# HG changeset patch # User iuc # Date 1526580675 14400 # Node ID b48e673af4e8dda5aead790ddb463b90dde2d04d # Parent 793225b112029011888d89f02af25b815d49e69f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b diff -r 793225b11202 -r b48e673af4e8 fimo_wrapper.py --- a/fimo_wrapper.py Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,194 +0,0 @@ -#!/usr/bin/env python -import argparse -import os -import shutil -import string -import subprocess -import sys -import tempfile - -BUFFSIZE = 1048576 -# Translation table for reverse Complement, with ambiguity codes. -DNA_COMPLEMENT = string.maketrans("ACGTRYKMBDHVacgtrykmbdhv", "TGCAYRMKVHDBtgcayrmkvhdb") - - -def get_stderr(tmp_stderr): - tmp_stderr.seek(0) - stderr = '' - try: - while True: - stderr += tmp_stderr.read(BUFFSIZE) - if not stderr or len(stderr) % BUFFSIZE != 0: - break - except OverflowError: - pass - return stderr - - -def reverse(sequence): - # Reverse sequence string. - return sequence[::-1] - - -def dna_complement(sequence): - # Complement DNA sequence string. - return sequence.translate(DNA_COMPLEMENT) - - -def dna_reverse_complement(sequence): - # Returns the reverse complement of the sequence. - sequence = reverse(sequence) - return dna_complement(sequence) - - -def stop_err(msg): - sys.stderr.write(msg) - sys.exit(1) - - -parser = argparse.ArgumentParser() -parser.add_argument('--input_motifs', dest='input_motifs', help='MEME output formatted files for input to fimo') -parser.add_argument('--input_fasta', dest='input_fasta', help='Fassta sequence file') -parser.add_argument('--options_type', dest='options_type', help='Basic or Advance options') -parser.add_argument('--input_psp', dest='input_psp', default=None, help='File containing position specific priors') -parser.add_argument('--input_prior_dist', dest='input_prior_dist', default=None, help='File containing binned distribution of priors') -parser.add_argument('--alpha', dest='alpha', type=float, default=1.0, help='The alpha parameter for calculating position specific priors') -parser.add_argument('--bgfile', dest='bgfile', default=None, help='Background file type, used only if not "default"') -parser.add_argument('--max_strand', action='store_true', help='If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score') -parser.add_argument('--max_stored_scores', dest='max_stored_scores', type=int, help='Maximum score count to store') -parser.add_argument('--motif', dest='motifs', action='append', default=[], help='Specify motif by id') -parser.add_argument('--output_separate_motifs', dest='output_separate_motifs', default='no', help='Output one dataset per motif') -parser.add_argument('--motif_pseudo', dest='motif_pseudo', type=float, default=0.1, help='Pseudocount to add to counts in motif matrix') -parser.add_argument('--no_qvalue', action='store_true', help='Do not compute a q-value for each p-value') -parser.add_argument('--norc', action='store_true', help='Do not score the reverse complement DNA strand') -parser.add_argument('--output_path', dest='output_path', help='Output files directory') -parser.add_argument('--parse_genomic_coord', dest='parse_genomic_coord', default='no', help='Check each sequence header for UCSC style genomic coordinates') -parser.add_argument('--remove_duplicate_coords', dest='remove_duplicate_coords', default='no', help='Remove duplicate entries in unique GFF coordinates') -parser.add_argument('--qv_thresh', action='store_true', help='Use q-values for the output threshold') -parser.add_argument('--thresh', dest='thresh', type=float, help='p-value threshold') -parser.add_argument('--gff_output', dest='gff_output', help='Gff output file') -parser.add_argument('--html_output', dest='html_output', help='HTML output file') -parser.add_argument('--interval_output', dest='interval_output', help='Interval output file') -parser.add_argument('--txt_output', dest='txt_output', help='Text output file') -parser.add_argument('--xml_output', dest='xml_output', help='XML output file') -args = parser.parse_args() - -fimo_cmd_list = ['fimo'] -if args.options_type == 'advanced': - fimo_cmd_list.append('--alpha %4f' % args.alpha) - if args.bgfile is not None: - fimo_cmd_list.append('--bgfile "%s"' % args.bgfile) - if args.max_strand: - fimo_cmd_list.append('--max-strand') - fimo_cmd_list.append('--max-stored-scores %d' % args.max_stored_scores) - if len(args.motifs) > 0: - for motif in args.motifs: - fimo_cmd_list.append('--motif "%s"' % motif) - fimo_cmd_list.append('--motif-pseudo %4f' % args.motif_pseudo) - if args.no_qvalue: - fimo_cmd_list.append('--no-qvalue') - if args.norc: - fimo_cmd_list.append('--norc') - if args.parse_genomic_coord == 'yes': - fimo_cmd_list.append('--parse-genomic-coord') - if args.qv_thresh: - fimo_cmd_list.append('--qv-thresh') - fimo_cmd_list.append('--thresh %4f' % args.thresh) - if args.input_psp is not None: - fimo_cmd_list.append('--psp "%s"' % args.input_psp) - if args.input_prior_dist is not None: - fimo_cmd_list.append('--prior-dist "%s"' % args.input_prior_dist) -fimo_cmd_list.append('--o "%s"' % (args.output_path)) -fimo_cmd_list.append('--verbosity 1') -fimo_cmd_list.append(args.input_motifs) -fimo_cmd_list.append(args.input_fasta) - -fimo_cmd = ' '.join(fimo_cmd_list) - -try: - tmp_stderr = tempfile.NamedTemporaryFile() - proc = subprocess.Popen(args=fimo_cmd, shell=True, stderr=tmp_stderr) - returncode = proc.wait() - if returncode != 0: - stderr = get_stderr(tmp_stderr) - stop_err(stderr) -except Exception as e: - stop_err('Error running FIMO:\n%s' % e) - -shutil.move(os.path.join(args.output_path, 'fimo.txt'), args.txt_output) - -gff_file = os.path.join(args.output_path, 'fimo.gff') -if args.remove_duplicate_coords == 'yes': - tmp_stderr = tempfile.NamedTemporaryFile() - # Identify and eliminating identical motif occurrences. These - # are identical if the combination of chrom, start, end and - # motif id are identical. - cmd = 'sort -k1,1 -k4,4n -k5,5n -k9.1,9.6 -u -o %s %s' % (gff_file, gff_file) - proc = subprocess.Popen(args=cmd, stderr=tmp_stderr, shell=True) - returncode = proc.wait() - if returncode != 0: - stderr = get_stderr(tmp_stderr) - stop_err(stderr) - # Sort GFF output by a combination of chrom, score, start. - cmd = 'sort -k1,1 -k4,4n -k6,6n -o %s %s' % (gff_file, gff_file) - proc = subprocess.Popen(args=cmd, stderr=tmp_stderr, shell=True) - returncode = proc.wait() - if returncode != 0: - stderr = get_stderr(tmp_stderr) - stop_err(stderr) -if args.output_separate_motifs == 'yes': - # Create the collection output directory. - collection_path = (os.path.join(os.getcwd(), 'output')) - # Keep track of motif occurrences. - header_line = None - motif_ids = [] - file_handles = [] - for line in open(gff_file, 'r'): - if line.startswith('#'): - if header_line is None: - header_line = line - continue - items = line.split('\t') - attribute = items[8] - attributes = attribute.split(';') - name = attributes[0] - motif_id = name.split('=')[1] - file_name = os.path.join(collection_path, 'MOTIF%s.gff' % motif_id) - if motif_id in motif_ids: - i = motif_ids.index(motif_id) - fh = file_handles[i] - fh.write(line) - else: - fh = open(file_name, 'wb') - if header_line is not None: - fh.write(header_line) - fh.write(line) - motif_ids.append(motif_id) - file_handles.append(fh) - for file_handle in file_handles: - file_handle.close() -else: - shutil.move(gff_file, args.gff_output) -shutil.move(os.path.join(args.output_path, 'fimo.xml'), args.xml_output) -shutil.move(os.path.join(args.output_path, 'fimo.html'), args.html_output) - -out_file = open(args.interval_output, 'wb') -out_file.write("#%s\n" % "\t".join(("chr", "start", "end", "pattern name", "score", "strand", "matched sequence", "p-value", "q-value"))) -for line in open(args.txt_output): - if line.startswith('#'): - continue - fields = line.rstrip("\n\r").split("\t") - start, end = int(fields[2]), int(fields[3]) - sequence = fields[7] - if start > end: - # Flip start and end and set strand. - start, end = end, start - strand = "-" - # We want sequences relative to strand; FIMO always provides + stranded sequence. - sequence = dna_reverse_complement(sequence) - else: - strand = "+" - # Make 0-based start position. - start -= 1 - out_file.write("%s\n" % "\t".join([fields[1], str(start), str(end), fields[0], fields[4], strand, sequence, fields[5], fields[6]])) -out_file.close() diff -r 793225b11202 -r b48e673af4e8 macros.xml --- a/macros.xml Wed Apr 25 12:13:08 2018 -0400 +++ b/macros.xml Thu May 17 14:11:15 2018 -0400 @@ -1,10 +1,11 @@ - 4.11.2 + 4.12.0 graphicsmagick - meme + meme + diff -r 793225b11202 -r b48e673af4e8 meme_psp_gen.xml --- a/meme_psp_gen.xml Wed Apr 25 12:13:08 2018 -0400 +++ b/meme_psp_gen.xml Thu May 17 14:11:15 2018 -0400 @@ -5,9 +5,11 @@ - - + + diff -r 793225b11202 -r b48e673af4e8 test-data/dreme1.html --- a/test-data/dreme1.html Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6199 +0,0 @@ - - - - - DREME - - - - - - - - - - - - - - -
-

Help poup.

- -
- -
-

- The name of the motif uses the IUPAC codes for nucleotides which has - a different letter to represent each of the 15 possible combinations. -

-

- The name is itself a representation of the motif though the position - weight matrix is not directly equalivant as it is generated from the - sites found that matched the letters given in the name. -

-

- - Read more about the MEME suite's use of the IUPAC alphabets. - - -

- -
- - -
-

The E-value is the enrichment p-value times the number of candidate - motifs tested.

-

The enrichment p-value is calculated using Fisher's Exact Test for - enrichment of the motif in the positive sequences.

-

Note that the counts used in Fisher's Exact Test are made after - erasing sites that match previously found motifs.

- -
-
-

The E-value of the motif calculated without erasing the sites of - previously found motifs.

- -
-
-

Show more information on the motif.

- -
-
-

Submit your motif to another MEME Suite program or download your motif.

-
Supported Programs
-
-
Tomtom
-
Tomtom is a tool for searching for similar known motifs. -
-
MAST
-
MAST is a tool for searching biological sequence databases for - sequences that contain one or more of a group of known motifs. -
-
FIMO
-
FIMO is a tool for searching biological sequence databases for - sequences that contain one or more known motifs. -
-
GOMO
-
GOMO is a tool for identifying possible roles (Gene Ontology - terms) for DNA binding motifs. -
-
SpaMo
-
SpaMo is a tool for inferring possible transcription factor - complexes by finding motifs with enriched spacings. -
-
- -
-
-

# positive sequences matching the motif / # positive sequences.

-

Note these counts are made after erasing sites that match previously - found motifs.

- -
-
-

# negative sequences matching the motif / # negative sequences.

-

Note these counts are made after erasing sites that match previously - found motifs.

- -
-
-

The p-value of Fisher's Exact Test for enrichment of the motif in - the positive sequences.

-

Note that the counts used in Fisher's Exact Test are made after - erasing sites that match previously found motifs.

- -
-
-

The E-value is the motif p-value times the number of candidate motifs - tested.

-

Note that the p-value was calculated with counts made after - erasing sites that match previously found motifs.

- -
-
-

The E-value of the motif calculated without erasing the sites of - previously found motifs.

- -
-
-

All words matching the motif whose uncorrected p-value is less than - .

- - -
-
-

# positive sequences with matches to the word / # positive sequences.

-

Note these counts are made after erasing sites that match previously - found motifs.

- -
-
-

# negative sequences with matches to the word / # negative sequences.

-

Note these counts are made after erasing sites that match previously - found motifs.

- -
-
-

The p-value of Fisher's Exact Test for enrichment of the word in - the positive sequences.

-

Note that the counts used in Fisher's Exact Test are made after - erasing sites that match previously found motifs.

- -
-
-

The word p-value times the number of candidates tested.

-

Note that the p-value was calculated with counts made after - erasing sites that match previously found motifs.

- -
- -
-

The sequence file used by DREME to find the motifs.

- -
-
-

The alphabet of the sequences.

- -
-
-

The count of the sequences.

- -
- -
-

The name of the alphabet symbol.

- -
- -
-

The frequency of the alphabet symbol in the control dataset.

- -
- - - -
-
- - -
-

Details

- - - - - - - - - - - - - - - - - - - -
Positives
Negatives
P-value
E-value
Unerased E-value
- / - - / -
-

Enriched Matching Words

-
-
- - - - - - - -
- -

- For further information on how to interpret these results or to get a - copy of the MEME software please access - http://meme.nbcr.net. -

-

- If you use DREME in your research please cite the following paper:
- - Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", Bioinformatics, 27(12):1653-1659, 2011. - [full text] - -

-
- -
- Discovered Motifs -   |   - Inputs & Settings -   |   - Program information -
- - -

Your browser does not support canvas!

- - - - - -
-

Discovered Motifs

- Next Top -
-
-

No motifs were discovered!

-
- - -
-

Inputs & Settings

- Previous Next Top -
-
-

Sequences

- - - - - - - - - - -
Source
Alphabet
Sequence Count
- -

Control Sequences

- - - - - - - - -
Source
Sequence Count
- -

Background

- - -

Other Settings

- - - - - - - - - - -
Strand Handling - This alphabet only has one strand - Only the given strand is processed - Both the given and reverse complement strands are processed -
# REs to Generalize
Shuffle Seed
E-value Threshold
Max Motif Count
Max Run Time
- -
- -
- -
-
DREME version
- - (Release date: )
-
- -
-
Reference
- - Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", Bioinformatics, 27(12):1653-1659, 2011. - [full text] - -
-
-
Command line
- - -
-
- - - diff -r 793225b11202 -r b48e673af4e8 test-data/dreme1.txt --- a/test-data/dreme1.txt Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,102 +0,0 @@ -# DREME 4.12.0 -# command: dreme -oc dreme_out -rna -norc -p dreme_test_sites.fa -e 0.05 -mink 3 -maxk 8 -# positives: 1000 from dreme_test_sites.fa (Thu Apr 19 19:09:45 CEST 2018) -# negatives: 1000 from shuffled positives -# host: ThinkPad-T450s -# when: Thu Apr 19 19:11:17 CEST 2018 - -MEME version 4.12.0 - -ALPHABET "RNA" RNA-LIKE -A "Adenine" CC0000 -C "Cytosine" 0000CC -G "Guanine" FFB300 -U "Uracil" 008000 -N "Any base" = ACGU -X = ACGU -. = ACGU -V "Not U" = ACG -H "Not G" = ACU -D "Not C" = AGU -B "Not A" = CGU -M "Amino" = AC -R "Purine" = AG -W "Weak" = AU -S "Strong" = CG -Y "Pyrimidine" = CU -K "Keto" = GU -T = U -END ALPHABET - -Background letter frequencies (from dataset): -A 0.221 C 0.245 G 0.221 U 0.312 - - -MOTIF UUYUCY DREME-1 - -# Word Pos Neg P-value E-value -# BEST UUYUCY 387 210 2.6e-018 1.2e-013 -# UUUUCC 147 75 1.8e-007 8.1e-003 -# UUUUCU 155 94 2.2e-005 1.0e+000 -# UUCUCU 94 51 1.3e-004 6.1e+000 -# UUCUCC 75 42 1.1e-003 5.0e+001 - -letter-probability matrix: alength= 4 w= 6 nsites= 459 E= 1.2e-013 -0.000000 0.000000 0.000000 1.000000 -0.000000 0.000000 0.000000 1.000000 -0.000000 0.294118 0.000000 0.705882 -0.000000 0.000000 0.000000 1.000000 -0.000000 1.000000 0.000000 0.000000 -0.000000 0.474946 0.000000 0.525054 - - -MOTIF YAGG DREME-2 - -# Word Pos Neg P-value E-value -# BEST YAGG 600 416 1.1e-016 5.1e-012 -# CAGG 441 304 1.5e-010 6.6e-006 -# UAGG 232 165 1.1e-004 4.7e+000 - -letter-probability matrix: alength= 4 w= 4 nsites= 793 E= 5.1e-012 -0.000000 0.692308 0.000000 0.307692 -1.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 1.000000 0.000000 -0.000000 0.000000 1.000000 0.000000 - - -MOTIF GAAGAW DREME-3 - -# Word Pos Neg P-value E-value -# BEST GAAGAW 81 22 8.2e-010 3.4e-005 -# GAAGAU 45 7 2.4e-008 9.9e-004 -# GAAGAA 40 16 7.9e-004 3.3e+001 - -letter-probability matrix: alength= 4 w= 6 nsites= 89 E= 3.4e-005 -0.000000 0.000000 1.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 1.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 -0.494382 0.000000 0.000000 0.505618 - - -MOTIF SMUGGA DREME-4 - -# Word Pos Neg P-value E-value -# BEST SMUGGA 110 47 9.1e-008 3.7e-003 -# GAUGGA 22 6 1.7e-003 7.1e+001 -# GCUGGA 33 14 3.6e-003 1.5e+002 -# CCUGGA 32 15 8.6e-003 3.5e+002 -# CAUGGA 29 13 9.1e-003 3.7e+002 - -letter-probability matrix: alength= 4 w= 6 nsites= 119 E= 3.7e-003 -0.000000 0.529412 0.470588 0.000000 -0.428571 0.571429 0.000000 0.000000 -0.000000 0.000000 0.000000 1.000000 -0.000000 0.000000 1.000000 0.000000 -0.000000 0.000000 1.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 - - -# Stopping reason: E-value threshold exceeded -# Running time: 13.45 seconds diff -r 793225b11202 -r b48e673af4e8 test-data/dreme1.xml --- a/test-data/dreme1.xml Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,32 +0,0 @@ - - - dreme -oc dreme_out -rna -norc -p dreme_test_sites.fa -e 0 - - - - - - - - - - - - - - - - - - - - none - - - 100 - 0.01 - 1 - ThinkPad-T450s - Thu Apr 19 19:40:08 CEST 2018 - - diff -r 793225b11202 -r b48e673af4e8 test-data/dreme2.html --- a/test-data/dreme2.html Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6118 +0,0 @@ - - - - - DREME - - - - - - - - - - - - - - -
-

Help poup.

- -
- -
-

- The name of the motif uses the IUPAC codes for nucleotides which has - a different letter to represent each of the 15 possible combinations. -

-

- The name is itself a representation of the motif though the position - weight matrix is not directly equalivant as it is generated from the - sites found that matched the letters given in the name. -

-

- - Read more about the MEME suite's use of the IUPAC alphabets. - - -

- -
- - -
-

The E-value is the enrichment p-value times the number of candidate - motifs tested.

-

The enrichment p-value is calculated using Fisher's Exact Test for - enrichment of the motif in the positive sequences.

-

Note that the counts used in Fisher's Exact Test are made after - erasing sites that match previously found motifs.

- -
-
-

The E-value of the motif calculated without erasing the sites of - previously found motifs.

- -
-
-

Show more information on the motif.

- -
-
-

Submit your motif to another MEME Suite program or download your motif.

-
Supported Programs
-
-
Tomtom
-
Tomtom is a tool for searching for similar known motifs. -
-
MAST
-
MAST is a tool for searching biological sequence databases for - sequences that contain one or more of a group of known motifs. -
-
FIMO
-
FIMO is a tool for searching biological sequence databases for - sequences that contain one or more known motifs. -
-
GOMO
-
GOMO is a tool for identifying possible roles (Gene Ontology - terms) for DNA binding motifs. -
-
SpaMo
-
SpaMo is a tool for inferring possible transcription factor - complexes by finding motifs with enriched spacings. -
-
- -
-
-

# positive sequences matching the motif / # positive sequences.

-

Note these counts are made after erasing sites that match previously - found motifs.

- -
-
-

# negative sequences matching the motif / # negative sequences.

-

Note these counts are made after erasing sites that match previously - found motifs.

- -
-
-

The p-value of Fisher's Exact Test for enrichment of the motif in - the positive sequences.

-

Note that the counts used in Fisher's Exact Test are made after - erasing sites that match previously found motifs.

- -
-
-

The E-value is the motif p-value times the number of candidate motifs - tested.

-

Note that the p-value was calculated with counts made after - erasing sites that match previously found motifs.

- -
-
-

The E-value of the motif calculated without erasing the sites of - previously found motifs.

- -
-
-

All words matching the motif whose uncorrected p-value is less than - .

- - -
-
-

# positive sequences with matches to the word / # positive sequences.

-

Note these counts are made after erasing sites that match previously - found motifs.

- -
-
-

# negative sequences with matches to the word / # negative sequences.

-

Note these counts are made after erasing sites that match previously - found motifs.

- -
-
-

The p-value of Fisher's Exact Test for enrichment of the word in - the positive sequences.

-

Note that the counts used in Fisher's Exact Test are made after - erasing sites that match previously found motifs.

- -
-
-

The word p-value times the number of candidates tested.

-

Note that the p-value was calculated with counts made after - erasing sites that match previously found motifs.

- -
- -
-

The sequence file used by DREME to find the motifs.

- -
-
-

The alphabet of the sequences.

- -
-
-

The count of the sequences.

- -
- -
-

The name of the alphabet symbol.

- -
- -
-

The frequency of the alphabet symbol in the control dataset.

- -
- - - -
-
- - -
-

Details

- - - - - - - - - - - - - - - - - - - -
Positives
Negatives
P-value
E-value
Unerased E-value
- / - - / -
-

Enriched Matching Words

-
-
- - - - - - - -
- -

- For further information on how to interpret these results or to get a - copy of the MEME software please access - http://meme.nbcr.net. -

-

- If you use DREME in your research please cite the following paper:
- - Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", Bioinformatics, 27(12):1653-1659, 2011. - [full text] - -

-
- -
- Discovered Motifs -   |   - Inputs & Settings -   |   - Program information -
- - -

Your browser does not support canvas!

- - - - - -
-

Discovered Motifs

- Next Top -
-
-

No motifs were discovered!

-
- - -
-

Inputs & Settings

- Previous Next Top -
-
-

Sequences

- - - - - - - - - - -
Source
Alphabet
Sequence Count
- -

Control Sequences

- - - - - - - - -
Source
Sequence Count
- -

Background

- - -

Other Settings

- - - - - - - - - - -
Strand Handling - This alphabet only has one strand - Only the given strand is processed - Both the given and reverse complement strands are processed -
# REs to Generalize
Shuffle Seed
E-value Threshold
Max Motif Count
Max Run Time
- -
- -
- -
-
DREME version
- - (Release date: )
-
- -
-
Reference
- - Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", Bioinformatics, 27(12):1653-1659, 2011. - [full text] - -
-
-
Command line
- - -
-
- - - diff -r 793225b11202 -r b48e673af4e8 test-data/dreme2.txt --- a/test-data/dreme2.txt Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,68 +0,0 @@ -# DREME 4.12.0 -# command: dreme -oc dreme_out_adv -rna -norc -p dreme_test_sites.fa -e 0.00001 -mink 4 -maxk 10 -# positives: 1000 from dreme_test_sites.fa (Thu Apr 19 19:09:45 CEST 2018) -# negatives: 1000 from shuffled positives -# host: ThinkPad-T450s -# when: Tue Apr 24 18:44:36 CEST 2018 - -MEME version 4.12.0 - -ALPHABET "RNA" RNA-LIKE -A "Adenine" CC0000 -C "Cytosine" 0000CC -G "Guanine" FFB300 -U "Uracil" 008000 -N "Any base" = ACGU -X = ACGU -. = ACGU -V "Not U" = ACG -H "Not G" = ACU -D "Not C" = AGU -B "Not A" = CGU -M "Amino" = AC -R "Purine" = AG -W "Weak" = AU -S "Strong" = CG -Y "Pyrimidine" = CU -K "Keto" = GU -T = U -END ALPHABET - -Background letter frequencies (from dataset): -A 0.221 C 0.245 G 0.221 U 0.312 - - -MOTIF UUYUCY DREME-1 - -# Word Pos Neg P-value E-value -# BEST UUYUCY 387 210 2.6e-018 3.3e-013 -# UUUUCC 147 75 1.8e-007 2.2e-002 -# UUUUCU 155 94 2.2e-005 2.8e+000 -# UUCUCU 94 51 1.3e-004 1.7e+001 -# UUCUCC 75 42 1.1e-003 1.4e+002 - -letter-probability matrix: alength= 4 w= 6 nsites= 459 E= 3.3e-013 -0.000000 0.000000 0.000000 1.000000 -0.000000 0.000000 0.000000 1.000000 -0.000000 0.294118 0.000000 0.705882 -0.000000 0.000000 0.000000 1.000000 -0.000000 1.000000 0.000000 0.000000 -0.000000 0.474946 0.000000 0.525054 - - -MOTIF YAGG DREME-2 - -# Word Pos Neg P-value E-value -# BEST YAGG 600 416 1.1e-016 1.4e-011 -# CAGG 441 304 1.5e-010 1.8e-005 -# UAGG 232 165 1.1e-004 1.3e+001 - -letter-probability matrix: alength= 4 w= 4 nsites= 793 E= 1.4e-011 -0.000000 0.692308 0.000000 0.307692 -1.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 1.000000 0.000000 -0.000000 0.000000 1.000000 0.000000 - - -# Stopping reason: E-value threshold exceeded -# Running time: 18.17 seconds diff -r 793225b11202 -r b48e673af4e8 test-data/dreme_fimo_input_1.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dreme_fimo_input_1.xml Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,99 @@ + + + dreme -oc dreme_out -norc -p input.fa + + + + + + + + + + + + + + + + + + + + given + + + 100 + 0.01 + 1 + ThinkPad-T450s + Wed May 02 16:45:34 CEST 2018 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 793225b11202 -r b48e673af4e8 test-data/dreme_output_test1.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dreme_output_test1.html Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,6198 @@ + + + + + DREME + + + + + + + + + + + + + + +
+

Help poup.

+ +
+ +
+

+ The name of the motif uses the IUPAC codes for nucleotides which has + a different letter to represent each of the 15 possible combinations. +

+

+ The name is itself a representation of the motif though the position + weight matrix is not directly equalivant as it is generated from the + sites found that matched the letters given in the name. +

+

+ + Read more about the MEME suite's use of the IUPAC alphabets. + + +

+ +
+ + +
+

The E-value is the enrichment p-value times the number of candidate + motifs tested.

+

The enrichment p-value is calculated using Fisher's Exact Test for + enrichment of the motif in the positive sequences.

+

Note that the counts used in Fisher's Exact Test are made after + erasing sites that match previously found motifs.

+ +
+
+

The E-value of the motif calculated without erasing the sites of + previously found motifs.

+ +
+
+

Show more information on the motif.

+ +
+
+

Submit your motif to another MEME Suite program or download your motif.

+
Supported Programs
+
+
Tomtom
+
Tomtom is a tool for searching for similar known motifs. +
+
MAST
+
MAST is a tool for searching biological sequence databases for + sequences that contain one or more of a group of known motifs. +
+
FIMO
+
FIMO is a tool for searching biological sequence databases for + sequences that contain one or more known motifs. +
+
GOMO
+
GOMO is a tool for identifying possible roles (Gene Ontology + terms) for DNA binding motifs. +
+
SpaMo
+
SpaMo is a tool for inferring possible transcription factor + complexes by finding motifs with enriched spacings. +
+
+ +
+
+

# positive sequences matching the motif / # positive sequences.

+

Note these counts are made after erasing sites that match previously + found motifs.

+ +
+
+

# negative sequences matching the motif / # negative sequences.

+

Note these counts are made after erasing sites that match previously + found motifs.

+ +
+
+

The p-value of Fisher's Exact Test for enrichment of the motif in + the positive sequences.

+

Note that the counts used in Fisher's Exact Test are made after + erasing sites that match previously found motifs.

+ +
+
+

The E-value is the motif p-value times the number of candidate motifs + tested.

+

Note that the p-value was calculated with counts made after + erasing sites that match previously found motifs.

+ +
+
+

The E-value of the motif calculated without erasing the sites of + previously found motifs.

+ +
+
+

All words matching the motif whose uncorrected p-value is less than + .

+ + +
+
+

# positive sequences with matches to the word / # positive sequences.

+

Note these counts are made after erasing sites that match previously + found motifs.

+ +
+
+

# negative sequences with matches to the word / # negative sequences.

+

Note these counts are made after erasing sites that match previously + found motifs.

+ +
+
+

The p-value of Fisher's Exact Test for enrichment of the word in + the positive sequences.

+

Note that the counts used in Fisher's Exact Test are made after + erasing sites that match previously found motifs.

+ +
+
+

The word p-value times the number of candidates tested.

+

Note that the p-value was calculated with counts made after + erasing sites that match previously found motifs.

+ +
+ +
+

The sequence file used by DREME to find the motifs.

+ +
+
+

The alphabet of the sequences.

+ +
+
+

The count of the sequences.

+ +
+ +
+

The name of the alphabet symbol.

+ +
+ +
+

The frequency of the alphabet symbol in the control dataset.

+ +
+ + + +
+
+ + +
+

Details

+ + + + + + + + + + + + + + + + + + + +
Positives
Negatives
P-value
E-value
Unerased E-value
+ / + + / +
+

Enriched Matching Words

+
+
+ + + + + + + +
+ +

+ For further information on how to interpret these results or to get a + copy of the MEME software please access + http://meme.nbcr.net. +

+

+ If you use DREME in your research please cite the following paper:
+ + Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", Bioinformatics, 27(12):1653-1659, 2011. + [full text] + +

+
+ +
+ Discovered Motifs +   |   + Inputs & Settings +   |   + Program information +
+ + +

Your browser does not support canvas!

+ + + + + +
+

Discovered Motifs

+ Next Top +
+
+

No motifs were discovered!

+
+ + +
+

Inputs & Settings

+ Previous Next Top +
+
+

Sequences

+ + + + + + + + + + +
Source
Alphabet
Sequence Count
+ +

Control Sequences

+ + + + + + + + +
Source
Sequence Count
+ +

Background

+ + +

Other Settings

+ + + + + + + + + + +
Strand Handling + This alphabet only has one strand + Only the given strand is processed + Both the given and reverse complement strands are processed +
# REs to Generalize
Shuffle Seed
E-value Threshold
Max Motif Count
Max Run Time
+ +
+ +
+ +
+
DREME version
+ + (Release date: )
+
+ +
+
Reference
+ + Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", Bioinformatics, 27(12):1653-1659, 2011. + [full text] + +
+
+
Command line
+ + +
+
+ + + diff -r 793225b11202 -r b48e673af4e8 test-data/dreme_output_test1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dreme_output_test1.txt Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,102 @@ +# DREME 4.12.0 +# command: dreme -o ./dreme_test1_out -p dreme_test_sites.fa -norc -rna -s 1 +# positives: 1000 from dreme_test_sites.fa (Thu Apr 26 15:09:03 CEST 2018) +# negatives: 1000 from shuffled positives +# host: ThinkPad-T450s +# when: Thu May 03 13:22:29 CEST 2018 + +MEME version 4.12.0 + +ALPHABET "RNA" RNA-LIKE +A "Adenine" CC0000 +C "Cytosine" 0000CC +G "Guanine" FFB300 +U "Uracil" 008000 +N "Any base" = ACGU +X = ACGU +. = ACGU +V "Not U" = ACG +H "Not G" = ACU +D "Not C" = AGU +B "Not A" = CGU +M "Amino" = AC +R "Purine" = AG +W "Weak" = AU +S "Strong" = CG +Y "Pyrimidine" = CU +K "Keto" = GU +T = U +END ALPHABET + +Background letter frequencies (from dataset): +A 0.221 C 0.245 G 0.221 U 0.312 + + +MOTIF UUYUCY DREME-1 + +# Word Pos Neg P-value E-value +# BEST UUYUCY 387 210 2.6e-018 1.2e-013 +# UUUUCC 147 75 1.8e-007 8.1e-003 +# UUUUCU 155 94 2.2e-005 1.0e+000 +# UUCUCU 94 51 1.3e-004 6.1e+000 +# UUCUCC 75 42 1.1e-003 5.0e+001 + +letter-probability matrix: alength= 4 w= 6 nsites= 459 E= 1.2e-013 +0.000000 0.000000 0.000000 1.000000 +0.000000 0.000000 0.000000 1.000000 +0.000000 0.294118 0.000000 0.705882 +0.000000 0.000000 0.000000 1.000000 +0.000000 1.000000 0.000000 0.000000 +0.000000 0.474946 0.000000 0.525054 + + +MOTIF YAGG DREME-2 + +# Word Pos Neg P-value E-value +# BEST YAGG 600 416 1.1e-016 5.1e-012 +# CAGG 441 304 1.5e-010 6.6e-006 +# UAGG 232 165 1.1e-004 4.7e+000 + +letter-probability matrix: alength= 4 w= 4 nsites= 793 E= 5.1e-012 +0.000000 0.692308 0.000000 0.307692 +1.000000 0.000000 0.000000 0.000000 +0.000000 0.000000 1.000000 0.000000 +0.000000 0.000000 1.000000 0.000000 + + +MOTIF GAAGAW DREME-3 + +# Word Pos Neg P-value E-value +# BEST GAAGAW 81 22 8.2e-010 3.4e-005 +# GAAGAU 45 7 2.4e-008 9.9e-004 +# GAAGAA 40 16 7.9e-004 3.3e+001 + +letter-probability matrix: alength= 4 w= 6 nsites= 89 E= 3.4e-005 +0.000000 0.000000 1.000000 0.000000 +1.000000 0.000000 0.000000 0.000000 +1.000000 0.000000 0.000000 0.000000 +0.000000 0.000000 1.000000 0.000000 +1.000000 0.000000 0.000000 0.000000 +0.494382 0.000000 0.000000 0.505618 + + +MOTIF SMUGGA DREME-4 + +# Word Pos Neg P-value E-value +# BEST SMUGGA 110 47 9.1e-008 3.7e-003 +# GAUGGA 22 6 1.7e-003 7.1e+001 +# GCUGGA 33 14 3.6e-003 1.5e+002 +# CCUGGA 32 15 8.6e-003 3.5e+002 +# CAUGGA 29 13 9.1e-003 3.7e+002 + +letter-probability matrix: alength= 4 w= 6 nsites= 119 E= 3.7e-003 +0.000000 0.529412 0.470588 0.000000 +0.428571 0.571429 0.000000 0.000000 +0.000000 0.000000 0.000000 1.000000 +0.000000 0.000000 1.000000 0.000000 +0.000000 0.000000 1.000000 0.000000 +1.000000 0.000000 0.000000 0.000000 + + +# Stopping reason: E-value threshold exceeded +# Running time: 13.95 seconds diff -r 793225b11202 -r b48e673af4e8 test-data/dreme_output_test1.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dreme_output_test1.xml Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,77 @@ + + + dreme -o ./dreme_test1_out -p dreme_test_sites.fa -norc -rna -s 1 + + + + + + + + + + + + + + + + + + + + none + + + 100 + 0.01 + 1 + ThinkPad-T450s + Thu May 03 13:22:29 CEST 2018 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 793225b11202 -r b48e673af4e8 test-data/dreme_output_test2.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dreme_output_test2.html Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,6119 @@ + + + + + DREME + + + + + + + + + + + + + + +
+

Help poup.

+ +
+ +
+

+ The name of the motif uses the IUPAC codes for nucleotides which has + a different letter to represent each of the 15 possible combinations. +

+

+ The name is itself a representation of the motif though the position + weight matrix is not directly equalivant as it is generated from the + sites found that matched the letters given in the name. +

+

+ + Read more about the MEME suite's use of the IUPAC alphabets. + + +

+ +
+ + +
+

The E-value is the enrichment p-value times the number of candidate + motifs tested.

+

The enrichment p-value is calculated using Fisher's Exact Test for + enrichment of the motif in the positive sequences.

+

Note that the counts used in Fisher's Exact Test are made after + erasing sites that match previously found motifs.

+ +
+
+

The E-value of the motif calculated without erasing the sites of + previously found motifs.

+ +
+
+

Show more information on the motif.

+ +
+
+

Submit your motif to another MEME Suite program or download your motif.

+
Supported Programs
+
+
Tomtom
+
Tomtom is a tool for searching for similar known motifs. +
+
MAST
+
MAST is a tool for searching biological sequence databases for + sequences that contain one or more of a group of known motifs. +
+
FIMO
+
FIMO is a tool for searching biological sequence databases for + sequences that contain one or more known motifs. +
+
GOMO
+
GOMO is a tool for identifying possible roles (Gene Ontology + terms) for DNA binding motifs. +
+
SpaMo
+
SpaMo is a tool for inferring possible transcription factor + complexes by finding motifs with enriched spacings. +
+
+ +
+
+

# positive sequences matching the motif / # positive sequences.

+

Note these counts are made after erasing sites that match previously + found motifs.

+ +
+
+

# negative sequences matching the motif / # negative sequences.

+

Note these counts are made after erasing sites that match previously + found motifs.

+ +
+
+

The p-value of Fisher's Exact Test for enrichment of the motif in + the positive sequences.

+

Note that the counts used in Fisher's Exact Test are made after + erasing sites that match previously found motifs.

+ +
+
+

The E-value is the motif p-value times the number of candidate motifs + tested.

+

Note that the p-value was calculated with counts made after + erasing sites that match previously found motifs.

+ +
+
+

The E-value of the motif calculated without erasing the sites of + previously found motifs.

+ +
+
+

All words matching the motif whose uncorrected p-value is less than + .

+ + +
+
+

# positive sequences with matches to the word / # positive sequences.

+

Note these counts are made after erasing sites that match previously + found motifs.

+ +
+
+

# negative sequences with matches to the word / # negative sequences.

+

Note these counts are made after erasing sites that match previously + found motifs.

+ +
+
+

The p-value of Fisher's Exact Test for enrichment of the word in + the positive sequences.

+

Note that the counts used in Fisher's Exact Test are made after + erasing sites that match previously found motifs.

+ +
+
+

The word p-value times the number of candidates tested.

+

Note that the p-value was calculated with counts made after + erasing sites that match previously found motifs.

+ +
+ +
+

The sequence file used by DREME to find the motifs.

+ +
+
+

The alphabet of the sequences.

+ +
+
+

The count of the sequences.

+ +
+ +
+

The name of the alphabet symbol.

+ +
+ +
+

The frequency of the alphabet symbol in the control dataset.

+ +
+ + + +
+
+ + +
+

Details

+ + + + + + + + + + + + + + + + + + + +
Positives
Negatives
P-value
E-value
Unerased E-value
+ / + + / +
+

Enriched Matching Words

+
+
+ + + + + + + +
+ +

+ For further information on how to interpret these results or to get a + copy of the MEME software please access + http://meme.nbcr.net. +

+

+ If you use DREME in your research please cite the following paper:
+ + Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", Bioinformatics, 27(12):1653-1659, 2011. + [full text] + +

+
+ +
+ Discovered Motifs +   |   + Inputs & Settings +   |   + Program information +
+ + +

Your browser does not support canvas!

+ + + + + +
+

Discovered Motifs

+ Next Top +
+
+

No motifs were discovered!

+
+ + +
+

Inputs & Settings

+ Previous Next Top +
+
+

Sequences

+ + + + + + + + + + +
Source
Alphabet
Sequence Count
+ +

Control Sequences

+ + + + + + + + +
Source
Sequence Count
+ +

Background

+ + +

Other Settings

+ + + + + + + + + + +
Strand Handling + This alphabet only has one strand + Only the given strand is processed + Both the given and reverse complement strands are processed +
# REs to Generalize
Shuffle Seed
E-value Threshold
Max Motif Count
Max Run Time
+ +
+ +
+ +
+
DREME version
+ + (Release date: )
+
+ +
+
Reference
+ + Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", Bioinformatics, 27(12):1653-1659, 2011. + [full text] + +
+
+
Command line
+ + +
+
+ + + diff -r 793225b11202 -r b48e673af4e8 test-data/dreme_output_test2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dreme_output_test2.txt Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,68 @@ +# DREME 4.12.0 +# command: dreme -o ./dreme_test2_out -p dreme_test_sites.fa -norc -rna -s 1 -e 1e-05 -g 100 -mink 4 -maxk 10 +# positives: 1000 from dreme_test_sites.fa (Thu Apr 26 15:09:03 CEST 2018) +# negatives: 1000 from shuffled positives +# host: ThinkPad-T450s +# when: Thu May 03 13:22:11 CEST 2018 + +MEME version 4.12.0 + +ALPHABET "RNA" RNA-LIKE +A "Adenine" CC0000 +C "Cytosine" 0000CC +G "Guanine" FFB300 +U "Uracil" 008000 +N "Any base" = ACGU +X = ACGU +. = ACGU +V "Not U" = ACG +H "Not G" = ACU +D "Not C" = AGU +B "Not A" = CGU +M "Amino" = AC +R "Purine" = AG +W "Weak" = AU +S "Strong" = CG +Y "Pyrimidine" = CU +K "Keto" = GU +T = U +END ALPHABET + +Background letter frequencies (from dataset): +A 0.221 C 0.245 G 0.221 U 0.312 + + +MOTIF UUYUCY DREME-1 + +# Word Pos Neg P-value E-value +# BEST UUYUCY 387 210 2.6e-018 3.3e-013 +# UUUUCC 147 75 1.8e-007 2.2e-002 +# UUUUCU 155 94 2.2e-005 2.8e+000 +# UUCUCU 94 51 1.3e-004 1.7e+001 +# UUCUCC 75 42 1.1e-003 1.4e+002 + +letter-probability matrix: alength= 4 w= 6 nsites= 459 E= 3.3e-013 +0.000000 0.000000 0.000000 1.000000 +0.000000 0.000000 0.000000 1.000000 +0.000000 0.294118 0.000000 0.705882 +0.000000 0.000000 0.000000 1.000000 +0.000000 1.000000 0.000000 0.000000 +0.000000 0.474946 0.000000 0.525054 + + +MOTIF YAGG DREME-2 + +# Word Pos Neg P-value E-value +# BEST YAGG 600 416 1.1e-016 1.4e-011 +# CAGG 441 304 1.5e-010 1.8e-005 +# UAGG 232 165 1.1e-004 1.3e+001 + +letter-probability matrix: alength= 4 w= 4 nsites= 793 E= 1.4e-011 +0.000000 0.692308 0.000000 0.307692 +1.000000 0.000000 0.000000 0.000000 +0.000000 0.000000 1.000000 0.000000 +0.000000 0.000000 1.000000 0.000000 + + +# Stopping reason: E-value threshold exceeded +# Running time: 15.97 seconds diff -r 793225b11202 -r b48e673af4e8 test-data/dreme_output_test2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dreme_output_test2.xml Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,55 @@ + + + dreme -o ./dreme_test2_out -p dreme_test_sites.fa -norc -rna -s 1 -e 1e-05 -g 100 -mink 4 -maxk 10 + + + + + + + + + + + + + + + + + + + + none + + + 100 + 0.01 + 1 + ThinkPad-T450s + Thu May 03 13:22:11 CEST 2018 + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 793225b11202 -r b48e673af4e8 test-data/fimo_background_probs_hsa_chrM.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_background_probs_hsa_chrM.txt Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,7 @@ +# 0-order Markov frequencies from file hsa_chrM.fa +# seqs: 1 min: 16569 max: 16569 avg: 16569.0 sum: 16569 alph: DNA +# order 0 +A 3.093e-01 +C 3.127e-01 +G 1.309e-01 +T 2.471e-01 diff -r 793225b11202 -r b48e673af4e8 test-data/fimo_output_almost-gff_1.txt --- a/test-data/fimo_output_almost-gff_1.txt Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -##gff-version 3 -phiX174 fimo polypeptide_motif 1388 1398 102 + . Name=1;ID=1-1-phiX174;pvalue=6.36e-11;qvalue= 1.25e-09;sequence=AATATCTATAA; -phiX174 fimo polypeptide_motif 847 857 102 + . Name=1;ID=1-2-phiX174;pvalue=7.02e-11;qvalue= 1.25e-09;sequence=AATGTCTAAAG; -phiX174 fimo polypeptide_motif 2301 2311 99.6 + . Name=1;ID=1-3-phiX174;pvalue=1.08e-10;qvalue= 1.29e-09;sequence=AGGTTATAACG; -phiX174 fimo polypeptide_motif 5063 5073 95.6 + . Name=1;ID=1-4-phiX174;pvalue=2.73e-10;qvalue= 2.25e-09;sequence=AGGAGCTAAAG; -phiX174 fimo polypeptide_motif 989 999 95 + . Name=1;ID=1-5-phiX174;pvalue=3.15e-10;qvalue= 2.25e-09;sequence=TGAGGATAAAT; -phiX174 fimo polypeptide_motif 4713 4723 91.1 + . Name=1;ID=1-6-phiX174;pvalue=7.74e-10;qvalue= 3.48e-09;sequence=GACTGCTATCA; -phiX174 fimo polypeptide_motif 5048 5058 90.7 + . Name=1;ID=1-7-phiX174;pvalue=8.51e-10;qvalue= 3.48e-09;sequence=TGCTGCTAAAG; -phiX174 fimo polypeptide_motif 855 865 90.6 + . Name=1;ID=1-8-phiX174;pvalue=8.64e-10;qvalue= 3.48e-09;sequence=AAGGTAAAAAA; -phiX174 fimo polypeptide_motif 3155 3165 90.1 + . Name=1;ID=1-9-phiX174;pvalue=9.76e-10;qvalue= 3.48e-09;sequence=TATGGCTAAAG; -phiX174 fimo polypeptide_motif 5009 5019 90.1 + . Name=1;ID=1-10-phiX174;pvalue=9.76e-10;qvalue= 3.48e-09;sequence=TGTGGCTAAAT; -phiX174 fimo polypeptide_motif 814 824 88.9 + . Name=1;ID=1-11-phiX174;pvalue=1.28e-09;qvalue= 4.14e-09;sequence=TGCGTCAAAAA; -phiX174 fimo polypeptide_motif 2832 2842 88.5 + . Name=1;ID=1-12-phiX174;pvalue=1.42e-09;qvalue= 4.23e-09;sequence=TTGGTCTAACT; -phiX174 fimo polypeptide_motif 3830 3840 87.7 + . Name=1;ID=1-13-phiX174;pvalue=1.7e-09;qvalue= 4.68e-09;sequence=TATTGATAAAG; -phiX174 fimo polypeptide_motif 3560 3570 87.2 + . Name=1;ID=1-14-phiX174;pvalue=1.89e-09;qvalue= 4.82e-09;sequence=TGCGTCTATTA; -phiX174 fimo polypeptide_motif 2882 2892 86.4 + . Name=1;ID=1-15-phiX174;pvalue=2.29e-09;qvalue= 5.46e-09;sequence=AGGTTATTAAA; -phiX174 fimo polypeptide_motif 4453 4463 85.9 + . Name=1;ID=1-16-phiX174;pvalue=2.58e-09;qvalue= 5.75e-09;sequence=AAGGTATTAAG; -phiX174 fimo polypeptide_motif 2493 2503 85.1 + . Name=1;ID=1-17-phiX174;pvalue=3.06e-09;qvalue= 5.79e-09;sequence=GACACCTAAAG; -phiX174 fimo polypeptide_motif 4104 4114 85.1 + . Name=1;ID=1-18-phiX174;pvalue=3.08e-09;qvalue= 5.79e-09;sequence=GGCTTCCATAA; -phiX174 fimo polypeptide_motif 4955 4965 85.1 + . Name=1;ID=1-19-phiX174;pvalue=3.08e-09;qvalue= 5.79e-09;sequence=TGATGCTAAAG; -phiX174 fimo polypeptide_motif 1885 1895 84.4 + . Name=1;ID=1-20-phiX174;pvalue=3.61e-09;qvalue= 6.45e-09;sequence=TGCGACTAAAG; -phiX174 fimo polypeptide_motif 3376 3386 84.2 + . Name=1;ID=1-21-phiX174;pvalue=3.81e-09;qvalue= 6.48e-09;sequence=AGAATCAAAAA; -phiX174 fimo polypeptide_motif 52 62 83.9 + . Name=1;ID=1-22-phiX174;pvalue=4.06e-09;qvalue= 6.58e-09;sequence=TGAGTCGAAAA; -phiX174 fimo polypeptide_motif 1390 1400 83.7 + . Name=1;ID=1-23-phiX174;pvalue=4.26e-09;qvalue= 6.61e-09;sequence=TATCTATAACA; -phiX174 fimo polypeptide_motif 2017 2027 83.4 + . Name=1;ID=1-24-phiX174;pvalue=4.6e-09;qvalue= 6.85e-09;sequence=TTCGTCTAAGA; -phiX174 fimo polypeptide_motif 1000 1010 83.1 + . Name=1;ID=1-25-phiX174;pvalue=4.88e-09;qvalue= 6.97e-09;sequence=TATGTCTAATA; -phiX174 fimo polypeptide_motif 1555 1565 82.5 + . Name=1;ID=1-26-phiX174;pvalue=5.58e-09;qvalue= 7.37e-09;sequence=GACTTCTACCA; -phiX174 fimo polypeptide_motif 4430 4440 82.5 + . Name=1;ID=1-27-phiX174;pvalue=5.62e-09;qvalue= 7.37e-09;sequence=TGAGTATAATT; -phiX174 fimo polypeptide_motif 1927 1937 82.3 + . Name=1;ID=1-28-phiX174;pvalue=5.82e-09;qvalue= 7.37e-09;sequence=GACTTATACCG; -phiX174 fimo polypeptide_motif 2981 2991 82.1 + . Name=1;ID=1-29-phiX174;pvalue=6.13e-09;qvalue= 7.37e-09;sequence=CATGTCTAAAT; -phiX174 fimo polypeptide_motif 4203 4213 82 + . Name=1;ID=1-30-phiX174;pvalue=6.34e-09;qvalue= 7.37e-09;sequence=GACGGCCATAA; -phiX174 fimo polypeptide_motif 1669 1679 81.9 + . Name=1;ID=1-31-phiX174;pvalue=6.4e-09;qvalue= 7.37e-09;sequence=TGGAGGTAAAA; -phiX174 fimo polypeptide_motif 3260 3270 81.5 + . Name=1;ID=1-32-phiX174;pvalue=7.01e-09;qvalue= 7.82e-09;sequence=CGCTGATAAAG; -phiX174 fimo polypeptide_motif 3047 3057 81.3 + . Name=1;ID=1-33-phiX174;pvalue=7.4e-09;qvalue= 7.85e-09;sequence=TACCGATAACA; -phiX174 fimo polypeptide_motif 4176 4186 81.2 + . Name=1;ID=1-34-phiX174;pvalue=7.6e-09;qvalue= 7.85e-09;sequence=GAGTTCGATAA; -phiX174 fimo polypeptide_motif 4118 4128 81.1 + . Name=1;ID=1-35-phiX174;pvalue=7.7e-09;qvalue= 7.85e-09;sequence=GATGGATAACC; -phiX174 fimo polypeptide_motif 5370 5380 80.9 + . Name=1;ID=1-36-phiX174;pvalue=8.03e-09;qvalue= 7.87e-09;sequence=GGCGTATCCAA; -phiX174 fimo polypeptide_motif 1242 1252 80.5 + . Name=1;ID=1-37-phiX174;pvalue=8.94e-09;qvalue= 7.87e-09;sequence=AGTGGATTAAG; -phiX174 fimo polypeptide_motif 2583 2593 80.5 + . Name=1;ID=1-38-phiX174;pvalue=8.94e-09;qvalue= 7.87e-09;sequence=TACATCTGTCA; -phiX174 fimo polypeptide_motif 698 708 80.4 + . Name=1;ID=1-39-phiX174;pvalue=9.13e-09;qvalue= 7.87e-09;sequence=TACGGAAAACA; -phiX174 fimo polypeptide_motif 2299 2309 80.3 + . Name=1;ID=1-40-phiX174;pvalue=9.26e-09;qvalue= 7.87e-09;sequence=TGAGGTTATAA; -phiX174 fimo polypeptide_motif 4189 4199 80.1 + . Name=1;ID=1-41-phiX174;pvalue=9.69e-09;qvalue= 7.87e-09;sequence=GTGATATGTAT; -phiX174 fimo polypeptide_motif 275 285 80.1 + . Name=1;ID=1-42-phiX174;pvalue=9.85e-09;qvalue= 7.87e-09;sequence=GGTTTAGATAT; -phiX174 fimo polypeptide_motif 1801 1811 80 + . Name=1;ID=1-43-phiX174;pvalue=1e-08;qvalue= 7.87e-09;sequence=GACCTATAAAC; -phiX174 fimo polypeptide_motif 1386 1396 79.9 + . Name=1;ID=1-44-phiX174;pvalue=1.03e-08;qvalue= 7.87e-09;sequence=TGAATATCTAT; -phiX174 fimo polypeptide_motif 1303 1313 79.8 + . Name=1;ID=1-45-phiX174;pvalue=1.03e-08;qvalue= 7.87e-09;sequence=TGGTTATATTG; -phiX174 fimo polypeptide_motif 3772 3782 79.8 + . Name=1;ID=1-46-phiX174;pvalue=1.04e-08;qvalue= 7.87e-09;sequence=AGGATATTTCT; -phiX174 fimo polypeptide_motif 1288 1298 79.8 + . Name=1;ID=1-47-phiX174;pvalue=1.04e-08;qvalue= 7.87e-09;sequence=GACTGTTAACA; -phiX174 fimo polypeptide_motif 2577 2587 79.7 + . Name=1;ID=1-48-phiX174;pvalue=1.08e-08;qvalue= 7.87e-09;sequence=GATGGATACAT; -phiX174 fimo polypeptide_motif 937 947 79.6 + . Name=1;ID=1-49-phiX174;pvalue=1.08e-08;qvalue= 7.87e-09;sequence=TTGGTATGTAG; -phiX174 fimo polypeptide_motif 904 914 79.5 + . Name=1;ID=1-50-phiX174;pvalue=1.11e-08;qvalue= 7.93e-09;sequence=AGGTACTAAAG; -phiX174 fimo polypeptide_motif 2279 2289 79.4 + . Name=1;ID=1-51-phiX174;pvalue=1.13e-08;qvalue= 7.93e-09;sequence=TCGTGATAAAA; -phiX174 fimo polypeptide_motif 3164 3174 79.3 + . Name=1;ID=1-52-phiX174;pvalue=1.16e-08;qvalue= 7.98e-09;sequence=AGCTGGTAAAG; -phiX174 fimo polypeptide_motif 24 34 79.1 + . Name=1;ID=1-53-phiX174;pvalue=1.23e-08;qvalue= 8.24e-09;sequence=AGAAGTTAACA; -phiX174 fimo polypeptide_motif 838 848 78.9 + . Name=1;ID=1-54-phiX174;pvalue=1.27e-08;qvalue= 8.24e-09;sequence=GAGTGATGTAA; -phiX174 fimo polypeptide_motif 853 863 78.9 + . Name=1;ID=1-55-phiX174;pvalue=1.27e-08;qvalue= 8.24e-09;sequence=TAAAGGTAAAA; -phiX174 fimo polypeptide_motif 1984 1994 78.6 + . Name=1;ID=1-56-phiX174;pvalue=1.36e-08;qvalue= 8.68e-09;sequence=AATTTCTATGA; -phiX174 fimo polypeptide_motif 1 11 78.3 + . Name=1;ID=1-57-phiX174;pvalue=1.46e-08;qvalue= 9.05e-09;sequence=GAGTTTTATCG; -phiX174 fimo polypeptide_motif 4307 4317 78.3 + . Name=1;ID=1-58-phiX174;pvalue=1.47e-08;qvalue= 9.05e-09;sequence=TATTAATAACA; -phiX174 fimo polypeptide_motif 4303 4313 78.2 + . Name=1;ID=1-59-phiX174;pvalue=1.52e-08;qvalue= 9.19e-09;sequence=TTGATATTAAT; -phiX174 fimo polypeptide_motif 5033 5043 78 + . Name=1;ID=1-60-phiX174;pvalue=1.58e-08;qvalue= 9.41e-09;sequence=GTCAGATATGG; -phiX174 fimo polypeptide_motif 2579 2589 77.6 + . Name=1;ID=1-61-phiX174;pvalue=1.73e-08;qvalue= 1.01e-08;sequence=TGGATACATCT; -phiX174 fimo polypeptide_motif 322 332 77.4 + . Name=1;ID=1-62-phiX174;pvalue=1.82e-08;qvalue= 1.05e-08;sequence=GACATTTTAAA; -phiX174 fimo polypeptide_motif 5001 5011 76.8 + . Name=1;ID=1-63-phiX174;pvalue=2.09e-08;qvalue= 1.19e-08;sequence=GGTTTCTATGT; -phiX174 fimo polypeptide_motif 4217 4227 76.7 + . Name=1;ID=1-64-phiX174;pvalue=2.15e-08;qvalue= 1.2e-08;sequence=TGCTTCTGACG; -phiX174 fimo polypeptide_motif 4262 4272 76.6 + . Name=1;ID=1-65-phiX174;pvalue=2.18e-08;qvalue= 1.2e-08;sequence=AATGGATGAAT; -phiX174 fimo polypeptide_motif 3569 3579 76.5 + . Name=1;ID=1-66-phiX174;pvalue=2.26e-08;qvalue= 1.22e-08;sequence=TATGGAAAACA; -phiX174 fimo polypeptide_motif 194 204 76.4 + . Name=1;ID=1-67-phiX174;pvalue=2.29e-08;qvalue= 1.22e-08;sequence=ATCAACTAACG; -phiX174 fimo polypeptide_motif 131 141 76 + . Name=1;ID=1-68-phiX174;pvalue=2.49e-08;qvalue= 1.31e-08;sequence=AAATGAGAAAA; -phiX174 fimo polypeptide_motif 1491 1501 75.9 + . Name=1;ID=1-69-phiX174;pvalue=2.55e-08;qvalue= 1.32e-08;sequence=GCCATCTCAAA; -phiX174 fimo polypeptide_motif 434 444 75.7 + . Name=1;ID=1-70-phiX174;pvalue=2.67e-08;qvalue= 1.36e-08;sequence=GGCCTCTATTA; -phiX174 fimo polypeptide_motif 4565 4575 75.6 + . Name=1;ID=1-71-phiX174;pvalue=2.73e-08;qvalue= 1.36e-08;sequence=TTGGTTTATCG; -phiX174 fimo polypeptide_motif 102 112 75.6 + . Name=1;ID=1-72-phiX174;pvalue=2.75e-08;qvalue= 1.36e-08;sequence=GAATTAAATCG; -phiX174 fimo polypeptide_motif 903 913 75.5 + . Name=1;ID=1-73-phiX174;pvalue=2.82e-08;qvalue= 1.38e-08;sequence=GAGGTACTAAA; -phiX174 fimo polypeptide_motif 4748 4758 75.2 + . Name=1;ID=1-74-phiX174;pvalue=3.01e-08;qvalue= 1.45e-08;sequence=TACAGCTAATG; -phiX174 fimo polypeptide_motif 2622 2632 75 + . Name=1;ID=1-75-phiX174;pvalue=3.16e-08;qvalue= 1.5e-08;sequence=TGCTGATATTG; -phiX174 fimo polypeptide_motif 467 477 74.7 + . Name=1;ID=1-76-phiX174;pvalue=3.35e-08;qvalue= 1.57e-08;sequence=TTTGGATTTAA; -phiX174 fimo polypeptide_motif 4033 4043 74.6 + . Name=1;ID=1-77-phiX174;pvalue=3.44e-08;qvalue= 1.58e-08;sequence=AGCGTATCGAG; -phiX174 fimo polypeptide_motif 1348 1358 74.6 + . Name=1;ID=1-78-phiX174;pvalue=3.46e-08;qvalue= 1.58e-08;sequence=TACCAATAAAA; -phiX174 fimo polypeptide_motif 239 249 74.4 + . Name=1;ID=1-79-phiX174;pvalue=3.62e-08;qvalue= 1.64e-08;sequence=AGTGGCTTAAT; -phiX174 fimo polypeptide_motif 500 510 74.1 + . Name=1;ID=1-80-phiX174;pvalue=3.84e-08;qvalue= 1.71e-08;sequence=GACGAGTAACA; -phiX174 fimo polypeptide_motif 3001 3011 74 + . Name=1;ID=1-81-phiX174;pvalue=3.93e-08;qvalue= 1.73e-08;sequence=GCGGTCAAAAA; -phiX174 fimo polypeptide_motif 3776 3786 74 + . Name=1;ID=1-82-phiX174;pvalue=3.98e-08;qvalue= 1.73e-08;sequence=TATTTCTAATG; -phiX174 fimo polypeptide_motif 2026 2036 73.9 + . Name=1;ID=1-83-phiX174;pvalue=4.06e-08;qvalue= 1.75e-08;sequence=GAAGTTTAAGA; -phiX174 fimo polypeptide_motif 4237 4247 73.8 + . Name=1;ID=1-84-phiX174;pvalue=4.12e-08;qvalue= 1.75e-08;sequence=AGTTTGTATCT; -phiX174 fimo polypeptide_motif 803 813 73.7 + . Name=1;ID=1-85-phiX174;pvalue=4.24e-08;qvalue= 1.78e-08;sequence=AGAAGAAAACG; -phiX174 fimo polypeptide_motif 3770 3780 73.6 + . Name=1;ID=1-86-phiX174;pvalue=4.35e-08;qvalue= 1.81e-08;sequence=AAAGGATATTT; -phiX174 fimo polypeptide_motif 3429 3439 73.5 + . Name=1;ID=1-87-phiX174;pvalue=4.45e-08;qvalue= 1.82e-08;sequence=GAGATGCAAAA; -phiX174 fimo polypeptide_motif 99 109 73.5 + . Name=1;ID=1-88-phiX174;pvalue=4.48e-08;qvalue= 1.82e-08;sequence=TACGAATTAAA; -phiX174 fimo polypeptide_motif 67 77 73.2 + . Name=1;ID=1-89-phiX174;pvalue=4.78e-08;qvalue= 1.92e-08;sequence=TCTTGATAAAG; -phiX174 fimo polypeptide_motif 5332 5342 72.9 + . Name=1;ID=1-90-phiX174;pvalue=5.13e-08;qvalue= 2.01e-08;sequence=ATCTGCTCAAA; -phiX174 fimo polypeptide_motif 277 287 72.9 + . Name=1;ID=1-91-phiX174;pvalue=5.14e-08;qvalue= 2.01e-08;sequence=TTTAGATATGA; -phiX174 fimo polypeptide_motif 4338 4348 72.8 + . Name=1;ID=1-92-phiX174;pvalue=5.18e-08;qvalue= 2.01e-08;sequence=GGGGACGAAAA; -phiX174 fimo polypeptide_motif 3812 3822 72.8 + . Name=1;ID=1-93-phiX174;pvalue=5.28e-08;qvalue= 2.03e-08;sequence=GGTTGATATTT; -phiX174 fimo polypeptide_motif 1909 1919 72.6 + . Name=1;ID=1-94-phiX174;pvalue=5.51e-08;qvalue= 2.08e-08;sequence=TAACGCTAAAG; -phiX174 fimo polypeptide_motif 3000 3010 72.6 + . Name=1;ID=1-95-phiX174;pvalue=5.54e-08;qvalue= 2.08e-08;sequence=GGCGGTCAAAA; -phiX174 fimo polypeptide_motif 3891 3901 72.4 + . Name=1;ID=1-96-phiX174;pvalue=5.75e-08;qvalue= 2.11e-08;sequence=ATTGGCTCTAA; -phiX174 fimo polypeptide_motif 3079 3089 72.4 + . Name=1;ID=1-97-phiX174;pvalue=5.76e-08;qvalue= 2.11e-08;sequence=CTGGTATTAAA; -phiX174 fimo polypeptide_motif 37 47 72.4 + . Name=1;ID=1-98-phiX174;pvalue=5.79e-08;qvalue= 2.11e-08;sequence=TTCGGATATTT; -phiX174 fimo polypeptide_motif 380 390 72.2 + . Name=1;ID=1-99-phiX174;pvalue=6.01e-08;qvalue= 2.17e-08;sequence=GTAAGAAATCA; diff -r 793225b11202 -r b48e673af4e8 test-data/fimo_output_almost-gff_2.txt --- a/test-data/fimo_output_almost-gff_2.txt Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -##gff-version 3 -phiX174 fimo polypeptide_motif 1388 1398 102 + . Name=1;ID=1-1-phiX174;pvalue=6.36e-11;sequence=AATATCTATAA; -phiX174 fimo polypeptide_motif 847 857 102 + . Name=1;ID=1-2-phiX174;pvalue=7.02e-11;sequence=AATGTCTAAAG; -phiX174 fimo polypeptide_motif 2301 2311 99.6 + . Name=1;ID=1-3-phiX174;pvalue=1.08e-10;sequence=AGGTTATAACG; -phiX174 fimo polypeptide_motif 5063 5073 95.6 + . Name=1;ID=1-4-phiX174;pvalue=2.73e-10;sequence=AGGAGCTAAAG; -phiX174 fimo polypeptide_motif 989 999 95 + . Name=1;ID=1-5-phiX174;pvalue=3.15e-10;sequence=TGAGGATAAAT; -phiX174 fimo polypeptide_motif 4713 4723 91.1 + . Name=1;ID=1-6-phiX174;pvalue=7.74e-10;sequence=GACTGCTATCA; -phiX174 fimo polypeptide_motif 5048 5058 90.7 + . Name=1;ID=1-7-phiX174;pvalue=8.51e-10;sequence=TGCTGCTAAAG; -phiX174 fimo polypeptide_motif 855 865 90.6 + . Name=1;ID=1-8-phiX174;pvalue=8.64e-10;sequence=AAGGTAAAAAA; -phiX174 fimo polypeptide_motif 3155 3165 90.1 + . Name=1;ID=1-9-phiX174;pvalue=9.76e-10;sequence=TATGGCTAAAG; -phiX174 fimo polypeptide_motif 5009 5019 90.1 + . Name=1;ID=1-10-phiX174;pvalue=9.76e-10;sequence=TGTGGCTAAAT; -phiX174 fimo polypeptide_motif 814 824 88.9 + . Name=1;ID=1-11-phiX174;pvalue=1.28e-09;sequence=TGCGTCAAAAA; -phiX174 fimo polypeptide_motif 2832 2842 88.5 + . Name=1;ID=1-12-phiX174;pvalue=1.42e-09;sequence=TTGGTCTAACT; -phiX174 fimo polypeptide_motif 3830 3840 87.7 + . Name=1;ID=1-13-phiX174;pvalue=1.7e-09;sequence=TATTGATAAAG; -phiX174 fimo polypeptide_motif 3560 3570 87.2 + . Name=1;ID=1-14-phiX174;pvalue=1.89e-09;sequence=TGCGTCTATTA; -phiX174 fimo polypeptide_motif 2882 2892 86.4 + . Name=1;ID=1-15-phiX174;pvalue=2.29e-09;sequence=AGGTTATTAAA; -phiX174 fimo polypeptide_motif 4453 4463 85.9 + . Name=1;ID=1-16-phiX174;pvalue=2.58e-09;sequence=AAGGTATTAAG; -phiX174 fimo polypeptide_motif 2493 2503 85.1 + . Name=1;ID=1-17-phiX174;pvalue=3.06e-09;sequence=GACACCTAAAG; -phiX174 fimo polypeptide_motif 4104 4114 85.1 + . Name=1;ID=1-18-phiX174;pvalue=3.08e-09;sequence=GGCTTCCATAA; -phiX174 fimo polypeptide_motif 4955 4965 85.1 + . Name=1;ID=1-19-phiX174;pvalue=3.08e-09;sequence=TGATGCTAAAG; -phiX174 fimo polypeptide_motif 1885 1895 84.4 + . Name=1;ID=1-20-phiX174;pvalue=3.61e-09;sequence=TGCGACTAAAG; -phiX174 fimo polypeptide_motif 3376 3386 84.2 + . Name=1;ID=1-21-phiX174;pvalue=3.81e-09;sequence=AGAATCAAAAA; -phiX174 fimo polypeptide_motif 52 62 83.9 + . Name=1;ID=1-22-phiX174;pvalue=4.06e-09;sequence=TGAGTCGAAAA; -phiX174 fimo polypeptide_motif 1390 1400 83.7 + . Name=1;ID=1-23-phiX174;pvalue=4.26e-09;sequence=TATCTATAACA; -phiX174 fimo polypeptide_motif 2017 2027 83.4 + . Name=1;ID=1-24-phiX174;pvalue=4.6e-09;sequence=TTCGTCTAAGA; -phiX174 fimo polypeptide_motif 1000 1010 83.1 + . Name=1;ID=1-25-phiX174;pvalue=4.88e-09;sequence=TATGTCTAATA; -phiX174 fimo polypeptide_motif 1555 1565 82.5 + . Name=1;ID=1-26-phiX174;pvalue=5.58e-09;sequence=GACTTCTACCA; -phiX174 fimo polypeptide_motif 4430 4440 82.5 + . Name=1;ID=1-27-phiX174;pvalue=5.62e-09;sequence=TGAGTATAATT; -phiX174 fimo polypeptide_motif 1927 1937 82.3 + . Name=1;ID=1-28-phiX174;pvalue=5.82e-09;sequence=GACTTATACCG; -phiX174 fimo polypeptide_motif 2981 2991 82.1 + . Name=1;ID=1-29-phiX174;pvalue=6.13e-09;sequence=CATGTCTAAAT; -phiX174 fimo polypeptide_motif 4203 4213 82 + . Name=1;ID=1-30-phiX174;pvalue=6.34e-09;sequence=GACGGCCATAA; -phiX174 fimo polypeptide_motif 1669 1679 81.9 + . Name=1;ID=1-31-phiX174;pvalue=6.4e-09;sequence=TGGAGGTAAAA; -phiX174 fimo polypeptide_motif 3260 3270 81.5 + . Name=1;ID=1-32-phiX174;pvalue=7.01e-09;sequence=CGCTGATAAAG; -phiX174 fimo polypeptide_motif 3047 3057 81.3 + . Name=1;ID=1-33-phiX174;pvalue=7.4e-09;sequence=TACCGATAACA; -phiX174 fimo polypeptide_motif 4176 4186 81.2 + . Name=1;ID=1-34-phiX174;pvalue=7.6e-09;sequence=GAGTTCGATAA; -phiX174 fimo polypeptide_motif 4118 4128 81.1 + . Name=1;ID=1-35-phiX174;pvalue=7.7e-09;sequence=GATGGATAACC; -phiX174 fimo polypeptide_motif 5370 5380 80.9 + . Name=1;ID=1-36-phiX174;pvalue=8.03e-09;sequence=GGCGTATCCAA; -phiX174 fimo polypeptide_motif 1242 1252 80.5 + . Name=1;ID=1-37-phiX174;pvalue=8.94e-09;sequence=AGTGGATTAAG; -phiX174 fimo polypeptide_motif 2583 2593 80.5 + . Name=1;ID=1-38-phiX174;pvalue=8.94e-09;sequence=TACATCTGTCA; -phiX174 fimo polypeptide_motif 698 708 80.4 + . Name=1;ID=1-39-phiX174;pvalue=9.13e-09;sequence=TACGGAAAACA; -phiX174 fimo polypeptide_motif 2299 2309 80.3 + . Name=1;ID=1-40-phiX174;pvalue=9.26e-09;sequence=TGAGGTTATAA; -phiX174 fimo polypeptide_motif 4189 4199 80.1 + . Name=1;ID=1-41-phiX174;pvalue=9.69e-09;sequence=GTGATATGTAT; -phiX174 fimo polypeptide_motif 275 285 80.1 + . Name=1;ID=1-42-phiX174;pvalue=9.85e-09;sequence=GGTTTAGATAT; -phiX174 fimo polypeptide_motif 1801 1811 80 + . Name=1;ID=1-43-phiX174;pvalue=1e-08;sequence=GACCTATAAAC; -phiX174 fimo polypeptide_motif 1386 1396 79.9 + . Name=1;ID=1-44-phiX174;pvalue=1.03e-08;sequence=TGAATATCTAT; -phiX174 fimo polypeptide_motif 1303 1313 79.8 + . Name=1;ID=1-45-phiX174;pvalue=1.03e-08;sequence=TGGTTATATTG; -phiX174 fimo polypeptide_motif 3772 3782 79.8 + . Name=1;ID=1-46-phiX174;pvalue=1.04e-08;sequence=AGGATATTTCT; -phiX174 fimo polypeptide_motif 1288 1298 79.8 + . Name=1;ID=1-47-phiX174;pvalue=1.04e-08;sequence=GACTGTTAACA; -phiX174 fimo polypeptide_motif 2577 2587 79.7 + . Name=1;ID=1-48-phiX174;pvalue=1.08e-08;sequence=GATGGATACAT; -phiX174 fimo polypeptide_motif 937 947 79.6 + . Name=1;ID=1-49-phiX174;pvalue=1.08e-08;sequence=TTGGTATGTAG; -phiX174 fimo polypeptide_motif 904 914 79.5 + . Name=1;ID=1-50-phiX174;pvalue=1.11e-08;sequence=AGGTACTAAAG; -phiX174 fimo polypeptide_motif 2279 2289 79.4 + . Name=1;ID=1-51-phiX174;pvalue=1.13e-08;sequence=TCGTGATAAAA; -phiX174 fimo polypeptide_motif 3164 3174 79.3 + . Name=1;ID=1-52-phiX174;pvalue=1.16e-08;sequence=AGCTGGTAAAG; -phiX174 fimo polypeptide_motif 24 34 79.1 + . Name=1;ID=1-53-phiX174;pvalue=1.23e-08;sequence=AGAAGTTAACA; -phiX174 fimo polypeptide_motif 838 848 78.9 + . Name=1;ID=1-54-phiX174;pvalue=1.27e-08;sequence=GAGTGATGTAA; -phiX174 fimo polypeptide_motif 853 863 78.9 + . Name=1;ID=1-55-phiX174;pvalue=1.27e-08;sequence=TAAAGGTAAAA; -phiX174 fimo polypeptide_motif 1984 1994 78.6 + . Name=1;ID=1-56-phiX174;pvalue=1.36e-08;sequence=AATTTCTATGA; -phiX174 fimo polypeptide_motif 1 11 78.3 + . Name=1;ID=1-57-phiX174;pvalue=1.46e-08;sequence=GAGTTTTATCG; -phiX174 fimo polypeptide_motif 4307 4317 78.3 + . Name=1;ID=1-58-phiX174;pvalue=1.47e-08;sequence=TATTAATAACA; -phiX174 fimo polypeptide_motif 4303 4313 78.2 + . Name=1;ID=1-59-phiX174;pvalue=1.52e-08;sequence=TTGATATTAAT; -phiX174 fimo polypeptide_motif 5033 5043 78 + . Name=1;ID=1-60-phiX174;pvalue=1.58e-08;sequence=GTCAGATATGG; -phiX174 fimo polypeptide_motif 2579 2589 77.6 + . Name=1;ID=1-61-phiX174;pvalue=1.73e-08;sequence=TGGATACATCT; -phiX174 fimo polypeptide_motif 322 332 77.4 + . Name=1;ID=1-62-phiX174;pvalue=1.82e-08;sequence=GACATTTTAAA; -phiX174 fimo polypeptide_motif 5001 5011 76.8 + . Name=1;ID=1-63-phiX174;pvalue=2.09e-08;sequence=GGTTTCTATGT; -phiX174 fimo polypeptide_motif 4217 4227 76.7 + . Name=1;ID=1-64-phiX174;pvalue=2.15e-08;sequence=TGCTTCTGACG; -phiX174 fimo polypeptide_motif 4262 4272 76.6 + . Name=1;ID=1-65-phiX174;pvalue=2.18e-08;sequence=AATGGATGAAT; -phiX174 fimo polypeptide_motif 3569 3579 76.5 + . Name=1;ID=1-66-phiX174;pvalue=2.26e-08;sequence=TATGGAAAACA; -phiX174 fimo polypeptide_motif 194 204 76.4 + . Name=1;ID=1-67-phiX174;pvalue=2.29e-08;sequence=ATCAACTAACG; -phiX174 fimo polypeptide_motif 131 141 76 + . Name=1;ID=1-68-phiX174;pvalue=2.49e-08;sequence=AAATGAGAAAA; -phiX174 fimo polypeptide_motif 1491 1501 75.9 + . Name=1;ID=1-69-phiX174;pvalue=2.55e-08;sequence=GCCATCTCAAA; -phiX174 fimo polypeptide_motif 434 444 75.7 + . Name=1;ID=1-70-phiX174;pvalue=2.67e-08;sequence=GGCCTCTATTA; -phiX174 fimo polypeptide_motif 4565 4575 75.6 + . Name=1;ID=1-71-phiX174;pvalue=2.73e-08;sequence=TTGGTTTATCG; -phiX174 fimo polypeptide_motif 102 112 75.6 + . Name=1;ID=1-72-phiX174;pvalue=2.75e-08;sequence=GAATTAAATCG; -phiX174 fimo polypeptide_motif 903 913 75.5 + . Name=1;ID=1-73-phiX174;pvalue=2.82e-08;sequence=GAGGTACTAAA; -phiX174 fimo polypeptide_motif 4748 4758 75.2 + . Name=1;ID=1-74-phiX174;pvalue=3.01e-08;sequence=TACAGCTAATG; -phiX174 fimo polypeptide_motif 2622 2632 75 + . Name=1;ID=1-75-phiX174;pvalue=3.16e-08;sequence=TGCTGATATTG; -phiX174 fimo polypeptide_motif 467 477 74.7 + . Name=1;ID=1-76-phiX174;pvalue=3.35e-08;sequence=TTTGGATTTAA; -phiX174 fimo polypeptide_motif 4033 4043 74.6 + . Name=1;ID=1-77-phiX174;pvalue=3.44e-08;sequence=AGCGTATCGAG; -phiX174 fimo polypeptide_motif 1348 1358 74.6 + . Name=1;ID=1-78-phiX174;pvalue=3.46e-08;sequence=TACCAATAAAA; -phiX174 fimo polypeptide_motif 239 249 74.4 + . Name=1;ID=1-79-phiX174;pvalue=3.62e-08;sequence=AGTGGCTTAAT; -phiX174 fimo polypeptide_motif 500 510 74.1 + . Name=1;ID=1-80-phiX174;pvalue=3.84e-08;sequence=GACGAGTAACA; -phiX174 fimo polypeptide_motif 3001 3011 74 + . Name=1;ID=1-81-phiX174;pvalue=3.93e-08;sequence=GCGGTCAAAAA; -phiX174 fimo polypeptide_motif 3776 3786 74 + . Name=1;ID=1-82-phiX174;pvalue=3.98e-08;sequence=TATTTCTAATG; -phiX174 fimo polypeptide_motif 2026 2036 73.9 + . Name=1;ID=1-83-phiX174;pvalue=4.06e-08;sequence=GAAGTTTAAGA; -phiX174 fimo polypeptide_motif 4237 4247 73.8 + . Name=1;ID=1-84-phiX174;pvalue=4.12e-08;sequence=AGTTTGTATCT; -phiX174 fimo polypeptide_motif 803 813 73.7 + . Name=1;ID=1-85-phiX174;pvalue=4.24e-08;sequence=AGAAGAAAACG; -phiX174 fimo polypeptide_motif 3770 3780 73.6 + . Name=1;ID=1-86-phiX174;pvalue=4.35e-08;sequence=AAAGGATATTT; -phiX174 fimo polypeptide_motif 3429 3439 73.5 + . Name=1;ID=1-87-phiX174;pvalue=4.45e-08;sequence=GAGATGCAAAA; -phiX174 fimo polypeptide_motif 99 109 73.5 + . Name=1;ID=1-88-phiX174;pvalue=4.48e-08;sequence=TACGAATTAAA; -phiX174 fimo polypeptide_motif 67 77 73.2 + . Name=1;ID=1-89-phiX174;pvalue=4.78e-08;sequence=TCTTGATAAAG; -phiX174 fimo polypeptide_motif 5332 5342 72.9 + . Name=1;ID=1-90-phiX174;pvalue=5.13e-08;sequence=ATCTGCTCAAA; -phiX174 fimo polypeptide_motif 277 287 72.9 + . Name=1;ID=1-91-phiX174;pvalue=5.14e-08;sequence=TTTAGATATGA; -phiX174 fimo polypeptide_motif 4338 4348 72.8 + . Name=1;ID=1-92-phiX174;pvalue=5.18e-08;sequence=GGGGACGAAAA; -phiX174 fimo polypeptide_motif 3812 3822 72.8 + . Name=1;ID=1-93-phiX174;pvalue=5.28e-08;sequence=GGTTGATATTT; -phiX174 fimo polypeptide_motif 1909 1919 72.6 + . Name=1;ID=1-94-phiX174;pvalue=5.51e-08;sequence=TAACGCTAAAG; -phiX174 fimo polypeptide_motif 3000 3010 72.6 + . Name=1;ID=1-95-phiX174;pvalue=5.54e-08;sequence=GGCGGTCAAAA; -phiX174 fimo polypeptide_motif 3891 3901 72.4 + . Name=1;ID=1-96-phiX174;pvalue=5.75e-08;sequence=ATTGGCTCTAA; -phiX174 fimo polypeptide_motif 3079 3089 72.4 + . Name=1;ID=1-97-phiX174;pvalue=5.76e-08;sequence=CTGGTATTAAA; -phiX174 fimo polypeptide_motif 37 47 72.4 + . Name=1;ID=1-98-phiX174;pvalue=5.79e-08;sequence=TTCGGATATTT; -phiX174 fimo polypeptide_motif 380 390 72.2 + . Name=1;ID=1-99-phiX174;pvalue=6.01e-08;sequence=GTAAGAAATCA; diff -r 793225b11202 -r b48e673af4e8 test-data/fimo_output_html_1.html --- a/test-data/fimo_output_html_1.html Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,97 +0,0 @@ - - - - - -FIMO Results - - - - -
- - - - - - -
Database and MotifsHigh-scoring Motif OccurencesDebugging Information
-
-
-
-
FIMO - Motif search tool
-
-

-For further information on how to interpret these results -or to get a copy of the FIMO software please access -http://meme.nbcr.net

-

If you use FIMO in your research, please cite the following paper:
-Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, -"FIMO: Scanning for occurrences of a given motif", -Bioinformatics, 27(7):1017-1018, 2011. -[full text]

-
-
DATABASE AND MOTIFS
-
-
-

-
- Database contains 1 sequences, 5386 residues -

-

- - - - - - - - - - - - - - - -
MOTIFWIDTH - BEST POSSIBLE MATCH -
111GGGGTATAAAA
-

-

-Random model letter frequencies (from non-redundant database): -
- -A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058 -L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064 -W 0.013 Y 0.033

-
-
-
SECTION I: HIGH-SCORING MOTIF OCCURENCES
-
-
    -
  • -There were 1937 motif occurences with a p-value less than 0.0001. -Only the most significant 1000 matches are shown here. - -The full set of motif occurences can be seen in the -tab-delimited plain text output file -fimo.txt, -the GFF file -fimo.gff -which may be suitable for uploading to the -UCSC Genome Table Browser -(assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format), -or the XML file -fimo.xml. -
  • -
  • -The p-value of a motif occurrence is defined as the -probability of a random sequence of the same length as the motif -matching that position of the sequence with as good or better a score. -
  • -
  • -The score for the match of a position in a sequence to a motif diff -r 793225b11202 -r b48e673af4e8 test-data/fimo_output_html_2.html --- a/test-data/fimo_output_html_2.html Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,97 +0,0 @@ - - - - - -FIMO Results - - - - -
    - - - - - - -
    Database and MotifsHigh-scoring Motif OccurencesDebugging Information
    -
    -
    -
    -
    FIMO - Motif search tool
    -
    -

    -For further information on how to interpret these results -or to get a copy of the FIMO software please access -http://meme.nbcr.net

    -

    If you use FIMO in your research, please cite the following paper:
    -Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, -"FIMO: Scanning for occurrences of a given motif", -Bioinformatics, 27(7):1017-1018, 2011. -[full text]

    -
    -
    DATABASE AND MOTIFS
    -
    -
    -

    -
    - Database contains 1 sequences, 5386 residues -

    -

    - - - - - - - - - - - - - - - -
    MOTIFWIDTH - BEST POSSIBLE MATCH -
    111GGGGTATAAAA
    -

    -

    -Random model letter frequencies (from non-redundant database): -
    - -A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058 -L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064 -W 0.013 Y 0.033

    -
    -
    -
    SECTION I: HIGH-SCORING MOTIF OCCURENCES
    -
    -
      -
    • -There were 1937 motif occurences with a p-value less than 0.0001. -Only the most significant 1000 matches are shown here. - -The full set of motif occurences can be seen in the -tab-delimited plain text output file -fimo.txt, -the GFF file -fimo.gff -which may be suitable for uploading to the -UCSC Genome Table Browser -(assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format), -or the XML file -fimo.xml. -
    • -
    • -The p-value of a motif occurrence is defined as the -probability of a random sequence of the same length as the motif -matching that position of the sequence with as good or better a score. -
    • -
    • -The score for the match of a position in a sequence to a motif diff -r 793225b11202 -r b48e673af4e8 test-data/fimo_output_interval_1.txt --- a/test-data/fimo_output_interval_1.txt Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -#chr start end pattern name score strand matched sequence p-value q-value -phiX174 1387 1398 1 + + 1.25e-09 29.4024 6.36e-11 -phiX174 846 857 1 + + 1.25e-09 29.122 7.02e-11 -phiX174 2300 2311 1 + + 1.29e-09 27.6463 1.08e-10 -phiX174 5062 5073 1 + + 2.25e-09 25.5366 2.73e-10 -phiX174 988 999 1 + + 2.25e-09 25.3049 3.15e-10 -phiX174 4712 4723 1 + + 3.48e-09 23.622 7.74e-10 -phiX174 5047 5058 1 + + 3.48e-09 23.3293 8.51e-10 -phiX174 854 865 1 + + 3.48e-09 23.3049 8.64e-10 -phiX174 3154 3165 1 + + 3.48e-09 23.0366 9.76e-10 -phiX174 5008 5019 1 + + 3.48e-09 23.0366 9.76e-10 -phiX174 813 824 1 + + 4.14e-09 22.5854 1.28e-09 -phiX174 2831 2842 1 + + 4.23e-09 22.3415 1.42e-09 -phiX174 3829 3840 1 + + 4.68e-09 21.8293 1.7e-09 -phiX174 3559 3570 1 + + 4.82e-09 21.5976 1.89e-09 -phiX174 2881 2892 1 + + 5.46e-09 21.1951 2.29e-09 -phiX174 4452 4463 1 + + 5.75e-09 20.8902 2.58e-09 -phiX174 2492 2503 1 + + 5.79e-09 20.3415 3.06e-09 -phiX174 4103 4114 1 + + 5.79e-09 20.3171 3.08e-09 -phiX174 4954 4965 1 + + 5.79e-09 20.3171 3.08e-09 -phiX174 1884 1895 1 + + 6.45e-09 19.9268 3.61e-09 -phiX174 3375 3386 1 + + 6.48e-09 19.7683 3.81e-09 -phiX174 51 62 1 + + 6.58e-09 19.5732 4.06e-09 -phiX174 1389 1400 1 + + 6.61e-09 19.378 4.26e-09 -phiX174 2016 2027 1 + + 6.85e-09 19.0854 4.6e-09 -phiX174 999 1010 1 + + 6.97e-09 18.878 4.88e-09 -phiX174 1554 1565 1 + + 7.37e-09 18.439 5.58e-09 -phiX174 4429 4440 1 + + 7.37e-09 18.4268 5.62e-09 -phiX174 1926 1937 1 + + 7.37e-09 18.2927 5.82e-09 -phiX174 2980 2991 1 + + 7.37e-09 18.0732 6.13e-09 -phiX174 4202 4213 1 + + 7.37e-09 17.9268 6.34e-09 -phiX174 1668 1679 1 + + 7.37e-09 17.8659 6.4e-09 -phiX174 3259 3270 1 + + 7.82e-09 17.5 7.01e-09 -phiX174 3046 3057 1 + + 7.85e-09 17.2805 7.4e-09 -phiX174 4175 4186 1 + + 7.85e-09 17.1829 7.6e-09 -phiX174 4117 4128 1 + + 7.85e-09 17.1341 7.7e-09 -phiX174 5369 5380 1 + + 7.87e-09 16.9878 8.03e-09 -phiX174 1241 1252 1 + + 7.87e-09 16.5122 8.94e-09 -phiX174 2582 2593 1 + + 7.87e-09 16.5122 8.94e-09 -phiX174 697 708 1 + + 7.87e-09 16.4146 9.13e-09 -phiX174 2298 2309 1 + + 7.87e-09 16.3537 9.26e-09 -phiX174 4188 4199 1 + + 7.87e-09 16.1707 9.69e-09 -phiX174 274 285 1 + + 7.87e-09 16.0976 9.85e-09 -phiX174 1800 1811 1 + + 7.87e-09 16.0366 1e-08 -phiX174 1385 1396 1 + + 7.87e-09 15.9268 1.03e-08 -phiX174 1302 1313 1 + + 7.87e-09 15.9024 1.03e-08 -phiX174 3771 3782 1 + + 7.87e-09 15.878 1.04e-08 -phiX174 1287 1298 1 + + 7.87e-09 15.8659 1.04e-08 -phiX174 2576 2587 1 + + 7.87e-09 15.7683 1.08e-08 -phiX174 936 947 1 + + 7.87e-09 15.7561 1.08e-08 -phiX174 903 914 1 + + 7.93e-09 15.6585 1.11e-08 -phiX174 2278 2289 1 + + 7.93e-09 15.5854 1.13e-08 -phiX174 3163 3174 1 + + 7.98e-09 15.5 1.16e-08 -phiX174 23 34 1 + + 8.24e-09 15.3293 1.23e-08 -phiX174 837 848 1 + + 8.24e-09 15.2561 1.27e-08 -phiX174 852 863 1 + + 8.24e-09 15.2561 1.27e-08 -phiX174 1983 1994 1 + + 8.68e-09 15.0244 1.36e-08 -phiX174 0 11 1 + + 9.05e-09 14.8293 1.46e-08 -phiX174 4306 4317 1 + + 9.05e-09 14.7927 1.47e-08 -phiX174 4302 4313 1 + + 9.19e-09 14.6585 1.52e-08 -phiX174 5032 5043 1 + + 9.41e-09 14.561 1.58e-08 -phiX174 2578 2589 1 + + 1.01e-08 14.2927 1.73e-08 -phiX174 321 332 1 + + 1.05e-08 14.1951 1.82e-08 -phiX174 5000 5011 1 + + 1.19e-08 13.8902 2.09e-08 -phiX174 4216 4227 1 + + 1.2e-08 13.8171 2.15e-08 -phiX174 4261 4272 1 + + 1.2e-08 13.7805 2.18e-08 -phiX174 3568 3579 1 + + 1.22e-08 13.7073 2.26e-08 -phiX174 193 204 1 + + 1.22e-08 13.6829 2.29e-08 -phiX174 130 141 1 + + 1.31e-08 13.4756 2.49e-08 -phiX174 1490 1501 1 + + 1.32e-08 13.4024 2.55e-08 -phiX174 433 444 1 + + 1.36e-08 13.2805 2.67e-08 -phiX174 4564 4575 1 + + 1.36e-08 13.2439 2.73e-08 -phiX174 101 112 1 + + 1.36e-08 13.2195 2.75e-08 -phiX174 902 913 1 + + 1.38e-08 13.1463 2.82e-08 -phiX174 4747 4758 1 + + 1.45e-08 12.9756 3.01e-08 -phiX174 2621 2632 1 + + 1.5e-08 12.8659 3.16e-08 -phiX174 466 477 1 + + 1.57e-08 12.7317 3.35e-08 -phiX174 4032 4043 1 + + 1.58e-08 12.6829 3.44e-08 -phiX174 1347 1358 1 + + 1.58e-08 12.6707 3.46e-08 -phiX174 238 249 1 + + 1.64e-08 12.5732 3.62e-08 -phiX174 499 510 1 + + 1.71e-08 12.4634 3.84e-08 -phiX174 3000 3011 1 + + 1.73e-08 12.4146 3.93e-08 -phiX174 3775 3786 1 + + 1.73e-08 12.378 3.98e-08 -phiX174 2025 2036 1 + + 1.75e-08 12.3293 4.06e-08 -phiX174 4236 4247 1 + + 1.75e-08 12.3049 4.12e-08 -phiX174 802 813 1 + + 1.78e-08 12.2439 4.24e-08 -phiX174 3769 3780 1 + + 1.81e-08 12.1829 4.35e-08 -phiX174 3428 3439 1 + + 1.82e-08 12.122 4.45e-08 -phiX174 98 109 1 + + 1.82e-08 12.1098 4.48e-08 -phiX174 66 77 1 + + 1.92e-08 11.9268 4.78e-08 -phiX174 5331 5342 1 + + 2.01e-08 11.7195 5.13e-08 -phiX174 276 287 1 + + 2.01e-08 11.7073 5.14e-08 -phiX174 4337 4348 1 + + 2.01e-08 11.6951 5.18e-08 -phiX174 3811 3822 1 + + 2.03e-08 11.6585 5.28e-08 -phiX174 1908 1919 1 + + 2.08e-08 11.5488 5.51e-08 -phiX174 2999 3010 1 + + 2.08e-08 11.5366 5.54e-08 -phiX174 3890 3901 1 + + 2.11e-08 11.439 5.75e-08 -phiX174 3078 3089 1 + + 2.11e-08 11.4268 5.76e-08 -phiX174 36 47 1 + + 2.11e-08 11.4146 5.79e-08 -phiX174 379 390 1 + + 2.17e-08 11.3293 6.01e-08 diff -r 793225b11202 -r b48e673af4e8 test-data/fimo_output_interval_2.txt --- a/test-data/fimo_output_interval_2.txt Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -#chr start end pattern name score strand matched sequence p-value q-value -phiX174 1387 1398 1 + + 0 29.4024 6.36e-11 -phiX174 846 857 1 + + 0 29.122 7.02e-11 -phiX174 2300 2311 1 + + 0 27.6463 1.08e-10 -phiX174 5062 5073 1 + + 0 25.5366 2.73e-10 -phiX174 988 999 1 + + 0 25.3049 3.15e-10 -phiX174 4712 4723 1 + + 0 23.622 7.74e-10 -phiX174 5047 5058 1 + + 0 23.3293 8.51e-10 -phiX174 854 865 1 + + 0 23.3049 8.64e-10 -phiX174 3154 3165 1 + + 0 23.0366 9.76e-10 -phiX174 5008 5019 1 + + 0 23.0366 9.76e-10 -phiX174 813 824 1 + + 0 22.5854 1.28e-09 -phiX174 2831 2842 1 + + 0 22.3415 1.42e-09 -phiX174 3829 3840 1 + + 0 21.8293 1.7e-09 -phiX174 3559 3570 1 + + 0 21.5976 1.89e-09 -phiX174 2881 2892 1 + + 0 21.1951 2.29e-09 -phiX174 4452 4463 1 + + 0 20.8902 2.58e-09 -phiX174 2492 2503 1 + + 0 20.3415 3.06e-09 -phiX174 4103 4114 1 + + 0 20.3171 3.08e-09 -phiX174 4954 4965 1 + + 0 20.3171 3.08e-09 -phiX174 1884 1895 1 + + 0 19.9268 3.61e-09 -phiX174 3375 3386 1 + + 0 19.7683 3.81e-09 -phiX174 51 62 1 + + 0 19.5732 4.06e-09 -phiX174 1389 1400 1 + + 0 19.378 4.26e-09 -phiX174 2016 2027 1 + + 0 19.0854 4.6e-09 -phiX174 999 1010 1 + + 0 18.878 4.88e-09 -phiX174 1554 1565 1 + + 0 18.439 5.58e-09 -phiX174 4429 4440 1 + + 0 18.4268 5.62e-09 -phiX174 1926 1937 1 + + 0 18.2927 5.82e-09 -phiX174 2980 2991 1 + + 0 18.0732 6.13e-09 -phiX174 4202 4213 1 + + 0 17.9268 6.34e-09 -phiX174 1668 1679 1 + + 0 17.8659 6.4e-09 -phiX174 3259 3270 1 + + 0 17.5 7.01e-09 -phiX174 3046 3057 1 + + 0 17.2805 7.4e-09 -phiX174 4175 4186 1 + + 0 17.1829 7.6e-09 -phiX174 4117 4128 1 + + 0 17.1341 7.7e-09 -phiX174 5369 5380 1 + + 0 16.9878 8.03e-09 -phiX174 1241 1252 1 + + 0 16.5122 8.94e-09 -phiX174 2582 2593 1 + + 0 16.5122 8.94e-09 -phiX174 697 708 1 + + 0 16.4146 9.13e-09 -phiX174 2298 2309 1 + + 0 16.3537 9.26e-09 -phiX174 4188 4199 1 + + 0 16.1707 9.69e-09 -phiX174 274 285 1 + + 0 16.0976 9.85e-09 -phiX174 1800 1811 1 + + 0 16.0366 1e-08 -phiX174 1385 1396 1 + + 0 15.9268 1.03e-08 -phiX174 1302 1313 1 + + 0 15.9024 1.03e-08 -phiX174 3771 3782 1 + + 0 15.878 1.04e-08 -phiX174 1287 1298 1 + + 0 15.8659 1.04e-08 -phiX174 2576 2587 1 + + 0 15.7683 1.08e-08 -phiX174 936 947 1 + + 0 15.7561 1.08e-08 -phiX174 903 914 1 + + 0 15.6585 1.11e-08 -phiX174 2278 2289 1 + + 0 15.5854 1.13e-08 -phiX174 3163 3174 1 + + 0 15.5 1.16e-08 -phiX174 23 34 1 + + 0 15.3293 1.23e-08 -phiX174 837 848 1 + + 0 15.2561 1.27e-08 -phiX174 852 863 1 + + 0 15.2561 1.27e-08 -phiX174 1983 1994 1 + + 0 15.0244 1.36e-08 -phiX174 0 11 1 + + 0 14.8293 1.46e-08 -phiX174 4306 4317 1 + + 0 14.7927 1.47e-08 -phiX174 4302 4313 1 + + 0 14.6585 1.52e-08 -phiX174 5032 5043 1 + + 0 14.561 1.58e-08 -phiX174 2578 2589 1 + + 0 14.2927 1.73e-08 -phiX174 321 332 1 + + 0 14.1951 1.82e-08 -phiX174 5000 5011 1 + + 0 13.8902 2.09e-08 -phiX174 4216 4227 1 + + 0 13.8171 2.15e-08 -phiX174 4261 4272 1 + + 0 13.7805 2.18e-08 -phiX174 3568 3579 1 + + 0 13.7073 2.26e-08 -phiX174 193 204 1 + + 0 13.6829 2.29e-08 -phiX174 130 141 1 + + 0 13.4756 2.49e-08 -phiX174 1490 1501 1 + + 0 13.4024 2.55e-08 -phiX174 433 444 1 + + 0 13.2805 2.67e-08 -phiX174 4564 4575 1 + + 0 13.2439 2.73e-08 -phiX174 101 112 1 + + 0 13.2195 2.75e-08 -phiX174 902 913 1 + + 0 13.1463 2.82e-08 -phiX174 4747 4758 1 + + 0 12.9756 3.01e-08 -phiX174 2621 2632 1 + + 0 12.8659 3.16e-08 -phiX174 466 477 1 + + 0 12.7317 3.35e-08 -phiX174 4032 4043 1 + + 0 12.6829 3.44e-08 -phiX174 1347 1358 1 + + 0 12.6707 3.46e-08 -phiX174 238 249 1 + + 0 12.5732 3.62e-08 -phiX174 499 510 1 + + 0 12.4634 3.84e-08 -phiX174 3000 3011 1 + + 0 12.4146 3.93e-08 -phiX174 3775 3786 1 + + 0 12.378 3.98e-08 -phiX174 2025 2036 1 + + 0 12.3293 4.06e-08 -phiX174 4236 4247 1 + + 0 12.3049 4.12e-08 -phiX174 802 813 1 + + 0 12.2439 4.24e-08 -phiX174 3769 3780 1 + + 0 12.1829 4.35e-08 -phiX174 3428 3439 1 + + 0 12.122 4.45e-08 -phiX174 98 109 1 + + 0 12.1098 4.48e-08 -phiX174 66 77 1 + + 0 11.9268 4.78e-08 -phiX174 5331 5342 1 + + 0 11.7195 5.13e-08 -phiX174 276 287 1 + + 0 11.7073 5.14e-08 -phiX174 4337 4348 1 + + 0 11.6951 5.18e-08 -phiX174 3811 3822 1 + + 0 11.6585 5.28e-08 -phiX174 1908 1919 1 + + 0 11.5488 5.51e-08 -phiX174 2999 3010 1 + + 0 11.5366 5.54e-08 -phiX174 3890 3901 1 + + 0 11.439 5.75e-08 -phiX174 3078 3089 1 + + 0 11.4268 5.76e-08 -phiX174 36 47 1 + + 0 11.4146 5.79e-08 -phiX174 379 390 1 + + 0 11.3293 6.01e-08 diff -r 793225b11202 -r b48e673af4e8 test-data/fimo_output_test1.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_test1.gff Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,12 @@ +##gff-version 3 +chrM fimo nucleotide_motif 2299 2306 46.6 - . Name=TACTAAYM_chrM-;Alias=MEME-1;ID=TACTAAYM-MEME-1-1-chrM;pvalue=2.18e-05;qvalue= 0.142;sequence=TACTAACA; +chrM fimo nucleotide_motif 6529 6536 46.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-2-chrM;pvalue=2.18e-05;qvalue= 0.142;sequence=TACTAACA; +chrM fimo nucleotide_motif 7741 7748 46.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-3-chrM;pvalue=2.18e-05;qvalue= 0.142;sequence=TACTAACA; +chrM fimo nucleotide_motif 13656 13663 46.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-4-chrM;pvalue=2.18e-05;qvalue= 0.142;sequence=TACTAACA; +chrM fimo nucleotide_motif 13740 13747 46.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-5-chrM;pvalue=2.18e-05;qvalue= 0.142;sequence=TACTAACA; +chrM fimo nucleotide_motif 861 868 44 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-6-chrM;pvalue=3.96e-05;qvalue= 0.185;sequence=TACTAACC; +chrM fimo nucleotide_motif 9346 9353 44 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-7-chrM;pvalue=3.96e-05;qvalue= 0.185;sequence=TACTAACC; +chrM fimo nucleotide_motif 3767 3774 41.8 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-8-chrM;pvalue=6.62e-05;qvalue= 0.216;sequence=TACTAATA; +chrM fimo nucleotide_motif 5497 5504 41.8 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-9-chrM;pvalue=6.62e-05;qvalue= 0.216;sequence=TACTAATA; +chrM fimo nucleotide_motif 10105 10112 41.8 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-10-chrM;pvalue=6.62e-05;qvalue= 0.216;sequence=TACTAATA; +chrM fimo nucleotide_motif 10959 10966 40.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-11-chrM;pvalue=8.79e-05;qvalue= 0.261;sequence=TACTAACT; diff -r 793225b11202 -r b48e673af4e8 test-data/fimo_output_test1.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_test1.html Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,300 @@ + + + + + +FIMO Results + + + + +
      + + + + + + +
      Database and MotifsHigh-scoring Motif OccurencesDebugging Information
      +
      +
      +
      +
      FIMO - Motif search tool
      +
      +

      +FIMO version 4.12.0, (Release date: Tue Jun 27 16:22:50 2017 -0700) +

      +

      +For further information on how to interpret these results +or to get a copy of the FIMO software please access +http://meme.nbcr.net

      +

      If you use FIMO in your research, please cite the following paper:
      +Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, +"FIMO: Scanning for occurrences of a given motif", +Bioinformatics, 27(7):1017-1018, 2011. +[full text]

      +
      +
      DATABASE AND MOTIFS
      +
      +
      +

      + DATABASE hsa_chrM.fa +
      + Database contains 1 sequences, 16569 residues +

      +

      + MOTIFS meme_fimo_input_1.xml (DNA) + + + + + + + + + + + + + + + +
      MOTIFWIDTH + BEST POSSIBLE MATCH +
      TACTAAYM8TACTAACA
      +

      +

      +Random model letter frequencies (--nrdb--): +
      + +A 0.275 C 0.225 G 0.225 T 0.275

      +
      +
      +
      SECTION I: HIGH-SCORING MOTIF OCCURENCES
      +
      +
        +
      • +There were 11 motif occurences with a p-value less than 0.0001. + +The full set of motif occurences can be seen in the +tab-delimited plain text output file +fimo.txt, +the GFF file +fimo.gff +which may be suitable for uploading to the +UCSC Genome Table Browser +(assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format), +or the XML file +fimo.xml. +
      • +
      • +The p-value of a motif occurrence is defined as the +probability of a random sequence of the same length as the motif +matching that position of the sequence with as good or better a score. +
      • +
      • +The score for the match of a position in a sequence to a motif +is computed by summing the appropriate entries from each column of +the position-dependent scoring matrix that represents the motif. +
      • +
      • +The q-value of a motif occurrence is defined as the +false discovery rate if the occurrence is accepted as significant. +
      • +
      • The table is sorted by increasing p-value.
      • +
      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Motif IDAlt IDSequence NameStrandStartEndp-valueq-valueMatched Sequence
      TACTAAYMMEME-1chrM-229923062.18e-050.142TACTAACA
      TACTAAYMMEME-1chrM+652965362.18e-050.142TACTAACA
      TACTAAYMMEME-1chrM+774177482.18e-050.142TACTAACA
      TACTAAYMMEME-1chrM+13656136632.18e-050.142TACTAACA
      TACTAAYMMEME-1chrM+13740137472.18e-050.142TACTAACA
      TACTAAYMMEME-1chrM+8618683.96e-050.185TACTAACC
      TACTAAYMMEME-1chrM+934693533.96e-050.185TACTAACC
      TACTAAYMMEME-1chrM+376737746.62e-050.216TACTAATA
      TACTAAYMMEME-1chrM+549755046.62e-050.216TACTAATA
      TACTAAYMMEME-1chrM+10105101126.62e-050.216TACTAATA
      TACTAAYMMEME-1chrM+10959109668.79e-050.261TACTAACT
      + +
      +
      DEBUGGING INFORMATION
      +
      +

      +Command line: +

      +
      +fimo -oc fimo_test1_out meme_fimo_input_1.xml hsa_chrM.fa
      +
      +

      +Settings: +

      +
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      output_directory = fimo_test1_outMEME file name = meme_fimo_input_1.xmlsequence file name = hsa_chrM.fa
      background file name = --nrdb--alphabet = DNAmax stored scores = 100000
      allow clobber = truecompute q-values = trueparse genomic coord. = false
      text only = falsescan both strands = truemax strand = false
      threshold type = p-valueoutput theshold = 0.0001pseudocount = 0.1
      alpha = 1verbosity = 2
      +
      +

      +This information can be useful in the event you wish to report a +problem with the FIMO software. +

      +
      +Go to top + + diff -r 793225b11202 -r b48e673af4e8 test-data/fimo_output_test1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_test1.txt Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,12 @@ +# motif_id motif_alt_id sequence_name start stop strand score p-value q-value matched_sequence +TACTAAYM MEME-1 chrM 2299 2306 - 12.9701 2.18e-05 0.142 TACTAACA +TACTAAYM MEME-1 chrM 6529 6536 + 12.9701 2.18e-05 0.142 TACTAACA +TACTAAYM MEME-1 chrM 7741 7748 + 12.9701 2.18e-05 0.142 TACTAACA +TACTAAYM MEME-1 chrM 13656 13663 + 12.9701 2.18e-05 0.142 TACTAACA +TACTAAYM MEME-1 chrM 13740 13747 + 12.9701 2.18e-05 0.142 TACTAACA +TACTAAYM MEME-1 chrM 861 868 + 12.2836 3.96e-05 0.185 TACTAACC +TACTAAYM MEME-1 chrM 9346 9353 + 12.2836 3.96e-05 0.185 TACTAACC +TACTAAYM MEME-1 chrM 3767 3774 + 11.7164 6.62e-05 0.216 TACTAATA +TACTAAYM MEME-1 chrM 5497 5504 + 11.7164 6.62e-05 0.216 TACTAATA +TACTAAYM MEME-1 chrM 10105 10112 + 11.7164 6.62e-05 0.216 TACTAATA +TACTAAYM MEME-1 chrM 10959 10966 + 11.6567 8.79e-05 0.261 TACTAACT diff -r 793225b11202 -r b48e673af4e8 test-data/fimo_output_test1.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_test1.xml Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,50 @@ + + + + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation= xmlns:fimo="http://noble.gs.washington.edu/schema/fimo" +> +fimo -oc fimo_test1_out meme_fimo_input_1.xml hsa_chrM.fa + +fimo_test1_out +meme_fimo_input_1.xml +hsa_chrM.fa +--nrdb-- +true +true +false +false +true +0.0001 +p-value +100000 +0.1 +2 + + + + + + + + + + + + + + + + + + + + + +0.275 +0.225 +0.225 +0.275 + +cisml.xml + diff -r 793225b11202 -r b48e673af4e8 test-data/fimo_output_test2.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_test2.gff Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,12 @@ +##gff-version 3 +chrM fimo nucleotide_motif 440 446 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-1-chrM;pvalue=8.2e-05;qvalue= 0.327;sequence=ACTAACA; +chrM fimo nucleotide_motif 2093 2099 40.9 - . Name=ACTAAYH_chrM-;Alias=DREME-1;ID=ACTAAYH-DREME-1-2-chrM;pvalue=8.2e-05;qvalue= 0.327;sequence=ACTAACA; +chrM fimo nucleotide_motif 2299 2305 40.9 - . Name=ACTAAYH_chrM-;Alias=DREME-1;ID=ACTAAYH-DREME-1-3-chrM;pvalue=8.2e-05;qvalue= 0.327;sequence=ACTAACA; +chrM fimo nucleotide_motif 5186 5192 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-4-chrM;pvalue=8.2e-05;qvalue= 0.327;sequence=ACTAACA; +chrM fimo nucleotide_motif 6530 6536 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-5-chrM;pvalue=8.2e-05;qvalue= 0.327;sequence=ACTAACA; +chrM fimo nucleotide_motif 7742 7748 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-6-chrM;pvalue=8.2e-05;qvalue= 0.327;sequence=ACTAACA; +chrM fimo nucleotide_motif 13657 13663 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-7-chrM;pvalue=8.2e-05;qvalue= 0.327;sequence=ACTAACA; +chrM fimo nucleotide_motif 13741 13747 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-8-chrM;pvalue=8.2e-05;qvalue= 0.327;sequence=ACTAACA; +chrM fimo nucleotide_motif 510 516 43.8 + . Name=CCAGCAY_chrM+;Alias=DREME-5;ID=CCAGCAY-DREME-5-1-chrM;pvalue=4.15e-05;qvalue= 0.668;sequence=CCAGCAC; +chrM fimo nucleotide_motif 5137 5143 43.8 + . Name=CCAGCAY_chrM+;Alias=DREME-5;ID=CCAGCAY-DREME-5-2-chrM;pvalue=4.15e-05;qvalue= 0.668;sequence=CCAGCAC; +chrM fimo nucleotide_motif 4241 4247 40.3 + . Name=CCAGCAY_chrM+;Alias=DREME-5;ID=CCAGCAY-DREME-5-3-chrM;pvalue=9.37e-05;qvalue= 1;sequence=CCAGCAT; diff -r 793225b11202 -r b48e673af4e8 test-data/fimo_output_test2.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_test2.html Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,325 @@ + + + + + +FIMO Results + + + + +
      + + + + + + +
      Database and MotifsHigh-scoring Motif OccurencesDebugging Information
      +
      +
      +
      +
      FIMO - Motif search tool
      +
      +

      +FIMO version 4.12.0, (Release date: Tue Jun 27 16:22:50 2017 -0700) +

      +

      +For further information on how to interpret these results +or to get a copy of the FIMO software please access +http://meme.nbcr.net

      +

      If you use FIMO in your research, please cite the following paper:
      +Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, +"FIMO: Scanning for occurrences of a given motif", +Bioinformatics, 27(7):1017-1018, 2011. +[full text]

      +
      +
      DATABASE AND MOTIFS
      +
      +
      +

      + DATABASE hsa_chrM.fa +
      + Database contains 1 sequences, 16569 residues +

      +

      + MOTIFS dreme_fimo_input_1.xml (DNA) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      MOTIFWIDTH + BEST POSSIBLE MATCH +
      ACTAAYH7ACTAACA
      YTAACA6TTAACA
      TCTGT5TCTGT
      SCCAGG6CCCAGG
      CCAGCAY7CCAGCAC
      GMATGT6GAATGT
      +

      +

      +Random model letter frequencies (fimo_background_probs_hsa_chrM.txt): +
      + +A 0.278 C 0.222 G 0.222 T 0.278

      +
      +
      +
      SECTION I: HIGH-SCORING MOTIF OCCURENCES
      +
      +
        +
      • +There were 11 motif occurences with a p-value less than 0.0001. + +The full set of motif occurences can be seen in the +tab-delimited plain text output file +fimo.txt, +the GFF file +fimo.gff +which may be suitable for uploading to the +UCSC Genome Table Browser +(assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format), +or the XML file +fimo.xml. +
      • +
      • +The p-value of a motif occurrence is defined as the +probability of a random sequence of the same length as the motif +matching that position of the sequence with as good or better a score. +
      • +
      • +The score for the match of a position in a sequence to a motif +is computed by summing the appropriate entries from each column of +the position-dependent scoring matrix that represents the motif. +
      • +
      • +The q-value of a motif occurrence is defined as the +false discovery rate if the occurrence is accepted as significant. +
      • +
      • The table is sorted by increasing p-value.
      • +
      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Motif IDAlt IDSequence NameStrandStartEndp-valueq-valueMatched Sequence
      CCAGCAYDREME-5chrM+5105164.15e-050.668CCAGCAC
      CCAGCAYDREME-5chrM+513751434.15e-050.668CCAGCAC
      ACTAAYHDREME-1chrM+4404468.2e-050.327ACTAACA
      ACTAAYHDREME-1chrM-209320998.2e-050.327ACTAACA
      ACTAAYHDREME-1chrM-229923058.2e-050.327ACTAACA
      ACTAAYHDREME-1chrM+518651928.2e-050.327ACTAACA
      ACTAAYHDREME-1chrM+653065368.2e-050.327ACTAACA
      ACTAAYHDREME-1chrM+774277488.2e-050.327ACTAACA
      ACTAAYHDREME-1chrM+13657136638.2e-050.327ACTAACA
      ACTAAYHDREME-1chrM+13741137478.2e-050.327ACTAACA
      CCAGCAYDREME-5chrM+424142479.37e-051CCAGCAT
      + +
      +
      DEBUGGING INFORMATION
      +
      +

      +Command line: +

      +
      +fimo -oc fimo_test2_out --bgfile fimo_background_probs_hsa_chrM.txt dreme_fimo_input_1.xml hsa_chrM.fa
      +
      +

      +Settings: +

      +
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      +
      output_directory = fimo_test2_outMEME file name = dreme_fimo_input_1.xmlsequence file name = hsa_chrM.fa
      background file name = fimo_background_probs_hsa_chrM.txtalphabet = DNAmax stored scores = 100000
      allow clobber = truecompute q-values = trueparse genomic coord. = false
      text only = falsescan both strands = truemax strand = false
      threshold type = p-valueoutput theshold = 0.0001pseudocount = 0.1
      alpha = 1verbosity = 2
      +
      +

      +This information can be useful in the event you wish to report a +problem with the FIMO software. +

      +
      +Go to top + + diff -r 793225b11202 -r b48e673af4e8 test-data/fimo_output_test2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_test2.txt Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,12 @@ +# motif_id motif_alt_id sequence_name start stop strand score p-value q-value matched_sequence +CCAGCAY DREME-5 chrM 510 516 + 13.5843 4.15e-05 0.668 CCAGCAC +CCAGCAY DREME-5 chrM 5137 5143 + 13.5843 4.15e-05 0.668 CCAGCAC +ACTAAYH DREME-1 chrM 440 446 + 11.7385 8.2e-05 0.327 ACTAACA +ACTAAYH DREME-1 chrM 2093 2099 - 11.7385 8.2e-05 0.327 ACTAACA +ACTAAYH DREME-1 chrM 2299 2305 - 11.7385 8.2e-05 0.327 ACTAACA +ACTAAYH DREME-1 chrM 5186 5192 + 11.7385 8.2e-05 0.327 ACTAACA +ACTAAYH DREME-1 chrM 6530 6536 + 11.7385 8.2e-05 0.327 ACTAACA +ACTAAYH DREME-1 chrM 7742 7748 + 11.7385 8.2e-05 0.327 ACTAACA +ACTAAYH DREME-1 chrM 13657 13663 + 11.7385 8.2e-05 0.327 ACTAACA +ACTAAYH DREME-1 chrM 13741 13747 + 11.7385 8.2e-05 0.327 ACTAACA +CCAGCAY DREME-5 chrM 4241 4247 + 13.1461 9.37e-05 1 CCAGCAT diff -r 793225b11202 -r b48e673af4e8 test-data/fimo_output_test2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_test2.xml Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,55 @@ + + + + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation= xmlns:fimo="http://noble.gs.washington.edu/schema/fimo" +> +fimo -oc fimo_test2_out --bgfile fimo_background_probs_hsa_chrM.txt dreme_fimo_input_1.xml hsa_chrM.fa + +fimo_test2_out +dreme_fimo_input_1.xml +hsa_chrM.fa +fimo_background_probs_hsa_chrM.txt +true +true +false +false +true +0.0001 +p-value +100000 +0.1 +2 + + + + + + + + + + + + + + + + + + + + + + + + + + +0.278 +0.222 +0.222 +0.278 + +cisml.xml + diff -r 793225b11202 -r b48e673af4e8 test-data/fimo_output_test3.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_test3.html Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,5891 @@ + + + + + +FIMO Results + + + + +
      + + + + + + +
      Database and MotifsHigh-scoring Motif OccurencesDebugging Information
      +
      +
      +
      +
      FIMO - Motif search tool
      +
      +

      +FIMO version 4.12.0, (Release date: Tue Jun 27 16:22:50 2017 -0700) +

      +

      +For further information on how to interpret these results +or to get a copy of the FIMO software please access +http://meme.nbcr.net

      +

      If you use FIMO in your research, please cite the following paper:
      +Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, +"FIMO: Scanning for occurrences of a given motif", +Bioinformatics, 27(7):1017-1018, 2011. +[full text]

      +
      +
      DATABASE AND MOTIFS
      +
      +
      +

      + DATABASE hsa_chrM.fa +
      + Database contains 1 sequences, 16569 residues +

      +

      + MOTIFS dreme_fimo_input_1.xml (DNA) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      MOTIFWIDTH + BEST POSSIBLE MATCH +
      ACTAAYH7ACTAACA
      YTAACA6TTAACA
      TCTGT5TCTGT
      SCCAGG6CCCAGG
      CCAGCAY7CCAGCAC
      GMATGT6GAATGT
      +

      +

      +Random model letter frequencies (--uniform--): +
      + +A 0.250 C 0.250 G 0.250 T 0.250

      +
      +
      +
      SECTION I: HIGH-SCORING MOTIF OCCURENCES
      +
      +
        +
      • +There were 517 motif occurences with a p-value less than 0.01. + +The full set of motif occurences can be seen in the +tab-delimited plain text output file +fimo.txt, +the GFF file +fimo.gff +which may be suitable for uploading to the +UCSC Genome Table Browser +(assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format), +or the XML file +fimo.xml. +
      • +
      • +The p-value of a motif occurrence is defined as the +probability of a random sequence of the same length as the motif +matching that position of the sequence with as good or better a score. +
      • +
      • +The score for the match of a position in a sequence to a motif +is computed by summing the appropriate entries from each column of +the position-dependent scoring matrix that represents the motif. +
      • +
      • +The q-value of a motif occurrence is defined as the +false discovery rate if the occurrence is accepted as significant. +
      • +
      • The table is sorted by increasing p-value.
      • +
      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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      Motif IDAlt IDSequence NameStrandStartEndp-valueq-valueMatched Sequence
      ACTAAYHDREME-1chrM+4404466.1e-050.239ACTAACA
      ACTAAYHDREME-1chrM-209320996.1e-050.239ACTAACA
      ACTAAYHDREME-1chrM-229923056.1e-050.239ACTAACA
      ACTAAYHDREME-1chrM+518651926.1e-050.239ACTAACA
      ACTAAYHDREME-1chrM+653065366.1e-050.239ACTAACA
      ACTAAYHDREME-1chrM+774277486.1e-050.239ACTAACA
      ACTAAYHDREME-1chrM+13657136636.1e-050.239ACTAACA
      ACTAAYHDREME-1chrM+13741137476.1e-050.239ACTAACA
      ACTAAYHDREME-1chrM+376837740.0001220.239ACTAATA
      ACTAAYHDREME-1chrM+549855040.0001220.239ACTAATA
      ACTAAYHDREME-1chrM+773677420.0001220.239ACTAATA
      ACTAAYHDREME-1chrM+987298780.0001220.239ACTAATA
      ACTAAYHDREME-1chrM+10106101120.0001220.239ACTAATA
      ACTAAYHDREME-1chrM+10313103190.0001220.239ACTAATA
      ACTAAYHDREME-1chrM+11818118240.0001220.239ACTAATA
      ACTAAYHDREME-1chrM+15903159090.0001220.239ACTAATA
      ACTAAYHDREME-1chrM+773277380.0001830.294ACTAACT
      ACTAAYHDREME-1chrM+10960109660.0001830.294ACTAACT
      ACTAAYHDREME-1chrM+8628680.0002440.294ACTAACC
      ACTAAYHDREME-1chrM+183218380.0002440.294ACTAACC
      ACTAAYHDREME-1chrM+867986850.0002440.294ACTAACC
      ACTAAYHDREME-1chrM+877087760.0002440.294ACTAACC
      ACTAAYHDREME-1chrM+934793530.0002440.294ACTAACC
      ACTAAYHDREME-1chrM+935993650.0002440.294ACTAACC
      ACTAAYHDREME-1chrM+10302103080.0002440.294ACTAACC
      ACTAAYHDREME-1chrM+14765147710.0002440.294ACTAACC
      ACTAAYHDREME-1chrM+446644720.0003050.302ACTAATT
      ACTAAYHDREME-1chrM+11248112540.0003050.302ACTAATT
      ACTAAYHDREME-1chrM+4754810.0003660.302ACTAATC
      ACTAAYHDREME-1chrM+793079360.0003660.302ACTAATC
      ACTAAYHDREME-1chrM+864986550.0003660.302ACTAATC
      ACTAAYHDREME-1chrM+867086760.0003660.302ACTAATC
      ACTAAYHDREME-1chrM+10768107740.0003660.302ACTAATC
      ACTAAYHDREME-1chrM+11053110590.0003660.302ACTAATC
      ACTAAYHDREME-1chrM+11101111070.0003660.302ACTAATC
      ACTAAYHDREME-1chrM+12720127260.0003660.302ACTAATC
      ACTAAYHDREME-1chrM+13149131550.0003660.302ACTAATC
      ACTAAYHDREME-1chrM+14216142220.0003660.302ACTAATC
      ACTAAYHDREME-1chrM-6786840.0005490.366ACTAAGA
      ACTAAYHDREME-1chrM+143514410.0005490.366ACTAAGA
      ACTAAYHDREME-1chrM+152415300.0005490.366ACTAAAA
      ACTAAYHDREME-1chrM-203520410.0005490.366ACTAAGA
      ACTAAYHDREME-1chrM+844084460.0005490.366ACTAAAA
      ACTAAYHDREME-1chrM-9995100010.0005490.366ACTAAAA
      ACTAAYHDREME-1chrM-10225102310.0005490.366ACTAAGA
      ACTAAYHDREME-1chrM-12725127310.0005490.366ACTAAGA
      ACTAAYHDREME-1chrM+14393143990.0005490.366ACTAAAA
      ACTAAYHDREME-1chrM+229423000.000610.398ACTAATG
      ACTAAYHDREME-1chrM-2062120.001650.441ATTAACA
      ACTAAYHDREME-1chrM+2372430.001650.441AATAACA
      ACTAAYHDREME-1chrM+3703760.001650.441CCTAACA
      ACTAAYHDREME-1chrM+163016360.001650.441ACTTACA
      ACTAAYHDREME-1chrM+170217080.001650.441ACTACCA
      ACTAAYHDREME-1chrM+230923150.001650.441AGTAACA
      ACTAAYHDREME-1chrM+236323690.001650.441ACTGACA
      ACTAAYHDREME-1chrM+237023760.001650.441ATTAACA
      ACTAAYHDREME-1chrM+239524010.001650.441ACCAACA
      ACTAAYHDREME-1chrM+276127670.001650.441CCTAACA
      ACTAAYHDREME-1chrM+278427900.001650.441ACTACCA
      ACTAAYHDREME-1chrM-319131970.001650.441ACTAAGT
      ACTAAYHDREME-1chrM+375637620.001650.441ACTATCA
      ACTAAYHDREME-1chrM+387338790.001650.441ACTAGCA
      ACTAAYHDREME-1chrM+399139970.001650.441ACAAACA
      ACTAAYHDREME-1chrM-444544510.001650.441ACCAACA
      ACTAAYHDREME-1chrM+473447400.001650.441ACTACCA
      ACTAAYHDREME-1chrM+506150670.001650.441CCTAACA
      ACTAAYHDREME-1chrM+517751830.001650.441GCTAACA
      ACTAAYHDREME-1chrM+539153970.001650.441TCTAACA
      ACTAAYHDREME-1chrM+568056860.001650.441ACAAACA
      ACTAAYHDREME-1chrM-568656920.001650.441ACTAAGT
      ACTAAYHDREME-1chrM+659566010.001650.441ACCAACA
      ACTAAYHDREME-1chrM+714671520.001650.441ACTATCA
      ACTAAYHDREME-1chrM+728672920.001650.441TCTAACA
      ACTAAYHDREME-1chrM+771477200.001650.441CCTAACA
      ACTAAYHDREME-1chrM+772077260.001650.441ACTCACA
      ACTAAYHDREME-1chrM+834483500.001650.441ACCAACA
      ACTAAYHDREME-1chrM+837483800.001650.441ACTAAAT
      ACTAAYHDREME-1chrM+846084660.001650.441ACTACCA
      ACTAAYHDREME-1chrM+901090160.001650.441GCTAACA
      ACTAAYHDREME-1chrM+925792630.001650.441CCTAACA
      ACTAAYHDREME-1chrM+935193570.001650.441ACCAACA
      ACTAAYHDREME-1chrM+10127101330.001650.441ACTACCA
      ACTAAYHDREME-1chrM+10295103010.001650.441ACAAACA
      ACTAAYHDREME-1chrM+10496105020.001650.441ACTAGCA
      ACTAAYHDREME-1chrM+10792107980.001650.441ACTACCA
      ACTAAYHDREME-1chrM+10798108040.001650.441ACTGACA
      ACTAAYHDREME-1chrM+10939109450.001650.441CCTAACA
      ACTAAYHDREME-1chrM+11023110290.001650.441ACTATCA
      ACTAAYHDREME-1chrM+11258112640.001650.441ACTCACA
      ACTAAYHDREME-1chrM+11314113200.001650.441ACTATCA
      ACTAAYHDREME-1chrM+11593115990.001650.441ACAAACA
      ACTAAYHDREME-1chrM+11650116560.001650.441AGTAACA
      ACTAAYHDREME-1chrM+11768117740.001650.441ACTCACA
      ACTAAYHDREME-1chrM-11901119070.001650.441ACTAGCA
      ACTAAYHDREME-1chrM+11941119470.001650.441ACTTACA
      ACTAAYHDREME-1chrM+12026120320.001650.441ATTAACA
      ACTAAYHDREME-1chrM+12245122510.001650.441TCTAACA
      ACTAAYHDREME-1chrM+12412124180.001650.441CCTAACA
      ACTAAYHDREME-1chrM+12530125360.001650.441ACTGACA
      ACTAAYHDREME-1chrM-12617126230.001650.441ACGAACA
      ACTAAYHDREME-1chrM+12736127420.001650.441GCTAACA
      ACTAAYHDREME-1chrM+13161131670.001650.441TCTAACA
      ACTAAYHDREME-1chrM+13626136320.001650.441CCTAACA
      ACTAAYHDREME-1chrM+13797138030.001650.441ACTCACA
      ACTAAYHDREME-1chrM+13830138360.001650.441TCTAACA
      ACTAAYHDREME-1chrM+13858138640.001650.441ACCAACA
      ACTAAYHDREME-1chrM+14185141910.001650.441ACCAACA
      ACTAAYHDREME-1chrM+14189141950.001650.441ACAAACA
      ACTAAYHDREME-1chrM+14548145540.001650.441AATAACA
      ACTAAYHDREME-1chrM+14569145750.001650.441GCTAACA
      ACTAAYHDREME-1chrM+15469154750.001650.441ATTAACA
      ACTAAYHDREME-1chrM+15599156050.001650.441CCTAACA
      ACTAAYHDREME-1chrM+16227162330.001650.441ACTATCA
      ACTAAYHDREME-1chrM+16277162830.001650.441ACCAACA
      ACTAAYHDREME-1chrM+8528580.001770.441ACTAAGC
      ACTAAYHDREME-1chrM-144914550.001770.441ACTAAGC
      ACTAAYHDREME-1chrM+491349190.001770.441ACTAAAC
      ACTAAYHDREME-1chrM+11278112840.001770.441ACTAAAC
      ACTAAYHDREME-1chrM+13686136920.001770.441ACTAAAC
      ACTAAYHDREME-1chrM+14582145880.001770.441ACTAAAC
      ACTAAYHDREME-1chrM+14636146420.001770.441ACTAAAC
      ACTAAYHDREME-1chrM+15703157090.001770.441ACTAAGC
      ACTAAYHDREME-1chrM-1521580.002690.441AATAATA
      ACTAAYHDREME-1chrM+2342400.002690.441AATAATA
      ACTAAYHDREME-1chrM+4724780.002690.441ACTACTA
      ACTAAYHDREME-1chrM+6456510.002690.441ACAAATA
      ACTAAYHDREME-1chrM-6716770.002690.441GCTAATA
      ACTAAYHDREME-1chrM-230523110.002690.441ACTTATA
      ACTAAYHDREME-1chrM-252925350.002690.441TCTAATA
      ACTAAYHDREME-1chrM-274427500.002690.441ATTAATA
      ACTAAYHDREME-1chrM+288028860.002690.441ACTACTA
      ACTAAYHDREME-1chrM+415841640.002690.441ACTCATA
      ACTAAYHDREME-1chrM+420642120.002690.441ACTTATA
      ACTAAYHDREME-1chrM+430143070.002690.441AATAATA
      ACTAAYHDREME-1chrM+467946850.002690.441TCTAATA
      ACTAAYHDREME-1chrM+472847340.002690.441ACCAATA
      ACTAAYHDREME-1chrM+475447600.002690.441ATTAATA
      ACTAAYHDREME-1chrM+503650420.002690.441AATAATA
      ACTAAYHDREME-1chrM+510351090.002690.441ACTACTA
      ACTAAYHDREME-1chrM+515351590.002690.441ACTACTA
      ACTAAYHDREME-1chrM-596259680.002690.441AATAATA
      ACTAAYHDREME-1chrM+611061160.002690.441AGTAATA
      ACTAAYHDREME-1chrM+615561610.002690.441CCTAATA
      ACTAAYHDREME-1chrM+652765330.002690.441ACTACTA
      ACTAAYHDREME-1chrM-697369790.002690.441GCTAATA
      ACTAAYHDREME-1chrM+729573010.002690.441AGTAATA
      ACTAAYHDREME-1chrM+730173070.002690.441ATTAATA
      ACTAAYHDREME-1chrM-730073060.002690.441ATTAATA
      ACTAAYHDREME-1chrM+734973550.002690.441CCTAATA
      ACTAAYHDREME-1chrM-735173570.002690.441ACTATTA
      ACTAAYHDREME-1chrM-752275280.002690.441TCTAATA
      ACTAAYHDREME-1chrM+873987450.002690.441ACTAGTA
      ACTAAYHDREME-1chrM-873887440.002690.441ACTAGTA
      ACTAAYHDREME-1chrM-894589510.002690.441ACTAGTA
      ACTAAYHDREME-1chrM+898289880.002690.441ACCAATA
      ACTAAYHDREME-1chrM-961396190.002690.441AGTAATA
      ACTAAYHDREME-1chrM+965696620.002690.441TCTAATA
      ACTAAYHDREME-1chrM+10055100610.002690.441AGTAATA
      ACTAAYHDREME-1chrM+10103101090.002690.441ACTACTA
      ACTAAYHDREME-1chrM-10246102520.002690.441AATAATA
      ACTAAYHDREME-1chrM-10315103210.002690.441ACTATTA
      ACTAAYHDREME-1chrM-10336103420.002690.441ATTAATA
      ACTAAYHDREME-1chrM-10368103740.002690.441ACTCATA
      ACTAAYHDREME-1chrM+10526105320.002690.441ACTAGTA
      ACTAAYHDREME-1chrM-10525105310.002690.441ACTAGTA
      ACTAAYHDREME-1chrM+10574105800.002690.441AATAATA
      ACTAAYHDREME-1chrM-10657106630.002690.441ACTAGTA
      ACTAAYHDREME-1chrM-10699107050.002690.441ACTAGTA
      ACTAAYHDREME-1chrM-10788107940.002690.441AGTAATA
      ACTAAYHDREME-1chrM-10858108640.002690.441GCTAATA
      ACTAAYHDREME-1chrM+10954109600.002690.441CCTAATA
      ACTAAYHDREME-1chrM+11873118790.002690.441ACTATTA
      ACTAAYHDREME-1chrM-11958119640.002690.441ACTAGTA
      ACTAAYHDREME-1chrM+12333123390.002690.441AGTAATA
      ACTAAYHDREME-1chrM+12349123550.002690.441ACTACTA
      ACTAAYHDREME-1chrM+12425124310.002690.441ACTCATA
      ACTAAYHDREME-1chrM-12471124770.002690.441ACTGATA
      ACTAAYHDREME-1chrM+12933129390.002690.441ACAAATA
      ACTAAYHDREME-1chrM+12972129780.002690.441ACTACTA
      ACTAAYHDREME-1chrM+13269132750.002690.441ACTCATA
      ACTAAYHDREME-1chrM-13274132800.002690.441ACTATTA
      ACTAAYHDREME-1chrM-13566135720.002690.441AGTAATA
      ACTAAYHDREME-1chrM+14210142160.002690.441ACTACTA
      ACTAAYHDREME-1chrM+14213142190.002690.441ACTACTA
      ACTAAYHDREME-1chrM+14251142570.002690.441ACCAATA
      ACTAAYHDREME-1chrM+14314143200.002690.441ACTATTA
      ACTAAYHDREME-1chrM+14510145160.002690.441ACTATTA
      ACTAAYHDREME-1chrM+14545145510.002690.441AATAATA
      ACTAAYHDREME-1chrM+14773147790.002690.441CCTAATA
      ACTAAYHDREME-1chrM-15627156330.002690.441AGTAATA
      ACTAAYHDREME-1chrM+15838158440.002690.441CCTAATA
      ACTAAYHDREME-1chrM+1931990.00360.501ACTTACT
      ACTAAYHDREME-1chrM-7147200.00360.501ACTCACT
      ACTAAYHDREME-1chrM+186018660.00360.501ATTAACT
      ACTAAYHDREME-1chrM+187018760.00360.501AATAACT
      ACTAAYHDREME-1chrM+222022260.00360.501ACTACCT
      ACTAAYHDREME-1chrM+290129070.00360.501AATAACT
      ACTAAYHDREME-1chrM+415441600.00360.501ACCAACT
      ACTAAYHDREME-1chrM-428342890.00360.501AGTAACT
      ACTAAYHDREME-1chrM+509951050.00360.501CCTAACT
      ACTAAYHDREME-1chrM+515651620.00360.501ACTATCT
      ACTAAYHDREME-1chrM-555555610.00360.501ACTTACT
      ACTAAYHDREME-1chrM+614261480.00360.501ACTGACT
      ACTAAYHDREME-1chrM+667866840.00360.501ACTTACT
      ACTAAYHDREME-1chrM+716971750.00360.501TCTAACT
      ACTAAYHDREME-1chrM+830483100.00360.501GCTAACT
      ACTAAYHDREME-1chrM+845684620.00360.501ACAAACT
      ACTAAYHDREME-1chrM+881788230.00360.501ACTATCT
      ACTAAYHDREME-1chrM-894989550.00360.501AATAACT
      ACTAAYHDREME-1chrM+912091260.00360.501ACTGACT
      ACTAAYHDREME-1chrM+985298580.00360.501ACTATCT
      ACTAAYHDREME-1chrM+10025100310.00360.501ATTAACT
      ACTAAYHDREME-1chrM+10964109700.00360.501ACTACCT
      ACTAAYHDREME-1chrM+11293112990.00360.501ACTCACT
      ACTAAYHDREME-1chrM+11347113530.00360.501ACTAGCT
      ACTAAYHDREME-1chrM+12226122320.00360.501GCTAACT
      ACTAAYHDREME-1chrM-12516125220.00360.501AATAACT
      ACTAAYHDREME-1chrM+13850138560.00360.501ACTACCT
      ACTAAYHDREME-1chrM+13862138680.00360.501ACAAACT
      ACTAAYHDREME-1chrM+14206142120.00360.501AGTAACT
      ACTAAYHDREME-1chrM+15185151910.00360.501ACAAACT
      ACTAAYHDREME-1chrM+15189151950.00360.501ACTTACT
      ACTAAYHDREME-1chrM+15603156090.00360.501ACAAACT
      ACTAAYHDREME-1chrM+15844158500.00360.501ACCAACT
      ACTAAYHDREME-1chrM+15848158540.00360.501ACTATCT
      ACTAAYHDREME-1chrM+21270.004520.505ATTAACC
      ACTAAYHDREME-1chrM+3813870.004520.505CCTAACC
      ACTAAYHDREME-1chrM+5295350.004520.505GCTAACC
      ACTAAYHDREME-1chrM+5475530.004520.505ACCAACC
      ACTAAYHDREME-1chrM+8238290.004520.505ATTAACC
      ACTAAYHDREME-1chrM-8738790.004520.505ACCAACC
      ACTAAYHDREME-1chrM+9109160.004520.505ATTAACC
      ACTAAYHDREME-1chrM+9789840.004520.505ACTCACC
      ACTAAYHDREME-1chrM-156915750.004520.505ACTTACC
      ACTAAYHDREME-1chrM+159616020.004520.505ACGAACC
      ACTAAYHDREME-1chrM+199119970.004520.505ACAAACC
      ACTAAYHDREME-1chrM+257825840.004520.505CCTAACC
      ACTAAYHDREME-1chrM+276527710.004520.505ACAAACC
      ACTAAYHDREME-1chrM-303130370.004520.505ACGAACC
      ACTAAYHDREME-1chrM-322532310.004520.505ACAAACC
      ACTAAYHDREME-1chrM+388338890.004520.505ACCAACC
      ACTAAYHDREME-1chrM+410141070.004520.505TCTAACC
      ACTAAYHDREME-1chrM+419141970.004520.505ACTCACC
      ACTAAYHDREME-1chrM+459846040.004520.505TCTAACC
      ACTAAYHDREME-1chrM+487448800.004520.505ACTAGCC
      ACTAAYHDREME-1chrM+523752430.004520.505GCTAACC
      ACTAAYHDREME-1chrM+583958450.004520.505CCTAACC
      ACTAAYHDREME-1chrM+593159370.004520.505ACAAACC
      ACTAAYHDREME-1chrM+633563410.004520.505CCTAACC
      ACTAAYHDREME-1chrM+722872340.004520.505ACTACCC
      ACTAAYHDREME-1chrM+778177870.004520.505ACTATCC
      ACTAAYHDREME-1chrM+831583210.004520.505ATTAACC
      ACTAAYHDREME-1chrM+850885140.004520.505ACAAACC
      ACTAAYHDREME-1chrM+872187270.004520.505ACGAACC
      ACTAAYHDREME-1chrM+880588110.004520.505ACCAACC
      ACTAAYHDREME-1chrM+900390090.004520.505CCTAACC
      ACTAAYHDREME-1chrM+907690820.004520.505ATTAACC
      ACTAAYHDREME-1chrM+912491300.004520.505ACTATCC
      ACTAAYHDREME-1chrM+11548115540.004520.505ACTATCC
      ACTAAYHDREME-1chrM+11852118580.004520.505GCTAACC
      ACTAAYHDREME-1chrM+11876118820.004520.505ATTAACC
      ACTAAYHDREME-1chrM+11905119110.004520.505AGTAACC
      ACTAAYHDREME-1chrM+12013120190.004520.505ACTCACC
      ACTAAYHDREME-1chrM+12336123420.004520.505AATAACC
      ACTAAYHDREME-1chrM+12363123690.004520.505CCTAACC
      ACTAAYHDREME-1chrM+13295133010.004520.505ACCAACC
      ACTAAYHDREME-1chrM+13672136780.004520.505AATAACC
      ACTAAYHDREME-1chrM+13854138600.004520.505CCTAACC
      ACTAAYHDREME-1chrM+13998140040.004520.505CCTAACC
      ACTAAYHDREME-1chrM+14124141300.004520.505CCTAACC
      ACTAAYHDREME-1chrM+14384143900.004520.505GCTAACC
      ACTAAYHDREME-1chrM+14401144070.004520.505ACTCACC
      ACTAAYHDREME-1chrM+14624146300.004520.505ACAAACC
      ACTAAYHDREME-1chrM+14786147920.004520.505ATTAACC
      ACTAAYHDREME-1chrM+14910149160.004520.505ACTCACC
      ACTAAYHDREME-1chrM+15193151990.004520.505ACTATCC
      ACTAAYHDREME-1chrM+15631156370.004520.505ACTATCC
      ACTAAYHDREME-1chrM+15748157540.004520.505TCTAACC
      ACTAAYHDREME-1chrM+16066160720.004520.505ACTCACC
      ACTAAYHDREME-1chrM+16281162870.004520.505ACAAACC
      ACTAAYHDREME-1chrM+2112170.005430.514ATTAATT
      ACTAAYHDREME-1chrM-2102160.005430.514ATTAATT
      ACTAAYHDREME-1chrM-2142200.005430.514ATTAATT
      ACTAAYHDREME-1chrM-196119670.005430.514ACTATTT
      ACTAAYHDREME-1chrM+218821940.005430.514ACCAATT
      ACTAAYHDREME-1chrM-377137770.005430.514ACTTATT
      ACTAAYHDREME-1chrM-392339290.005430.514ACTAGTT
      ACTAAYHDREME-1chrM-446944750.005430.514ATTAATT
      ACTAAYHDREME-1chrM+454345490.005430.514ACTGATT
      ACTAAYHDREME-1chrM+508550910.005430.514ACTATTT
      ACTAAYHDREME-1chrM+614661520.005430.514ACTAGTT
      ACTAAYHDREME-1chrM+708770930.005430.514ACTGATT
      ACTAAYHDREME-1chrM+730473100.005430.514AATAATT
      ACTAAYHDREME-1chrM+804180470.005430.514AATAATT
      ACTAAYHDREME-1chrM+822182270.005430.514ATTAATT
      ACTAAYHDREME-1chrM-822082260.005430.514ATTAATT
      ACTAAYHDREME-1chrM+879588010.005430.514ACTCATT
      ACTAAYHDREME-1chrM+894689520.005430.514ACTAGTT
      ACTAAYHDREME-1chrM+897389790.005430.514ACTCATT
      ACTAAYHDREME-1chrM+904290480.005430.514CCTAATT
      ACTAAYHDREME-1chrM+911191170.005430.514TCTAATT
      ACTAAYHDREME-1chrM-953895440.005430.514CCTAATT
      ACTAAYHDREME-1chrM+968096860.005430.514AATAATT
      ACTAAYHDREME-1chrM+995399590.005430.514ACTATTT
      ACTAAYHDREME-1chrM-10004100100.005430.514ACTATTT
      ACTAAYHDREME-1chrM+10029100350.005430.514ACTAGTT
      ACTAAYHDREME-1chrM-10028100340.005430.514ACTAGTT
      ACTAAYHDREME-1chrM+10109101150.005430.514AATAATT
      ACTAAYHDREME-1chrM-10112101180.005430.514AATAATT
      ACTAAYHDREME-1chrM-10402104080.005430.514ACCAATT
      ACTAAYHDREME-1chrM+10438104440.005430.514ACTCATT
      ACTAAYHDREME-1chrM+10852108580.005430.514CCTAATT
      ACTAAYHDREME-1chrM-10855108610.005430.514AATAATT
      ACTAAYHDREME-1chrM+10876108820.005430.514ACTATTT
      ACTAAYHDREME-1chrM+11500115060.005430.514ACTCATT
      ACTAAYHDREME-1chrM+12378123840.005430.514CCTAATT
      ACTAAYHDREME-1chrM+12584125900.005430.514ACTACTT
      ACTAAYHDREME-1chrM-12679126850.005430.514ACTGATT
      ACTAAYHDREME-1chrM+12708127140.005430.514CCTAATT
      ACTAAYHDREME-1chrM-13013130190.005430.514CCTAATT
      ACTAAYHDREME-1chrM+13350133560.005430.514ACTATTT
      ACTAAYHDREME-1chrM+13611136170.005430.514AATAATT
      ACTAAYHDREME-1chrM-14296143020.005430.514AATAATT
      ACTAAYHDREME-1chrM+14782147880.005430.514ATTAATT
      ACTAAYHDREME-1chrM-14781147870.005430.514ATTAATT
      ACTAAYHDREME-1chrM+14793147990.005430.514ACTCATT
      ACTAAYHDREME-1chrM+15178151840.005430.514AGTAATT
      ACTAAYHDREME-1chrM+15856158620.005430.514CCTAATT
      ACTAAYHDREME-1chrM+16003160090.005430.514TCTAATT
      ACTAAYHDREME-1chrM-107410800.006350.514TCTAATC
      ACTAAYHDREME-1chrM+227022760.006350.514ACCAATC
      ACTAAYHDREME-1chrM+308130870.006350.514AGTAATC
      ACTAAYHDREME-1chrM+334533510.006350.514TCTAATC
      ACTAAYHDREME-1chrM-382438300.006350.514AGTAATC
      ACTAAYHDREME-1chrM+392439300.006350.514ACTAGTC
      ACTAAYHDREME-1chrM+447044760.006350.514ATTAATC
      ACTAAYHDREME-1chrM+452045260.006350.514ACTCATC
      ACTAAYHDREME-1chrM+473747430.006350.514ACCAATC
      ACTAAYHDREME-1chrM+474747530.006350.514ACTCATC
      ACTAAYHDREME-1chrM+475747630.006350.514AATAATC
      ACTAAYHDREME-1chrM+512051260.006350.514ACTACTC
      ACTAAYHDREME-1chrM+535453600.006350.514CCTAATC
      ACTAAYHDREME-1chrM+537853840.006350.514ACTACTC
      ACTAAYHDREME-1chrM+545354590.006350.514ACTCATC
      ACTAAYHDREME-1chrM+550155070.006350.514AATAATC
      ACTAAYHDREME-1chrM+570757130.006350.514CCTAATC
      ACTAAYHDREME-1chrM+592159270.006350.514ACTATTC
      ACTAAYHDREME-1chrM+609561010.006350.514AATAATC
      ACTAAYHDREME-1chrM-614561510.006350.514ACTAGTC
      ACTAAYHDREME-1chrM+615861640.006350.514AATAATC
      ACTAAYHDREME-1chrM+630763130.006350.514ACTACTC
      ACTAAYHDREME-1chrM+646764730.006350.514CCTAATC
      ACTAAYHDREME-1chrM+665966650.006350.514AATAATC
      ACTAAYHDREME-1chrM+668266880.006350.514ACTACTC
      ACTAAYHDREME-1chrM+698269880.006350.514ACTCATC
      ACTAAYHDREME-1chrM-800780130.006350.514ACTACTC
      ACTAAYHDREME-1chrM+842284280.006350.514ACTATTC
      ACTAAYHDREME-1chrM+858985950.006350.514ACTGATC
      ACTAAYHDREME-1chrM+909390990.006350.514ACTTATC
      ACTAAYHDREME-1chrM+921492200.006350.514ACCAATC
      ACTAAYHDREME-1chrM+10079100850.006350.514AATAATC
      ACTAAYHDREME-1chrM+10337103430.006350.514ATTAATC
      ACTAAYHDREME-1chrM-10387103930.006350.514TCTAATC
      ACTAAYHDREME-1chrM+10658106640.006350.514ACTAGTC
      ACTAAYHDREME-1chrM+10700107060.006350.514ACTAGTC
      ACTAAYHDREME-1chrM+11007110130.006350.514ACTTATC
      ACTAAYHDREME-1chrM+11065110710.006350.514ACAAATC
      ACTAAYHDREME-1chrM+11134111400.006350.514ACTTATC
      ACTAAYHDREME-1chrM+11239112450.006350.514ACTCATC
      ACTAAYHDREME-1chrM+11290112960.006350.514ACTACTC
      ACTAAYHDREME-1chrM+11734117400.006350.514ACTATTC
      ACTAAYHDREME-1chrM+11959119650.006350.514ACTAGTC
      ACTAAYHDREME-1chrM+12676126820.006350.514ATTAATC
      ACTAAYHDREME-1chrM+12699127050.006350.514ACTCATC
      ACTAAYHDREME-1chrM+12952129580.006350.514GCTAATC
      ACTAAYHDREME-1chrM+13113131190.006350.514ACTCATC
      ACTAAYHDREME-1chrM+13419134250.006350.514ACTACTC
      ACTAAYHDREME-1chrM+14118141240.006350.514ACTCATC
      ACTAAYHDREME-1chrM+14136141420.006350.514CCTAATC
      ACTAAYHDREME-1chrM+14366143720.006350.514ACCAATC
      ACTAAYHDREME-1chrM+14890148960.006350.514ACTATTC
      ACTAAYHDREME-1chrM+14907149130.006350.514ACTACTC
      ACTAAYHDREME-1chrM+15475154810.006350.514ACTATTC
      ACTAAYHDREME-1chrM+15652156580.006350.514AATAATC
      ACTAAYHDREME-1chrM+15832158380.006350.514CCTAATC
      ACTAAYHDREME-1chrM+15951159570.006350.514ACAAATC
      ACTAAYHDREME-1chrM+16013160190.006350.514ACTATTC
      ACTAAYHDREME-1chrM+1972030.006470.521ACTAAAG
      ACTAAYHDREME-1chrM+871387190.006470.521ACTAAAG
      ACTAAYHDREME-1chrM+28340.007390.559ACTCACG
      ACTAAYHDREME-1chrM-132213280.007390.559CCTAACG
      ACTAAYHDREME-1chrM+291029160.007390.559ACCAACG
      ACTAAYHDREME-1chrM-303530410.007390.559ACAAACG
      ACTAAYHDREME-1chrM+510651120.007390.559ACTACCG
      ACTAAYHDREME-1chrM-721872240.007390.559AGTAACG
      ACTAAYHDREME-1chrM+838183870.007390.559ACTACCG
      ACTAAYHDREME-1chrM+10580105860.007390.559ACTATCG
      ACTAAYHDREME-1chrM+11760117660.007390.559ACGAACG
      ACTAAYHDREME-1chrM+13546135520.007390.559ACAAACG
      ACTAAYHDREME-1chrM+13663136690.007390.559ATTAACG
      ACTAAYHDREME-1chrM-57630.009220.559ACGAAAA
      ACTAAYHDREME-1chrM+2842900.009220.559ACAAAAA
      ACTAAYHDREME-1chrM+3313370.009220.559ACTTAAA
      ACTAAYHDREME-1chrM+3613670.009220.559ACAAAGA
      ACTAAYHDREME-1chrM+6086140.009220.559ACTGAAA
      ACTAAYHDREME-1chrM+6826880.009220.559AGTAAGA
      ACTAAYHDREME-1chrM-9469520.009220.559TCTAAAA
      ACTAAYHDREME-1chrM+9729780.009220.559GCTAAAA
      ACTAAYHDREME-1chrM+101910250.009220.559ACTACGA
      ACTAAYHDREME-1chrM+105710630.009220.559GCTAAGA
      ACTAAYHDREME-1chrM+114211480.009220.559ACTACGA
      ACTAAYHDREME-1chrM+116211680.009220.559ACTCAAA
      ACTAAYHDREME-1chrM+138413900.009220.559ACTACGA
      ACTAAYHDREME-1chrM+186418700.009220.559ACTAGAA
      ACTAAYHDREME-1chrM+189419000.009220.559GCTAAGA
      ACTAAYHDREME-1chrM+192219280.009220.559CCTAAGA
      ACTAAYHDREME-1chrM+193219380.009220.559GCTAAAA
      ACTAAYHDREME-1chrM+212421300.009220.559ACTAGGA
      ACTAAYHDREME-1chrM+214821540.009220.559AGTAAAA
      ACTAAYHDREME-1chrM+217521810.009220.559CCTAAAA
      ACTAAYHDREME-1chrM+219221980.009220.559ATTAAGA
      ACTAAYHDREME-1chrM+222422300.009220.559CCTAAAA
      ACTAAYHDREME-1chrM+235023560.009220.559ATTAAAA
      ACTAAYHDREME-1chrM+246324690.009220.559AGTAAAA
      ACTAAYHDREME-1chrM+250025060.009220.559ACCAAAA
      ACTAAYHDREME-1chrM-265826640.009220.559AGTAAGA
      ACTAAYHDREME-1chrM+279828040.009220.559ATTAAAA
      ACTAAYHDREME-1chrM+285528610.009220.559GCTAAGA
      ACTAAYHDREME-1chrM-306530710.009220.559ACTCAGA
      ACTAAYHDREME-1chrM+326232680.009220.559ACTTAAA
      ACTAAYHDREME-1chrM+337833840.009220.559ACGAAAA
      ACTAAYHDREME-1chrM+344134470.009220.559ACTACAA
      ACTAAYHDREME-1chrM+348634920.009220.559CCTAAAA
      ACTAAYHDREME-1chrM+355835640.009220.559ACTATGA
      ACTAAYHDREME-1chrM+367736830.009220.559ACTCAAA
      ACTAAYHDREME-1chrM+402140270.009220.559ACTACAA
      ACTAAYHDREME-1chrM+408740930.009220.559ACCAAGA
      ACTAAYHDREME-1chrM+425942650.009220.559CCTAAGA
      ACTAAYHDREME-1chrM+433443400.009220.559ACTATGA
      ACTAAYHDREME-1chrM-458645920.009220.559AATAAAA
      ACTAAYHDREME-1chrM+460246080.009220.559ACCAAAA
      ACTAAYHDREME-1chrM+477847840.009220.559AATAAAA
      ACTAAYHDREME-1chrM+478447900.009220.559ACTAGGA
      ACTAAYHDREME-1chrM-480748130.009220.559ACTCAGA
      ACTAAYHDREME-1chrM+486848740.009220.559ACAAAAA
      ACTAAYHDREME-1chrM-500250080.009220.559GCTAAGA
      ACTAAYHDREME-1chrM-507550810.009220.559ATTAAGA
      ACTAAYHDREME-1chrM+512851340.009220.559ACTTAAA
      ACTAAYHDREME-1chrM+528052860.009220.559ACAAAAA
      ACTAAYHDREME-1chrM+540554110.009220.559AATAAAA
      ACTAAYHDREME-1chrM+553355390.009220.559ACCAAGA
      ACTAAYHDREME-1chrM+567056760.009220.559ACTTAAA
      ACTAAYHDREME-1chrM+593859440.009220.559ACAAAGA
      ACTAAYHDREME-1chrM-610661120.009220.559ACTATGA
      ACTAAYHDREME-1chrM-637663820.009220.559CCTAAGA
      ACTAAYHDREME-1chrM-645164570.009220.559ACGAAGA
      ACTAAYHDREME-1chrM+744574510.009220.559ACAAAAA
      ACTAAYHDREME-1chrM-758175870.009220.559ATTAAGA
      ACTAAYHDREME-1chrM-769276980.009220.559ACTAGGA
      ACTAAYHDREME-1chrM-780078060.009220.559ACTAGGA
      ACTAAYHDREME-1chrM+823082360.009220.559CCTAAAA
      ACTAAYHDREME-1chrM-832383290.009220.559ACTTAAA
      ACTAAYHDREME-1chrM+833583410.009220.559ATTAAGA
      ACTAAYHDREME-1chrM+849485000.009220.559AATAAAA
      ACTAAYHDREME-1chrM+852185270.009220.559ACCAAAA
      ACTAAYHDREME-1chrM+853185370.009220.559ACGAAAA
      ACTAAYHDREME-1chrM-875787630.009220.559AATAAAA
      ACTAAYHDREME-1chrM+888188870.009220.559TCTAAGA
      ACTAAYHDREME-1chrM+888788930.009220.559ATTAAAA
      ACTAAYHDREME-1chrM-917391790.009220.559ACTAGAA
      ACTAAYHDREME-1chrM+923692420.009220.559AGTAAAA
      ACTAAYHDREME-1chrM-970697120.009220.559AGTAAAA
      ACTAAYHDREME-1chrM-979698020.009220.559ACAAAAA
      ACTAAYHDREME-1chrM-998799930.009220.559AGTAAGA
      ACTAAYHDREME-1chrM-10075100810.009220.559ATTAAAA
      ACTAAYHDREME-1chrM-10243102490.009220.559AATAAGA
      ACTAAYHDREME-1chrM-10333103390.009220.559AATAAGA
      ACTAAYHDREME-1chrM+10376103820.009220.559ACTACAA
      ACTAAYHDREME-1chrM+10379103850.009220.559ACAAAAA
      ACTAAYHDREME-1chrM-10630106360.009220.559GCTAAGA
      ACTAAYHDREME-1chrM+10762107680.009220.559GCTAAAA
      ACTAAYHDREME-1chrM+11029110350.009220.559ACGAAAA
      ACTAAYHDREME-1chrM-11367113730.009220.559ACTATAA
      ACTAAYHDREME-1chrM+11602116080.009220.559CCTAAAA
      ACTAAYHDREME-1chrM-11646116520.009220.559ACTACGA
      ACTAAYHDREME-1chrM+11751117570.009220.559ACTCAAA
      ACTAAYHDREME-1chrM+11757117630.009220.559ACTACGA
      ACTAAYHDREME-1chrM+12152121580.009220.559ACCAAAA
      ACTAAYHDREME-1chrM-12295123010.009220.559CCTAAGA
      ACTAAYHDREME-1chrM-12311123170.009220.559ACCAAAA
      ACTAAYHDREME-1chrM+12327123330.009220.559AATAAAA
      ACTAAYHDREME-1chrM+12352123580.009220.559ACTATAA
      ACTAAYHDREME-1chrM+12416124220.009220.559ACAAAAA
      ACTAAYHDREME-1chrM+12509125150.009220.559ACCAAGA
      ACTAAYHDREME-1chrM+12662126680.009220.559ACTCAGA
      ACTAAYHDREME-1chrM-13109131150.009220.559AGTAAGA
      ACTAAYHDREME-1chrM+13263132690.009220.559ACTAGGA
      ACTAAYHDREME-1chrM+13422134280.009220.559ACTCAAA
      ACTAAYHDREME-1chrM+13667136730.009220.559ACGAAAA
      ACTAAYHDREME-1chrM+13791137970.009220.559CCTAAAA
      ACTAAYHDREME-1chrM+13866138720.009220.559ACTTAAA
      ACTAAYHDREME-1chrM+13872138780.009220.559AATAAAA
      ACTAAYHDREME-1chrM-13894139000.009220.559AATAAAA
      ACTAAYHDREME-1chrM+14007140130.009220.559ACTAGAA
      ACTAAYHDREME-1chrM+14023140290.009220.559CCTAAAA
      ACTAAYHDREME-1chrM+14405144110.009220.559ACCAAGA
      ACTAAYHDREME-1chrM+14501145070.009220.559ATTAAAA
      ACTAAYHDREME-1chrM+14687146930.009220.559ACTACAA
      ACTAAYHDREME-1chrM+14732147380.009220.559ACTACAA
      ACTAAYHDREME-1chrM+14776147820.009220.559AATAAAA
      ACTAAYHDREME-1chrM+15072150780.009220.559ACTCAGA
      ACTAAYHDREME-1chrM+15607156130.009220.559ACTAGGA
      ACTAAYHDREME-1chrM+15874158800.009220.559ACTCAAA
      ACTAAYHDREME-1chrM-15892158980.009220.559ACTACAA
      ACTAAYHDREME-1chrM+15995160010.009220.559GCTAAGA
      ACTAAYHDREME-1chrM+16269162750.009220.559ACTAGGA
      ACTAAYHDREME-1chrM+16553165590.009220.559AATAAGA
      + +
      +
      DEBUGGING INFORMATION
      +
      +

      +Command line: +

      +
      +fimo -o ./fimo_test4_out --thresh 0.01 --bgfile --uniform-- --max-stored-scores 100000 --motif ACTAAYH --motif-pseudo 0.1 dreme_fimo_input_1.xml hsa_chrM.fa
      +
      +

      +Settings: +

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      output_directory = ./fimo_test4_outMEME file name = dreme_fimo_input_1.xmlsequence file name = hsa_chrM.fa
      background file name = --uniform--alphabet = DNAmax stored scores = 100000
      allow clobber = falsecompute q-values = trueparse genomic coord. = false
      text only = falsescan both strands = truemax strand = false
      threshold type = p-valueoutput theshold = 0.01pseudocount = 0.1
      alpha = 1verbosity = 2
      +
      +

      +This information can be useful in the event you wish to report a +problem with the FIMO software. +

      +
      +Go to top + + diff -r 793225b11202 -r b48e673af4e8 test-data/fimo_output_test3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_test3.txt Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,518 @@ +# motif_id motif_alt_id sequence_name start stop strand score p-value q-value matched_sequence +ACTAAYH DREME-1 chrM 440 446 + 12.1831 6.1e-05 0.239 ACTAACA +ACTAAYH DREME-1 chrM 2093 2099 - 12.1831 6.1e-05 0.239 ACTAACA +ACTAAYH DREME-1 chrM 2299 2305 - 12.1831 6.1e-05 0.239 ACTAACA +ACTAAYH DREME-1 chrM 5186 5192 + 12.1831 6.1e-05 0.239 ACTAACA +ACTAAYH DREME-1 chrM 6530 6536 + 12.1831 6.1e-05 0.239 ACTAACA +ACTAAYH DREME-1 chrM 7742 7748 + 12.1831 6.1e-05 0.239 ACTAACA +ACTAAYH DREME-1 chrM 13657 13663 + 12.1831 6.1e-05 0.239 ACTAACA +ACTAAYH DREME-1 chrM 13741 13747 + 12.1831 6.1e-05 0.239 ACTAACA +ACTAAYH DREME-1 chrM 3768 3774 + 11.5915 0.000122 0.239 ACTAATA +ACTAAYH DREME-1 chrM 5498 5504 + 11.5915 0.000122 0.239 ACTAATA +ACTAAYH DREME-1 chrM 7736 7742 + 11.5915 0.000122 0.239 ACTAATA +ACTAAYH DREME-1 chrM 9872 9878 + 11.5915 0.000122 0.239 ACTAATA +ACTAAYH DREME-1 chrM 10106 10112 + 11.5915 0.000122 0.239 ACTAATA +ACTAAYH DREME-1 chrM 10313 10319 + 11.5915 0.000122 0.239 ACTAATA +ACTAAYH DREME-1 chrM 11818 11824 + 11.5915 0.000122 0.239 ACTAATA +ACTAAYH DREME-1 chrM 15903 15909 + 11.5915 0.000122 0.239 ACTAATA +ACTAAYH DREME-1 chrM 7732 7738 + 11.4507 0.000183 0.294 ACTAACT +ACTAAYH DREME-1 chrM 10960 10966 + 11.4507 0.000183 0.294 ACTAACT +ACTAAYH DREME-1 chrM 862 868 + 11.2394 0.000244 0.294 ACTAACC +ACTAAYH DREME-1 chrM 1832 1838 + 11.2394 0.000244 0.294 ACTAACC +ACTAAYH DREME-1 chrM 8679 8685 + 11.2394 0.000244 0.294 ACTAACC +ACTAAYH DREME-1 chrM 8770 8776 + 11.2394 0.000244 0.294 ACTAACC +ACTAAYH DREME-1 chrM 9347 9353 + 11.2394 0.000244 0.294 ACTAACC +ACTAAYH DREME-1 chrM 9359 9365 + 11.2394 0.000244 0.294 ACTAACC +ACTAAYH DREME-1 chrM 10302 10308 + 11.2394 0.000244 0.294 ACTAACC +ACTAAYH DREME-1 chrM 14765 14771 + 11.2394 0.000244 0.294 ACTAACC +ACTAAYH DREME-1 chrM 4466 4472 + 10.8592 0.000305 0.302 ACTAATT +ACTAAYH DREME-1 chrM 11248 11254 + 10.8592 0.000305 0.302 ACTAATT +ACTAAYH DREME-1 chrM 475 481 + 10.6479 0.000366 0.302 ACTAATC +ACTAAYH DREME-1 chrM 7930 7936 + 10.6479 0.000366 0.302 ACTAATC +ACTAAYH DREME-1 chrM 8649 8655 + 10.6479 0.000366 0.302 ACTAATC +ACTAAYH DREME-1 chrM 8670 8676 + 10.6479 0.000366 0.302 ACTAATC +ACTAAYH DREME-1 chrM 10768 10774 + 10.6479 0.000366 0.302 ACTAATC +ACTAAYH DREME-1 chrM 11053 11059 + 10.6479 0.000366 0.302 ACTAATC +ACTAAYH DREME-1 chrM 11101 11107 + 10.6479 0.000366 0.302 ACTAATC +ACTAAYH DREME-1 chrM 12720 12726 + 10.6479 0.000366 0.302 ACTAATC +ACTAAYH DREME-1 chrM 13149 13155 + 10.6479 0.000366 0.302 ACTAATC +ACTAAYH DREME-1 chrM 14216 14222 + 10.6479 0.000366 0.302 ACTAATC +ACTAAYH DREME-1 chrM 678 684 - -1.07042 0.000549 0.366 ACTAAGA +ACTAAYH DREME-1 chrM 1435 1441 + -1.07042 0.000549 0.366 ACTAAGA +ACTAAYH DREME-1 chrM 1524 1530 + -1.07042 0.000549 0.366 ACTAAAA +ACTAAYH DREME-1 chrM 2035 2041 - -1.07042 0.000549 0.366 ACTAAGA +ACTAAYH DREME-1 chrM 8440 8446 + -1.07042 0.000549 0.366 ACTAAAA +ACTAAYH DREME-1 chrM 9995 10001 - -1.07042 0.000549 0.366 ACTAAAA +ACTAAYH DREME-1 chrM 10225 10231 - -1.07042 0.000549 0.366 ACTAAGA +ACTAAYH DREME-1 chrM 12725 12731 - -1.07042 0.000549 0.366 ACTAAGA +ACTAAYH DREME-1 chrM 14393 14399 + -1.07042 0.000549 0.366 ACTAAAA +ACTAAYH DREME-1 chrM 2294 2300 + -1.30986 0.00061 0.398 ACTAATG +ACTAAYH DREME-1 chrM 206 212 - -1.80282 0.00165 0.441 ATTAACA +ACTAAYH DREME-1 chrM 237 243 + -1.80282 0.00165 0.441 AATAACA +ACTAAYH DREME-1 chrM 370 376 + -1.80282 0.00165 0.441 CCTAACA +ACTAAYH DREME-1 chrM 1630 1636 + -1.80282 0.00165 0.441 ACTTACA +ACTAAYH DREME-1 chrM 1702 1708 + -1.80282 0.00165 0.441 ACTACCA +ACTAAYH DREME-1 chrM 2309 2315 + -1.80282 0.00165 0.441 AGTAACA +ACTAAYH DREME-1 chrM 2363 2369 + -1.80282 0.00165 0.441 ACTGACA +ACTAAYH DREME-1 chrM 2370 2376 + -1.80282 0.00165 0.441 ATTAACA +ACTAAYH DREME-1 chrM 2395 2401 + -1.80282 0.00165 0.441 ACCAACA +ACTAAYH DREME-1 chrM 2761 2767 + -1.80282 0.00165 0.441 CCTAACA +ACTAAYH DREME-1 chrM 2784 2790 + -1.80282 0.00165 0.441 ACTACCA +ACTAAYH DREME-1 chrM 3191 3197 - -1.80282 0.00165 0.441 ACTAAGT +ACTAAYH DREME-1 chrM 3756 3762 + -1.80282 0.00165 0.441 ACTATCA +ACTAAYH DREME-1 chrM 3873 3879 + -1.80282 0.00165 0.441 ACTAGCA +ACTAAYH DREME-1 chrM 3991 3997 + -1.80282 0.00165 0.441 ACAAACA +ACTAAYH DREME-1 chrM 4445 4451 - -1.80282 0.00165 0.441 ACCAACA +ACTAAYH DREME-1 chrM 4734 4740 + -1.80282 0.00165 0.441 ACTACCA +ACTAAYH DREME-1 chrM 5061 5067 + -1.80282 0.00165 0.441 CCTAACA +ACTAAYH DREME-1 chrM 5177 5183 + -1.80282 0.00165 0.441 GCTAACA +ACTAAYH DREME-1 chrM 5391 5397 + -1.80282 0.00165 0.441 TCTAACA +ACTAAYH DREME-1 chrM 5680 5686 + -1.80282 0.00165 0.441 ACAAACA +ACTAAYH DREME-1 chrM 5686 5692 - -1.80282 0.00165 0.441 ACTAAGT +ACTAAYH DREME-1 chrM 6595 6601 + -1.80282 0.00165 0.441 ACCAACA +ACTAAYH DREME-1 chrM 7146 7152 + -1.80282 0.00165 0.441 ACTATCA +ACTAAYH DREME-1 chrM 7286 7292 + -1.80282 0.00165 0.441 TCTAACA +ACTAAYH DREME-1 chrM 7714 7720 + -1.80282 0.00165 0.441 CCTAACA +ACTAAYH DREME-1 chrM 7720 7726 + -1.80282 0.00165 0.441 ACTCACA +ACTAAYH DREME-1 chrM 8344 8350 + -1.80282 0.00165 0.441 ACCAACA +ACTAAYH DREME-1 chrM 8374 8380 + -1.80282 0.00165 0.441 ACTAAAT +ACTAAYH DREME-1 chrM 8460 8466 + -1.80282 0.00165 0.441 ACTACCA +ACTAAYH DREME-1 chrM 9010 9016 + -1.80282 0.00165 0.441 GCTAACA +ACTAAYH DREME-1 chrM 9257 9263 + -1.80282 0.00165 0.441 CCTAACA +ACTAAYH DREME-1 chrM 9351 9357 + -1.80282 0.00165 0.441 ACCAACA +ACTAAYH DREME-1 chrM 10127 10133 + -1.80282 0.00165 0.441 ACTACCA +ACTAAYH DREME-1 chrM 10295 10301 + -1.80282 0.00165 0.441 ACAAACA +ACTAAYH DREME-1 chrM 10496 10502 + -1.80282 0.00165 0.441 ACTAGCA +ACTAAYH DREME-1 chrM 10792 10798 + -1.80282 0.00165 0.441 ACTACCA +ACTAAYH DREME-1 chrM 10798 10804 + -1.80282 0.00165 0.441 ACTGACA +ACTAAYH DREME-1 chrM 10939 10945 + -1.80282 0.00165 0.441 CCTAACA +ACTAAYH DREME-1 chrM 11023 11029 + -1.80282 0.00165 0.441 ACTATCA +ACTAAYH DREME-1 chrM 11258 11264 + -1.80282 0.00165 0.441 ACTCACA +ACTAAYH DREME-1 chrM 11314 11320 + -1.80282 0.00165 0.441 ACTATCA +ACTAAYH DREME-1 chrM 11593 11599 + -1.80282 0.00165 0.441 ACAAACA +ACTAAYH DREME-1 chrM 11650 11656 + -1.80282 0.00165 0.441 AGTAACA +ACTAAYH DREME-1 chrM 11768 11774 + -1.80282 0.00165 0.441 ACTCACA +ACTAAYH DREME-1 chrM 11901 11907 - -1.80282 0.00165 0.441 ACTAGCA +ACTAAYH DREME-1 chrM 11941 11947 + -1.80282 0.00165 0.441 ACTTACA +ACTAAYH DREME-1 chrM 12026 12032 + -1.80282 0.00165 0.441 ATTAACA +ACTAAYH DREME-1 chrM 12245 12251 + -1.80282 0.00165 0.441 TCTAACA +ACTAAYH DREME-1 chrM 12412 12418 + -1.80282 0.00165 0.441 CCTAACA +ACTAAYH DREME-1 chrM 12530 12536 + -1.80282 0.00165 0.441 ACTGACA +ACTAAYH DREME-1 chrM 12617 12623 - -1.80282 0.00165 0.441 ACGAACA +ACTAAYH DREME-1 chrM 12736 12742 + -1.80282 0.00165 0.441 GCTAACA +ACTAAYH DREME-1 chrM 13161 13167 + -1.80282 0.00165 0.441 TCTAACA +ACTAAYH DREME-1 chrM 13626 13632 + -1.80282 0.00165 0.441 CCTAACA +ACTAAYH DREME-1 chrM 13797 13803 + -1.80282 0.00165 0.441 ACTCACA +ACTAAYH DREME-1 chrM 13830 13836 + -1.80282 0.00165 0.441 TCTAACA +ACTAAYH DREME-1 chrM 13858 13864 + -1.80282 0.00165 0.441 ACCAACA +ACTAAYH DREME-1 chrM 14185 14191 + -1.80282 0.00165 0.441 ACCAACA +ACTAAYH DREME-1 chrM 14189 14195 + -1.80282 0.00165 0.441 ACAAACA +ACTAAYH DREME-1 chrM 14548 14554 + -1.80282 0.00165 0.441 AATAACA +ACTAAYH DREME-1 chrM 14569 14575 + -1.80282 0.00165 0.441 GCTAACA +ACTAAYH DREME-1 chrM 15469 15475 + -1.80282 0.00165 0.441 ATTAACA +ACTAAYH DREME-1 chrM 15599 15605 + -1.80282 0.00165 0.441 CCTAACA +ACTAAYH DREME-1 chrM 16227 16233 + -1.80282 0.00165 0.441 ACTATCA +ACTAAYH DREME-1 chrM 16277 16283 + -1.80282 0.00165 0.441 ACCAACA +ACTAAYH DREME-1 chrM 852 858 + -2.01408 0.00177 0.441 ACTAAGC +ACTAAYH DREME-1 chrM 1449 1455 - -2.01408 0.00177 0.441 ACTAAGC +ACTAAYH DREME-1 chrM 4913 4919 + -2.01408 0.00177 0.441 ACTAAAC +ACTAAYH DREME-1 chrM 11278 11284 + -2.01408 0.00177 0.441 ACTAAAC +ACTAAYH DREME-1 chrM 13686 13692 + -2.01408 0.00177 0.441 ACTAAAC +ACTAAYH DREME-1 chrM 14582 14588 + -2.01408 0.00177 0.441 ACTAAAC +ACTAAYH DREME-1 chrM 14636 14642 + -2.01408 0.00177 0.441 ACTAAAC +ACTAAYH DREME-1 chrM 15703 15709 + -2.01408 0.00177 0.441 ACTAAGC +ACTAAYH DREME-1 chrM 152 158 - -2.39437 0.00269 0.441 AATAATA +ACTAAYH DREME-1 chrM 234 240 + -2.39437 0.00269 0.441 AATAATA +ACTAAYH DREME-1 chrM 472 478 + -2.39437 0.00269 0.441 ACTACTA +ACTAAYH DREME-1 chrM 645 651 + -2.39437 0.00269 0.441 ACAAATA +ACTAAYH DREME-1 chrM 671 677 - -2.39437 0.00269 0.441 GCTAATA +ACTAAYH DREME-1 chrM 2305 2311 - -2.39437 0.00269 0.441 ACTTATA +ACTAAYH DREME-1 chrM 2529 2535 - -2.39437 0.00269 0.441 TCTAATA +ACTAAYH DREME-1 chrM 2744 2750 - -2.39437 0.00269 0.441 ATTAATA +ACTAAYH DREME-1 chrM 2880 2886 + -2.39437 0.00269 0.441 ACTACTA +ACTAAYH DREME-1 chrM 4158 4164 + -2.39437 0.00269 0.441 ACTCATA +ACTAAYH DREME-1 chrM 4206 4212 + -2.39437 0.00269 0.441 ACTTATA +ACTAAYH DREME-1 chrM 4301 4307 + -2.39437 0.00269 0.441 AATAATA +ACTAAYH DREME-1 chrM 4679 4685 + -2.39437 0.00269 0.441 TCTAATA +ACTAAYH DREME-1 chrM 4728 4734 + -2.39437 0.00269 0.441 ACCAATA +ACTAAYH DREME-1 chrM 4754 4760 + -2.39437 0.00269 0.441 ATTAATA +ACTAAYH DREME-1 chrM 5036 5042 + -2.39437 0.00269 0.441 AATAATA +ACTAAYH DREME-1 chrM 5103 5109 + -2.39437 0.00269 0.441 ACTACTA +ACTAAYH DREME-1 chrM 5153 5159 + -2.39437 0.00269 0.441 ACTACTA +ACTAAYH DREME-1 chrM 5962 5968 - -2.39437 0.00269 0.441 AATAATA +ACTAAYH DREME-1 chrM 6110 6116 + -2.39437 0.00269 0.441 AGTAATA +ACTAAYH DREME-1 chrM 6155 6161 + -2.39437 0.00269 0.441 CCTAATA +ACTAAYH DREME-1 chrM 6527 6533 + -2.39437 0.00269 0.441 ACTACTA +ACTAAYH DREME-1 chrM 6973 6979 - -2.39437 0.00269 0.441 GCTAATA +ACTAAYH DREME-1 chrM 7295 7301 + -2.39437 0.00269 0.441 AGTAATA +ACTAAYH DREME-1 chrM 7301 7307 + -2.39437 0.00269 0.441 ATTAATA +ACTAAYH DREME-1 chrM 7300 7306 - -2.39437 0.00269 0.441 ATTAATA +ACTAAYH DREME-1 chrM 7349 7355 + -2.39437 0.00269 0.441 CCTAATA +ACTAAYH DREME-1 chrM 7351 7357 - -2.39437 0.00269 0.441 ACTATTA +ACTAAYH DREME-1 chrM 7522 7528 - -2.39437 0.00269 0.441 TCTAATA +ACTAAYH DREME-1 chrM 8739 8745 + -2.39437 0.00269 0.441 ACTAGTA +ACTAAYH DREME-1 chrM 8738 8744 - -2.39437 0.00269 0.441 ACTAGTA +ACTAAYH DREME-1 chrM 8945 8951 - -2.39437 0.00269 0.441 ACTAGTA +ACTAAYH DREME-1 chrM 8982 8988 + -2.39437 0.00269 0.441 ACCAATA +ACTAAYH DREME-1 chrM 9613 9619 - -2.39437 0.00269 0.441 AGTAATA +ACTAAYH DREME-1 chrM 9656 9662 + -2.39437 0.00269 0.441 TCTAATA +ACTAAYH DREME-1 chrM 10055 10061 + -2.39437 0.00269 0.441 AGTAATA +ACTAAYH DREME-1 chrM 10103 10109 + -2.39437 0.00269 0.441 ACTACTA +ACTAAYH DREME-1 chrM 10246 10252 - -2.39437 0.00269 0.441 AATAATA +ACTAAYH DREME-1 chrM 10315 10321 - -2.39437 0.00269 0.441 ACTATTA +ACTAAYH DREME-1 chrM 10336 10342 - -2.39437 0.00269 0.441 ATTAATA +ACTAAYH DREME-1 chrM 10368 10374 - -2.39437 0.00269 0.441 ACTCATA +ACTAAYH DREME-1 chrM 10526 10532 + -2.39437 0.00269 0.441 ACTAGTA +ACTAAYH DREME-1 chrM 10525 10531 - -2.39437 0.00269 0.441 ACTAGTA +ACTAAYH DREME-1 chrM 10574 10580 + -2.39437 0.00269 0.441 AATAATA +ACTAAYH DREME-1 chrM 10657 10663 - -2.39437 0.00269 0.441 ACTAGTA +ACTAAYH DREME-1 chrM 10699 10705 - -2.39437 0.00269 0.441 ACTAGTA +ACTAAYH DREME-1 chrM 10788 10794 - -2.39437 0.00269 0.441 AGTAATA +ACTAAYH DREME-1 chrM 10858 10864 - -2.39437 0.00269 0.441 GCTAATA +ACTAAYH DREME-1 chrM 10954 10960 + -2.39437 0.00269 0.441 CCTAATA +ACTAAYH DREME-1 chrM 11873 11879 + -2.39437 0.00269 0.441 ACTATTA +ACTAAYH DREME-1 chrM 11958 11964 - -2.39437 0.00269 0.441 ACTAGTA +ACTAAYH DREME-1 chrM 12333 12339 + -2.39437 0.00269 0.441 AGTAATA +ACTAAYH DREME-1 chrM 12349 12355 + -2.39437 0.00269 0.441 ACTACTA +ACTAAYH DREME-1 chrM 12425 12431 + -2.39437 0.00269 0.441 ACTCATA +ACTAAYH DREME-1 chrM 12471 12477 - -2.39437 0.00269 0.441 ACTGATA +ACTAAYH DREME-1 chrM 12933 12939 + -2.39437 0.00269 0.441 ACAAATA +ACTAAYH DREME-1 chrM 12972 12978 + -2.39437 0.00269 0.441 ACTACTA +ACTAAYH DREME-1 chrM 13269 13275 + -2.39437 0.00269 0.441 ACTCATA +ACTAAYH DREME-1 chrM 13274 13280 - -2.39437 0.00269 0.441 ACTATTA +ACTAAYH DREME-1 chrM 13566 13572 - -2.39437 0.00269 0.441 AGTAATA +ACTAAYH DREME-1 chrM 14210 14216 + -2.39437 0.00269 0.441 ACTACTA +ACTAAYH DREME-1 chrM 14213 14219 + -2.39437 0.00269 0.441 ACTACTA +ACTAAYH DREME-1 chrM 14251 14257 + -2.39437 0.00269 0.441 ACCAATA +ACTAAYH DREME-1 chrM 14314 14320 + -2.39437 0.00269 0.441 ACTATTA +ACTAAYH DREME-1 chrM 14510 14516 + -2.39437 0.00269 0.441 ACTATTA +ACTAAYH DREME-1 chrM 14545 14551 + -2.39437 0.00269 0.441 AATAATA +ACTAAYH DREME-1 chrM 14773 14779 + -2.39437 0.00269 0.441 CCTAATA +ACTAAYH DREME-1 chrM 15627 15633 - -2.39437 0.00269 0.441 AGTAATA +ACTAAYH DREME-1 chrM 15838 15844 + -2.39437 0.00269 0.441 CCTAATA +ACTAAYH DREME-1 chrM 193 199 + -2.53521 0.0036 0.501 ACTTACT +ACTAAYH DREME-1 chrM 714 720 - -2.53521 0.0036 0.501 ACTCACT +ACTAAYH DREME-1 chrM 1860 1866 + -2.53521 0.0036 0.501 ATTAACT +ACTAAYH DREME-1 chrM 1870 1876 + -2.53521 0.0036 0.501 AATAACT +ACTAAYH DREME-1 chrM 2220 2226 + -2.53521 0.0036 0.501 ACTACCT +ACTAAYH DREME-1 chrM 2901 2907 + -2.53521 0.0036 0.501 AATAACT +ACTAAYH DREME-1 chrM 4154 4160 + -2.53521 0.0036 0.501 ACCAACT +ACTAAYH DREME-1 chrM 4283 4289 - -2.53521 0.0036 0.501 AGTAACT +ACTAAYH DREME-1 chrM 5099 5105 + -2.53521 0.0036 0.501 CCTAACT +ACTAAYH DREME-1 chrM 5156 5162 + -2.53521 0.0036 0.501 ACTATCT +ACTAAYH DREME-1 chrM 5555 5561 - -2.53521 0.0036 0.501 ACTTACT +ACTAAYH DREME-1 chrM 6142 6148 + -2.53521 0.0036 0.501 ACTGACT +ACTAAYH DREME-1 chrM 6678 6684 + -2.53521 0.0036 0.501 ACTTACT +ACTAAYH DREME-1 chrM 7169 7175 + -2.53521 0.0036 0.501 TCTAACT +ACTAAYH DREME-1 chrM 8304 8310 + -2.53521 0.0036 0.501 GCTAACT +ACTAAYH DREME-1 chrM 8456 8462 + -2.53521 0.0036 0.501 ACAAACT +ACTAAYH DREME-1 chrM 8817 8823 + -2.53521 0.0036 0.501 ACTATCT +ACTAAYH DREME-1 chrM 8949 8955 - -2.53521 0.0036 0.501 AATAACT +ACTAAYH DREME-1 chrM 9120 9126 + -2.53521 0.0036 0.501 ACTGACT +ACTAAYH DREME-1 chrM 9852 9858 + -2.53521 0.0036 0.501 ACTATCT +ACTAAYH DREME-1 chrM 10025 10031 + -2.53521 0.0036 0.501 ATTAACT +ACTAAYH DREME-1 chrM 10964 10970 + -2.53521 0.0036 0.501 ACTACCT +ACTAAYH DREME-1 chrM 11293 11299 + -2.53521 0.0036 0.501 ACTCACT +ACTAAYH DREME-1 chrM 11347 11353 + -2.53521 0.0036 0.501 ACTAGCT +ACTAAYH DREME-1 chrM 12226 12232 + -2.53521 0.0036 0.501 GCTAACT +ACTAAYH DREME-1 chrM 12516 12522 - -2.53521 0.0036 0.501 AATAACT +ACTAAYH DREME-1 chrM 13850 13856 + -2.53521 0.0036 0.501 ACTACCT +ACTAAYH DREME-1 chrM 13862 13868 + -2.53521 0.0036 0.501 ACAAACT +ACTAAYH DREME-1 chrM 14206 14212 + -2.53521 0.0036 0.501 AGTAACT +ACTAAYH DREME-1 chrM 15185 15191 + -2.53521 0.0036 0.501 ACAAACT +ACTAAYH DREME-1 chrM 15189 15195 + -2.53521 0.0036 0.501 ACTTACT +ACTAAYH DREME-1 chrM 15603 15609 + -2.53521 0.0036 0.501 ACAAACT +ACTAAYH DREME-1 chrM 15844 15850 + -2.53521 0.0036 0.501 ACCAACT +ACTAAYH DREME-1 chrM 15848 15854 + -2.53521 0.0036 0.501 ACTATCT +ACTAAYH DREME-1 chrM 21 27 + -2.74648 0.00452 0.505 ATTAACC +ACTAAYH DREME-1 chrM 381 387 + -2.74648 0.00452 0.505 CCTAACC +ACTAAYH DREME-1 chrM 529 535 + -2.74648 0.00452 0.505 GCTAACC +ACTAAYH DREME-1 chrM 547 553 + -2.74648 0.00452 0.505 ACCAACC +ACTAAYH DREME-1 chrM 823 829 + -2.74648 0.00452 0.505 ATTAACC +ACTAAYH DREME-1 chrM 873 879 - -2.74648 0.00452 0.505 ACCAACC +ACTAAYH DREME-1 chrM 910 916 + -2.74648 0.00452 0.505 ATTAACC +ACTAAYH DREME-1 chrM 978 984 + -2.74648 0.00452 0.505 ACTCACC +ACTAAYH DREME-1 chrM 1569 1575 - -2.74648 0.00452 0.505 ACTTACC +ACTAAYH DREME-1 chrM 1596 1602 + -2.74648 0.00452 0.505 ACGAACC +ACTAAYH DREME-1 chrM 1991 1997 + -2.74648 0.00452 0.505 ACAAACC +ACTAAYH DREME-1 chrM 2578 2584 + -2.74648 0.00452 0.505 CCTAACC +ACTAAYH DREME-1 chrM 2765 2771 + -2.74648 0.00452 0.505 ACAAACC +ACTAAYH DREME-1 chrM 3031 3037 - -2.74648 0.00452 0.505 ACGAACC +ACTAAYH DREME-1 chrM 3225 3231 - -2.74648 0.00452 0.505 ACAAACC +ACTAAYH DREME-1 chrM 3883 3889 + -2.74648 0.00452 0.505 ACCAACC +ACTAAYH DREME-1 chrM 4101 4107 + -2.74648 0.00452 0.505 TCTAACC +ACTAAYH DREME-1 chrM 4191 4197 + -2.74648 0.00452 0.505 ACTCACC +ACTAAYH DREME-1 chrM 4598 4604 + -2.74648 0.00452 0.505 TCTAACC +ACTAAYH DREME-1 chrM 4874 4880 + -2.74648 0.00452 0.505 ACTAGCC +ACTAAYH DREME-1 chrM 5237 5243 + -2.74648 0.00452 0.505 GCTAACC +ACTAAYH DREME-1 chrM 5839 5845 + -2.74648 0.00452 0.505 CCTAACC +ACTAAYH DREME-1 chrM 5931 5937 + -2.74648 0.00452 0.505 ACAAACC +ACTAAYH DREME-1 chrM 6335 6341 + -2.74648 0.00452 0.505 CCTAACC +ACTAAYH DREME-1 chrM 7228 7234 + -2.74648 0.00452 0.505 ACTACCC +ACTAAYH DREME-1 chrM 7781 7787 + -2.74648 0.00452 0.505 ACTATCC +ACTAAYH DREME-1 chrM 8315 8321 + -2.74648 0.00452 0.505 ATTAACC +ACTAAYH DREME-1 chrM 8508 8514 + -2.74648 0.00452 0.505 ACAAACC +ACTAAYH DREME-1 chrM 8721 8727 + -2.74648 0.00452 0.505 ACGAACC +ACTAAYH DREME-1 chrM 8805 8811 + -2.74648 0.00452 0.505 ACCAACC +ACTAAYH DREME-1 chrM 9003 9009 + -2.74648 0.00452 0.505 CCTAACC +ACTAAYH DREME-1 chrM 9076 9082 + -2.74648 0.00452 0.505 ATTAACC +ACTAAYH DREME-1 chrM 9124 9130 + -2.74648 0.00452 0.505 ACTATCC +ACTAAYH DREME-1 chrM 11548 11554 + -2.74648 0.00452 0.505 ACTATCC +ACTAAYH DREME-1 chrM 11852 11858 + -2.74648 0.00452 0.505 GCTAACC +ACTAAYH DREME-1 chrM 11876 11882 + -2.74648 0.00452 0.505 ATTAACC +ACTAAYH DREME-1 chrM 11905 11911 + -2.74648 0.00452 0.505 AGTAACC +ACTAAYH DREME-1 chrM 12013 12019 + -2.74648 0.00452 0.505 ACTCACC +ACTAAYH DREME-1 chrM 12336 12342 + -2.74648 0.00452 0.505 AATAACC +ACTAAYH DREME-1 chrM 12363 12369 + -2.74648 0.00452 0.505 CCTAACC +ACTAAYH DREME-1 chrM 13295 13301 + -2.74648 0.00452 0.505 ACCAACC +ACTAAYH DREME-1 chrM 13672 13678 + -2.74648 0.00452 0.505 AATAACC +ACTAAYH DREME-1 chrM 13854 13860 + -2.74648 0.00452 0.505 CCTAACC +ACTAAYH DREME-1 chrM 13998 14004 + -2.74648 0.00452 0.505 CCTAACC +ACTAAYH DREME-1 chrM 14124 14130 + -2.74648 0.00452 0.505 CCTAACC +ACTAAYH DREME-1 chrM 14384 14390 + -2.74648 0.00452 0.505 GCTAACC +ACTAAYH DREME-1 chrM 14401 14407 + -2.74648 0.00452 0.505 ACTCACC +ACTAAYH DREME-1 chrM 14624 14630 + -2.74648 0.00452 0.505 ACAAACC +ACTAAYH DREME-1 chrM 14786 14792 + -2.74648 0.00452 0.505 ATTAACC +ACTAAYH DREME-1 chrM 14910 14916 + -2.74648 0.00452 0.505 ACTCACC +ACTAAYH DREME-1 chrM 15193 15199 + -2.74648 0.00452 0.505 ACTATCC +ACTAAYH DREME-1 chrM 15631 15637 + -2.74648 0.00452 0.505 ACTATCC +ACTAAYH DREME-1 chrM 15748 15754 + -2.74648 0.00452 0.505 TCTAACC +ACTAAYH DREME-1 chrM 16066 16072 + -2.74648 0.00452 0.505 ACTCACC +ACTAAYH DREME-1 chrM 16281 16287 + -2.74648 0.00452 0.505 ACAAACC +ACTAAYH DREME-1 chrM 211 217 + -3.12676 0.00543 0.514 ATTAATT +ACTAAYH DREME-1 chrM 210 216 - -3.12676 0.00543 0.514 ATTAATT +ACTAAYH DREME-1 chrM 214 220 - -3.12676 0.00543 0.514 ATTAATT +ACTAAYH DREME-1 chrM 1961 1967 - -3.12676 0.00543 0.514 ACTATTT +ACTAAYH DREME-1 chrM 2188 2194 + -3.12676 0.00543 0.514 ACCAATT +ACTAAYH DREME-1 chrM 3771 3777 - -3.12676 0.00543 0.514 ACTTATT +ACTAAYH DREME-1 chrM 3923 3929 - -3.12676 0.00543 0.514 ACTAGTT +ACTAAYH DREME-1 chrM 4469 4475 - -3.12676 0.00543 0.514 ATTAATT +ACTAAYH DREME-1 chrM 4543 4549 + -3.12676 0.00543 0.514 ACTGATT +ACTAAYH DREME-1 chrM 5085 5091 + -3.12676 0.00543 0.514 ACTATTT +ACTAAYH DREME-1 chrM 6146 6152 + -3.12676 0.00543 0.514 ACTAGTT +ACTAAYH DREME-1 chrM 7087 7093 + -3.12676 0.00543 0.514 ACTGATT +ACTAAYH DREME-1 chrM 7304 7310 + -3.12676 0.00543 0.514 AATAATT +ACTAAYH DREME-1 chrM 8041 8047 + -3.12676 0.00543 0.514 AATAATT +ACTAAYH DREME-1 chrM 8221 8227 + -3.12676 0.00543 0.514 ATTAATT +ACTAAYH DREME-1 chrM 8220 8226 - -3.12676 0.00543 0.514 ATTAATT +ACTAAYH DREME-1 chrM 8795 8801 + -3.12676 0.00543 0.514 ACTCATT +ACTAAYH DREME-1 chrM 8946 8952 + -3.12676 0.00543 0.514 ACTAGTT +ACTAAYH DREME-1 chrM 8973 8979 + -3.12676 0.00543 0.514 ACTCATT +ACTAAYH DREME-1 chrM 9042 9048 + -3.12676 0.00543 0.514 CCTAATT +ACTAAYH DREME-1 chrM 9111 9117 + -3.12676 0.00543 0.514 TCTAATT +ACTAAYH DREME-1 chrM 9538 9544 - -3.12676 0.00543 0.514 CCTAATT +ACTAAYH DREME-1 chrM 9680 9686 + -3.12676 0.00543 0.514 AATAATT +ACTAAYH DREME-1 chrM 9953 9959 + -3.12676 0.00543 0.514 ACTATTT +ACTAAYH DREME-1 chrM 10004 10010 - -3.12676 0.00543 0.514 ACTATTT +ACTAAYH DREME-1 chrM 10029 10035 + -3.12676 0.00543 0.514 ACTAGTT +ACTAAYH DREME-1 chrM 10028 10034 - -3.12676 0.00543 0.514 ACTAGTT +ACTAAYH DREME-1 chrM 10109 10115 + -3.12676 0.00543 0.514 AATAATT +ACTAAYH DREME-1 chrM 10112 10118 - -3.12676 0.00543 0.514 AATAATT +ACTAAYH DREME-1 chrM 10402 10408 - -3.12676 0.00543 0.514 ACCAATT +ACTAAYH DREME-1 chrM 10438 10444 + -3.12676 0.00543 0.514 ACTCATT +ACTAAYH DREME-1 chrM 10852 10858 + -3.12676 0.00543 0.514 CCTAATT +ACTAAYH DREME-1 chrM 10855 10861 - -3.12676 0.00543 0.514 AATAATT +ACTAAYH DREME-1 chrM 10876 10882 + -3.12676 0.00543 0.514 ACTATTT +ACTAAYH DREME-1 chrM 11500 11506 + -3.12676 0.00543 0.514 ACTCATT +ACTAAYH DREME-1 chrM 12378 12384 + -3.12676 0.00543 0.514 CCTAATT +ACTAAYH DREME-1 chrM 12584 12590 + -3.12676 0.00543 0.514 ACTACTT +ACTAAYH DREME-1 chrM 12679 12685 - -3.12676 0.00543 0.514 ACTGATT +ACTAAYH DREME-1 chrM 12708 12714 + -3.12676 0.00543 0.514 CCTAATT +ACTAAYH DREME-1 chrM 13013 13019 - -3.12676 0.00543 0.514 CCTAATT +ACTAAYH DREME-1 chrM 13350 13356 + -3.12676 0.00543 0.514 ACTATTT +ACTAAYH DREME-1 chrM 13611 13617 + -3.12676 0.00543 0.514 AATAATT +ACTAAYH DREME-1 chrM 14296 14302 - -3.12676 0.00543 0.514 AATAATT +ACTAAYH DREME-1 chrM 14782 14788 + -3.12676 0.00543 0.514 ATTAATT +ACTAAYH DREME-1 chrM 14781 14787 - -3.12676 0.00543 0.514 ATTAATT +ACTAAYH DREME-1 chrM 14793 14799 + -3.12676 0.00543 0.514 ACTCATT +ACTAAYH DREME-1 chrM 15178 15184 + -3.12676 0.00543 0.514 AGTAATT +ACTAAYH DREME-1 chrM 15856 15862 + -3.12676 0.00543 0.514 CCTAATT +ACTAAYH DREME-1 chrM 16003 16009 + -3.12676 0.00543 0.514 TCTAATT +ACTAAYH DREME-1 chrM 1074 1080 - -3.33803 0.00635 0.514 TCTAATC +ACTAAYH DREME-1 chrM 2270 2276 + -3.33803 0.00635 0.514 ACCAATC +ACTAAYH DREME-1 chrM 3081 3087 + -3.33803 0.00635 0.514 AGTAATC +ACTAAYH DREME-1 chrM 3345 3351 + -3.33803 0.00635 0.514 TCTAATC +ACTAAYH DREME-1 chrM 3824 3830 - -3.33803 0.00635 0.514 AGTAATC +ACTAAYH DREME-1 chrM 3924 3930 + -3.33803 0.00635 0.514 ACTAGTC +ACTAAYH DREME-1 chrM 4470 4476 + -3.33803 0.00635 0.514 ATTAATC +ACTAAYH DREME-1 chrM 4520 4526 + -3.33803 0.00635 0.514 ACTCATC +ACTAAYH DREME-1 chrM 4737 4743 + -3.33803 0.00635 0.514 ACCAATC +ACTAAYH DREME-1 chrM 4747 4753 + -3.33803 0.00635 0.514 ACTCATC +ACTAAYH DREME-1 chrM 4757 4763 + -3.33803 0.00635 0.514 AATAATC +ACTAAYH DREME-1 chrM 5120 5126 + -3.33803 0.00635 0.514 ACTACTC +ACTAAYH DREME-1 chrM 5354 5360 + -3.33803 0.00635 0.514 CCTAATC +ACTAAYH DREME-1 chrM 5378 5384 + -3.33803 0.00635 0.514 ACTACTC +ACTAAYH DREME-1 chrM 5453 5459 + -3.33803 0.00635 0.514 ACTCATC +ACTAAYH DREME-1 chrM 5501 5507 + -3.33803 0.00635 0.514 AATAATC +ACTAAYH DREME-1 chrM 5707 5713 + -3.33803 0.00635 0.514 CCTAATC +ACTAAYH DREME-1 chrM 5921 5927 + -3.33803 0.00635 0.514 ACTATTC +ACTAAYH DREME-1 chrM 6095 6101 + -3.33803 0.00635 0.514 AATAATC +ACTAAYH DREME-1 chrM 6145 6151 - -3.33803 0.00635 0.514 ACTAGTC +ACTAAYH DREME-1 chrM 6158 6164 + -3.33803 0.00635 0.514 AATAATC +ACTAAYH DREME-1 chrM 6307 6313 + -3.33803 0.00635 0.514 ACTACTC +ACTAAYH DREME-1 chrM 6467 6473 + -3.33803 0.00635 0.514 CCTAATC +ACTAAYH DREME-1 chrM 6659 6665 + -3.33803 0.00635 0.514 AATAATC +ACTAAYH DREME-1 chrM 6682 6688 + -3.33803 0.00635 0.514 ACTACTC +ACTAAYH DREME-1 chrM 6982 6988 + -3.33803 0.00635 0.514 ACTCATC +ACTAAYH DREME-1 chrM 8007 8013 - -3.33803 0.00635 0.514 ACTACTC +ACTAAYH DREME-1 chrM 8422 8428 + -3.33803 0.00635 0.514 ACTATTC +ACTAAYH DREME-1 chrM 8589 8595 + -3.33803 0.00635 0.514 ACTGATC +ACTAAYH DREME-1 chrM 9093 9099 + -3.33803 0.00635 0.514 ACTTATC +ACTAAYH DREME-1 chrM 9214 9220 + -3.33803 0.00635 0.514 ACCAATC +ACTAAYH DREME-1 chrM 10079 10085 + -3.33803 0.00635 0.514 AATAATC +ACTAAYH DREME-1 chrM 10337 10343 + -3.33803 0.00635 0.514 ATTAATC +ACTAAYH DREME-1 chrM 10387 10393 - -3.33803 0.00635 0.514 TCTAATC +ACTAAYH DREME-1 chrM 10658 10664 + -3.33803 0.00635 0.514 ACTAGTC +ACTAAYH DREME-1 chrM 10700 10706 + -3.33803 0.00635 0.514 ACTAGTC +ACTAAYH DREME-1 chrM 11007 11013 + -3.33803 0.00635 0.514 ACTTATC +ACTAAYH DREME-1 chrM 11065 11071 + -3.33803 0.00635 0.514 ACAAATC +ACTAAYH DREME-1 chrM 11134 11140 + -3.33803 0.00635 0.514 ACTTATC +ACTAAYH DREME-1 chrM 11239 11245 + -3.33803 0.00635 0.514 ACTCATC +ACTAAYH DREME-1 chrM 11290 11296 + -3.33803 0.00635 0.514 ACTACTC +ACTAAYH DREME-1 chrM 11734 11740 + -3.33803 0.00635 0.514 ACTATTC +ACTAAYH DREME-1 chrM 11959 11965 + -3.33803 0.00635 0.514 ACTAGTC +ACTAAYH DREME-1 chrM 12676 12682 + -3.33803 0.00635 0.514 ATTAATC +ACTAAYH DREME-1 chrM 12699 12705 + -3.33803 0.00635 0.514 ACTCATC +ACTAAYH DREME-1 chrM 12952 12958 + -3.33803 0.00635 0.514 GCTAATC +ACTAAYH DREME-1 chrM 13113 13119 + -3.33803 0.00635 0.514 ACTCATC +ACTAAYH DREME-1 chrM 13419 13425 + -3.33803 0.00635 0.514 ACTACTC +ACTAAYH DREME-1 chrM 14118 14124 + -3.33803 0.00635 0.514 ACTCATC +ACTAAYH DREME-1 chrM 14136 14142 + -3.33803 0.00635 0.514 CCTAATC +ACTAAYH DREME-1 chrM 14366 14372 + -3.33803 0.00635 0.514 ACCAATC +ACTAAYH DREME-1 chrM 14890 14896 + -3.33803 0.00635 0.514 ACTATTC +ACTAAYH DREME-1 chrM 14907 14913 + -3.33803 0.00635 0.514 ACTACTC +ACTAAYH DREME-1 chrM 15475 15481 + -3.33803 0.00635 0.514 ACTATTC +ACTAAYH DREME-1 chrM 15652 15658 + -3.33803 0.00635 0.514 AATAATC +ACTAAYH DREME-1 chrM 15832 15838 + -3.33803 0.00635 0.514 CCTAATC +ACTAAYH DREME-1 chrM 15951 15957 + -3.33803 0.00635 0.514 ACAAATC +ACTAAYH DREME-1 chrM 16013 16019 + -3.33803 0.00635 0.514 ACTATTC +ACTAAYH DREME-1 chrM 197 203 + -13.9718 0.00647 0.521 ACTAAAG +ACTAAYH DREME-1 chrM 8713 8719 + -13.9718 0.00647 0.521 ACTAAAG +ACTAAYH DREME-1 chrM 28 34 + -14.7042 0.00739 0.559 ACTCACG +ACTAAYH DREME-1 chrM 1322 1328 - -14.7042 0.00739 0.559 CCTAACG +ACTAAYH DREME-1 chrM 2910 2916 + -14.7042 0.00739 0.559 ACCAACG +ACTAAYH DREME-1 chrM 3035 3041 - -14.7042 0.00739 0.559 ACAAACG +ACTAAYH DREME-1 chrM 5106 5112 + -14.7042 0.00739 0.559 ACTACCG +ACTAAYH DREME-1 chrM 7218 7224 - -14.7042 0.00739 0.559 AGTAACG +ACTAAYH DREME-1 chrM 8381 8387 + -14.7042 0.00739 0.559 ACTACCG +ACTAAYH DREME-1 chrM 10580 10586 + -14.7042 0.00739 0.559 ACTATCG +ACTAAYH DREME-1 chrM 11760 11766 + -14.7042 0.00739 0.559 ACGAACG +ACTAAYH DREME-1 chrM 13546 13552 + -14.7042 0.00739 0.559 ACAAACG +ACTAAYH DREME-1 chrM 13663 13669 + -14.7042 0.00739 0.559 ATTAACG +ACTAAYH DREME-1 chrM 57 63 - -15.0563 0.00922 0.559 ACGAAAA +ACTAAYH DREME-1 chrM 284 290 + -15.0563 0.00922 0.559 ACAAAAA +ACTAAYH DREME-1 chrM 331 337 + -15.0563 0.00922 0.559 ACTTAAA +ACTAAYH DREME-1 chrM 361 367 + -15.0563 0.00922 0.559 ACAAAGA +ACTAAYH DREME-1 chrM 608 614 + -15.0563 0.00922 0.559 ACTGAAA +ACTAAYH DREME-1 chrM 682 688 + -15.0563 0.00922 0.559 AGTAAGA +ACTAAYH DREME-1 chrM 946 952 - -15.0563 0.00922 0.559 TCTAAAA +ACTAAYH DREME-1 chrM 972 978 + -15.0563 0.00922 0.559 GCTAAAA +ACTAAYH DREME-1 chrM 1019 1025 + -15.0563 0.00922 0.559 ACTACGA +ACTAAYH DREME-1 chrM 1057 1063 + -15.0563 0.00922 0.559 GCTAAGA +ACTAAYH DREME-1 chrM 1142 1148 + -15.0563 0.00922 0.559 ACTACGA +ACTAAYH DREME-1 chrM 1162 1168 + -15.0563 0.00922 0.559 ACTCAAA +ACTAAYH DREME-1 chrM 1384 1390 + -15.0563 0.00922 0.559 ACTACGA +ACTAAYH DREME-1 chrM 1864 1870 + -15.0563 0.00922 0.559 ACTAGAA +ACTAAYH DREME-1 chrM 1894 1900 + -15.0563 0.00922 0.559 GCTAAGA +ACTAAYH DREME-1 chrM 1922 1928 + -15.0563 0.00922 0.559 CCTAAGA +ACTAAYH DREME-1 chrM 1932 1938 + -15.0563 0.00922 0.559 GCTAAAA +ACTAAYH DREME-1 chrM 2124 2130 + -15.0563 0.00922 0.559 ACTAGGA +ACTAAYH DREME-1 chrM 2148 2154 + -15.0563 0.00922 0.559 AGTAAAA +ACTAAYH DREME-1 chrM 2175 2181 + -15.0563 0.00922 0.559 CCTAAAA +ACTAAYH DREME-1 chrM 2192 2198 + -15.0563 0.00922 0.559 ATTAAGA +ACTAAYH DREME-1 chrM 2224 2230 + -15.0563 0.00922 0.559 CCTAAAA +ACTAAYH DREME-1 chrM 2350 2356 + -15.0563 0.00922 0.559 ATTAAAA +ACTAAYH DREME-1 chrM 2463 2469 + -15.0563 0.00922 0.559 AGTAAAA +ACTAAYH DREME-1 chrM 2500 2506 + -15.0563 0.00922 0.559 ACCAAAA +ACTAAYH DREME-1 chrM 2658 2664 - -15.0563 0.00922 0.559 AGTAAGA +ACTAAYH DREME-1 chrM 2798 2804 + -15.0563 0.00922 0.559 ATTAAAA +ACTAAYH DREME-1 chrM 2855 2861 + -15.0563 0.00922 0.559 GCTAAGA +ACTAAYH DREME-1 chrM 3065 3071 - -15.0563 0.00922 0.559 ACTCAGA +ACTAAYH DREME-1 chrM 3262 3268 + -15.0563 0.00922 0.559 ACTTAAA +ACTAAYH DREME-1 chrM 3378 3384 + -15.0563 0.00922 0.559 ACGAAAA +ACTAAYH DREME-1 chrM 3441 3447 + -15.0563 0.00922 0.559 ACTACAA +ACTAAYH DREME-1 chrM 3486 3492 + -15.0563 0.00922 0.559 CCTAAAA +ACTAAYH DREME-1 chrM 3558 3564 + -15.0563 0.00922 0.559 ACTATGA +ACTAAYH DREME-1 chrM 3677 3683 + -15.0563 0.00922 0.559 ACTCAAA +ACTAAYH DREME-1 chrM 4021 4027 + -15.0563 0.00922 0.559 ACTACAA +ACTAAYH DREME-1 chrM 4087 4093 + -15.0563 0.00922 0.559 ACCAAGA +ACTAAYH DREME-1 chrM 4259 4265 + -15.0563 0.00922 0.559 CCTAAGA +ACTAAYH DREME-1 chrM 4334 4340 + -15.0563 0.00922 0.559 ACTATGA +ACTAAYH DREME-1 chrM 4586 4592 - -15.0563 0.00922 0.559 AATAAAA +ACTAAYH DREME-1 chrM 4602 4608 + -15.0563 0.00922 0.559 ACCAAAA +ACTAAYH DREME-1 chrM 4778 4784 + -15.0563 0.00922 0.559 AATAAAA +ACTAAYH DREME-1 chrM 4784 4790 + -15.0563 0.00922 0.559 ACTAGGA +ACTAAYH DREME-1 chrM 4807 4813 - -15.0563 0.00922 0.559 ACTCAGA +ACTAAYH DREME-1 chrM 4868 4874 + -15.0563 0.00922 0.559 ACAAAAA +ACTAAYH DREME-1 chrM 5002 5008 - -15.0563 0.00922 0.559 GCTAAGA +ACTAAYH DREME-1 chrM 5075 5081 - -15.0563 0.00922 0.559 ATTAAGA +ACTAAYH DREME-1 chrM 5128 5134 + -15.0563 0.00922 0.559 ACTTAAA +ACTAAYH DREME-1 chrM 5280 5286 + -15.0563 0.00922 0.559 ACAAAAA +ACTAAYH DREME-1 chrM 5405 5411 + -15.0563 0.00922 0.559 AATAAAA +ACTAAYH DREME-1 chrM 5533 5539 + -15.0563 0.00922 0.559 ACCAAGA +ACTAAYH DREME-1 chrM 5670 5676 + -15.0563 0.00922 0.559 ACTTAAA +ACTAAYH DREME-1 chrM 5938 5944 + -15.0563 0.00922 0.559 ACAAAGA +ACTAAYH DREME-1 chrM 6106 6112 - -15.0563 0.00922 0.559 ACTATGA +ACTAAYH DREME-1 chrM 6376 6382 - -15.0563 0.00922 0.559 CCTAAGA +ACTAAYH DREME-1 chrM 6451 6457 - -15.0563 0.00922 0.559 ACGAAGA +ACTAAYH DREME-1 chrM 7445 7451 + -15.0563 0.00922 0.559 ACAAAAA +ACTAAYH DREME-1 chrM 7581 7587 - -15.0563 0.00922 0.559 ATTAAGA +ACTAAYH DREME-1 chrM 7692 7698 - -15.0563 0.00922 0.559 ACTAGGA +ACTAAYH DREME-1 chrM 7800 7806 - -15.0563 0.00922 0.559 ACTAGGA +ACTAAYH DREME-1 chrM 8230 8236 + -15.0563 0.00922 0.559 CCTAAAA +ACTAAYH DREME-1 chrM 8323 8329 - -15.0563 0.00922 0.559 ACTTAAA +ACTAAYH DREME-1 chrM 8335 8341 + -15.0563 0.00922 0.559 ATTAAGA +ACTAAYH DREME-1 chrM 8494 8500 + -15.0563 0.00922 0.559 AATAAAA +ACTAAYH DREME-1 chrM 8521 8527 + -15.0563 0.00922 0.559 ACCAAAA +ACTAAYH DREME-1 chrM 8531 8537 + -15.0563 0.00922 0.559 ACGAAAA +ACTAAYH DREME-1 chrM 8757 8763 - -15.0563 0.00922 0.559 AATAAAA +ACTAAYH DREME-1 chrM 8881 8887 + -15.0563 0.00922 0.559 TCTAAGA +ACTAAYH DREME-1 chrM 8887 8893 + -15.0563 0.00922 0.559 ATTAAAA +ACTAAYH DREME-1 chrM 9173 9179 - -15.0563 0.00922 0.559 ACTAGAA +ACTAAYH DREME-1 chrM 9236 9242 + -15.0563 0.00922 0.559 AGTAAAA +ACTAAYH DREME-1 chrM 9706 9712 - -15.0563 0.00922 0.559 AGTAAAA +ACTAAYH DREME-1 chrM 9796 9802 - -15.0563 0.00922 0.559 ACAAAAA +ACTAAYH DREME-1 chrM 9987 9993 - -15.0563 0.00922 0.559 AGTAAGA +ACTAAYH DREME-1 chrM 10075 10081 - -15.0563 0.00922 0.559 ATTAAAA +ACTAAYH DREME-1 chrM 10243 10249 - -15.0563 0.00922 0.559 AATAAGA +ACTAAYH DREME-1 chrM 10333 10339 - -15.0563 0.00922 0.559 AATAAGA +ACTAAYH DREME-1 chrM 10376 10382 + -15.0563 0.00922 0.559 ACTACAA +ACTAAYH DREME-1 chrM 10379 10385 + -15.0563 0.00922 0.559 ACAAAAA +ACTAAYH DREME-1 chrM 10630 10636 - -15.0563 0.00922 0.559 GCTAAGA +ACTAAYH DREME-1 chrM 10762 10768 + -15.0563 0.00922 0.559 GCTAAAA +ACTAAYH DREME-1 chrM 11029 11035 + -15.0563 0.00922 0.559 ACGAAAA +ACTAAYH DREME-1 chrM 11367 11373 - -15.0563 0.00922 0.559 ACTATAA +ACTAAYH DREME-1 chrM 11602 11608 + -15.0563 0.00922 0.559 CCTAAAA +ACTAAYH DREME-1 chrM 11646 11652 - -15.0563 0.00922 0.559 ACTACGA +ACTAAYH DREME-1 chrM 11751 11757 + -15.0563 0.00922 0.559 ACTCAAA +ACTAAYH DREME-1 chrM 11757 11763 + -15.0563 0.00922 0.559 ACTACGA +ACTAAYH DREME-1 chrM 12152 12158 + -15.0563 0.00922 0.559 ACCAAAA +ACTAAYH DREME-1 chrM 12295 12301 - -15.0563 0.00922 0.559 CCTAAGA +ACTAAYH DREME-1 chrM 12311 12317 - -15.0563 0.00922 0.559 ACCAAAA +ACTAAYH DREME-1 chrM 12327 12333 + -15.0563 0.00922 0.559 AATAAAA +ACTAAYH DREME-1 chrM 12352 12358 + -15.0563 0.00922 0.559 ACTATAA +ACTAAYH DREME-1 chrM 12416 12422 + -15.0563 0.00922 0.559 ACAAAAA +ACTAAYH DREME-1 chrM 12509 12515 + -15.0563 0.00922 0.559 ACCAAGA +ACTAAYH DREME-1 chrM 12662 12668 + -15.0563 0.00922 0.559 ACTCAGA +ACTAAYH DREME-1 chrM 13109 13115 - -15.0563 0.00922 0.559 AGTAAGA +ACTAAYH DREME-1 chrM 13263 13269 + -15.0563 0.00922 0.559 ACTAGGA +ACTAAYH DREME-1 chrM 13422 13428 + -15.0563 0.00922 0.559 ACTCAAA +ACTAAYH DREME-1 chrM 13667 13673 + -15.0563 0.00922 0.559 ACGAAAA +ACTAAYH DREME-1 chrM 13791 13797 + -15.0563 0.00922 0.559 CCTAAAA +ACTAAYH DREME-1 chrM 13866 13872 + -15.0563 0.00922 0.559 ACTTAAA +ACTAAYH DREME-1 chrM 13872 13878 + -15.0563 0.00922 0.559 AATAAAA +ACTAAYH DREME-1 chrM 13894 13900 - -15.0563 0.00922 0.559 AATAAAA +ACTAAYH DREME-1 chrM 14007 14013 + -15.0563 0.00922 0.559 ACTAGAA +ACTAAYH DREME-1 chrM 14023 14029 + -15.0563 0.00922 0.559 CCTAAAA +ACTAAYH DREME-1 chrM 14405 14411 + -15.0563 0.00922 0.559 ACCAAGA +ACTAAYH DREME-1 chrM 14501 14507 + -15.0563 0.00922 0.559 ATTAAAA +ACTAAYH DREME-1 chrM 14687 14693 + -15.0563 0.00922 0.559 ACTACAA +ACTAAYH DREME-1 chrM 14732 14738 + -15.0563 0.00922 0.559 ACTACAA +ACTAAYH DREME-1 chrM 14776 14782 + -15.0563 0.00922 0.559 AATAAAA +ACTAAYH DREME-1 chrM 15072 15078 + -15.0563 0.00922 0.559 ACTCAGA +ACTAAYH DREME-1 chrM 15607 15613 + -15.0563 0.00922 0.559 ACTAGGA +ACTAAYH DREME-1 chrM 15874 15880 + -15.0563 0.00922 0.559 ACTCAAA +ACTAAYH DREME-1 chrM 15892 15898 - -15.0563 0.00922 0.559 ACTACAA +ACTAAYH DREME-1 chrM 15995 16001 + -15.0563 0.00922 0.559 GCTAAGA +ACTAAYH DREME-1 chrM 16269 16275 + -15.0563 0.00922 0.559 ACTAGGA +ACTAAYH DREME-1 chrM 16553 16559 + -15.0563 0.00922 0.559 AATAAGA diff -r 793225b11202 -r b48e673af4e8 test-data/fimo_output_test3.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_test3.xml Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,56 @@ + + + + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation= xmlns:fimo="http://noble.gs.washington.edu/schema/fimo" +> +fimo -o ./fimo_test4_out --thresh 0.01 --bgfile --uniform-- --max-stored-scores 100000 --motif ACTAAYH --motif-pseudo 0.1 dreme_fimo_input_1.xml hsa_chrM.fa + +./fimo_test4_out +dreme_fimo_input_1.xml +hsa_chrM.fa +--uniform-- +false +true +false +false +true +0.01 +p-value +100000 +0.1 +2 +ACTAAYH + + + + + + + + + + + + + + + + + + + + + + + + + + +0.250 +0.250 +0.250 +0.250 + +cisml.xml + diff -r 793225b11202 -r b48e673af4e8 test-data/fimo_output_txt_1.txt --- a/test-data/fimo_output_txt_1.txt Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -#pattern name sequence name start stop strand score p-value q-value matched sequence -1 phiX174 1388 1398 + 29.4024 6.36e-11 1.25e-09 AATATCTATAA -1 phiX174 847 857 + 29.122 7.02e-11 1.25e-09 AATGTCTAAAG -1 phiX174 2301 2311 + 27.6463 1.08e-10 1.29e-09 AGGTTATAACG -1 phiX174 5063 5073 + 25.5366 2.73e-10 2.25e-09 AGGAGCTAAAG -1 phiX174 989 999 + 25.3049 3.15e-10 2.25e-09 TGAGGATAAAT -1 phiX174 4713 4723 + 23.622 7.74e-10 3.48e-09 GACTGCTATCA -1 phiX174 5048 5058 + 23.3293 8.51e-10 3.48e-09 TGCTGCTAAAG -1 phiX174 855 865 + 23.3049 8.64e-10 3.48e-09 AAGGTAAAAAA -1 phiX174 3155 3165 + 23.0366 9.76e-10 3.48e-09 TATGGCTAAAG -1 phiX174 5009 5019 + 23.0366 9.76e-10 3.48e-09 TGTGGCTAAAT -1 phiX174 814 824 + 22.5854 1.28e-09 4.14e-09 TGCGTCAAAAA -1 phiX174 2832 2842 + 22.3415 1.42e-09 4.23e-09 TTGGTCTAACT -1 phiX174 3830 3840 + 21.8293 1.7e-09 4.68e-09 TATTGATAAAG -1 phiX174 3560 3570 + 21.5976 1.89e-09 4.82e-09 TGCGTCTATTA -1 phiX174 2882 2892 + 21.1951 2.29e-09 5.46e-09 AGGTTATTAAA -1 phiX174 4453 4463 + 20.8902 2.58e-09 5.75e-09 AAGGTATTAAG -1 phiX174 2493 2503 + 20.3415 3.06e-09 5.79e-09 GACACCTAAAG -1 phiX174 4104 4114 + 20.3171 3.08e-09 5.79e-09 GGCTTCCATAA -1 phiX174 4955 4965 + 20.3171 3.08e-09 5.79e-09 TGATGCTAAAG -1 phiX174 1885 1895 + 19.9268 3.61e-09 6.45e-09 TGCGACTAAAG -1 phiX174 3376 3386 + 19.7683 3.81e-09 6.48e-09 AGAATCAAAAA -1 phiX174 52 62 + 19.5732 4.06e-09 6.58e-09 TGAGTCGAAAA -1 phiX174 1390 1400 + 19.378 4.26e-09 6.61e-09 TATCTATAACA -1 phiX174 2017 2027 + 19.0854 4.6e-09 6.85e-09 TTCGTCTAAGA -1 phiX174 1000 1010 + 18.878 4.88e-09 6.97e-09 TATGTCTAATA -1 phiX174 1555 1565 + 18.439 5.58e-09 7.37e-09 GACTTCTACCA -1 phiX174 4430 4440 + 18.4268 5.62e-09 7.37e-09 TGAGTATAATT -1 phiX174 1927 1937 + 18.2927 5.82e-09 7.37e-09 GACTTATACCG -1 phiX174 2981 2991 + 18.0732 6.13e-09 7.37e-09 CATGTCTAAAT -1 phiX174 4203 4213 + 17.9268 6.34e-09 7.37e-09 GACGGCCATAA -1 phiX174 1669 1679 + 17.8659 6.4e-09 7.37e-09 TGGAGGTAAAA -1 phiX174 3260 3270 + 17.5 7.01e-09 7.82e-09 CGCTGATAAAG -1 phiX174 3047 3057 + 17.2805 7.4e-09 7.85e-09 TACCGATAACA -1 phiX174 4176 4186 + 17.1829 7.6e-09 7.85e-09 GAGTTCGATAA -1 phiX174 4118 4128 + 17.1341 7.7e-09 7.85e-09 GATGGATAACC -1 phiX174 5370 5380 + 16.9878 8.03e-09 7.87e-09 GGCGTATCCAA -1 phiX174 1242 1252 + 16.5122 8.94e-09 7.87e-09 AGTGGATTAAG -1 phiX174 2583 2593 + 16.5122 8.94e-09 7.87e-09 TACATCTGTCA -1 phiX174 698 708 + 16.4146 9.13e-09 7.87e-09 TACGGAAAACA -1 phiX174 2299 2309 + 16.3537 9.26e-09 7.87e-09 TGAGGTTATAA -1 phiX174 4189 4199 + 16.1707 9.69e-09 7.87e-09 GTGATATGTAT -1 phiX174 275 285 + 16.0976 9.85e-09 7.87e-09 GGTTTAGATAT -1 phiX174 1801 1811 + 16.0366 1e-08 7.87e-09 GACCTATAAAC -1 phiX174 1386 1396 + 15.9268 1.03e-08 7.87e-09 TGAATATCTAT -1 phiX174 1303 1313 + 15.9024 1.03e-08 7.87e-09 TGGTTATATTG -1 phiX174 3772 3782 + 15.878 1.04e-08 7.87e-09 AGGATATTTCT -1 phiX174 1288 1298 + 15.8659 1.04e-08 7.87e-09 GACTGTTAACA -1 phiX174 2577 2587 + 15.7683 1.08e-08 7.87e-09 GATGGATACAT -1 phiX174 937 947 + 15.7561 1.08e-08 7.87e-09 TTGGTATGTAG -1 phiX174 904 914 + 15.6585 1.11e-08 7.93e-09 AGGTACTAAAG -1 phiX174 2279 2289 + 15.5854 1.13e-08 7.93e-09 TCGTGATAAAA -1 phiX174 3164 3174 + 15.5 1.16e-08 7.98e-09 AGCTGGTAAAG -1 phiX174 24 34 + 15.3293 1.23e-08 8.24e-09 AGAAGTTAACA -1 phiX174 838 848 + 15.2561 1.27e-08 8.24e-09 GAGTGATGTAA -1 phiX174 853 863 + 15.2561 1.27e-08 8.24e-09 TAAAGGTAAAA -1 phiX174 1984 1994 + 15.0244 1.36e-08 8.68e-09 AATTTCTATGA -1 phiX174 1 11 + 14.8293 1.46e-08 9.05e-09 GAGTTTTATCG -1 phiX174 4307 4317 + 14.7927 1.47e-08 9.05e-09 TATTAATAACA -1 phiX174 4303 4313 + 14.6585 1.52e-08 9.19e-09 TTGATATTAAT -1 phiX174 5033 5043 + 14.561 1.58e-08 9.41e-09 GTCAGATATGG -1 phiX174 2579 2589 + 14.2927 1.73e-08 1.01e-08 TGGATACATCT -1 phiX174 322 332 + 14.1951 1.82e-08 1.05e-08 GACATTTTAAA -1 phiX174 5001 5011 + 13.8902 2.09e-08 1.19e-08 GGTTTCTATGT -1 phiX174 4217 4227 + 13.8171 2.15e-08 1.2e-08 TGCTTCTGACG -1 phiX174 4262 4272 + 13.7805 2.18e-08 1.2e-08 AATGGATGAAT -1 phiX174 3569 3579 + 13.7073 2.26e-08 1.22e-08 TATGGAAAACA -1 phiX174 194 204 + 13.6829 2.29e-08 1.22e-08 ATCAACTAACG -1 phiX174 131 141 + 13.4756 2.49e-08 1.31e-08 AAATGAGAAAA -1 phiX174 1491 1501 + 13.4024 2.55e-08 1.32e-08 GCCATCTCAAA -1 phiX174 434 444 + 13.2805 2.67e-08 1.36e-08 GGCCTCTATTA -1 phiX174 4565 4575 + 13.2439 2.73e-08 1.36e-08 TTGGTTTATCG -1 phiX174 102 112 + 13.2195 2.75e-08 1.36e-08 GAATTAAATCG -1 phiX174 903 913 + 13.1463 2.82e-08 1.38e-08 GAGGTACTAAA -1 phiX174 4748 4758 + 12.9756 3.01e-08 1.45e-08 TACAGCTAATG -1 phiX174 2622 2632 + 12.8659 3.16e-08 1.5e-08 TGCTGATATTG -1 phiX174 467 477 + 12.7317 3.35e-08 1.57e-08 TTTGGATTTAA -1 phiX174 4033 4043 + 12.6829 3.44e-08 1.58e-08 AGCGTATCGAG -1 phiX174 1348 1358 + 12.6707 3.46e-08 1.58e-08 TACCAATAAAA -1 phiX174 239 249 + 12.5732 3.62e-08 1.64e-08 AGTGGCTTAAT -1 phiX174 500 510 + 12.4634 3.84e-08 1.71e-08 GACGAGTAACA -1 phiX174 3001 3011 + 12.4146 3.93e-08 1.73e-08 GCGGTCAAAAA -1 phiX174 3776 3786 + 12.378 3.98e-08 1.73e-08 TATTTCTAATG -1 phiX174 2026 2036 + 12.3293 4.06e-08 1.75e-08 GAAGTTTAAGA -1 phiX174 4237 4247 + 12.3049 4.12e-08 1.75e-08 AGTTTGTATCT -1 phiX174 803 813 + 12.2439 4.24e-08 1.78e-08 AGAAGAAAACG -1 phiX174 3770 3780 + 12.1829 4.35e-08 1.81e-08 AAAGGATATTT -1 phiX174 3429 3439 + 12.122 4.45e-08 1.82e-08 GAGATGCAAAA -1 phiX174 99 109 + 12.1098 4.48e-08 1.82e-08 TACGAATTAAA -1 phiX174 67 77 + 11.9268 4.78e-08 1.92e-08 TCTTGATAAAG -1 phiX174 5332 5342 + 11.7195 5.13e-08 2.01e-08 ATCTGCTCAAA -1 phiX174 277 287 + 11.7073 5.14e-08 2.01e-08 TTTAGATATGA -1 phiX174 4338 4348 + 11.6951 5.18e-08 2.01e-08 GGGGACGAAAA -1 phiX174 3812 3822 + 11.6585 5.28e-08 2.03e-08 GGTTGATATTT -1 phiX174 1909 1919 + 11.5488 5.51e-08 2.08e-08 TAACGCTAAAG -1 phiX174 3000 3010 + 11.5366 5.54e-08 2.08e-08 GGCGGTCAAAA -1 phiX174 3891 3901 + 11.439 5.75e-08 2.11e-08 ATTGGCTCTAA -1 phiX174 3079 3089 + 11.4268 5.76e-08 2.11e-08 CTGGTATTAAA -1 phiX174 37 47 + 11.4146 5.79e-08 2.11e-08 TTCGGATATTT -1 phiX174 380 390 + 11.3293 6.01e-08 2.17e-08 GTAAGAAATCA diff -r 793225b11202 -r b48e673af4e8 test-data/fimo_output_txt_2.txt --- a/test-data/fimo_output_txt_2.txt Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -#pattern name sequence name start stop strand score p-value q-value matched sequence -1 phiX174 1388 1398 + 29.4024 6.36e-11 0 AATATCTATAA -1 phiX174 847 857 + 29.122 7.02e-11 0 AATGTCTAAAG -1 phiX174 2301 2311 + 27.6463 1.08e-10 0 AGGTTATAACG -1 phiX174 5063 5073 + 25.5366 2.73e-10 0 AGGAGCTAAAG -1 phiX174 989 999 + 25.3049 3.15e-10 0 TGAGGATAAAT -1 phiX174 4713 4723 + 23.622 7.74e-10 0 GACTGCTATCA -1 phiX174 5048 5058 + 23.3293 8.51e-10 0 TGCTGCTAAAG -1 phiX174 855 865 + 23.3049 8.64e-10 0 AAGGTAAAAAA -1 phiX174 3155 3165 + 23.0366 9.76e-10 0 TATGGCTAAAG -1 phiX174 5009 5019 + 23.0366 9.76e-10 0 TGTGGCTAAAT -1 phiX174 814 824 + 22.5854 1.28e-09 0 TGCGTCAAAAA -1 phiX174 2832 2842 + 22.3415 1.42e-09 0 TTGGTCTAACT -1 phiX174 3830 3840 + 21.8293 1.7e-09 0 TATTGATAAAG -1 phiX174 3560 3570 + 21.5976 1.89e-09 0 TGCGTCTATTA -1 phiX174 2882 2892 + 21.1951 2.29e-09 0 AGGTTATTAAA -1 phiX174 4453 4463 + 20.8902 2.58e-09 0 AAGGTATTAAG -1 phiX174 2493 2503 + 20.3415 3.06e-09 0 GACACCTAAAG -1 phiX174 4104 4114 + 20.3171 3.08e-09 0 GGCTTCCATAA -1 phiX174 4955 4965 + 20.3171 3.08e-09 0 TGATGCTAAAG -1 phiX174 1885 1895 + 19.9268 3.61e-09 0 TGCGACTAAAG -1 phiX174 3376 3386 + 19.7683 3.81e-09 0 AGAATCAAAAA -1 phiX174 52 62 + 19.5732 4.06e-09 0 TGAGTCGAAAA -1 phiX174 1390 1400 + 19.378 4.26e-09 0 TATCTATAACA -1 phiX174 2017 2027 + 19.0854 4.6e-09 0 TTCGTCTAAGA -1 phiX174 1000 1010 + 18.878 4.88e-09 0 TATGTCTAATA -1 phiX174 1555 1565 + 18.439 5.58e-09 0 GACTTCTACCA -1 phiX174 4430 4440 + 18.4268 5.62e-09 0 TGAGTATAATT -1 phiX174 1927 1937 + 18.2927 5.82e-09 0 GACTTATACCG -1 phiX174 2981 2991 + 18.0732 6.13e-09 0 CATGTCTAAAT -1 phiX174 4203 4213 + 17.9268 6.34e-09 0 GACGGCCATAA -1 phiX174 1669 1679 + 17.8659 6.4e-09 0 TGGAGGTAAAA -1 phiX174 3260 3270 + 17.5 7.01e-09 0 CGCTGATAAAG -1 phiX174 3047 3057 + 17.2805 7.4e-09 0 TACCGATAACA -1 phiX174 4176 4186 + 17.1829 7.6e-09 0 GAGTTCGATAA -1 phiX174 4118 4128 + 17.1341 7.7e-09 0 GATGGATAACC -1 phiX174 5370 5380 + 16.9878 8.03e-09 0 GGCGTATCCAA -1 phiX174 1242 1252 + 16.5122 8.94e-09 0 AGTGGATTAAG -1 phiX174 2583 2593 + 16.5122 8.94e-09 0 TACATCTGTCA -1 phiX174 698 708 + 16.4146 9.13e-09 0 TACGGAAAACA -1 phiX174 2299 2309 + 16.3537 9.26e-09 0 TGAGGTTATAA -1 phiX174 4189 4199 + 16.1707 9.69e-09 0 GTGATATGTAT -1 phiX174 275 285 + 16.0976 9.85e-09 0 GGTTTAGATAT -1 phiX174 1801 1811 + 16.0366 1e-08 0 GACCTATAAAC -1 phiX174 1386 1396 + 15.9268 1.03e-08 0 TGAATATCTAT -1 phiX174 1303 1313 + 15.9024 1.03e-08 0 TGGTTATATTG -1 phiX174 3772 3782 + 15.878 1.04e-08 0 AGGATATTTCT -1 phiX174 1288 1298 + 15.8659 1.04e-08 0 GACTGTTAACA -1 phiX174 2577 2587 + 15.7683 1.08e-08 0 GATGGATACAT -1 phiX174 937 947 + 15.7561 1.08e-08 0 TTGGTATGTAG -1 phiX174 904 914 + 15.6585 1.11e-08 0 AGGTACTAAAG -1 phiX174 2279 2289 + 15.5854 1.13e-08 0 TCGTGATAAAA -1 phiX174 3164 3174 + 15.5 1.16e-08 0 AGCTGGTAAAG -1 phiX174 24 34 + 15.3293 1.23e-08 0 AGAAGTTAACA -1 phiX174 838 848 + 15.2561 1.27e-08 0 GAGTGATGTAA -1 phiX174 853 863 + 15.2561 1.27e-08 0 TAAAGGTAAAA -1 phiX174 1984 1994 + 15.0244 1.36e-08 0 AATTTCTATGA -1 phiX174 1 11 + 14.8293 1.46e-08 0 GAGTTTTATCG -1 phiX174 4307 4317 + 14.7927 1.47e-08 0 TATTAATAACA -1 phiX174 4303 4313 + 14.6585 1.52e-08 0 TTGATATTAAT -1 phiX174 5033 5043 + 14.561 1.58e-08 0 GTCAGATATGG -1 phiX174 2579 2589 + 14.2927 1.73e-08 0 TGGATACATCT -1 phiX174 322 332 + 14.1951 1.82e-08 0 GACATTTTAAA -1 phiX174 5001 5011 + 13.8902 2.09e-08 0 GGTTTCTATGT -1 phiX174 4217 4227 + 13.8171 2.15e-08 0 TGCTTCTGACG -1 phiX174 4262 4272 + 13.7805 2.18e-08 0 AATGGATGAAT -1 phiX174 3569 3579 + 13.7073 2.26e-08 0 TATGGAAAACA -1 phiX174 194 204 + 13.6829 2.29e-08 0 ATCAACTAACG -1 phiX174 131 141 + 13.4756 2.49e-08 0 AAATGAGAAAA -1 phiX174 1491 1501 + 13.4024 2.55e-08 0 GCCATCTCAAA -1 phiX174 434 444 + 13.2805 2.67e-08 0 GGCCTCTATTA -1 phiX174 4565 4575 + 13.2439 2.73e-08 0 TTGGTTTATCG -1 phiX174 102 112 + 13.2195 2.75e-08 0 GAATTAAATCG -1 phiX174 903 913 + 13.1463 2.82e-08 0 GAGGTACTAAA -1 phiX174 4748 4758 + 12.9756 3.01e-08 0 TACAGCTAATG -1 phiX174 2622 2632 + 12.8659 3.16e-08 0 TGCTGATATTG -1 phiX174 467 477 + 12.7317 3.35e-08 0 TTTGGATTTAA -1 phiX174 4033 4043 + 12.6829 3.44e-08 0 AGCGTATCGAG -1 phiX174 1348 1358 + 12.6707 3.46e-08 0 TACCAATAAAA -1 phiX174 239 249 + 12.5732 3.62e-08 0 AGTGGCTTAAT -1 phiX174 500 510 + 12.4634 3.84e-08 0 GACGAGTAACA -1 phiX174 3001 3011 + 12.4146 3.93e-08 0 GCGGTCAAAAA -1 phiX174 3776 3786 + 12.378 3.98e-08 0 TATTTCTAATG -1 phiX174 2026 2036 + 12.3293 4.06e-08 0 GAAGTTTAAGA -1 phiX174 4237 4247 + 12.3049 4.12e-08 0 AGTTTGTATCT -1 phiX174 803 813 + 12.2439 4.24e-08 0 AGAAGAAAACG -1 phiX174 3770 3780 + 12.1829 4.35e-08 0 AAAGGATATTT -1 phiX174 3429 3439 + 12.122 4.45e-08 0 GAGATGCAAAA -1 phiX174 99 109 + 12.1098 4.48e-08 0 TACGAATTAAA -1 phiX174 67 77 + 11.9268 4.78e-08 0 TCTTGATAAAG -1 phiX174 5332 5342 + 11.7195 5.13e-08 0 ATCTGCTCAAA -1 phiX174 277 287 + 11.7073 5.14e-08 0 TTTAGATATGA -1 phiX174 4338 4348 + 11.6951 5.18e-08 0 GGGGACGAAAA -1 phiX174 3812 3822 + 11.6585 5.28e-08 0 GGTTGATATTT -1 phiX174 1909 1919 + 11.5488 5.51e-08 0 TAACGCTAAAG -1 phiX174 3000 3010 + 11.5366 5.54e-08 0 GGCGGTCAAAA -1 phiX174 3891 3901 + 11.439 5.75e-08 0 ATTGGCTCTAA -1 phiX174 3079 3089 + 11.4268 5.76e-08 0 CTGGTATTAAA -1 phiX174 37 47 + 11.4146 5.79e-08 0 TTCGGATATTT -1 phiX174 380 390 + 11.3293 6.01e-08 0 GTAAGAAATCA diff -r 793225b11202 -r b48e673af4e8 test-data/fimo_output_xml_1.xml --- a/test-data/fimo_output_xml_1.xml Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,66 +0,0 @@ - - - -false -true -false -false -false -0.0001 -p-value -100000 -0.1 -1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -0.073 -0.018 -0.052 -0.062 -0.040 -0.069 -0.022 -0.056 -0.058 -0.092 -0.023 -0.046 -0.051 -0.041 -0.052 -0.074 -0.059 -0.064 -0.013 -0.033 - -cisml.xml - diff -r 793225b11202 -r b48e673af4e8 test-data/fimo_output_xml_2.xml --- a/test-data/fimo_output_xml_2.xml Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ - - - -false -false -false -false -0.0001 -p-value -100000 -0.1 -1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -0.073 -0.018 -0.052 -0.062 -0.040 -0.069 -0.022 -0.056 -0.058 -0.092 -0.023 -0.046 -0.051 -0.041 -0.052 -0.074 -0.059 -0.064 -0.013 -0.033 - -cisml.xml - diff -r 793225b11202 -r b48e673af4e8 test-data/hsa_chrM.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hsa_chrM.fa Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,238 @@ +>chrM +GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG +GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC +CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA +ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC +ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA +AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC +TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA +CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC +AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC +ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA +GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC +AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA +ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA +TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT +CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC +ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC +AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC +CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA +CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC +AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT +GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA +AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA +TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA +GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA +GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG +ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA +ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC +AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA +AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT +AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC +CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG +TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC +ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG +TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC +AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA +AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC +ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA +AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT +TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA +TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT +AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG +TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA +GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG +ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG +AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT +ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA +ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT +TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA +TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC +CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC +ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC +CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG +CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC +AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC +TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG +CCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTCGACCTTGCCGAAGGGGAGTC +CGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATAC +ACAAACATTATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCC +CTGAACTCTACACAACATATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAAC +AGCATACCCCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTA +GCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAACCTAAGAAATAT +GTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTAGGACTATGA +GAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAAGTAAGGTC +AGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAATTAATCCCCT +GGCCCAACCCGTCATCTACTCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTT +TTTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCCTC +GTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTAT +CCTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAATACTACCAATCAATACTCATCATTAATA +ATCATAATAGCTATAGCAATAAAACTAGGAATAGCCCCCTTTCACTTCTGAGTCCCAGAGGTTACCCAAG +GCACCCCTCTGACATCCGGCCTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCA +AATCTCTCCCTCACTAAACGTAAGCCTTCTCCTCACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGA +GGTGGATTAAACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAA +TAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATCCTAACTACTAC +CGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACCCTACTACTATCTCGCACCTGAAACAAGCTA +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTTT +TGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCAC +CATCACCCTCCTTAACCTCTACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATA +TCTAACAACGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCATCG +CCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACTAATAATCTTATAGAAATTTAGGTTAAATAC +AGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGTAACAGCTAAGGACTGCAAAA +CCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTACTAGACCAATGGGA +CTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCC +GCCGGGAAAAAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGA +AAATCACCTCGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTCA +GCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGG +AACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTCTAAGCCTCCTTATTCGAGCC +GAGCTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCACATCTACAACGTTATCGTCACAGCCCATGCAT +TTGTAATAATCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAAT +AATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTC +CTACTCCTGCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTAG +CAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCTAGCAGGTGTCTC +CTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAAACCCCCTGCCATAACCCAATAC +CAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCTCCCAGTCCTAG +CTGCTGGCATCACTATACTACTAACAGACCGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGG +AGACCCCATTCTATACCAACACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCA +GGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGGTA +TGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGG +AATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAA +GTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGAAATGATCTGCTGCAGTGCTCTGAGCCCTAG +GATTCATCTTTCTTTTCACCGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGT +ACTACACGACACGTACTACGTTGTAGCCCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATC +ATAGGAGGCTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCC +ATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGCCTATCCGGAAT +GCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACATCCTATCATCTGTAGGCTCATTC +ATTTCTCTAACAGCAGTAATATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCC +TAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGA +AGAACCCGTATACATAAAATCTAGACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAA +CCCCATGGCCTCCATGACTTTTTCAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAAT +TATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCT +ATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCC +TGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAAATAGA +AACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTAC +ATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACG +AGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGA +CCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACA +TCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTC +TAAACCAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGC +AAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTT +ACCCTATAGCACCCCCTCTACCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTT +AAAGATTAAGAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCAT +AATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACAAACTACCACCTA +CCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCT +GTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCTATTTCCCCCT +CTATTGATCCCCACCTCCAAATATCTCATCAACAACCGACTAATCACCACCCAACAATGACTAATCAAAC +TAACCTCAAAACAAATGATAACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTT +AATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAACTA +TCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCACAGTGATTATAGGCTTTCGCTCTAAGATTA +AAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAGTTATTATCGA +AACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTAACCGCTAACATTACTGCAGGCCAC +CTACTCATGCACCTAATTGGAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCA +TCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCAC +ACTTCTAGTAAGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGTAA +AACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATT +TCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACACACTAACCATATACCAATGATGG +CGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACG +GGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAG +CCTAGCCCCTACCCCCCAATTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAA +GTCCCACTCCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCTAA +TAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCTCTATTTTACCCT +CCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTT +GTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCTCACTATCTGCTTCATCCGCC +AACTAATATTTCACTTTACATCCAAACATCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGT +AGATGTGGTTTGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGT +ACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTTAA +TAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACAT +AGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCCCGCGTCCCTTTCTCCATAAAA +TTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAG +CCCTACAAACAACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAG +TCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAACCGAATTGGTATATAGTTTAAACAAAACGAAT +GATTTCGACTCATTAAATTATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTAG +CATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCTACTATGCCTAGA +AGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAAT +ATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCTACTAGTCTCAA +TCTCCAACACATATGGCCTAGACTACGTACATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCA +ACAATTATATTACTACCACTGACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACA +GCCTAATTATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCCCC +AACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATC +ATGGCAAGCCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAACTCTACCTCTCTATACTAATCT +CCCTACAAATCTCCTTAATTATAACATTCACAGCCACAGAACTAATCATATTTTATATCTTCTTCGAAAC +CACACTTATCCCCACCTTGGCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACA +TACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCC +TAGGCTCACTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTT +AATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACTTATGACTCCCT +AAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCAGTACTCTTAAAACTAGGCGGCT +ATGGTATAATACGCCTCACACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACT +ATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCA +TACTCTTCAATCAGCCACATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCG +GCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTA +CGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTT +TGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTG +TGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGC +CCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAA +CCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACC +CCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAA +CAGAGGCTTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCATGTCTAAC +AACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCA +ACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCC +ATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCAT +CCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAA +CTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAATA +TTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATATAAACTCAGACC +CAAACATTAATCAGTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA +CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA +TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT +TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA +CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT +CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA +TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC +TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC +AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC +CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC +CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC +ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA +AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC +TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC +ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC +TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA +CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC +AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA +TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT +AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA +ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA +TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA +CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA +CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC +TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC +CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC +CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG +ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC +CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC +CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC +CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA +ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA +CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC +ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC +TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC +AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC +TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA +GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT +CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC +ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT +TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC +TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA +GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC +AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT +AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC +TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC +CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA +GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC +ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA +TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA +ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA +ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG +TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC +TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG +CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC +ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG diff -r 793225b11202 -r b48e673af4e8 test-data/meme_fimo_input_1.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme_fimo_input_1.xml Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,8739 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+TTAACAACAG + + +C + + + + + + + + + + +TAATATAGTG + + +TAAATCTTAA + + + + + + + + + + +CAAGTAAAAA + + +CACTGT + + + + + + + + + + +ATTGAACTTC + + +GTGACAGAGC + + + + + + + + + + +AACTAACTAA + + +TTTTAAATTG + + + + + + + + + + +GACATGTTTG + + +AACTAATTCC + + + + + + + + + + +CCTTAAGAGT + + + + + + + + + + + + + +TGTAACAATA + + +ACAAGGGAGG + + + + + + + + + + +ACACATGTGT + + +CCCCTCCCTG + + + + + + + + + + +TCTGCACTCT + + +ATTCTTTAAG + + + + + + + + + + +GAATGTACTG + + +TAACTTTCTC + + + + + + + + + + +TTCCCCTGCT + + +T + + + + + + + + + + +CAAATGCTAA + + +GAATTAATAA + + + + + + + + + + +TCTCGGGTGA + + +GATTTGCTT + + + + + + + + + + +ATTTGGCTTG + + +AATGGGCTAA + + + + + + + + + + +GCCACGAACC + + +TCTTTTATT + + + + + + + + + + +TACTGTAGAG + + +ATTTTTTCTT + + + + + + + + + + +CTTCACTTAA + + +GTTCATGGAA + + + + + + + + + + +TAATGTTAAC + + +TTTAAAAAAT + + + + + + + + + + +TTAGGGGAAA + + +TTAAAAAT + + + + + + + + + + +TAGGCAACTT + + +CAAATCGGGA + + + + + + + + + + +TTCTATAGGC + + +TTAATAAC + + + + + + + + + + +TTTATTGCAT + + +ATCCAATGCA + + + + + + + + + + +TAATCAGTCT + + +TATTAACTTC + + + + + + + + + + +TTTCTATAAC + + +GCCAACTTCA + + + + + + + + + + +ATACTGTATA + + +CTGGAAGTTA + + + + + + + + + + +TCGGCTGTAG + + +ACACCTAGAA + + + + + + + + + + +CTTCCTTAGT + + +CTTCTAAA + + + + + + + + + + +TTCCAGTGTT + + +TAATTGTGTA + + + + + + + + + + +AAGACCTGAG + + +ACTAAG + + + + + + + + + + +CTTTCATTGT + + +GCATTTCCCA + + + + + + + + + + +TTTAGCTCTC + + +CATGATAACC + + + + + + + + + + +CA + + +CCCAGAGTCC + + + + + + + + + + +ATTACCAGGG + + +CCTAAGAAAC + + + + + + + + + + +T + + +AGCTAACTTC + + + + + + + + + + +CATTATCCTT + + +TTTTCTAACC + + + + + + + + + + +ACGGTTCTGA + + +TAACAGTTAC + + + + + + + + + + +ATCCGGTAGA + + +TTTATAAGGG + + + + + + + + + + +CCATTCATGA + + +ATAGCAT + + + + + + + + + + +CATCCTTTAG + + +GTTGCATTCG + + + + + + + + + + +TATATGTAGT + + +TTACTTATAC + + + + + + + + + + +AAAAAGATTT + + +AGATAGATAG + + + + + + + + + + +TTTGTGAGAA + + + + + + + + + + + + + +ACATAATATT + + +TAATGTACTC + + + + + + + + + + +AATTGT + + +AATATGTCAT + + + + + + + + + + +ATAGTCAACA + + +TTCTACTTCC + + + + + + + + + + +ACTGCTCTCT + + +CTTTATTAAT + + + + + + + + + + +ACTTAGTCTA + + +TATCTGTTAG + + + + + + + + + + +CTACTCCTAC + + +ACTTAGCAAG + + + + + + + + + + +TATAAAGAAG + + +TATACTTCTT + + + + + + + + + + +AA + + +AC + + + + + + + + + + +TTCTATTGTA + + +GTATTCATAG + + + + + + + + + + +TTTTCTGGTA + + +TAAATGTCTT + + + + + + + + + + +ATCTACCTCC + + +CTTGCCTTCT + + + + + + + + + + +CCCCATTCTT + + +ATTGAACGTA + + + + + + + + + + +TTGATGTGTG + + +ATTCAATTCT + + + + + + + + + + +ACTCTGTGTG + + +AATATATATA + + + + + + + + + + +ACTCTGTCAC + + +GGCTTTATCT + + + + + + + + + + +CAGTCCCCAC + + +CTTATCTACC + + + + + + + + + + +CTTGTTAGAG + + +TTAACTCCAC + + + + + + + + + + +TATTCTAATT + + +TATTTGAATG + + + + + + + + + + +ATGGCATGTA + + +TTTTACT + + + + + + + + + + +TGGACACTGG + + +TTTATAAAGT + + + + + + + + + + +TGATCAGGGA + + +CCCTAAACCT + + + + + + + + + + +ATGCCTCATG + + +TACATGAAAA + + + + + + + + + + +ACATAATATT + + +CTGTTTAAAA + + + + + + + + + + +CACATAAATT + + +ATCATTAATA + + + + + + + + + + +AGAAAAATTG + + +TATATGAAAT + + + + + + + + + + +AACTTTCAG + + +ACCCCTCTT + + + + + + + + + + +TACTTGCTTC + + +GGAGTATACA + + + + + + + + + + +CATGTAAAGT + + +TGCTCTAATA + + + + + + + + + + +CTTTACTTAT + + +ATTC + + + + + + + + + + +TGAAAGTAGA + + +CCTCACCACT + + + + + + + + + + +GTATCTCCTC + + +A + + + + + + + + + + +TTTGTTATTC + + +TGAATCGGAA + + + + + + + + + + +TTAACACAAA + + +TCCTCTTCTT + + + + + + + + + + +CCTGTGCCTT + + +GCCTTAATTT + + + + + + + + + + +TATGCTATCA + + +CCATTGTCTC + + + + + + + + + + +GGCAGTGTTG + + +GTTCATTTT + + + + + + + + + + +CTTTAGCTCT + + +TGAACTTTGC + + + + + + + + + + +ATTGTTGATT + + +AGACTTAAGG + + + + + + + + + + +AAGGAGCAGG + + +AA + + + + + + + + + + +ACACTAATTT + + +ATCTTTTTTC + + + + + + + + + + +TATAGTTATG + + +CTTCTCT + + + + + + + + + + +TATAACTTCT + + +CCTAGAGTAA + + + + + + + + + + +ATTCTGCCCA + + +TTGAATCATA + + + + + + + + + + +ACAAATGGAT + + +TTTGTTTAGT + + + + + + + + + + +CCTCTAGCTC + + +CTCTCTTAAT + + + + + + + + + + +TTATAGATTA + + +TTTCTGACTA + + + + + + + + + + +GTGTATATAG + + +ATACATAAGT + + + + + + + + + + +CTTTCTTGTT + + +TACCATCAAT + + + + + + + + + + +CTCACATATT + + +GCTCTTAACC + + + + + + + + + + +TTTCTTCTTT + + +TTAATGTATC + + + + + + + + + + +ATTCCACTTC + + +TAGCTT + + + + + + + + + + +AGTACTGACT + + +TGGTTGTACC + + + + + + + + + + +AATCTCTTTT + + +AATGTTAACT + + + + + + + + + + +CGGGTTCTGT + + +CC + + + + + + + + + + +TTAGACTTTC + + +CTTCTAACCA + + + + + + + + + + +CAGAACCCTT + + +CAATTAAATT + + + + + + + + + + +CACTTATTAG + + +CTATT + + + + + + + + + + +TCTCTTCATT + + +CTTCC + + + + + + + + + + +TTAAAACAAA + + +TCATCCCTCT + + + + + + + + + + +ATCATCCTAG + + +GATATAATTT + + + + + + + + + + +ATAAGAACTT + + + + + + + + + + + + + +TTTTCTCTGT + + +TACTGTCTTG + + + + + + + + + + +TCTTCCTAAC + + +CCAACCCTAA + + + + + + + + + + +ATAACCCTAA + + +TTAAACCCCA + + + + + + + + + + +ATTGCTCTTG + + +TTTTCTTCT + + + + + + + + + + +CTCCCTTTTC + + +GCTGGCACTG + + + + + + + + + + +ACTTAACATG + + +ATAAACTTCC + + + + + + + + + + +TTCCCTAAAC + + +TACTATATGC + + + + + + + + + + +CTAACAGCTC + + +TCCCAGCCTC + + + + + + + + + + +AT + + +TGAAGGCAGT + + + + + + + + + + +CTATATGAAC + + +TAACCTTTAG + + + + + + + + + + +TAAACCTCCT + + +GCTTTCTTTT + + + + + + + + + + +TTGGAATGAT + + +CTTTT + + + + + + + + + + +ATTTTAAGCT + + +TAAATGTA + + + + + + + + + + +TTTTAAGGTC + + +CCAATTAATT + + + + + + + + + + +AATTTATTGG + + +GAACTAGTAG + + + + + + + + + + +CAGGGAGCTC + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 793225b11202 -r b48e673af4e8 test-data/meme_output_html_1.html --- a/test-data/meme_output_html_1.html Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,95 +0,0 @@ - - - - - MEME - + + + + + + + + + + + + + + + +
      +

      Help poup.

      +
      [ + close ]
      +
      +
      +

      The statistical significance of the motif. MEME usually finds the most + statistically significant (low E-value) motifs first. It is unusual to + consider a motif with an E-value larger than 0.05 significant so, as an + additional indicator, MEME displays these partially transparent.

      +

      The E-value of a motif is based on its log likelihood ratio, width, + sites, the background letter frequencies (given in the command line + summary), and the size of the training set.

      +

      The E-value is an estimate of the expected number of motifs with the + given log likelihood ratio (or higher), and with the same width and site + count, that one would find in a similarly sized set of random + sequences (sequences where each position is independent and letters are + chosen according to the background letter frequencies).

      +
      [ + close ]
      +
      +
      +

      The number of sites contributing to the construction of the motif.

      +
      [ + close ]
      +
      +
      +

      The width of the motif. Each motif describes a pattern of a fixed + width, as no gaps are allowed in MEME motifs.

      +
      [ + close ]
      +
      +
      +

      Click on the blue symbol below to reveal more information about this motif.

      +
      [ + close ]
      +
      +
      +

      Click on the blue symbol below to reveal options allowing you + to submit this motif to another MEME Suite motif analysis program, to download this + motif in various text formats, or to download a sequence "logo" of + this motif PNG or EPS format.

      +
      Supported Programs
      +
      +
      Tomtom
      +
      Tomtom is a tool for searching for similar known motifs. + [manual]
      +
      MAST
      +
      MAST is a tool for searching biological sequence databases for + sequences that contain one or more of a group of known motifs. + [manual]
      +
      FIMO
      +
      FIMO is a tool for searching biological sequence databases for + sequences that contain one or more known motifs. + [manual]
      +
      GOMO
      +
      GOMO is a tool for identifying possible roles (Gene Ontology + terms) for DNA binding motifs. + [manual]
      +
      SpaMo
      +
      SpaMo is a tool for inferring possible transcription factor + complexes by finding motifs with enriched spacings. + [manual]
      +
      +
      [ + close ]
      +
      +
      +

      The log likelihood ratio of the motif.The log likelihood ratio is the + logarithm of the ratio of the probability of the occurrences of the motif + given the motif model (likelihood given the motif) versus their + probability given the background model (likelihood given the null model). + (Normally the background model is a 0-order Markov model using the + background letter frequencies, but higher order Markov models may be + specified via the -bfile option to MEME.).

      +
      [ + close ]
      +
      +
      +

      The information content of the motif in bits. It is equal to the sum + of the uncorrected information content, R(), in the columns of the pwm. + This is equal relative entropy of the motif relative to a uniform + background frequency model.

      +
      [ + close ]
      +
      +
      +

      The relative entropy of the motif.

      + +

      re = llr / (sites * ln(2))

      +
      [ + close ]
      +
      +
      +

      The Bayes Threshold.

      +
      [ + close ]
      +
      +
      +

      The strand used for the motif site.

      +
      +
      +
      +
      The motif site was found in the sequence as it was supplied.
      +
      -
      +
      The motif site was found in the reverse complement of the supplied sequence.
      +
      +
      [ + close ]
      +
      +
      +

      The position in the sequence where the motif site starts. If a motif + started right at the begining of a sequence it would be described as + starting at position 1.

      +
      [ + close ]
      +
      +
      +

      The probability that an equal or better site would be found in a + random sequence of the same length conforming to the background letter + frequencies.

      +
      [ + close ]
      +
      +
      +

      A motif site with the 10 flanking letters on either side.

      +

      When the site is not on the given strand then the site + and both flanks are reverse complemented so they align.

      +
      [ + close ]
      +
      + +
      +

      The name of the sequences as given in the FASTA file.

      +

      The number to the left of the sequence name is the ordinal + of the sequence.

      +
      [ + close ]
      +
      + +
      +

      These are the motif sites predicted by MEME and used to build the motif.

      +

      These sites are shown in solid color and hovering the cursor + over a site will reveal details about the site. Only sequences + that contain a motif site are shown.

      +
      [ + close ]
      +
      + +
      +

      These are the motif sites predicted by MEME plus + any additional sites detected using a motif scanning + algorithm.

      +

      These MEME sites are shown in solid color and + additional scanned sites are shown in transparent color. + Hovering the cursor over a site will reveal details about the site. + Only sequences containing a predicted or scanned motif site are shown.

      +

      The scanned sites are predicted using a + log-odds scoring matrix constructed from the MEME sites. + Only scanned sites with position p-values less + than 0.0001 are shown.

      +
      [ + close ]
      +
      + +
      +

      These are the same sites as shown by selecting the + "Motif Sites + Scanned Sites" button except that all + sequences, including those with no sites, are included + in the diagram.

      +
      [ + close ]
      +
      + +
      +

      This is the combined match p-value.

      +

      The combined match p-value is defined as the probability that a + random sequence (with the same length and conforming to the background) + would have position p-values such that the product is smaller + or equal to the value calulated for the sequence under test.

      +

      The position p-value is defined as the probability that a + random sequence (with the same length and conforming to the background) + would have a match to the motif under test with a score greater or equal + to the largest found in the sequence under test.

      +

      Hovering your mouse over a motif site in the motif location + block diagram will show its position p-value and other information + about the site.

      + +
      [ + close ]
      +
      +
      +

      This diagram shows the location of motif sites.

      +

      Each block shows the position and strength of a motif + site. The height of a block gives an indication of the + significance of the site as taller blocks are more significant. + The height is calculated to be proportional to the negative + logarithm of the p-value of the site, truncated at + the height for a p-value of 1e-10.

      +

      For complementable alphabets (like DNA), sites on the + positive strand are shown above the line, + sites on the negative strand are shown below.

      +

      Placing the cursor + over a motif site will reveal more information about the site + including its position p-value. (See the help + for the p-value column for an explanation of position + p-values.)

      +
      [ + close ]
      +
      + +
      +

      The name of the file of sequences input to MEME.

      +
      [ + close ]
      +
      +
      +

      The position specific priors file used by MEME to find the motifs.

      +
      [ + close ]
      +
      +
      +

      The alphabet used by the sequences.

      +
      [ + close ]
      +
      +
      +

      The number of sequences provided as input to MEME.

      +
      [ + close ]
      +
      + +
      +

      The name of the alphabet symbol.

      +
      [ + close ]
      +
      +
      +

      The frequency of the alphabet symbol in the dataset with a pseudocount + so it is never zero.

      +
      [ + close ]
      +
      +
      +

      The frequency of the alphabet symbol as defined by the background model.

      +
      [ + close ]
      +
      + + +
      +
      +
      + + +
      +
      + + + +
      + + + + + +
      Motif1
      p-value8.23e-7
      Start23
      End33
      +
      + +
      +
      Scanned Site
      + + + + + + +
      Motif1
      p-value8.23e-7
      Start23
      End33
      +
      + +
      +
      +
      + . +
      +
      +
      +
      +
      +
      + E-value: + +
      +
      +
      + Site Count: + +
      +
      +
      + Width: + +
      +
      +
      +
      + +
      +
      + StandardReverse + Complement +
      +
      +
      + Log Likelihood Ratio: + +
      +
      +
      + Information Content: + +
      +
      +
      + Relative Entropy: + +
      +
      +
      + Bayes Threshold: + +
      +
      +
      +
      +
      + + + + + + + +
      + +

      + For further information on how to interpret these results or to get a + copy of the MEME software please access + http://meme-suite.org. +

      +

      If you use MEME in your research, please cite the following paper:
      + + Timothy L. Bailey and Charles Elkan, + "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", + Proceedings of the Second International Conference on Intelligent Systems + for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. + [pdf] + +

      +
      + +
      + Discovered Motifs +   |   + Motif Locations +   |   + Inputs & Settings +   |   + Program information +
      + + +

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      + +

      Discovered Motifs

      +
      +

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      +

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      +
      +

      Motif Locations

      +
      +

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      +

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      +
      +

      Inputs & Settings

      +
      +

      Sequences

      + + + + + + + + + + + + +
      Source
      PSP Source
      Alphabet
      Sequence Count
      + +

      Background

      + + +

      Other Settings

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Motif Site Distribution + ZOOPS: Zero or one site per sequence + OOPS: Exactly one site per sequence + ANR: Any number of sites per sequence +
      Site Strand Handling + This alphabet only has one strand + Sites must be on the given strand + Sites may be on either strand +
      Maximum Number of Motifs
      Motif E-value Threshold
      Minimum Motif Width
      Maximum Motif Width
      Minimum Sites per Motif
      Maximum Sites per Motif
      Bias on Number of Sites
      Sequence Prior + Simple Dirichlet + Dirichlets Mix + Mega-weight Dirichlets Mix + Mega-weight Dirichlets Mix Plus + Add One +
      Sequence Prior Strength
      EM Starting Point Source + From substrings in input sequences + From strings on command line (-cons) +
      EM Starting Point Map Type + Uniform + Point Accepted Mutation +
      EM Starting Point Fuzz
      EM Maximum Iterations
      EM Improvement Threshold
      Trim Gap Open Cost
      Trim Gap Extend Cost
      End Gap Treatment + No cost + Same cost as other gaps +
      + + Show Advanced Settings + Hide Advanced Settings + +
      + +
      + +
      +
      +
      MEME version
      + + (Release date: )
      +
      + +
      +
      Reference
      + + Timothy L. Bailey and Charles Elkan, + "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", + Proceedings of the Second International Conference on Intelligent Systems + for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. + +
      +
      +
      Command line
      + + +
      +
      + + + diff -r 793225b11202 -r b48e673af4e8 test-data/meme_output_test1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme_output_test1.txt Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,325 @@ +******************************************************************************** +MEME - Motif discovery tool +******************************************************************************** +MEME version 4.12.0 (Release date: Tue Jun 27 16:22:50 2017 -0700) + +For further information on how to interpret these results or to get +a copy of the MEME software please access http://meme-suite.org . + +This file may be used as input to the MAST algorithm for searching +sequence databases for matches to groups of motifs. MAST is available +for interactive use and downloading at http://meme-suite.org . +******************************************************************************** + + +******************************************************************************** +REFERENCE +******************************************************************************** +If you use this program in your research, please cite: + +Timothy L. Bailey and Charles Elkan, +"Fitting a mixture model by expectation maximization to discover +motifs in biopolymers", Proceedings of the Second International +Conference on Intelligent Systems for Molecular Biology, pp. 28-36, +AAAI Press, Menlo Park, California, 1994. +******************************************************************************** + + +******************************************************************************** +TRAINING SET +******************************************************************************** +DATAFILE= meme_input_1.fasta +ALPHABET= ACDEFGHIKLMNPQRSTVWY +Sequence name Weight Length Sequence name Weight Length +------------- ------ ------ ------------- ------ ------ +chr21_19617074_19617124_ 1.0000 50 chr21_26934381_26934431_ 1.0000 50 +chr21_28217753_28217803_ 1.0000 50 chr21_31710037_31710087_ 1.0000 50 +chr21_31744582_31744632_ 1.0000 50 chr21_31768316_31768366_ 1.0000 50 +chr21_31914206_31914256_ 1.0000 50 chr21_31933633_31933683_ 1.0000 50 +chr21_31962741_31962791_ 1.0000 50 chr21_31964683_31964733_ 1.0000 50 +chr21_31973364_31973414_ 1.0000 50 chr21_31992870_31992920_ 1.0000 50 +chr21_32185595_32185645_ 1.0000 50 chr21_32202076_32202126_ 1.0000 50 +chr21_32253899_32253949_ 1.0000 50 chr21_32410820_32410870_ 1.0000 50 +chr21_36411748_36411798_ 1.0000 50 chr21_37838750_37838800_ 1.0000 50 +chr21_45705687_45705737_ 1.0000 50 chr21_45971413_45971463_ 1.0000 50 +chr21_45978668_45978718_ 1.0000 50 chr21_45993530_45993580_ 1.0000 50 +chr21_46020421_46020471_ 1.0000 50 chr21_46031920_46031970_ 1.0000 50 +chr21_46046964_46047014_ 1.0000 50 chr21_46057197_46057247_ 1.0000 50 +chr21_46086869_46086919_ 1.0000 50 chr21_46102103_46102153_ 1.0000 50 +chr21_47517957_47518007_ 1.0000 50 chr21_47575506_47575556_ 1.0000 50 +******************************************************************************** + +******************************************************************************** +COMMAND LINE SUMMARY +******************************************************************************** +This information can also be useful in the event you wish to report a +problem with the MEME software. + +command: meme meme_input_1.fasta -o meme_test1_out -nostatus -maxsize 1000000 + +model: mod= zoops nmotifs= 1 evt= inf +object function= E-value of product of p-values +width: minw= 8 maxw= 50 +width: wg= 11 ws= 1 endgaps= yes +nsites: minsites= 2 maxsites= 30 wnsites= 0.8 +theta: spmap= pam spfuzz= 120 +global: substring= yes branching= no wbranch= no +em: prior= megap b= 7500 maxiter= 50 + distance= 1e-05 +data: n= 1500 N= 30 shuffle= -1 + +sample: seed= 0 ctfrac= -1 maxwords= -1 +Dirichlet mixture priors file: prior30.plib +Letter frequencies in dataset: +A 0.294 C 0.231 D 0.000 E 0.000 F 0.000 G 0.257 H 0.000 I 0.000 K 0.000 +L 0.000 M 0.000 N 0.000 P 0.000 Q 0.000 R 0.000 S 0.000 T 0.217 V 0.000 +W 0.000 Y 0.000 +Background letter frequencies (from dataset with add-one prior applied): +A 0.291 C 0.229 D 0.001 E 0.001 F 0.001 G 0.255 H 0.001 I 0.001 K 0.001 +L 0.001 M 0.001 N 0.001 P 0.001 Q 0.001 R 0.001 S 0.001 T 0.215 V 0.001 +W 0.001 Y 0.001 +******************************************************************************** + + +******************************************************************************** +MOTIF GGGGTATAAAA MEME-1 width = 11 sites = 25 llr = 239 E-value = 2.4e-011 +******************************************************************************** +-------------------------------------------------------------------------------- + Motif GGGGTATAAAA MEME-1 Description +-------------------------------------------------------------------------------- +Simplified A 2323:a:a8a8 +pos.-specific C ::3:::::::: +probability D ::::::::::: +matrix E ::::::::::: + F ::::::::::: + G 7746::::::1 + H ::::::::::: + I ::::::::::: + K ::::::::::: + L ::::::::::: + M ::::::::::: + N ::::::::::: + P ::::::::::: + Q ::::::::::: + R ::::::::::: + S ::::::::::: + T 1:2:a:a:2:: + V ::::::::::: + W ::::::::::: + Y ::::::::::: + + bits 10.6 + 9.5 + 8.5 + 7.4 +Relative 6.3 +Entropy 5.3 +(13.8 bits) 4.2 + 3.2 + 2.1 * ** + 1.1 ** ******** + 0.0 ----------- + +Multilevel GGGGTATAAAA +consensus AACA T +sequence + + +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif GGGGTATAAAA MEME-1 sites sorted by position p-value +-------------------------------------------------------------------------------- +Sequence name Start P-value Site +------------- ----- --------- ----------- +chr21_46046964_46047014_ 13 1.06e-06 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC +chr21_46057197_46057247_ 37 3.41e-06 ACAGGCCCTG GGCATATAAAA GCC +chr21_45971413_45971463_ 10 3.41e-06 CAGGCCCTG GGCATATAAAA GCCCCAGCAG +chr21_31964683_31964733_ 14 3.41e-06 GATTCACTGA GGCATATAAAA GGCCCTCTGC +chr21_45993530_45993580_ 8 4.00e-06 CCAAGGA GGAGTATAAAA GCCCCACAAA +chr21_32202076_32202126_ 14 5.01e-06 CCACCAGCTT GAGGTATAAAA AGCCCTGTAC +chr21_46031920_46031970_ 16 6.06e-06 ATACCCAGGG AGGGTATAAAA CCTCAGCAGC +chr21_32410820_32410870_ 22 8.67e-06 AATCACTGAG GATGTATAAAA GTCCCAGGGA +chr21_32185595_32185645_ 19 8.67e-06 CACCAGAGCT GGGATATATAA AGAAGGTTCT +chr21_31992870_31992920_ 17 8.67e-06 CACTATTGAA GATGTATAAAA TTTCATTTGC +chr21_46020421_46020471_ 3 1.21e-05 GA GACATATAAAA GCCAACATCC +chr21_47517957_47518007_ 33 1.59e-05 CCGGCGGGGC GGGGTATAAAG GGGGCGG +chr21_45978668_45978718_ 5 1.59e-05 CAGA GGGGTATAAAG GTTCCGACCA +chr21_31914206_31914256_ 16 1.68e-05 CCCACTACTT AGAGTATAAAA TCATTCTGAG +chr21_32253899_32253949_ 20 2.03e-05 CACCAGCAAG GATATATAAAA GCTCAGGAGT +chr21_31744582_31744632_ 13 3.06e-05 CAGGTCTAAG AGCATATATAA CTTGGAGTCC +chr21_19617074_19617124_ 40 3.06e-05 CCTCGGGACG TGGGTATATAA +chr21_45705687_45705737_ 38 3.82e-05 CGTGGTCGCG GGGGTATAACA GC +chr21_31768316_31768366_ 1 3.82e-05 . AACGTATATAA ATGGTCCTGT +chr21_47575506_47575556_ 31 4.02e-05 GCTGCCGGTG AGCGTATAAAG GCCCTGGCG +chr21_26934381_26934431_ 28 5.52e-05 AGTCACAAGT GAGTTATAAAA GGGTCGCACG +chr21_31710037_31710087_ 15 5.94e-05 CCCAGGTTTC TGAGTATATAA TCGCCGCACC +chr21_36411748_36411798_ 23 6.78e-05 AGTTTCAGTT GGCATCtaaaa attatataac +chr21_31933633_31933683_ 3 2.08e-04 TC AGAGTATATAT AAATGTTCCT +chr21_31962741_31962791_ 14 4.05e-04 TATAACTCAG GTTGGATAAAA TAATTTGTAC +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif GGGGTATAAAA MEME-1 block diagrams +-------------------------------------------------------------------------------- +SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM +------------- ---------------- ------------- +chr21_46046964_46047014_ 1.1e-06 12_[1]_27 +chr21_46057197_46057247_ 3.4e-06 36_[1]_3 +chr21_45971413_45971463_ 3.4e-06 9_[1]_30 +chr21_31964683_31964733_ 3.4e-06 13_[1]_26 +chr21_45993530_45993580_ 4e-06 7_[1]_32 +chr21_32202076_32202126_ 5e-06 13_[1]_26 +chr21_46031920_46031970_ 6.1e-06 15_[1]_24 +chr21_32410820_32410870_ 8.7e-06 21_[1]_18 +chr21_32185595_32185645_ 8.7e-06 18_[1]_21 +chr21_31992870_31992920_ 8.7e-06 16_[1]_23 +chr21_46020421_46020471_ 1.2e-05 2_[1]_37 +chr21_47517957_47518007_ 1.6e-05 32_[1]_7 +chr21_45978668_45978718_ 1.6e-05 4_[1]_35 +chr21_31914206_31914256_ 1.7e-05 15_[1]_24 +chr21_32253899_32253949_ 2e-05 19_[1]_20 +chr21_31744582_31744632_ 3.1e-05 12_[1]_27 +chr21_19617074_19617124_ 3.1e-05 39_[1] +chr21_45705687_45705737_ 3.8e-05 37_[1]_2 +chr21_31768316_31768366_ 3.8e-05 [1]_39 +chr21_47575506_47575556_ 4e-05 30_[1]_9 +chr21_26934381_26934431_ 5.5e-05 27_[1]_12 +chr21_31710037_31710087_ 5.9e-05 14_[1]_25 +chr21_36411748_36411798_ 6.8e-05 22_[1]_17 +chr21_31933633_31933683_ 0.00021 2_[1]_37 +chr21_31962741_31962791_ 0.0004 13_[1]_26 +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif GGGGTATAAAA MEME-1 in BLOCKS format +-------------------------------------------------------------------------------- +BL MOTIF GGGGTATAAAA width=11 seqs=25 +chr21_46046964_46047014_ ( 13) GGGGTATAAAA 1 +chr21_46057197_46057247_ ( 37) GGCATATAAAA 1 +chr21_45971413_45971463_ ( 10) GGCATATAAAA 1 +chr21_31964683_31964733_ ( 14) GGCATATAAAA 1 +chr21_45993530_45993580_ ( 8) GGAGTATAAAA 1 +chr21_32202076_32202126_ ( 14) GAGGTATAAAA 1 +chr21_46031920_46031970_ ( 16) AGGGTATAAAA 1 +chr21_32410820_32410870_ ( 22) GATGTATAAAA 1 +chr21_32185595_32185645_ ( 19) GGGATATATAA 1 +chr21_31992870_31992920_ ( 17) GATGTATAAAA 1 +chr21_46020421_46020471_ ( 3) GACATATAAAA 1 +chr21_47517957_47518007_ ( 33) GGGGTATAAAG 1 +chr21_45978668_45978718_ ( 5) GGGGTATAAAG 1 +chr21_31914206_31914256_ ( 16) AGAGTATAAAA 1 +chr21_32253899_32253949_ ( 20) GATATATAAAA 1 +chr21_31744582_31744632_ ( 13) AGCATATATAA 1 +chr21_19617074_19617124_ ( 40) TGGGTATATAA 1 +chr21_45705687_45705737_ ( 38) GGGGTATAACA 1 +chr21_31768316_31768366_ ( 1) AACGTATATAA 1 +chr21_47575506_47575556_ ( 31) AGCGTATAAAG 1 +chr21_26934381_26934431_ ( 28) GAGTTATAAAA 1 +chr21_31710037_31710087_ ( 15) TGAGTATATAA 1 +chr21_36411748_36411798_ ( 23) GGCATCTAAAA 1 +chr21_31933633_31933683_ ( 3) AGAGTATATAT 1 +chr21_31962741_31962791_ ( 14) GTTGGATAAAA 1 +// + +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif GGGGTATAAAA MEME-1 position-specific scoring matrix +-------------------------------------------------------------------------------- +log-odds matrix: alength= 20 w= 11 n= 1200 bayes= 5.33554 E= 2.4e-011 + -32 -680 91 77 7 138 -20 55 64 107 11 150 142 72 87 396 -148 221 -140 -36 + -11 -680 89 76 7 137 -21 55 63 107 10 149 141 71 87 396 -239 220 -140 -36 + -79 41 4 21 -7 44 -62 42 -5 99 0 99 138 52 42 399 -46 223 -173 -68 + 11 -677 48 47 -2 127 -43 46 27 101 3 124 138 60 62 397 -235 220 -160 -55 + -596 -820 12 -21 -53 -267 -74 37 16 44 -37 98 31 9 19 319 212 127 -193 -95 + 165 -261 70 110 77 -521 -4 147 95 201 90 121 124 91 107 425 -527 314 -95 8 + -838 -990 -89 -149 -151 -841 -161 -117 -113 -66 -209 -68 -69 -129 -91 111 221 -55 -255 -173 + 176 -858 -79 -103 -115 -717 -148 -95 -108 -17 -162 -61 -12 -95 -69 193 -737 52 -240 -153 + 134 -686 0 16 -12 -553 -68 44 -8 96 -9 88 124 41 36 384 11 216 -177 -71 + 165 -261 70 110 77 -521 -4 147 95 201 90 121 124 91 107 425 -527 314 -95 8 + 147 -614 89 129 93 -121 12 160 113 217 108 144 144 111 125 447 -241 332 -81 22 +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif GGGGTATAAAA MEME-1 position-specific probability matrix +-------------------------------------------------------------------------------- +letter-probability matrix: alength= 20 w= 11 nsites= 25 E= 2.4e-011 + 0.240000 0.000000 0.000000 0.000000 0.000000 0.680000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.080000 0.000000 0.000000 0.000000 + 0.280000 0.000000 0.000000 0.000000 0.000000 0.680000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 + 0.160000 0.320000 0.000000 0.000000 0.000000 0.360000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.160000 0.000000 0.000000 0.000000 + 0.320000 0.000000 0.000000 0.000000 0.000000 0.640000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.960000 0.000000 0.000000 0.000000 + 0.960000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 + 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.760000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.240000 0.000000 0.000000 0.000000 + 0.960000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.840000 0.000000 0.000000 0.000000 0.000000 0.120000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif GGGGTATAAAA MEME-1 regular expression +-------------------------------------------------------------------------------- +[GA][GA][GC][GA]TATA[AT]AA +-------------------------------------------------------------------------------- + + + + +Time 0.77 secs. + +******************************************************************************** + + +******************************************************************************** +SUMMARY OF MOTIFS +******************************************************************************** + +-------------------------------------------------------------------------------- + Combined block diagrams: non-overlapping sites with p-value < 0.0001 +-------------------------------------------------------------------------------- +SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM +------------- ---------------- ------------- +chr21_19617074_19617124_ 1.22e-03 39_[1(3.06e-05)] +chr21_26934381_26934431_ 2.21e-03 27_[1(5.52e-05)]_12 +chr21_28217753_28217803_ 7.29e-01 50 +chr21_31710037_31710087_ 2.37e-03 14_[1(5.94e-05)]_25 +chr21_31744582_31744632_ 1.22e-03 12_[1(3.06e-05)]_27 +chr21_31768316_31768366_ 1.53e-03 [1(3.82e-05)]_39 +chr21_31914206_31914256_ 6.70e-04 15_[1(1.68e-05)]_24 +chr21_31933633_31933683_ 1.81e-03 4_[1(4.54e-05)]_35 +chr21_31962741_31962791_ 1.61e-02 50 +chr21_31964683_31964733_ 1.36e-04 13_[1(3.41e-06)]_26 +chr21_31973364_31973414_ 1.99e-01 50 +chr21_31992870_31992920_ 3.47e-04 16_[1(8.67e-06)]_23 +chr21_32185595_32185645_ 3.47e-04 18_[1(8.67e-06)]_21 +chr21_32202076_32202126_ 2.01e-04 13_[1(5.01e-06)]_26 +chr21_32253899_32253949_ 8.11e-04 19_[1(2.03e-05)]_20 +chr21_32410820_32410870_ 3.47e-04 21_[1(8.67e-06)]_18 +chr21_36411748_36411798_ 2.71e-03 22_[1(6.78e-05)]_17 +chr21_37838750_37838800_ 8.23e-02 50 +chr21_45705687_45705737_ 1.53e-03 37_[1(3.82e-05)]_2 +chr21_45971413_45971463_ 1.36e-04 9_[1(3.41e-06)]_30 +chr21_45978668_45978718_ 6.37e-04 4_[1(1.59e-05)]_35 +chr21_45993530_45993580_ 1.60e-04 7_[1(4.00e-06)]_32 +chr21_46020421_46020471_ 4.83e-04 2_[1(1.21e-05)]_37 +chr21_46031920_46031970_ 2.43e-04 15_[1(6.06e-06)]_24 +chr21_46046964_46047014_ 4.26e-05 12_[1(1.06e-06)]_27 +chr21_46057197_46057247_ 1.36e-04 36_[1(3.41e-06)]_3 +chr21_46086869_46086919_ 4.30e-02 50 +chr21_46102103_46102153_ 4.30e-02 50 +chr21_47517957_47518007_ 6.37e-04 32_[1(1.59e-05)]_7 +chr21_47575506_47575556_ 1.61e-03 30_[1(4.02e-05)]_9 +-------------------------------------------------------------------------------- + +******************************************************************************** + + +******************************************************************************** +Stopped because requested number of motifs (1) found. +******************************************************************************** + +CPU: ThinkPad-T450s + +******************************************************************************** diff -r 793225b11202 -r b48e673af4e8 test-data/meme_output_test1.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme_output_test1.xml Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,1292 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0.294 +0.231 +0.000 +0.000 +0.000 +0.257 +0.000 +0.000 +0.000 +0.000 +0.000 +0.000 +0.000 +0.000 +0.000 +0.000 +0.217 +0.000 +0.000 +0.000 + + + + +meme meme_input_1.fasta -o meme_test1_out -nostatus -maxsize 1000000 +ThinkPad-T450s +zoops +1 +inf +E-value of product of p-values +0 +8 +50 +11 +1 +yes +yes +2 +30 +0.8 +pam +120 +megap +7500 +50 +1e-05 +30 +1500 +0 +-1 +-1 +none +prior30.plib +Stopped because requested number of motifs (1) found. + + +0.291 +0.229 +0.001 +0.001 +0.001 +0.255 +0.001 +0.001 +0.001 +0.001 +0.001 +0.001 +0.001 +0.001 +0.001 +0.001 +0.215 +0.001 +0.001 +0.001 + + + + + + + + +-32 +-680 +91 +77 +7 +138 +-20 +55 +64 +107 +11 +150 +142 +72 +87 +396 +-148 +221 +-140 +-36 + + +-11 +-680 +89 +76 +7 +137 +-21 +55 +63 +107 +10 +149 +141 +71 +87 +396 +-239 +220 +-140 +-36 + + +-79 +41 +4 +21 +-7 +44 +-62 +42 +-5 +99 +0 +99 +138 +52 +42 +399 +-46 +223 +-173 +-68 + + +11 +-677 +48 +47 +-2 +127 +-43 +46 +27 +101 +3 +124 +138 +60 +62 +397 +-235 +220 +-160 +-55 + + +-596 +-820 +12 +-21 +-53 +-267 +-74 +37 +16 +44 +-37 +98 +31 +9 +19 +319 +212 +127 +-193 +-95 + + +165 +-261 +70 +110 +77 +-521 +-4 +147 +95 +201 +90 +121 +124 +91 +107 +425 +-527 +314 +-95 +8 + + +-838 +-990 +-89 +-149 +-151 +-841 +-161 +-117 +-113 +-66 +-209 +-68 +-69 +-129 +-91 +111 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+CCACCAGCTT + + + + + + + + + + + + + +AGCCCTGTAC + + +ATACCCAGGG + + + + + + + + + + + + + +CCTCAGCAGC + + +AATCACTGAG + + + + + + + + + + + + + +GTCCCAGGGA + + +CACCAGAGCT + + + + + + + + + + + + + +AGAAGGTTCT + + +CACTATTGAA + + + + + + + + + + + + + +TTTCATTTGC + + +GA + + + + + + + + + + + + + +GCCAACATCC + + +CCGGCGGGGC + + + + + + + + + + + + + +GGGGCGG + + +CAGA + + + + + + + + + + + + + +GTTCCGACCA + + +CCCACTACTT + + + + + + + + + + + + + +TCATTCTGAG + + +CACCAGCAAG + + + + + + + + + + + + + +GCTCAGGAGT + + +CAGGTCTAAG + + + + + + + + + + + + + +CTTGGAGTCC + + +CCTCGGGACG + + + + + + + + + + + + + + + + +CGTGGTCGCG + + + + + + + + + + + + + +GC + + + + + + + + + + + + + + + + +ATGGTCCTGT + + +GCTGCCGGTG + + + + + + + + + + + + + +GCCCTGGCG + + +AGTCACAAGT + + + + + + + + + + + + + +GGGTCGCACG + + +CCCAGGTTTC + + + + + + + + + + + + + +TCGCCGCACC + + +AGTTTCAGTT + + + + + + + + + + + + + +attatataac + + +TC + + + + + + + + + + + + + +AAATGTTCCT + + +TATAACTCAG + + + + + + + + + + + + + +TAATTTGTAC + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 793225b11202 -r b48e673af4e8 test-data/meme_output_test2.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme_output_test2.html Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,7937 @@ + + + + + MEME + + + + + + + + + + + + + + + + +
      +

      Help poup.

      +
      [ + close ]
      +
      +
      +

      The statistical significance of the motif. MEME usually finds the most + statistically significant (low E-value) motifs first. It is unusual to + consider a motif with an E-value larger than 0.05 significant so, as an + additional indicator, MEME displays these partially transparent.

      +

      The E-value of a motif is based on its log likelihood ratio, width, + sites, the background letter frequencies (given in the command line + summary), and the size of the training set.

      +

      The E-value is an estimate of the expected number of motifs with the + given log likelihood ratio (or higher), and with the same width and site + count, that one would find in a similarly sized set of random + sequences (sequences where each position is independent and letters are + chosen according to the background letter frequencies).

      +
      [ + close ]
      +
      +
      +

      The number of sites contributing to the construction of the motif.

      +
      [ + close ]
      +
      +
      +

      The width of the motif. Each motif describes a pattern of a fixed + width, as no gaps are allowed in MEME motifs.

      +
      [ + close ]
      +
      +
      +

      Click on the blue symbol below to reveal more information about this motif.

      +
      [ + close ]
      +
      +
      +

      Click on the blue symbol below to reveal options allowing you + to submit this motif to another MEME Suite motif analysis program, to download this + motif in various text formats, or to download a sequence "logo" of + this motif PNG or EPS format.

      +
      Supported Programs
      +
      +
      Tomtom
      +
      Tomtom is a tool for searching for similar known motifs. + [manual]
      +
      MAST
      +
      MAST is a tool for searching biological sequence databases for + sequences that contain one or more of a group of known motifs. + [manual]
      +
      FIMO
      +
      FIMO is a tool for searching biological sequence databases for + sequences that contain one or more known motifs. + [manual]
      +
      GOMO
      +
      GOMO is a tool for identifying possible roles (Gene Ontology + terms) for DNA binding motifs. + [manual]
      +
      SpaMo
      +
      SpaMo is a tool for inferring possible transcription factor + complexes by finding motifs with enriched spacings. + [manual]
      +
      +
      [ + close ]
      +
      +
      +

      The log likelihood ratio of the motif.The log likelihood ratio is the + logarithm of the ratio of the probability of the occurrences of the motif + given the motif model (likelihood given the motif) versus their + probability given the background model (likelihood given the null model). + (Normally the background model is a 0-order Markov model using the + background letter frequencies, but higher order Markov models may be + specified via the -bfile option to MEME.).

      +
      [ + close ]
      +
      +
      +

      The information content of the motif in bits. It is equal to the sum + of the uncorrected information content, R(), in the columns of the pwm. + This is equal relative entropy of the motif relative to a uniform + background frequency model.

      +
      [ + close ]
      +
      +
      +

      The relative entropy of the motif.

      + +

      re = llr / (sites * ln(2))

      +
      [ + close ]
      +
      +
      +

      The Bayes Threshold.

      +
      [ + close ]
      +
      +
      +

      The strand used for the motif site.

      +
      +
      +
      +
      The motif site was found in the sequence as it was supplied.
      +
      -
      +
      The motif site was found in the reverse complement of the supplied sequence.
      +
      +
      [ + close ]
      +
      +
      +

      The position in the sequence where the motif site starts. If a motif + started right at the begining of a sequence it would be described as + starting at position 1.

      +
      [ + close ]
      +
      +
      +

      The probability that an equal or better site would be found in a + random sequence of the same length conforming to the background letter + frequencies.

      +
      [ + close ]
      +
      +
      +

      A motif site with the 10 flanking letters on either side.

      +

      When the site is not on the given strand then the site + and both flanks are reverse complemented so they align.

      +
      [ + close ]
      +
      + +
      +

      The name of the sequences as given in the FASTA file.

      +

      The number to the left of the sequence name is the ordinal + of the sequence.

      +
      [ + close ]
      +
      + +
      +

      These are the motif sites predicted by MEME and used to build the motif.

      +

      These sites are shown in solid color and hovering the cursor + over a site will reveal details about the site. Only sequences + that contain a motif site are shown.

      +
      [ + close ]
      +
      + +
      +

      These are the motif sites predicted by MEME plus + any additional sites detected using a motif scanning + algorithm.

      +

      These MEME sites are shown in solid color and + additional scanned sites are shown in transparent color. + Hovering the cursor over a site will reveal details about the site. + Only sequences containing a predicted or scanned motif site are shown.

      +

      The scanned sites are predicted using a + log-odds scoring matrix constructed from the MEME sites. + Only scanned sites with position p-values less + than 0.0001 are shown.

      +
      [ + close ]
      +
      + +
      +

      These are the same sites as shown by selecting the + "Motif Sites + Scanned Sites" button except that all + sequences, including those with no sites, are included + in the diagram.

      +
      [ + close ]
      +
      + +
      +

      This is the combined match p-value.

      +

      The combined match p-value is defined as the probability that a + random sequence (with the same length and conforming to the background) + would have position p-values such that the product is smaller + or equal to the value calulated for the sequence under test.

      +

      The position p-value is defined as the probability that a + random sequence (with the same length and conforming to the background) + would have a match to the motif under test with a score greater or equal + to the largest found in the sequence under test.

      +

      Hovering your mouse over a motif site in the motif location + block diagram will show its position p-value and other information + about the site.

      + +
      [ + close ]
      +
      +
      +

      This diagram shows the location of motif sites.

      +

      Each block shows the position and strength of a motif + site. The height of a block gives an indication of the + significance of the site as taller blocks are more significant. + The height is calculated to be proportional to the negative + logarithm of the p-value of the site, truncated at + the height for a p-value of 1e-10.

      +

      For complementable alphabets (like DNA), sites on the + positive strand are shown above the line, + sites on the negative strand are shown below.

      +

      Placing the cursor + over a motif site will reveal more information about the site + including its position p-value. (See the help + for the p-value column for an explanation of position + p-values.)

      +
      [ + close ]
      +
      + +
      +

      The name of the file of sequences input to MEME.

      +
      [ + close ]
      +
      +
      +

      The position specific priors file used by MEME to find the motifs.

      +
      [ + close ]
      +
      +
      +

      The alphabet used by the sequences.

      +
      [ + close ]
      +
      +
      +

      The number of sequences provided as input to MEME.

      +
      [ + close ]
      +
      + +
      +

      The name of the alphabet symbol.

      +
      [ + close ]
      +
      +
      +

      The frequency of the alphabet symbol in the dataset with a pseudocount + so it is never zero.

      +
      [ + close ]
      +
      +
      +

      The frequency of the alphabet symbol as defined by the background model.

      +
      [ + close ]
      +
      + + +
      +
      +
      + + +
      +
      + + + +
      + + + + + +
      Motif1
      p-value8.23e-7
      Start23
      End33
      +
      + +
      +
      Scanned Site
      + + + + + + +
      Motif1
      p-value8.23e-7
      Start23
      End33
      +
      + +
      +
      +
      + . +
      +
      +
      +
      +
      +
      + E-value: + +
      +
      +
      + Site Count: + +
      +
      +
      + Width: + +
      +
      +
      +
      + +
      +
      + StandardReverse + Complement +
      +
      +
      + Log Likelihood Ratio: + +
      +
      +
      + Information Content: + +
      +
      +
      + Relative Entropy: + +
      +
      +
      + Bayes Threshold: + +
      +
      +
      +
      +
      + + + + + + + +
      + +

      + For further information on how to interpret these results or to get a + copy of the MEME software please access + http://meme-suite.org. +

      +

      If you use MEME in your research, please cite the following paper:
      + + Timothy L. Bailey and Charles Elkan, + "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", + Proceedings of the Second International Conference on Intelligent Systems + for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. + [pdf] + +

      +
      + +
      + Discovered Motifs +   |   + Motif Locations +   |   + Inputs & Settings +   |   + Program information +
      + + +

      Your browser does not support canvas!

      + +

      Discovered Motifs

      +
      +

      Please wait... Loading...

      +

      If the page has fully loaded and this message does not disappear then an error may have occurred.

      +
      +

      Motif Locations

      +
      +

      Please wait... Loading...

      +

      If the page has fully loaded and this message does not disappear then an error may have occurred.

      +
      +

      Inputs & Settings

      +
      +

      Sequences

      + + + + + + + + + + + + +
      Source
      PSP Source
      Alphabet
      Sequence Count
      + +

      Background

      + + +

      Other Settings

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Motif Site Distribution + ZOOPS: Zero or one site per sequence + OOPS: Exactly one site per sequence + ANR: Any number of sites per sequence +
      Site Strand Handling + This alphabet only has one strand + Sites must be on the given strand + Sites may be on either strand +
      Maximum Number of Motifs
      Motif E-value Threshold
      Minimum Motif Width
      Maximum Motif Width
      Minimum Sites per Motif
      Maximum Sites per Motif
      Bias on Number of Sites
      Sequence Prior + Simple Dirichlet + Dirichlets Mix + Mega-weight Dirichlets Mix + Mega-weight Dirichlets Mix Plus + Add One +
      Sequence Prior Strength
      EM Starting Point Source + From substrings in input sequences + From strings on command line (-cons) +
      EM Starting Point Map Type + Uniform + Point Accepted Mutation +
      EM Starting Point Fuzz
      EM Maximum Iterations
      EM Improvement Threshold
      Trim Gap Open Cost
      Trim Gap Extend Cost
      End Gap Treatment + No cost + Same cost as other gaps +
      + + Show Advanced Settings + Hide Advanced Settings + +
      + +
      + +
      +
      +
      MEME version
      + + (Release date: )
      +
      + +
      +
      Reference
      + + Timothy L. Bailey and Charles Elkan, + "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", + Proceedings of the Second International Conference on Intelligent Systems + for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. + +
      +
      +
      Command line
      + + +
      +
      + + + diff -r 793225b11202 -r b48e673af4e8 test-data/meme_output_test2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme_output_test2.txt Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,319 @@ +******************************************************************************** +MEME - Motif discovery tool +******************************************************************************** +MEME version 4.12.0 (Release date: Tue Jun 27 16:22:50 2017 -0700) + +For further information on how to interpret these results or to get +a copy of the MEME software please access http://meme-suite.org . + +This file may be used as input to the MAST algorithm for searching +sequence databases for matches to groups of motifs. MAST is available +for interactive use and downloading at http://meme-suite.org . +******************************************************************************** + + +******************************************************************************** +REFERENCE +******************************************************************************** +If you use this program in your research, please cite: + +Timothy L. Bailey and Charles Elkan, +"Fitting a mixture model by expectation maximization to discover +motifs in biopolymers", Proceedings of the Second International +Conference on Intelligent Systems for Molecular Biology, pp. 28-36, +AAAI Press, Menlo Park, California, 1994. +******************************************************************************** + + +******************************************************************************** +TRAINING SET +******************************************************************************** +DATAFILE= Galaxy_FASTA_Input +ALPHABET= ACGT +Sequence name Weight Length Sequence name Weight Length +------------- ------ ------ ------------- ------ ------ +chr21_19617074_19617124_ 1.0000 50 chr21_26934381_26934431_ 1.0000 50 +chr21_28217753_28217803_ 1.0000 50 chr21_31710037_31710087_ 1.0000 50 +chr21_31744582_31744632_ 1.0000 50 chr21_31768316_31768366_ 1.0000 50 +chr21_31914206_31914256_ 1.0000 50 chr21_31933633_31933683_ 1.0000 50 +chr21_31962741_31962791_ 1.0000 50 chr21_31964683_31964733_ 1.0000 50 +chr21_31973364_31973414_ 1.0000 50 chr21_31992870_31992920_ 1.0000 50 +chr21_32185595_32185645_ 1.0000 50 chr21_32202076_32202126_ 1.0000 50 +chr21_32253899_32253949_ 1.0000 50 chr21_32410820_32410870_ 1.0000 50 +chr21_36411748_36411798_ 1.0000 50 chr21_37838750_37838800_ 1.0000 50 +chr21_45705687_45705737_ 1.0000 50 chr21_45971413_45971463_ 1.0000 50 +chr21_45978668_45978718_ 1.0000 50 chr21_45993530_45993580_ 1.0000 50 +chr21_46020421_46020471_ 1.0000 50 chr21_46031920_46031970_ 1.0000 50 +chr21_46046964_46047014_ 1.0000 50 chr21_46057197_46057247_ 1.0000 50 +chr21_46086869_46086919_ 1.0000 50 chr21_46102103_46102153_ 1.0000 50 +chr21_47517957_47518007_ 1.0000 50 chr21_47575506_47575556_ 1.0000 50 +******************************************************************************** + +******************************************************************************** +COMMAND LINE SUMMARY +******************************************************************************** +This information can also be useful in the event you wish to report a +problem with the MEME software. + +command: meme meme_input_1.fasta -o meme_test2_out -nostatus -maxsize 1000000 -sf Galaxy_FASTA_Input -dna -mod zoops -nmotifs 1 -wnsites 0.8 -minw 8 -maxw 50 -wg 11 -ws 1 -maxiter 50 -distance 0.001 -prior dirichlet -b 0.01 -plib prior30.plib -spmap uni -spfuzz 0.5 + +model: mod= zoops nmotifs= 1 evt= inf +object function= E-value of product of p-values +width: minw= 8 maxw= 50 +width: wg= 11 ws= 1 endgaps= yes +nsites: minsites= 2 maxsites= 30 wnsites= 0.8 +theta: spmap= uni spfuzz= 0.5 +global: substring= yes branching= no wbranch= no +em: prior= dirichlet b= 0.01 maxiter= 50 + distance= 0.001 +data: n= 1500 N= 30 shuffle= -1 +strands: + +sample: seed= 0 ctfrac= -1 maxwords= -1 +Dirichlet mixture priors file: prior30.plib +Letter frequencies in dataset: +A 0.294 C 0.231 G 0.257 T 0.217 +Background letter frequencies (from dataset with add-one prior applied): +A 0.294 C 0.231 G 0.257 T 0.217 +******************************************************************************** + + +******************************************************************************** +MOTIF GGSRTATAAAA MEME-1 width = 11 sites = 30 llr = 254 E-value = 5.1e-040 +******************************************************************************** +-------------------------------------------------------------------------------- + Motif GGSRTATAAAA MEME-1 Description +-------------------------------------------------------------------------------- +Simplified A 3313:9:a798 +pos.-specific C 1:3::1:::1: +probability G 6756::::::2 +matrix T 1:11a1a:3:: + + bits 2.2 * + 2.0 * * + 1.8 * * + 1.5 * ** * +Relative 1.3 * ** * +Entropy 1.1 ****** +(12.2 bits) 0.9 * ******* + 0.7 * ******* + 0.4 ** ******** + 0.2 *********** + 0.0 ----------- + +Multilevel GGGGTATAAAA +consensus AACA T +sequence + +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif GGSRTATAAAA MEME-1 sites sorted by position p-value +-------------------------------------------------------------------------------- +Sequence name Start P-value Site +------------- ----- --------- ----------- +chr21_46046964_46047014_ 13 4.51e-07 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC +chr21_46031920_46031970_ 16 2.22e-06 ATACCCAGGG AGGGTATAAAA CCTCAGCAGC +chr21_32202076_32202126_ 14 2.74e-06 CCACCAGCTT GAGGTATAAAA AGCCCTGTAC +chr21_46057197_46057247_ 37 4.86e-06 ACAGGCCCTG GGCATATAAAA GCC +chr21_45993530_45993580_ 8 4.86e-06 CCAAGGA GGAGTATAAAA GCCCCACAAA +chr21_45971413_45971463_ 10 4.86e-06 CAGGCCCTG GGCATATAAAA GCCCCAGCAG +chr21_31964683_31964733_ 14 4.86e-06 GATTCACTGA GGCATATAAAA GGCCCTCTGC +chr21_47517957_47518007_ 33 6.48e-06 CCGGCGGGGC GGGGTATAAAG GGGGCGG +chr21_45978668_45978718_ 5 6.48e-06 CAGA GGGGTATAAAG GTTCCGACCA +chr21_32185595_32185645_ 19 6.48e-06 CACCAGAGCT GGGATATATAA AGAAGGTTCT +chr21_32410820_32410870_ 22 1.38e-05 AATCACTGAG GATGTATAAAA GTCCCAGGGA +chr21_31992870_31992920_ 17 1.38e-05 CACTATTGAA GATGTATAAAA TTTCATTTGC +chr21_19617074_19617124_ 40 1.41e-05 CCTCGGGACG TGGGTATATAA +chr21_31914206_31914256_ 16 1.61e-05 CCCACTACTT AGAGTATAAAA TCATTCTGAG +chr21_46020421_46020471_ 3 1.95e-05 GA GACATATAAAA GCCAACATCC +chr21_32253899_32253949_ 18 1.95e-05 CCCACCAGCA AGGATATATAA AAGCTCAGGA +chr21_45705687_45705737_ 38 2.16e-05 CGTGGTCGCG GGGGTATAACA GC +chr21_47575506_47575556_ 31 3.04e-05 GCTGCCGGTG AGCGTATAAAG GCCCTGGCG +chr21_31744582_31744632_ 13 3.04e-05 CAGGTCTAAG AGCATATATAA CTTGGAGTCC +chr21_31768316_31768366_ 1 3.67e-05 . AACGTATATAA ATGGTCCTGT +chr21_26934381_26934431_ 28 3.93e-05 AGTCACAAGT GAGTTATAAAA GGGTCGCACG +chr21_31933633_31933683_ 5 5.65e-05 TCAG AGTATATATAA ATGTTCCTGT +chr21_31710037_31710087_ 15 6.24e-05 CCCAGGTTTC TGAGTATATAA TCGCCGCACC +chr21_36411748_36411798_ 23 7.15e-05 AGTTTCAGTT GGCATCtaaaa attatataac +chr21_46102103_46102153_ 37 1.39e-04 TGCCTGGGTC CAGGTATAAAG GCT +chr21_46086869_46086919_ 38 1.39e-04 TGCCTGGGCC CAGGTATAAAG GC +chr21_37838750_37838800_ 3 4.81e-04 ga tggttttataa ggggcctcac +chr21_31962741_31962791_ 14 8.57e-04 TATAACTCAG GTTGGATAAAA TAATTTGTAC +chr21_31973364_31973414_ 8 1.47e-03 aaactta aaactctataa acttaaaact +chr21_28217753_28217803_ 27 2.64e-03 GGTGGGGGTG GGGGTTTCACT GGTCCACTAT +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif GGSRTATAAAA MEME-1 block diagrams +-------------------------------------------------------------------------------- +SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM +------------- ---------------- ------------- +chr21_46046964_46047014_ 4.5e-07 12_[+1]_27 +chr21_46031920_46031970_ 2.2e-06 15_[+1]_24 +chr21_32202076_32202126_ 2.7e-06 13_[+1]_26 +chr21_46057197_46057247_ 4.9e-06 36_[+1]_3 +chr21_45993530_45993580_ 4.9e-06 7_[+1]_32 +chr21_45971413_45971463_ 4.9e-06 9_[+1]_30 +chr21_31964683_31964733_ 4.9e-06 13_[+1]_26 +chr21_47517957_47518007_ 6.5e-06 32_[+1]_7 +chr21_45978668_45978718_ 6.5e-06 4_[+1]_35 +chr21_32185595_32185645_ 6.5e-06 18_[+1]_21 +chr21_32410820_32410870_ 1.4e-05 21_[+1]_18 +chr21_31992870_31992920_ 1.4e-05 16_[+1]_23 +chr21_19617074_19617124_ 1.4e-05 39_[+1] +chr21_31914206_31914256_ 1.6e-05 15_[+1]_24 +chr21_46020421_46020471_ 1.9e-05 2_[+1]_37 +chr21_32253899_32253949_ 1.9e-05 17_[+1]_22 +chr21_45705687_45705737_ 2.2e-05 37_[+1]_2 +chr21_47575506_47575556_ 3e-05 30_[+1]_9 +chr21_31744582_31744632_ 3e-05 12_[+1]_27 +chr21_31768316_31768366_ 3.7e-05 [+1]_39 +chr21_26934381_26934431_ 3.9e-05 27_[+1]_12 +chr21_31933633_31933683_ 5.6e-05 4_[+1]_35 +chr21_31710037_31710087_ 6.2e-05 14_[+1]_25 +chr21_36411748_36411798_ 7.1e-05 22_[+1]_17 +chr21_46102103_46102153_ 0.00014 36_[+1]_3 +chr21_46086869_46086919_ 0.00014 37_[+1]_2 +chr21_37838750_37838800_ 0.00048 2_[+1]_37 +chr21_31962741_31962791_ 0.00086 13_[+1]_26 +chr21_31973364_31973414_ 0.0015 7_[+1]_32 +chr21_28217753_28217803_ 0.0026 26_[+1]_13 +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif GGSRTATAAAA MEME-1 in BLOCKS format +-------------------------------------------------------------------------------- +BL MOTIF GGSRTATAAAA width=11 seqs=30 +chr21_46046964_46047014_ ( 13) GGGGTATAAAA 1 +chr21_46031920_46031970_ ( 16) AGGGTATAAAA 1 +chr21_32202076_32202126_ ( 14) GAGGTATAAAA 1 +chr21_46057197_46057247_ ( 37) GGCATATAAAA 1 +chr21_45993530_45993580_ ( 8) GGAGTATAAAA 1 +chr21_45971413_45971463_ ( 10) GGCATATAAAA 1 +chr21_31964683_31964733_ ( 14) GGCATATAAAA 1 +chr21_47517957_47518007_ ( 33) GGGGTATAAAG 1 +chr21_45978668_45978718_ ( 5) GGGGTATAAAG 1 +chr21_32185595_32185645_ ( 19) GGGATATATAA 1 +chr21_32410820_32410870_ ( 22) GATGTATAAAA 1 +chr21_31992870_31992920_ ( 17) GATGTATAAAA 1 +chr21_19617074_19617124_ ( 40) TGGGTATATAA 1 +chr21_31914206_31914256_ ( 16) AGAGTATAAAA 1 +chr21_46020421_46020471_ ( 3) GACATATAAAA 1 +chr21_32253899_32253949_ ( 18) AGGATATATAA 1 +chr21_45705687_45705737_ ( 38) GGGGTATAACA 1 +chr21_47575506_47575556_ ( 31) AGCGTATAAAG 1 +chr21_31744582_31744632_ ( 13) AGCATATATAA 1 +chr21_31768316_31768366_ ( 1) AACGTATATAA 1 +chr21_26934381_26934431_ ( 28) GAGTTATAAAA 1 +chr21_31933633_31933683_ ( 5) AGTATATATAA 1 +chr21_31710037_31710087_ ( 15) TGAGTATATAA 1 +chr21_36411748_36411798_ ( 23) GGCATCTAAAA 1 +chr21_46102103_46102153_ ( 37) CAGGTATAAAG 1 +chr21_46086869_46086919_ ( 38) CAGGTATAAAG 1 +chr21_37838750_37838800_ ( 3) TGGTTTTATAA 1 +chr21_31962741_31962791_ ( 14) GTTGGATAAAA 1 +chr21_31973364_31973414_ ( 8) AAACTCTATAA 1 +chr21_28217753_28217803_ ( 27) GGGGTTTCACT 1 +// + +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif GGSRTATAAAA MEME-1 position-specific scoring matrix +-------------------------------------------------------------------------------- +log-odds matrix: alength= 4 w= 11 n= 1200 bayes= 5.2854 E= 5.1e-040 + -14 -179 114 -112 + 3 -1155 137 -270 + -114 20 86 -71 + 3 -279 122 -170 + -1155 -1155 -295 215 + 156 -179 -1155 -170 + -1155 -1155 -1155 220 + 172 -279 -1155 -1155 + 125 -1155 -1155 46 + 167 -179 -1155 -1155 + 144 -1155 -63 -270 +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif GGSRTATAAAA MEME-1 position-specific probability matrix +-------------------------------------------------------------------------------- +letter-probability matrix: alength= 4 w= 11 nsites= 30 E= 5.1e-040 + 0.266667 0.066667 0.566667 0.100000 + 0.300000 0.000000 0.666667 0.033333 + 0.133333 0.266667 0.466667 0.133333 + 0.300000 0.033333 0.600000 0.066667 + 0.000000 0.000000 0.033333 0.966667 + 0.866667 0.066667 0.000000 0.066667 + 0.000000 0.000000 0.000000 1.000000 + 0.966667 0.033333 0.000000 0.000000 + 0.700000 0.000000 0.000000 0.300000 + 0.933333 0.066667 0.000000 0.000000 + 0.800000 0.000000 0.166667 0.033333 +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif GGSRTATAAAA MEME-1 regular expression +-------------------------------------------------------------------------------- +[GA][GA][GC][GA]TATA[AT]AA +-------------------------------------------------------------------------------- + + + + +Time 0.38 secs. + +******************************************************************************** + + +******************************************************************************** +SUMMARY OF MOTIFS +******************************************************************************** + +-------------------------------------------------------------------------------- + Combined block diagrams: non-overlapping sites with p-value < 0.0001 +-------------------------------------------------------------------------------- +SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM +------------- ---------------- ------------- +chr21_19617074_19617124_ 5.63e-04 39_[+1(1.41e-05)] +chr21_26934381_26934431_ 1.57e-03 27_[+1(3.93e-05)]_12 +chr21_28217753_28217803_ 1.00e-01 50 +chr21_31710037_31710087_ 2.49e-03 14_[+1(6.24e-05)]_25 +chr21_31744582_31744632_ 1.22e-03 12_[+1(3.04e-05)]_27 +chr21_31768316_31768366_ 1.47e-03 [+1(3.67e-05)]_39 +chr21_31914206_31914256_ 6.45e-04 15_[+1(1.61e-05)]_24 +chr21_31933633_31933683_ 2.26e-03 4_[+1(5.65e-05)]_35 +chr21_31962741_31962791_ 3.37e-02 50 +chr21_31964683_31964733_ 1.95e-04 13_[+1(4.86e-06)]_26 +chr21_31973364_31973414_ 5.73e-02 50 +chr21_31992870_31992920_ 5.52e-04 16_[+1(1.38e-05)]_23 +chr21_32185595_32185645_ 2.59e-04 18_[+1(6.48e-06)]_21 +chr21_32202076_32202126_ 1.10e-04 13_[+1(2.74e-06)]_26 +chr21_32253899_32253949_ 7.78e-04 17_[+1(1.95e-05)]_22 +chr21_32410820_32410870_ 5.52e-04 21_[+1(1.38e-05)]_18 +chr21_36411748_36411798_ 2.85e-03 22_[+1(7.15e-05)]_17 +chr21_37838750_37838800_ 1.90e-02 50 +chr21_45705687_45705737_ 8.63e-04 37_[+1(2.16e-05)]_2 +chr21_45971413_45971463_ 1.95e-04 9_[+1(4.86e-06)]_30 +chr21_45978668_45978718_ 2.59e-04 4_[+1(6.48e-06)]_35 +chr21_45993530_45993580_ 1.95e-04 7_[+1(4.86e-06)]_32 +chr21_46020421_46020471_ 7.78e-04 2_[+1(1.95e-05)]_37 +chr21_46031920_46031970_ 8.89e-05 15_[+1(2.22e-06)]_24 +chr21_46046964_46047014_ 1.80e-05 12_[+1(4.51e-07)]_27 +chr21_46057197_46057247_ 1.95e-04 36_[+1(4.86e-06)]_3 +chr21_46086869_46086919_ 5.54e-03 50 +chr21_46102103_46102153_ 5.54e-03 50 +chr21_47517957_47518007_ 2.59e-04 32_[+1(6.48e-06)]_7 +chr21_47575506_47575556_ 1.22e-03 30_[+1(3.04e-05)]_9 +-------------------------------------------------------------------------------- + +******************************************************************************** + + +******************************************************************************** +Stopped because requested number of motifs (1) found. +******************************************************************************** + +CPU: ThinkPad-T450s + +******************************************************************************** diff -r 793225b11202 -r b48e673af4e8 test-data/meme_output_test2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme_output_test2.xml Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,984 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0.294 +0.231 +0.257 +0.217 + + + + +meme meme_input_1.fasta -o meme_test2_out -nostatus -maxsize 1000000 -sf Galaxy_FASTA_Input -dna -mod zoops -nmotifs 1 -wnsites 0.8 -minw 8 -maxw 50 -wg 11 -ws 1 -maxiter 50 -distance 0.001 -prior dirichlet -b 0.01 -plib prior30.plib -spmap uni -spfuzz 0.5 +ThinkPad-T450s +zoops +1 +inf +E-value of product of p-values +0 +8 +50 +11 +1 +yes +yes +2 +30 +0.8 +uni +0.5 +dirichlet +0.01 +50 +0.001 +30 +1500 +0 +-1 +-1 +forward +prior30.plib +Stopped because requested number of motifs (1) found. + + +0.294 +0.231 +0.257 +0.217 + + + + + + + + +-14 +-179 +114 +-112 + + +3 +-1155 +137 +-270 + + +-114 +20 +86 +-71 + + +3 +-279 +122 +-170 + + +-1155 +-1155 +-295 +215 + + +156 +-179 +-1155 +-170 + + +-1155 +-1155 +-1155 +220 + + +172 +-279 +-1155 +-1155 + + +125 +-1155 +-1155 +46 + + +167 +-179 +-1155 +-1155 + + +144 +-1155 +-63 +-270 + + + + + + +0.266667 +0.066667 +0.566667 +0.100000 + + +0.300000 +0.000000 +0.666667 +0.033333 + + +0.133333 +0.266667 +0.466667 +0.133333 + + +0.300000 +0.033333 +0.600000 +0.066667 + + +0.000000 +0.000000 +0.033333 +0.966667 + + +0.866667 +0.066667 +0.000000 +0.066667 + + +0.000000 +0.000000 +0.000000 +1.000000 + + +0.966667 +0.033333 +0.000000 +0.000000 + + +0.700000 +0.000000 +0.000000 +0.300000 + + +0.933333 +0.066667 +0.000000 +0.000000 + + +0.800000 +0.000000 +0.166667 +0.033333 + + + + +[GA][GA][GC][GA]TATA[AT]AA + + + +AAGGCCAGGA + + + + + + + + + + + + + +GCCTGAGAGC + + +ATACCCAGGG + + + + + + + + + + + + + +CCTCAGCAGC + + +CCACCAGCTT + + + + + + + + + + + + + +AGCCCTGTAC + + +ACAGGCCCTG + + + + + + + + + + + + + +GCC + + +CCAAGGA + + + + + + + + + + + + + +GCCCCACAAA + + +CAGGCCCTG + + + + + + + + + + + + + +GCCCCAGCAG + + +GATTCACTGA + + + + + + + + + + + + + +GGCCCTCTGC + + +CCGGCGGGGC + + + + + + + + + + + + + +GGGGCGG + + +CAGA + + + + + + + + + + + + + +GTTCCGACCA + + +CACCAGAGCT + + + + + + + + + + + + + +AGAAGGTTCT + + +AATCACTGAG + + + + + + + + + + + + + +GTCCCAGGGA + + +CACTATTGAA + + + + + + + + + + + + + +TTTCATTTGC + + +CCTCGGGACG + + + + + + + + + + + + + + + + +CCCACTACTT + + + + + + + + + + + + + +TCATTCTGAG + + +GA + + + + + + + + + + + + + +GCCAACATCC + + +CCCACCAGCA + + + + + + + + + + + + + +AAGCTCAGGA + + +CGTGGTCGCG + + + + + + + + + + + + + +GC + + +GCTGCCGGTG + + + + + + + + + + + + + +GCCCTGGCG + + +CAGGTCTAAG + + + + + + + + + + + + + +CTTGGAGTCC + + + + + + + + + + + + + + + + +ATGGTCCTGT + + +AGTCACAAGT + + + + + + + + + + + + + +GGGTCGCACG + + +TCAG + + + + + + + + + + + + + +ATGTTCCTGT + + +CCCAGGTTTC + + + + + + + + + + + + + +TCGCCGCACC + + +AGTTTCAGTT + + + + + + + + + + + + + +attatataac + + +TGCCTGGGTC + + + + + + + + + + + + + +GCT + + +TGCCTGGGCC + + + + + + + + + + + + + +GC + + +ga + + + + + + + + + + + + + +ggggcctcac + + +TATAACTCAG + + + + + + + + + + + + + +TAATTTGTAC + + +aaactta + + + + + + + + + + + + + +acttaaaact + + +GGTGGGGGTG + + + + + + + + + + + + + +GGTCCACTAT + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 793225b11202 -r b48e673af4e8 test-data/meme_output_txt_1.txt --- a/test-data/meme_output_txt_1.txt Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,325 +0,0 @@ -******************************************************************************** -MEME - Motif discovery tool -******************************************************************************** -MEME version 4.11.2 (Release date: Thu May 05 14:58:55 2016 -0700) - -For further information on how to interpret these results or to get -a copy of the MEME software please access http://meme-suite.org . - -This file may be used as input to the MAST algorithm for searching -sequence databases for matches to groups of motifs. MAST is available -for interactive use and downloading at http://meme-suite.org . -******************************************************************************** - - -******************************************************************************** -REFERENCE -******************************************************************************** -If you use this program in your research, please cite: - -Timothy L. Bailey and Charles Elkan, -"Fitting a mixture model by expectation maximization to discover -motifs in biopolymers", Proceedings of the Second International -Conference on Intelligent Systems for Molecular Biology, pp. 28-36, -AAAI Press, Menlo Park, California, 1994. -******************************************************************************** - - -******************************************************************************** -TRAINING SET -******************************************************************************** -DATAFILE= /tmp/tmpCNK6l0/files/000/dataset_22.dat -ALPHABET= ACDEFGHIKLMNPQRSTVWY -Sequence name Weight Length Sequence name Weight Length -------------- ------ ------ ------------- ------ ------ -chr21_19617074_19617124_ 1.0000 50 chr21_26934381_26934431_ 1.0000 50 -chr21_28217753_28217803_ 1.0000 50 chr21_31710037_31710087_ 1.0000 50 -chr21_31744582_31744632_ 1.0000 50 chr21_31768316_31768366_ 1.0000 50 -chr21_31914206_31914256_ 1.0000 50 chr21_31933633_31933683_ 1.0000 50 -chr21_31962741_31962791_ 1.0000 50 chr21_31964683_31964733_ 1.0000 50 -chr21_31973364_31973414_ 1.0000 50 chr21_31992870_31992920_ 1.0000 50 -chr21_32185595_32185645_ 1.0000 50 chr21_32202076_32202126_ 1.0000 50 -chr21_32253899_32253949_ 1.0000 50 chr21_32410820_32410870_ 1.0000 50 -chr21_36411748_36411798_ 1.0000 50 chr21_37838750_37838800_ 1.0000 50 -chr21_45705687_45705737_ 1.0000 50 chr21_45971413_45971463_ 1.0000 50 -chr21_45978668_45978718_ 1.0000 50 chr21_45993530_45993580_ 1.0000 50 -chr21_46020421_46020471_ 1.0000 50 chr21_46031920_46031970_ 1.0000 50 -chr21_46046964_46047014_ 1.0000 50 chr21_46057197_46057247_ 1.0000 50 -chr21_46086869_46086919_ 1.0000 50 chr21_46102103_46102153_ 1.0000 50 -chr21_47517957_47518007_ 1.0000 50 chr21_47575506_47575556_ 1.0000 50 -******************************************************************************** - -******************************************************************************** -COMMAND LINE SUMMARY -******************************************************************************** -This information can also be useful in the event you wish to report a -problem with the MEME software. - -command: meme /tmp/tmpCNK6l0/files/000/dataset_22.dat -o /tmp/tmpCNK6l0/job_working_directory/000/11/dataset_23_files -nostatus -maxsize 1000000 - -model: mod= zoops nmotifs= 1 evt= inf -object function= E-value of product of p-values -width: minw= 8 maxw= 50 -width: wg= 11 ws= 1 endgaps= yes -nsites: minsites= 2 maxsites= 30 wnsites= 0.8 -theta: spmap= pam spfuzz= 120 -global: substring= yes branching= no wbranch= no -em: prior= megap b= 7500 maxiter= 50 - distance= 1e-05 -data: n= 1500 N= 30 shuffle= -1 - -sample: seed= 0 ctfrac= -1 maxwords= -1 -Dirichlet mixture priors file: prior30.plib -Letter frequencies in dataset: -A 0.294 C 0.231 D 0.000 E 0.000 F 0.000 G 0.257 H 0.000 I 0.000 K 0.000 -L 0.000 M 0.000 N 0.000 P 0.000 Q 0.000 R 0.000 S 0.000 T 0.217 V 0.000 -W 0.000 Y 0.000 -Background letter frequencies (from dataset with add-one prior applied): -A 0.291 C 0.229 D 0.001 E 0.001 F 0.001 G 0.255 H 0.001 I 0.001 K 0.001 -L 0.001 M 0.001 N 0.001 P 0.001 Q 0.001 R 0.001 S 0.001 T 0.215 V 0.001 -W 0.001 Y 0.001 -******************************************************************************** - - -******************************************************************************** -MOTIF 1 MEME width = 11 sites = 25 llr = 239 E-value = 2.4e-011 -******************************************************************************** --------------------------------------------------------------------------------- - Motif 1 Description --------------------------------------------------------------------------------- -Simplified A 2323:a:a8a8 -pos.-specific C ::3:::::::: -probability D ::::::::::: -matrix E ::::::::::: - F ::::::::::: - G 7746::::::1 - H ::::::::::: - I ::::::::::: - K ::::::::::: - L ::::::::::: - M ::::::::::: - N ::::::::::: - P ::::::::::: - Q ::::::::::: - R ::::::::::: - S ::::::::::: - T 1:2:a:a:2:: - V ::::::::::: - W ::::::::::: - Y ::::::::::: - - bits 10.6 - 9.5 - 8.5 - 7.4 -Relative 6.3 -Entropy 5.3 -(13.8 bits) 4.2 - 3.2 - 2.1 * ** - 1.1 ** ******** - 0.0 ----------- - -Multilevel GGGGTATAAAA -consensus AACA T -sequence - - --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 sites sorted by position p-value --------------------------------------------------------------------------------- -Sequence name Start P-value Site -------------- ----- --------- ----------- -chr21_46046964_46047014_ 13 1.06e-06 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC -chr21_46057197_46057247_ 37 3.41e-06 ACAGGCCCTG GGCATATAAAA GCC -chr21_45971413_45971463_ 10 3.41e-06 CAGGCCCTG GGCATATAAAA GCCCCAGCAG -chr21_31964683_31964733_ 14 3.41e-06 GATTCACTGA GGCATATAAAA GGCCCTCTGC -chr21_45993530_45993580_ 8 4.00e-06 CCAAGGA GGAGTATAAAA GCCCCACAAA -chr21_32202076_32202126_ 14 5.01e-06 CCACCAGCTT GAGGTATAAAA AGCCCTGTAC -chr21_46031920_46031970_ 16 6.06e-06 ATACCCAGGG AGGGTATAAAA CCTCAGCAGC -chr21_32410820_32410870_ 22 8.67e-06 AATCACTGAG GATGTATAAAA GTCCCAGGGA -chr21_32185595_32185645_ 19 8.67e-06 CACCAGAGCT GGGATATATAA AGAAGGTTCT -chr21_31992870_31992920_ 17 8.67e-06 CACTATTGAA GATGTATAAAA TTTCATTTGC -chr21_46020421_46020471_ 3 1.21e-05 GA GACATATAAAA GCCAACATCC -chr21_47517957_47518007_ 33 1.59e-05 CCGGCGGGGC GGGGTATAAAG GGGGCGG -chr21_45978668_45978718_ 5 1.59e-05 CAGA GGGGTATAAAG GTTCCGACCA -chr21_31914206_31914256_ 16 1.68e-05 CCCACTACTT AGAGTATAAAA TCATTCTGAG -chr21_32253899_32253949_ 20 2.03e-05 CACCAGCAAG GATATATAAAA GCTCAGGAGT -chr21_31744582_31744632_ 13 3.06e-05 CAGGTCTAAG AGCATATATAA CTTGGAGTCC -chr21_19617074_19617124_ 40 3.06e-05 CCTCGGGACG TGGGTATATAA -chr21_45705687_45705737_ 38 3.82e-05 CGTGGTCGCG GGGGTATAACA GC -chr21_31768316_31768366_ 1 3.82e-05 . AACGTATATAA ATGGTCCTGT -chr21_47575506_47575556_ 31 4.02e-05 GCTGCCGGTG AGCGTATAAAG GCCCTGGCG -chr21_26934381_26934431_ 28 5.52e-05 AGTCACAAGT GAGTTATAAAA GGGTCGCACG -chr21_31710037_31710087_ 15 5.94e-05 CCCAGGTTTC TGAGTATATAA TCGCCGCACC -chr21_36411748_36411798_ 23 6.78e-05 AGTTTCAGTT GGCATCtaaaa attatataac -chr21_31933633_31933683_ 3 2.08e-04 TC AGAGTATATAT AAATGTTCCT -chr21_31962741_31962791_ 14 4.05e-04 TATAACTCAG GTTGGATAAAA TAATTTGTAC --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 block diagrams --------------------------------------------------------------------------------- -SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM -------------- ---------------- ------------- -chr21_46046964_46047014_ 1.1e-06 12_[1]_27 -chr21_46057197_46057247_ 3.4e-06 36_[1]_3 -chr21_45971413_45971463_ 3.4e-06 9_[1]_30 -chr21_31964683_31964733_ 3.4e-06 13_[1]_26 -chr21_45993530_45993580_ 4e-06 7_[1]_32 -chr21_32202076_32202126_ 5e-06 13_[1]_26 -chr21_46031920_46031970_ 6.1e-06 15_[1]_24 -chr21_32410820_32410870_ 8.7e-06 21_[1]_18 -chr21_32185595_32185645_ 8.7e-06 18_[1]_21 -chr21_31992870_31992920_ 8.7e-06 16_[1]_23 -chr21_46020421_46020471_ 1.2e-05 2_[1]_37 -chr21_47517957_47518007_ 1.6e-05 32_[1]_7 -chr21_45978668_45978718_ 1.6e-05 4_[1]_35 -chr21_31914206_31914256_ 1.7e-05 15_[1]_24 -chr21_32253899_32253949_ 2e-05 19_[1]_20 -chr21_31744582_31744632_ 3.1e-05 12_[1]_27 -chr21_19617074_19617124_ 3.1e-05 39_[1] -chr21_45705687_45705737_ 3.8e-05 37_[1]_2 -chr21_31768316_31768366_ 3.8e-05 [1]_39 -chr21_47575506_47575556_ 4e-05 30_[1]_9 -chr21_26934381_26934431_ 5.5e-05 27_[1]_12 -chr21_31710037_31710087_ 5.9e-05 14_[1]_25 -chr21_36411748_36411798_ 6.8e-05 22_[1]_17 -chr21_31933633_31933683_ 0.00021 2_[1]_37 -chr21_31962741_31962791_ 0.0004 13_[1]_26 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 in BLOCKS format --------------------------------------------------------------------------------- -BL MOTIF 1 width=11 seqs=25 -chr21_46046964_46047014_ ( 13) GGGGTATAAAA 1 -chr21_46057197_46057247_ ( 37) GGCATATAAAA 1 -chr21_45971413_45971463_ ( 10) GGCATATAAAA 1 -chr21_31964683_31964733_ ( 14) GGCATATAAAA 1 -chr21_45993530_45993580_ ( 8) GGAGTATAAAA 1 -chr21_32202076_32202126_ ( 14) GAGGTATAAAA 1 -chr21_46031920_46031970_ ( 16) AGGGTATAAAA 1 -chr21_32410820_32410870_ ( 22) GATGTATAAAA 1 -chr21_32185595_32185645_ ( 19) GGGATATATAA 1 -chr21_31992870_31992920_ ( 17) GATGTATAAAA 1 -chr21_46020421_46020471_ ( 3) GACATATAAAA 1 -chr21_47517957_47518007_ ( 33) GGGGTATAAAG 1 -chr21_45978668_45978718_ ( 5) GGGGTATAAAG 1 -chr21_31914206_31914256_ ( 16) AGAGTATAAAA 1 -chr21_32253899_32253949_ ( 20) GATATATAAAA 1 -chr21_31744582_31744632_ ( 13) AGCATATATAA 1 -chr21_19617074_19617124_ ( 40) TGGGTATATAA 1 -chr21_45705687_45705737_ ( 38) GGGGTATAACA 1 -chr21_31768316_31768366_ ( 1) AACGTATATAA 1 -chr21_47575506_47575556_ ( 31) AGCGTATAAAG 1 -chr21_26934381_26934431_ ( 28) GAGTTATAAAA 1 -chr21_31710037_31710087_ ( 15) TGAGTATATAA 1 -chr21_36411748_36411798_ ( 23) GGCATCTAAAA 1 -chr21_31933633_31933683_ ( 3) AGAGTATATAT 1 -chr21_31962741_31962791_ ( 14) GTTGGATAAAA 1 -// - --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 position-specific scoring matrix --------------------------------------------------------------------------------- -log-odds matrix: alength= 20 w= 11 n= 1200 bayes= 5.33554 E= 2.4e-011 - -32 -680 91 77 7 138 -20 55 64 107 11 150 142 72 87 396 -148 221 -140 -36 - -11 -680 89 76 7 137 -21 55 63 107 10 149 141 71 87 396 -239 220 -140 -36 - -79 41 4 21 -7 44 -62 42 -5 99 0 99 138 52 42 399 -46 223 -173 -68 - 11 -677 48 47 -2 127 -43 46 27 101 3 124 138 60 62 397 -235 220 -160 -55 - -596 -820 12 -21 -53 -267 -74 37 16 44 -37 98 31 9 19 319 212 127 -193 -95 - 165 -261 70 110 77 -521 -4 147 95 201 90 121 124 91 107 425 -527 314 -95 8 - -838 -990 -89 -149 -151 -841 -161 -117 -113 -66 -209 -68 -69 -129 -91 111 221 -55 -255 -173 - 176 -858 -79 -103 -115 -717 -148 -95 -108 -17 -162 -61 -12 -95 -69 193 -737 52 -240 -153 - 134 -686 0 16 -12 -553 -68 44 -8 96 -9 88 124 41 36 384 11 216 -177 -71 - 165 -261 70 110 77 -521 -4 147 95 201 90 121 124 91 107 425 -527 314 -95 8 - 147 -614 89 129 93 -121 12 160 113 217 108 144 144 111 125 447 -241 332 -81 22 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 position-specific probability matrix --------------------------------------------------------------------------------- -letter-probability matrix: alength= 20 w= 11 nsites= 25 E= 2.4e-011 - 0.240000 0.000000 0.000000 0.000000 0.000000 0.680000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.080000 0.000000 0.000000 0.000000 - 0.280000 0.000000 0.000000 0.000000 0.000000 0.680000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 - 0.160000 0.320000 0.000000 0.000000 0.000000 0.360000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.160000 0.000000 0.000000 0.000000 - 0.320000 0.000000 0.000000 0.000000 0.000000 0.640000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 - 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.960000 0.000000 0.000000 0.000000 - 0.960000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 - 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 0.760000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.240000 0.000000 0.000000 0.000000 - 0.960000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 0.840000 0.000000 0.000000 0.000000 0.000000 0.120000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 regular expression --------------------------------------------------------------------------------- -[GA][GA][GC][GA]TATA[AT]AA --------------------------------------------------------------------------------- - - - - -Time 0.72 secs. - -******************************************************************************** - - -******************************************************************************** -SUMMARY OF MOTIFS -******************************************************************************** - --------------------------------------------------------------------------------- - Combined block diagrams: non-overlapping sites with p-value < 0.0001 --------------------------------------------------------------------------------- -SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM -------------- ---------------- ------------- -chr21_19617074_19617124_ 1.22e-03 39_[1(3.06e-05)] -chr21_26934381_26934431_ 2.21e-03 27_[1(5.52e-05)]_12 -chr21_28217753_28217803_ 7.29e-01 50 -chr21_31710037_31710087_ 2.37e-03 14_[1(5.94e-05)]_25 -chr21_31744582_31744632_ 1.22e-03 12_[1(3.06e-05)]_27 -chr21_31768316_31768366_ 1.53e-03 [1(3.82e-05)]_39 -chr21_31914206_31914256_ 6.70e-04 15_[1(1.68e-05)]_24 -chr21_31933633_31933683_ 1.81e-03 4_[1(4.54e-05)]_35 -chr21_31962741_31962791_ 1.61e-02 50 -chr21_31964683_31964733_ 1.36e-04 13_[1(3.41e-06)]_26 -chr21_31973364_31973414_ 1.99e-01 50 -chr21_31992870_31992920_ 3.47e-04 16_[1(8.67e-06)]_23 -chr21_32185595_32185645_ 3.47e-04 18_[1(8.67e-06)]_21 -chr21_32202076_32202126_ 2.01e-04 13_[1(5.01e-06)]_26 -chr21_32253899_32253949_ 8.11e-04 19_[1(2.03e-05)]_20 -chr21_32410820_32410870_ 3.47e-04 21_[1(8.67e-06)]_18 -chr21_36411748_36411798_ 2.71e-03 22_[1(6.78e-05)]_17 -chr21_37838750_37838800_ 8.23e-02 50 -chr21_45705687_45705737_ 1.53e-03 37_[1(3.82e-05)]_2 -chr21_45971413_45971463_ 1.36e-04 9_[1(3.41e-06)]_30 -chr21_45978668_45978718_ 6.37e-04 4_[1(1.59e-05)]_35 -chr21_45993530_45993580_ 1.60e-04 7_[1(4.00e-06)]_32 -chr21_46020421_46020471_ 4.83e-04 2_[1(1.21e-05)]_37 -chr21_46031920_46031970_ 2.43e-04 15_[1(6.06e-06)]_24 -chr21_46046964_46047014_ 4.26e-05 12_[1(1.06e-06)]_27 -chr21_46057197_46057247_ 1.36e-04 36_[1(3.41e-06)]_3 -chr21_46086869_46086919_ 4.30e-02 50 -chr21_46102103_46102153_ 4.30e-02 50 -chr21_47517957_47518007_ 6.37e-04 32_[1(1.59e-05)]_7 -chr21_47575506_47575556_ 1.61e-03 30_[1(4.02e-05)]_9 --------------------------------------------------------------------------------- - -******************************************************************************** - - -******************************************************************************** -Stopped because requested number of motifs (1) found. -******************************************************************************** - -CPU: bigsky - -******************************************************************************** diff -r 793225b11202 -r b48e673af4e8 test-data/meme_output_txt_2.txt --- a/test-data/meme_output_txt_2.txt Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,319 +0,0 @@ -******************************************************************************** -MEME - Motif discovery tool -******************************************************************************** -MEME version 4.11.2 (Release date: Thu May 05 14:58:55 2016 -0700) - -For further information on how to interpret these results or to get -a copy of the MEME software please access http://meme-suite.org . - -This file may be used as input to the MAST algorithm for searching -sequence databases for matches to groups of motifs. MAST is available -for interactive use and downloading at http://meme-suite.org . -******************************************************************************** - - -******************************************************************************** -REFERENCE -******************************************************************************** -If you use this program in your research, please cite: - -Timothy L. Bailey and Charles Elkan, -"Fitting a mixture model by expectation maximization to discover -motifs in biopolymers", Proceedings of the Second International -Conference on Intelligent Systems for Molecular Biology, pp. 28-36, -AAAI Press, Menlo Park, California, 1994. -******************************************************************************** - - -******************************************************************************** -TRAINING SET -******************************************************************************** -DATAFILE= Galaxy_FASTA_Input -ALPHABET= ACGT -Sequence name Weight Length Sequence name Weight Length -------------- ------ ------ ------------- ------ ------ -chr21_19617074_19617124_ 1.0000 50 chr21_26934381_26934431_ 1.0000 50 -chr21_28217753_28217803_ 1.0000 50 chr21_31710037_31710087_ 1.0000 50 -chr21_31744582_31744632_ 1.0000 50 chr21_31768316_31768366_ 1.0000 50 -chr21_31914206_31914256_ 1.0000 50 chr21_31933633_31933683_ 1.0000 50 -chr21_31962741_31962791_ 1.0000 50 chr21_31964683_31964733_ 1.0000 50 -chr21_31973364_31973414_ 1.0000 50 chr21_31992870_31992920_ 1.0000 50 -chr21_32185595_32185645_ 1.0000 50 chr21_32202076_32202126_ 1.0000 50 -chr21_32253899_32253949_ 1.0000 50 chr21_32410820_32410870_ 1.0000 50 -chr21_36411748_36411798_ 1.0000 50 chr21_37838750_37838800_ 1.0000 50 -chr21_45705687_45705737_ 1.0000 50 chr21_45971413_45971463_ 1.0000 50 -chr21_45978668_45978718_ 1.0000 50 chr21_45993530_45993580_ 1.0000 50 -chr21_46020421_46020471_ 1.0000 50 chr21_46031920_46031970_ 1.0000 50 -chr21_46046964_46047014_ 1.0000 50 chr21_46057197_46057247_ 1.0000 50 -chr21_46086869_46086919_ 1.0000 50 chr21_46102103_46102153_ 1.0000 50 -chr21_47517957_47518007_ 1.0000 50 chr21_47575506_47575556_ 1.0000 50 -******************************************************************************** - -******************************************************************************** -COMMAND LINE SUMMARY -******************************************************************************** -This information can also be useful in the event you wish to report a -problem with the MEME software. - -command: meme /tmp/tmpCNK6l0/files/000/dataset_26.dat -o /tmp/tmpCNK6l0/job_working_directory/000/14/dataset_28_files -nostatus -maxsize 1000000 -sf Galaxy_FASTA_Input -dna -mod zoops -nmotifs 1 -wnsites 0.8 -evt inf -minw 8 -maxw 50 -wg 11 -ws 1 -maxiter 50 -distance 0.001 -prior dirichlet -b 0.01 -plib /tmp/tmpCNK6l0/files/000/dataset_27.dat -spmap uni -spfuzz 0.5 - -model: mod= zoops nmotifs= 1 evt= inf -object function= E-value of product of p-values -width: minw= 8 maxw= 50 -width: wg= 11 ws= 1 endgaps= yes -nsites: minsites= 2 maxsites= 30 wnsites= 0.8 -theta: spmap= uni spfuzz= 0.5 -global: substring= yes branching= no wbranch= no -em: prior= dirichlet b= 0.01 maxiter= 50 - distance= 0.001 -data: n= 1500 N= 30 shuffle= -1 -strands: + -sample: seed= 0 ctfrac= -1 maxwords= -1 -Dirichlet mixture priors file: dataset_27.dat -Letter frequencies in dataset: -A 0.294 C 0.231 G 0.257 T 0.217 -Background letter frequencies (from dataset with add-one prior applied): -A 0.294 C 0.231 G 0.257 T 0.217 -******************************************************************************** - - -******************************************************************************** -MOTIF 1 MEME width = 11 sites = 30 llr = 254 E-value = 5.1e-040 -******************************************************************************** --------------------------------------------------------------------------------- - Motif 1 Description --------------------------------------------------------------------------------- -Simplified A 3313:9:a798 -pos.-specific C 1:3::1:::1: -probability G 6756::::::2 -matrix T 1:11a1a:3:: - - bits 2.2 * - 2.0 * * - 1.8 * * - 1.5 * ** * -Relative 1.3 * ** * -Entropy 1.1 ****** -(12.2 bits) 0.9 * ******* - 0.7 * ******* - 0.4 ** ******** - 0.2 *********** - 0.0 ----------- - -Multilevel GGGGTATAAAA -consensus AACA T -sequence - --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 sites sorted by position p-value --------------------------------------------------------------------------------- -Sequence name Start P-value Site -------------- ----- --------- ----------- -chr21_46046964_46047014_ 13 4.51e-07 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC -chr21_46031920_46031970_ 16 2.22e-06 ATACCCAGGG AGGGTATAAAA CCTCAGCAGC -chr21_32202076_32202126_ 14 2.74e-06 CCACCAGCTT GAGGTATAAAA AGCCCTGTAC -chr21_46057197_46057247_ 37 4.86e-06 ACAGGCCCTG GGCATATAAAA GCC -chr21_45993530_45993580_ 8 4.86e-06 CCAAGGA GGAGTATAAAA GCCCCACAAA -chr21_45971413_45971463_ 10 4.86e-06 CAGGCCCTG GGCATATAAAA GCCCCAGCAG -chr21_31964683_31964733_ 14 4.86e-06 GATTCACTGA GGCATATAAAA GGCCCTCTGC -chr21_47517957_47518007_ 33 6.48e-06 CCGGCGGGGC GGGGTATAAAG GGGGCGG -chr21_45978668_45978718_ 5 6.48e-06 CAGA GGGGTATAAAG GTTCCGACCA -chr21_32185595_32185645_ 19 6.48e-06 CACCAGAGCT GGGATATATAA AGAAGGTTCT -chr21_32410820_32410870_ 22 1.38e-05 AATCACTGAG GATGTATAAAA GTCCCAGGGA -chr21_31992870_31992920_ 17 1.38e-05 CACTATTGAA GATGTATAAAA TTTCATTTGC -chr21_19617074_19617124_ 40 1.41e-05 CCTCGGGACG TGGGTATATAA -chr21_31914206_31914256_ 16 1.61e-05 CCCACTACTT AGAGTATAAAA TCATTCTGAG -chr21_46020421_46020471_ 3 1.95e-05 GA GACATATAAAA GCCAACATCC -chr21_32253899_32253949_ 18 1.95e-05 CCCACCAGCA AGGATATATAA AAGCTCAGGA -chr21_45705687_45705737_ 38 2.16e-05 CGTGGTCGCG GGGGTATAACA GC -chr21_47575506_47575556_ 31 3.04e-05 GCTGCCGGTG AGCGTATAAAG GCCCTGGCG -chr21_31744582_31744632_ 13 3.04e-05 CAGGTCTAAG AGCATATATAA CTTGGAGTCC -chr21_31768316_31768366_ 1 3.67e-05 . AACGTATATAA ATGGTCCTGT -chr21_26934381_26934431_ 28 3.93e-05 AGTCACAAGT GAGTTATAAAA GGGTCGCACG -chr21_31933633_31933683_ 5 5.65e-05 TCAG AGTATATATAA ATGTTCCTGT -chr21_31710037_31710087_ 15 6.24e-05 CCCAGGTTTC TGAGTATATAA TCGCCGCACC -chr21_36411748_36411798_ 23 7.15e-05 AGTTTCAGTT GGCATCtaaaa attatataac -chr21_46102103_46102153_ 37 1.39e-04 TGCCTGGGTC CAGGTATAAAG GCT -chr21_46086869_46086919_ 38 1.39e-04 TGCCTGGGCC CAGGTATAAAG GC -chr21_37838750_37838800_ 3 4.81e-04 ga tggttttataa ggggcctcac -chr21_31962741_31962791_ 14 8.57e-04 TATAACTCAG GTTGGATAAAA TAATTTGTAC -chr21_31973364_31973414_ 8 1.47e-03 aaactta aaactctataa acttaaaact -chr21_28217753_28217803_ 27 2.64e-03 GGTGGGGGTG GGGGTTTCACT GGTCCACTAT --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 block diagrams --------------------------------------------------------------------------------- -SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM -------------- ---------------- ------------- -chr21_46046964_46047014_ 4.5e-07 12_[+1]_27 -chr21_46031920_46031970_ 2.2e-06 15_[+1]_24 -chr21_32202076_32202126_ 2.7e-06 13_[+1]_26 -chr21_46057197_46057247_ 4.9e-06 36_[+1]_3 -chr21_45993530_45993580_ 4.9e-06 7_[+1]_32 -chr21_45971413_45971463_ 4.9e-06 9_[+1]_30 -chr21_31964683_31964733_ 4.9e-06 13_[+1]_26 -chr21_47517957_47518007_ 6.5e-06 32_[+1]_7 -chr21_45978668_45978718_ 6.5e-06 4_[+1]_35 -chr21_32185595_32185645_ 6.5e-06 18_[+1]_21 -chr21_32410820_32410870_ 1.4e-05 21_[+1]_18 -chr21_31992870_31992920_ 1.4e-05 16_[+1]_23 -chr21_19617074_19617124_ 1.4e-05 39_[+1] -chr21_31914206_31914256_ 1.6e-05 15_[+1]_24 -chr21_46020421_46020471_ 1.9e-05 2_[+1]_37 -chr21_32253899_32253949_ 1.9e-05 17_[+1]_22 -chr21_45705687_45705737_ 2.2e-05 37_[+1]_2 -chr21_47575506_47575556_ 3e-05 30_[+1]_9 -chr21_31744582_31744632_ 3e-05 12_[+1]_27 -chr21_31768316_31768366_ 3.7e-05 [+1]_39 -chr21_26934381_26934431_ 3.9e-05 27_[+1]_12 -chr21_31933633_31933683_ 5.6e-05 4_[+1]_35 -chr21_31710037_31710087_ 6.2e-05 14_[+1]_25 -chr21_36411748_36411798_ 7.1e-05 22_[+1]_17 -chr21_46102103_46102153_ 0.00014 36_[+1]_3 -chr21_46086869_46086919_ 0.00014 37_[+1]_2 -chr21_37838750_37838800_ 0.00048 2_[+1]_37 -chr21_31962741_31962791_ 0.00086 13_[+1]_26 -chr21_31973364_31973414_ 0.0015 7_[+1]_32 -chr21_28217753_28217803_ 0.0026 26_[+1]_13 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 in BLOCKS format --------------------------------------------------------------------------------- -BL MOTIF 1 width=11 seqs=30 -chr21_46046964_46047014_ ( 13) GGGGTATAAAA 1 -chr21_46031920_46031970_ ( 16) AGGGTATAAAA 1 -chr21_32202076_32202126_ ( 14) GAGGTATAAAA 1 -chr21_46057197_46057247_ ( 37) GGCATATAAAA 1 -chr21_45993530_45993580_ ( 8) GGAGTATAAAA 1 -chr21_45971413_45971463_ ( 10) GGCATATAAAA 1 -chr21_31964683_31964733_ ( 14) GGCATATAAAA 1 -chr21_47517957_47518007_ ( 33) GGGGTATAAAG 1 -chr21_45978668_45978718_ ( 5) GGGGTATAAAG 1 -chr21_32185595_32185645_ ( 19) GGGATATATAA 1 -chr21_32410820_32410870_ ( 22) GATGTATAAAA 1 -chr21_31992870_31992920_ ( 17) GATGTATAAAA 1 -chr21_19617074_19617124_ ( 40) TGGGTATATAA 1 -chr21_31914206_31914256_ ( 16) AGAGTATAAAA 1 -chr21_46020421_46020471_ ( 3) GACATATAAAA 1 -chr21_32253899_32253949_ ( 18) AGGATATATAA 1 -chr21_45705687_45705737_ ( 38) GGGGTATAACA 1 -chr21_47575506_47575556_ ( 31) AGCGTATAAAG 1 -chr21_31744582_31744632_ ( 13) AGCATATATAA 1 -chr21_31768316_31768366_ ( 1) AACGTATATAA 1 -chr21_26934381_26934431_ ( 28) GAGTTATAAAA 1 -chr21_31933633_31933683_ ( 5) AGTATATATAA 1 -chr21_31710037_31710087_ ( 15) TGAGTATATAA 1 -chr21_36411748_36411798_ ( 23) GGCATCTAAAA 1 -chr21_46102103_46102153_ ( 37) CAGGTATAAAG 1 -chr21_46086869_46086919_ ( 38) CAGGTATAAAG 1 -chr21_37838750_37838800_ ( 3) TGGTTTTATAA 1 -chr21_31962741_31962791_ ( 14) GTTGGATAAAA 1 -chr21_31973364_31973414_ ( 8) AAACTCTATAA 1 -chr21_28217753_28217803_ ( 27) GGGGTTTCACT 1 -// - --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 position-specific scoring matrix --------------------------------------------------------------------------------- -log-odds matrix: alength= 4 w= 11 n= 1200 bayes= 5.2854 E= 5.1e-040 - -14 -179 114 -112 - 3 -1155 137 -270 - -114 20 86 -71 - 3 -279 122 -170 - -1155 -1155 -295 215 - 156 -179 -1155 -170 - -1155 -1155 -1155 220 - 172 -279 -1155 -1155 - 125 -1155 -1155 46 - 167 -179 -1155 -1155 - 144 -1155 -63 -270 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 position-specific probability matrix --------------------------------------------------------------------------------- -letter-probability matrix: alength= 4 w= 11 nsites= 30 E= 5.1e-040 - 0.266667 0.066667 0.566667 0.100000 - 0.300000 0.000000 0.666667 0.033333 - 0.133333 0.266667 0.466667 0.133333 - 0.300000 0.033333 0.600000 0.066667 - 0.000000 0.000000 0.033333 0.966667 - 0.866667 0.066667 0.000000 0.066667 - 0.000000 0.000000 0.000000 1.000000 - 0.966667 0.033333 0.000000 0.000000 - 0.700000 0.000000 0.000000 0.300000 - 0.933333 0.066667 0.000000 0.000000 - 0.800000 0.000000 0.166667 0.033333 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 regular expression --------------------------------------------------------------------------------- -[GA][GA][GC][GA]TATA[AT]AA --------------------------------------------------------------------------------- - - - - -Time 0.32 secs. - -******************************************************************************** - - -******************************************************************************** -SUMMARY OF MOTIFS -******************************************************************************** - --------------------------------------------------------------------------------- - Combined block diagrams: non-overlapping sites with p-value < 0.0001 --------------------------------------------------------------------------------- -SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM -------------- ---------------- ------------- -chr21_19617074_19617124_ 5.63e-04 39_[+1(1.41e-05)] -chr21_26934381_26934431_ 1.57e-03 27_[+1(3.93e-05)]_12 -chr21_28217753_28217803_ 1.00e-01 50 -chr21_31710037_31710087_ 2.49e-03 14_[+1(6.24e-05)]_25 -chr21_31744582_31744632_ 1.22e-03 12_[+1(3.04e-05)]_27 -chr21_31768316_31768366_ 1.47e-03 [+1(3.67e-05)]_39 -chr21_31914206_31914256_ 6.45e-04 15_[+1(1.61e-05)]_24 -chr21_31933633_31933683_ 2.26e-03 4_[+1(5.65e-05)]_35 -chr21_31962741_31962791_ 3.37e-02 50 -chr21_31964683_31964733_ 1.95e-04 13_[+1(4.86e-06)]_26 -chr21_31973364_31973414_ 5.73e-02 50 -chr21_31992870_31992920_ 5.52e-04 16_[+1(1.38e-05)]_23 -chr21_32185595_32185645_ 2.59e-04 18_[+1(6.48e-06)]_21 -chr21_32202076_32202126_ 1.10e-04 13_[+1(2.74e-06)]_26 -chr21_32253899_32253949_ 7.78e-04 17_[+1(1.95e-05)]_22 -chr21_32410820_32410870_ 5.52e-04 21_[+1(1.38e-05)]_18 -chr21_36411748_36411798_ 2.85e-03 22_[+1(7.15e-05)]_17 -chr21_37838750_37838800_ 1.90e-02 50 -chr21_45705687_45705737_ 8.63e-04 37_[+1(2.16e-05)]_2 -chr21_45971413_45971463_ 1.95e-04 9_[+1(4.86e-06)]_30 -chr21_45978668_45978718_ 2.59e-04 4_[+1(6.48e-06)]_35 -chr21_45993530_45993580_ 1.95e-04 7_[+1(4.86e-06)]_32 -chr21_46020421_46020471_ 7.78e-04 2_[+1(1.95e-05)]_37 -chr21_46031920_46031970_ 8.89e-05 15_[+1(2.22e-06)]_24 -chr21_46046964_46047014_ 1.80e-05 12_[+1(4.51e-07)]_27 -chr21_46057197_46057247_ 1.95e-04 36_[+1(4.86e-06)]_3 -chr21_46086869_46086919_ 5.54e-03 50 -chr21_46102103_46102153_ 5.54e-03 50 -chr21_47517957_47518007_ 2.59e-04 32_[+1(6.48e-06)]_7 -chr21_47575506_47575556_ 1.22e-03 30_[+1(3.04e-05)]_9 --------------------------------------------------------------------------------- - -******************************************************************************** - - -******************************************************************************** -Stopped because requested number of motifs (1) found. -******************************************************************************** - -CPU: bigsky - -******************************************************************************** diff -r 793225b11202 -r b48e673af4e8 test-data/meme_output_xml_1.xml --- a/test-data/meme_output_xml_1.xml Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1285 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -]> - - - - - - - - - - - - - - - - - - - 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- - -CAGGTCTAAG - - - - - - - - - - - - - -CTTGGAGTCC - - -CCTCGGGACG - - - - - - - - - - - - - - - - -CGTGGTCGCG - - - - - - - - - - - - - -GC - - - - - - - - - - - - - - - - -ATGGTCCTGT - - -GCTGCCGGTG - - - - - - - - - - - - - -GCCCTGGCG - - -AGTCACAAGT - - - - - - - - - - - - - -GGGTCGCACG - - -CCCAGGTTTC - - - - - - - - - - - - - -TCGCCGCACC - - -AGTTTCAGTT - - - - - - - - - - - - - -attatataac - - -TC - - - - - - - - - - - - - -AAATGTTCCT - - -TATAACTCAG - - - - - - - - - - - - - -TAATTTGTAC - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 793225b11202 -r b48e673af4e8 test-data/meme_output_xml_2.xml --- a/test-data/meme_output_xml_2.xml Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,977 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -0.294 -0.231 -0.257 -0.217 - - - - -meme /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2490.dat -o /Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1929/dataset_2578_files -nostatus -sf Galaxy_FASTA_Input -dna -mod zoops -nmotifs 1 -wnsites 0.8 -minw 8 -maxw 50 -wg 11 -ws 1 -maxiter 50 -distance 0.001 -prior dirichlet -b 0.01 -plib /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2577.dat -spmap uni -spfuzz 0.5 -MacBook-Pro-2.local -zoops -1 -inf -E-value of product of p-values -0 -8 -50 -11 -1 -yes -yes -2 -30 -0.8 -uni -0.5 -dirichlet -0.01 -50 -0.001 -30 -1500 -0 --1 --1 -forward -dataset_2577.dat -Stopped because requested number of motifs (1) found. - - -0.294 -0.231 -0.257 -0.217 - - - - - - - - --14 --179 -114 --112 - - -3 --1155 -137 --270 - - --114 -20 -86 --71 - - -3 --279 -122 --170 - - --1155 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-TGCCTGGGCC - - - - - - - - - - - - - -GC - - -ga - - - - - - - - - - - - - -ggggcctcac - - -TATAACTCAG - - - - - - - - - - - - - -TAATTTGTAC - - -aaactta - - - - - - - - - - - - - -acttaaaact - - -GGTGGGGGTG - - - - - - - - - - - - - -GGTCCACTAT - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 793225b11202 -r b48e673af4e8 test-data/meme_psp_gen_reports_output.tabular --- a/test-data/meme_psp_gen_reports_output.tabular Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ -540 bases or amino acids -0.5 0.5 4 4 -0.5 0.5 6 6 -0.5 0.5 7 7 -0.5 0.5 8 8 -0.5 0.5 9 9 -0.5 0.5 10 10 -0.5 0.5 11 11 -0.5 0.5 12 12 -0.5 0.5 13 13 -0.5 0.5 14 14 -0.5 0.5 15 15 -0.5 0.5 16 16 -0.5 0.5 17 17 -0.5 0.5 18 18 -0.5 0.5 19 19 -0.5 0.5 20 20 - -score 0.9 occurred 483 times diff -r 793225b11202 -r b48e673af4e8 test-data/meme_psp_output_test1.memepsp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme_psp_output_test1.memepsp Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,6 @@ +>BBP_PIEBR 20 scaledmin = 0.1 scaledmax = 0.9 +0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +>ICYA_MANSE 20 scaledmin = 0.1 scaledmax = 0.9 +0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +>LACB_BOVIN 20 scaledmin = 0.1 scaledmax = 0.9 +0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff -r 793225b11202 -r b48e673af4e8 test-data/meme_psp_output_test1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme_psp_output_test1.tabular Thu May 17 14:11:15 2018 -0400 @@ -0,0 +1,21 @@ +meme_psp_input_pos.fa: 540 bases or amino acids +meme_psp_input_neg.fa: 540 bases or amino acids +meme_psp_input_pos.fa meme_psp_input_neg.fa 0.5 0.5 4 4 +meme_psp_input_pos.fa meme_psp_input_neg.fa 0.5 0.5 5 5 +meme_psp_input_pos.fa meme_psp_input_neg.fa 0.5 0.5 6 6 +meme_psp_input_pos.fa meme_psp_input_neg.fa 0.5 0.5 7 7 +meme_psp_input_pos.fa meme_psp_input_neg.fa 0.5 0.5 8 8 +meme_psp_input_pos.fa meme_psp_input_neg.fa 0.5 0.5 9 9 +meme_psp_input_pos.fa meme_psp_input_neg.fa 0.5 0.5 10 10 +meme_psp_input_pos.fa meme_psp_input_neg.fa 0.5 0.5 11 11 +meme_psp_input_pos.fa meme_psp_input_neg.fa 0.5 0.5 12 12 +meme_psp_input_pos.fa meme_psp_input_neg.fa 0.5 0.5 13 13 +meme_psp_input_pos.fa meme_psp_input_neg.fa 0.5 0.5 14 14 +meme_psp_input_pos.fa meme_psp_input_neg.fa 0.5 0.5 15 15 +meme_psp_input_pos.fa meme_psp_input_neg.fa 0.5 0.5 16 16 +meme_psp_input_pos.fa meme_psp_input_neg.fa 0.5 0.5 17 17 +meme_psp_input_pos.fa meme_psp_input_neg.fa 0.5 0.5 18 18 +meme_psp_input_pos.fa meme_psp_input_neg.fa 0.5 0.5 19 19 +meme_psp_input_pos.fa meme_psp_input_neg.fa 0.5 0.5 20 20 + +score 0.9 occurred 483 times diff -r 793225b11202 -r b48e673af4e8 test-data/meme_psp_protein_input.fasta --- a/test-data/meme_psp_protein_input.fasta Wed Apr 25 12:13:08 2018 -0400 +++ b/test-data/meme_psp_protein_input.fasta Thu May 17 14:11:15 2018 -0400 @@ -3,13 +3,11 @@ DGKKASVYNSFVSNGVKEYMEGDLEIAPDAKYTKQGKYVMTFKFGQRVVN LVPWVLATDYKNYAINYNCDYHPDKKAHSIHAWILSKSKVLEGNTKEVVD NVLKTFSHLIDASKFISNDFSEAACQYSTTYSLTGPDRH - >LACB_BOVIN MKCLLLALALTCGAQALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDA QSAPLRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAEKTKIPAVFKI DALNENKVLVLDTDYKKYLLFCMENSAEPEQSLACQCLVRTPEVDDEALE KFDKALKALPMHIRLSFNPTQLEEQCHI - >BBP_PIEBR NVYHDGACPEVKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCGWAEYTPE GKSVKVSNYHVIHGKEYFIEGTAYPVGDSKIGKIYHKLTYGGVTKENVFN diff -r 793225b11202 -r b48e673af4e8 test-data/motif1.gff --- a/test-data/motif1.gff Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -##gff-version 3 -phiX174 fimo polypeptide_motif 1 11 78.3 + . Name=1;ID=1-57-phiX174;pvalue=1.46e-08;sequence=GAGTTTTATCG; -phiX174 fimo polypeptide_motif 3 13 57.5 + . Name=1;ID=1-471-phiX174;pvalue=1.79e-06;sequence=GTTTTATCGCT; -phiX174 fimo polypeptide_motif 7 17 45 + . Name=1;ID=1-1378-phiX174;pvalue=3.18e-05;sequence=TATCGCTTCCA; -phiX174 fimo polypeptide_motif 10 20 53.9 + . Name=1;ID=1-605-phiX174;pvalue=4.1e-06;sequence=CGCTTCCATGA; -phiX174 fimo polypeptide_motif 17 27 40.2 + . Name=1;ID=1-1887-phiX174;pvalue=9.55e-05;sequence=ATGACGCAGAA; -phiX174 fimo polypeptide_motif 18 28 45.3 + . Name=1;ID=1-1349-phiX174;pvalue=2.98e-05;sequence=TGACGCAGAAG; -phiX174 fimo polypeptide_motif 19 29 55.8 + . Name=1;ID=1-527-phiX174;pvalue=2.6e-06;sequence=GACGCAGAAGT; -phiX174 fimo polypeptide_motif 21 31 41.5 + . Name=1;ID=1-1705-phiX174;pvalue=7.07e-05;sequence=CGCAGAAGTTA; -phiX174 fimo polypeptide_motif 22 32 44.6 + . Name=1;ID=1-1404-phiX174;pvalue=3.44e-05;sequence=GCAGAAGTTAA; -phiX174 fimo polypeptide_motif 24 34 79.1 + . Name=1;ID=1-53-phiX174;pvalue=1.23e-08;sequence=AGAAGTTAACA; -phiX174 fimo polypeptide_motif 25 35 45.3 + . Name=1;ID=1-1347-phiX174;pvalue=2.97e-05;sequence=GAAGTTAACAC; -phiX174 fimo polypeptide_motif 26 36 59.2 + . Name=1;ID=1-417-phiX174;pvalue=1.19e-06;sequence=AAGTTAACACT; -phiX174 fimo polypeptide_motif 30 40 44.7 + . Name=1;ID=1-1399-phiX174;pvalue=3.4e-05;sequence=TAACACTTTCG; -phiX174 fimo polypeptide_motif 37 47 72.4 + . Name=1;ID=1-98-phiX174;pvalue=5.79e-08;sequence=TTCGGATATTT; -phiX174 fimo polypeptide_motif 39 49 65.3 + . Name=1;ID=1-213-phiX174;pvalue=2.92e-07;sequence=CGGATATTTCT; -phiX174 fimo polypeptide_motif 41 51 55.3 + . Name=1;ID=1-548-phiX174;pvalue=2.97e-06;sequence=GATATTTCTGA; -phiX174 fimo polypeptide_motif 43 53 58.4 + . Name=1;ID=1-442-phiX174;pvalue=1.43e-06;sequence=TATTTCTGATG; -phiX174 fimo polypeptide_motif 46 56 53.7 + . Name=1;ID=1-617-phiX174;pvalue=4.23e-06;sequence=TTCTGATGAGT; -phiX174 fimo polypeptide_motif 50 60 45.4 + . Name=1;ID=1-1333-phiX174;pvalue=2.86e-05;sequence=GATGAGTCGAA; -phiX174 fimo polypeptide_motif 51 61 48.4 + . Name=1;ID=1-1094-phiX174;pvalue=1.44e-05;sequence=ATGAGTCGAAA; -phiX174 fimo polypeptide_motif 52 62 83.9 + . Name=1;ID=1-22-phiX174;pvalue=4.06e-09;sequence=TGAGTCGAAAA; -phiX174 fimo polypeptide_motif 53 63 53.9 + . Name=1;ID=1-601-phiX174;pvalue=4.03e-06;sequence=GAGTCGAAAAA; -phiX174 fimo polypeptide_motif 54 64 62.9 + . Name=1;ID=1-297-phiX174;pvalue=5.16e-07;sequence=AGTCGAAAAAT; -phiX174 fimo polypeptide_motif 55 65 52.8 + . Name=1;ID=1-675-phiX174;pvalue=5.26e-06;sequence=GTCGAAAAATT; -phiX174 fimo polypeptide_motif 56 66 41.4 + . Name=1;ID=1-1713-phiX174;pvalue=7.2e-05;sequence=TCGAAAAATTA; -phiX174 fimo polypeptide_motif 58 68 43.4 + . Name=1;ID=1-1500-phiX174;pvalue=4.56e-05;sequence=GAAAAATTATC; -phiX174 fimo polypeptide_motif 59 69 59.6 + . Name=1;ID=1-409-phiX174;pvalue=1.1e-06;sequence=AAAAATTATCT; -phiX174 fimo polypeptide_motif 61 71 61.8 + . Name=1;ID=1-329-phiX174;pvalue=6.52e-07;sequence=AAATTATCTTG; -phiX174 fimo polypeptide_motif 63 73 59.2 + . Name=1;ID=1-419-phiX174;pvalue=1.2e-06;sequence=ATTATCTTGAT; -phiX174 fimo polypeptide_motif 65 75 53.3 + . Name=1;ID=1-643-phiX174;pvalue=4.66e-06;sequence=TATCTTGATAA; -phiX174 fimo polypeptide_motif 66 76 51.8 + . Name=1;ID=1-737-phiX174;pvalue=6.54e-06;sequence=ATCTTGATAAA; -phiX174 fimo polypeptide_motif 67 77 73.2 + . Name=1;ID=1-89-phiX174;pvalue=4.78e-08;sequence=TCTTGATAAAG; -phiX174 fimo polypeptide_motif 69 79 63.8 + . Name=1;ID=1-268-phiX174;pvalue=4.15e-07;sequence=TTGATAAAGCA; -phiX174 fimo polypeptide_motif 71 81 40.2 + . Name=1;ID=1-1882-phiX174;pvalue=9.49e-05;sequence=GATAAAGCAGG; -phiX174 fimo polypeptide_motif 73 83 45.4 + . Name=1;ID=1-1334-phiX174;pvalue=2.87e-05;sequence=TAAAGCAGGAA; -phiX174 fimo polypeptide_motif 74 84 50.9 + . Name=1;ID=1-832-phiX174;pvalue=8.05e-06;sequence=AAAGCAGGAAT; -phiX174 fimo polypeptide_motif 76 86 52.2 + . Name=1;ID=1-710-phiX174;pvalue=5.96e-06;sequence=AGCAGGAATTA; -phiX174 fimo polypeptide_motif 78 88 51.8 + . Name=1;ID=1-741-phiX174;pvalue=6.65e-06;sequence=CAGGAATTACT; -phiX174 fimo polypeptide_motif 79 89 45 + . Name=1;ID=1-1369-phiX174;pvalue=3.16e-05;sequence=AGGAATTACTA; -phiX174 fimo polypeptide_motif 80 90 43.3 + . Name=1;ID=1-1511-phiX174;pvalue=4.63e-05;sequence=GGAATTACTAC; -phiX174 fimo polypeptide_motif 81 91 59.8 + . Name=1;ID=1-402-phiX174;pvalue=1.05e-06;sequence=GAATTACTACT; -phiX174 fimo polypeptide_motif 82 92 46.9 + . Name=1;ID=1-1205-phiX174;pvalue=2.03e-05;sequence=AATTACTACTG; -phiX174 fimo polypeptide_motif 88 98 41.2 + . Name=1;ID=1-1744-phiX174;pvalue=7.51e-05;sequence=TACTGCTTGTT; -phiX174 fimo polypeptide_motif 91 101 53.6 + . Name=1;ID=1-621-phiX174;pvalue=4.33e-06;sequence=TGCTTGTTTAC; -phiX174 fimo polypeptide_motif 92 102 44.8 + . Name=1;ID=1-1388-phiX174;pvalue=3.31e-05;sequence=GCTTGTTTACG; -phiX174 fimo polypeptide_motif 93 103 43.2 + . Name=1;ID=1-1525-phiX174;pvalue=4.82e-05;sequence=CTTGTTTACGA; -phiX174 fimo polypeptide_motif 95 105 61.9 + . Name=1;ID=1-327-phiX174;pvalue=6.5e-07;sequence=TGTTTACGAAT; -phiX174 fimo polypeptide_motif 96 106 42.9 + . Name=1;ID=1-1553-phiX174;pvalue=5.08e-05;sequence=GTTTACGAATT; -phiX174 fimo polypeptide_motif 98 108 45.4 + . Name=1;ID=1-1340-phiX174;pvalue=2.9e-05;sequence=TTACGAATTAA; -phiX174 fimo polypeptide_motif 99 109 73.5 + . Name=1;ID=1-88-phiX174;pvalue=4.48e-08;sequence=TACGAATTAAA; -phiX174 fimo polypeptide_motif 100 110 53 + . Name=1;ID=1-661-phiX174;pvalue=4.99e-06;sequence=ACGAATTAAAT; -phiX174 fimo polypeptide_motif 102 112 75.6 + . Name=1;ID=1-72-phiX174;pvalue=2.75e-08;sequence=GAATTAAATCG; -phiX174 fimo polypeptide_motif 104 114 52.2 + . Name=1;ID=1-713-phiX174;pvalue=6.05e-06;sequence=ATTAAATCGAA; -phiX174 fimo polypeptide_motif 106 116 59.6 + . Name=1;ID=1-407-phiX174;pvalue=1.09e-06;sequence=TAAATCGAAGT; -phiX174 fimo polypeptide_motif 112 122 41.6 + . Name=1;ID=1-1683-phiX174;pvalue=6.85e-05;sequence=GAAGTGGACTG; -phiX174 fimo polypeptide_motif 114 124 45.3 + . Name=1;ID=1-1342-phiX174;pvalue=2.92e-05;sequence=AGTGGACTGCT; -phiX174 fimo polypeptide_motif 118 128 56.2 + . Name=1;ID=1-512-phiX174;pvalue=2.38e-06;sequence=GACTGCTGGCG; -phiX174 fimo polypeptide_motif 122 132 51.4 + . Name=1;ID=1-774-phiX174;pvalue=7.15e-06;sequence=GCTGGCGGAAA; -phiX174 fimo polypeptide_motif 123 133 43.1 + . Name=1;ID=1-1533-phiX174;pvalue=4.93e-05;sequence=CTGGCGGAAAA; -phiX174 fimo polypeptide_motif 124 134 48.6 + . Name=1;ID=1-1085-phiX174;pvalue=1.38e-05;sequence=TGGCGGAAAAT; -phiX174 fimo polypeptide_motif 125 135 68.3 + . Name=1;ID=1-146-phiX174;pvalue=1.49e-07;sequence=GGCGGAAAATG; -phiX174 fimo polypeptide_motif 126 136 46.4 + . Name=1;ID=1-1243-phiX174;pvalue=2.27e-05;sequence=GCGGAAAATGA; -phiX174 fimo polypeptide_motif 128 138 58.3 + . Name=1;ID=1-446-phiX174;pvalue=1.48e-06;sequence=GGAAAATGAGA; -phiX174 fimo polypeptide_motif 129 139 43.2 + . Name=1;ID=1-1522-phiX174;pvalue=4.78e-05;sequence=GAAAATGAGAA; -phiX174 fimo polypeptide_motif 130 140 54.1 + . Name=1;ID=1-595-phiX174;pvalue=3.92e-06;sequence=AAAATGAGAAA; -phiX174 fimo polypeptide_motif 131 141 76 + . Name=1;ID=1-68-phiX174;pvalue=2.49e-08;sequence=AAATGAGAAAA; -phiX174 fimo polypeptide_motif 132 142 51.2 + . Name=1;ID=1-800-phiX174;pvalue=7.57e-06;sequence=AATGAGAAAAT; -phiX174 fimo polypeptide_motif 133 143 56.2 + . Name=1;ID=1-513-phiX174;pvalue=2.41e-06;sequence=ATGAGAAAATT; -phiX174 fimo polypeptide_motif 134 144 41.1 + . Name=1;ID=1-1761-phiX174;pvalue=7.83e-05;sequence=TGAGAAAATTC; -phiX174 fimo polypeptide_motif 135 145 50.3 + . Name=1;ID=1-910-phiX174;pvalue=9.39e-06;sequence=GAGAAAATTCG; -phiX174 fimo polypeptide_motif 136 146 43.3 + . Name=1;ID=1-1517-phiX174;pvalue=4.66e-05;sequence=AGAAAATTCGA; -phiX174 fimo polypeptide_motif 139 149 54.2 + . Name=1;ID=1-588-phiX174;pvalue=3.75e-06;sequence=AAATTCGACCT; -phiX174 fimo polypeptide_motif 141 151 42.2 + . Name=1;ID=1-1625-phiX174;pvalue=6.01e-05;sequence=ATTCGACCTAT; -phiX174 fimo polypeptide_motif 143 153 50 + . Name=1;ID=1-938-phiX174;pvalue=9.94e-06;sequence=TCGACCTATCC; -phiX174 fimo polypeptide_motif 145 155 44.6 + . Name=1;ID=1-1403-phiX174;pvalue=3.42e-05;sequence=GACCTATCCTT; -phiX174 fimo polypeptide_motif 155 165 51.3 + . Name=1;ID=1-787-phiX174;pvalue=7.35e-06;sequence=TGCGCAGCTCG; -phiX174 fimo polypeptide_motif 157 167 51.1 + . Name=1;ID=1-807-phiX174;pvalue=7.68e-06;sequence=CGCAGCTCGAG; -phiX174 fimo polypeptide_motif 159 169 44.5 + . Name=1;ID=1-1420-phiX174;pvalue=3.56e-05;sequence=CAGCTCGAGAA; -phiX174 fimo polypeptide_motif 160 170 40 + . Name=1;ID=1-1921-phiX174;pvalue=9.89e-05;sequence=AGCTCGAGAAG; -phiX174 fimo polypeptide_motif 166 176 60.9 + . Name=1;ID=1-365-phiX174;pvalue=8.02e-07;sequence=AGAAGCTCTTA; -phiX174 fimo polypeptide_motif 168 178 62.3 + . Name=1;ID=1-311-phiX174;pvalue=5.87e-07;sequence=AAGCTCTTACT; -phiX174 fimo polypeptide_motif 181 191 49.9 + . Name=1;ID=1-946-phiX174;pvalue=1.01e-05;sequence=GCGACCTTTCG; -phiX174 fimo polypeptide_motif 187 197 52.5 + . Name=1;ID=1-694-phiX174;pvalue=5.64e-06;sequence=TTTCGCCATCA; -phiX174 fimo polypeptide_motif 191 201 46.6 + . Name=1;ID=1-1232-phiX174;pvalue=2.2e-05;sequence=GCCATCAACTA; -phiX174 fimo polypeptide_motif 194 204 76.4 + . Name=1;ID=1-67-phiX174;pvalue=2.29e-08;sequence=ATCAACTAACG; -phiX174 fimo polypeptide_motif 201 211 40.1 + . Name=1;ID=1-1908-phiX174;pvalue=9.77e-05;sequence=AACGATTCTGT; -phiX174 fimo polypeptide_motif 203 213 63 + . Name=1;ID=1-291-phiX174;pvalue=5e-07;sequence=CGATTCTGTCA; -phiX174 fimo polypeptide_motif 205 215 53.8 + . Name=1;ID=1-610-phiX174;pvalue=4.16e-06;sequence=ATTCTGTCAAA; -phiX174 fimo polypeptide_motif 206 216 59.1 + . Name=1;ID=1-421-phiX174;pvalue=1.23e-06;sequence=TTCTGTCAAAA; -phiX174 fimo polypeptide_motif 207 217 68 + . Name=1;ID=1-153-phiX174;pvalue=1.58e-07;sequence=TCTGTCAAAAA; -phiX174 fimo polypeptide_motif 209 219 49.6 + . Name=1;ID=1-988-phiX174;pvalue=1.09e-05;sequence=TGTCAAAAACT; -phiX174 fimo polypeptide_motif 210 220 40.8 + . Name=1;ID=1-1810-phiX174;pvalue=8.33e-05;sequence=GTCAAAAACTG; -phiX174 fimo polypeptide_motif 213 223 59.7 + . Name=1;ID=1-404-phiX174;pvalue=1.06e-06;sequence=AAAAACTGACG; -phiX174 fimo polypeptide_motif 223 233 42 + . Name=1;ID=1-1654-phiX174;pvalue=6.36e-05;sequence=GCGTTGGATGA; -phiX174 fimo polypeptide_motif 225 235 61.4 + . Name=1;ID=1-349-phiX174;pvalue=7.16e-07;sequence=GTTGGATGAGG; -phiX174 fimo polypeptide_motif 227 237 40.3 + . Name=1;ID=1-1874-phiX174;pvalue=9.32e-05;sequence=TGGATGAGGAG; -phiX174 fimo polypeptide_motif 228 238 49.9 + . Name=1;ID=1-947-phiX174;pvalue=1.01e-05;sequence=GGATGAGGAGA; -phiX174 fimo polypeptide_motif 229 239 45 + . Name=1;ID=1-1370-phiX174;pvalue=3.16e-05;sequence=GATGAGGAGAA; -phiX174 fimo polypeptide_motif 230 240 44.8 + . Name=1;ID=1-1395-phiX174;pvalue=3.33e-05;sequence=ATGAGGAGAAG; diff -r 793225b11202 -r b48e673af4e8 test-data/output.memepsp --- a/test-data/output.memepsp Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ ->BBP_PIEBR 20 scaledmin = 0.1 scaledmax = 0.9 -0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ->ICYA_MANSE 20 scaledmin = 0.1 scaledmax = 0.9 -0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ->LACB_BOVIN 20 scaledmin = 0.1 scaledmax = 0.9 -0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff -r 793225b11202 -r b48e673af4e8 test-data/phiX.fasta --- a/test-data/phiX.fasta Wed Apr 25 12:13:08 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,79 +0,0 @@ ->phiX174 -GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT -GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA -ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG -TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA -GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC -TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT -TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT -CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT -TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG -TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC -GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA -CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG -TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT -AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC -CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA -TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC -TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA -CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA -GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT -GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA -ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC -TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT -TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC -ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC -CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT -GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC -CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC -TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG -TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT -TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA -AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT -TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT -ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC -GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC -TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT -TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA -TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG -TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC -CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG -AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC -CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT -TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG -CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA -AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT -GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG -GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA -TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT -CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG -TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA -GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC -CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA -TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA -AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC -TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT -CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA -TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG -TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT -CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT -TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC -ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG -TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA -ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG -GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC -CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT -GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG -GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT -ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG -CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC -CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC -GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT -CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG -CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA -TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT -TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG -TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC -AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC -TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA -