(title+seqs+"\n") + break + else: + #print(x[1],x[0],y[0].split("_")[1],"blast_score:",y[1],"identity%:",str(round(y[2]*100,2))+"%",str(min(y[-1]))+" to "+str(max(y[-1]))) + log_file.write(x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antigen\n") + title=">"+x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antigen\n" + seqs="" + for z in handle_fasta: + if x[1]==z.description: + seqs=str(z.seq) + extract_file.write(title+seqs+"\n") + if x[0]=="fliC": + if y[0].split("_")[1] not in H1_cont_stat: + H1_cont_stat[y[0].split("_")[1]]=y[2] + else: + H1_cont_stat[y[0].split("_")[1]]+=y[2] + if x[0]=="fljB": + if y[0].split("_")[1] not in H2_cont_stat: + H2_cont_stat[y[0].split("_")[1]]=y[2] + else: + H2_cont_stat[y[0].split("_")[1]]+=y[2] + break + #detect contaminations + #print(H1_cont_stat) + #print(H2_cont_stat) + H1_cont_stat_list=[x for x in H1_cont_stat if H1_cont_stat[x]>0.2] + H2_cont_stat_list=[x for x in H2_cont_stat if H2_cont_stat[x]>0.2] + contamination_H="" + if len(H1_cont_stat_list)>1 or len(H2_cont_stat_list)>1: + contamination_H="potential contamination from H antigen signals" + elif len(H2_cont_stat_list)==1 and fljB_contig=="NA": + contamination_H="potential contamination from H antigen signals, uncommon weak fljB signals detected" + #get additional antigens + """ + if ("O-9,46_wbaV" in O_list or "O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254" in O_list) and O_list_less_contamination[0].startswith("O-9,"):#not sure should use and float(O9_wbaV)/float(num_1) > 0.1 + if "O-9,46_wzy" in O_list:#and float(O946_wzy)/float(num_1) > 0.1 + O_choice="O-9,46" + #print "$$$Most possilble Otype: O-9,46" + elif "O-9,46,27_partial_wzy" in O_list:#and float(O94627)/float(num_1) > 0.1 + O_choice="O-9,46,27" + #print "$$$Most possilble Otype: O-9,46,27" + elif ("O-3,10_wzx" in O_list) and ("O-9,46_wzy" in O_list) and (O_list[0].startswith("O-3,10") or O_list_less_contamination[0].startswith("O-9,46_wzy")):#and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1 + if "O-3,10_not_in_1,3,19" in O_list:#and float(O310_no_1319)/float(num_1) > 0.1 + O_choice="O-3,10" + #print "$$$Most possilble Otype: O-3,10 (contain O-3,10_not_in_1,3,19)" + else: + O_choice="O-1,3,19" + #print "$$$Most possilble Otype: O-1,3,19 (not contain O-3,10_not_in_1,3,19)" + ### end of special test for O9,46 and O3,10 family + + if O_choice=="O-9,46,27" or O_choice=="O-3,10" or O_choice=="O-1,3,19": + if len(Otypes_uniq)>2: + contamination_O="potential contamination from O antigen signals" + else: + if len(Otypes_uniq)>1: + if O_choice=="O-4" and len(Otypes_uniq)==2 and "O-9,46,27" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund + contamination_O="" + elif O_choice=="O-9,46" and len(Otypes_uniq)==2 and "O-9,46_wbaV" in Otypes_uniq and "O-9,46_wzy" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund + contamination_O="" + """ + additonal_antigents=[] + #print(contamination_O) + #print(contamination_H) + log_file.write(contamination_O+"\n") + log_file.write(contamination_H+"\n") + log_file.close() + return O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H,Otypes_uniq,H1_cont_stat_list,H2_cont_stat_list + +def get_input_K(input_file,lib_dict,data_type,k_size): + #kmer mode; get input_Ks from dict and data_type + kmers = [] + for h in lib_dict: + kmers += lib_dict[h] + if data_type == '4': + input_Ks = target_multifasta_kmerizer(input_file, k_size, set(kmers)) + elif data_type == '1' or data_type == '2' or data_type == '3':#set it for now, will change later + input_Ks = target_read_kmerizer(input_file, k_size, set(kmers)) + elif data_type == '5':#minion_2d_fasta + input_Ks = minion_fasta_kmerizer(input_file, k_size, set(kmers)) + if data_type == '6':#minion_2d_fastq + input_Ks = minion_fastq_kmerizer(input_file, k_size, set(kmers)) + return input_Ks + +def get_kmer_dict(lib_dict,input_Ks): + #kmer mode; get predicted types + O_dict = {} + H_dict = {} + Special_dict = {} + for h in lib_dict: + score = (len(lib_dict[h] & input_Ks) / len(lib_dict[h])) * 100 + if score > 1: # Arbitrary cut-off for similarity score very low but seems necessary to detect O-3,10 in some cases + if h.startswith('O-') and score > 25: + O_dict[h] = score + if h.startswith('fl') and score > 40: + H_dict[h] = score + if (h[:2] != 'fl') and (h[:2] != 'O-'): + Special_dict[h] = score + return O_dict,H_dict,Special_dict + +def call_O_and_H_type(O_dict,H_dict,Special_dict,make_dir): + log_file=open("SeqSero_log.txt","a") + log_file.write("O_scores:\n") + #call O: + highest_O = '-' + if len(O_dict) == 0: + pass + else: + for x in O_dict: + log_file.write(x+"\t"+str(O_dict[x])+"\n") + if ('O-9,46_wbaV__1002' in O_dict and O_dict['O-9,46_wbaV__1002']>70) or ("O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002" in O_dict and O_dict['O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002']>70): # not sure should use and float(O9_wbaV)/float(num_1) > 0.1 + #if 'O-9,46_wzy__1191' in O_dict or "O-9,46_wzy_partial__216" in O_dict: # and float(O946_wzy)/float(num_1) > 0.1 + #modified to fix miscall of O-9,46 + if ('O-9,46_wzy__1191' in O_dict and O_dict['O-9,46_wzy__1191']>40) or ("O-9,46_wzy_partial__216" in O_dict and O_dict["O-9,46_wzy_partial__216"]>40): # and float(O946_wzy)/float(num_1) > 0.1 + highest_O = "O-9,46" + elif "O-9,46,27_partial_wzy__1019" in O_dict: # and float(O94627)/float(num_1) > 0.1 + highest_O = "O-9,46,27" + else: + highest_O = "O-9" # next, detect O9 vs O2? + O2 = 0 + O9 = 0 + for z in Special_dict: + if "tyr-O-9" in z: + O9 = float(Special_dict[z]) + if "tyr-O-2" in z: + O2 = float(Special_dict[z]) + if O2 > O9: + highest_O = "O-2" + elif ("O-3,10_wzx__1539" in O_dict) and ( + "O-9,46_wzy__1191" in O_dict + ): # and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1 + if "O-3,10_not_in_1,3,19__1519" in O_dict: # and float(O310_no_1319)/float(num_1) > 0.1 + highest_O = "O-3,10" + else: + highest_O = "O-1,3,19" + ### end of special test for O9,46 and O3,10 family + else: + try: + max_score = 0 + for x in O_dict: + if float(O_dict[x]) >= max_score: + max_score = float(O_dict[x]) + #highest_O = x.split("_")[0] + # ed_SL_12182019: modified to fix the O-9,46 error example1 + if (x == 'O-9,46_wbaV__1002' or x == 'O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002') and ('O-9,46_wzy__1191' not in O_dict and 'O-9,46_wzy_partial__216' not in O_dict): + highest_O = "O-9" + else: + highest_O = x.split("_")[0] + if highest_O == "O-1,3,19": + highest_O = '-' + max_score = 0 + for x in O_dict: + if x == 'O-1,3,19_not_in_3,10__130': + pass + else: + if float(O_dict[x]) >= max_score: + max_score = float(O_dict[x]) + #highest_O = x.split("_")[0] + # ed_SL_12182019: modified to fix the O-9,46 error example1 + if (x == 'O-9,46_wbaV__1002' or x == 'O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002') and ('O-9,46_wzy__1191' not in O_dict and 'O-9,46_wzy_partial__216' not in O_dict): + highest_O = "O-9" + else: + highest_O = x.split("_")[0] + except: + pass + #call_fliC: + if len(H_dict)!=0: + highest_H_score_both_BC=H_dict[max(H_dict.keys(), key=(lambda k: H_dict[k]))] #used to detect whether fljB existed or not + else: + highest_H_score_both_BC=0 + highest_fliC = '-' + highest_fliC_raw = '-' + highest_Score = 0 + log_file.write("\nH_scores:\n") + for s in H_dict: + log_file.write(s+"\t"+str(H_dict[s])+"\n") + if s.startswith('fliC'): + if float(H_dict[s]) > highest_Score: + highest_fliC = s.split('_')[1] + highest_fliC_raw = s + highest_Score = float(H_dict[s]) + #call_fljB + highest_fljB = '-' + highest_fljB_raw = '-' + highest_Score = 0 + for s in H_dict: + if s.startswith('fljB'): + if float(H_dict[s]) > highest_Score and float(H_dict[s]) > highest_H_score_both_BC * 0.65: #fljB is special, so use highest_H_score_both_BC to give a general estimate of coverage, currently 0.65 seems pretty good; the reason use a high (0.65) is some fliC and fljB shared with each other + #highest_fljB = s.split('_')[1] + #highest_fljB_raw = s + #highest_Score = float(H_dict[s]) + if s.split('_')[1]!=highest_fliC: + highest_fljB = s.split('_')[1] + highest_fljB_raw = s + highest_Score = float(H_dict[s]) + log_file.write("\nSpecial_scores:\n") + for s in Special_dict: + log_file.write(s+"\t"+str(Special_dict[s])+"\n") + log_file.close() + return highest_O,highest_fliC,highest_fljB + +def get_temp_file_names(for_fq,rev_fq): + #seqsero2 -a; get temp file names + sam=for_fq+".sam" + bam=for_fq+".bam" + sorted_bam=for_fq+"_sorted.bam" + mapped_fq1=for_fq+"_mapped.fq" + mapped_fq2=rev_fq+"_mapped.fq" + combined_fq=for_fq+"_combined.fq" + for_sai=for_fq+".sai" + rev_sai=rev_fq+".sai" + return sam,bam,sorted_bam,mapped_fq1,mapped_fq2,combined_fq,for_sai,rev_sai + +def map_and_sort(threads,database,fnameA,fnameB,sam,bam,for_sai,rev_sai,sorted_bam,mapping_mode): + #seqsero2 -a; do mapping and sort + print("building database...") + subprocess.check_call("bwa index "+database+ " 2>> data_log.txt",shell=True) + print("mapping...") + if mapping_mode=="mem": + subprocess.check_call("bwa mem -k 17 -t "+threads+" "+database+" "+fnameA+" "+fnameB+" > "+sam+ " 2>> data_log.txt",shell=True) + elif mapping_mode=="sam": + if fnameB!="": + subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameA+" > "+for_sai+ " 2>> data_log.txt",shell=True) + subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameB+" > "+rev_sai+ " 2>> data_log.txt",shell=True) + subprocess.check_call("bwa sampe "+database+" "+for_sai+" "+ rev_sai+" "+fnameA+" "+fnameB+" > "+sam+ " 2>> data_log.txt",shell=True) + else: + subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameA+" > "+for_sai+ " 2>> data_log.txt",shell=True) + subprocess.check_call("bwa samse "+database+" "+for_sai+" "+for_fq+" > "+sam) + subprocess.check_call("samtools view -@ "+threads+" -F 4 -Sh "+sam+" > "+bam,shell=True) + ### check the version of samtools then use differnt commands + samtools_version=subprocess.Popen(["samtools"],stdout=subprocess.PIPE,stderr=subprocess.PIPE) + out, err = samtools_version.communicate() + version = str(err).split("ersion:")[1].strip().split(" ")[0].strip() + print("check samtools version:",version) + ### end of samtools version check and its analysis + if LooseVersion(version)<=LooseVersion("1.2"): + subprocess.check_call("samtools sort -@ "+threads+" -n "+bam+" "+fnameA+"_sorted",shell=True) + else: + subprocess.check_call("samtools sort -@ "+threads+" -n "+bam+" >"+sorted_bam,shell=True) + +def extract_mapped_reads_and_do_assembly_and_blast(current_time,sorted_bam,combined_fq,mapped_fq1,mapped_fq2,threads,fnameA,fnameB,database,mapping_mode): + #seqsero2 -a; extract, assembly and blast + subprocess.check_call("bamToFastq -i "+sorted_bam+" -fq "+combined_fq,shell=True) + #print("fnameA:",fnameA) + #print("fnameB:",fnameB) + if fnameB!="": + subprocess.check_call("bamToFastq -i "+sorted_bam+" -fq "+mapped_fq1+" -fq2 "+mapped_fq2 + " 2>> data_log.txt",shell=True)#2> /dev/null if want no output + else: + pass + outdir=current_time+"_temp" + print("assembling...") + if int(threads)>4: + t="4" + else: + t=threads + if os.path.getsize(combined_fq)>100 and (fnameB=="" or os.path.getsize(mapped_fq1)>100):#if not, then it's "-:-:-" + if fnameB!="": + subprocess.check_call("spades.py --careful --pe1-s "+combined_fq+" --pe1-1 "+mapped_fq1+" --pe1-2 "+mapped_fq2+" -t "+t+" -o "+outdir+ " >> data_log.txt 2>&1",shell=True) + else: + subprocess.check_call("spades.py --careful --pe1-s "+combined_fq+" -t "+t+" -o "+outdir+ " >> data_log.txt 2>&1",shell=True) + new_fasta=fnameA+"_"+database+"_"+mapping_mode+".fasta" + #new_fasta=fnameA+"_"+database.split('/')[-1]+"_"+mapping_mode+".fasta" # change path to databse for packaging + subprocess.check_call("mv "+outdir+"/contigs.fasta "+new_fasta+ " 2> /dev/null",shell=True) + #os.system("mv "+outdir+"/scaffolds.fasta "+new_fasta+ " 2> /dev/null") contigs.fasta + subprocess.check_call("rm -rf "+outdir+ " 2> /dev/null",shell=True) + print("blasting...","\n") + xmlfile="blasted_output.xml"#fnameA+"-extracted_vs_"+database+"_"+mapping_mode+".xml" + subprocess.check_call('makeblastdb -in '+new_fasta+' -out '+new_fasta+'_db '+'-dbtype nucl >> data_log.txt 2>&1',shell=True) #temp.txt is to forbid the blast result interrupt the output of our program###1/27/2015 + subprocess.check_call("blastn -query "+database+" -db "+new_fasta+"_db -out "+xmlfile+" -outfmt 5 >> data_log.txt 2>&1",shell=True)###1/27/2015; 08272018, remove "-word_size 10" + else: + xmlfile="NA" + return xmlfile,new_fasta + +def judge_subspecies(fnameA): + #seqsero2 -a; judge subspecies on just forward raw reads fastq + salmID_output=subprocess.Popen("SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE) + out, err = salmID_output.communicate() + out=out.decode("utf-8") + file=open("data_log.txt","a") + file.write(out) + file.close() + salm_species_scores=out.split("\n")[1].split("\t")[6:] + salm_species_results=out.split("\n")[0].split("\t")[6:] + max_score=0 + max_score_index=1 #default is 1, means "I" + for i in range(len(salm_species_scores)): + if max_score float(out.split("\n")[1].split("\t")[5]): #bongori and enterica compare + if float(out.split("\n")[1].split("\t")[4]) > 10 and float(out.split("\n")[1].split("\t")[4]) > float(out.split("\n")[1].split("\t")[5]): ## ed_SL_0318: change SalmID_ssp_threshold + prediction="bongori" #if not, the prediction would always be enterica, since they are located in the later part + #if max_score<10: ## ed_SL_0318: change SalmID_ssp_threshold + if max_score<60: + prediction="-" + return prediction + +def judge_subspecies_Kmer(Special_dict): + #seqsero2 -k; + max_score=0 + prediction="-" #default should be I + for x in Special_dict: + #if "mer" in x: ## ed_SL_0318: change ssp_threshold + if "mer" in x and float(Special_dict[x]) > 60: + if max_score95:#if bongori already, then no need to test enterica + prediction="bongori" + break + return prediction + +## ed_SL_11232019: add notes for missing antigen +def check_antigens(ssp,O_antigen,H1_antigen,H2_antigen,NA_note): + antigen_note = '' + if ssp != '-': + if O_antigen != '-' and H1_antigen == '-' and H2_antigen == '-': # O:-:- + antigen_note = 'H antigens were not detected. This is an atypical result that should be further investigated. Most Salmonella strains have at least fliC, encoding the Phase 1 H antigen, even if it is not expressed. ' + NA_note = '' + elif O_antigen != '-' and H1_antigen == '-' and H2_antigen != '-': # O:-:H2 + antigen_note = 'fliC was not detected. This is an atypical result that should be further investigated. Most Salmonella strains have fliC, encoding the Phase 1 H antigen, even if it is not expressed. ' + NA_note = '' + elif O_antigen == '-' and H1_antigen != '-': # -:H1:X + antigen_note = 'O antigen was not detected. This result may be due to a rough strain that has deleted the rfb region. For raw reads input, the k-mer workflow is sometimes more sensitive than the microassembly workflow in detecting O antigen. Caution should be used with this approach because the k-mer result may be due to low levels of contamination. ' + NA_note = '' + elif O_antigen == '-' and H1_antigen == '-' and H2_antigen == '-': # -:-:- + antigen_note = 'No serotype antigens were detected. This is an atypical result that should be further investigated. ' + NA_note = '' + else: + antigen_note = 'The input genome cannot be identified as Salmonella. Check the input for taxonomic ID, contamination, or sequencing quality. ' + NA_note = '' +# if [O_antigen, H1_antigen, H2_antigen].count('-') >= 2: +# antigen_note = 'No subspecies marker was detected and less than 2 serotype antigens were detected; further, this genome was not identified as Salmonella. This is an atypical result that should be further investigated. ' +# else: +# antigen_note = 'No subspecies marker was detected. This genome may not be Salmonella. This is an atypical result that should be further investigated. ' + return (antigen_note,NA_note) + +def main(): + #combine SeqSeroK and SeqSero2, also with SalmID + args = parse_args() + input_file = args.i + data_type = args.t + analysis_mode = args.m + mapping_mode=args.b + threads=args.p + make_dir=args.d + clean_mode=args.c + sample_name=args.n + ingore_header=args.s + k_size=27 #will change for bug fixing + dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__))) + ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019: add ex_dir for packaging + seqsero2_db=ex_dir+"/H_and_O_and_specific_genes.fasta" # ed_SL_11092019: change path to database for packaging + database="H_and_O_and_specific_genes.fasta" + note="Note: " + NA_note="This predicted serotype is not in the Kauffman-White scheme. " # ed_SL_09272019: add for new output format + if len(sys.argv)==1: + subprocess.check_call(dirpath+"/SeqSero2_package.py -h",shell=True)#change name of python file + else: + request_id = time.strftime("%m_%d_%Y_%H_%M_%S", time.localtime()) + request_id += str(random.randint(1, 10000000)) + if make_dir is None: + make_dir="SeqSero_result_"+request_id + make_dir=os.path.abspath(make_dir) + if os.path.isdir(make_dir): + pass + else: + subprocess.check_call("mkdir -p "+make_dir,shell=True) + #subprocess.check_call("cp "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) + #subprocess.check_call("ln -sr "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) + subprocess.check_call("ln -f -s "+seqsero2_db+" "+" ".join(input_file)+" "+make_dir,shell=True) # ed_SL_11092019: change path to database for packaging + #subprocess.check_call("ln -f -s "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) ### use -f option to force the replacement of links, remove -r and use absolute path instead to avoid link issue (use 'type=os.path.abspath' in -i argument). + ############################begin the real analysis + if analysis_mode=="a": + if data_type in ["1","2","3"]:#use allele mode + for_fq,rev_fq=get_input_files(make_dir,input_file,data_type,dirpath) + os.chdir(make_dir) + ###add a function to tell input files + fnameA=for_fq.split("/")[-1] + fnameB=rev_fq.split("/")[-1] + current_time=time.strftime("%Y_%m_%d_%H_%M_%S", time.localtime()) + sam,bam,sorted_bam,mapped_fq1,mapped_fq2,combined_fq,for_sai,rev_sai=get_temp_file_names(fnameA,fnameB) #get temp files id + map_and_sort(threads,database,fnameA,fnameB,sam,bam,for_sai,rev_sai,sorted_bam,mapping_mode) #do mapping and sort + ### avoid error out when micro assembly fails. ed_SL_03172020 + try: + xmlfile,new_fasta=extract_mapped_reads_and_do_assembly_and_blast(current_time,sorted_bam,combined_fq,mapped_fq1,mapped_fq2,threads,fnameA,fnameB,database,mapping_mode) #extract the mapped reads and do micro assembly and blast + except (UnboundLocalError, subprocess.CalledProcessError): + xmlfile="NA" + H1_cont_stat_list=[] + H2_cont_stat_list=[] + ### + if xmlfile=="NA": + O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H=("-","-","-",[],"","") + else: + Final_list=xml_parse_score_comparision_seqsero(xmlfile) #analyze xml and get parsed results + file=open("data_log.txt","a") + for x in Final_list: + file.write("\t".join(str(y) for y in x)+"\n") + file.close() + Final_list_passed=[x for x in Final_list if float(x[0].split("_cov_")[1].split("_")[0])>=0.9 and (x[1]>=int(x[0].split("__")[1]) or x[1]>=int(x[0].split("___")[1].split("_")[3]) or x[1]>1000)] + O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H,Otypes_uniq,H1_cont_stat_list,H2_cont_stat_list=predict_O_and_H_types(Final_list,Final_list_passed,new_fasta) #predict O, fliC and fljB + subspecies=judge_subspecies(fnameA) #predict subspecies + ###output + predict_form,predict_sero,star,star_line,claim=seqsero_from_formula_to_serotypes(O_choice,fliC_choice,fljB_choice,special_gene_list,subspecies) + claim="" #04132019, disable claim for new report requirement + contamination_report="" + H_list=["fliC_"+x for x in H1_cont_stat_list if len(x)>0]+["fljB_"+x for x in H2_cont_stat_list if len(x)>0] + if contamination_O!="" and contamination_H=="": + contamination_report="#Potential inter-serotype contamination detected from O antigen signals. All O-antigens detected:"+"\t".join(Otypes_uniq)+"." + elif contamination_O=="" and contamination_H!="": + contamination_report="#Potential inter-serotype contamination detected or potential thrid H phase from H antigen signals. All H-antigens detected:"+"\t".join(H_list)+"." + elif contamination_O!="" and contamination_H!="": + contamination_report="#Potential inter-serotype contamination detected from both O and H antigen signals.All O-antigens detected:"+"\t".join(Otypes_uniq)+". All H-antigens detected:"+"\t".join(H_list)+"." + if contamination_report!="": + #contamination_report="potential inter-serotype contamination detected (please refer below antigen signal report for details)." #above contamination_reports are for back-up and bug fixing #web-based mode need to be re-used, 04132019 + contamination_report="Co-existence of multiple serotypes detected, indicating potential inter-serotype contamination. See 'Extracted_antigen_alleles.fasta' for detected serotype determinant alleles. " + #claim="\n"+open("Extracted_antigen_alleles.fasta","r").read()#used to store H and O antigen sequeences #04132019, need to change if using web-version + #if contamination_report+star_line+claim=="": #0413, new output style + # note="" + #else: + # note="Note:" + + ### ed_SL_11232019: add notes for missing antigen + if O_choice=="": + O_choice="-" + antigen_note,NA_note=check_antigens(subspecies,O_choice,fliC_choice,fljB_choice,NA_note) + if sample_name: + print ("Sample name:\t"+sample_name) + ### + + if clean_mode: + subprocess.check_call("rm -rf ../"+make_dir,shell=True) + make_dir="none-output-directory due to '-c' flag" + else: + new_file=open("SeqSero_result.txt","w") + ### ed_SL_01152020: add new output + conta_note="yes" if "inter-serotype contamination" in contamination_report else "no" + tsv_file=open("SeqSero_result.tsv","w") + if ingore_header: + pass + else: + tsv_file.write("Sample name\tOutput directory\tInput files\tO antigen prediction\tH1 antigen prediction(fliC)\tH2 antigen prediction(fljB)\tPredicted subspecies\tPredicted antigenic profile\tPredicted serotype\tPotential inter-serotype contamination\tNote\n") + if sample_name: + new_file.write("Sample name:\t"+sample_name+"\n") + tsv_file.write(sample_name+'\t') + else: + tsv_file.write(input_file[0].split('/')[-1]+'\t') + ### + if "N/A" not in predict_sero: + new_file.write("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+"\t".join(input_file)+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ + "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+predict_sero+"\n"+ + note+contamination_report+star_line+claim+antigen_note+"\n")#+## + tsv_file.write(make_dir+"\t"+" ".join(input_file)+"\t"+O_choice+"\t"+fliC_choice+"\t"+fljB_choice+"\t"+subspecies+"\t"+predict_form+"\t"+predict_sero+"\t"+conta_note+"\t"+contamination_report+star_line+claim+antigen_note+"\n") + else: + #star_line=star_line.strip()+"\tNone such antigenic formula in KW.\n" + star_line="" #04132019, for new output requirement, diable star_line if "NA" in output + new_file.write("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+"\t".join(input_file)+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ + "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, add subspecies + note+NA_note+contamination_report+star_line+claim+antigen_note+"\n")#+## + tsv_file.write(make_dir+"\t"+" ".join(input_file)+"\t"+O_choice+"\t"+fliC_choice+"\t"+fljB_choice+"\t"+subspecies+"\t"+predict_form+"\t"+subspecies+' '+predict_form+"\t"+conta_note+"\t"+NA_note+contamination_report+star_line+claim+antigen_note+"\n") + new_file.close() + tsv_file.close() + #subprocess.check_call("cat Seqsero_result.txt",shell=True) + #subprocess.call("rm H_and_O_and_specific_genes.fasta* *.sra *.bam *.sam *.fastq *.gz *.fq temp.txt *.xml "+fnameA+"*_db* 2> /dev/null",shell=True) + subprocess.call("rm H_and_O_and_specific_genes.fasta* *.sra *.bam *.sam *.fastq *.gz *.fq temp.txt "+fnameA+"*_db* 2> /dev/null",shell=True) + if "N/A" not in predict_sero: + #print("Output_directory:"+make_dir+"\nInput files:\t"+for_fq+" "+rev_fq+"\n"+"O antigen prediction:\t"+O_choice+"\n"+"H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+"H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+"Predicted antigenic profile:\t"+predict_form+"\n"+"Predicted subspecies:\t"+subspecies+"\n"+"Predicted serotype(s):\t"+predict_sero+star+"\nNote:"+contamination_report+star+star_line+claim+"\n")#+## + print("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+"\t".join(input_file)+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ + "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+predict_sero+"\n"+ + note+contamination_report+star_line+claim+antigen_note+"\n")#+## + else: + print("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+"\t".join(input_file)+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ + "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, subspecies + note+NA_note+contamination_report+star_line+claim+antigen_note+"\n") + else: + print("Allele modes only support raw reads datatype, i.e. '-t 1 or 2 or 3'; please use '-m k'") + elif analysis_mode=="k": + #ex_dir = os.path.dirname(os.path.realpath(__file__)) + ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019: change ex_dir for packaging + #output_mode = args.mode + for_fq,rev_fq=get_input_files(make_dir,input_file,data_type,dirpath) + input_file = for_fq #-k will just use forward because not all reads were used + os.chdir(make_dir) + f = open(ex_dir + '/antigens.pickle', 'rb') + lib_dict = pickle.load(f) + f.close + input_Ks=get_input_K(input_file,lib_dict,data_type,k_size) + O_dict,H_dict,Special_dict=get_kmer_dict(lib_dict,input_Ks) + highest_O,highest_fliC,highest_fljB=call_O_and_H_type(O_dict,H_dict,Special_dict,make_dir) + subspecies=judge_subspecies_Kmer(Special_dict) + if subspecies=="IIb" or subspecies=="IIa": + subspecies="II" + predict_form,predict_sero,star,star_line,claim = seqsero_from_formula_to_serotypes( + highest_O.split('-')[1], highest_fliC, highest_fljB, Special_dict,subspecies) + claim="" #no claim any more based on new output requirement + #if star_line+claim=="": #0413, new output style + # note="" + #else: + # note="Note:" + + ### ed_SL_11232019: add notes for missing antigen + if highest_O.split('-')[-1]=="": + O_choice="-" + else: + O_choice=highest_O.split('-')[-1] + antigen_note,NA_note=check_antigens(subspecies,O_choice,highest_fliC,highest_fljB,NA_note) + if sample_name: + print ("Sample name:\t"+sample_name) + ### + + if clean_mode: + subprocess.check_call("rm -rf ../"+make_dir,shell=True) + make_dir="none-output-directory due to '-c' flag" + # ### ed_SL_05282019, fix the assignment issue of variable 'O_choice' using "-m k -c" + # if highest_O.split('-')[-1]=="": + # O_choice="-" + # else: + # O_choice=highest_O.split('-')[-1] + # ### + else: + # if highest_O.split('-')[-1]=="": + # O_choice="-" + # else: + # O_choice=highest_O.split('-')[-1] + #print("Output_directory:"+make_dir+"\tInput_file:"+input_file+"\tPredicted subpecies:"+subspecies + '\tPredicted antigenic profile:' + predict_form + '\tPredicted serotype(s):' + predict_sero) + new_file=open("SeqSero_result.txt","w") + #new_file.write("Output_directory:"+make_dir+"\nInput files:\t"+input_file+"\n"+"O antigen prediction:\t"+O_choice+"\n"+"H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+"H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+"Predicted antigenic profile:\t"+predict_form+"\n"+"Predicted subspecies:\t"+subspecies+"\n"+"Predicted serotype(s):\t"+predict_sero+star+"\n"+star+star_line+claim+"\n")#+## + ### ed_SL_01152020: add new output + tsv_file=open("SeqSero_result.tsv","w") + if ingore_header: + pass + else: + tsv_file.write("Sample name\tOutput directory\tInput files\tO antigen prediction\tH1 antigen prediction(fliC)\tH2 antigen prediction(fljB)\tPredicted subspecies\tPredicted antigenic profile\tPredicted serotype\tNote\n") + if sample_name: + new_file.write("Sample name:\t"+sample_name+"\n") + tsv_file.write(sample_name+'\t') + else: + tsv_file.write(input_file.split('/')[-1]+'\t') + ### + if "N/A" not in predict_sero: + new_file.write("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+input_file+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ + "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+predict_sero+"\n"+ + note+star_line+claim+antigen_note+"\n")#+## + tsv_file.write(make_dir+"\t"+input_file+"\t"+O_choice+"\t"+highest_fliC+"\t"+highest_fljB+"\t"+subspecies+"\t"+predict_form+"\t"+predict_sero+"\t"+star_line+claim+antigen_note+"\n") + else: + #star_line=star_line.strip()+"\tNone such antigenic formula in KW.\n" + star_line = "" #changed for new output requirement, 04132019 + new_file.write("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+input_file+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ + "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, subspecies + note+NA_note+star_line+claim+antigen_note+"\n")#+## + tsv_file.write(make_dir+"\t"+input_file+"\t"+O_choice+"\t"+highest_fliC+"\t"+highest_fljB+"\t"+subspecies+"\t"+predict_form+"\t"+subspecies+' '+predict_form+"\t"+NA_note+star_line+claim+antigen_note+"\n") + new_file.close() + tsv_file.close() + subprocess.call("rm *.fasta* *.fastq *.gz *.fq temp.txt *.sra 2> /dev/null",shell=True) + if "N/A" not in predict_sero: + print("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+input_file+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ + "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+predict_sero+"\n"+ + note+star_line+claim+antigen_note+"\n")#+## + else: + print("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+input_file+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ + "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, subspecies + note+NA_note+star_line+claim+antigen_note+"\n")#+## + +if __name__ == '__main__': + main() diff -r 43f6b7f6ebb3 -r e6437d423693 build/scripts-3.6/SeqSero2_update_kmer_database.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/scripts-3.6/SeqSero2_update_kmer_database.py Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,113 @@ +#!/Users/charles.strittmatter/miniconda3/bin/python + +import argparse +import os,subprocess +import pickle + +### SeqSero Kmer +def parse_args(): + "Parse the input arguments, use '-h' for help." + parser = argparse.ArgumentParser(usage='Just type "SeqSero2_update_kmer_database.py", it will update kmer database automatically') + return parser.parse_args() + +def reverse_complement(sequence): + complement = { + 'A': 'T', + 'C': 'G', + 'G': 'C', + 'T': 'A', + 'N': 'N', + 'M': 'K', + 'R': 'Y', + 'W': 'W', + 'S': 'S', + 'Y': 'R', + 'K': 'M', + 'V': 'B', + 'H': 'D', + 'D': 'H', + 'B': 'V' + } + return "".join(complement[base] for base in reversed(sequence)) + +def multifasta_dict(multifasta): + multifasta_list = [ + line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0 + ] + headers = [i for i in multifasta_list if i[0] == '>'] + multifasta_dict = {} + for h in headers: + start = multifasta_list.index(h) + for element in multifasta_list[start + 1:]: + if element[0] == '>': + break + else: + if h[1:] in multifasta_dict: + multifasta_dict[h[1:]] += element + else: + multifasta_dict[h[1:]] = element + return multifasta_dict + +def createKmerDict_reads(list_of_strings, kmer): + kmer_table = {} + for string in list_of_strings: + sequence = string.strip('\n') + for i in range(len(sequence) - kmer + 1): + new_mer = sequence[i:i + kmer].upper() + new_mer_rc = reverse_complement(new_mer) + if new_mer in kmer_table: + kmer_table[new_mer.upper()] += 1 + else: + kmer_table[new_mer.upper()] = 1 + if new_mer_rc in kmer_table: + kmer_table[new_mer_rc.upper()] += 1 + else: + kmer_table[new_mer_rc.upper()] = 1 + return kmer_table + +def multifasta_to_kmers_dict(multifasta): + multi_seq_dict = multifasta_dict(multifasta) + lib_dict = {} + for h in multi_seq_dict: + lib_dict[h] = set( + [k for k in createKmerDict_reads([multi_seq_dict[h]], 27)]) + return lib_dict + +def get_salmid_invA_database(ex_dir): + # read invA kmer and return it + a = open(ex_dir + '/invA_mers_dict', 'rb') + invA_dict = pickle.load(a) + try: + del invA_dict['version'] + except: + pass + return invA_dict + +def get_salmid_rpoB_database(ex_dir): + # read invA kmer and return it + a = open(ex_dir + '/rpoB_mers_dict', 'rb') + rpoB_dict = pickle.load(a) + try: + del rpoB_dict['version'] + except: + pass + return rpoB_dict + +def main(): + args = parse_args() + ex_dir = os.path.dirname(os.path.realpath(__file__)) + lib_dict = multifasta_to_kmers_dict(ex_dir + '/H_and_O_and_specific_genes.fasta') + invA_dict=get_salmid_invA_database(ex_dir) + #rpoB_dict=get_salmid_rpoB_database(ex_dir) + lib_dict_new = lib_dict.copy() + #print(len(lib_dict_new)) + lib_dict_new.update(invA_dict) + #print(len(lib_dict_new)) + #lib_dict_new.update(rpoB_dict) + #print(len(lib_dict_new)) + f = open(ex_dir + '/antigens.pickle', "wb") + pickle.dump(lib_dict_new, f) + f.close() + +if __name__ == '__main__': + main() diff -r 43f6b7f6ebb3 -r e6437d423693 build/scripts-3.6/deinterleave_fastq.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/scripts-3.6/deinterleave_fastq.sh Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,30 @@ +#!/bin/bash +# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress] +# +# Deinterleaves a FASTQ file of paired reads into two FASTQ +# files specified on the command line. Optionally GZip compresses the output +# FASTQ files using pigz if the 3rd command line argument is the word "compress" +# +# Can deinterleave 100 million paired reads (200 million total +# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s) +# +# Latest code: https://gist.github.com/3521724 +# Also see my interleaving script: https://gist.github.com/4544979 +# +# Inspired by Torsten Seemann's blog post: +# http://thegenomefactory.blogspot.com.au/2012/05/cool-use-of-unix-paste-with-ngs.html + +# Set up some defaults +GZIP_OUTPUT=0 +PIGZ_COMPRESSION_THREADS=10 + +# If the third argument is the word "compress" then we'll compress the output using pigz +if [[ $3 == "compress" ]]; then + GZIP_OUTPUT=1 +fi + +if [[ ${GZIP_OUTPUT} == 0 ]]; then + paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" > $1) | cut -f 5-8 | tr "\t" "\n" > $2 +else + paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $1) | cut -f 5-8 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $2 +fi diff -r 43f6b7f6ebb3 -r e6437d423693 core.py --- a/core.py Thu Apr 30 21:47:42 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,386 +0,0 @@ -#!/usr/bin/env python3 - - -import gzip -import io -import pickle -import os -import sys - -from argparse import ArgumentParser -try: - from .version import SalmID_version -except ImportError: - SalmID_version = "version unknown" - - -def reverse_complement(sequence): - """return the reverse complement of a nucleotide (including IUPAC ambiguous nuceotide codes)""" - complement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'N': 'N', 'M': 'K', 'R': 'Y', 'W': 'W', - 'S': 'S', 'Y': 'R', 'K': 'M', 'V': 'B', 'H': 'D', 'D': 'H', 'B': 'V'} - return "".join(complement[base] for base in reversed(sequence)) - - -def parse_args(): - "Parse the input arguments, use '-h' for help." - parser = ArgumentParser(description='SalmID - rapid Kmer based Salmonella identifier from sequence data') - # inputs - parser.add_argument('-v', '--version', action='version', version='%(prog)s ' + SalmID_version) - parser.add_argument( - '-i', '--input_file', type=str, required=False, default='None', metavar='your_fastqgz', - help='Single fastq.gz file input, include path to file if file is not in same directory ') - parser.add_argument( - '-e', '--extension', type=str, required=False, default='.fastq.gz', metavar='file_extension', - help='File extension, if specified without "--input_dir", SalmID will attempt to ID all files\n' + - ' with this extension in current directory, otherwise files in input directory') - - parser.add_argument( - '-d', '--input_dir', type=str, required=False, default='.', metavar='directory', - help='Directory which contains data for identification, when not specified files in current directory will be analyzed.') - parser.add_argument( - '-r', '--report', type=str, required=False, default='percentage', metavar='percentage, coverage or taxonomy', - help='Report either percentage ("percentage") of clade specific kmers recovered, average kmer-coverage ("cov"), or ' - 'taxonomy (taxonomic species ID, plus observed mean k-mer coverages and expected coverage).') - parser.add_argument( - '-m', '--mode', type=str, required=False, default='quick', metavar='quick or thorough', - help='Quick [quick] or thorough [thorough] mode') - if len(sys.argv) == 1: - parser.print_help(sys.stderr) - sys.exit(1) - return parser.parse_args() - - -def get_av_read_length(file): - """Samples the first 100 reads from a fastq file and return the average read length.""" - i = 1 - n_reads = 0 - total_length = 0 - if file.endswith(".gz"): - file_content = io.BufferedReader(gzip.open(file)) - else: - file_content = open(file, "r").readlines() - for line in file_content: - if i % 4 == 2: - total_length += len(line.strip()) - n_reads += 1 - i += 1 - if n_reads == 100: - break - return total_length / 100 - - -def createKmerDict_reads(list_of_strings, kmer): - """Count occurence of K-mers in a list of strings - - Args: - list_of_strings(list of str): nucleotide sequences as a list of strings - kmer(int): length of the K-mer to count - - Returns: - dict: dictionary with kmers as keys, counts for each kmer as values""" - kmer_table = {} - for string in list_of_strings: - sequence = string.strip('\n') - if len(sequence) >= kmer: - for i in range(len(sequence) - kmer + 1): - new_mer = sequence[i:i + kmer] - new_mer_rc = reverse_complement(new_mer) - if new_mer in kmer_table: - kmer_table[new_mer.upper()] += 1 - else: - kmer_table[new_mer.upper()] = 1 - if new_mer_rc in kmer_table: - kmer_table[new_mer_rc.upper()] += 1 - else: - kmer_table[new_mer_rc.upper()] = 1 - return kmer_table - - -def target_read_kmerizer_multi(file, k, kmerDict_1, kmerDict_2, mode): - mean_1 = None - mean_2 = None - i = 1 - n_reads_1 = 0 - n_reads_2 = 0 - total_coverage_1 = 0 - total_coverage_2 = 0 - reads_1 = [] - reads_2 = [] - total_reads = 0 - if file.endswith(".gz"): - file_content = io.BufferedReader(gzip.open(file)) - else: - file_content = open(file, "r").readlines() - for line in file_content: - start = int((len(line) - k) // 2) - if i % 4 == 2: - total_reads += 1 - if file.endswith(".gz"): - s1 = line[start:k + start].decode() - line = line.decode() - else: - s1 = line[start:k + start] - if s1 in kmerDict_1: - n_reads_1 += 1 - total_coverage_1 += len(line) - reads_1.append(line) - if s1 in kmerDict_2: - n_reads_2 += 1 - total_coverage_2 += len(line) - reads_2.append(line) - i += 1 - if mode == 'quick': - if total_coverage_2 >= 800000: - break - - if len(reads_1) == 0: - kmer_Dict1 = {} - else: - kmer_Dict1 = createKmerDict_reads(reads_1, k) - mers_1 = set([key for key in kmer_Dict1]) - mean_1 = sum([kmer_Dict1[key] for key in kmer_Dict1]) / len(mers_1) - if len(reads_2) == 0: - kmer_Dict2 = {} - else: - kmer_Dict2 = createKmerDict_reads(reads_2, k) - mers_2 = set([key for key in kmer_Dict2]) - mean_2 = sum([kmer_Dict2[key] for key in kmer_Dict2]) / len(mers_2) - return kmer_Dict1, kmer_Dict2, mean_1, mean_2, total_reads - - -def mean_cov_selected_kmers(iterable, kmer_dict, clade_specific_kmers): - ''' - Given an iterable (list, set, dictrionary) returns mean coverage for the kmers in iterable - :param iterable: set, list or dictionary containing kmers - :param kmer_dict: dictionary with kmers as keys, kmer-frequency as value - :param clade_specific_kmers: list, dict or set of clade specific kmers - :return: mean frequency as float - ''' - if len(iterable) == 0: - return 0 - return sum([kmer_dict[value] for value in iterable]) / len(clade_specific_kmers) - - -def kmer_lists(query_fastq_gz, k, - allmers, allmers_rpoB, - uniqmers_bongori, - uniqmers_I, - uniqmers_IIa, - uniqmers_IIb, - uniqmers_IIIa, - uniqmers_IIIb, - uniqmers_IV, - uniqmers_VI, - uniqmers_VII, - uniqmers_VIII, - uniqmers_bongori_rpoB, - uniqmers_S_enterica_rpoB, - uniqmers_Escherichia_rpoB, - uniqmers_Listeria_ss_rpoB, - uniqmers_Lmono_rpoB, - mode): - dict_invA, dict_rpoB, mean_invA, mean_rpoB, total_reads = target_read_kmerizer_multi(query_fastq_gz, k, allmers, - allmers_rpoB, mode) - target_mers_invA = set([key for key in dict_invA]) - target_mers_rpoB = set([key for key in dict_rpoB]) - if target_mers_invA == 0: - print('No reads found matching invA, no Salmonella in sample?') - else: - p_bongori = (len(uniqmers_bongori & target_mers_invA) / len(uniqmers_bongori)) * 100 - p_I = (len(uniqmers_I & target_mers_invA) / len(uniqmers_I)) * 100 - p_IIa = (len(uniqmers_IIa & target_mers_invA) / len(uniqmers_IIa)) * 100 - p_IIb = (len(uniqmers_IIb & target_mers_invA) / len(uniqmers_IIb)) * 100 - p_IIIa = (len(uniqmers_IIIa & target_mers_invA) / len(uniqmers_IIIa)) * 100 - p_IIIb = (len(uniqmers_IIIb & target_mers_invA) / len(uniqmers_IIIb)) * 100 - p_VI = (len(uniqmers_VI & target_mers_invA) / len(uniqmers_VI)) * 100 - p_IV = (len(uniqmers_IV & target_mers_invA) / len(uniqmers_IV)) * 100 - p_VII = (len(uniqmers_VII & target_mers_invA) / len(uniqmers_VII)) * 100 - p_VIII = (len(uniqmers_VIII & target_mers_invA) / len(uniqmers_VIII)) * 100 - p_bongori_rpoB = (len(uniqmers_bongori_rpoB & target_mers_rpoB) / len(uniqmers_bongori_rpoB)) * 100 - p_Senterica = (len(uniqmers_S_enterica_rpoB & target_mers_rpoB) / len(uniqmers_S_enterica_rpoB)) * 100 - p_Escherichia = (len(uniqmers_Escherichia_rpoB & target_mers_rpoB) / len(uniqmers_Escherichia_rpoB)) * 100 - p_Listeria_ss = (len(uniqmers_Listeria_ss_rpoB & target_mers_rpoB) / len(uniqmers_Listeria_ss_rpoB)) * 100 - p_Lmono = (len(uniqmers_Lmono_rpoB & target_mers_rpoB) / len(uniqmers_Lmono_rpoB)) * 100 - bongori_invA_cov = mean_cov_selected_kmers(uniqmers_bongori & target_mers_invA, dict_invA, uniqmers_bongori) - I_invA_cov = mean_cov_selected_kmers(uniqmers_I & target_mers_invA, dict_invA, uniqmers_I) - IIa_invA_cov = mean_cov_selected_kmers(uniqmers_IIa & target_mers_invA, dict_invA, uniqmers_IIa) - IIb_invA_cov = mean_cov_selected_kmers(uniqmers_IIb & target_mers_invA, dict_invA, uniqmers_IIb) - IIIa_invA_cov = mean_cov_selected_kmers(uniqmers_IIIa & target_mers_invA, dict_invA, uniqmers_IIIa) - IIIb_invA_cov = mean_cov_selected_kmers(uniqmers_IIIb & target_mers_invA, dict_invA, uniqmers_IIIb) - IV_invA_cov = mean_cov_selected_kmers(uniqmers_IV & target_mers_invA, dict_invA, uniqmers_IV) - VI_invA_cov = mean_cov_selected_kmers(uniqmers_VI & target_mers_invA, dict_invA, uniqmers_VI) - VII_invA_cov = mean_cov_selected_kmers(uniqmers_VII & target_mers_invA, dict_invA, uniqmers_VII) - VIII_invA_cov = mean_cov_selected_kmers(uniqmers_VIII & target_mers_invA, dict_invA, uniqmers_VIII) - S_enterica_rpoB_cov = mean_cov_selected_kmers((uniqmers_S_enterica_rpoB & target_mers_rpoB), dict_rpoB, - uniqmers_S_enterica_rpoB) - S_bongori_rpoB_cov = mean_cov_selected_kmers((uniqmers_bongori_rpoB & target_mers_rpoB), dict_rpoB, - uniqmers_bongori_rpoB) - Escherichia_rpoB_cov = mean_cov_selected_kmers((uniqmers_Escherichia_rpoB & target_mers_rpoB), dict_rpoB, - uniqmers_Escherichia_rpoB) - Listeria_ss_rpoB_cov = mean_cov_selected_kmers((uniqmers_Listeria_ss_rpoB & target_mers_rpoB), dict_rpoB, - uniqmers_Listeria_ss_rpoB) - Lmono_rpoB_cov = mean_cov_selected_kmers((uniqmers_Lmono_rpoB & target_mers_rpoB), dict_rpoB, - uniqmers_Lmono_rpoB) - coverages = [Listeria_ss_rpoB_cov, Lmono_rpoB_cov, Escherichia_rpoB_cov, S_bongori_rpoB_cov, - S_enterica_rpoB_cov, bongori_invA_cov, I_invA_cov, IIa_invA_cov, IIb_invA_cov, - IIIa_invA_cov, IIIb_invA_cov, IV_invA_cov, VI_invA_cov, VII_invA_cov, VIII_invA_cov] - locus_scores = [p_Listeria_ss, p_Lmono, p_Escherichia, p_bongori_rpoB, p_Senterica, p_bongori, - p_I, p_IIa, p_IIb, p_IIIa, p_IIIb, p_IV, p_VI, p_VII, p_VIII] - return locus_scores, coverages, total_reads - - -def report_taxon(locus_covs, average_read_length, number_of_reads): - list_taxa = [ 'Listeria ss', 'Listeria monocytogenes', 'Escherichia sp.', # noqa: E201 - 'Salmonella bongori (rpoB)', 'Salmonella enterica (rpoB)', - 'Salmonella bongori (invA)', 'S. enterica subsp. enterica (invA)', - 'S. enterica subsp. salamae (invA: clade a)', 'S. enterica subsp. salamae (invA: clade b)', - 'S. enterica subsp. arizonae (invA)', 'S. enterica subsp. diarizonae (invA)', - 'S. enterica subsp. houtenae (invA)', 'S. enterica subsp. indica (invA)', - 'S. enterica subsp. VII (invA)', 'S. enterica subsp. salamae (invA: clade VIII)' ] # noqa: E202 - if sum(locus_covs) < 1: - rpoB = ('No rpoB matches!', 0) - invA = ('No invA matches!', 0) - return rpoB, invA, 0.0 - else: - # given list of scores get taxon - if sum(locus_covs[0:5]) > 0: - best_rpoB = max(range(len(locus_covs[1:5])), key=lambda x: locus_covs[1:5][x]) + 1 - all_rpoB = max(range(len(locus_covs[0:5])), key=lambda x: locus_covs[0:5][x]) - if (locus_covs[best_rpoB] != 0) & (all_rpoB == 0): - rpoB = (list_taxa[best_rpoB], locus_covs[best_rpoB]) - elif (all_rpoB == 0) & (round(sum(locus_covs[1:5]), 1) < 1): - rpoB = (list_taxa[0], locus_covs[0]) - else: - rpoB = (list_taxa[best_rpoB], locus_covs[best_rpoB]) - else: - rpoB = ('No rpoB matches!', 0) - if sum(locus_covs[5:]) > 0: - best_invA = max(range(len(locus_covs[5:])), key=lambda x: locus_covs[5:][x]) + 5 - invA = (list_taxa[best_invA], locus_covs[best_invA]) - else: - invA = ('No invA matches!', 0) - if 'Listeria' in rpoB[0]: - return rpoB, invA, (average_read_length * number_of_reads) / 3000000 - else: - return rpoB, invA, (average_read_length * number_of_reads) / 5000000 - - -def main(): - ex_dir = os.path.dirname(os.path.realpath(__file__)) - args = parse_args() - input_file = args.input_file - if input_file != 'None': - files = [input_file] - else: - extension = args.extension - inputdir = args.input_dir - files = [inputdir + '/' + f for f in os.listdir(inputdir) if f.endswith(extension)] - report = args.report - mode = args.mode - f_invA = open(ex_dir + "/invA_mers_dict", "rb") - sets_dict_invA = pickle.load(f_invA) - f_invA.close() - allmers = sets_dict_invA['allmers'] - uniqmers_I = sets_dict_invA['uniqmers_I'] - uniqmers_IIa = sets_dict_invA['uniqmers_IIa'] - uniqmers_IIb = sets_dict_invA['uniqmers_IIb'] - uniqmers_IIIa = sets_dict_invA['uniqmers_IIIa'] - uniqmers_IIIb = sets_dict_invA['uniqmers_IIIb'] - uniqmers_IV = sets_dict_invA['uniqmers_IV'] - uniqmers_VI = sets_dict_invA['uniqmers_VI'] - uniqmers_VII = sets_dict_invA['uniqmers_VII'] - uniqmers_VIII = sets_dict_invA['uniqmers_VIII'] - uniqmers_bongori = sets_dict_invA['uniqmers_bongori'] - - f = open(ex_dir + "/rpoB_mers_dict", "rb") - sets_dict = pickle.load(f) - f.close() - - allmers_rpoB = sets_dict['allmers'] - uniqmers_bongori_rpoB = sets_dict['uniqmers_bongori'] - uniqmers_S_enterica_rpoB = sets_dict['uniqmers_S_enterica'] - uniqmers_Escherichia_rpoB = sets_dict['uniqmers_Escherichia'] - uniqmers_Listeria_ss_rpoB = sets_dict['uniqmers_Listeria_ss'] - uniqmers_Lmono_rpoB = sets_dict['uniqmers_L_mono'] - # todo: run kmer_lists() once, create list of tuples containing data to be used fro different reports - if report == 'taxonomy': - print('file\trpoB\tinvA\texpected coverage') - for f in files: - locus_scores, coverages, reads = kmer_lists(f, 27, - allmers, allmers_rpoB, - uniqmers_bongori, - uniqmers_I, - uniqmers_IIa, - uniqmers_IIb, - uniqmers_IIIa, - uniqmers_IIIb, - uniqmers_IV, - uniqmers_VI, - uniqmers_VII, - uniqmers_VIII, - uniqmers_bongori_rpoB, - uniqmers_S_enterica_rpoB, - uniqmers_Escherichia_rpoB, - uniqmers_Listeria_ss_rpoB, - uniqmers_Lmono_rpoB, - mode) - pretty_covs = [round(cov, 1) for cov in coverages] - report = report_taxon(pretty_covs, get_av_read_length(f), reads) - print(f.split('/')[-1] + '\t' + report[0][0] + '[' + str(report[0][1]) + ']' + '\t' + report[1][0] + - '[' + str(report[1][1]) + ']' + - '\t' + str(round(report[2], 1))) - else: - print( - 'file\tListeria sensu stricto (rpoB)\tL. monocytogenes (rpoB)\tEscherichia spp. (rpoB)\tS. bongori (rpoB)\tS. enterica' + # noqa: E122 - '(rpoB)\tS. bongori (invA)\tsubsp. I (invA)\tsubsp. II (clade a: invA)\tsubsp. II' + # noqa: E122 - ' (clade b: invA)\tsubsp. IIIa (invA)\tsubsp. IIIb (invA)\tsubsp.IV (invA)\tsubsp. VI (invA)\tsubsp. VII (invA)' + # noqa: E122 - '\tsubsp. II (clade VIII : invA)') - if report == 'percentage': - for f in files: - locus_scores, coverages, reads = kmer_lists(f, 27, - allmers, allmers_rpoB, - uniqmers_bongori, - uniqmers_I, - uniqmers_IIa, - uniqmers_IIb, - uniqmers_IIIa, - uniqmers_IIIb, - uniqmers_IV, - uniqmers_VI, - uniqmers_VII, - uniqmers_VIII, - uniqmers_bongori_rpoB, - uniqmers_S_enterica_rpoB, - uniqmers_Escherichia_rpoB, - uniqmers_Listeria_ss_rpoB, - uniqmers_Lmono_rpoB, - mode) - pretty_scores = [str(round(score)) for score in locus_scores] - print(f.split('/')[-1] + '\t' + '\t'.join(pretty_scores)) - else: - for f in files: - locus_scores, coverages, reads = kmer_lists(f, 27, - allmers, allmers_rpoB, - uniqmers_bongori, - uniqmers_I, - uniqmers_IIa, - uniqmers_IIb, - uniqmers_IIIa, - uniqmers_IIIb, - uniqmers_IV, - uniqmers_VI, - uniqmers_VII, - uniqmers_VIII, - uniqmers_bongori_rpoB, - uniqmers_S_enterica_rpoB, - uniqmers_Escherichia_rpoB, - uniqmers_Listeria_ss_rpoB, - uniqmers_Lmono_rpoB, - mode) - pretty_covs = [str(round(cov, 1)) for cov in coverages] - print(f.split('/')[-1] + '\t' + '\t'.join(pretty_covs)) - - -if __name__ == '__main__': - main() - diff -r 43f6b7f6ebb3 -r e6437d423693 deinterleave_fastq.sh --- a/deinterleave_fastq.sh Thu Apr 30 21:47:42 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -#!/bin/bash -# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress] -# -# Deinterleaves a FASTQ file of paired reads into two FASTQ -# files specified on the command line. Optionally GZip compresses the output -# FASTQ files using pigz if the 3rd command line argument is the word "compress" -# -# Can deinterleave 100 million paired reads (200 million total -# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s) -# -# Latest code: https://gist.github.com/3521724 -# Also see my interleaving script: https://gist.github.com/4544979 -# -# Inspired by Torsten Seemann's blog post: -# http://thegenomefactory.blogspot.com.au/2012/05/cool-use-of-unix-paste-with-ngs.html - -# Set up some defaults -GZIP_OUTPUT=0 -PIGZ_COMPRESSION_THREADS=10 - -# If the third argument is the word "compress" then we'll compress the output using pigz -if [[ $3 == "compress" ]]; then - GZIP_OUTPUT=1 -fi - -if [[ ${GZIP_OUTPUT} == 0 ]]; then - paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" > $1) | cut -f 5-8 | tr "\t" "\n" > $2 -else - paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $1) | cut -f 5-8 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $2 -fi diff -r 43f6b7f6ebb3 -r e6437d423693 dist/SeqSero2-1.1.1-py3.6.egg Binary file dist/SeqSero2-1.1.1-py3.6.egg has changed diff -r 43f6b7f6ebb3 -r e6437d423693 pyproject.toml --- a/pyproject.toml Thu Apr 30 21:47:42 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ -[tool.poetry] -name = "salmid" -version = "0.1.23" -description = "Rapid tool to check taxonomic ID of single isolate samples. Currently only IDs Salmonella species and subspecies, and some common contaminants (Listeria, Escherichia)." -authors = ["Henk den Bakker "] -license = "MIT" -include = [ 'salmid/invA_mers_dict', 'salmid/rpoB_mers_dict' ] - -[tool.poetry.dependencies] -python = "^3.5" - -[tool.poetry.dev-dependencies] - -[tool.poetry.scripts] -'SalmID.py' = 'salmid.core:main' - -[build-system] -requires = ["poetry>=0.12"] -build-backend = "poetry.masonry.api"