# HG changeset patch
# User greg
# Date 1467815106 14400
# Node ID 4df8e9f58a53dea878569fbc7d46426fcc5aadb6
# Parent  e85346ab5054727009e169cf8f738f2a97c5fba2
Uploaded

diff -r e85346ab5054 -r 4df8e9f58a53 fimo.xml
--- a/fimo.xml	Thu Jun 16 08:07:03 2016 -0400
+++ b/fimo.xml	Wed Jul 06 10:25:06 2016 -0400
@@ -1,8 +1,8 @@
-<tool id="meme_fimo" name="FIMO" version="4.11.0.3">
+<tool id="meme_fimo" name="FIMO" version="4.11.1.0">
     <description>- Scan a set of sequences for motifs.</description>
     <requirements>
-        <requirement type="package" version="6.9.3">imagemagick</requirement>
-        <requirement type="package" version="4.11.0">meme</requirement>
+        <requirement type="package" version="1.3.20">graphicsmagick</requirement>
+        <requirement type="package" version="4.11.1">meme</requirement>
     </requirements>
     <command>
         <![CDATA[
@@ -117,7 +117,10 @@
                         <option value="yes">Yes</option>
                     </param>
                     <when value="yes">
-                        <param name="remove_duplicate_coords" type="boolean" truevalue="yes" falsevalue="no" label="Remove duplicate entries in unique GFF coordinates?" help="Remove duplicate entries as defined by the unique GFF coordinates" />
+                        <param name="remove_duplicate_coords" type="select" label="Remove duplicate entries in unique GFF coordinates?" help="Remove duplicate entries as defined by the unique GFF coordinates">
+                        <option value="no" selected="true">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
                     </when>
                     <when value="no"/>
                 </conditional>
@@ -178,7 +181,7 @@
             </actions>
         </data>
         <data format="tabular" name="gff_outfile" label="${tool.name} on ${on_string} (almost-gff)">
-            <filter>options_type['output_separate_motifs'] == 'no'</filter>
+            <filter>options_type['options_type_selector'] == 'basic' or (options_type['options_type_selector'] == 'advanced' and options_type['output_separate_motifs'] == 'no')</filter>
             <actions>
                 <conditional name="fasta_type.fasta_type_selector">
                     <when value="cached">
@@ -193,7 +196,7 @@
         </data>
         <collection name="motifs" type="list" label="Motifs: ${tool.name} on ${on_string}">
             <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output" ext="gff" visible="false" />
-            <filter>options_type['output_separate_motifs'] == 'yes'</filter>
+            <filter>options_type['options_type_selector'] == 'advanced' and options_type['output_separate_motifs'] == 'yes'</filter>
         </collection>
         <data format="cisml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)">
             <actions>
diff -r e85346ab5054 -r 4df8e9f58a53 fimo_wrapper.py
--- a/fimo_wrapper.py	Thu Jun 16 08:07:03 2016 -0400
+++ b/fimo_wrapper.py	Wed Jul 06 10:25:06 2016 -0400
@@ -56,13 +56,13 @@
 parser.add_argument('--max_strand', action='store_true', help='If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score')
 parser.add_argument('--max_stored_scores', dest='max_stored_scores', type=int, help='Maximum score count to store')
 parser.add_argument('--motif', dest='motifs', action='append', default=[], help='Specify motif by id')
-parser.add_argument('--output_separate_motifs', default="no", help='Output one dataset per motif')
+parser.add_argument('--output_separate_motifs', dest='output_separate_motifs', default='no', help='Output one dataset per motif')
 parser.add_argument('--motif_pseudo', dest='motif_pseudo', type=float, default=0.1, help='Pseudocount to add to counts in motif matrix')
 parser.add_argument('--no_qvalue', action='store_true', help='Do not compute a q-value for each p-value')
 parser.add_argument('--norc', action='store_true', help='Do not score the reverse complement DNA strand')
 parser.add_argument('--output_path', dest='output_path', help='Output files directory')
-parser.add_argument('--parse_genomic_coord', default='no', help='Check each sequence header for UCSC style genomic coordinates')
-parser.add_argument('--remove_duplicate_coords', default='no', help='Remove duplicate entries in unique GFF coordinates')
+parser.add_argument('--parse_genomic_coord', dest='parse_genomic_coord', default='no', help='Check each sequence header for UCSC style genomic coordinates')
+parser.add_argument('--remove_duplicate_coords', dest='remove_duplicate_coords', default='no', help='Remove duplicate entries in unique GFF coordinates')
 parser.add_argument('--qv_thresh', action='store_true', help='Use q-values for the output threshold')
 parser.add_argument('--thresh', dest='thresh', type=float, help='p-value threshold')
 parser.add_argument('--gff_output', dest='gff_output', help='Gff output file')
diff -r e85346ab5054 -r 4df8e9f58a53 test-data/fimo_output_html_1.html
--- a/test-data/fimo_output_html_1.html	Thu Jun 16 08:07:03 2016 -0400
+++ b/test-data/fimo_output_html_1.html	Wed Jul 06 10:25:06 2016 -0400
@@ -41,12 +41,10 @@
 <hr>
 <div style="padding-left: 0.75in; line-height: 1em; font-family: monospace;">
 <p>
-  DATABASE /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat
   <br />
   Database contains 1 sequences, 5386 residues
 </p>
 <p>
-  MOTIFS /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat (Protein)
   <table>
     <thead>
       <tr>
@@ -98,3 +96,5 @@
 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.
 </li>
+<li>
+The score for the match of a position in a sequence to a motif
diff -r e85346ab5054 -r 4df8e9f58a53 test-data/fimo_output_html_2.html
--- a/test-data/fimo_output_html_2.html	Thu Jun 16 08:07:03 2016 -0400
+++ b/test-data/fimo_output_html_2.html	Wed Jul 06 10:25:06 2016 -0400
@@ -96,3 +96,5 @@
 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.
 </li>
+<li>
+The score for the match of a position in a sequence to a motif
diff -r e85346ab5054 -r 4df8e9f58a53 test-data/fimo_output_xml_1.xml
--- a/test-data/fimo_output_xml_1.xml	Thu Jun 16 08:07:03 2016 -0400
+++ b/test-data/fimo_output_xml_1.xml	Wed Jul 06 10:25:06 2016 -0400
@@ -4,11 +4,7 @@
   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
   xsi:schemaLocation=  xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
 >
-<command-line>fimo --o /Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1973/dataset_2713_files --verbosity 1 /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat</command-line>
 <settings>
-<setting name="output directory">/Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1973/dataset_2713_files</setting>
-<setting name="MEME file name">/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat</setting>
-<setting name="sequence file name">/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat</setting>
 <setting name="allow clobber">false</setting>
 <setting name="compute q-values">true</setting>
 <setting name="parse genomic coord.">false</setting>
diff -r e85346ab5054 -r 4df8e9f58a53 test-data/fimo_output_xml_2.xml
--- a/test-data/fimo_output_xml_2.xml	Thu Jun 16 08:07:03 2016 -0400
+++ b/test-data/fimo_output_xml_2.xml	Wed Jul 06 10:25:06 2016 -0400
@@ -4,14 +4,9 @@
   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
   xsi:schemaLocation=  xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
 >
-<command-line>fimo --alpha 1.000000 --max-stored-scores 100000 --motif-pseudo 0.100000 --no-qvalue --thresh 0.000100 --o /Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1978/dataset_2738_files --verbosity 1 /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat</command-line>
 <settings>
-<setting name="output directory">/Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1978/dataset_2738_files</setting>
-<setting name="MEME file name">/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat</setting>
-<setting name="sequence file name">/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat</setting>
 <setting name="allow clobber">false</setting>
 <setting name="compute q-values">false</setting>
-<setting name="parse genomic coord.">false</setting>
 <setting name="text only">false</setting>
 <setting name="scan both strands">false</setting>
 <setting name="output threshold">0.0001</setting>
diff -r e85346ab5054 -r 4df8e9f58a53 test-data/meme_output_html_1.html
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/meme_output_html_1.html	Wed Jul 06 10:25:06 2016 -0400
@@ -0,0 +1,97 @@
+<!DOCTYPE HTML>
+<html>
+  <head>
+    <meta charset="UTF-8">
+    <title>MEME</title>
+    <script>
+      // @JSON_VAR data
+      var data = {
+        "program": "MEME",
+        "version": "4.11.0",
+        "release": "Thu Nov 26 17:48:49 2015 +1000",
+        "stop_reason": "Stopped because requested number of motifs (1) found.",
+        "cmd": [
+          "meme",
+          "-nostatus"
+        ],
+        "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",
diff -r e85346ab5054 -r 4df8e9f58a53 test-data/meme_output_html_2.html
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/meme_output_html_2.html	Wed Jul 06 10:25:06 2016 -0400
@@ -0,0 +1,91 @@
+<!DOCTYPE HTML>
+<html>
+  <head>
+    <meta charset="UTF-8">
+    <title>MEME</title>
+    <script>
+      // @JSON_VAR data
+      var data = {
+        "program": "MEME",
+        "version": "4.11.0",
+        "release": "Thu Nov 26 17:48:49 2015 +1000",
+        "stop_reason": "Stopped because requested number of motifs (1) found.",
+        "cmd": [
+          "meme",
+        ],
+        "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"
diff -r e85346ab5054 -r 4df8e9f58a53 test-data/meme_output_txt_1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/meme_output_txt_1.txt	Wed Jul 06 10:25:06 2016 -0400
@@ -0,0 +1,325 @@
+********************************************************************************
+MEME - Motif discovery tool
+********************************************************************************
+MEME version 4.11.0 (Release date: Thu Nov 26 17:48:49 2015 +1000)
+
+For further information on how to interpret these results or to get
+a copy of the MEME software please access http://meme-suite.org .
+
+This file may be used as input to the MAST algorithm for searching
+sequence databases for matches to groups of motifs.  MAST is available
+for interactive use and downloading at http://meme-suite.org .
+********************************************************************************
+
+
+********************************************************************************
+REFERENCE
+********************************************************************************
+If you use this program in your research, please cite:
+
+Timothy L. Bailey and Charles Elkan,
+"Fitting a mixture model by expectation maximization to discover
+motifs in biopolymers", Proceedings of the Second International
+Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
+AAAI Press, Menlo Park, California, 1994.
+********************************************************************************
+
+
+********************************************************************************
+TRAINING SET
+********************************************************************************
+DATAFILE=
+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 
+
+model:  mod=         zoops    nmotifs=         1    evt=           inf
+object function=  E-value of product of p-values
+width:  minw=            8    maxw=           50
+width:  wg=             11    ws=              1    endgaps=       yes
+nsites: minsites=        2    maxsites=       30    wnsites=       0.8
+theta:  spmap=         pam    spfuzz=        120
+global: substring=     yes    branching=      no    wbranch=        no
+em:     prior=       megap    b=            7500    maxiter=        50
+        distance=    1e-05
+data:   n=            1500    N=              30    shuffle=        -1
+
+sample: seed=            0    ctfrac=         -1    maxwords=       -1
+Dirichlet mixture priors file: prior30.plib
+Letter frequencies in dataset:
+A 0.294 C 0.231 D 0.000 E 0.000 F 0.000 G 0.257 H 0.000 I 0.000 K 0.000 
+L 0.000 M 0.000 N 0.000 P 0.000 Q 0.000 R 0.000 S 0.000 T 0.217 V 0.000 
+W 0.000 Y 0.000 
+Background letter frequencies (from dataset with add-one prior applied):
+A 0.291 C 0.229 D 0.001 E 0.001 F 0.001 G 0.255 H 0.001 I 0.001 K 0.001 
+L 0.001 M 0.001 N 0.001 P 0.001 Q 0.001 R 0.001 S 0.001 T 0.215 V 0.001 
+W 0.001 Y 0.001 
+********************************************************************************
+
+
+********************************************************************************
+MOTIF  1 MEME	width =  11  sites =  25  llr = 239  E-value = 2.4e-011
+********************************************************************************
+--------------------------------------------------------------------------------
+	Motif 1 Description
+--------------------------------------------------------------------------------
+Simplified        A  2323:a:a8a8
+pos.-specific     C  ::3::::::::
+probability       D  :::::::::::
+matrix            E  :::::::::::
+                  F  :::::::::::
+                  G  7746::::::1
+                  H  :::::::::::
+                  I  :::::::::::
+                  K  :::::::::::
+                  L  :::::::::::
+                  M  :::::::::::
+                  N  :::::::::::
+                  P  :::::::::::
+                  Q  :::::::::::
+                  R  :::::::::::
+                  S  :::::::::::
+                  T  1:2:a:a:2::
+                  V  :::::::::::
+                  W  :::::::::::
+                  Y  :::::::::::
+
+         bits   10.6            
+                 9.5            
+                 8.5            
+                 7.4            
+Relative         6.3            
+Entropy          5.3            
+(13.8 bits)      4.2            
+                 3.2            
+                 2.1     * **   
+                 1.1 ** ********
+                 0.0 -----------
+
+Multilevel           GGGGTATAAAA
+consensus            AACA    T  
+sequence                        
+                                
+                                
+--------------------------------------------------------------------------------
+
+--------------------------------------------------------------------------------
+	Motif 1 sites sorted by position p-value
+--------------------------------------------------------------------------------
+Sequence name             Start   P-value               Site  
+-------------             ----- ---------            -----------
+chr21_46046964_46047014_     13  1.06e-06 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC
+chr21_46057197_46057247_     37  3.41e-06 ACAGGCCCTG GGCATATAAAA GCC       
+chr21_45971413_45971463_     10  3.41e-06  CAGGCCCTG GGCATATAAAA GCCCCAGCAG
+chr21_31964683_31964733_     14  3.41e-06 GATTCACTGA GGCATATAAAA GGCCCTCTGC
+chr21_45993530_45993580_      8  4.00e-06    CCAAGGA GGAGTATAAAA GCCCCACAAA
+chr21_32202076_32202126_     14  5.01e-06 CCACCAGCTT GAGGTATAAAA AGCCCTGTAC
+chr21_46031920_46031970_     16  6.06e-06 ATACCCAGGG AGGGTATAAAA CCTCAGCAGC
+chr21_32410820_32410870_     22  8.67e-06 AATCACTGAG GATGTATAAAA GTCCCAGGGA
+chr21_32185595_32185645_     19  8.67e-06 CACCAGAGCT GGGATATATAA AGAAGGTTCT
+chr21_31992870_31992920_     17  8.67e-06 CACTATTGAA GATGTATAAAA TTTCATTTGC
+chr21_46020421_46020471_      3  1.21e-05         GA GACATATAAAA GCCAACATCC
+chr21_47517957_47518007_     33  1.59e-05 CCGGCGGGGC GGGGTATAAAG GGGGCGG   
+chr21_45978668_45978718_      5  1.59e-05       CAGA GGGGTATAAAG GTTCCGACCA
+chr21_31914206_31914256_     16  1.68e-05 CCCACTACTT AGAGTATAAAA TCATTCTGAG
+chr21_32253899_32253949_     20  2.03e-05 CACCAGCAAG GATATATAAAA GCTCAGGAGT
+chr21_31744582_31744632_     13  3.06e-05 CAGGTCTAAG AGCATATATAA CTTGGAGTCC
+chr21_19617074_19617124_     40  3.06e-05 CCTCGGGACG TGGGTATATAA           
+chr21_45705687_45705737_     38  3.82e-05 CGTGGTCGCG GGGGTATAACA GC        
+chr21_31768316_31768366_      1  3.82e-05          . AACGTATATAA ATGGTCCTGT
+chr21_47575506_47575556_     31  4.02e-05 GCTGCCGGTG AGCGTATAAAG GCCCTGGCG 
+chr21_26934381_26934431_     28  5.52e-05 AGTCACAAGT GAGTTATAAAA GGGTCGCACG
+chr21_31710037_31710087_     15  5.94e-05 CCCAGGTTTC TGAGTATATAA TCGCCGCACC
+chr21_36411748_36411798_     23  6.78e-05 AGTTTCAGTT GGCATCtaaaa attatataac
+chr21_31933633_31933683_      3  2.08e-04         TC AGAGTATATAT AAATGTTCCT
+chr21_31962741_31962791_     14  4.05e-04 TATAACTCAG GTTGGATAAAA TAATTTGTAC
+--------------------------------------------------------------------------------
+
+--------------------------------------------------------------------------------
+	Motif 1 block diagrams
+--------------------------------------------------------------------------------
+SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
+-------------            ----------------  -------------
+chr21_46046964_46047014_          1.1e-06  12_[1]_27
+chr21_46057197_46057247_          3.4e-06  36_[1]_3
+chr21_45971413_45971463_          3.4e-06  9_[1]_30
+chr21_31964683_31964733_          3.4e-06  13_[1]_26
+chr21_45993530_45993580_            4e-06  7_[1]_32
+chr21_32202076_32202126_            5e-06  13_[1]_26
+chr21_46031920_46031970_          6.1e-06  15_[1]_24
+chr21_32410820_32410870_          8.7e-06  21_[1]_18
+chr21_32185595_32185645_          8.7e-06  18_[1]_21
+chr21_31992870_31992920_          8.7e-06  16_[1]_23
+chr21_46020421_46020471_          1.2e-05  2_[1]_37
+chr21_47517957_47518007_          1.6e-05  32_[1]_7
+chr21_45978668_45978718_          1.6e-05  4_[1]_35
+chr21_31914206_31914256_          1.7e-05  15_[1]_24
+chr21_32253899_32253949_            2e-05  19_[1]_20
+chr21_31744582_31744632_          3.1e-05  12_[1]_27
+chr21_19617074_19617124_          3.1e-05  39_[1]
+chr21_45705687_45705737_          3.8e-05  37_[1]_2
+chr21_31768316_31768366_          3.8e-05  [1]_39
+chr21_47575506_47575556_            4e-05  30_[1]_9
+chr21_26934381_26934431_          5.5e-05  27_[1]_12
+chr21_31710037_31710087_          5.9e-05  14_[1]_25
+chr21_36411748_36411798_          6.8e-05  22_[1]_17
+chr21_31933633_31933683_          0.00021  2_[1]_37
+chr21_31962741_31962791_           0.0004  13_[1]_26
+--------------------------------------------------------------------------------
+
+--------------------------------------------------------------------------------
+	Motif 1 in BLOCKS format
+--------------------------------------------------------------------------------
+BL   MOTIF 1 width=11 seqs=25
+chr21_46046964_46047014_ (   13) GGGGTATAAAA  1 
+chr21_46057197_46057247_ (   37) GGCATATAAAA  1 
+chr21_45971413_45971463_ (   10) GGCATATAAAA  1 
+chr21_31964683_31964733_ (   14) GGCATATAAAA  1 
+chr21_45993530_45993580_ (    8) GGAGTATAAAA  1 
+chr21_32202076_32202126_ (   14) GAGGTATAAAA  1 
+chr21_46031920_46031970_ (   16) AGGGTATAAAA  1 
+chr21_32410820_32410870_ (   22) GATGTATAAAA  1 
+chr21_32185595_32185645_ (   19) GGGATATATAA  1 
+chr21_31992870_31992920_ (   17) GATGTATAAAA  1 
+chr21_46020421_46020471_ (    3) GACATATAAAA  1 
+chr21_47517957_47518007_ (   33) GGGGTATAAAG  1 
+chr21_45978668_45978718_ (    5) GGGGTATAAAG  1 
+chr21_31914206_31914256_ (   16) AGAGTATAAAA  1 
+chr21_32253899_32253949_ (   20) GATATATAAAA  1 
+chr21_31744582_31744632_ (   13) AGCATATATAA  1 
+chr21_19617074_19617124_ (   40) TGGGTATATAA  1 
+chr21_45705687_45705737_ (   38) GGGGTATAACA  1 
+chr21_31768316_31768366_ (    1) AACGTATATAA  1 
+chr21_47575506_47575556_ (   31) AGCGTATAAAG  1 
+chr21_26934381_26934431_ (   28) GAGTTATAAAA  1 
+chr21_31710037_31710087_ (   15) TGAGTATATAA  1 
+chr21_36411748_36411798_ (   23) GGCATCTAAAA  1 
+chr21_31933633_31933683_ (    3) AGAGTATATAT  1 
+chr21_31962741_31962791_ (   14) GTTGGATAAAA  1 
+//
+
+--------------------------------------------------------------------------------
+
+--------------------------------------------------------------------------------
+	Motif 1 position-specific scoring matrix
+--------------------------------------------------------------------------------
+log-odds matrix: alength= 20 w= 11 n= 1200 bayes= 5.33554 E= 2.4e-011 
+   -32   -680     91     77      7    138    -20     55     64    107     11    150    142     72     87    396   -148    221   -140    -36 
+   -11   -680     89     76      7    137    -21     55     63    107     10    149    141     71     87    396   -239    220   -140    -36 
+   -79     41      4     21     -7     44    -62     42     -5     99      0     99    138     52     42    399    -46    223   -173    -68 
+    11   -677     48     47     -2    127    -43     46     27    101      3    124    138     60     62    397   -235    220   -160    -55 
+  -596   -820     12    -21    -53   -267    -74     37     16     44    -37     98     31      9     19    319    212    127   -193    -95 
+   165   -261     70    110     77   -521     -4    147     95    201     90    121    124     91    107    425   -527    314    -95      8 
+  -838   -990    -89   -149   -151   -841   -161   -117   -113    -66   -209    -68    -69   -129    -91    111    221    -55   -255   -173 
+   176   -858    -79   -103   -115   -717   -148    -95   -108    -17   -162    -61    -12    -95    -69    193   -737     52   -240   -153 
+   134   -686      0     16    -12   -553    -68     44     -8     96     -9     88    124     41     36    384     11    216   -177    -71 
+   165   -261     70    110     77   -521     -4    147     95    201     90    121    124     91    107    425   -527    314    -95      8 
+   147   -614     89    129     93   -121     12    160    113    217    108    144    144    111    125    447   -241    332    -81     22 
+--------------------------------------------------------------------------------
+
+--------------------------------------------------------------------------------
+	Motif 1 position-specific probability matrix
+--------------------------------------------------------------------------------
+letter-probability matrix: alength= 20 w= 11 nsites= 25 E= 2.4e-011 
+ 0.240000  0.000000  0.000000  0.000000  0.000000  0.680000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.080000  0.000000  0.000000  0.000000 
+ 0.280000  0.000000  0.000000  0.000000  0.000000  0.680000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.040000  0.000000  0.000000  0.000000 
+ 0.160000  0.320000  0.000000  0.000000  0.000000  0.360000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.160000  0.000000  0.000000  0.000000 
+ 0.320000  0.000000  0.000000  0.000000  0.000000  0.640000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.040000  0.000000  0.000000  0.000000 
+ 0.000000  0.000000  0.000000  0.000000  0.000000  0.040000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.960000  0.000000  0.000000  0.000000 
+ 0.960000  0.040000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
+ 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000 
+ 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
+ 0.760000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.240000  0.000000  0.000000  0.000000 
+ 0.960000  0.040000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
+ 0.840000  0.000000  0.000000  0.000000  0.000000  0.120000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.040000  0.000000  0.000000  0.000000 
+--------------------------------------------------------------------------------
+
+--------------------------------------------------------------------------------
+	Motif 1 regular expression
+--------------------------------------------------------------------------------
+[GA][GA][GC][GA]TATA[AT]AA
+--------------------------------------------------------------------------------
+
+
+
+
+Time
+
+********************************************************************************
+
+
+********************************************************************************
+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:
+
+********************************************************************************
diff -r e85346ab5054 -r 4df8e9f58a53 test-data/meme_output_txt_2.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/meme_output_txt_2.txt	Wed Jul 06 10:25:06 2016 -0400
@@ -0,0 +1,319 @@
+********************************************************************************
+MEME - Motif discovery tool
+********************************************************************************
+MEME version 4.11.0 (Release date: Thu Nov 26 17:48:49 2015 +1000)
+
+For further information on how to interpret these results or to get
+a copy of the MEME software please access http://meme-suite.org .
+
+This file may be used as input to the MAST algorithm for searching
+sequence databases for matches to groups of motifs.  MAST is available
+for interactive use and downloading at http://meme-suite.org .
+********************************************************************************
+
+
+********************************************************************************
+REFERENCE
+********************************************************************************
+If you use this program in your research, please cite:
+
+Timothy L. Bailey and Charles Elkan,
+"Fitting a mixture model by expectation maximization to discover
+motifs in biopolymers", Proceedings of the Second International
+Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
+AAAI Press, Menlo Park, California, 1994.
+********************************************************************************
+
+
+********************************************************************************
+TRAINING SET
+********************************************************************************
+DATAFILE= Galaxy_FASTA_Input
+ALPHABET= ACGT
+Sequence name            Weight Length  Sequence name            Weight Length  
+-------------            ------ ------  -------------            ------ ------  
+chr21_19617074_19617124_ 1.0000     50  chr21_26934381_26934431_ 1.0000     50  
+chr21_28217753_28217803_ 1.0000     50  chr21_31710037_31710087_ 1.0000     50  
+chr21_31744582_31744632_ 1.0000     50  chr21_31768316_31768366_ 1.0000     50  
+chr21_31914206_31914256_ 1.0000     50  chr21_31933633_31933683_ 1.0000     50  
+chr21_31962741_31962791_ 1.0000     50  chr21_31964683_31964733_ 1.0000     50  
+chr21_31973364_31973414_ 1.0000     50  chr21_31992870_31992920_ 1.0000     50  
+chr21_32185595_32185645_ 1.0000     50  chr21_32202076_32202126_ 1.0000     50  
+chr21_32253899_32253949_ 1.0000     50  chr21_32410820_32410870_ 1.0000     50  
+chr21_36411748_36411798_ 1.0000     50  chr21_37838750_37838800_ 1.0000     50  
+chr21_45705687_45705737_ 1.0000     50  chr21_45971413_45971463_ 1.0000     50  
+chr21_45978668_45978718_ 1.0000     50  chr21_45993530_45993580_ 1.0000     50  
+chr21_46020421_46020471_ 1.0000     50  chr21_46031920_46031970_ 1.0000     50  
+chr21_46046964_46047014_ 1.0000     50  chr21_46057197_46057247_ 1.0000     50  
+chr21_46086869_46086919_ 1.0000     50  chr21_46102103_46102153_ 1.0000     50  
+chr21_47517957_47518007_ 1.0000     50  chr21_47575506_47575556_ 1.0000     50  
+********************************************************************************
+
+********************************************************************************
+COMMAND LINE SUMMARY
+********************************************************************************
+This information can also be useful in the event you wish to report a
+problem with the MEME software.
+
+command: meme 
+
+model:  mod=         zoops    nmotifs=         1    evt=           inf
+object function=  E-value of product of p-values
+width:  minw=            8    maxw=           50
+width:  wg=             11    ws=              1    endgaps=       yes
+nsites: minsites=        2    maxsites=       30    wnsites=       0.8
+theta:  spmap=         uni    spfuzz=        0.5
+global: substring=     yes    branching=      no    wbranch=        no
+em:     prior=   dirichlet    b=            0.01    maxiter=        50
+        distance=    0.001
+data:   n=            1500    N=              30    shuffle=        -1
+strands: +
+sample: seed=            0    ctfrac=         -1    maxwords=       -1
+Dirichlet mixture priors file:
+Letter frequencies in dataset:
+A 0.294 C 0.231 G 0.257 T 0.217 
+Background letter frequencies (from dataset with add-one prior applied):
+A 0.294 C 0.231 G 0.257 T 0.217 
+********************************************************************************
+
+
+********************************************************************************
+MOTIF  1 MEME	width =  11  sites =  30  llr = 254  E-value = 5.1e-040
+********************************************************************************
+--------------------------------------------------------------------------------
+	Motif 1 Description
+--------------------------------------------------------------------------------
+Simplified        A  3313:9:a798
+pos.-specific     C  1:3::1:::1:
+probability       G  6756::::::2
+matrix            T  1:11a1a:3::
+
+         bits    2.2       *    
+                 2.0     * *    
+                 1.8     * *    
+                 1.5     * ** * 
+Relative         1.3     * ** * 
+Entropy          1.1     ****** 
+(12.2 bits)      0.9  *  *******
+                 0.7  *  *******
+                 0.4 ** ********
+                 0.2 ***********
+                 0.0 -----------
+
+Multilevel           GGGGTATAAAA
+consensus            AACA    T  
+sequence                        
+                                
+--------------------------------------------------------------------------------
+
+--------------------------------------------------------------------------------
+	Motif 1 sites sorted by position p-value
+--------------------------------------------------------------------------------
+Sequence name             Start   P-value               Site  
+-------------             ----- ---------            -----------
+chr21_46046964_46047014_     13  4.51e-07 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC
+chr21_46031920_46031970_     16  2.22e-06 ATACCCAGGG AGGGTATAAAA CCTCAGCAGC
+chr21_32202076_32202126_     14  2.74e-06 CCACCAGCTT GAGGTATAAAA AGCCCTGTAC
+chr21_46057197_46057247_     37  4.86e-06 ACAGGCCCTG GGCATATAAAA GCC       
+chr21_45993530_45993580_      8  4.86e-06    CCAAGGA GGAGTATAAAA GCCCCACAAA
+chr21_45971413_45971463_     10  4.86e-06  CAGGCCCTG GGCATATAAAA GCCCCAGCAG
+chr21_31964683_31964733_     14  4.86e-06 GATTCACTGA GGCATATAAAA GGCCCTCTGC
+chr21_47517957_47518007_     33  6.48e-06 CCGGCGGGGC GGGGTATAAAG GGGGCGG   
+chr21_45978668_45978718_      5  6.48e-06       CAGA GGGGTATAAAG GTTCCGACCA
+chr21_32185595_32185645_     19  6.48e-06 CACCAGAGCT GGGATATATAA AGAAGGTTCT
+chr21_32410820_32410870_     22  1.38e-05 AATCACTGAG GATGTATAAAA GTCCCAGGGA
+chr21_31992870_31992920_     17  1.38e-05 CACTATTGAA GATGTATAAAA TTTCATTTGC
+chr21_19617074_19617124_     40  1.41e-05 CCTCGGGACG TGGGTATATAA           
+chr21_31914206_31914256_     16  1.61e-05 CCCACTACTT AGAGTATAAAA TCATTCTGAG
+chr21_46020421_46020471_      3  1.95e-05         GA GACATATAAAA GCCAACATCC
+chr21_32253899_32253949_     18  1.95e-05 CCCACCAGCA AGGATATATAA AAGCTCAGGA
+chr21_45705687_45705737_     38  2.16e-05 CGTGGTCGCG GGGGTATAACA GC        
+chr21_47575506_47575556_     31  3.04e-05 GCTGCCGGTG AGCGTATAAAG GCCCTGGCG 
+chr21_31744582_31744632_     13  3.04e-05 CAGGTCTAAG AGCATATATAA CTTGGAGTCC
+chr21_31768316_31768366_      1  3.67e-05          . AACGTATATAA ATGGTCCTGT
+chr21_26934381_26934431_     28  3.93e-05 AGTCACAAGT GAGTTATAAAA GGGTCGCACG
+chr21_31933633_31933683_      5  5.65e-05       TCAG AGTATATATAA ATGTTCCTGT
+chr21_31710037_31710087_     15  6.24e-05 CCCAGGTTTC TGAGTATATAA TCGCCGCACC
+chr21_36411748_36411798_     23  7.15e-05 AGTTTCAGTT GGCATCtaaaa attatataac
+chr21_46102103_46102153_     37  1.39e-04 TGCCTGGGTC CAGGTATAAAG GCT       
+chr21_46086869_46086919_     38  1.39e-04 TGCCTGGGCC CAGGTATAAAG GC        
+chr21_37838750_37838800_      3  4.81e-04         ga tggttttataa ggggcctcac
+chr21_31962741_31962791_     14  8.57e-04 TATAACTCAG GTTGGATAAAA TAATTTGTAC
+chr21_31973364_31973414_      8  1.47e-03    aaactta aaactctataa acttaaaact
+chr21_28217753_28217803_     27  2.64e-03 GGTGGGGGTG GGGGTTTCACT GGTCCACTAT
+--------------------------------------------------------------------------------
+
+--------------------------------------------------------------------------------
+	Motif 1 block diagrams
+--------------------------------------------------------------------------------
+SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
+-------------            ----------------  -------------
+chr21_46046964_46047014_          4.5e-07  12_[+1]_27
+chr21_46031920_46031970_          2.2e-06  15_[+1]_24
+chr21_32202076_32202126_          2.7e-06  13_[+1]_26
+chr21_46057197_46057247_          4.9e-06  36_[+1]_3
+chr21_45993530_45993580_          4.9e-06  7_[+1]_32
+chr21_45971413_45971463_          4.9e-06  9_[+1]_30
+chr21_31964683_31964733_          4.9e-06  13_[+1]_26
+chr21_47517957_47518007_          6.5e-06  32_[+1]_7
+chr21_45978668_45978718_          6.5e-06  4_[+1]_35
+chr21_32185595_32185645_          6.5e-06  18_[+1]_21
+chr21_32410820_32410870_          1.4e-05  21_[+1]_18
+chr21_31992870_31992920_          1.4e-05  16_[+1]_23
+chr21_19617074_19617124_          1.4e-05  39_[+1]
+chr21_31914206_31914256_          1.6e-05  15_[+1]_24
+chr21_46020421_46020471_          1.9e-05  2_[+1]_37
+chr21_32253899_32253949_          1.9e-05  17_[+1]_22
+chr21_45705687_45705737_          2.2e-05  37_[+1]_2
+chr21_47575506_47575556_            3e-05  30_[+1]_9
+chr21_31744582_31744632_            3e-05  12_[+1]_27
+chr21_31768316_31768366_          3.7e-05  [+1]_39
+chr21_26934381_26934431_          3.9e-05  27_[+1]_12
+chr21_31933633_31933683_          5.6e-05  4_[+1]_35
+chr21_31710037_31710087_          6.2e-05  14_[+1]_25
+chr21_36411748_36411798_          7.1e-05  22_[+1]_17
+chr21_46102103_46102153_          0.00014  36_[+1]_3
+chr21_46086869_46086919_          0.00014  37_[+1]_2
+chr21_37838750_37838800_          0.00048  2_[+1]_37
+chr21_31962741_31962791_          0.00086  13_[+1]_26
+chr21_31973364_31973414_           0.0015  7_[+1]_32
+chr21_28217753_28217803_           0.0026  26_[+1]_13
+--------------------------------------------------------------------------------
+
+--------------------------------------------------------------------------------
+	Motif 1 in BLOCKS format
+--------------------------------------------------------------------------------
+BL   MOTIF 1 width=11 seqs=30
+chr21_46046964_46047014_ (   13) GGGGTATAAAA  1 
+chr21_46031920_46031970_ (   16) AGGGTATAAAA  1 
+chr21_32202076_32202126_ (   14) GAGGTATAAAA  1 
+chr21_46057197_46057247_ (   37) GGCATATAAAA  1 
+chr21_45993530_45993580_ (    8) GGAGTATAAAA  1 
+chr21_45971413_45971463_ (   10) GGCATATAAAA  1 
+chr21_31964683_31964733_ (   14) GGCATATAAAA  1 
+chr21_47517957_47518007_ (   33) GGGGTATAAAG  1 
+chr21_45978668_45978718_ (    5) GGGGTATAAAG  1 
+chr21_32185595_32185645_ (   19) GGGATATATAA  1 
+chr21_32410820_32410870_ (   22) GATGTATAAAA  1 
+chr21_31992870_31992920_ (   17) GATGTATAAAA  1 
+chr21_19617074_19617124_ (   40) TGGGTATATAA  1 
+chr21_31914206_31914256_ (   16) AGAGTATAAAA  1 
+chr21_46020421_46020471_ (    3) GACATATAAAA  1 
+chr21_32253899_32253949_ (   18) AGGATATATAA  1 
+chr21_45705687_45705737_ (   38) GGGGTATAACA  1 
+chr21_47575506_47575556_ (   31) AGCGTATAAAG  1 
+chr21_31744582_31744632_ (   13) AGCATATATAA  1 
+chr21_31768316_31768366_ (    1) AACGTATATAA  1 
+chr21_26934381_26934431_ (   28) GAGTTATAAAA  1 
+chr21_31933633_31933683_ (    5) AGTATATATAA  1 
+chr21_31710037_31710087_ (   15) TGAGTATATAA  1 
+chr21_36411748_36411798_ (   23) GGCATCTAAAA  1 
+chr21_46102103_46102153_ (   37) CAGGTATAAAG  1 
+chr21_46086869_46086919_ (   38) CAGGTATAAAG  1 
+chr21_37838750_37838800_ (    3) TGGTTTTATAA  1 
+chr21_31962741_31962791_ (   14) GTTGGATAAAA  1 
+chr21_31973364_31973414_ (    8) AAACTCTATAA  1 
+chr21_28217753_28217803_ (   27) GGGGTTTCACT  1 
+//
+
+--------------------------------------------------------------------------------
+
+--------------------------------------------------------------------------------
+	Motif 1 position-specific scoring matrix
+--------------------------------------------------------------------------------
+log-odds matrix: alength= 4 w= 11 n= 1200 bayes= 5.2854 E= 5.1e-040 
+   -14   -179    114   -112 
+     3  -1155    137   -270 
+  -114     20     86    -71 
+     3   -279    122   -170 
+ -1155  -1155   -295    215 
+   156   -179  -1155   -170 
+ -1155  -1155  -1155    220 
+   172   -279  -1155  -1155 
+   125  -1155  -1155     46 
+   167   -179  -1155  -1155 
+   144  -1155    -63   -270 
+--------------------------------------------------------------------------------
+
+--------------------------------------------------------------------------------
+	Motif 1 position-specific probability matrix
+--------------------------------------------------------------------------------
+letter-probability matrix: alength= 4 w= 11 nsites= 30 E= 5.1e-040 
+ 0.266667  0.066667  0.566667  0.100000 
+ 0.300000  0.000000  0.666667  0.033333 
+ 0.133333  0.266667  0.466667  0.133333 
+ 0.300000  0.033333  0.600000  0.066667 
+ 0.000000  0.000000  0.033333  0.966667 
+ 0.866667  0.066667  0.000000  0.066667 
+ 0.000000  0.000000  0.000000  1.000000 
+ 0.966667  0.033333  0.000000  0.000000 
+ 0.700000  0.000000  0.000000  0.300000 
+ 0.933333  0.066667  0.000000  0.000000 
+ 0.800000  0.000000  0.166667  0.033333 
+--------------------------------------------------------------------------------
+
+--------------------------------------------------------------------------------
+	Motif 1 regular expression
+--------------------------------------------------------------------------------
+[GA][GA][GC][GA]TATA[AT]AA
+--------------------------------------------------------------------------------
+
+
+
+
+Time  
+
+********************************************************************************
+
+
+********************************************************************************
+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:
+
+********************************************************************************
diff -r e85346ab5054 -r 4df8e9f58a53 test-data/meme_output_xml_2.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/meme_output_xml_2.xml	Wed Jul 06 10:25:06 2016 -0400
@@ -0,0 +1,977 @@
+<?xml version='1.0' encoding='UTF-8' standalone='yes'?>
+<!-- Document definition -->
+<!DOCTYPE MEME[
+<!ELEMENT MEME (
+  training_set,
+  model, 
+  motifs, 
+  scanned_sites_summary?
+)>
+<!ATTLIST MEME 
+  version CDATA #REQUIRED
+  release CDATA #REQUIRED
+>
+<!-- Training-set elements -->
+<!ELEMENT training_set (alphabet, ambigs, sequence*, letter_frequencies)>
+<!ATTLIST training_set datafile CDATA #REQUIRED length CDATA #REQUIRED>
+<!ELEMENT alphabet (letter*)>
+<!ATTLIST alphabet name CDATA #REQUIRED>
+<!ELEMENT ambigs (letter*)>
+<!ELEMENT letter EMPTY>
+<!ATTLIST letter id ID #REQUIRED>
+<!ATTLIST letter symbol CDATA #REQUIRED>
+<!ATTLIST letter equals CDATA #IMPLIED>
+<!ATTLIST letter aliases CDATA #IMPLIED>
+<!ATTLIST letter complement CDATA #IMPLIED>
+<!ATTLIST letter name CDATA #IMPLIED>
+<!ATTLIST letter colour CDATA #IMPLIED>
+<!ELEMENT sequence EMPTY>
+<!ATTLIST sequence id ID #REQUIRED
+                   name CDATA #REQUIRED
+                   length CDATA #REQUIRED
+                   weight CDATA #REQUIRED
+>
+<!ELEMENT letter_frequencies (alphabet_array)>
+
+<!-- Model elements -->
+<!ELEMENT model (
+  command_line,
+  host,
+  type,
+  nmotifs,
+  evalue_threshold,
+  object_function,
+  min_width,
+  max_width,
+  minic,
+  wg,
+  ws,
+  endgaps,
+  minsites,
+  maxsites,
+  wnsites,
+  prob,
+  spmap,
+  spfuzz,
+  prior,
+  beta,
+  maxiter,
+  distance,
+  num_sequences,
+  num_positions,
+  seed,
+  seqfrac,
+  strands,
+  priors_file,
+  reason_for_stopping,
+  background_frequencies
+)>
+<!ELEMENT command_line (#PCDATA)*>
+<!ELEMENT host (#PCDATA)*>
+<!ELEMENT type (#PCDATA)*>
+<!ELEMENT nmotifs (#PCDATA)*>
+<!ELEMENT evalue_threshold (#PCDATA)*>
+<!ELEMENT object_function (#PCDATA)*>
+<!ELEMENT min_width (#PCDATA)*>
+<!ELEMENT max_width (#PCDATA)*>
+<!ELEMENT minic (#PCDATA)*>
+<!ELEMENT wg (#PCDATA)*>
+<!ELEMENT ws (#PCDATA)*>
+<!ELEMENT endgaps (#PCDATA)*>
+<!ELEMENT minsites (#PCDATA)*>
+<!ELEMENT maxsites (#PCDATA)*>
+<!ELEMENT wnsites (#PCDATA)*>
+<!ELEMENT prob (#PCDATA)*>
+<!ELEMENT spmap (#PCDATA)*>
+<!ELEMENT spfuzz (#PCDATA)*>
+<!ELEMENT prior (#PCDATA)*>
+<!ELEMENT beta (#PCDATA)*>
+<!ELEMENT maxiter (#PCDATA)*>
+<!ELEMENT distance (#PCDATA)*>
+<!ELEMENT num_sequences (#PCDATA)*>
+<!ELEMENT num_positions (#PCDATA)*>
+<!ELEMENT seed (#PCDATA)*>
+<!ELEMENT seqfrac (#PCDATA)*>
+<!ELEMENT strands (#PCDATA)*>
+<!ELEMENT priors_file (#PCDATA)*>
+<!ELEMENT reason_for_stopping (#PCDATA)*>
+<!ELEMENT background_frequencies (alphabet_array)>
+<!ATTLIST background_frequencies source CDATA #REQUIRED>
+
+<!-- Motif elements -->
+<!ELEMENT motifs (motif*)>
+<!ELEMENT motif (scores, probabilities, regular_expression?, contributing_sites)>
+<!ATTLIST motif id ID #REQUIRED
+                name CDATA #REQUIRED
+                width CDATA #REQUIRED
+                sites CDATA #REQUIRED
+                llr CDATA #REQUIRED
+                ic CDATA #REQUIRED
+                re CDATA #REQUIRED
+                bayes_threshold CDATA #REQUIRED
+                e_value CDATA #REQUIRED
+                elapsed_time CDATA #REQUIRED
+                url CDATA ""
+>
+<!ELEMENT scores (alphabet_matrix)>
+<!ELEMENT probabilities (alphabet_matrix)>
+<!ELEMENT regular_expression (#PCDATA)*>
+
+<!-- Contributing site elements -->
+<!-- Contributing sites are motif occurences found during the motif discovery phase -->
+<!ELEMENT contributing_sites (contributing_site*)>
+<!ELEMENT contributing_site (left_flank, site, right_flank)>
+<!ATTLIST contributing_site sequence_id IDREF #REQUIRED
+                          position CDATA #REQUIRED
+                          strand (plus|minus|none) 'none'
+                          pvalue CDATA #REQUIRED
+>
+<!-- The left_flank contains the sequence for 10 bases to the left of the motif start -->
+<!ELEMENT left_flank (#PCDATA)>
+<!-- The site contains the sequence for the motif instance -->
+<!ELEMENT site (letter_ref*)>
+<!-- The right_flank contains the sequence for 10 bases to the right of the motif end -->
+<!ELEMENT right_flank (#PCDATA)>
+
+<!-- Scanned site elements -->
+<!-- Scanned sites are motif occurences found during the sequence scan phase -->
+<!ELEMENT scanned_sites_summary (scanned_sites*)>
+<!ATTLIST scanned_sites_summary p_thresh CDATA #REQUIRED>
+<!ELEMENT scanned_sites (scanned_site*)>
+<!ATTLIST scanned_sites sequence_id IDREF #REQUIRED
+                        pvalue CDATA #REQUIRED
+                        num_sites CDATA #REQUIRED>
+<!ELEMENT scanned_site EMPTY>
+<!ATTLIST scanned_site  motif_id IDREF #REQUIRED
+                        strand (plus|minus|none) 'none'
+                        position CDATA #REQUIRED
+                        pvalue CDATA #REQUIRED>
+
+<!-- Utility elements -->
+<!-- A reference to a letter in the alphabet -->
+<!ELEMENT letter_ref EMPTY>
+<!ATTLIST letter_ref letter_id IDREF #REQUIRED>
+<!-- A alphabet-array contains one floating point value for each letter in an alphabet -->
+<!ELEMENT alphabet_array (value*)>
+<!ELEMENT value (#PCDATA)>
+<!ATTLIST value letter_id IDREF #REQUIRED>
+
+<!-- A alphabet_matrix contains one alphabet_array for each position in a motif -->
+<!ELEMENT alphabet_matrix (alphabet_array*)>
+
+]>
+<!-- Begin document body -->
+<MEME version="4.11.0" release="Thu Nov 26 17:48:49 2015 +1000">
+<training_set datafile="Galaxy_FASTA_Input" length="30">
+<alphabet name="DNA" like="dna">
+<letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/>
+<letter id="C" symbol="C" complement="G" name="Cytosine" colour="0000CC"/>
+<letter id="G" symbol="G" complement="C" name="Guanine" colour="FFB300"/>
+<letter id="T" symbol="T" aliases="U" complement="A" name="Thymine" colour="008000"/>
+<letter id="N" symbol="N" aliases="X." equals="ACGT" name="Any base"/>
+<letter id="V" symbol="V" equals="ACG" name="Not T"/>
+<letter id="H" symbol="H" equals="ACT" name="Not G"/>
+<letter id="D" symbol="D" equals="AGT" name="Not C"/>
+<letter id="B" symbol="B" equals="CGT" name="Not A"/>
+<letter id="M" symbol="M" equals="AC" name="Amino"/>
+<letter id="R" symbol="R" equals="AG" name="Purine"/>
+<letter id="W" symbol="W" equals="AT" name="Weak"/>
+<letter id="S" symbol="S" equals="CG" name="Strong"/>
+<letter id="Y" symbol="Y" equals="CT" name="Pyrimidine"/>
+<letter id="K" symbol="K" equals="GT" name="Keto"/>
+</alphabet>
+<sequence id="sequence_0" name="chr21_19617074_19617124_+" length="50" weight="1.000000" />
+<sequence id="sequence_1" name="chr21_26934381_26934431_+" length="50" weight="1.000000" />
+<sequence id="sequence_2" name="chr21_28217753_28217803_-" length="50" weight="1.000000" />
+<sequence id="sequence_3" name="chr21_31710037_31710087_-" length="50" weight="1.000000" />
+<sequence id="sequence_4" name="chr21_31744582_31744632_-" length="50" weight="1.000000" />
+<sequence id="sequence_5" name="chr21_31768316_31768366_+" length="50" weight="1.000000" />
+<sequence id="sequence_6" name="chr21_31914206_31914256_-" length="50" weight="1.000000" />
+<sequence id="sequence_7" name="chr21_31933633_31933683_-" length="50" weight="1.000000" />
+<sequence id="sequence_8" name="chr21_31962741_31962791_-" length="50" weight="1.000000" />
+<sequence id="sequence_9" name="chr21_31964683_31964733_+" length="50" weight="1.000000" />
+<sequence id="sequence_10" name="chr21_31973364_31973414_+" length="50" weight="1.000000" />
+<sequence id="sequence_11" name="chr21_31992870_31992920_+" length="50" weight="1.000000" />
+<sequence id="sequence_12" name="chr21_32185595_32185645_-" length="50" weight="1.000000" />
+<sequence id="sequence_13" name="chr21_32202076_32202126_-" length="50" weight="1.000000" />
+<sequence id="sequence_14" name="chr21_32253899_32253949_-" length="50" weight="1.000000" />
+<sequence id="sequence_15" name="chr21_32410820_32410870_-" length="50" weight="1.000000" />
+<sequence id="sequence_16" name="chr21_36411748_36411798_-" length="50" weight="1.000000" />
+<sequence id="sequence_17" name="chr21_37838750_37838800_-" length="50" weight="1.000000" />
+<sequence id="sequence_18" name="chr21_45705687_45705737_+" length="50" weight="1.000000" />
+<sequence id="sequence_19" name="chr21_45971413_45971463_-" length="50" weight="1.000000" />
+<sequence id="sequence_20" name="chr21_45978668_45978718_-" length="50" weight="1.000000" />
+<sequence id="sequence_21" name="chr21_45993530_45993580_+" length="50" weight="1.000000" />
+<sequence id="sequence_22" name="chr21_46020421_46020471_+" length="50" weight="1.000000" />
+<sequence id="sequence_23" name="chr21_46031920_46031970_+" length="50" weight="1.000000" />
+<sequence id="sequence_24" name="chr21_46046964_46047014_+" length="50" weight="1.000000" />
+<sequence id="sequence_25" name="chr21_46057197_46057247_+" length="50" weight="1.000000" />
+<sequence id="sequence_26" name="chr21_46086869_46086919_-" length="50" weight="1.000000" />
+<sequence id="sequence_27" name="chr21_46102103_46102153_-" length="50" weight="1.000000" />
+<sequence id="sequence_28" name="chr21_47517957_47518007_+" length="50" weight="1.000000" />
+<sequence id="sequence_29" name="chr21_47575506_47575556_-" length="50" weight="1.000000" />
+<letter_frequencies>
+<alphabet_array>
+<value letter_id="A">0.294</value>
+<value letter_id="C">0.231</value>
+<value letter_id="G">0.257</value>
+<value letter_id="T">0.217</value>
+</alphabet_array>
+</letter_frequencies>
+</training_set>
+<model>
+<command_line>meme /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2490.dat -o /Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1929/dataset_2578_files -nostatus -sf Galaxy_FASTA_Input -dna -mod zoops -nmotifs 1 -wnsites 0.8 -minw 8 -maxw 50 -wg 11 -ws 1 -maxiter 50 -distance 0.001 -prior dirichlet -b 0.01 -plib /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2577.dat -spmap uni -spfuzz 0.5 </command_line>
+<host>MacBook-Pro-2.local</host>
+<type>zoops</type>
+<nmotifs>1</nmotifs>
+<evalue_threshold>inf</evalue_threshold>
+<object_function>E-value of product of p-values</object_function>
+<use_llr>0</use_llr>
+<min_width>8</min_width>
+<max_width>50</max_width>
+<wg>11</wg>
+<ws>1</ws>
+<endgaps>yes</endgaps>
+<substring>yes</substring>
+<minsites>2</minsites>
+<maxsites>30</maxsites>
+<wnsites>0.8</wnsites>
+<spmap>uni</spmap>
+<spfuzz>0.5</spfuzz>
+<prior>dirichlet</prior>
+<beta>0.01</beta>
+<maxiter>50</maxiter>
+<distance>0.001</distance>
+<num_sequences>30</num_sequences>
+<num_positions>1500</num_positions>
+<seed>0</seed>
+<ctfrac>-1</ctfrac>
+<maxwords>-1</maxwords>
+<strands>forward</strands>
+<priors_file>dataset_2577.dat</priors_file>
+<reason_for_stopping>Stopped because requested number of motifs (1) found.</reason_for_stopping>
+<background_frequencies source="dataset with add-one prior applied">
+<alphabet_array>
+<value letter_id="A">0.294</value>
+<value letter_id="C">0.231</value>
+<value letter_id="G">0.257</value>
+<value letter_id="T">0.217</value>
+</alphabet_array>
+</background_frequencies>
+</model>
+<motifs>
+<motif id="motif_1" name="1" width="11" sites="30" ic="13.0" re="12.2" llr="254" e_value="5.1e-040" bayes_threshold="5.2854" elapsed_time="0.168106">
+<scores>
+<alphabet_matrix>
+<alphabet_array>
+<value letter_id="A">-14</value>
+<value letter_id="C">-179</value>
+<value letter_id="G">114</value>
+<value letter_id="T">-112</value>
+</alphabet_array>
+<alphabet_array>
+<value letter_id="A">3</value>
+<value letter_id="C">-1155</value>
+<value letter_id="G">137</value>
+<value letter_id="T">-270</value>
+</alphabet_array>
+<alphabet_array>
+<value letter_id="A">-114</value>
+<value letter_id="C">20</value>
+<value letter_id="G">86</value>
+<value letter_id="T">-71</value>
+</alphabet_array>
+<alphabet_array>
+<value letter_id="A">3</value>
+<value letter_id="C">-279</value>
+<value letter_id="G">122</value>
+<value letter_id="T">-170</value>
+</alphabet_array>
+<alphabet_array>
+<value letter_id="A">-1155</value>
+<value letter_id="C">-1155</value>
+<value letter_id="G">-295</value>
+<value letter_id="T">215</value>
+</alphabet_array>
+<alphabet_array>
+<value letter_id="A">156</value>
+<value letter_id="C">-179</value>
+<value letter_id="G">-1155</value>
+<value letter_id="T">-170</value>
+</alphabet_array>
+<alphabet_array>
+<value letter_id="A">-1155</value>
+<value letter_id="C">-1155</value>
+<value letter_id="G">-1155</value>
+<value letter_id="T">220</value>
+</alphabet_array>
+<alphabet_array>
+<value letter_id="A">172</value>
+<value letter_id="C">-279</value>
+<value letter_id="G">-1155</value>
+<value letter_id="T">-1155</value>
+</alphabet_array>
+<alphabet_array>
+<value letter_id="A">125</value>
+<value letter_id="C">-1155</value>
+<value letter_id="G">-1155</value>
+<value letter_id="T">46</value>
+</alphabet_array>
+<alphabet_array>
+<value letter_id="A">167</value>
+<value letter_id="C">-179</value>
+<value letter_id="G">-1155</value>
+<value letter_id="T">-1155</value>
+</alphabet_array>
+<alphabet_array>
+<value letter_id="A">144</value>
+<value letter_id="C">-1155</value>
+<value letter_id="G">-63</value>
+<value letter_id="T">-270</value>
+</alphabet_array>
+</alphabet_matrix>
+</scores>
+<probabilities>
+<alphabet_matrix>
+<alphabet_array>
+<value letter_id="A">0.266667</value>
+<value letter_id="C">0.066667</value>
+<value letter_id="G">0.566667</value>
+<value letter_id="T">0.100000</value>
+</alphabet_array>
+<alphabet_array>
+<value letter_id="A">0.300000</value>
+<value letter_id="C">0.000000</value>
+<value letter_id="G">0.666667</value>
+<value letter_id="T">0.033333</value>
+</alphabet_array>
+<alphabet_array>
+<value letter_id="A">0.133333</value>
+<value letter_id="C">0.266667</value>
+<value letter_id="G">0.466667</value>
+<value letter_id="T">0.133333</value>
+</alphabet_array>
+<alphabet_array>
+<value letter_id="A">0.300000</value>
+<value letter_id="C">0.033333</value>
+<value letter_id="G">0.600000</value>
+<value letter_id="T">0.066667</value>
+</alphabet_array>
+<alphabet_array>
+<value letter_id="A">0.000000</value>
+<value letter_id="C">0.000000</value>
+<value letter_id="G">0.033333</value>
+<value letter_id="T">0.966667</value>
+</alphabet_array>
+<alphabet_array>
+<value letter_id="A">0.866667</value>
+<value letter_id="C">0.066667</value>
+<value letter_id="G">0.000000</value>
+<value letter_id="T">0.066667</value>
+</alphabet_array>
+<alphabet_array>
+<value letter_id="A">0.000000</value>
+<value letter_id="C">0.000000</value>
+<value letter_id="G">0.000000</value>
+<value letter_id="T">1.000000</value>
+</alphabet_array>
+<alphabet_array>
+<value letter_id="A">0.966667</value>
+<value letter_id="C">0.033333</value>
+<value letter_id="G">0.000000</value>
+<value letter_id="T">0.000000</value>
+</alphabet_array>
+<alphabet_array>
+<value letter_id="A">0.700000</value>
+<value letter_id="C">0.000000</value>
+<value letter_id="G">0.000000</value>
+<value letter_id="T">0.300000</value>
+</alphabet_array>
+<alphabet_array>
+<value letter_id="A">0.933333</value>
+<value letter_id="C">0.066667</value>
+<value letter_id="G">0.000000</value>
+<value letter_id="T">0.000000</value>
+</alphabet_array>
+<alphabet_array>
+<value letter_id="A">0.800000</value>
+<value letter_id="C">0.000000</value>
+<value letter_id="G">0.166667</value>
+<value letter_id="T">0.033333</value>
+</alphabet_array>
+</alphabet_matrix>
+</probabilities>
+<regular_expression>
+[GA][GA][GC][GA]TATA[AT]AA
+</regular_expression>
+<contributing_sites>
+<contributing_site sequence_id="sequence_24" position="12" strand="plus" pvalue="4.51e-07" >
+<left_flank>AAGGCCAGGA</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>GCCTGAGAGC</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_23" position="15" strand="plus" pvalue="2.22e-06" >
+<left_flank>ATACCCAGGG</left_flank>
+<site>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>CCTCAGCAGC</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_13" position="13" strand="plus" pvalue="2.74e-06" >
+<left_flank>CCACCAGCTT</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>AGCCCTGTAC</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_25" position="36" strand="plus" pvalue="4.86e-06" >
+<left_flank>ACAGGCCCTG</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>GCC</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_21" position="7" strand="plus" pvalue="4.86e-06" >
+<left_flank>CCAAGGA</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>GCCCCACAAA</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_19" position="9" strand="plus" pvalue="4.86e-06" >
+<left_flank>CAGGCCCTG</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>GCCCCAGCAG</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_9" position="13" strand="plus" pvalue="4.86e-06" >
+<left_flank>GATTCACTGA</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>GGCCCTCTGC</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_28" position="32" strand="plus" pvalue="6.48e-06" >
+<left_flank>CCGGCGGGGC</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+</site>
+<right_flank>GGGGCGG</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_20" position="4" strand="plus" pvalue="6.48e-06" >
+<left_flank>CAGA</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+</site>
+<right_flank>GTTCCGACCA</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_12" position="18" strand="plus" pvalue="6.48e-06" >
+<left_flank>CACCAGAGCT</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>AGAAGGTTCT</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_15" position="21" strand="plus" pvalue="1.38e-05" >
+<left_flank>AATCACTGAG</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>GTCCCAGGGA</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_11" position="16" strand="plus" pvalue="1.38e-05" >
+<left_flank>CACTATTGAA</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>TTTCATTTGC</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_0" position="39" strand="plus" pvalue="1.41e-05" >
+<left_flank>CCTCGGGACG</left_flank>
+<site>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank></right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_6" position="15" strand="plus" pvalue="1.61e-05" >
+<left_flank>CCCACTACTT</left_flank>
+<site>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>TCATTCTGAG</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_22" position="2" strand="plus" pvalue="1.95e-05" >
+<left_flank>GA</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>GCCAACATCC</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_14" position="17" strand="plus" pvalue="1.95e-05" >
+<left_flank>CCCACCAGCA</left_flank>
+<site>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>AAGCTCAGGA</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_18" position="37" strand="plus" pvalue="2.16e-05" >
+<left_flank>CGTGGTCGCG</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>GC</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_29" position="30" strand="plus" pvalue="3.04e-05" >
+<left_flank>GCTGCCGGTG</left_flank>
+<site>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+</site>
+<right_flank>GCCCTGGCG</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_4" position="12" strand="plus" pvalue="3.04e-05" >
+<left_flank>CAGGTCTAAG</left_flank>
+<site>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>CTTGGAGTCC</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_5" position="0" strand="plus" pvalue="3.67e-05" >
+<left_flank></left_flank>
+<site>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>ATGGTCCTGT</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_1" position="27" strand="plus" pvalue="3.93e-05" >
+<left_flank>AGTCACAAGT</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>GGGTCGCACG</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_7" position="4" strand="plus" pvalue="5.65e-05" >
+<left_flank>TCAG</left_flank>
+<site>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>ATGTTCCTGT</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_3" position="14" strand="plus" pvalue="6.24e-05" >
+<left_flank>CCCAGGTTTC</left_flank>
+<site>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>TCGCCGCACC</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_16" position="22" strand="plus" pvalue="7.15e-05" >
+<left_flank>AGTTTCAGTT</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>attatataac</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_27" position="36" strand="plus" pvalue="1.39e-04" >
+<left_flank>TGCCTGGGTC</left_flank>
+<site>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+</site>
+<right_flank>GCT</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_26" position="37" strand="plus" pvalue="1.39e-04" >
+<left_flank>TGCCTGGGCC</left_flank>
+<site>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+</site>
+<right_flank>GC</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_17" position="2" strand="plus" pvalue="4.81e-04" >
+<left_flank>ga</left_flank>
+<site>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>ggggcctcac</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_8" position="13" strand="plus" pvalue="8.57e-04" >
+<left_flank>TATAACTCAG</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>TAATTTGTAC</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_10" position="7" strand="plus" pvalue="1.47e-03" >
+<left_flank>aaactta</left_flank>
+<site>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>acttaaaact</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_2" position="26" strand="plus" pvalue="2.64e-03" >
+<left_flank>GGTGGGGGTG</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="T"/>
+</site>
+<right_flank>GGTCCACTAT</right_flank>
+</contributing_site>
+</contributing_sites>
+</motif>
+</motifs>
+<scanned_sites_summary p_thresh="0.0001">
+<scanned_sites sequence_id="sequence_0" pvalue="5.63e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="39" pvalue="1.41e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_1" pvalue="1.57e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="27" pvalue="3.93e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_2" pvalue="1.00e-01" num_sites="0"></scanned_sites>
+<scanned_sites sequence_id="sequence_3" pvalue="2.49e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="14" pvalue="6.24e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_4" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="12" pvalue="3.04e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_5" pvalue="1.47e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="0" pvalue="3.67e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_6" pvalue="6.45e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="15" pvalue="1.61e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_7" pvalue="2.26e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="4" pvalue="5.65e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_8" pvalue="3.37e-02" num_sites="0"></scanned_sites>
+<scanned_sites sequence_id="sequence_9" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="13" pvalue="4.86e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_10" pvalue="5.73e-02" num_sites="0"></scanned_sites>
+<scanned_sites sequence_id="sequence_11" pvalue="5.52e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="16" pvalue="1.38e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_12" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="18" pvalue="6.48e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_13" pvalue="1.10e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="13" pvalue="2.74e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_14" pvalue="7.78e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="17" pvalue="1.95e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_15" pvalue="5.52e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="21" pvalue="1.38e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_16" pvalue="2.85e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="22" pvalue="7.15e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_17" pvalue="1.90e-02" num_sites="0"></scanned_sites>
+<scanned_sites sequence_id="sequence_18" pvalue="8.63e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="37" pvalue="2.16e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_19" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="9" pvalue="4.86e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_20" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="4" pvalue="6.48e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_21" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="7" pvalue="4.86e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_22" pvalue="7.78e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="2" pvalue="1.95e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_23" pvalue="8.89e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="15" pvalue="2.22e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_24" pvalue="1.80e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="12" pvalue="4.51e-07"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_25" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="36" pvalue="4.86e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_26" pvalue="5.54e-03" num_sites="0"></scanned_sites>
+<scanned_sites sequence_id="sequence_27" pvalue="5.54e-03" num_sites="0"></scanned_sites>
+<scanned_sites sequence_id="sequence_28" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="32" pvalue="6.48e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_29" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="30" pvalue="3.04e-05"/>
+</scanned_sites>
+</scanned_sites_summary>
+</MEME>
diff -r e85346ab5054 -r 4df8e9f58a53 test-data/motif1.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif1.gff	Wed Jul 06 10:25:06 2016 -0400
@@ -0,0 +1,100 @@
+##gff-version 3
+phiX174	fimo	polypeptide_motif	1	11	78.3	+	.	Name=1;ID=1-57-phiX174;pvalue=1.46e-08;sequence=GAGTTTTATCG;
+phiX174	fimo	polypeptide_motif	3	13	57.5	+	.	Name=1;ID=1-471-phiX174;pvalue=1.79e-06;sequence=GTTTTATCGCT;
+phiX174	fimo	polypeptide_motif	7	17	 45	+	.	Name=1;ID=1-1378-phiX174;pvalue=3.18e-05;sequence=TATCGCTTCCA;
+phiX174	fimo	polypeptide_motif	10	20	53.9	+	.	Name=1;ID=1-605-phiX174;pvalue=4.1e-06;sequence=CGCTTCCATGA;
+phiX174	fimo	polypeptide_motif	17	27	40.2	+	.	Name=1;ID=1-1887-phiX174;pvalue=9.55e-05;sequence=ATGACGCAGAA;
+phiX174	fimo	polypeptide_motif	18	28	45.3	+	.	Name=1;ID=1-1349-phiX174;pvalue=2.98e-05;sequence=TGACGCAGAAG;
+phiX174	fimo	polypeptide_motif	19	29	55.8	+	.	Name=1;ID=1-527-phiX174;pvalue=2.6e-06;sequence=GACGCAGAAGT;
+phiX174	fimo	polypeptide_motif	21	31	41.5	+	.	Name=1;ID=1-1705-phiX174;pvalue=7.07e-05;sequence=CGCAGAAGTTA;
+phiX174	fimo	polypeptide_motif	22	32	44.6	+	.	Name=1;ID=1-1404-phiX174;pvalue=3.44e-05;sequence=GCAGAAGTTAA;
+phiX174	fimo	polypeptide_motif	24	34	79.1	+	.	Name=1;ID=1-53-phiX174;pvalue=1.23e-08;sequence=AGAAGTTAACA;
+phiX174	fimo	polypeptide_motif	25	35	45.3	+	.	Name=1;ID=1-1347-phiX174;pvalue=2.97e-05;sequence=GAAGTTAACAC;
+phiX174	fimo	polypeptide_motif	26	36	59.2	+	.	Name=1;ID=1-417-phiX174;pvalue=1.19e-06;sequence=AAGTTAACACT;
+phiX174	fimo	polypeptide_motif	30	40	44.7	+	.	Name=1;ID=1-1399-phiX174;pvalue=3.4e-05;sequence=TAACACTTTCG;
+phiX174	fimo	polypeptide_motif	37	47	72.4	+	.	Name=1;ID=1-98-phiX174;pvalue=5.79e-08;sequence=TTCGGATATTT;
+phiX174	fimo	polypeptide_motif	39	49	65.3	+	.	Name=1;ID=1-213-phiX174;pvalue=2.92e-07;sequence=CGGATATTTCT;
+phiX174	fimo	polypeptide_motif	41	51	55.3	+	.	Name=1;ID=1-548-phiX174;pvalue=2.97e-06;sequence=GATATTTCTGA;
+phiX174	fimo	polypeptide_motif	43	53	58.4	+	.	Name=1;ID=1-442-phiX174;pvalue=1.43e-06;sequence=TATTTCTGATG;
+phiX174	fimo	polypeptide_motif	46	56	53.7	+	.	Name=1;ID=1-617-phiX174;pvalue=4.23e-06;sequence=TTCTGATGAGT;
+phiX174	fimo	polypeptide_motif	50	60	45.4	+	.	Name=1;ID=1-1333-phiX174;pvalue=2.86e-05;sequence=GATGAGTCGAA;
+phiX174	fimo	polypeptide_motif	51	61	48.4	+	.	Name=1;ID=1-1094-phiX174;pvalue=1.44e-05;sequence=ATGAGTCGAAA;
+phiX174	fimo	polypeptide_motif	52	62	83.9	+	.	Name=1;ID=1-22-phiX174;pvalue=4.06e-09;sequence=TGAGTCGAAAA;
+phiX174	fimo	polypeptide_motif	53	63	53.9	+	.	Name=1;ID=1-601-phiX174;pvalue=4.03e-06;sequence=GAGTCGAAAAA;
+phiX174	fimo	polypeptide_motif	54	64	62.9	+	.	Name=1;ID=1-297-phiX174;pvalue=5.16e-07;sequence=AGTCGAAAAAT;
+phiX174	fimo	polypeptide_motif	55	65	52.8	+	.	Name=1;ID=1-675-phiX174;pvalue=5.26e-06;sequence=GTCGAAAAATT;
+phiX174	fimo	polypeptide_motif	56	66	41.4	+	.	Name=1;ID=1-1713-phiX174;pvalue=7.2e-05;sequence=TCGAAAAATTA;
+phiX174	fimo	polypeptide_motif	58	68	43.4	+	.	Name=1;ID=1-1500-phiX174;pvalue=4.56e-05;sequence=GAAAAATTATC;
+phiX174	fimo	polypeptide_motif	59	69	59.6	+	.	Name=1;ID=1-409-phiX174;pvalue=1.1e-06;sequence=AAAAATTATCT;
+phiX174	fimo	polypeptide_motif	61	71	61.8	+	.	Name=1;ID=1-329-phiX174;pvalue=6.52e-07;sequence=AAATTATCTTG;
+phiX174	fimo	polypeptide_motif	63	73	59.2	+	.	Name=1;ID=1-419-phiX174;pvalue=1.2e-06;sequence=ATTATCTTGAT;
+phiX174	fimo	polypeptide_motif	65	75	53.3	+	.	Name=1;ID=1-643-phiX174;pvalue=4.66e-06;sequence=TATCTTGATAA;
+phiX174	fimo	polypeptide_motif	66	76	51.8	+	.	Name=1;ID=1-737-phiX174;pvalue=6.54e-06;sequence=ATCTTGATAAA;
+phiX174	fimo	polypeptide_motif	67	77	73.2	+	.	Name=1;ID=1-89-phiX174;pvalue=4.78e-08;sequence=TCTTGATAAAG;
+phiX174	fimo	polypeptide_motif	69	79	63.8	+	.	Name=1;ID=1-268-phiX174;pvalue=4.15e-07;sequence=TTGATAAAGCA;
+phiX174	fimo	polypeptide_motif	71	81	40.2	+	.	Name=1;ID=1-1882-phiX174;pvalue=9.49e-05;sequence=GATAAAGCAGG;
+phiX174	fimo	polypeptide_motif	73	83	45.4	+	.	Name=1;ID=1-1334-phiX174;pvalue=2.87e-05;sequence=TAAAGCAGGAA;
+phiX174	fimo	polypeptide_motif	74	84	50.9	+	.	Name=1;ID=1-832-phiX174;pvalue=8.05e-06;sequence=AAAGCAGGAAT;
+phiX174	fimo	polypeptide_motif	76	86	52.2	+	.	Name=1;ID=1-710-phiX174;pvalue=5.96e-06;sequence=AGCAGGAATTA;
+phiX174	fimo	polypeptide_motif	78	88	51.8	+	.	Name=1;ID=1-741-phiX174;pvalue=6.65e-06;sequence=CAGGAATTACT;
+phiX174	fimo	polypeptide_motif	79	89	 45	+	.	Name=1;ID=1-1369-phiX174;pvalue=3.16e-05;sequence=AGGAATTACTA;
+phiX174	fimo	polypeptide_motif	80	90	43.3	+	.	Name=1;ID=1-1511-phiX174;pvalue=4.63e-05;sequence=GGAATTACTAC;
+phiX174	fimo	polypeptide_motif	81	91	59.8	+	.	Name=1;ID=1-402-phiX174;pvalue=1.05e-06;sequence=GAATTACTACT;
+phiX174	fimo	polypeptide_motif	82	92	46.9	+	.	Name=1;ID=1-1205-phiX174;pvalue=2.03e-05;sequence=AATTACTACTG;
+phiX174	fimo	polypeptide_motif	88	98	41.2	+	.	Name=1;ID=1-1744-phiX174;pvalue=7.51e-05;sequence=TACTGCTTGTT;
+phiX174	fimo	polypeptide_motif	91	101	53.6	+	.	Name=1;ID=1-621-phiX174;pvalue=4.33e-06;sequence=TGCTTGTTTAC;
+phiX174	fimo	polypeptide_motif	92	102	44.8	+	.	Name=1;ID=1-1388-phiX174;pvalue=3.31e-05;sequence=GCTTGTTTACG;
+phiX174	fimo	polypeptide_motif	93	103	43.2	+	.	Name=1;ID=1-1525-phiX174;pvalue=4.82e-05;sequence=CTTGTTTACGA;
+phiX174	fimo	polypeptide_motif	95	105	61.9	+	.	Name=1;ID=1-327-phiX174;pvalue=6.5e-07;sequence=TGTTTACGAAT;
+phiX174	fimo	polypeptide_motif	96	106	42.9	+	.	Name=1;ID=1-1553-phiX174;pvalue=5.08e-05;sequence=GTTTACGAATT;
+phiX174	fimo	polypeptide_motif	98	108	45.4	+	.	Name=1;ID=1-1340-phiX174;pvalue=2.9e-05;sequence=TTACGAATTAA;
+phiX174	fimo	polypeptide_motif	99	109	73.5	+	.	Name=1;ID=1-88-phiX174;pvalue=4.48e-08;sequence=TACGAATTAAA;
+phiX174	fimo	polypeptide_motif	100	110	 53	+	.	Name=1;ID=1-661-phiX174;pvalue=4.99e-06;sequence=ACGAATTAAAT;
+phiX174	fimo	polypeptide_motif	102	112	75.6	+	.	Name=1;ID=1-72-phiX174;pvalue=2.75e-08;sequence=GAATTAAATCG;
+phiX174	fimo	polypeptide_motif	104	114	52.2	+	.	Name=1;ID=1-713-phiX174;pvalue=6.05e-06;sequence=ATTAAATCGAA;
+phiX174	fimo	polypeptide_motif	106	116	59.6	+	.	Name=1;ID=1-407-phiX174;pvalue=1.09e-06;sequence=TAAATCGAAGT;
+phiX174	fimo	polypeptide_motif	112	122	41.6	+	.	Name=1;ID=1-1683-phiX174;pvalue=6.85e-05;sequence=GAAGTGGACTG;
+phiX174	fimo	polypeptide_motif	114	124	45.3	+	.	Name=1;ID=1-1342-phiX174;pvalue=2.92e-05;sequence=AGTGGACTGCT;
+phiX174	fimo	polypeptide_motif	118	128	56.2	+	.	Name=1;ID=1-512-phiX174;pvalue=2.38e-06;sequence=GACTGCTGGCG;
+phiX174	fimo	polypeptide_motif	122	132	51.4	+	.	Name=1;ID=1-774-phiX174;pvalue=7.15e-06;sequence=GCTGGCGGAAA;
+phiX174	fimo	polypeptide_motif	123	133	43.1	+	.	Name=1;ID=1-1533-phiX174;pvalue=4.93e-05;sequence=CTGGCGGAAAA;
+phiX174	fimo	polypeptide_motif	124	134	48.6	+	.	Name=1;ID=1-1085-phiX174;pvalue=1.38e-05;sequence=TGGCGGAAAAT;
+phiX174	fimo	polypeptide_motif	125	135	68.3	+	.	Name=1;ID=1-146-phiX174;pvalue=1.49e-07;sequence=GGCGGAAAATG;
+phiX174	fimo	polypeptide_motif	126	136	46.4	+	.	Name=1;ID=1-1243-phiX174;pvalue=2.27e-05;sequence=GCGGAAAATGA;
+phiX174	fimo	polypeptide_motif	128	138	58.3	+	.	Name=1;ID=1-446-phiX174;pvalue=1.48e-06;sequence=GGAAAATGAGA;
+phiX174	fimo	polypeptide_motif	129	139	43.2	+	.	Name=1;ID=1-1522-phiX174;pvalue=4.78e-05;sequence=GAAAATGAGAA;
+phiX174	fimo	polypeptide_motif	130	140	54.1	+	.	Name=1;ID=1-595-phiX174;pvalue=3.92e-06;sequence=AAAATGAGAAA;
+phiX174	fimo	polypeptide_motif	131	141	 76	+	.	Name=1;ID=1-68-phiX174;pvalue=2.49e-08;sequence=AAATGAGAAAA;
+phiX174	fimo	polypeptide_motif	132	142	51.2	+	.	Name=1;ID=1-800-phiX174;pvalue=7.57e-06;sequence=AATGAGAAAAT;
+phiX174	fimo	polypeptide_motif	133	143	56.2	+	.	Name=1;ID=1-513-phiX174;pvalue=2.41e-06;sequence=ATGAGAAAATT;
+phiX174	fimo	polypeptide_motif	134	144	41.1	+	.	Name=1;ID=1-1761-phiX174;pvalue=7.83e-05;sequence=TGAGAAAATTC;
+phiX174	fimo	polypeptide_motif	135	145	50.3	+	.	Name=1;ID=1-910-phiX174;pvalue=9.39e-06;sequence=GAGAAAATTCG;
+phiX174	fimo	polypeptide_motif	136	146	43.3	+	.	Name=1;ID=1-1517-phiX174;pvalue=4.66e-05;sequence=AGAAAATTCGA;
+phiX174	fimo	polypeptide_motif	139	149	54.2	+	.	Name=1;ID=1-588-phiX174;pvalue=3.75e-06;sequence=AAATTCGACCT;
+phiX174	fimo	polypeptide_motif	141	151	42.2	+	.	Name=1;ID=1-1625-phiX174;pvalue=6.01e-05;sequence=ATTCGACCTAT;
+phiX174	fimo	polypeptide_motif	143	153	 50	+	.	Name=1;ID=1-938-phiX174;pvalue=9.94e-06;sequence=TCGACCTATCC;
+phiX174	fimo	polypeptide_motif	145	155	44.6	+	.	Name=1;ID=1-1403-phiX174;pvalue=3.42e-05;sequence=GACCTATCCTT;
+phiX174	fimo	polypeptide_motif	155	165	51.3	+	.	Name=1;ID=1-787-phiX174;pvalue=7.35e-06;sequence=TGCGCAGCTCG;
+phiX174	fimo	polypeptide_motif	157	167	51.1	+	.	Name=1;ID=1-807-phiX174;pvalue=7.68e-06;sequence=CGCAGCTCGAG;
+phiX174	fimo	polypeptide_motif	159	169	44.5	+	.	Name=1;ID=1-1420-phiX174;pvalue=3.56e-05;sequence=CAGCTCGAGAA;
+phiX174	fimo	polypeptide_motif	160	170	 40	+	.	Name=1;ID=1-1921-phiX174;pvalue=9.89e-05;sequence=AGCTCGAGAAG;
+phiX174	fimo	polypeptide_motif	166	176	60.9	+	.	Name=1;ID=1-365-phiX174;pvalue=8.02e-07;sequence=AGAAGCTCTTA;
+phiX174	fimo	polypeptide_motif	168	178	62.3	+	.	Name=1;ID=1-311-phiX174;pvalue=5.87e-07;sequence=AAGCTCTTACT;
+phiX174	fimo	polypeptide_motif	181	191	49.9	+	.	Name=1;ID=1-946-phiX174;pvalue=1.01e-05;sequence=GCGACCTTTCG;
+phiX174	fimo	polypeptide_motif	187	197	52.5	+	.	Name=1;ID=1-694-phiX174;pvalue=5.64e-06;sequence=TTTCGCCATCA;
+phiX174	fimo	polypeptide_motif	191	201	46.6	+	.	Name=1;ID=1-1232-phiX174;pvalue=2.2e-05;sequence=GCCATCAACTA;
+phiX174	fimo	polypeptide_motif	194	204	76.4	+	.	Name=1;ID=1-67-phiX174;pvalue=2.29e-08;sequence=ATCAACTAACG;
+phiX174	fimo	polypeptide_motif	201	211	40.1	+	.	Name=1;ID=1-1908-phiX174;pvalue=9.77e-05;sequence=AACGATTCTGT;
+phiX174	fimo	polypeptide_motif	203	213	 63	+	.	Name=1;ID=1-291-phiX174;pvalue=5e-07;sequence=CGATTCTGTCA;
+phiX174	fimo	polypeptide_motif	205	215	53.8	+	.	Name=1;ID=1-610-phiX174;pvalue=4.16e-06;sequence=ATTCTGTCAAA;
+phiX174	fimo	polypeptide_motif	206	216	59.1	+	.	Name=1;ID=1-421-phiX174;pvalue=1.23e-06;sequence=TTCTGTCAAAA;
+phiX174	fimo	polypeptide_motif	207	217	 68	+	.	Name=1;ID=1-153-phiX174;pvalue=1.58e-07;sequence=TCTGTCAAAAA;
+phiX174	fimo	polypeptide_motif	209	219	49.6	+	.	Name=1;ID=1-988-phiX174;pvalue=1.09e-05;sequence=TGTCAAAAACT;
+phiX174	fimo	polypeptide_motif	210	220	40.8	+	.	Name=1;ID=1-1810-phiX174;pvalue=8.33e-05;sequence=GTCAAAAACTG;
+phiX174	fimo	polypeptide_motif	213	223	59.7	+	.	Name=1;ID=1-404-phiX174;pvalue=1.06e-06;sequence=AAAAACTGACG;
+phiX174	fimo	polypeptide_motif	223	233	 42	+	.	Name=1;ID=1-1654-phiX174;pvalue=6.36e-05;sequence=GCGTTGGATGA;
+phiX174	fimo	polypeptide_motif	225	235	61.4	+	.	Name=1;ID=1-349-phiX174;pvalue=7.16e-07;sequence=GTTGGATGAGG;
+phiX174	fimo	polypeptide_motif	227	237	40.3	+	.	Name=1;ID=1-1874-phiX174;pvalue=9.32e-05;sequence=TGGATGAGGAG;
+phiX174	fimo	polypeptide_motif	228	238	49.9	+	.	Name=1;ID=1-947-phiX174;pvalue=1.01e-05;sequence=GGATGAGGAGA;
+phiX174	fimo	polypeptide_motif	229	239	 45	+	.	Name=1;ID=1-1370-phiX174;pvalue=3.16e-05;sequence=GATGAGGAGAA;
+phiX174	fimo	polypeptide_motif	230	240	44.8	+	.	Name=1;ID=1-1395-phiX174;pvalue=3.33e-05;sequence=ATGAGGAGAAG;
diff -r e85346ab5054 -r 4df8e9f58a53 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jun 16 08:07:03 2016 -0400
+++ b/tool_dependencies.xml	Wed Jul 06 10:25:06 2016 -0400
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="imagemagick" version="6.9.3">
-        <repository changeset_revision="1cb6eed50cd2" name="package_imagemagick_6_9_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="graphicsmagick" version="1.3.20">
+        <repository changeset_revision="25002de17a97" name="package_graphicsmagick_1_3_20" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="meme" version="4.11.0">
-        <repository changeset_revision="1c44baf77b0e" name="package_meme_4_11_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="meme" version="4.11.1">
+        <repository changeset_revision="fd41eab672cd" name="package_meme_4_11_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>