# HG changeset patch # User iuc # Date 1576105535 18000 # Node ID 0c5239d1aa652c5bf84f1df5d20d9fbeda9aeac7 # Parent c1a9a297ba8b3ac6cad273065fc7a8a22a1d59cc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0" diff -r c1a9a297ba8b -r 0c5239d1aa65 fimo.xml --- a/fimo.xml Wed Dec 12 02:50:48 2018 -0500 +++ b/fimo.xml Wed Dec 11 18:05:35 2019 -0500 @@ -47,7 +47,7 @@ '${fasta_type.input_database.fields.path}' #end if && mv ./out/fimo.html '${html_outfile}' -&& mv ./out/fimo.txt '${txt_outfile}' +&& mv ./out/fimo.tsv '${txt_outfile}' && mv ./out/fimo.xml '${xml_outfile}' && mv ./out/fimo.gff '${gff_outfile}' ]]> @@ -235,10 +235,10 @@ - - - - + + + + @@ -252,10 +252,10 @@ - - - - + + + + @@ -273,9 +273,9 @@ - - - + + + diff -r c1a9a297ba8b -r 0c5239d1aa65 macros.xml --- a/macros.xml Wed Dec 12 02:50:48 2018 -0500 +++ b/macros.xml Wed Dec 11 18:05:35 2019 -0500 @@ -1,10 +1,9 @@ - 4.12.0 + 5.0.5 - graphicsmagick - meme + meme diff -r c1a9a297ba8b -r 0c5239d1aa65 test-data/dreme_output_test1.html --- a/test-data/dreme_output_test1.html Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/dreme_output_test1.html Wed Dec 11 18:05:35 2019 -0500 @@ -7,10 +7,9 @@ // @JSON_VAR data var data = { "program": "dreme", - "version": "4.12.0", - "release": "Tue Jun 27 16:22:50 2017 -0700", + "version": "5.0.5", "cmd": [ - "dreme", "-o", "./dreme_test1_out", "-p", "dreme_test_sites.fa", + "dreme", "-o", "./dreme_out", "-p", "-norc", "-rna", "-s", "1" ], "options": { @@ -20,95 +19,19 @@ "seed": 1, "stop": { "evalue": "0.05" - } - }, "alphabet": { "name": "RNA", "like": "rna", "ncore": 4, "symbols": [ - { - "symbol": "A", - "name": "Adenine", - "colour": "CC0000" - }, { - "symbol": "C", - "name": "Cytosine", - "colour": "0000CC" - }, { - "symbol": "G", - "name": "Guanine", - "colour": "FFB300" - }, { - "symbol": "U", - "aliases": "T", - "name": "Uracil", - "colour": "008000" - }, { - "symbol": "N", - "aliases": "X.", - "name": "Any base", - "equals": "ACGU" - }, { - "symbol": "V", - "name": "Not U", - "equals": "ACG" - }, { - "symbol": "H", - "name": "Not G", - "equals": "ACU" - }, { - "symbol": "D", - "name": "Not C", - "equals": "AGU" - }, { - "symbol": "B", - "name": "Not A", - "equals": "CGU" - }, { - "symbol": "M", - "name": "Amino", - "equals": "AC" - }, { - "symbol": "R", - "name": "Purine", - "equals": "AG" - }, { - "symbol": "W", - "name": "Weak", - "equals": "AU" - }, { - "symbol": "S", - "name": "Strong", - "equals": "CG" - }, { - "symbol": "Y", - "name": "Pyrimidine", - "equals": "CU" - }, { - "symbol": "K", - "name": "Keto", - "equals": "GU" - } - ] - }, "background": { "freqs": [0.221, 0.245, 0.221, 0.312] - }, - "sequence_db": { - "name": "dreme test sites", - "file": "dreme_test_sites.fa", - "lmod": "Thu Apr 26 15:09:03 CEST 2018", - "count": 1000 - }, "control_db": { "name": "shuffled positive sequences", "from": "shuffled", "count": 1000, "freqs": [0.221, 0.245, 0.221, 0.312] - }, "motifs": [ - { "db": 0, "id": "UUYUCY", "alt": "DREME-1", @@ -126,9 +49,7 @@ [0.000000, 0.000000, 0.000000, 1.000000], [0.000000, 1.000000, 0.000000, 0.000000], [0.000000, 0.474946, 0.000000, 0.525054] - ], "matches": [ - { "seq": "UUUUCC", "p": 147, "n": 75, @@ -140,6059 +61,53 @@ "n": 94, "pvalue": "2.2e-005", "evalue": "1.0e+000" - }, { "seq": "UUCUCU", "p": 94, "n": 51, "pvalue": "1.3e-004", "evalue": "6.1e+000" - }, { "seq": "UUCUCC", "p": 75, "n": 42, "pvalue": "1.1e-003", "evalue": "5.0e+001" - } - ] - }, { - "db": 0, - "id": "YAGG", - "alt": "DREME-2", - "len": 4, - "nsites": 793, - "evalue": "5.1e-012", - "p": 600, - "n": 416, - "pvalue": "1.1e-016", - "unerased_evalue": "2.4e-012", - "pwm": [ - [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] - ], - "matches": [ - { - "seq": "CAGG", - "p": 441, - "n": 304, - "pvalue": "1.5e-010", - "evalue": "6.6e-006" - }, { - "seq": "UAGG", - "p": 232, - "n": 165, - "pvalue": "1.1e-004", - "evalue": "4.7e+000" - } - ] - }, { - "db": 0, - "id": "GAAGAW", - "alt": "DREME-3", - "len": 6, - "nsites": 89, - "evalue": "3.4e-005", - "p": 81, - "n": 22, - "pvalue": "8.2e-010", - "unerased_evalue": "3.5e-004", - "pwm": [ - [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] - ], - "matches": [ - { - "seq": "GAAGAU", - "p": 45, - "n": 7, - "pvalue": "2.4e-008", - "evalue": "9.9e-004" - }, { - "seq": "GAAGAA", - "p": 40, - "n": 16, - "pvalue": "7.9e-004", - "evalue": "3.3e+001" - } - ] - }, { - "db": 0, - "id": "SMUGGA", - "alt": "DREME-4", - "len": 6, - "nsites": 119, - "evalue": "3.7e-003", - "p": 110, - "n": 47, - "pvalue": "9.1e-008", - "unerased_evalue": "2.6e-005", - "pwm": [ - [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] - ], - "matches": [ - { - "seq": "GAUGGA", - "p": 22, - "n": 6, - "pvalue": "1.7e-003", - "evalue": "7.1e+001" - }, { - "seq": "GCUGGA", - "p": 33, - "n": 14, - "pvalue": "3.6e-003", - "evalue": "1.5e+002" - }, { - "seq": "CCUGGA", - "p": 32, - "n": 15, - "pvalue": "8.6e-003", - "evalue": "3.5e+002" - }, { - "seq": "CAUGGA", - "p": 29, - "n": 13, - "pvalue": "9.1e-003", - "evalue": "3.7e+002" - } - ] - } - ], - "runtime": { - "host": "ThinkPad-T450s", - "when": "Thu May 03 13:22:29 CEST 2018", - "cpu": 13.95, - "real": 13.95, - "stop": "evalue" - } - }; - - - - - - - - - - - -
-

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 + weight matrix is not directly equivalent 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 +
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 -
- - -

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- - - - - -
-

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 c1a9a297ba8b -r 0c5239d1aa65 test-data/dreme_output_test1.txt --- a/test-data/dreme_output_test1.txt Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/dreme_output_test1.txt Wed Dec 11 18:05:35 2019 -0500 @@ -1,12 +1,7 @@ -# 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) +# DREME 5.0.5 # negatives: 1000 from shuffled positives -# host: ThinkPad-T450s -# when: Thu May 03 13:22:29 CEST 2018 -MEME version 4.12.0 - +MEME version 5.0.5 ALPHABET "RNA" RNA-LIKE A "Adenine" CC0000 C "Cytosine" 0000CC @@ -27,20 +22,15 @@ 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 @@ -48,29 +38,21 @@ 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 @@ -78,17 +60,13 @@ 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 @@ -96,7 +74,4 @@ 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 c1a9a297ba8b -r 0c5239d1aa65 test-data/dreme_output_test1.xml --- a/test-data/dreme_output_test1.xml Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/dreme_output_test1.xml Wed Dec 11 18:05:35 2019 -0500 @@ -1,7 +1,5 @@ - + - dreme -o ./dreme_test1_out -p dreme_test_sites.fa -norc -rna -s 1 - @@ -26,8 +24,6 @@ 100 0.01 1 - ThinkPad-T450s - Thu May 03 13:22:29 CEST 2018 @@ -73,5 +69,4 @@ - diff -r c1a9a297ba8b -r 0c5239d1aa65 test-data/dreme_output_test2.html --- a/test-data/dreme_output_test2.html Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/dreme_output_test2.html Wed Dec 11 18:05:35 2019 -0500 @@ -7,10 +7,10 @@ // @JSON_VAR data var data = { "program": "dreme", - "version": "4.12.0", - "release": "Tue Jun 27 16:22:50 2017 -0700", + "version": "5.0.5", + "release": "Mon Mar 18 20:12:19 2019 -0700", "cmd": [ - "dreme", "-o", "./dreme_test2_out", "-p", "dreme_test_sites.fa", + "dreme", "-o", "./dreme_out", "-p", "-norc", "-rna", "-s", "1", "-e", "1e-05", "-g", "100", "-mink", "4", "-maxk", "10" ], @@ -36,80 +36,57 @@ "symbol": "C", "name": "Cytosine", "colour": "0000CC" - }, { "symbol": "G", "name": "Guanine", "colour": "FFB300" - }, { "symbol": "U", "aliases": "T", "name": "Uracil", "colour": "008000" - }, { "symbol": "N", "aliases": "X.", "name": "Any base", "equals": "ACGU" - }, { "symbol": "V", "name": "Not U", "equals": "ACG" - }, { "symbol": "H", "name": "Not G", "equals": "ACU" - }, { "symbol": "D", "name": "Not C", "equals": "AGU" - }, { "symbol": "B", "name": "Not A", "equals": "CGU" - }, { "symbol": "M", "name": "Amino", "equals": "AC" - }, { "symbol": "R", "name": "Purine", "equals": "AG" - }, { "symbol": "W", "name": "Weak", "equals": "AU" - }, { "symbol": "S", "name": "Strong", "equals": "CG" - }, { "symbol": "Y", "name": "Pyrimidine", "equals": "CU" - }, { "symbol": "K", "name": "Keto", "equals": "GU" - } - ] - }, "background": { "freqs": [0.221, 0.245, 0.221, 0.312] - }, "sequence_db": { - "name": "dreme test sites", - "file": "dreme_test_sites.fa", - "lmod": "Thu Apr 26 15:09:03 CEST 2018", "count": 1000 - }, "control_db": { "name": "shuffled positive sequences", "from": "shuffled", "count": 1000, "freqs": [0.221, 0.245, 0.221, 0.312] - }, "motifs": [ - { "db": 0, "id": "UUYUCY", "alt": "DREME-1", @@ -127,5993 +104,64 @@ [0.000000, 0.000000, 0.000000, 1.000000], [0.000000, 1.000000, 0.000000, 0.000000], [0.000000, 0.474946, 0.000000, 0.525054] - ], "matches": [ - { "seq": "UUUUCC", "p": 147, "n": 75, "pvalue": "1.8e-007", "evalue": "2.2e-002" - }, { - "seq": "UUUUCU", - "p": 155, - "n": 94, - "pvalue": "2.2e-005", - "evalue": "2.8e+000" - }, { - "seq": "UUCUCU", - "p": 94, - "n": 51, - "pvalue": "1.3e-004", - "evalue": "1.7e+001" - }, { - "seq": "UUCUCC", - "p": 75, - "n": 42, - "pvalue": "1.1e-003", - "evalue": "1.4e+002" - } - ] - }, { - "db": 0, - "id": "YAGG", - "alt": "DREME-2", - "len": 4, - "nsites": 793, - "evalue": "1.4e-011", - "p": 600, - "n": 416, - "pvalue": "1.1e-016", - "unerased_evalue": "6.3e-012", - "pwm": [ - [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] - ], - "matches": [ - { - "seq": "CAGG", - "p": 441, - "n": 304, - "pvalue": "1.5e-010", - "evalue": "1.8e-005" - }, { - "seq": "UAGG", - "p": 232, - "n": 165, - "pvalue": "1.1e-004", - "evalue": "1.3e+001" - } - ] - } - ], - "runtime": { - "host": "ThinkPad-T450s", - "when": "Thu May 03 13:22:11 CEST 2018", - "cpu": 15.97, - "real": 15.97, - "stop": "evalue" - } - }; - - - - - - - - - -
-

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 + weight matrix is not directly equivalent 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 +
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. -

-

+ For further information on how to interpret these results please access + To get a copy of the MEME software please access 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 -
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Discovered Motifs

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No motifs were discovered!

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Inputs & Settings

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Sequences

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

Control Sequences

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Source
Sequence Count
- -

Background

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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
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- -
- -
-
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 c1a9a297ba8b -r 0c5239d1aa65 test-data/dreme_output_test2.txt --- a/test-data/dreme_output_test2.txt Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/dreme_output_test2.txt Wed Dec 11 18:05:35 2019 -0500 @@ -1,12 +1,7 @@ -# 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) +# DREME 5.0.5 # negatives: 1000 from shuffled positives -# host: ThinkPad-T450s -# when: Thu May 03 13:22:11 CEST 2018 -MEME version 4.12.0 - +MEME version 5.0.5 ALPHABET "RNA" RNA-LIKE A "Adenine" CC0000 C "Cytosine" 0000CC @@ -27,20 +22,15 @@ 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 @@ -48,21 +38,14 @@ 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 c1a9a297ba8b -r 0c5239d1aa65 test-data/dreme_output_test2.xml --- a/test-data/dreme_output_test2.xml Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/dreme_output_test2.xml Wed Dec 11 18:05:35 2019 -0500 @@ -1,7 +1,5 @@ - + - dreme -o ./dreme_test2_out -p dreme_test_sites.fa -norc -rna -s 1 -e 1e-05 -g 100 -mink 4 -maxk 10 - @@ -26,8 +24,6 @@ 100 0.01 1 - ThinkPad-T450s - Thu May 03 13:22:11 CEST 2018 @@ -51,5 +47,4 @@ - diff -r c1a9a297ba8b -r 0c5239d1aa65 test-data/fimo_output_test1.gff --- a/test-data/fimo_output_test1.gff Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/fimo_output_test1.gff Wed Dec 11 18:05:35 2019 -0500 @@ -1,9 +1,9 @@ ##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 6529 6536 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 7741 7748 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 13656 13663 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 13740 13747 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 2299 2306 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; diff -r c1a9a297ba8b -r 0c5239d1aa65 test-data/fimo_output_test1.html --- a/test-data/fimo_output_test1.html Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/fimo_output_test1.html Wed Dec 11 18:05:35 2019 -0500 @@ -7,9 +7,8 @@ - +
@@ -17,98 +16,36 @@ + +
Database and Motifs High-scoring Motif Occurences Debugging InformationResults in TSV FormatResults in GFF3 Format
-
-
-
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

+FIMO version 5.0.5, (Release date: Mon Mar 18 20:12:19 2019 -0700) +For further information on how to interpret these results please access http://meme-suite.org/doc/fimo-output-format.html.
+To get a copy of the FIMO software please access http://meme-suite.org

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 +TSV (tab-delimited values) output file +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.
  • -
- - - +
  • The table is sorted by increasing p-value.
  • @@ -118,21 +55,6 @@ - - - - - - - - - - - - - - - @@ -142,159 +64,10 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Motif ID Alt ID Sequence Namep-value q-value Matched Sequence
    TACTAAYMMEME-1chrM-229923062.18e-050.142TACTAACA
    TACTAAYM MEME-1 chrM2.18e-05 0.142 TACTAACA
    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 c1a9a297ba8b -r 0c5239d1aa65 test-data/fimo_output_test1.txt --- a/test-data/fimo_output_test1.txt Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/fimo_output_test1.txt Wed Dec 11 18:05:35 2019 -0500 @@ -1,9 +1,9 @@ -# 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 +motif_id motif_alt_id sequence_name start stop strand score p-value q-value matched_sequence 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 2299 2306 - 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 diff -r c1a9a297ba8b -r 0c5239d1aa65 test-data/fimo_output_test1.xml --- a/test-data/fimo_output_test1.xml Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/fimo_output_test1.xml Wed Dec 11 18:05:35 2019 -0500 @@ -1,16 +1,12 @@ - + 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 +false true false false diff -r c1a9a297ba8b -r 0c5239d1aa65 test-data/fimo_output_test2.gff --- a/test-data/fimo_output_test2.gff Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/fimo_output_test2.gff Wed Dec 11 18:05:35 2019 -0500 @@ -1,12 +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 440 446 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-1-chrM;pvalue=8.2e-05;qvalue= 0.332;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= 0.332;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= 0.332;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= 0.332;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= 0.332;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= 0.332;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= 0.332;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= 0.332;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= 0.683;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= 0.683;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 c1a9a297ba8b -r 0c5239d1aa65 test-data/fimo_output_test2.html --- a/test-data/fimo_output_test2.html Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/fimo_output_test2.html Wed Dec 11 18:05:35 2019 -0500 @@ -9,7 +9,7 @@ td.right {text-align: right; padding-right: 1cm;} - +
    @@ -17,123 +17,44 @@ + +
    Database and Motifs High-scoring Motif Occurences Debugging InformationResults in TSV FormatResults in GFF3 Format
    -
    -
    -
    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

    +FIMO version 5.0.5, (Release date: Mon Mar 18 20:12:19 2019 -0700) +For further information on how to interpret these results please access http://meme-suite.org/doc/fimo-output-format.html.
    +To get a copy of the FIMO software please access http://meme-suite.org

    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 +TSV (tab-delimited values) output file +the GFF3 file 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 +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.
    • -
    - - - +
  • The table is sorted by increasing p-value.
  • @@ -143,9 +64,6 @@ - - - @@ -154,172 +72,19 @@ - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - -
    Motif ID Alt ID Sequence Namep-value q-value Matched Sequence
    CCAGCAY DREME-5510 516 4.15e-050.668CCAGCAC
    CCAGCAYDREME-5chrM+513751434.15e-050.6680.683 CCAGCAC
    ACTAAYHDREME-1chrM+4404468.2e-050.327ACTAACA
    ACTAAYHDREME-1chrM- 2093 2099 8.2e-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-050.3270.332 ACTAACA
    ACTAAYHDREME-1chrM+13741137478.2e-050.327ACTAACA
    CCAGCAYDREME-5chrM+424142479.37e-051CCAGCAT
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    DEBUGGING INFORMATION
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    Command line: -

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    -fimo -oc fimo_test2_out --bgfile fimo_background_probs_hsa_chrM.txt dreme_fimo_input_1.xml hsa_chrM.fa
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    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
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    This information can be useful in the event you wish to report a problem with the FIMO software. -

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    -Go to top diff -r c1a9a297ba8b -r 0c5239d1aa65 test-data/fimo_output_test2.txt --- a/test-data/fimo_output_test2.txt Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/fimo_output_test2.txt Wed Dec 11 18:05:35 2019 -0500 @@ -1,12 +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 +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 0.683 CCAGCAC +CCAGCAY DREME-5 chrM 5137 5143 + 13.5843 4.15e-05 0.683 CCAGCAC +ACTAAYH DREME-1 chrM 440 446 + 11.7286 8.2e-05 0.332 ACTAACA +ACTAAYH DREME-1 chrM 2093 2099 - 11.7286 8.2e-05 0.332 ACTAACA +ACTAAYH DREME-1 chrM 2299 2305 - 11.7286 8.2e-05 0.332 ACTAACA +ACTAAYH DREME-1 chrM 5186 5192 + 11.7286 8.2e-05 0.332 ACTAACA +ACTAAYH DREME-1 chrM 6530 6536 + 11.7286 8.2e-05 0.332 ACTAACA +ACTAAYH DREME-1 chrM 7742 7748 + 11.7286 8.2e-05 0.332 ACTAACA +ACTAAYH DREME-1 chrM 13657 13663 + 11.7286 8.2e-05 0.332 ACTAACA +ACTAAYH DREME-1 chrM 13741 13747 + 11.7286 8.2e-05 0.332 ACTAACA CCAGCAY DREME-5 chrM 4241 4247 + 13.1461 9.37e-05 1 CCAGCAT diff -r c1a9a297ba8b -r 0c5239d1aa65 test-data/fimo_output_test2.xml --- a/test-data/fimo_output_test2.xml Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/fimo_output_test2.xml Wed Dec 11 18:05:35 2019 -0500 @@ -1,16 +1,11 @@ - + 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 +false true false false @@ -45,7 +40,6 @@ - 0.278 0.222 0.222 diff -r c1a9a297ba8b -r 0c5239d1aa65 test-data/fimo_output_test3.html --- a/test-data/fimo_output_test3.html Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/fimo_output_test3.html Wed Dec 11 18:05:35 2019 -0500 @@ -5,48 +5,23 @@ FIMO Results - - -
    - - + - -
    Database and Motifs High-scoring Motif Occurences Debugging Information
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    +Results in TSV Format +Results in GFF3 Format
    FIMO - Motif search tool
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    -

    -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

    +FIMO version 5.0.5, (Release date: Mon Mar 18 20:12:19 2019 -0700) +For further information on how to interpret these results please access http://meme-suite.org/doc/fimo-output-format.html.
    +To get a copy of the FIMO software please access http://meme-suite.org

    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]

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    DATABASE AND MOTIFS
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    - DATABASE hsa_chrM.fa -
    Database contains 1 sequences, 16569 residues -

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    - MOTIFS dreme_fimo_input_1.xml (DNA) @@ -63,74 +38,29 @@ - - - - - - - - - - - - - - - - - - - - - - - - -
    7 ACTAACA
    YTAACA6TTAACA
    TCTGT5TCTGT
    SCCAGG6CCCAGG
    CCAGCAY7CCAGCAC
    GMATGT6GAATGT

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

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    SECTION I: HIGH-SCORING MOTIF OCCURENCES
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    • 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 +TSV (tab-delimited values) output file +the GFF3 file 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 +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.
    • -
    +
  • The table is sorted by increasing p-value.
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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    ACTAAYHDREME-1chrM-2102160.005430.514ATTAATT
    ACTAAYHDREME-1chrM-2142200.005430.514ATTAATT
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    ACTAAYHDREME-1chrM+308130870.006350.514AGTAATC
    ACTAAYHDREME-1chrM+334533510.006350.514TCTAATC
    ACTAAYHDREME-1chrM-382438300.006350.514AGTAATC
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    ACTAAYHDREME-1chrM+12699127050.006350.514ACTCATC
    ACTAAYHDREME-1chrM+12952129580.006350.514GCTAATC
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    ACTAAYHDREME-1chrM+13419134250.006350.514ACTACTC
    ACTAAYHDREME-1chrM+14118141240.006350.514ACTCATC
    ACTAAYHDREME-1chrM+14136141420.006350.514CCTAATC
    ACTAAYHDREME-1chrM+14366143720.006350.514ACCAATC
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    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
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    DEBUGGING INFORMATION
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    -

    -Command line: -

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    -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
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    -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
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    -

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

    -
    -Go to top diff -r c1a9a297ba8b -r 0c5239d1aa65 test-data/fimo_output_test3.txt --- a/test-data/fimo_output_test3.txt Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/fimo_output_test3.txt Wed Dec 11 18:05:35 2019 -0500 @@ -1,4 +1,4 @@ -# motif_id motif_alt_id sequence_name start stop strand score p-value q-value matched_sequence +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 @@ -20,499 +20,3 @@ 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 c1a9a297ba8b -r 0c5239d1aa65 test-data/fimo_output_test3.xml --- a/test-data/fimo_output_test3.xml Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/fimo_output_test3.xml Wed Dec 11 18:05:35 2019 -0500 @@ -1,14 +1,10 @@ - + 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 diff -r c1a9a297ba8b -r 0c5239d1aa65 test-data/meme_output_test1.html --- a/test-data/meme_output_test1.html Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/meme_output_test1.html Wed Dec 11 18:05:35 2019 -0500 @@ -7,7999 +7,18 @@ // @JSON_VAR data var data = { "program": "MEME", - "version": "4.12.0", - "release": "Tue Jun 27 16:22:50 2017 -0700", + "version": "5.0.5", + "release": "Mon Mar 18 20:12:19 2019 -0700", "stop_reason": "Stopped because requested number of motifs (1) found.", "cmd": [ - "meme", "meme_input_1.fasta", "-o", "meme_test1_out", "-nostatus", - "-maxsize", "1000000" + "meme", + "-o", + "-nostatus", "-maxsize", "1000000" ], "options": { - "mod": "zoops", - "revcomp": false, - "nmotifs": 1, - "minw": 8, - "maxw": 50, - "minsites": 2, - "maxsites": 30, - "wnsites": 0.8, - "spmap": "pam", - "spfuzz": 120, - "maxwords": -1, - "prior": "megap", - "b": 7500, - "maxiter": 50, - "distance": 1e-05, - "wg": 11, - "ws": 1, - "noendgaps": false, - "substring": true - }, - "alphabet": { - "name": "Protein", - "like": "protein", - "ncore": 20, - "symbols": [ - { - "symbol": "A", - "name": "Alanine", - "colour": "0000CC" - }, { - "symbol": "C", - "name": "Cysteine", - "colour": "0000CC" - }, { - "symbol": "D", - "name": "Aspartic acid", - "colour": "FF00FF" - }, { - "symbol": "E", - "name": "Glutamic acid", - "colour": "FF00FF" - }, { - "symbol": "F", - "name": "Phenylalanine", - "colour": "0000CC" - }, { - "symbol": "G", - "name": "Glycine", - "colour": "FFB300" - }, { - "symbol": "H", - "name": "Histidine", - "colour": "FFCCCC" - }, { - "symbol": "I", - "name": "Isoleucine", - "colour": "0000CC" - }, { - "symbol": "K", - "name": "Lysine", - "colour": "CC0000" - }, { - "symbol": "L", - "name": "Leucine", - "colour": "0000CC" - }, { - "symbol": "M", - "name": "Methionine", - "colour": "0000CC" - }, { - "symbol": "N", - "name": "Asparagine", - "colour": "008000" - }, { - "symbol": "P", - "name": "Proline", - "colour": "FFFF00" - }, { - "symbol": "Q", - "name": "Glutamine", - "colour": "008000" - }, { - "symbol": "R", - "name": "Arginine", - "colour": "CC0000" - }, { - "symbol": "S", - "name": "Serine", - "colour": "008000" - }, { - "symbol": "T", - "name": "Threonine", - "colour": "008000" - }, { - "symbol": "V", - "name": "Valine", - "colour": "0000CC" - }, { - "symbol": "W", - "name": "Tryptophan", - "colour": "0000CC" - }, { - "symbol": "Y", - "name": "Tyrosine", - "colour": "33E6CC" - }, { - "symbol": "X", - "aliases": "*.", - "name": "Any amino acid", - "equals": "ACDEFGHIKLMNPQRSTVWY" - }, { - "symbol": "B", - "name": "Asparagine or Aspartic acid", - "equals": "DN" - }, { - "symbol": "Z", - "name": "Glutamine or Glutamic acid", - "equals": "EQ" - }, { - "symbol": "J", - "name": "Leucine or Isoleucine", - "equals": "IL" - } - ] - }, - "background": { - "freqs": [ - 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 - ] - }, - "sequence_db": { - "source": "meme_input_1.fasta", - "psp_source": "prior30.plib", - "freqs": [ - 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 - ], - "sequences": [ - { - "name": "chr21_19617074_19617124_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_26934381_26934431_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_28217753_28217803_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_31710037_31710087_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_31744582_31744632_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_31768316_31768366_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_31914206_31914256_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_31933633_31933683_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_31962741_31962791_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_31964683_31964733_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_31973364_31973414_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_31992870_31992920_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_32185595_32185645_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_32202076_32202126_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_32253899_32253949_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_32410820_32410870_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_36411748_36411798_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_37838750_37838800_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_45705687_45705737_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_45971413_45971463_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_45978668_45978718_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_45993530_45993580_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_46020421_46020471_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_46031920_46031970_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_46046964_46047014_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_46057197_46057247_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_46086869_46086919_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_46102103_46102153_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_47517957_47518007_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_47575506_47575556_-", - "length": 50, - "weight": 1.000000 - } - ] }, "motifs": [ - { - "db": 0, - "id": "GGGGTATAAAA", - "alt": "MEME-1", - "len": 11, - "nsites": 25, - "evalue": "2.4e-011", - "ic": 40.0, - "re": 13.8, - "llr": 239, - "bt": 5.33554, - "time": 0.772000, - "psm": [ - [ - -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, - 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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 - ] - ], - "sites": [ - { - "seq": 24, - "pos": 12, - "rc": false, - "pvalue": 1.06e-06, - "lflank": "AAGGCCAGGA", - "match": "GGGGTATAAAA", - "rflank": "GCCTGAGAGC" - }, { - "seq": 25, - "pos": 36, - "rc": false, - "pvalue": 3.41e-06, - "lflank": "ACAGGCCCTG", - "match": "GGCATATAAAA", - "rflank": "GCC" - }, { - "seq": 19, - "pos": 9, - "rc": false, - "pvalue": 3.41e-06, - "lflank": "CAGGCCCTG", - "match": "GGCATATAAAA", - "rflank": "GCCCCAGCAG" - }, { - "seq": 9, - "pos": 13, - "rc": false, - "pvalue": 3.41e-06, - "lflank": "GATTCACTGA", - "match": "GGCATATAAAA", - "rflank": "GGCCCTCTGC" - }, { - "seq": 21, - "pos": 7, - "rc": false, - "pvalue": 4.00e-06, - "lflank": "CCAAGGA", - "match": "GGAGTATAAAA", - "rflank": "GCCCCACAAA" - }, { - "seq": 13, - "pos": 13, - "rc": false, - "pvalue": 5.01e-06, - "lflank": "CCACCAGCTT", - "match": "GAGGTATAAAA", - "rflank": "AGCCCTGTAC" - }, { - "seq": 23, - "pos": 15, - "rc": false, - "pvalue": 6.06e-06, - "lflank": "ATACCCAGGG", - "match": "AGGGTATAAAA", - "rflank": "CCTCAGCAGC" - }, { - "seq": 15, - "pos": 21, - "rc": false, - "pvalue": 8.67e-06, - "lflank": "AATCACTGAG", - "match": "GATGTATAAAA", - "rflank": "GTCCCAGGGA" - }, { - "seq": 12, - "pos": 18, - "rc": false, - "pvalue": 8.67e-06, - "lflank": "CACCAGAGCT", - "match": "GGGATATATAA", - "rflank": "AGAAGGTTCT" - }, { - "seq": 11, - "pos": 16, - "rc": false, - "pvalue": 8.67e-06, - "lflank": "CACTATTGAA", - "match": "GATGTATAAAA", - "rflank": "TTTCATTTGC" - }, { - "seq": 22, - "pos": 2, - "rc": false, - "pvalue": 1.21e-05, - "lflank": "GA", - "match": "GACATATAAAA", - "rflank": "GCCAACATCC" - }, { - "seq": 28, - "pos": 32, - "rc": false, - "pvalue": 1.59e-05, - "lflank": "CCGGCGGGGC", - "match": "GGGGTATAAAG", - "rflank": "GGGGCGG" - }, { - "seq": 20, - "pos": 4, - "rc": false, - "pvalue": 1.59e-05, - "lflank": "CAGA", - "match": "GGGGTATAAAG", - "rflank": "GTTCCGACCA" - }, { - "seq": 6, - "pos": 15, - "rc": false, - "pvalue": 1.68e-05, - "lflank": "CCCACTACTT", - "match": "AGAGTATAAAA", - "rflank": "TCATTCTGAG" - }, { - "seq": 14, - "pos": 19, - "rc": false, - "pvalue": 2.03e-05, - "lflank": "CACCAGCAAG", - "match": "GATATATAAAA", - "rflank": "GCTCAGGAGT" - }, { - "seq": 4, - "pos": 12, - "rc": false, - "pvalue": 3.06e-05, - "lflank": "CAGGTCTAAG", - "match": "AGCATATATAA", - "rflank": "CTTGGAGTCC" - }, { - "seq": 0, - "pos": 39, - "rc": false, - "pvalue": 3.06e-05, - "lflank": "CCTCGGGACG", - "match": "TGGGTATATAA", - "rflank": "" - }, { - "seq": 18, - "pos": 37, - "rc": false, - "pvalue": 3.82e-05, - "lflank": "CGTGGTCGCG", - "match": "GGGGTATAACA", - "rflank": "GC" - }, { - "seq": 5, - "pos": 0, - "rc": false, - "pvalue": 3.82e-05, - "lflank": "", - "match": "AACGTATATAA", - "rflank": "ATGGTCCTGT" - }, { - "seq": 29, - "pos": 30, - "rc": false, - "pvalue": 4.02e-05, - "lflank": "GCTGCCGGTG", - "match": "AGCGTATAAAG", - "rflank": "GCCCTGGCG" - }, { - "seq": 1, - "pos": 27, - "rc": false, - "pvalue": 5.52e-05, - "lflank": "AGTCACAAGT", - "match": "GAGTTATAAAA", - "rflank": "GGGTCGCACG" - }, { - "seq": 3, - "pos": 14, - "rc": false, - "pvalue": 5.94e-05, - "lflank": "CCCAGGTTTC", - "match": "TGAGTATATAA", - "rflank": "TCGCCGCACC" - }, { - "seq": 16, - "pos": 22, - "rc": false, - "pvalue": 6.78e-05, - "lflank": "AGTTTCAGTT", - "match": "GGCATCTAAAA", - "rflank": "attatataac" - }, { - "seq": 7, - "pos": 2, - "rc": false, - "pvalue": 2.08e-04, - "lflank": "TC", - "match": "AGAGTATATAT", - "rflank": "AAATGTTCCT" - }, { - "seq": 8, - "pos": 13, - "rc": false, - "pvalue": 4.05e-04, - "lflank": "TATAACTCAG", - "match": "GTTGGATAAAA", - "rflank": "TAATTTGTAC" - } - ] - } - ], "scan": [ - { - "pvalue": 1.22e-03, - "sites": [ - { - "motif": 0, - "pos": 39, - "rc": false, - "pvalue": 3.06e-05 - } - ] - }, { - "pvalue": 2.21e-03, - "sites": [ - { - "motif": 0, - "pos": 27, - "rc": false, - "pvalue": 5.52e-05 - } - ] - }, { - "pvalue": 7.29e-01, - "sites": [] - }, { - "pvalue": 2.37e-03, - "sites": [ - { - "motif": 0, - "pos": 14, - "rc": false, - "pvalue": 5.94e-05 - } - ] - }, { - "pvalue": 1.22e-03, - "sites": [ - { - "motif": 0, - "pos": 12, - "rc": false, - "pvalue": 3.06e-05 - } - ] - }, { - "pvalue": 1.53e-03, - "sites": [ - { - "motif": 0, - "pos": 0, - "rc": false, - "pvalue": 3.82e-05 - } - ] - }, { - "pvalue": 6.70e-04, - "sites": [ - { - "motif": 0, - "pos": 15, - "rc": false, - "pvalue": 1.68e-05 - } - ] - }, { - "pvalue": 1.81e-03, - "sites": [ - { - "motif": 0, - "pos": 4, - "rc": false, - "pvalue": 4.54e-05 - } - ] - }, { - "pvalue": 1.61e-02, - "sites": [] - }, { - "pvalue": 1.36e-04, - "sites": [ - { - "motif": 0, - "pos": 13, - "rc": false, - "pvalue": 3.41e-06 - } - ] - }, { - "pvalue": 1.99e-01, - "sites": [] - }, { - "pvalue": 3.47e-04, - "sites": [ - { - "motif": 0, - "pos": 16, - "rc": false, - "pvalue": 8.67e-06 - } - ] - }, { - "pvalue": 3.47e-04, - "sites": [ - { - "motif": 0, - "pos": 18, - "rc": false, - "pvalue": 8.67e-06 - } - ] - }, { - "pvalue": 2.01e-04, - "sites": [ - { - "motif": 0, - "pos": 13, - "rc": false, - "pvalue": 5.01e-06 - } - ] - }, { - "pvalue": 8.11e-04, - "sites": [ - { - "motif": 0, - "pos": 19, - "rc": false, - "pvalue": 2.03e-05 - } - ] - }, { - "pvalue": 3.47e-04, - "sites": [ - { - "motif": 0, - "pos": 21, - "rc": false, - "pvalue": 8.67e-06 - } - ] - }, { - "pvalue": 2.71e-03, - "sites": [ - { - "motif": 0, - "pos": 22, - "rc": false, - "pvalue": 6.78e-05 - } - ] - }, { - "pvalue": 8.23e-02, - "sites": [] - }, { - "pvalue": 1.53e-03, - "sites": [ - { - "motif": 0, - "pos": 37, - "rc": false, - "pvalue": 3.82e-05 - } - ] - }, { - "pvalue": 1.36e-04, - "sites": [ - { - "motif": 0, - "pos": 9, - "rc": false, - "pvalue": 3.41e-06 - } - ] - }, { - "pvalue": 6.37e-04, - "sites": [ - { - "motif": 0, - "pos": 4, - "rc": false, - "pvalue": 1.59e-05 - } - ] - }, { - "pvalue": 1.60e-04, - "sites": [ - { - "motif": 0, - "pos": 7, - "rc": false, - "pvalue": 4.00e-06 - } - ] - }, { - "pvalue": 4.83e-04, - "sites": [ - { - "motif": 0, - "pos": 2, - "rc": false, - "pvalue": 1.21e-05 - } - ] - }, { - "pvalue": 2.43e-04, - "sites": [ - { - "motif": 0, - "pos": 15, - "rc": false, - "pvalue": 6.06e-06 - } - ] - }, { - "pvalue": 4.26e-05, - "sites": [ - { - "motif": 0, - "pos": 12, - "rc": false, - "pvalue": 1.06e-06 - } - ] - }, { - "pvalue": 1.36e-04, - "sites": [ - { - "motif": 0, - "pos": 36, - "rc": false, - "pvalue": 3.41e-06 - } - ] - }, { - "pvalue": 4.30e-02, - "sites": [] - }, { - "pvalue": 4.30e-02, - "sites": [] - }, { - "pvalue": 6.37e-04, - "sites": [ - { - "motif": 0, - "pos": 32, - "rc": false, - "pvalue": 1.59e-05 - } - ] - }, { - "pvalue": 1.61e-03, - "sites": [ - { - "motif": 0, - "pos": 30, - "rc": false, - "pvalue": 4.02e-05 - } - ] - } - ] - }; - - - - - - - - - - - - - - - -
    -

    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 ]
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    -
    -

    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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    Motif Locations

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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 c1a9a297ba8b -r 0c5239d1aa65 test-data/meme_output_test1.txt --- a/test-data/meme_output_test1.txt Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/meme_output_test1.txt Wed Dec 11 18:05:35 2019 -0500 @@ -1,325 +1,61 @@ ******************************************************************************** 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 . -******************************************************************************** - - -******************************************************************************** +MEME version 5.0.5 (Release date: Mon Mar 18 20:12:19 2019 -0700) 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 +CONTROL SEQUENCES= --none-- 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 +objective function: em= E-value of product of p-values + starts= 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 +trim: wg= 11 ws= 1 endgaps= yes +data: n= 1500 N= 30 +sample: seed= 0 hsfrac= 0 + searchsize= 1500 norand= no csites= 1000 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 -******************************************************************************** - - -******************************************************************************** +A 0.294 C 0.231 D 0 E 0 F 0 G 0.257 H 0 I 0 K 0 +L 0 M 0 N 0 P 0 Q 0 R 0 S 0 T 0.217 V 0 +W 0 Y 0 +Background letter frequencies (from file dataset with add-one prior applied): +A 0.291 C 0.229 D 0.000658 E 0.000658 F 0.000658 G 0.255 H 0.000658 I 0.000658 K 0.000658 +L 0.000658 M 0.000658 N 0.000658 P 0.000658 Q 0.000658 R 0.000658 S 0.000658 T 0.215 V 0.000658 +W 0.000658 Y 0.000658 +Background model order: 0 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 c1a9a297ba8b -r 0c5239d1aa65 test-data/meme_output_test1.xml --- a/test-data/meme_output_test1.xml Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/meme_output_test1.xml Wed Dec 11 18:05:35 2019 -0500 @@ -10,136 +10,29 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -153,7 +46,6 @@ strand (plus|minus|none) 'none' position CDATA #REQUIRED pvalue CDATA #REQUIRED> - @@ -162,643 +54,44 @@ - - ]> - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 -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 - - - - - - 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 - @@ -809,484 +102,17 @@ AAGGCCAGGA - - - - - - - - - - GCCTGAGAGC ACAGGCCCTG - - - - - - - - - - - - - GCC CAGGCCCTG - - - - - - - - - - - - - GCCCCAGCAG - - -GATTCACTGA - - - - - - - - - - - - - -GGCCCTCTGC - - -CCAAGGA - - - - - - - - - - - - - -GCCCCACAAA - - -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 c1a9a297ba8b -r 0c5239d1aa65 test-data/meme_output_test2.html --- a/test-data/meme_output_test2.html Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/meme_output_test2.html Wed Dec 11 18:05:35 2019 -0500 @@ -7,7931 +7,21 @@ // @JSON_VAR data var data = { "program": "MEME", - "version": "4.12.0", - "release": "Tue Jun 27 16:22:50 2017 -0700", + "version": "5.0.5", + "release": "Mon Mar 18 20:12:19 2019 -0700", "stop_reason": "Stopped because requested number of motifs (1) found.", "cmd": [ - "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" + "meme", + "-o", + "-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", + "-spmap", "uni", "-spfuzz", "0.5" ], - "options": { - "mod": "zoops", - "revcomp": false, - "nmotifs": 1, - "minw": 8, - "maxw": 50, - "minsites": 2, - "maxsites": 30, - "wnsites": 0.8, - "spmap": "uni", - "spfuzz": 0.5, - "maxwords": -1, - "prior": "dirichlet", - "b": 0.01, - "maxiter": 50, - "distance": 0.001, - "wg": 11, - "ws": 1, - "noendgaps": false, - "substring": true - }, - "alphabet": { - "name": "DNA", - "like": "dna", - "ncore": 4, - "symbols": [ - { - "symbol": "A", - "name": "Adenine", - "colour": "CC0000", - "complement": "T" - }, { - "symbol": "C", - "name": "Cytosine", - "colour": "0000CC", - "complement": "G" - }, { - "symbol": "G", - "name": "Guanine", - "colour": "FFB300", - "complement": "C" - }, { - "symbol": "T", - "aliases": "U", - "name": "Thymine", - "colour": "008000", - "complement": "A" - }, { - "symbol": "N", - "aliases": "X.", - "name": "Any base", - "equals": "ACGT" - }, { - "symbol": "V", - "name": "Not T", - "equals": "ACG" - }, { - "symbol": "H", - "name": "Not G", - "equals": "ACT" - }, { - "symbol": "D", - "name": "Not C", - "equals": "AGT" - }, { - "symbol": "B", - "name": "Not A", - "equals": "CGT" - }, { - "symbol": "M", - "name": "Amino", - "equals": "AC" - }, { - "symbol": "R", - "name": "Purine", - "equals": "AG" - }, { - "symbol": "W", - "name": "Weak", - "equals": "AT" - }, { - "symbol": "S", - "name": "Strong", - "equals": "CG" - }, { - "symbol": "Y", - "name": "Pyrimidine", - "equals": "CT" - }, { - "symbol": "K", - "name": "Keto", - "equals": "GT" - } - ] - }, - "background": { - "freqs": [0.294, 0.231, 0.257, 0.217] - }, - "sequence_db": { - "source": "Galaxy_FASTA_Input", - "psp_source": "prior30.plib", - "freqs": [0.294, 0.231, 0.257, 0.217], - "sequences": [ - { - "name": "chr21_19617074_19617124_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_26934381_26934431_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_28217753_28217803_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_31710037_31710087_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_31744582_31744632_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_31768316_31768366_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_31914206_31914256_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_31933633_31933683_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_31962741_31962791_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_31964683_31964733_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_31973364_31973414_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_31992870_31992920_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_32185595_32185645_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_32202076_32202126_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_32253899_32253949_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_32410820_32410870_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_36411748_36411798_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_37838750_37838800_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_45705687_45705737_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_45971413_45971463_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_45978668_45978718_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_45993530_45993580_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_46020421_46020471_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_46031920_46031970_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_46046964_46047014_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_46057197_46057247_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_46086869_46086919_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_46102103_46102153_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_47517957_47518007_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_47575506_47575556_-", - "length": 50, - "weight": 1.000000 - } - ] - }, "motifs": [ - { - "db": 0, - "id": "GGSRTATAAAA", - "alt": "MEME-1", - "len": 11, - "nsites": 30, - "evalue": "5.1e-040", - "ic": 13.0, - "re": 12.2, - "llr": 254, - "bt": 5.2854, - "time": 0.376000, - "psm": [ - [-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] - ], - "pwm": [ - [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] - ], - "sites": [ - { - "seq": 24, - "pos": 12, - "rc": false, - "pvalue": 4.51e-07, - "lflank": "AAGGCCAGGA", - "match": "GGGGTATAAAA", - "rflank": "GCCTGAGAGC" - }, { - "seq": 23, - "pos": 15, - "rc": false, - "pvalue": 2.22e-06, - "lflank": "ATACCCAGGG", - "match": "AGGGTATAAAA", - "rflank": "CCTCAGCAGC" - }, { - "seq": 13, - "pos": 13, - "rc": false, - "pvalue": 2.74e-06, - "lflank": "CCACCAGCTT", - "match": "GAGGTATAAAA", - "rflank": "AGCCCTGTAC" - }, { - "seq": 25, - "pos": 36, - "rc": false, - "pvalue": 4.86e-06, - "lflank": "ACAGGCCCTG", - "match": "GGCATATAAAA", - "rflank": "GCC" - }, { - "seq": 21, - "pos": 7, - "rc": false, - "pvalue": 4.86e-06, - "lflank": "CCAAGGA", - "match": "GGAGTATAAAA", - "rflank": "GCCCCACAAA" - }, { - "seq": 19, - "pos": 9, - "rc": false, - "pvalue": 4.86e-06, - "lflank": "CAGGCCCTG", - "match": "GGCATATAAAA", - "rflank": "GCCCCAGCAG" - }, { - "seq": 9, - "pos": 13, - "rc": false, - "pvalue": 4.86e-06, - "lflank": "GATTCACTGA", - "match": "GGCATATAAAA", - "rflank": "GGCCCTCTGC" - }, { - "seq": 28, - "pos": 32, - "rc": false, - "pvalue": 6.48e-06, - "lflank": "CCGGCGGGGC", - "match": "GGGGTATAAAG", - "rflank": "GGGGCGG" - }, { - "seq": 20, - "pos": 4, - "rc": false, - "pvalue": 6.48e-06, - "lflank": "CAGA", - "match": "GGGGTATAAAG", - "rflank": "GTTCCGACCA" - }, { - "seq": 12, - "pos": 18, - "rc": false, - "pvalue": 6.48e-06, - "lflank": "CACCAGAGCT", - "match": "GGGATATATAA", - "rflank": "AGAAGGTTCT" - }, { - "seq": 15, - "pos": 21, - "rc": false, - "pvalue": 1.38e-05, - "lflank": "AATCACTGAG", - "match": "GATGTATAAAA", - "rflank": "GTCCCAGGGA" - }, { - "seq": 11, - "pos": 16, - "rc": false, - "pvalue": 1.38e-05, - "lflank": "CACTATTGAA", - "match": "GATGTATAAAA", - "rflank": "TTTCATTTGC" - }, { - "seq": 0, - "pos": 39, - "rc": false, - "pvalue": 1.41e-05, - "lflank": "CCTCGGGACG", - "match": "TGGGTATATAA", - "rflank": "" - }, { - "seq": 6, - "pos": 15, - "rc": false, - "pvalue": 1.61e-05, - "lflank": "CCCACTACTT", - "match": "AGAGTATAAAA", - "rflank": "TCATTCTGAG" - }, { - "seq": 22, - "pos": 2, - "rc": false, - "pvalue": 1.95e-05, - "lflank": "GA", - "match": "GACATATAAAA", - "rflank": "GCCAACATCC" - }, { - "seq": 14, - "pos": 17, - "rc": false, - "pvalue": 1.95e-05, - "lflank": "CCCACCAGCA", - "match": "AGGATATATAA", - "rflank": "AAGCTCAGGA" - }, { - "seq": 18, - "pos": 37, - "rc": false, - "pvalue": 2.16e-05, - "lflank": "CGTGGTCGCG", - "match": "GGGGTATAACA", - "rflank": "GC" - }, { - "seq": 29, - "pos": 30, - "rc": false, - "pvalue": 3.04e-05, - "lflank": "GCTGCCGGTG", - "match": "AGCGTATAAAG", - "rflank": "GCCCTGGCG" - }, { - "seq": 4, - "pos": 12, - "rc": false, - "pvalue": 3.04e-05, - "lflank": "CAGGTCTAAG", - "match": "AGCATATATAA", - "rflank": "CTTGGAGTCC" - }, { - "seq": 5, - "pos": 0, - "rc": false, - "pvalue": 3.67e-05, - "lflank": "", - "match": "AACGTATATAA", - "rflank": "ATGGTCCTGT" - }, { - "seq": 1, - "pos": 27, - "rc": false, - "pvalue": 3.93e-05, - "lflank": "AGTCACAAGT", - "match": "GAGTTATAAAA", - "rflank": "GGGTCGCACG" - }, { - "seq": 7, - "pos": 4, - "rc": false, - "pvalue": 5.65e-05, - "lflank": "TCAG", - "match": "AGTATATATAA", - "rflank": "ATGTTCCTGT" - }, { - "seq": 3, - "pos": 14, - "rc": false, - "pvalue": 6.24e-05, - "lflank": "CCCAGGTTTC", - "match": "TGAGTATATAA", - "rflank": "TCGCCGCACC" - }, { - "seq": 16, - "pos": 22, - "rc": false, - "pvalue": 7.15e-05, - "lflank": "AGTTTCAGTT", - "match": "GGCATCTAAAA", - "rflank": "attatataac" - }, { - "seq": 27, - "pos": 36, - "rc": false, - "pvalue": 1.39e-04, - "lflank": "TGCCTGGGTC", - "match": "CAGGTATAAAG", - "rflank": "GCT" - }, { - "seq": 26, - "pos": 37, - "rc": false, - "pvalue": 1.39e-04, - "lflank": "TGCCTGGGCC", - "match": "CAGGTATAAAG", - "rflank": "GC" - }, { - "seq": 17, - "pos": 2, - "rc": false, - "pvalue": 4.81e-04, - "lflank": "ga", - "match": "TGGTTTTATAA", - "rflank": "ggggcctcac" - }, { - "seq": 8, - 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"pos": 0, - "rc": false, - "pvalue": 3.67e-05 - } - ] - }, { - "pvalue": 6.45e-04, - "sites": [ - { - "motif": 0, - "pos": 15, - "rc": false, - "pvalue": 1.61e-05 - } - ] - }, { - "pvalue": 2.26e-03, - "sites": [ - { - "motif": 0, - "pos": 4, - "rc": false, - "pvalue": 5.65e-05 - } - ] - }, { - "pvalue": 3.37e-02, - "sites": [] - }, { - "pvalue": 1.95e-04, - "sites": [ - { - "motif": 0, - "pos": 13, - "rc": false, - "pvalue": 4.86e-06 - } - ] - }, { - "pvalue": 5.73e-02, - "sites": [] - }, { - "pvalue": 5.52e-04, - "sites": [ - { - "motif": 0, - "pos": 16, - "rc": false, - "pvalue": 1.38e-05 - } - ] - }, { - "pvalue": 2.59e-04, - "sites": [ - { - "motif": 0, - "pos": 18, - "rc": false, - "pvalue": 6.48e-06 - } - ] - }, { - "pvalue": 1.10e-04, - "sites": [ - { - "motif": 0, - "pos": 13, - "rc": false, - "pvalue": 2.74e-06 - } - ] - }, { - "pvalue": 7.78e-04, - "sites": [ - { - "motif": 0, - "pos": 17, - "rc": false, - "pvalue": 1.95e-05 - } - ] - }, { - "pvalue": 5.52e-04, - "sites": [ - { - "motif": 0, - "pos": 21, - "rc": false, - "pvalue": 1.38e-05 - } - ] - }, { - "pvalue": 2.85e-03, - "sites": [ - { - "motif": 0, - "pos": 22, - "rc": false, - "pvalue": 7.15e-05 - } - ] - }, { - "pvalue": 1.90e-02, - "sites": [] - }, { - "pvalue": 8.63e-04, - "sites": [ - { - "motif": 0, - "pos": 37, - "rc": false, - "pvalue": 2.16e-05 - } - ] - }, { - "pvalue": 1.95e-04, - "sites": [ - { - "motif": 0, - "pos": 9, - "rc": false, - "pvalue": 4.86e-06 - } - ] - }, { - "pvalue": 2.59e-04, - "sites": [ - { - "motif": 0, - "pos": 4, - "rc": false, - "pvalue": 6.48e-06 - } - ] - }, { - "pvalue": 1.95e-04, - "sites": [ - { - "motif": 0, - "pos": 7, - "rc": false, - "pvalue": 4.86e-06 - } - ] - }, { - "pvalue": 7.78e-04, - "sites": [ - { - "motif": 0, - "pos": 2, - "rc": false, - "pvalue": 1.95e-05 - } - ] - }, { - "pvalue": 8.89e-05, - "sites": [ - { - "motif": 0, - "pos": 15, - "rc": false, - "pvalue": 2.22e-06 - } - ] - }, { - "pvalue": 1.80e-05, - "sites": [ - { - "motif": 0, - "pos": 12, - "rc": false, - "pvalue": 4.51e-07 - } - ] - }, { - "pvalue": 1.95e-04, - "sites": [ - { - "motif": 0, - "pos": 36, - "rc": false, - "pvalue": 4.86e-06 - } - ] - }, { - "pvalue": 5.54e-03, - "sites": [] - }, { - "pvalue": 5.54e-03, - "sites": [] - }, { - "pvalue": 2.59e-04, - "sites": [ - { - "motif": 0, - "pos": 32, - "rc": false, - "pvalue": 6.48e-06 - } - ] - }, { - "pvalue": 1.22e-03, - "sites": [ - { - "motif": 0, - "pos": 30, - "rc": false, - "pvalue": 3.04e-05 - } - ] - } ] }; - - - - - - - - - - - - - - - -
    -

    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]
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    GOMO
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    GOMO is a tool for identifying possible roles (Gene Ontology - terms) for DNA binding motifs. - [manual]
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    SpaMo
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    SpaMo is a tool for inferring possible transcription factor - complexes by finding motifs with enriched spacings. - [manual]
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    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.).

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    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.

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    The relative entropy of the motif.

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

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    The Bayes Threshold.

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    The strand used for the motif site.

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    The motif site was found in the sequence as it was supplied.
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    The motif site was found in the reverse complement of the supplied sequence.
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    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.

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    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.

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

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

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

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

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

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    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.

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

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    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.

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    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.

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    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.

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    This is the combined match p-value.

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    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.

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    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.

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    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.

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    This diagram shows the location of motif sites.

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    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.

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

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    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.)

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    The name of the file of sequences input to MEME.

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

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    The alphabet used by the sequences.

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    The number of sequences provided as input to MEME.

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    The name of the alphabet symbol.

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

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

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    Motif1
    p-value8.23e-7
    Start23
    End33
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    Motif1
    p-value8.23e-7
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    - E-value: - -
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    - StandardReverse - Complement -
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    - Log Likelihood Ratio: - -
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    - Relative Entropy: - -
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    - Bayes Threshold: - -
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    - -

    - 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] - -

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

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    Sequences

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    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
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    Trim Gap Open Cost
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    End Gap Treatment - No cost - Same cost as other gaps -
    - - Show Advanced Settings - Hide Advanced Settings - -
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    MEME version
    - - (Release date: )
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    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. - -
    -
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    Command line
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    - - - diff -r c1a9a297ba8b -r 0c5239d1aa65 test-data/meme_output_test2.txt --- a/test-data/meme_output_test2.txt Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/meme_output_test2.txt Wed Dec 11 18:05:35 2019 -0500 @@ -1,88 +1,36 @@ ******************************************************************************** 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 . -******************************************************************************** - - -******************************************************************************** +MEME version 5.0.5 (Release date: Mon Mar 18 20:12:19 2019 -0700) 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 +PRIMARY SEQUENCES= Galaxy_FASTA_Input +CONTROL SEQUENCES= --none-- 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 +objective function: em= E-value of product of p-values + starts= E-value of product of p-values +strands: + 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 +trim: wg= 11 ws= 1 endgaps= yes +data: n= 1500 N= 30 +sample: seed= 0 hsfrac= 0 + searchsize= 1500 norand= no csites= 1000 +Dirichlet mixture priors file: 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): +Background letter frequencies (from file dataset with add-one prior applied): A 0.294 C 0.231 G 0.257 T 0.217 -******************************************************************************** - - -******************************************************************************** +Background model order: 0 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 @@ -103,124 +51,17 @@ 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 @@ -233,87 +74,13 @@ 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 c1a9a297ba8b -r 0c5239d1aa65 test-data/meme_output_test2.xml --- a/test-data/meme_output_test2.xml Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/meme_output_test2.xml Wed Dec 11 18:05:35 2019 -0500 @@ -10,975 +10,73 @@ - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -]> - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -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 - - + +AGCCCTGTAC + 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -