# HG changeset patch
# User tyty
# Date 1416345844 18000
# Node ID d2817a631a7bd8e2f6ff9d77df3501be1ec79f6c
# Parent  36d912d5b1acdc0351cbb0a0461bd4ddb03828fb
Uploaded

diff -r 36d912d5b1ac -r d2817a631a7b Iterative_mapping/.DS_Store
Binary file Iterative_mapping/.DS_Store has changed
diff -r 36d912d5b1ac -r d2817a631a7b Iterative_mapping/._.DS_Store
Binary file Iterative_mapping/._.DS_Store has changed
diff -r 36d912d5b1ac -r d2817a631a7b Iterative_mapping/._iterative_map.xml
Binary file Iterative_mapping/._iterative_map.xml has changed
diff -r 36d912d5b1ac -r d2817a631a7b Iterative_mapping/iterative_map.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Iterative_mapping/iterative_map.py	Tue Nov 18 16:24:04 2014 -0500
@@ -0,0 +1,122 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import sys
+import os
+from read_file import *
+from read_s_file import *
+import random
+import string
+
+type_input = sys.argv[1]
+seq_file = sys.argv[2]
+ref_file = sys.argv[3]
+shift = sys.argv[4]
+length = sys.argv[5]
+t_end = sys.argv[6]
+map_type = sys.argv[7]
+output_file = sys.argv[8]
+
+
+if map_type!="default":
+    s = ""
+    sm = ""
+    s = s+"-v "+sys.argv[9]
+    sm = sm+"-v "+sys.argv[9]
+    sm = sm+" -5 "+sys.argv[10]
+    sm = sm+" -3 "+sys.argv[11]
+    s = s+" -k "+sys.argv[12]
+    sm = sm+" -k "+sys.argv[12]
+    if sys.argv[13]:
+        s = s+" -a"
+        sm = sm+" -a"
+    if int(sys.argv[14])>=1:
+        s = s+" -m "+sys.argv[14]
+        sm = sm+" -m "+sys.argv[14]
+    if sys.argv[15]:
+        s = s+" --best --strata "
+        sm = sm+" --best --strata "
+    
+else:
+    s = "-v 3 -a --best --strata "
+    sm = "-v 3 -a --best --strata "
+
+ospath = os.path.realpath(sys.argv[0])
+ost = ospath.split('/')
+syspath = ""
+for i in range(len(ost)-1):
+    syspath = syspath+ost[i].strip()
+    syspath = syspath+'/'
+
+syspathrs = os.getcwd()
+
+os.system("bowtie-build -f "+ref_file+" "+syspathrs+"ref > "+syspathrs+"log.txt")
+
+os.system("cp "+seq_file+" "+syspathrs+"seq0.fa")
+
+if type_input == "fasta":
+    tp = 'fasta'
+if type_input == "fastq":
+    tp = 'fastq'
+
+k = 0
+
+if type_input == "fasta":
+    os.system("bowtie "+sm+"-f "+syspathrs+"ref"+" "+syspathrs+"seq"+str(k)+".fa --quiet -S > "+syspathrs+"map"+str(k)+".sam")
+if type_input == "fastq":
+    os.system("bowtie "+sm+"-q "+syspathrs+"ref"+" "+syspathrs+"seq"+str(k)+".fa --quiet -S > "+syspathrs+"map"+str(k)+".sam")
+
+while(True):
+    os.system("samtools view -Sb -F 0xfff "+syspathrs+"map"+str(k)+".sam > "+syspathrs+"mapped"+str(k)+".bam 2>"+syspathrs+"log.txt") #get mapped reads
+    os.system("samtools view -Sb -f 0x4 "+syspathrs+"map"+str(k)+".sam > "+syspathrs+"umapped"+str(k)+".bam 2>"+syspathrs+"log.txt") #get unmapped reads
+    os.system("samtools view -Sb -f 0x10 "+syspathrs+"map"+str(k)+".sam > "+syspathrs+"rmapped"+str(k)+".bam 2>"+syspathrs+"log.txt") #get reversed mapped reads
+    os.system("samtools merge -f "+syspathrs+"unmapped"+str(k)+".bam "+syspathrs+"umapped"+str(k)+".bam "+syspathrs+"rmapped"+str(k)+".bam") #get reversed mapped reads
+    os.system("samtools view -h -o "+syspathrs+"unmapped"+str(k)+".sam "+syspathrs+"unmapped"+str(k)+".bam") #get reversed mapped reads
+    if k>0:
+        os.system("samtools view -h -o "+syspathrs+"mapped"+str(k)+".sam "+syspathrs+"mapped"+str(k)+".bam") #get reversed mapped reads
+        os.system("cut -f 1 "+syspathrs+"unmapped"+str(k)+".sam > "+syspathrs+"unmapped"+str(k)+".txt")
+        os.system("cut -f 1 "+syspathrs+"mapped"+str(k)+".sam > "+syspathrs+"mapped"+str(k)+".txt")
+        os.system("python "+syspath+"remove_map.py "+syspathrs+"unmapped"+str(k)+".txt "+syspathrs+"mapped"+str(k)+".txt "+syspathrs+"runmapped"+str(k)+".txt")
+        os.system("rm "+syspathrs+"mapped"+str(k)+".sam")
+        os.system("rm "+syspathrs+"mapped"+str(k)+".txt")
+        os.system("rm "+syspathrs+"unmapped"+str(k)+".txt")
+    else:
+        os.system("cut -f 1 "+syspathrs+"unmapped"+str(k)+".sam > "+syspathrs+"runmapped"+str(k)+".txt")
+    
+    os.system("rm "+syspathrs+"unmapped"+str(k)+".bam")
+    os.system("rm "+syspathrs+"umapped"+str(k)+".bam")
+    os.system("rm "+syspathrs+"rmapped"+str(k)+".bam")
+    os.system("python "+syspath+"seq_track.py "+syspathrs+"runmapped"+str(k)+".txt "+syspathrs+"seq"+str(k)+".fa "+syspathrs+"unmap_seq"+str(k)+".fa "+tp) #get unmapped sequence
+    os.system("python "+syspath+"truncate.py "+syspathrs+"unmap_seq"+str(k)+".fa "+shift+" "+syspathrs+"seq"+str(k+1)+".fa "+length+" "+t_end) #truncate unmapped sequence
+    os.system("rm "+syspathrs+"seq"+str(k)+".fa") #Remove sequences being mapped
+    os.system("rm "+syspathrs+"map"+str(k)+".sam") #Remove mapping file
+    os.system("rm "+syspathrs+"unmap_seq"+str(k)+".fa") #Remove unmapped sequnce
+    os.system("rm "+syspathrs+"runmapped"+str(k)+".txt")
+    os.system("rm "+syspathrs+"unmapped"+str(k)+".sam")
+    
+    os.system("wc -l "+syspathrs+"seq"+str(k+1)+".fa > "+syspathrs+"count"+str(k+1)+".txt")
+    c = read_sp_file(syspathrs+"count"+str(k+1)+".txt")
+    if c[0][0] == '0': #If no reads is in the sequence file, stop
+        os.system("rm "+syspathrs+"count"+str(k+1)+".txt")
+        os.system("rm "+syspathrs+"seq"+str(k+1)+".fa")
+        break
+    os.system("rm "+syspathrs+"count"+str(k+1)+".txt")
+    k = k+1
+    if type_input == "fasta":
+        os.system("bowtie "+s+"-f "+syspathrs+"ref"+" "+syspathrs+"seq"+str(k)+".fa --quiet -S > "+syspathrs+"map"+str(k)+".sam")
+    if type_input == "fastq":
+        os.system("bowtie "+s+"-q "+syspathrs+"ref"+" "+syspathrs+"seq"+str(k)+".fa --quiet -S > "+syspathrs+"map"+str(k)+".sam")
+
+
+ss = ""
+for i in range(0,k+1):
+    ss = ss+" "+syspathrs+"mapped"+str(i)+".bam"
+
+
+os.system("samtools merge -f "+output_file+" "+ss)
+#print("samtools merge mapped_all.bam"+ss)
+os.system("rm "+syspathrs+"mapped*.bam")
+os.system("rm "+syspathrs+"ref*")
+#os.system("rm -r "+syspathrs)
+
+
diff -r 36d912d5b1ac -r d2817a631a7b Iterative_mapping/iterative_map.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Iterative_mapping/iterative_map.xml	Tue Nov 18 16:24:04 2014 -0500
@@ -0,0 +1,96 @@
+<tool id="iterative_map_pipeline" name="Iterative Mapping" version="1.0">
+	<description></description>
+	<command interpreter="python">
+        #if $mapping_file.type == "user"
+            iterative_map.py $file_format.type $file_format.seq_file $reference_file $shift $length $t_end $mapping_file.type $output $mapping_file.param_v $mapping_file.param_five $mapping_file.param_three $mapping_file.param_k $mapping_file.param_a $mapping_file.param_m $mapping_file.param_best  
+        #else
+            iterative_map.py $file_format.type $file_format.seq_file $reference_file $shift $length $t_end $mapping_file.type $output
+        #end if
+    </command>
+        <requirements>
+                <requirement type="package" version="1.61">biopython</requirement>
+                <requirement type="package" version="1.7.1">numpy</requirement>
+                <requirement type="package" version="0.1.18">samtools</requirement>
+                <requirement type="package" version="0.12.7">bowtie</requirement>
+        </requirements>
+	<inputs>
+                <conditional name="file_format">
+                  <param name="type" type="select" label="File format of the reads (Default FASTQ)">
+                    <option value="fastq">FASTQ</option>
+                    <option value="fasta">FASTA</option>
+                  </param>
+                  <when value="fastq">
+                    <param name="seq_file" type="data" format="fastq" label="Fastq file"/>
+                  </when>
+                  <when value="fasta">
+                    <param name="seq_file" type="data" format="fasta" label="Fasta file"/>
+                  </when>
+                </conditional>
+		        <param name="reference_file" type="data" format="fasta" label="Reference genome/transcriptome"/>
+                <param name="shift" type="integer" value="1" label="Number of nucleotides trimmed each round"/>
+                <param name="length" type="integer" value="21" label="Minimum requirement of read length for mapping"/>
+                <param name="t_end" type="select" label="Trim from 5' or 3' end">
+                    <option value="five_end">5' end</option>
+                    <option value="three_end">3' end</option>
+                </param>
+                
+                <conditional name="mapping_file">
+                  <param name="type" type="select" label="Bowtie mapping flags (Default -v 0 -a --best --strata)">
+                    <option value="default">Default</option>
+                    <option value="user">User specified</option>
+                  </param>
+                  <when value="default"/>
+                  <when value="user"> 
+                    <param name="param_v" type="integer" value="0" label="Number of mismatches for SOAP-like alignment policy (-v)"/>
+                    <param name="param_five" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)"/>
+                    <param name="param_three" type="integer" value="0" label="Trim n bases from high-quality (right) end of each read before alignment (-3)"/>
+                    <param name="param_k" type="integer" value="1" label="Report up to n valid alignments per read (-k)"/>
+                    <param name="param_a" type="boolean" checked="False" truevalue = "1" falsevalue = "0" label="Whether or not to report all valid alignments per read (-a)"/>
+                    <param name="param_m" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m), -1 for unlimited"/>
+                    <param name="param_best" type="boolean" checked="False" truevalue = "1" falsevalue = "0" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best --strata)"/>
+                  </when>
+                </conditional>
+
+	</inputs>
+	<outputs>
+		<data name="output" type="data" format="bam"/>
+	</outputs>
+    <tests>
+        <test>
+            <param name="file_format.type" value="fasta" />
+            <param name="file_format.seq_file" value="sample.fasta" />
+	        <param name="reference_file" value="rRNA.txt" />
+            <param name="shift" value="1" />
+            <param name="length" value="21" />
+            <param name="mapping_file.type" value="default" />
+	        <output name="output" file="mapped.out" />
+        </test>
+    </tests>
+
+	<help>
+
+
+**TIPS**:
+
+-----
+
+**Input**:
+
+* 1. Sequence file type (FASTA/FASTQ)
+* 2. Sequence file (fasta/fastq format)
+* 3. Reference file (fasta) used to map the reads to
+* 4. “Shift” (The length of the sequence that will be trimmed at the 3’end of the reads before each round of mapping)
+* 5. “Length” (The minimum length of the reads for mapping after trimming)
+* [Optional]
+* 1. Bowtie mapping flags (options) [Default: -v 0 -a --best --strata] (-v flag indicates the number of allowed mismatches. Use -5/-3 flag to trim the nucleotides from 5'/3' end of the reads)
+
+-----
+
+**Output**:
+
+A bam file with all of the reads that are mapped	
+
+
+
+	</help>
+</tool>
diff -r 36d912d5b1ac -r d2817a631a7b Iterative_mapping/log.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Iterative_mapping/log.txt	Tue Nov 18 16:24:04 2014 -0500
@@ -0,0 +1,1 @@
+[samopen] SAM header is present: 4 sequences.
diff -r 36d912d5b1ac -r d2817a631a7b Iterative_mapping/map_ex.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Iterative_mapping/map_ex.py	Tue Nov 18 16:24:04 2014 -0500
@@ -0,0 +1,31 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import sys
+from read_file import *
+from Bio import SeqIO
+
+map_file = sys.argv[1]
+result_file = sys.argv[2]
+
+
+#reads = read_t_file(read_file);
+
+f = open(map_file);
+h = file(result_file, 'w')
+
+for aline in f.readlines():
+    tline = aline.strip();
+    tl = tline.split('\t');
+    if len(tl)>4:
+        if int(tl[1].strip())== 0:
+            h.write(tline)
+            h.write('\n')
+
+
+f.close();
+h.close()
+
+
+
+
diff -r 36d912d5b1ac -r d2817a631a7b Iterative_mapping/rRNA.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Iterative_mapping/rRNA.txt	Tue Nov 18 16:24:04 2014 -0500
@@ -0,0 +1,8 @@
+>25s rRNA 3375nts
+GCGACCCCAGGTCAGGCGGGATTACCCGCTGAGTTTAAGCATATCAATAAGCGGAGGAAAAGAAACTAACAAGGATTCCCTTAGTAACGGCGAGCGAACCGGGAAGAGCCCAGCTTGAAAATCGGACGTCTTCGGCGTTCGAATTGTAGTCTGGAGAAGCGTCCTCAGCGACGGACCGGGCCTAAGTTCCCTGGAAAGGGGCGCCAGAGAGGGTGAGAGCCCGTCGTGCCCGGACCCTGTCGCACCACGAGGCGCTGTCTACGAGTCGGGTTGTTTGGGAATGCAGCCCCAATCGGGCGGTAAATTCCGTCCAAGGCTAAATACGGGCGAGAGACCGATAGCGAACAAGTACCGCGAGGTAAAGATGAAAAGGACTTTGAAAAGAGAGTCAAAGAGTGCTTGAAATTGTCGGGAGGGAAGCGGATGGGGGCCGGCGATGCGTCCTGGTCGGATGCGGAACGGAGCAATCCGGTCCGCCGATCGATTCGGGGCGTGGACCGACGCGGATTACGGTGGCGGCCTAAGCCCGGGCTTTTGATACGCTTGTGGAGACGTCGCTGCCGTGATCGTGGTCTGCAGCACGCGCCTAACGGCGTGCCTCGGCATCAGCGTGCTCCGGGCGTCGGCCTGTGGGCTCCCCATTCGACCCGTCTTGAAACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAACGGGTGAGTAAACCCGTAAGGCGCAAGGAAGCTGATTGGCGGGATCCTCGCGGGTGCACCGCCGACCGACCTTGATCTTCTGAGAAGGGTTCGAGTGTGAGCATGCCTGTCGGGACCCGAAAGATGGTGAACTATGCCTGAGCGGGGTAAAGCCAGAGGAAACTCTGGTGGAAGCCCGCAGCGATACTGACGTGCAAATCGTTCGTCTGACTTGGGTATAGGGGCGAAAGACTAATCGAACCATCTAGTAGCTGGTTCCCTCCGAAGTTTCCCTCAGGATAGCTGGAGCTCGGACGCGAGTTCTATCGGGTAAAGCCAATGATTAGAGGCATTGGGGGCGCAACGCCTCGACCTATTCTCAAACTTTAAATAGGTAGGACGTGTCGGCTGCTTTGTTGAGCCGTCACACGGAATCGAGAGCTCCAAGTGGGCCATTTTTGGTAAGCAGAACTGGCGATGCGGGATGAACCGGAAGCCGGGTTACGGTGCCCAACTGCGCGCTAACCTAGAACCCACAAAGGGTGTTGGTCGATTAAGACAGCAGGACGGTGGTCATGGAAGTCGAAATCCGCTAAGGAGTGTGTAACAACTCACCTGCCGAATCAACTAGCCCCGAAAATGGATGGCGCTTAAGCGCGACCTATACCCGGCCGTCGGGGCAAGAGCCAGGCCTCGATGAGTAGGAGGGCGCGGCGGTCGCTGCAAAACCTAGGGCGCGAGGCGCGGAGCGGCCGTCGGTGCAGATCTTGGTGGTAGTAGCAAATATTCAAATGAGAACTTTGAAGGCCGAAGAGGGGAAAGGTTCCATGTGAACGGCACTTGCACATGGGTTAGTCGATCCTAAGAGTCGGGGGAAACCCGTCTGATAGCGCTTAAGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCGGAACCGGGACGTGGCGGTTGACGGCAACGTTAGGGAGTCCGGAGACGTCGGCGGGGGCCTCGGGAAGAGTTATCTTTTCTGTTTAACAGCCTGCCCACCCTGGAAACGGCTCAGCCGGAGGTAGGGTCCAGCGGCTGGAAGAGCACCGCACGTCGCGTGGTGTCCGGTGCGCCCCCGGGCGCCCTTGAAAATCCGGAGGACCGAGTGCCGCTCACGCCCGGTCGTACTCATAACCGCATCAGGTCTCCAAGGTGAACAGCCTCTGGTCGATGGAACAATGTAGGCAAGGGAAGTCGGCAAAATGGATCCGTAACTTCGGGAAAAGGATTGGCTCTGAGGGCTGGGCTCGGGGGTCCCAGTTCCGAACCCGTCGGCTGTCAGCGGACTGCTCGAGCTGCTTCCGCGGCGAGAGCGGGTCGCCGGCTGCCGGCCGGGGGACGACTGGGAACGGCTCTCTCGGGAGCTTTCCCCGGGCGTCGAACAGTCAGCTCAGAACTGGTACGGACAAGGGGAATCCGACTGTTTAATTAAAACAAAGCATTGCGATGGTCCCTGCGGATGCTAACGCAATGTGATTTCTGCCCAGTGCTCTGAATGTCAAAGTGAAGAAATTCAACCAAGCGCGGGTAAACGGCGGGAGTAACTATGACTCTCTTAAGGTAGCCAAATGCCTCGTCATCTAATTAGTGACGCGCATGAATGGATTAACGAGATTCCCACTGTCCCTGTCTACTATCCAGCGAAACCACAGCCAAGGGAACGGGCTTGGCAGAATCAGCGGGGAAAGAAGACCCTGTTGAGCTTGACTCTAGTCCGACTTTGTGAAATGACTTGAGAGGTGTAGGATAAGTGGGAGCTTCGGCGCAAGTGAAATACCACTACTTTTAACGTTATTTTACTTACTCCGTGAATCGGAGGCCGGGGTACAACCCCTGTTTTTGGTCCCAAGGCTCGCTTCGGCGGGTCGATCCGGGCGGAGGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTAAGATGAGCTCAACGAGAACAGAAATCTCGTGTGGAACAAAAGGGTAAAAGCTCGTTTGATTCTGATTTTCAGTACGAATACGAACCGTGAAAGCGTGGCCTATCGATCCTTTAGACTTCGGAATTTGAAGCTAGAGGTGTCAGAAAAGTTACCACAGGGATAACTGGCTTGTGGCAGCCAAGCGTTCATAGCGACGTTGCTTTTTGATCCTTCGATGTCGGCTCTTCCTATCATTGTGAAGCAGAATTCACCAAGTGTTGGATTGTTCACCCACCAATAGGGAACGTGAGCTGGGTTTAGACCGTCGTGAGACAGGTTAGTTTTACCCTACTGATGCCCGCGTCGCGATAGTAATTCAACCTAGTACGAGAGGAACCGTTGATTCGCACAATTGGTCATCGCGCTTGGTTGAAAAGCCAGTGGCGCGAAGCTACCGTGCGCTGGATTATGACTGAACGCCTCTAAGTCAGAATCCGGGCTAGAAGCGACGCATGCGCCCGCCGCCCGATTGCCGACCCTCAGTAGGAGCTTAGGCTCCAAAGGCACGTGTCGTTGGCTAAGTCCGTTCGGCGGAACGGTCGTTCGGACCGCCTTGAATTATAATTACCACCGAGCGGCGGGTAGAATCCTTTGCAGACGACTTAAATACGCGACGGGGTATTGTAAGTGGCAGAGTGGCCTTGCTGCCACGATCCACTGAGATTCAGCCCTTTGTCGCTAAGATTCGA
+>gi|20197903:2706-4513 Arabidopsis thaliana chromosome 2 BAC F23H14 genomic sequence, complete sequence
+TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTATGAACGAATTCAGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGATGGTAACTACTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCCGACTTATGGAAGGGACGCATTTATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCATGATAACTCGACGGATCGCATGGCCTCTGTGCTGGCGACGCATCATTCAAATTTCTGCCCTATCAACTTTCGATGGTAGGATAGTGGCCTACCATGGTGGTAACGGGTGACGGAGAATTAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCAATCCTGACACGGGGAGGTAGTGACAATAAATAACAATACTGGGCTCTTTCGAGTCTGGTAATTGGAATGAGTACAATCTAAATCCCTTAACGAGGATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGAACCTTGGGATGGGTCGGCCGGTCCGCCTTTGGTGTGCATTGGTCGGCTTGTCCCTTCGGTCGGCGATACGCTCCTGGTCTTAATTGGCCGGGTCGTGCCTCCGGCGCTGTTACTTTGAAGAAATTAGAGTGCTCAAAGCAAGCCTACGCTCTGGATACATTAGCATGGGATAACATCATAGGATTTCGATCCTATTGTGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATCAGCGGATGTTGCTTATAGGACTCCGCTGGCACCTTATGAGAAATCAAAGTTTTTGGGTTCCGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGGAAACTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAATGAACGAGACCTCAGCCTGCTAACTAGCTACGTGGAGGCATCCCTTCACGGCCGGCTTCTTAGAGGGACTATGGCCGTTTAGGCCAAGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTTCACACCTTGGCCGACAGGCCCGGGTAATCTTTGAAATTTCATCGTGATGGGGATAGATCATTGCAATTGTTGGTCTTCAACGAGGAATTCCTAGTAAGCGCGAGTCATCAGCTCGCGTTGACTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTCCTACCGATTGAATGATCCGGTGAAGTGTTCGGATCGCGGCGACGTGGGTGGTTCGCCGCCCGCGACGTCGCGAGAAGTCCACTAAACCTTATCATTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTG
+>Arabidopsis thaliana 1
+GGATGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCATCCCTC
+>gi|186498419|ref|NR_022453.1| Arabidopsis thaliana (AT2G01020) rRNA
+AAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCCAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACAA
\ No newline at end of file
diff -r 36d912d5b1ac -r d2817a631a7b Iterative_mapping/read_file.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Iterative_mapping/read_file.py	Tue Nov 18 16:24:04 2014 -0500
@@ -0,0 +1,21 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import sys
+
+
+
+def read_t_file(in_file):
+    f = open(in_file);
+    result = [];
+    for aline in f.readlines():
+        temp = [];
+        tline = aline.strip();
+        tl = tline.split('\t');
+        for i in range(0, len(tl)):
+            temp.append(tl[i].strip());
+        result.append(temp);
+    f.close();
+    return result;
+
+
diff -r 36d912d5b1ac -r d2817a631a7b Iterative_mapping/read_file.pyc
Binary file Iterative_mapping/read_file.pyc has changed
diff -r 36d912d5b1ac -r d2817a631a7b Iterative_mapping/read_s_file.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Iterative_mapping/read_s_file.py	Tue Nov 18 16:24:04 2014 -0500
@@ -0,0 +1,22 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import sys
+
+
+
+def read_sp_file(in_file):
+    f = open(in_file);
+    result = [];
+    for aline in f.readlines():
+        temp = [];
+        tline = aline.strip();
+        tl = tline.split(' ');
+        for i in range(0, len(tl)):
+            if len(tl[i].strip())>0:
+                temp.append(tl[i].strip());
+        result.append(temp);
+    f.close();
+    return result;
+
+
diff -r 36d912d5b1ac -r d2817a631a7b Iterative_mapping/read_s_file.pyc
Binary file Iterative_mapping/read_s_file.pyc has changed
diff -r 36d912d5b1ac -r d2817a631a7b Iterative_mapping/remove_map.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Iterative_mapping/remove_map.py	Tue Nov 18 16:24:04 2014 -0500
@@ -0,0 +1,29 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import sys
+from read_file import *
+
+
+unmap_file = sys.argv[1]
+map_file = sys.argv[2]
+result_file = sys.argv[3]
+
+
+unmap = read_t_file(unmap_file)
+mapped = read_t_file(map_file)
+h = file(result_file, 'w')
+
+maps = set()
+for i in range(len(mapped)):
+    maps.add(mapped[i][0])
+
+
+for i in range(len(unmap)):
+    name = unmap[i][0]
+    if name not in maps:
+        h.write(name)
+        h.write('\n')
+
+
+h.close()
diff -r 36d912d5b1ac -r d2817a631a7b Iterative_mapping/sample.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Iterative_mapping/sample.fasta	Tue Nov 18 16:24:04 2014 -0500
@@ -0,0 +1,1000 @@
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1415:1662#0/1
+TCATTCATCCATTTCCAGTGCTCAGCTAACCCCAACT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1359:1735#0/1
+TGCTGGCGACGCATCATTCAAATTTCTGCCCTATCAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1469:1743#0/1
+TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1750:1642#0/1
+AACCGGGACGTGGCGGTTGACGGCAACGTTAGGGAGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1899:1627#0/1
+AAAAACGACTCTCGGCAACGGATATCTCGGCTCTCGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1859:1668#0/1
+TACGCTCCTGGTCTTAATTGGCCGGGTCGTGCCCCCC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1830:1700#0/1
+ATTTCGATCCTATTGTGTTGGCCTTCGGGATCGGAGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2000:1705#0/1
+TTAATGATTAACAGGGACAGTCGGGGGCATTCGTATT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2149:1632#0/1
+GATCATACATTACTGACTAAAAGAAGCAAAATCTTGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2052:1637#0/1
+AGAACATGAAACCGTAAGCTCCCAAGCAGTGGGAGGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2036:1706#0/1
+AAAACTTAGCTGAGACGACGCAGAAACAGGTGAGATC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2183:1706#0/1
+TTCGAATTGTAGTCTGGAGAAGCGTCCTCAGCGACGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2068:1721#0/1
+AAGTAGCACGTCCCTCAGGAAAGAAGCTCTTCAGATT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2162:1740#0/1
+ATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2339:1628#0/1
+TGACGGCAACGTTAGGGAGTCCGGAGACGTCGGCCGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2338:1670#0/1
+TCGCGCGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2459:1678#0/1
+CCTCGTCGCTGCGTCTCTCTCCCGCAACCTTCGATTT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2492:1685#0/1
+AAAACGATGCCGACCAGGGATCAGCGGATGTTGCTTA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2286:1687#0/1
+AAGGCGGTGGAGGCCGCCCAGCATTGCCCGCACCTAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2283:1704#0/1
+ACTCTTGTTACAATGATTGTATGACATTCCTGATGGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2475:1719#0/1
+TTATGCAGAAATTGCTATAAGAAGAAACCTAAACTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2299:1733#0/1
+CTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2464:1744#0/1
+GTGTTTTTATCCAAATCCGGGGATAAACACATTTTGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2547:1662#0/1
+AGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2512:1664#0/1
+TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2675:1664#0/1
+GTACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2694:1675#0/1
+ACTACGAGAGGAACCGTTGATTCGCACAATTGGTCAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2558:1692#0/1
+ATCTTTCATATCCAGAGAGAGAGAAAGAGAACAAAAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2587:1709#0/1
+CAACCGTGAAAGCGTGGCCTATCGATCCTTTAGACCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2560:1727#0/1
+TTTCCGAGAGTATGCAGATTTTGTTTTCCAAGAATAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2960:1646#0/1
+CTTGCACATGGGTTAGTCGATCCTAAGAGTCGGGGGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2981:1669#0/1
+GATTCATCCCAAAACATTACAAAACGTTACAATGGCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2884:1740#0/1
+TCTCGCGCTTGTACGGCTTTGGCTCGGATTCGTCCGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3172:1696#0/1
+TCGAGTCTGGTAATTGGAATGAGTACAATCTAAATCC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3046:1703#0/1
+AGCGTCCTCAGCGACGGACCGGGCCTAAGTTCCCTGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3218:1717#0/1
+TCTCGCGCTTGTACGGCTTTGGCTCGGATTCGTCCGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3140:1732#0/1
+ATAAGAAGGTTATTGATTTGGTTAAAGAATACAATGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3212:1744#0/1
+TCCTGGTCTTAATTGGCCGGGTCGTGGCCCCCGCGCC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3277:1654#0/1
+TACTCGGATAACCGTAGTAATTCTAGAGCTAATACGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3373:1695#0/1
+CGTTTAGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3255:1702#0/1
+ACGCGGGCTCTGCCCGTTGCTCTGATGATTCATGATA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3391:1733#0/1
+AAATAGAAGGGTCAAAAGCTAAGGAAGAAAAGAAAGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3606:1635#0/1
+TTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3710:1652#0/1
+CCCCGTGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3551:1662#0/1
+AGAACATGAAACCGTAAGCTCCCAAGCAGTGGGAGGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3696:1663#0/1
+ACGCATTTATTAGATAAAAGGTCGACGCGGGCTCTGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3679:1667#0/1
+ACGGGGGGCAGCAGTGGGGAATCTTGGACAATGGGCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3622:1671#0/1
+TCATCCAATTGGAGACGAATCATATCGAGCGATGGAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3506:1682#0/1
+TGCGTTGTGGAAGTCGAAGAGGTTGATGAATATTGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3540:1687#0/1
+AAATTAAACCTCACCGACGGATTCAATTCTCTCGTTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3627:1725#0/1
+TCATCCAGATCTCAACTTTCTCTCATCTTCAAATTAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3710:1735#0/1
+GCGACCCCAGGTCAGGCGGGATTACCCGCTGAGTTTA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3787:1636#0/1
+AGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3996:1694#0/1
+AACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3942:1696#0/1
+TGTGCTGGCGACGCATCATTCAAATTTCTGCCCTATC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4104:1635#0/1
+AGGTCGGCGGTTCCATCACCACAACGCCGGACGACAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4243:1713#0/1
+AGATACTCCTTTGACCGAAGAAACCATAACGGAAGCC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4091:1714#0/1
+AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4229:1733#0/1
+GGGCCTGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4060:1745#0/1
+TGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4308:1693#0/1
+TCCTCGGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4384:1697#0/1
+AAAATTTCATCGTGATGGGGATAGATCATTGCAATTG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4506:1651#0/1
+GATAATAAAGAGATGGAGATTGTTTTGGAGCAACGGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4535:1654#0/1
+AAAAAGGGTAAAAGCTCGTTTGATTCTGATTTTCAGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4592:1677#0/1
+CTACCTGGTTAATCCTGCCAGTAGTCATATGCTTGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4726:1686#0/1
+TATGTTTTTGTTTGTTCGTAAATTCTTGACATCACTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4544:1694#0/1
+TGGAGCTCCGCTGAATTTTCTTTGCTCCATTTCCGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4604:1707#0/1
+TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4996:1665#0/1
+CTTATTTTACGAAGCTCCCCTCGGTTACAGCATTGAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4860:1668#0/1
+AGCGGCTGGAAGAGCACCGCACGTCGCGTGGTGTCCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4786:1671#0/1
+TATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4889:1691#0/1
+ATGGGGGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4843:1693#0/1
+AGGCAGTCCGATCCAACGGCTAGGCACTTACATGGCA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4977:1703#0/1
+ATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4791:1723#0/1
+TTGTGTTGGCCTTCGGGATCGGAGTAATGATTAACAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5019:1686#0/1
+ACAATGGAGCAACCACTCCTTCCGGCCTCGTCGCCGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5134:1686#0/1
+TCTGCTGTTGTAGAGCCTTACAACAGTGTGCTTTCAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5307:1664#0/1
+ACGTGCGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5278:1674#0/1
+GCATCAAAATCCTCCGACGATGACAACCATAGCTGCA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5486:1715#0/1
+TTGTGGTGGCGACGCATCATTCAAATTTCTGCCCTAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5541:1641#0/1
+TTCTCCCCGAAATGCGTTGAGGCGCAGCAGTTGACTG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5706:1646#0/1
+ACGAGGATCCATTGGAGGGCAAGTCTGGTGCCTGCAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5593:1651#0/1
+AAGGGGCTTCTTGTCATTGATGATGAGCTAGCCACCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5503:1695#0/1
+GAGAGGGAACTAATCATAAGAGATGCAATGAGTGTGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5581:1706#0/1
+ATAAAAACCAGAAGAATCCGTATAAATTATCCTAACA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5713:1729#0/1
+TCTCTTGGAGAGTTCGATCCTGGCTCAGGATGAACGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5831:1656#0/1
+TTCACGTGGCTCAAGTCACTAGCAATGCTCTTGCTTT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5942:1680#0/1
+TCCGGTGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5772:1711#0/1
+AGCGCGAACTTCGAAAGGGGATCTGGTTAAAATTCCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5957:1723#0/1
+TTACAATAAGTCTGCCTATAGTGGGAGAGGTGACAGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5981:1739#0/1
+GAGAAATTTGGAGTTTCGCCGGAATCTTCCTCTGTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6231:1644#0/1
+AATTGGAAAAGGTGGAGGAGTTGGCGGTGGCATCGGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6152:1724#0/1
+TGCAATTCTACCACGACCTCATCGACGAGCTCATAAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6100:1731#0/1
+TCCTCTGCGTTTTCACGAAACAGAGAACCTTATCGTT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6174:1733#0/1
+TCGAATTGTAGTCTGGAGAAGCGTCCTCAGCGACGGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6310:1648#0/1
+AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6287:1659#0/1
+TCAACGAGTTCACACCTTGGCCGACAGGCCCGGGTAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6332:1666#0/1
+TTTGGGTTCTCTCCTTATAGTTTGATGAACATTGTTG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6295:1704#0/1
+AGATAATCGGAACCTTCGTCCTTGTCTACACGGTCTT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6590:1655#0/1
+AGAAGCCACCTCCGGTTCCGGTTTACAAGCCCCCGCC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6585:1691#0/1
+CTTTTCCCAGAGAAGAAGCAATGACGGTATCTGGGGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6722:1719#0/1
+AACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6820:1642#0/1
+AAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:7000:1662#0/1
+GGGAAGCGTTGAGGCTTCACCCTCCACTCATCGTGTT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6873:1673#0/1
+AGCACTTTAGGATGGCATAGCCTTAAAGTTAAGGGTG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6770:1699#0/1
+AACTGTCTACAAAATCATTGAAGATCTACCCAAAAAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6782:1735#0/1
+GATCCGTCAAATTCAATTGATCCTCTCTCCAAATCAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:7159:1658#0/1
+ACCCACCTCCGGTTCCGGTTTACAAGCCACCGCCAAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:7183:1660#0/1
+ATTTCATCGTGATGGGGATAGATCATTGCAATTGTTG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:7167:1679#0/1
+TTCTGCCTCCGGCGCTGTTACTTTGAAGAAATTAGAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:7223:1688#0/1
+TTGGACGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:7410:1647#0/1
+ACCATGCAGTATCGGTTTATATAACATCCACATTGTT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:7387:1710#0/1
+TCTTCGAGTTTTGCTACTTGTATGGGATGATAAGACT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:7397:1741#0/1
+TTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:7624:1680#0/1
+AATTGTTGTTGTTATCTTCAACGATAGCGTTGTGCTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:7600:1744#0/1
+AGTTGTTGCAGTTAAAAAGCTCGTAGTTGAACCTTGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:7789:1676#0/1
+ACCCGTCTGATAGCGCTTAAGCGCGAACTTCGAAAGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:7950:1684#0/1
+TGAACGAGACCTCAGCCTGCTAACTAGCTACGTGGAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:7926:1706#0/1
+ACGGTATCTGGGGAATAAGCATCGGCTAACTCTGTGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:7757:1711#0/1
+TTGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:7970:1747#0/1
+TCGAAAGGGGATCCGGTTAAAATTCCGGAACCGGGAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8054:1672#0/1
+CGAAAGGGGATCCGGTTAAAATTCCGGAACCGGGACG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8245:1672#0/1
+GATATATAATCATAGATTCCAGAATTTGACATTTTCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8088:1710#0/1
+GAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8244:1713#0/1
+GGGACGCATTTATTAGATAAAAGGTCGACGCGGGCTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8069:1727#0/1
+TCGTCTACACCGTCTACGCCACAGCCGTTGACCCCAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8018:1745#0/1
+TTCTCTACTGGATTGCTCAGCTTCTTGGCTCCGTCGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8394:1647#0/1
+CTACAAGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8475:1658#0/1
+ACACTTGATCGGAATAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8367:1664#0/1
+GGGTGAGTAAACCCGTAAGGCGCAAGGAAGCTGATTG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8488:1695#0/1
+GCGACCCCAGGTCAGGCGGGATTACCCGCTGAGTTTA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8442:1727#0/1
+CGGTCGGCGATACGCTCCTGGTCTTAATTGGCCGGGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8328:1744#0/1
+TTGTCATTCTCTTCGCCGGAATCTAATCTCTCTCGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8520:1660#0/1
+TTGGCCGTTGTTTCCTTCTTCTTCTTCTTCTTCTTTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8563:1665#0/1
+AATTCAAATTTCTGCCCTATCAACTTTCGATGGTAGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8739:1667#0/1
+TCTCTCGGGAGCTTTCCCCGGGCGTCGAACAGTCAGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8596:1682#0/1
+TAGCCCACGAATGCGGTCACAACGCATTCAGCGACTA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8643:1688#0/1
+TTGCACGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8727:1745#0/1
+AGGGAGAGCTAATGCTTCTTGGGTATTTAGGTTTGAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8767:1649#0/1
+TCGGTACCAAATCGAGGCAAACTCTGAATACTAGATA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8932:1656#0/1
+GCTGGCGACGCATCATTCAAATTTCTGCCCTATCAAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8841:1666#0/1
+TCAAACGAGGAAAGGCTTACGGTGGATACCTAGGCAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8951:1673#0/1
+TGGTGGAGCTGGAGGAGGATTTGGTGGAGGAGCTGGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8876:1674#0/1
+AACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:8993:1737#0/1
+TTACCGTGCGCTGGATTATGACTGAACGCCTCTAAGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:9241:1664#0/1
+AAGTCACTCTTTCTTGTTGCCTTACTTGTCGGCTCTT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:9095:1710#0/1
+AGAACGAAAGTTGGGGGCTCGAAGACGATAAGATACC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:9231:1716#0/1
+TCGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:9171:1733#0/1
+AAAATTTCTGCCCTATCAACTTTCGATGGTAGGATAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:9471:1658#0/1
+GACACATACACACATAGCCATGGCCTCTTCTTTCTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:9383:1680#0/1
+TTCAGTGTTGATTCGTCTTCCTTCACGCCGTTCTTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:9627:1730#0/1
+ATTGTTTGTAAAGGGTGAGAGATTATTTTTCAGTGAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:9921:1680#0/1
+ATGGCTTCTCCGGTGAGATACCTGACTCGATTGGTTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:9931:1727#0/1
+AAAGCATCGGCTAACTCTGTGCCAGCAGCCGCGGTAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:10235:1668#0/1
+AAAAATCTTGAGTAAAAACAAATTTTCCTGTATCTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:10040:1686#0/1
+AAAACCCGTCTGATAGCGCTTAAGCGCGAACTTCGAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:10169:1689#0/1
+ACGGATCGCATGGCCTCTGTGCTGGCGACGCATCATT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:10213:1743#0/1
+GGCGCTTAAGCGCGCGACCTATACCCGGCCGTCGGGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:10021:1744#0/1
+CAAAGCAAGCCTACGCTCTGGATACATTAGCATGGGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:10294:1712#0/1
+TTCTCTCTCTAACATTCTTCAGAGAGGGAGACTTTAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:10392:1736#0/1
+TAGAGTGCTCAAAGCAAGCCTACGCTCTGGATACATT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:10582:1655#0/1
+ACGGTACTGGACAATGTGGAAGCTTCCCTTGTTCGGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:10777:1673#0/1
+CACTCTCACCCACAAGTTAGTCATAAAAAAAAAAAAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:10980:1714#0/1
+GTGGAGAGACTGAAAACCGCGAAGAGGATGTGAATGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:10931:1720#0/1
+TTGTAGTCTGGAGAAGCGTCCTCAGCGACGGACCGGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:11171:1717#0/1
+TGTGCTGGCGACGCATCATTCAAATTTCTGCCCTATC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:11458:1668#0/1
+GATCACAAGTTTTAAGCAGTATTTGTAAGAAAATGGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:11388:1696#0/1
+TTGTGCTGGCGACGCATCATTCAAATTTCTGCCCTAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:11317:1701#0/1
+ACAACTCAAGCTTCCATCAACTTGACCCACACCGAAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:11403:1706#0/1
+TAGATAACATCAAGACAACAACCGTCGGTCCCGGAAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:11291:1739#0/1
+GAAAATCAAATCTTTTCATTTACAATTATCTTTCTTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:11593:1673#0/1
+TCCCTTCACGGCCGGCTTCTTAGAGGGACTATGGCCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:11537:1726#0/1
+CCATCTCCGTATTGTCTTCTACGTAGACAATGTGCCC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:11709:1733#0/1
+CGAGGCGCTGTCTACGAGTCGGGTTGTTTGGGAATGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:11851:1657#0/1
+TAATCAAGATCGAAAGTTGGGGGCTCGAAGACGATCA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:11822:1687#0/1
+TTGACGGCAACGTTAGGGAGTCCGGAGACGTCGGCGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:11950:1691#0/1
+TTATGTTTACAGCTCTCCTCCTCCTCCGGTGAAGTCC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:11752:1704#0/1
+TGAACGGCACTTGCACATGGGTTAGTCGATCCTAAGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:11895:1708#0/1
+TTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:11756:1739#0/1
+TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:12136:1709#0/1
+ATGCGAAAAGTGTAAAGGTGGGAAGATCGGAATTGCA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:12070:1715#0/1
+ACGAGCAGCTCCCAACCACAGACTACTGAATTAATCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:12204:1724#0/1
+GAAAATTTTCCCCATTAAACAAAAAAAAATCAAATCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:12140:1746#0/1
+ACTACTCTCTCCACTAAACAAAAACACTAGAGTTAAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:12332:1664#0/1
+GCGAAAGCATTTGCCAAGGATGCTTTCATTAATCAAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:12455:1665#0/1
+ACAAGTCTTGTCTCTCGAGTGTTCTTCAAATGTTAGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:12252:1728#0/1
+GGAACTCCATGCGAATATGAAGCGCATGGATACAAGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:12315:1747#0/1
+TGGACCGGTAATTTCATTACATCGCCGGACGGCCGGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:12640:1665#0/1
+TCTCTTCTACAGTAAACAAAAAATGGCAATGAATGGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:12666:1668#0/1
+TTATTCTGCACTTGGAAGAAGAACTAGAAAAAGGAAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:12735:1728#0/1
+ATCCCTTCACGGCCGGCTTCTTAGAGGGACTATGGCC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:12751:1677#0/1
+TCCTCCTGTTTACAAGTCCCCACCACCACCGGTTAAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:12821:1679#0/1
+TCTTCTCCGGTGATTTACTTACTTAACAATCATGGCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:12935:1691#0/1
+ACTGCCTTCGGATTTGATTTGGTTCGTGGCACCAAGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:12996:1719#0/1
+TAATCTCTCTGTTTAATCTTATGATCTGCTGTTTTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:13223:1661#0/1
+GTTGATGTGTTTATTCCCAGAGATCGAAGGACTGGTG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:13442:1665#0/1
+TTTAACAGCCTGCCCACCCTGGAAACGGCTCAGCCGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:13331:1684#0/1
+GGGGGTCGCAGTGACCAGGCCCGGGCGACTGTTTACC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:13451:1685#0/1
+TGCTCAAATTTCTTCTTTAGAAGATTAAAAATCTTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:13309:1690#0/1
+TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:13312:1742#0/1
+AAAACGATGCCGACCAGGGATCAGCGGATGTTGCTTA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:13704:1696#0/1
+GACTCGGAGCAGAGATTTAGGGTCTGTAATTTGTATA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:13563:1703#0/1
+TATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:13735:1728#0/1
+AACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:13899:1667#0/1
+CGTTATTTTACTTACTCCGTGAATCGGAGGCGGGGTA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:13836:1707#0/1
+AACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:13886:1718#0/1
+GAACAGAAAATAGAAAGAAGTAACAAAACCAAAGCAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:13866:1724#0/1
+TCAATGAGCCATGGGTTTTCTCGCACGCTGGCTATGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:13943:1728#0/1
+TCGAAGACGATCAGATACCGTCCTAGTCTCAACCATA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:14097:1712#0/1
+CCCTCGACCTATTCTCAAACTTTAAATAGGTAGGACG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:14116:1729#0/1
+GTTCTCACGTTCGAAGACCATTTCTTGTTCTTTGGAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:14699:1669#0/1
+AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:14594:1718#0/1
+AATTTCCTCATGTTGAGAGGTACTTCTGGACTGTGGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:14743:1729#0/1
+AACTCACCTGCCGAATCAACTAGCCCCGAAAATGGAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:14510:1734#0/1
+TTCACCCACCGCAGCTTCACCACCGGCACCTCCGACG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:14821:1705#0/1
+AACTGGCTAACACGTATTGGGTTGAGTATCTCTCTAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:14892:1717#0/1
+CTTTCGGATATTCCACCAGTCTCTCGCAATCTTCGCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:14835:1743#0/1
+AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:15239:1702#0/1
+TCTGACGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:15059:1717#0/1
+TGTGCTGGCGACGCATCATTCAAATTTCTGCCCTATC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:15152:1718#0/1
+GGGCAGGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:15444:1702#0/1
+GATATCTATTTATTCAATAACCCTTACAACACCGAAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:15407:1747#0/1
+TCGGATACGGGTCGGGCTTCTTAGCTGTTTGAAGAAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:15681:1670#0/1
+AATTGCCACAACATGGGCGTTCTTCTTAGCAAGAATT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:15630:1695#0/1
+TTATTAGATAAAAGGTCGACGCGGGCTCTGCCCGGTG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:15506:1715#0/1
+TTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:15976:1688#0/1
+ATCATCCATCACATCTCCTCTTGCAAACCAACGTAAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:15940:1745#0/1
+AACAAGGTAGCCGTACTGGAAGGTGCGGCTGGATCAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:16043:1680#0/1
+ACGTATGTGGCAAAATACGGGGATGACTTGTGGCTAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:16175:1683#0/1
+ATCTAGTAGCTGGTTCCCTCCGAAGTTTCCCTCAGGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:16074:1695#0/1
+AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:16238:1700#0/1
+AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:16229:1727#0/1
+TCGAAGACGATCAGATACCGTCCTAGTCTCAACCATA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:16025:1727#0/1
+CCGGGAAGGACGCACCTCTGGTGTACCAGTTATCGTG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:16429:1678#0/1
+ACGGATCGCATGGCCTCTGTGCTGGCGACGCATCATT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:16255:1695#0/1
+CTAAGAAAGTTGATCCACCGCCGGTGCCAGTCCACAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:16494:1739#0/1
+AGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:16656:1687#0/1
+TTAAATCAGTTATAGTTTGTTTGATGGTAACTACTAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:16685:1715#0/1
+TAAAACGTCGTGGACTTTTTGAGTCTGACGCTGCATT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:16885:1690#0/1
+CTCAGGATCGGAAGAGCACACGTCTGAACTCCAGTCA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:16994:1709#0/1
+ATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:16768:1715#0/1
+TCGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:16899:1742#0/1
+GGTAAACTTCGAGCCTGTCCGACCCAGAAGGCACAAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:17201:1693#0/1
+TCTTTGGATAACAATATCCCAAACTGAAAATGGCTAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:17179:1704#0/1
+TTAAGTCCTCCGCTGCCTTCCCAGCCACCCGCAAGGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:17158:1711#0/1
+ACTAATGTAAAGGAAGCCTGTGCTTGGCTTGGATATA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:17051:1725#0/1
+ATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:17448:1685#0/1
+ACAATGACTGGGCCTCCACCTGCCATGGTGATGCCTG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:17551:1710#0/1
+GGTTTGTCTTCAAAATCGTCAGAAGAAGAAGAAGAAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:17662:1746#0/1
+GCAACACGGGGAAACTTACCAGGTCCAGACATAGTAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:17823:1706#0/1
+TCCCCCGGTTGGATTGAAGGGTTGAAAAAATTAGACA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:17951:1723#0/1
+TGATCGGAGGATGTTGCGACGGAGCCGTCCTTTGACC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:18174:1676#0/1
+ATTAAATCCTAAAATCCATTATTGATTGAATCTTCGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:18241:1694#0/1
+CCAAATCTAATAAATCTAAGTGTAGTTTTCGGTGTAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:18095:1727#0/1
+ACAAGCAACGGCGGAAGAGTTAACTGCATGCAGGTGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:18074:1746#0/1
+ACCACCAAATCGCCGCCATGTTTAAACAAGCTTCTCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:18318:1679#0/1
+GAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:18410:1680#0/1
+GCAAGCCTACGCTCTGGATACATTAGCATGGGATAAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:18290:1681#0/1
+TCAGGCCTTGGAGGACCGAACCCACGTATGTGGCAAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:18280:1722#0/1
+GAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:18429:1742#0/1
+TAGACTACGGATGGGACACCGCCGGACTTTCAGCTGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:18675:1682#0/1
+TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:18535:1684#0/1
+CCTTTGTACACACCGCCCGTCGCTCCTACCGATTGAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:18657:1722#0/1
+GAGAAGATAAAGAGATAAAGGAAAGACTAACGTTAAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:18618:1729#0/1
+TGAACACACACAAACACACACACACACAGCCTTTTTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:18823:1701#0/1
+ACCTGACCCAGATAGCGAGAAGTTTCATGGATAAGGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:19063:1699#0/1
+ACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:19104:1705#0/1
+AAAAACGACTCTCGGCAACGGATATCTCGGCTCTCGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:19019:1718#0/1
+AGACGATCAGATACCGTCCTGGTCTCAACCATAAACG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:19433:1728#0/1
+AAATAGCGTATATTTAAGTTGTTGCAGTTAAAAAGCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:19355:1731#0/1
+AATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:19500:1683#0/1
+TTGTAACACGGACCAAGGAGTCTGACATGTGTGCGAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:19657:1698#0/1
+GGGATTGGCTTTGGGCTTTTCCTGCGCAGCTTAGGTG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:19640:1749#0/1
+TTTAATTAATAACAATAAATGTTCTTTTTCAGTTTTG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:19866:1690#0/1
+AAGCCCGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:19966:1707#0/1
+AAAATGCCAAGACGGACGATCAGGATACGAGGCTTAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:20090:1682#0/1
+CAGGTCCCCGAGTGGCTCACACGATATGCTTCACGTG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:20183:1689#0/1
+GATATCGAGCGATGGATTTGGCAGAACTGTGGGCGAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:20206:1747#0/1
+TCGAAAGTTGGGGGCTCGAAGACGATCAGATGCCGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:20292:1695#0/1
+AGGAACGGAGACGGCAGGAACGATGAGTTCTATAGTA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:20306:1713#0/1
+CCGATGGTTGTGGACAACATGTATTATAAGAACATCA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:20402:1713#0/1
+TTACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:20275:1726#0/1
+AACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:20403:1737#0/1
+AAATAAGAAGACATATTTATCAACTTGATCAACTTGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:20539:1702#0/1
+CCTTCACGGCCGGCTTCTTAGAGGGACTATGGCCGTT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:20612:1731#0/1
+AGCGTCCTCAGCGACGGACCGGGCCTAAGTTCCCTGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:20566:1745#0/1
+AGTTCGGTCTCTCTGCCGGAGTCGGATCATTAAACGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:20889:1691#0/1
+CTTTCATTTCAGAGTCTTGGTGTTGTTTATGGTGATT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:20841:1709#0/1
+TTTGCTGGCATAATGGGAATGGGTTTTCCACCTTACA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:20980:1742#0/1
+TCCACTACTTTTAACGTTATTTTACTTACTCCGTGAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:21184:1708#0/1
+CGATCAGATACCGTCCTAGTCTCAACCATAAACGATG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:21173:1745#0/1
+TCGGTTGCTAATGGTTTGATCAATTTCCTCAACATAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:21427:1722#0/1
+CGTTAACGAACGAGACCTCAGCCTGCTAACTAGCTAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1449:1766#0/1
+TCAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1303:1793#0/1
+TAACCATAAACGATGCCGACCAGGGATCAGCGGATGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1430:1865#0/1
+TCTTCATCCTCGTCTACTGCACCGCCGGTATCTCTGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1450:1892#0/1
+AGCAACTGCCAAAGCACCCGCAACAAAATTATAAAGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1342:1935#0/1
+ATTGATGATGTCTTTACTTCTTCAAGAGGATCTACCA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1406:1941#0/1
+AACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1676:1764#0/1
+TGGTGAGACAAAAACGACGATATTTTCCTCTTCCTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1512:1774#0/1
+AAAAACAATAAACGAAAACTGAGAGAGAGATTGAAAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1677:1808#0/1
+ATTGGATCACTTTCAATGAGCCATGGGTTTTCTCGCA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1579:1824#0/1
+TTTTGTGTTTGTCCACCACCTCCTCCATGTTATTCTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1744:1840#0/1
+GGGTGAGAGCCCCGTTGTGCCCGGACCCTGTCGCACC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1579:1852#0/1
+AGAAGAAGAAGAAGAAAAAGTGGAGCAAGCTTCGTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1550:1869#0/1
+AACTCTGTGCCAGCAGCCGCGGTAATACAGAGGATGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1565:1898#0/1
+AGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1738:1918#0/1
+ACATTCCTCACCAAACCCTCTCCAAAACACACCCACA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1547:1922#0/1
+TCGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1732:1964#0/1
+TCTCGCGCTTGTACGGCTTTGGCTCGGATTCGTCCGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1654:1991#0/1
+GATTATATAAGGGAATGTTCAGTTCCAGTGACTGAGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1518:1992#0/1
+GGTGGAGGTTTACAAACACCACCAATCTTCTCTCTTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1865:1796#0/1
+GATTCATCCCAAAACATTACAAAACGTTACAATGGCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1886:1815#0/1
+GGGCGTAAAGCGTCTGTAGGTGGCTTTTTAAGTCCGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1855:1840#0/1
+TGGTATCGGTGGACTCGGCGGTGCAGGTGGGCTAGGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1960:1855#0/1
+ACCTCACTGCCGCCGATTAGACTCCGCCGGATGCAAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1808:1879#0/1
+TTACCATAAACGATGCCGACCAGGGATCAGCGGATGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1869:1890#0/1
+TGCTTCTTGGGTATTTAGGTTTGACACAGCTTCACAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1898:1925#0/1
+TCCCATGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:1765:1950#0/1
+AACTCATATCAACCTTCGCCGGAAATAATGGCTTTCC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2096:1773#0/1
+ATAGCACCGATAACAATCTACTCTCTTTAAAAGAAAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2186:1774#0/1
+TTGAGAAAATAAACGAGGAGGTGGCTCATCCTGAGAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2019:1774#0/1
+AAGACGATCAGATACCGTCCTAGTCTCAACCATAAAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2236:1797#0/1
+GTGTAGTCTGGAGAAGCGTCCTCAGCGACGGACCGGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2218:1825#0/1
+ACCTATCTCACTCTAAAATCTCTCTCTGCCAATCTCA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2067:1830#0/1
+ACATGTCTGTGAAGATGCGGACTACCTGCACCTGGAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2183:1833#0/1
+AGGGCGCGAGCCCGGGCGGAGCGGCCGTCGGTGCAGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2095:1843#0/1
+GACACAACACACCTCAAGCTTTATAACTTCTAAAACA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2184:1923#0/1
+AAGAGTCGGGGGAAACCCGTCTGATAGCGCTTAAGCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2086:1933#0/1
+AAAAACGACTCTCGGCAACGGATATCTCGGCTCTCGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2134:1944#0/1
+AGCGTCCTCAGCGACGGACCGGGCCTAAGTTCCCTGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2220:1966#0/1
+AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2066:1971#0/1
+TGAAGCATTTTCCAAAGAGAAAGAGAGAGAAATGGGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2239:1991#0/1
+ATTATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2113:1996#0/1
+TTTGGTGTGCATTGGTCGGCTTGTCCCTTCGGTCGGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2369:1755#0/1
+TGATCCTTTCGTCTTTTTCTGACTCTTCAATCTCTCC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2281:1791#0/1
+TTAATTCCGGAACCGGGACGTGGCGGTTGACGGCAAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2431:1837#0/1
+AAAATTTCATCGTGATGGGGATAGATCATTGCAATTG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2272:1843#0/1
+GGGGATCCGGTTAAAATTCCGGAACCGGGACGTGGCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2316:1843#0/1
+TGGCTTGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2451:1850#0/1
+TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2264:1872#0/1
+ATGATAACTCGACGGATCGCATGGCCTCTGTGCTGGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2443:1872#0/1
+ACAGGTCTGTGATGCCCTTAGATGTTCTGGGTCGCAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2297:1890#0/1
+ATAACATCATAGGATTTCGATCCTATTGTGTTGGCCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2472:1986#0/1
+ACTACCACTCTCCACCTCCTCCGGCGAAGTCCCCACC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2564:1768#0/1
+GGGGCCTGATAGGCGGTGGTTTACCCTGTGGCGGATG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2674:1786#0/1
+TAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2648:1802#0/1
+GCGATAATACAGAGGATGCAAGCGTTATCCGGAATGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2691:1831#0/1
+CAGTATAATCAATCAGAAAACAAGTAGAAACTTTAAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2560:1839#0/1
+TCGAAGACGATCAGATACCGTCCTAGTCTCGACCATA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2612:1876#0/1
+TCTTGGGCCTTTGCCACCAACTTTGTTCCCGGAAAGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2503:1919#0/1
+TCAGACGAGGAAAGGCTTACGGTGGATACCTAGGCAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2640:1953#0/1
+CACCGGGAGAAAATCCTCCTCCGCTGTCGTGAGAGCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2553:1969#0/1
+GATCATCACCTTCCCCACTAATACTCTATAGTTTGTT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2669:1987#0/1
+GGATCGTGAGACTCCGATGGTTGTGGACAACATGTAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2782:1800#0/1
+GACATTTTCTGTTTCCGTCTACAAGAACCACTTTGTT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2957:1811#0/1
+ATTAATTCACATTTAAACACTTCTCTGCATATATTTG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2990:1818#0/1
+TATTTTACTTACTCCGTGAATCGGAGGCGGGGTACAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2806:1852#0/1
+TGAAAATAAGCGTAGATCCGGAGATTCCCGAATAGGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2899:1856#0/1
+ACTGATGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2903:1882#0/1
+AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2913:1931#0/1
+TTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2816:1932#0/1
+GCATCAGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2795:1958#0/1
+TCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:2993:1984#0/1
+GACGATCAGATACCGTCCTAGTCTCAACCATAAACGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3163:1754#0/1
+AGGCAAGAGACAACCTGGCGAACTGAAACATCTTAGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3082:1793#0/1
+AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3054:1825#0/1
+TAGATGTTGAGACTCTAATCCCTAACCACAATGACTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3100:1835#0/1
+CTATCTTAAAACTTCTTACCTAAAATAGAAATTTGAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3199:1865#0/1
+TTTCTTAAAAATTGGATTTTGTGTTGGGTTTTTCTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3032:1907#0/1
+AGAGAGAAGAAGTAGGCAGACAAAGAAGAAGAAGAAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3232:1919#0/1
+ATCACAAGCAAACAAGAGAAAACATTTTATTGTTATT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3075:1937#0/1
+ACAGACTGTGAAACTGCGAATGGCTCATTAAATCAGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3005:1941#0/1
+TTTTAAGTCCGCCGTCAAATCCCAGGGCTCAACCCCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3026:1990#0/1
+AAGAAAGAGATTCCCCCGCCGGTTCCGGTTTACGATC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3131:1992#0/1
+GGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3319:1777#0/1
+GCGACCCCAGGTCAGGCGGGATTACCCGCTGAGTTTA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3337:1789#0/1
+GACGCGGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3416:1846#0/1
+AACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3292:1846#0/1
+AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3491:1888#0/1
+ATCTTTTCGAAGAGCGGAAGCTAAGGAGAGGCGAATT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3266:1903#0/1
+TATAGAAATGGCCAAAGACGTGGAAGGACCTGAGGGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3339:1904#0/1
+GTGAAGACACCAGAGACGCCTAGTTTGGTGGGAAAGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3435:1918#0/1
+AGCGTCCTCAGCGACGGACCGGGCCTAAGTTCCCTGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3478:1938#0/1
+CCGGAGAATAATATCCGATCTGCTAGTGCGGTTAATA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3381:1938#0/1
+ATCAGCGACTCTCCCACTCGCTCGTGTCGTCGAAGTT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3311:1972#0/1
+ACATTCATCCCAAAACATTACAAAACGTTACAATGGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3471:1996#0/1
+CCCATGTCCACCTAAATACAGTCCTCCTGTGGAGGTT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3408:1998#0/1
+AACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3714:1760#0/1
+TGTGCTGGCGACGCATCATTCAAATTTCTGCCCTATC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3734:1790#0/1
+ATACAGCAGCTGAAGCTGTGTATCGGAAAGCTCAATT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3699:1795#0/1
+ACAAAAGACAAGTTTTTAAACTGCAGAACCGCATTTA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3651:1798#0/1
+TCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3557:1799#0/1
+TGATAGTGCTTAAGCGCGAACTTCGAAAGGGGATCCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3531:1811#0/1
+TACAGACACACACGTGGCTCATCACCTGTTCTCGACA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3526:1856#0/1
+TCTTTGAAGAAATTAGAGTGCTCAAAGCAAGCCTACG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3693:1860#0/1
+AAAACAACTCTGCTTCACTCTCTATCTTTCTTAAGTA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3616:1916#0/1
+AGCTTGAAAATCGGACGTCTTCGGCGTTCGAATTGTA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3599:1930#0/1
+AGACGATCAGATACCGTCCTAGTCTCAACCATAAACG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3620:1956#0/1
+GAATCTCTCTGTGTTTTTTCTATCTCTCTCTTTCTTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3596:1973#0/1
+TGTAAGAGCTAGGCAGCAGGGATTATGTGTACGCAAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3721:1974#0/1
+AAGCCTGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3507:1998#0/1
+ACAAGGTGCTGGTGCTGGAGGAGGATATGGAGGTGGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3756:1769#0/1
+ACGCCCTCGACCTATTCTCAAACTTTAAATAGGTAGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3901:1846#0/1
+TACAAGTCTCCTCCGCCACCAACTCCGACATATGTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3892:1871#0/1
+ATCACCGCCTCCATATTCTTTCGCGTCTTTTGCTTCC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3765:1925#0/1
+AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3842:1953#0/1
+TCGAGCATTTTTGACGCCAAGGCTGGAATTGCATTCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3758:1970#0/1
+AACCCCGACTTATGGAAGGGACGCATTTATTAGATAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3931:1972#0/1
+CTCCGTGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:3828:1991#0/1
+CCTTCGGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4152:1771#0/1
+TCCTGAGATTTTTTATATATTTTCTCCAGATCTGCTA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4212:1780#0/1
+GACTCAACCAATTTCTTCTCAGGTAATACTCGTAAGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4130:1806#0/1
+TTGTGCTGGCGACGCATCATTCAAATTTCTGCCCTAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4183:1813#0/1
+AAGGCACGTGTCGTTGGCTAAGTCCGTTCGGCGGAAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4010:1857#0/1
+ACTCTGCTTCACTCTCTATCTTTCTTAAGTAAACAAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4206:1859#0/1
+TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4051:1895#0/1
+TCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4226:1939#0/1
+TGATCATCACTTTCACAATCTTCTTCATCGATTTCTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4381:1809#0/1
+GCAGCATCAGCAACAACAGAGCAGTCCTGGCTTTCTA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4456:1814#0/1
+TTCATGGACGTTGATAAGATCTTTCCATTTAGCAGCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4311:1831#0/1
+AAGAGTTATCTTTTCTGTTTAACAGCCTGCCCACCCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4464:1844#0/1
+TACGCTTGGGCCTTCGTCGCCAAGACTTCTCAAGTTA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4254:1850#0/1
+AAAAGGAGGTAGGGGTGCAGAGACAGCCAGGAGGTTT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4286:1883#0/1
+ATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGAAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4465:1887#0/1
+AACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4329:1895#0/1
+CCGTTCGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4379:1906#0/1
+ACTACTCTCTCCACTAAACAAAAACACTAGAGTTAAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4486:1907#0/1
+TAAGAGCCAAAGGTTGAGAATGTGACTCTTGGACCAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4456:1996#0/1
+GAGGATGCGAAAAGATACATCCGGCAACTTCCCAACT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4674:1782#0/1
+TTTATGACTGAACGCCTCTAAGTCAGAATCCGGGCTA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4634:1791#0/1
+GAATCACTTCACTCTCTCTAATCAAAAAGCTTTTAAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4501:1806#0/1
+TCGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4629:1820#0/1
+TGATCGTTCTTATTGACCCTAGCCGCTACACACTTTT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4590:1838#0/1
+ATTCATTTCAATCAATCTTCTTCTTCTTCTTCTTCTT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4741:1847#0/1
+AACGACTCTCGGCAACGGATATCTCGGCTCTCGCATC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4708:1892#0/1
+TTGTGCTGGCGACGCATCATTCAAATTTCTGCCCTAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4508:1902#0/1
+TTAGCATGGGATAACATCATAGGATTTCGATCCTATT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4691:1903#0/1
+AGTGAAATACCACTACTTTTTACGTTATTTTACTTAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4648:1966#0/1
+AAATTTCAAAATCAGATCCAACAAATCTTCTTCTTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4963:1798#0/1
+AGACGTCGGCGGGGGCCTCGGAAAGAGTTATCTTTTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4766:1882#0/1
+CTGTCGCACCACGAGGCGCTGTCTACGAGTCGGGTTG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4860:1888#0/1
+ATACTCGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4947:1899#0/1
+CATCAATACTCCTGTGAGAACAAAATGAAGCTTTCTT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4982:1926#0/1
+AGACTCGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4879:1942#0/1
+TCGAGTCAGGTAATTGGAATGAGTACAATCTAAATCC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:4914:1944#0/1
+GTGCAAAGGTTTCCTCGGGCCGGACGGAGATTGGCCC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5091:1754#0/1
+TTTATGTTTCTCATTATTACTGCGGGAATTTCAATTA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5145:1756#0/1
+TATCGGTAGGGGAGCGTTCCGCCTTAGGGGGAAGCAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5015:1781#0/1
+TTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5166:1833#0/1
+TTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5035:1836#0/1
+TGGCGACGCATCATTCAAATTTCTGCCCTATCAACTT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5195:1862#0/1
+TTCACCCATTTCTTGGCTTACAACAACAAATCTTAAA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5062:1871#0/1
+TTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5235:1878#0/1
+ACGGAAATGTCTTCATGGGTTCTTCCGAACATGTTCC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5231:1897#0/1
+GGAACGAACACACCACCTTCTCTCCAATCTGGATCTG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5168:1901#0/1
+ACTCACCTGCCGAATCAACTAGCCCCGAAAATGGATG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5220:1915#0/1
+CCACCTCCGGTTCCGGTTTACAAGCCCCCGCCAAAGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5013:1950#0/1
+ACTTTCAATGAGCCATGGGTTTTCTCGCACGCTGGCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5175:1985#0/1
+CGTGAAATACCACTACTTTTAACGTTATTTTACTTAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5145:1985#0/1
+ATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGAAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5453:1770#0/1
+CATCAAAACCCAGACGCTGTATGGTTATGGGGAATGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5412:1781#0/1
+ATGTCGGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5412:1816#0/1
+TAGGACTCCGCTGGCACCTTATGAGAAATCAAAGTTT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5496:1822#0/1
+AAAAACCTAAAACAAAAAAAATCTCTTTCCTTCTTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5346:1823#0/1
+AAGCCACCACCAAAGGTGGAGCTTCCACCGCCTATTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5333:1831#0/1
+TCGAGTCTGGTAATTGGAATGAGTACAATCTAAATCC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5305:1833#0/1
+AGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5371:1867#0/1
+GTAGCGTCCTCAGCAACGGACCGGGCCTAAGTTCCCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5374:1893#0/1
+ATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5377:1943#0/1
+TGTTCGGGAAACATTGACGACAAAGGAAAGTTTGGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5313:1973#0/1
+TGTATACAAGTCTCCTCCGCCACCAACTCCGACATAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5620:1756#0/1
+AAAAACTTTCTCTCAATTCTCTCTACCGTGATCAAGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5716:1779#0/1
+TCCCTTCACGGCCGGCTTCTTAGAGGGACTATGGCCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5667:1857#0/1
+GTATTCAACGAGTTCACACCTTGGCCGACAGGCCCGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5654:1887#0/1
+GTAACGGGTGACGGAGAATTAGGGTTCGATTCCGGAG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5636:1908#0/1
+TTCTCGCGCTTGTACGGCTTTGGCTCGGATTCGTCCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5715:1927#0/1
+CCGTCGGGGCAAGAGCCAGGCCTCGATGAGTAGGAGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5610:1936#0/1
+GAAGAAGCAATGACGGTATCTGGGGAATAAGCATCGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5832:1784#0/1
+GCCCGGATCGGAAGAGCACACGTCTGAACTCCAGTCA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5917:1794#0/1
+AGTCGCGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5769:1883#0/1
+AGCAAAGTTTTATGTAATCAAATCGTACAGTGAAGAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5796:1889#0/1
+TTGTGCTGGCGACGCATCATTCAAATTTCTGCCCTAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5992:1905#0/1
+ATGTGTGTATTAATTTATCTTCTTGTTTTAAAGAGAC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5885:1923#0/1
+AAGAAGAGCCAATGGCGATGAAGACATCACATGTTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5976:1937#0/1
+AGCGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:5957:1978#0/1
+TTAGTTGAACCTTGGGATGGGTCGGCCGGTCCGCCTT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6197:1781#0/1
+ACTTAGGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6180:1789#0/1
+ATTTTGGCTGGTGCTGAATACGGTAGTGGAAGTTCTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6038:1789#0/1
+TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6177:1825#0/1
+TTGATCCCGAGACTGAAGCTATGACCAGGAGAATTGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6159:1830#0/1
+CGGGCCGATCGGAAGAGCACACGTCTGAACTCCAGTC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6151:1878#0/1
+ATACGGTGTATGAATCCGAATTACACAGAGTTCAAGT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6123:1878#0/1
+AGCGCTAACTTCGAAAGGGGATCCGGTTAAAATTCCG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6196:1879#0/1
+ATTTCTGCCCTATCAACTTTCGATGGTAGGATAGTGG
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6237:1895#0/1
+AAGATCCCAGACGAAATGGCTCAGAAAGTGGTGCTGA
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6023:1896#0/1
+ACAACCGCTGAATATTTGGCTTATGAATGTGGAAAGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6123:1904#0/1
+ATGATAACTCGACGGATCGCATGGCCTCTGTGCTGGC
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6125:1922#0/1
+ATGGATCGTTGCACGTCGTCGTTTTTGCTTCCCACAT
+>DGM97JN1_120925_0255_AD166MACXX:4:1101:6184:1926#0/1
+GATCATCAAAAAACACCTCAAAGAATTATTCATTCAG
diff -r 36d912d5b1ac -r d2817a631a7b Iterative_mapping/seq_track.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Iterative_mapping/seq_track.py	Tue Nov 18 16:24:04 2014 -0500
@@ -0,0 +1,38 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import sys
+from read_file import *
+from Bio import SeqIO
+
+unmap_file = sys.argv[1]
+reads_file = sys.argv[2]
+result_file = sys.argv[3]
+tp = sys.argv[4]
+
+
+unmap = read_t_file(unmap_file);
+
+h = file(result_file, 'w')
+
+reads = SeqIO.parse(reads_file,tp)
+um = set()
+for i in range(0, len(unmap)):
+    id_r = unmap[i][0]
+    um.add(id_r)
+
+for read in reads:
+    if read.id in um:
+        h.write('>')
+        h.write(read.id)
+        h.write('\n')
+        h.write(read.seq.tostring())
+        h.write('\n')
+    
+
+
+h.close()
+
+
+
+
diff -r 36d912d5b1ac -r d2817a631a7b Iterative_mapping/truncate.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Iterative_mapping/truncate.py	Tue Nov 18 16:24:04 2014 -0500
@@ -0,0 +1,36 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import sys
+from Bio import SeqIO
+
+fasta_file = sys.argv[1]
+shift_in = sys.argv[2]
+result_file = sys.argv[3]
+length = sys.argv[4]
+t_end = sys.argv[5]
+
+shift = int(shift_in)
+    
+fasta_sequences = SeqIO.parse(open(fasta_file),'fasta');
+h = file(result_file,'w')
+for seq in fasta_sequences:
+        nuc = seq.id;
+        sequence = seq.seq.tostring();
+        if (len(sequence)-shift)>=int(length):
+                h.write('>'+nuc)
+                h.write('\n')
+                if t_end == 'three_end':
+                        h.write(sequence[0:(len(sequence)-shift)])
+                if t_end == 'five_end':
+                        h.write(sequence[(shift):(len(sequence))])
+                h.write('\n')
+
+
+
+
+h.close()
+
+
+
+
diff -r 36d912d5b1ac -r d2817a631a7b Iterative_mapping/unmap.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Iterative_mapping/unmap.py	Tue Nov 18 16:24:04 2014 -0500
@@ -0,0 +1,31 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import sys
+from read_file import *
+from Bio import SeqIO
+
+map_file = sys.argv[1]
+result_file = sys.argv[2]
+
+
+#reads = read_t_file(read_file);
+
+f = open(map_file);
+h = file(result_file, 'w')
+
+for aline in f.readlines():
+    tline = aline.strip();
+    tl = tline.split('\t');
+    if len(tl)>4:
+        if int(tl[1].strip()) != 0:
+            h.write(tl[0].strip());
+            h.write('\n');
+
+
+f.close();
+h.close()
+
+
+
+