| Next changeset 1:199e5afe498d (2018-07-04) |
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Commit message:
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy |
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added:
Tryp_G.py Tryp_T.py Tryp_V.py VAP.xml Vap.py data/Motifs/Phylotype1.hmm data/Motifs/Phylotype10a.hmm data/Motifs/Phylotype10b.hmm data/Motifs/Phylotype11.hmm data/Motifs/Phylotype11a.hmm data/Motifs/Phylotype11b.hmm data/Motifs/Phylotype12.hmm data/Motifs/Phylotype13a.hmm data/Motifs/Phylotype13b.hmm data/Motifs/Phylotype13c.hmm data/Motifs/Phylotype13d.hmm data/Motifs/Phylotype14.4.hmm data/Motifs/Phylotype14.hmm data/Motifs/Phylotype15.2.hmm data/Motifs/Phylotype15a.hmm data/Motifs/Phylotype15b.hmm data/Motifs/Phylotype15c.hmm data/Motifs/Phylotype2a.hmm data/Motifs/Phylotype2b.hmm data/Motifs/Phylotype3.hmm data/Motifs/Phylotype4.4.hmm data/Motifs/Phylotype4a.hmm data/Motifs/Phylotype4b.hmm data/Motifs/Phylotype4c.hmm data/Motifs/Phylotype5.1.hmm data/Motifs/Phylotype5.hmm data/Motifs/Phylotype6.hmm data/Motifs/Phylotype7.hmm data/Motifs/Phylotype8a.hmm data/Motifs/Phylotype8b.hmm data/Motifs/Phylotype9a.hmm data/Motifs/Phylotype9b.hmm data/Motifs/Phylotype9c.hmm data/Reference/148_prot.fasta data/Reference/IL3000.1.bt2 data/Reference/IL3000.2.bt2 data/Reference/IL3000.3.bt2 data/Reference/IL3000.4.bt2 data/Reference/IL3000.fasta data/Reference/IL3000.gtf data/Reference/IL3000.rev.1.bt2 data/Reference/IL3000.rev.2.bt2 data/Reference/IL3000_prot.fasta data/Reference/ORFAnnotation.gtf data/Reference/Tc148.1.bt2 data/Reference/Tc148.2.bt2 data/Reference/Tc148.3.bt2 data/Reference/Tc148.4.bt2 data/Reference/Tc148.rev.1.bt2 data/Reference/Tc148.rev.2.bt2 data/Reference/Tc148_contigs.fasta data/congodata.csv data/congodata_deviationfromthemean.csv data/geoTv.csv data/vivax/Database/Bin_2.fas data/vivax/Database/Bin_2.fas.nhr data/vivax/Database/Bin_2.fas.nin data/vivax/Database/Bin_2.fas.nsq data/vivax/Database/COGlist.txt data/vivax/Database/COGs.fas data/vivax/Database/COGs.fas.nhr data/vivax/Database/COGs.fas.nin data/vivax/Database/COGs.fas.nsq data/vivax/Database/binlist.txt data/vivax/TvDatabase.csv data/vivax/geoTv.csv |
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| diff -r 000000000000 -r 36cb22bd911d Tryp_G.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Tryp_G.py Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,462 @@\n+"""\r\n+ * Copyright 2018 University of Liverpool\r\n+ * Author: John Heap, Computational Biology Facility, UoL\r\n+ * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL\r\n+ *\r\n+ * Licensed under the Apache License, Version 2.0 (the "License");\r\n+ * you may not use this file except in compliance with the License.\r\n+ * You may obtain a copy of the License at\r\n+ *\r\n+ * http://www.apache.org/licenses/LICENSE-2.0\r\n+ *\r\n+ * Unless required by applicable law or agreed to in writing, software\r\n+ * distributed under the License is distributed on an "AS IS" BASIS,\r\n+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\r\n+ * See the License for the specific language governing permissions and\r\n+ * limitations under the License.\r\n+ *\r\n+ """\r\n+\r\n+import subprocess\r\n+import re\r\n+import os\r\n+import sys\r\n+import shutil\r\n+import pandas as pd\r\n+import numpy as np\r\n+import matplotlib as mpl\r\n+mpl.use(\'Agg\')\r\n+import matplotlib.pyplot as plt\r\n+from matplotlib.mlab import PCA\r\n+import seaborn as sns\r\n+\r\n+# some globals for convenience\r\n+\r\n+pList = [\'P1\', \'P2\', \'P3\', \'P4\', \'P5\', \'P6\', \'P7\', \'P8\', \'P9\', \'P10\', \'P11\', \'P12\', \'P13\', \'P14\', \'P15\']\r\n+\r\n+quietString = ""\t#" >>"+os.path.dirname(os.path.realpath(__file__))+"/log/Vap_log.txt 2>&1"\r\n+\r\n+def assembleWithVelvet(name, kmers, inslen, covcut, fastq1name,fastq2name):\r\n+ #argString = "velveth " + name + "_k65 65 -shortPaired -fastq " + name + "_R1.fastq " + name + "_R2.fastq"\r\n+ argString = "velveth " + name + "_k"+ kmers+" "+ kmers + " -shortPaired -fastq " + fastq1name+" "+fastq2name+quietString\r\n+ print(argString)\r\n+ returncode = subprocess.call(argString, shell=True)\r\n+ if returncode != 0:\r\n+ return "Error in velveth"\r\n+ argString = "velvetg " + name + "_k"+kmers+" -exp_cov auto -ins_length "+inslen+" -cov_cutoff "+covcut+" -clean yes -ins_length_sd 50 -min_pair_count 20"+quietString\r\n+ #argString = "velvetg " + name + "_k65 -exp_cov auto -ins_length 400 -cov_cutoff 5 -clean yes -ins_length_sd 50 -min_pair_count 20"+quietString\r\n+ print(argString)\r\n+ returncode = subprocess.call(argString, shell = True)\r\n+ if returncode != 0:\r\n+ return "Error in velvetg"\r\n+ shutil.copyfile(name + "_k"+kmers+"//contigs.fa",name + ".fa") # my $namechange = "mv ".$input."_k65/contigs.fa ".$input.".fa";\r\n+ return "ok"\r\n+\r\n+def contigTranslation(name):\r\n+ argString = "transeq " + name + ".fa " + name + "_6frame.fas -frame=6 " #+quietString\r\n+ print(argString)\r\n+ returncode = subprocess.call(argString, shell=True)\r\n+ #subprocess.call(\'ls -l *.fa\', shell = True)\r\n+ #sys.exit(1)\r\n+ #if returncode != 0:\r\n+ # return "Error in Transeq"\r\n+ #return \'ok\'\r\n+\r\n+\r\n+def HMMerMotifSearch(name):\r\n+ motifs = [\'1\', \'2a\', \'2b\', \'3\', \'4a\', \'4b\', \'4c\', \'5\', \'6\', \'7\', \'8a\', \'8b\', \'9a\', \'9b\',\r\n+ \'9c\', \'10a\', \'10b\', \'11a\', \'11b\', \'12\', \'13a\', \'13b\', \'13c\', \'13d\', \'14\', \'15a\', \'15b\', \'15c\']\r\n+ lineCounts = []\r\n+ compoundList = []\r\n+ dir_path = os.path.dirname(os.path.realpath(__file__))\r\n+ phylopath = dir_path + "/data/Motifs/Phylotype"\r\n+ for m in motifs:\r\n+ argString = "hmmsearch " + phylopath + m + ".hmm " + name + "_6frame.fas > Phy" + m + ".out" # +quietString\r\n+ # argString = "hmmsearch "+phylopath + m + ".hmm " + dir_path+"/data/Test_6frame.fas > Phy" + m + ".out"\r\n+ #print(argString)\r\n+ subprocess.call(argString, shell=True)\r\n+\r\n+ hmmResult = open("Phy" + m + ".out", \'r\')\r\n+ tempout = open(dir_path + "/data/" + "Phy" + m + ".txt", \'w\')\r\n+ #regex = r"NODE_[0-9]{1,7}_length_[0-9]{1,7}_cov_[0-9]{1,10}.[0-9]{1,7}_[0-9]{1,2}"\r\n+ n = 0\r\n+ outList = []\r\n+ for l in range(0,14):\r\n+ hmmResult.readline() #hacky? miss out the first 14 lines. data we want starts on line 15\r\n+\r\n+\r\n+ for line in hmmResult:\r\n+ if re.search(r"inclusion", line):\r\n+ '..b' contigs(args,dict):\r\n+ #argdict = {\'name\': 2, \'pdfexport\': 3, \'contigs\': 4, \'html_file\': 5, \'html_resource\': 6}\r\n+\r\n+ shutil.copyfile(args[dict[\'contigs\']], args[dict[\'name\']]+".fa")\r\n+\r\n+ \r\n+\r\n+ contigTranslation(args[dict[\'name\']])\r\n+ myCountList = HMMerMotifSearch(args[dict[\'name\']])\r\n+ myFreqList = relativeFrequencyTable(myCountList, args[dict[\'name\']],\r\n+ args[dict[\'html_resource\']]) # saves out inputname_relative_frequncy.csv\r\n+ # myFreqList = [0.111670020120724, 0.103621730382294, 0.0784708249496982, 0.0110663983903421,\r\n+ # 0.0543259557344064, 0.0563380281690141, 0.0734406438631791, 0.0160965794768612,\r\n+ # 0.0110663983903421, 0.028169014084507, 0.126760563380282, 0.0583501006036217, 0.062374245472837,\r\n+ # 0.0372233400402414, 0.17102615694165]\r\n+\r\n+\r\n+ myDevList = getDeviationFromMean(myFreqList, args[dict[\'name\']],\r\n+ args[dict[\'html_resource\']]) # saves out inputname_deviation_from_mean.csv\r\n+ relativeFrequencyHeatMap(args[dict[\'name\']], myFreqList, args[dict[\'pdfexport\']], args[dict[\'html_resource\']])\r\n+ deviationFromMeanHeatMap(args[dict[\'name\']], myDevList, args[dict[\'pdfexport\']], args[dict[\'html_resource\']])\r\n+ plotPCA(args[dict[\'name\']], myFreqList, args[dict[\'pdfexport\']], args[dict[\'html_resource\']])\r\n+ createHTML(args[dict[\'name\']], args[dict[\'html_file\']], myFreqList,\r\n+ myDevList) # assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource\r\n+\r\n+\r\n+def genomicProcess(inputname, exportpdf, forwardFN, reverseFN, htmlfile, htmlresource):\r\n+ assembleWithVelvet(inputname,forwardFN,reverseFN)\r\n+ contigTranslation(inputname)\r\n+ myCountList = HMMerMotifSearch(inputname)\r\n+ myFreqList = relativeFrequencyTable(myCountList, inputname, htmlresource) # saves out inputname_relative_frequncy.csv\r\n+ #myFreqList = [0.111670020120724, 0.103621730382294, 0.0784708249496982, 0.0110663983903421,\r\n+ # 0.0543259557344064, 0.0563380281690141, 0.0734406438631791, 0.0160965794768612,\r\n+ # 0.0110663983903421, 0.028169014084507, 0.126760563380282, 0.0583501006036217, 0.062374245472837,\r\n+ # 0.0372233400402414, 0.17102615694165]\r\n+\r\n+\r\n+ myDevList = getDeviationFromMean(myFreqList, inputname,htmlresource) # saves out inputname_deviation_from_mean.csv\r\n+\r\n+ relativeFrequencyHeatMap(inputname, myFreqList, exportpdf, htmlresource)\r\n+ deviationFromMeanHeatMap(inputname, myDevList, exportpdf, htmlresource)\r\n+ plotPCA(inputname, myFreqList, exportpdf, htmlresource)\r\n+ createHTML(inputname, htmlfile, myFreqList,myDevList) # assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource\r\n+ return\r\n+\r\n+\r\n+\r\n+if __name__ == "__main__":\r\n+ #contigTranslation(\'Tcongo\')\r\n+ #contigTranslation(\'Test\')\r\n+ #newHMMerMotifSearch(\'Test\')\r\n+ #HMMerMotifSearch(\'Tcongo\')\r\n+ #sys.exit()\r\n+\r\n+\r\n+ myFreqList = [0.111670020120724, 0.103621730382294, 0.0784708249496982, 0.0110663983903421,\r\n+ 0.0543259557344064, 0.0563380281690141, 0.0734406438631791, 0.0160965794768612,\r\n+ 0.0110663983903421, 0.028169014084507, 0.126760563380282, 0.0583501006036217, 0.062374245472837,\r\n+ 0.0372233400402414, 0.17102615694165]\r\n+ myDevList = [0.000790026,0.0073109,-0.001151769,-0.004502933,-0.013687421,-0.016159773,0.021689891,\r\n+ 0.007863809,-0.003133585,-0.001111709,-0.01313879,0.0036997,-0.00935284,0.005640693,0.015243802]\r\n+\r\n+ relativeFrequencyHeatMap(\'test\', myFreqList, "PDF_Yes","results")\r\n+ deviationFromMeanHeatMap(\'test\', myDevList, "PDF_Yes","results")\r\n+ plotPCA(\'test\',myFreqList,"PDF_Yes","results")\r\n+\r\n+ createHTML(\'test\',"results/test.html", myFreqList, myDevList)\r\n+ #contigTranslation("Test")\r\n+ #myCountList = HMMerMotifSearch("Test")\r\n+\r\n+\r\n+ sys.exit()\r\n' |
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| diff -r 000000000000 -r 36cb22bd911d Tryp_T.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Tryp_T.py Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,343 @@\n+"""\r\n+ * Copyright 2018 University of Liverpool\r\n+ * Author: John Heap, Computational Biology Facility, UoL\r\n+ * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL\r\n+ *\r\n+ * Licensed under the Apache License, Version 2.0 (the "License");\r\n+ * you may not use this file except in compliance with the License.\r\n+ * You may obtain a copy of the License at\r\n+ *\r\n+ * http://www.apache.org/licenses/LICENSE-2.0\r\n+ *\r\n+ * Unless required by applicable law or agreed to in writing, software\r\n+ * distributed under the License is distributed on an "AS IS" BASIS,\r\n+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\r\n+ * See the License for the specific language governing permissions and\r\n+ * limitations under the License.\r\n+ *\r\n+ """\r\n+\r\n+\r\n+import subprocess\r\n+import pandas as pd\r\n+import re\r\n+import os\r\n+import sys\r\n+import matplotlib as mpl\r\n+mpl.use(\'Agg\')\r\n+import matplotlib.pyplot as plt\r\n+\r\n+pList = [\'P1\', \'P2\', \'P3\', \'P4\', \'P5\', \'P6\', \'P7\', \'P8\', \'P9\', \'P10\', \'P11\', \'P12\', \'P13\', \'P14\', \'P15\']\r\n+quietString = "" #"">> Vap_log.txt 2>&1"\r\n+def transcriptMapping(inputname, strain, forwardFN,reverseFN):\r\n+ #where is our Reference data -\r\n+ dir_path = os.path.dirname(os.path.realpath(__file__))\r\n+ refName = dir_path+"/data/Reference/Tc148" #default\r\n+ if strain == "Tc148":\r\n+ refName = dir_path+"/data/Reference/Tc148"\r\n+ if strain == "IL3000":\r\n+ refName = dir_path+"/data/Reference/IL3000"\r\n+ #argString = "bowtie2 -x Refe4rence/IL3000 -1 data/"+forwardFN+" -2 data/"+reverseFN+" -S "+inputname+".sam" #>log.txt\r\n+ #argString = "bowtie2 -x Reference/Tc148 -1 data/"+forwardFN+" -2 data/"+reverseFN+" -S "+inputname+".sam" #>log.txt\r\n+ argString = "bowtie2 -x "+refName+" -1 "+forwardFN+" -2 "+reverseFN+" -S "+inputname+".sam"+quietString #>log.txt\r\n+ #print(argString)\r\n+ returncode = subprocess.call(argString, shell=True)\r\n+\r\n+def processSamFiles(inputname):\r\n+ #debug use a mapping sam file we have already found\r\n+ #dir_path = os.path.dirname(os.path.realpath(__file__))\r\n+ #bugName = dir_path+"/data/T_Test" #defasult\r\n+\r\n+ cur_path = os.getcwd()\r\n+ samName = cur_path+"/"+inputname\r\n+\r\n+ #argString = "samtools view -bS "+bugName+" > "+inputname+".bam"\r\n+ argString = "samtools view -bS "+inputname+".sam > "+samName+".bam"+quietString\r\n+ #print(argString)\r\n+ returncode = subprocess.call(argString, shell=True)\r\n+\r\n+\r\n+ #argString = "samtools sort "+bugName+" -o "+inputname+".sorted"\r\n+ argString = "samtools sort "+samName+".bam -o "+samName+".sorted"+quietString\r\n+ #print("argstring = "+argString)\r\n+ returncode = subprocess.call(argString, shell=True)\r\n+\r\n+ #argString = "samtools index "+bugName+".sorted "+inputname+".sorted.bai"\r\n+ argString = "samtools index "+samName+".sorted "+samName+".sorted.bai"+quietString\r\n+ #print("argstring = " + argString)\r\n+ returncode = subprocess.call(argString, shell=True)\r\n+\r\n+\r\n+\r\n+\r\n+def transcriptAbundance(inputname, strain):\r\n+ dir_path = os.path.dirname(os.path.realpath(__file__))\r\n+ refName = dir_path + "/data/Reference/ORFAnnotation.gtf" # defasult\r\n+ if strain == "Tc148":\r\n+ refName = dir_path + "/data/Reference/ORFAnnotation.gtf"\r\n+ if strain == "IL3000":\r\n+ refName = dir_path + "/data/Reference/IL3000.gtf"\r\n+ #argString = "cufflinks -G Reference/IL3000.gtf -o "+inputname+".cuff -u -p 8 "+inputname+".sorted"\r\n+ #argString = "cufflinks -G Reference/ORFAnnotation.gtf -o "+inputname+".cuff -u -p 8 "+inputname+".sorted"\r\n+ argString = "cufflinks -q -G "+refName+" -o "+inputname+".cuff -u -p 8 "+inputname+".sorted"+quietString\r\n+ returncode = subprocess.call(argString, shell = True)\r\n+\r\n+\r\n+def convertToFasta(inputName, strain): #equivalent to Sara\'s awk scripte\r\n+ dir_path = os.path.dirname(os.path.realpath(__file__))\r\n+ refName = dir_path + "/data/Reference/ORFAnnotation.gtf'..b'> table, th, tr, td {border: 1px solid black; border-collapse: collapse;}</style>"\r\n+\r\n+ htmlString += r"<table style=\'width:50%;margin-left:25%;text-align:center\'><tr><th>Phylotype</th><th>Relative Frequency</th><th>Weighted Frequency</th></tr>"\r\n+ tabString = ""\r\n+ # flush out table with correct values\r\n+ for i in range(0, 15):\r\n+ f = format(freqList[i], \'.4f\')\r\n+ w = format(weightList[i], \'.4f\')\r\n+ tabString += "<tr><td>phy" + str(i + 1) + "</td><td>" + f + "</td><td>" + w + "</td></tr>"\r\n+ htmlString += tabString + "</table><br><br><br><br><br>"\r\n+ htmlString += r"<p> <h3>Stacked Bar chart of Phylotype Frequency</h3> The \'weighted\' relative frequency of each phylotype alongside the VAP of selected strain.</p>"\r\n+ imgString = r"<img src = \'stackedbar.png\' alt=\'Stacked bar chart of phylotype variation\' style=\'max-width:100%\'><br><br>"\r\n+ htmlString += imgString\r\n+\r\n+# htmlString += r"<p><h3>The Deviation Heat Map and Dendogram</h3>The phylotype variation expressed as the deviation from your sample mean compared to the model dataset</p>"\r\n+# imgString = r"<img src = \'dheatmap.png\' alt=\'Deviation Heatmap\' style=\'max-width:100%\'><br><br>"\r\n+# htmlString += imgString\r\n+\r\n+# htmlString += r"<p><h3>The Variation PCA plot</h3>PCA analysis corresponding to absolute variation. Colour coded according to location</p>"\r\n+# imgString = r"<img src = \'vapPCA.png\' alt=\'PCA Analysis\' style=\'max-width:100%\'><br><br>"\r\n+# htmlString += imgString + r"</div></body></html>"\r\n+\r\n+ with open(htmlfn, "w") as htmlfile:\r\n+ htmlfile.write(htmlString)\r\n+\r\n+#argdict = {\'name\':2, \'pdfexport\': 3, \'strain\': 4, \'forward\': 5, \'reverse\': 6, \'html_file\': 7, \'html_resource\': 8}\r\n+def transcriptomicProcess(args,dict):\r\n+ transcriptMapping(args[dict[\'name\']], args[dict[\'strain\']], args[dict[\'forward\']], args[dict[\'reverse\']]) #uses bowtie\r\n+ processSamFiles(args[dict[\'name\']]) #uses samtools\r\n+ transcriptAbundance(args[dict[\'name\']],args[dict[\'strain\']]) #uses cufflinks -> ?.cuff/*.*\r\n+ cuff_df = convertToFasta(args[dict[\'name\']],args[dict[\'strain\']])\r\n+ countList, weightList = HMMerMotifSearch(args[dict[\'name\']],args[dict[\'strain\']], cuff_df)\r\n+ relFreqList = relativeFrequencyTable(countList,args[dict[\'name\']],args[dict[\'html_resource\']])\r\n+ relWeightList = weightedFrequencyTable(weightList,args[dict[\'name\']],args[dict[\'html_resource\']])\r\n+ createStackedBar(args[dict[\'name\']],relWeightList, args[dict[\'strain\']],args[dict[\'pdfexport\']],args[dict[\'html_resource\']])\r\n+ createHTML(args[dict[\'name\']],args[dict[\'html_file\']],args[dict[\'html_resource\']], relFreqList, relWeightList)\r\n+\r\n+if __name__ == "__main__":\r\n+ #print("Commencing Transcript Mapping")\r\n+ #transcriptMapping("T_Test", "Transcripts.1","Transcripts.2")\r\n+ #print("Processimg Sam Files")\r\n+ #processSamFiles("T_Test")\r\n+ #print("Assessing Transcript Abundance")\r\n+ #transcriptAbundance("T_Test")\r\n+ #print ("Converting to Fasta Subset")\r\n+ #cuff_df = convertToFasta("T_Test")\r\n+ #print("Commencing HMMer search")\r\n+ #countList, weightList = HMMerMotifSearch("T_Test",cuff_df)\r\n+ #relativeFrequencyTable(countList,\'T_Test\')\r\n+ #weightedFrequencyTable(weightList,\'T_Test\')\r\n+ relFreqList = [0.111842105,0.059210526,0.026315789,0.013157895,\r\n+ 0.006578947,0.013157895,0.032894737,0.019736842,\r\n+ 0.039473684,0.046052632,0.217105263,0.065789474,\r\n+ 0.151315789,0.059210526,0.138157895]\r\n+\r\n+ relWeightList = [0.07532571,0.05900545,0.009601452,0.042357532,0.01236219,0.001675663,0.04109726,\r\n+ 0.097464248,0.057491666,0.05826875,0.279457473,0.070004772,0.065329007,0.085361298,0.045197529]\r\n+\r\n+ createStackedBar(\'T_Test\',relWeightList, \'Tc148\',\'PDF_Yes\',\'results\')\r\n+ createHTML("t_test","results/t_test.html","results",relFreqList,relWeightList)\r\n' |
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| diff -r 000000000000 -r 36cb22bd911d Tryp_V.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Tryp_V.py Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,326 @@\n+"""\r\n+ * Copyright 2018 University of Liverpool\r\n+ * Author: John Heap, Computational Biology Facility, UoL\r\n+ * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL\r\n+ *\r\n+ * Licensed under the Apache License, Version 2.0 (the "License");\r\n+ * you may not use this file except in compliance with the License.\r\n+ * You may obtain a copy of the License at\r\n+ *\r\n+ * http://www.apache.org/licenses/LICENSE-2.0\r\n+ *\r\n+ * Unless required by applicable law or agreed to in writing, software\r\n+ * distributed under the License is distributed on an "AS IS" BASIS,\r\n+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\r\n+ * See the License for the specific language governing permissions and\r\n+ * limitations under the License.\r\n+ *\r\n+ """\r\n+\r\n+import matplotlib as mpl\r\n+mpl.use(\'Agg\')\r\n+\r\n+import subprocess\r\n+import shutil\r\n+import re\r\n+import pandas as pd\r\n+import os\r\n+\r\n+import sys\r\n+\r\n+import matplotlib.pyplot as plt\r\n+from matplotlib.patches import Patch\r\n+import seaborn as sns\r\n+\r\n+def assembleWithVelvet(name, kmers, inslen, covcut, fastq1name,fastq2name):\r\n+ #argString = "velveth " + name + "_k65 65 -shortPaired -fastq " + name + "_R1.fastq " + name + "_R2.fastq"\r\n+ argString = "velveth " + name + "_k"+ kmers+" "+ kmers + " -shortPaired -fastq " + fastq1name+" "+fastq2name\r\n+ print(argString)\r\n+ returncode = subprocess.call(argString, shell=True)\r\n+ if returncode != 0:\r\n+ return "Error in velveth"\r\n+ argString = "velvetg " + name + "_k"+kmers+" -exp_cov auto -ins_length "+inslen+" -clean yes -ins_length_sd 50 -min_pair_count 20"\r\n+ #argString = "velvetg " + name + "_k"+kmers+" -exp_cov auto -ins_length "+inslen+" -cov_cutoff "+covcut+" -clean yes -ins_length_sd 50 -min_pair_count 20"\r\n+ #argString = "velvetg " + name + "_k65 -exp_cov auto -ins_length 400 -cov_cutoff 5 -clean yes -ins_length_sd 50 -min_pair_count 20"+quietString\r\n+ print(argString)\r\n+ returncode = subprocess.call(argString, shell = True)\r\n+ if returncode != 0:\r\n+ return "Error in velvetg"\r\n+ shutil.copyfile(name + "_k"+kmers+"//contigs.fa",name + ".fa") # my $namechange = "mv ".$input."_k65/contigs.fa ".$input.".fa";\r\n+ return "ok"\r\n+\r\n+\r\n+def blastContigs(test_name,database):\r\n+ print(test_name)\r\n+ print(database)\r\n+ #db_path = os.path.dirname(os.path.realpath(__file__))+database\r\n+ db_path = database\r\n+ argString = "blastn -db "+db_path+" -query "+test_name+".fa -outfmt 10 -out "+test_name+"_blast.txt"\r\n+ print (argString)\r\n+ returncode = subprocess.call(argString, shell = True)\r\n+ if returncode != 0:\r\n+ return "Error in blastall"\r\n+ blast_df = pd.read_csv(""+test_name+"_blast.txt")\r\n+ #print (blast_df)\r\n+ #if ($temp[2] >= 98 & & $temp[3] > 100 & & $temp[10] < 0.001){\r\n+ #\'qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore\'\r\n+ blast_df.columns = [\'qaccver\', \'saccver\', \'pident\', \'length\', \'mismatch\', \'gapopen\', \'qstart\', \'qend\', \'sstart\', \'send\', \'evalue\',\'bitscore\']\r\n+ blastResult_df = blast_df[(blast_df[\'pident\']>=98) & (blast_df[\'length\'] > 100) & (blast_df[\'evalue\']<0.001) ]\r\n+ blastResult_df = blastResult_df[[\'qaccver\', \'saccver\', \'pident\']] #query accession.version, subject accession.version, Percentage of identical matches\r\n+\r\n+ return blastResult_df\r\n+\r\n+\r\n+\r\n+def getCogsPresent(blastResult_df,strain,cogOrBinList):\r\n+ blastResult_df.sort_values(\'pident\',axis = 0, ascending=False, inplace=True)\r\n+ nodeList = blastResult_df[\'qaccver\'].tolist()\r\n+ cogList = blastResult_df[\'saccver\'].tolist()\r\n+ cogSet = set(cogList) #get unique values\r\n+ cogList = sorted(cogSet) #sort them\r\n+\r\n+ #print (cogList)\r\n+ #print (len(cogList))\r\n+\r\n+ thereList = []\r\n+ dataList = []\r\n+ #dir_path = os.path.dirname(os.path.realpath(__file__))\r\n+ fname = cogOrBinList\r\n+ cnt = 0\r\n+ with open (fname) as f:\r\n+ for line'..b'[dict[\'name\']]+"_cogspresent.csv"\r\n+ cogPresence_df.to_csv(fname)\r\n+ current_df = addToCurrentData(cogPresence_df,args[dict[\'name\']]) # load in Tvdatabase and add cogPresence column to it.\r\n+ createClusterMap(current_df, args[dict[\'name\']],args[dict[\'html_resource\']],args[dict[\'pdfexport\']])\r\n+ createHTML(args[dict[\'name\']],args[dict[\'html_file\']],args[dict[\'html_resource\']])\r\n+\r\n+def test_cluster(args,dict):\r\n+ print ("name: %s",args[dict[\'name\']])\r\n+ cogPresence_df = pd.read_csv("test_cogspresent.csv")\r\n+ print(cogPresence_df)\r\n+ current_df = addToCurrentData(cogPresence_df,args[dict[\'name\']]) # load in Tvdatabase and add cogPresence column to it.\r\n+ createClusterMap(current_df, args[dict[\'name\']], args[dict[\'html_resource\']], args[dict[\'pdfexport\']])\r\n+\r\n+def vivax_contigs(args,dict):\r\n+# argdict = {\'name\': 2, \'pdfexport\': 3, \'contigs\': 4, \'html_file\': 5, \'html_resource\': 6}\r\n+\r\n+ #test_cluster(args,dict)\r\n+ #return;\r\n+\r\n+ #subprocess.call(\'echo $PATH\',shell = True)\r\n+ #sys.exit(1)\r\n+\r\n+ vivaxPath = os.path.dirname(os.path.realpath(__file__))+r"/data/vivax"\r\n+ shutil.copyfile(args[dict[\'contigs\']], args[dict[\'name\']]+".fa")\r\n+ blastResult_df = blastContigs(args[dict[\'name\']], vivaxPath+r"/Database/COGs.fas")\r\n+ orthPresence_df = getCogsPresent(blastResult_df, args[dict[\'name\']], vivaxPath+r"/Database/COGlist.txt")\r\n+\r\n+ binBlastResult_df = blastContigs(args[dict[\'name\']], vivaxPath+r"/Database/Bin_2.fas")\r\n+ binPresence_df = getCogsPresent(binBlastResult_df, args[dict[\'name\']], vivaxPath+r"/Database/binlist.txt")\r\n+ cogPresence_df = orthPresence_df.append(binPresence_df, ignore_index=True)\r\n+\r\n+ fname = args[dict[\'html_resource\']]+r"/"+ args[dict[\'name\']]+"_cogspresent.csv"\r\n+ cogPresence_df.to_csv(fname)\r\n+ current_df = addToCurrentData(cogPresence_df,args[dict[\'name\']]) # load in Tvdatabase and add cogPresence column to it.\r\n+ createClusterMap(current_df, args[dict[\'name\']], args[dict[\'html_resource\']], args[dict[\'pdfexport\']])\r\n+ createHTML(args[dict[\'name\']],args[dict[\'html_file\']],args[dict[\'html_resource\']])\r\n+\r\n+if __name__ == "__main__":\r\n+ #assembleWithVelvet("V2_Test",\'65\',\'400\', \'5\',"data/TviBrRp.1.clean","data/TviBrRp.2.clean")\r\n+ #assembleWithVelvet("V2_Test",\'65\',\'400\', \'5\',"data/Tv493.1","data/Tv493.2")\r\n+ #blastResult_df=blastContigs("V2_Test",r"/Database/COGs.fas")\r\n+ cogPresence_df = pd.read_csv("test_cogspresent.csv")\r\n+ print(cogPresence_df)\r\n+ current_df = addToCurrentData(cogPresence_df,"vTest") # load in Tvdatabase and add cogPresence column to it.\r\n+ createClusterMap(current_df, "vTest", "sausages","no")\r\n+ createHTML("vTest","vTest.html","sausages")\r\n+ sys.exit()\r\n+\r\n+ blastResult_df=blastContigs("Tv493",r"/Database/COGs.fas")\r\n+ orthPresence_df = getCogsPresent(blastResult_df,"Tv493",r"/Database/COGlist.txt")\r\n+\r\n+ #binBlastResult_df=blastContigs("V2_Test",r"/Database/Bin_2.fas")\r\n+\r\n+ binBlastResult_df=blastContigs("Tv493",r"/Database/Bin_2.fas")\r\n+ binPresence_df = getCogsPresent(binBlastResult_df,"Tv493",r"/Database/binlist.txt")\r\n+ cogPresence_df = orthPresence_df.append(binPresence_df, ignore_index=True)\r\n+ #now do the next bit?\r\n+ current_df = addToCurrentData(cogPresence_df) # load in Tvdatabase and add cogPresence column to it.\r\n+ createClusterMap(current_df,\'Test\',dict[\'html_resource\'] ,dict[\'pdfexport\'])\r\n+\r\n+\r\n+ #print(cogPresence_df)\r\n+ dir_path = os.path.dirname(os.path.realpath(__file__))\r\n+ fname = dir_path+r"/results/V2_TestPresence.csv"\r\n+ #fnameb = dir_path+r"/results/V2_Test_blastOrth.csv"\r\n+ #fnameb_bin = dir_path+r"/results/V2_Test_blastBin.csv"\r\n+ #binBlastResult_df.to_csv(fnameb_bin)\r\n+ #blastResult_df.to_csv(fnameb)\r\n+\r\n+ #cogPresence_df.to_csv(fname)\r\n+ cogPresence_df = pd.read_csv(fname)\r\n+\r\n+ current_df = addToCurrentData(cogPresence_df) #load in Tvdatabase and add cogPresence column to it.\r\n+\r\n+\r\n+\r\n+\r\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d VAP.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VAP.xml Wed Jul 04 16:39:13 2018 -0400 |
| b |
| @@ -0,0 +1,123 @@ +<tool id="VAP" name="VAP" version="0.0.5"> + <description>is a Variant Antigen Profiler that accurately quantifies the variant antigen diversity or presence in a Trypanosoma congolense or T.vivax isolate</description> + <requirements> + <requirement type="package" version="1.2.10">velvet</requirement> + <requirement type="package" version="3.1b2">HMMER</requirement> + <requirement type="package" version="2.2.6">bowtie2</requirement> + <requirement type="package" version="1.6">samtools</requirement> + <requirement type="package" version="2.2.1">cufflinks</requirement> + <requirement type="package" version="2.7.1">blast</requirement> + </requirements> + + + <command interpreter="python" detect_errors="exit_code"> + #if $TrypType.species == "Trypanosoma congolense": + #if $TrypType.GT.analysis == "Genomic": + #if $TrypType.GT.contigs.preassem == "Contig available": + <!-- name:2, pdfexport:3, contigs:4, html_file:5, html_resource:6 --> + Vap.py g_contigs $xname $P $TrypType.GT.contigs.contig $html_file $html_file.extra_files_path + #else + <!-- name = 2, pdfexport = 3, kmers = 4, inslen = 5, covcut = 6, forward = 7, reverse = 8, html_file = 9, html_resource = 10 --> + Vap.py g_assemble $xname $P $TrypType.GT.contigs.kmers $TrypType.GT.contigs.inslen $TrypType.GT.contigs.covcut $TrypType.GT.contigs.forward $TrypType.GT.contigs.reverse $html_file $html_file.extra_files_path + #end if + #else + <!-- name:2, pdfexport:3, strain:4, forward:5, reverse:6, html_file:7, html_resource:8 --> + Vap.py transcipt $xname $P $TrypType.GT.strain $TrypType.GT.forward $TrypType.GT.reverse $html_file $html_file.extra_files_path + #end if + #else + #if $TrypType.contigs.preassem == "Contig available": + <!-- name:2, pdfexport:3, contigs:4, html_file:5, html_resource:6 --> + Vap.py v_contigs $xname $P $TrypType.contigs.contig $html_file $html_file.extra_files_path + #else + <!-- name = 2, pdfexport = 3, kmers = 4, inslen = 5, covcut = 6, forward = 7, reverse = 8, html_file = 9, html_resource = 10 --> + Vap.py v_assemble $xname $P $TrypType.contigs.kmers $TrypType.contigs.inslen 0 $TrypType.contigs.forward $TrypType.contigs.reverse $html_file $html_file.extra_files_path + #end if + #end if + + </command> + + <inputs> + <param name="xname" size = "30" type="text" value = "Test" label="Prefix Name" /> + <conditional name = "TrypType"> + <param name = "species" type = 'select' label="Select Species"> + <option value = "Trypanosoma congolense" selected="true"></option> + <option value = "Trypanosoma vivax"></option> + </param> + <when value = "Trypanosoma congolense"> + <conditional name = "GT"> + <param name="analysis" type = "select" label = "Genomic or Transcriptomic Analysis?"> + <option value = "Genomic" selected = "true"></option> + <option value = "Transcriptomic"></option> + </param> + <when value = "Genomic"> + <conditional name = "contigs"> + <param name = "preassem" type = "select" label = "Contig file available?"> + <option value = "Full assembly" selected = "true"></option> + <option value = "Contig available"></option> + </param> + <when value = "Full assembly"> + <param name = "kmers" type="integer" value="65" min="31" max="99" label = "Specify kmers"></param> + <param name = "inslen" type="integer" value="400" min="1" max="999" label = "Insert length"></param> + <param name = "covcut" type="integer" value="5" min="1" max="999" label = "Coverage cut off"></param> + <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/> + <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/> + </when> + <when value = "Contig available"> + <param name="contig" type="data" format="fasta" label="Contig file"/> + </when> + </conditional> + </when> + <when value = "Transcriptomic"> + <param name = "strain" type="select" label = "Select Reference Strain"> + <option value = "Tc148"></option> + <option value = "IL3000"></option> + </param> + <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/> + <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/> + </when> + </conditional> + </when> + <when value="Trypanosoma vivax"> + <conditional name = "contigs"> + <param name = "preassem" type = "select" label = "Contig file available?"> + <option value = "Full assembly" selected = "true"></option> + <option value = "Contig available"></option> + </param> + <when value = "Full assembly"> + <param name = "kmers" type="integer" value="65" min="31" max="99" label = "Specify kmers"></param> + <param name = "inslen" type="integer" value="400" min="1" max="999" label = "Insert length"></param> + <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/> + <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/> + </when> + <when value = "Contig available"> + <param name="contig" type="data" format="fasta" label="Contig file"/> + </when> + </conditional> + </when> + </conditional> + + <param name="P" type="boolean" truevalue='PDF_Yes' falsevalue='PDF_No' label="Export PDF of figures" /> + </inputs> + + <outputs> + <data format="html" name = "html_file" label = "${xname.value}_html"/> + </outputs> + <tests> + <test> + <param name = "xname" value = "Test"/> + <conditional name = "TrypType"> + <param name = "species" value = "Trypanosoma congolense"/> + </conditional> + <conditional name = "GT"> + <param name = "analysis" value = "Genomic"/> + </conditional> + <conditional name = "contigs"> + <param name = "preassem" value = "Contig available"/> + <param name="contig" value = "Test.fa"/> + </conditional> + <param name = "P" value = 'PDF_No'/> + <output name = "html_file" file = 'Test_html' ftype = 'html'/> + </test> + </tests> +</tool> + |
| b |
| diff -r 000000000000 -r 36cb22bd911d Vap.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Vap.py Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| @@ -0,0 +1,91 @@ +""" + * Copyright 2018 University of Liverpool + * Author: John Heap, Computational Biology Facility, UoL + * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + """ +#import subprocess +#import re +import os +import sys +#import pandas as pd +#import numpy as np +#import seaborn as sns +#import matplotlib.pyplot as plt +#from matplotlib.mlab import PCA +import Tryp_G +import Tryp_T +import Tryp_V +import argparse +#Entry .sort out the arguments + +pdfExport = False +#parser = argparse.ArgumentParser(description='Variant Antigen Profiler - the VAP.') +#parser.add_argument('name') +#parser.add_argument('-t','-T', action = 'store_true', default = False, help = "Transciptomic Pathway") +#parser.add_argument('-p','-P', action = 'store_true', default = False, help = "Export PDFs to HTML directory") +#parser.add_argument('strain') +#parser.add_argument('Forward_Read_File') +#parser.add_argument('Reverse_Read_File') +#parser.add_argument('htmlfile') +#parser.add_argument('htmlresource') +#parser.add_argument('heatmapFile') +#parser.add_argument('PCAFile') +#parser.add_argument('devheatmapFile') +#args = parser.parse_args() + +#we have numerous parameters.... +#hard code it for differnt types? + + +arguments = sys.argv +htmldir = arguments[len(arguments)-1] #last argument is always html_resource +if not os.path.exists(htmldir): + os.mkdir(htmldir) + +if arguments[1] == 'g_assemble': + argdict = {'name':2, 'pdfexport':3, 'kmers':4,'inslen':5, 'covcut':6, 'forward':7, 'reverse':8, 'html_file':9, 'html_resource':10} + Tryp_G.assemble(arguments,argdict) +if arguments[1] == 'g_contigs': + argdict = {'name':2, 'pdfexport':3, 'contigs':4, 'html_file':5, 'html_resource':6} + Tryp_G.contigs(arguments,argdict) +if arguments[1] == 'transcipt': + argdict = {'name':2, 'pdfexport': 3, 'strain': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8} + Tryp_T.transcriptomicProcess(arguments,argdict) +if arguments[1] == 'v_assemble': + argdict = {'name':2, 'pdfexport':3, 'kmers':4,'inslen':5, 'covcut':6, 'forward':7, 'reverse':8, 'html_file':9, 'html_resource':10} + Tryp_V.vivax_assemble(arguments,argdict) +if arguments[1] == 'v_contigs': + argdict = {'name':2, 'pdfexport':3, 'contigs':4, 'html_file':5, 'html_resource':6} + Tryp_V.vivax_contigs(arguments,argdict) + + +sys.exit() + + + +#if not os.path.exists(args.htmlresource): +# os.mkdir(args.htmlresource) +#if args.p: +# pdfExport = True +#if args.t: +# print ("Transcriptomic Pathway") +# Tryp_T.transcriptomicProcess(args.name, pdfExport, args.strain, args.Forward_Read_File, args.Reverse_Read_File, args.htmlfile, args.htmlresource) +#else: + #print ('Genomic Pathway') + #Tryp_G.test_output(args.name, args.htmlfile, args.htmlresource, args.heatmapFile, args.PCAFile,args.devheatmapFile) +# Tryp_G.genomicProcess(args.name, pdfExport, args.Forward_Read_File, args.Reverse_Read_File, args.htmlfile, args.htmlresource) + + |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype1.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype1.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,82 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype1.2.2\n+LENG 20\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Wed Jul 22 16:28:52 2015\n+NSEQ 114\n+EFFN 16.452209\n+CKSUM 230921126\n+STATS LOCAL MSV -5.8517 0.72046\n+STATS LOCAL VITERBI -6.4341 0.72046\n+STATS LOCAL FORWARD -4.6617 0.72046\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 3.88091 6.11899 1.92851 2.01032 4.32208 4.24438 4.23469 3.00141 2.22197 1.74415 3.66285 2.79338 5.94754 4.01342 3.28923 2.90847 3.12039 4.23041 7.20112 2.74858\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00239 6.43270 7.15504 0.61958 0.77255 0.00000 *\n+ 1 5.93723 6.99655 7.95220 7.40640 4.86765 7.56972 7.82241 1.33088 7.34704 0.37080 4.56201 7.82516 7.22539 6.87530 7.13320 7.13995 6.11087 4.32050 7.33325 6.53626 1 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00239 6.43270 7.15504 0.61958 0.77255 0.48576 0.95510\n+ 2 5.20410 6.40045 7.26145 6.71767 4.95262 6.68808 3.86455 1.61092 6.59516 0.49989 4.70186 6.86812 6.76996 6.54000 6.57154 6.09561 5.42766 2.03821 7.14826 6.12827 2 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00239 6.43270 7.15504 0.61958 0.77255 0.48576 0.95510\n+ 3 3.94875 5.37457 5.60597 5.00051 3.70192 5.07981 2.74631 2.20975 2.54657 0.71200 4.42622 5.12903 5.43794 2.44525 4.89644 4.38022 4.17880 3.30167 5.97559 4.79527 3 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00239 6.43270 7.15504 0.61958 0.77255 0.48576 0.95510\n+ 4 6.01676 7.06650 8.00115 7.44444 4.83720 7.61022 7.80836 2.46472 7.37460 0.13772 4.53420 7.88217 7.23412 6.85920 7.13012 7.19336 6.17926 4.48385 7.30237 6.51492 4 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00239 6.43270 7.15504 0.61958 0.77255 0.48576 0.95510\n+ 5 5.67846 7.51901 6.14384 5.30024 7.31430 5.96347 5.72413 6.55895 0.11455 5.78227 6.73310 5.54785 6.31329 3.02471 3.90373 5.63503 5.73089 6.27508 7.60064 6.65052 5 K - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00239 6.43270 7.15504 0.61958 0.77255 0.48576 0.95510\n+ 6 7.25167 7.94884 7.54932 7.62724 5.13087 6.84171 6.63694 7.31549 7.63402 6.35385 7.78266 7.32174 7.37434 7.52813 7.39184 7.25451 7.55222 7.22206 6.73125 0.01946 12 Y - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00239 6.43270 7.15504 0.61958 0.77255 0.48576 0.95510\n+ 7 4.17392 3.92164 6.49393 6.40037 7.01002 2.07699 7.03629 6.53473 6.35021 6.21253 6.92808 1.3708'..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00239 6.43270 7.15504 0.61958 0.77255 0.48576 0.95510\n+ 13 5.23591 8.17310 3.12242 0.20363 7.37604 3.88269 5.88220 7.03796 5.20405 6.42617 7.42130 4.57210 5.88354 2.61367 6.04859 5.00165 5.58172 6.51328 8.57556 6.84123 19 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00239 6.43270 7.15504 0.61958 0.77255 0.48576 0.95510\n+ 14 2.59452 6.02323 6.30037 6.10527 1.72193 4.90099 6.71524 5.79134 6.05620 5.50800 6.33361 3.87144 5.73330 6.18281 6.13340 2.36282 0.52703 5.17514 7.74994 6.61688 20 T - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00239 6.43270 7.15504 0.61958 0.77255 0.48576 0.95510\n+ 15 1.51401 6.11373 3.28801 3.75781 5.48360 4.65924 3.13623 4.93584 3.81389 4.52058 5.32267 4.26675 5.11884 4.14807 4.28424 1.03701 2.49917 4.56640 6.73093 2.14411 21 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00239 6.43270 7.15504 0.61958 0.77255 0.48576 0.95510\n+ 16 5.11083 7.75657 3.94307 1.64973 7.32189 5.12958 5.93024 6.97917 5.21592 6.39379 7.35923 0.40114 5.87927 5.13700 5.98413 2.57227 5.49488 6.39587 8.52132 6.85226 22 N - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00239 6.43270 7.15504 0.61958 0.77255 0.48576 0.95510\n+ 17 5.97069 7.02550 7.97481 7.42279 4.85320 7.59149 7.81801 1.70149 7.35971 0.25771 4.54809 7.85136 7.22944 6.86747 7.13218 7.16505 6.13919 4.38670 7.31962 6.52901 23 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00239 6.43270 7.15504 0.61958 0.77255 0.48576 0.95510\n+ 18 5.39389 8.23124 0.27878 1.64388 7.50086 5.26098 6.03124 7.20969 5.38984 6.58320 7.60884 4.71401 6.00728 5.24483 6.25161 5.15819 5.74655 6.68226 8.63635 6.98785 24 D - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00239 6.43270 7.15504 0.61958 0.77255 0.48576 0.95510\n+ 19 5.23855 8.19119 0.45887 3.21780 7.37942 3.42800 2.63271 7.04400 5.21460 6.43203 7.42938 1.69056 5.88233 5.08477 6.07536 5.00163 5.58445 6.51922 8.58516 6.84249 25 D - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00239 6.43270 7.15504 0.61958 0.77255 0.48576 0.95510\n+ 20 3.84478 5.18293 5.68628 5.11650 4.30926 4.97779 5.29104 2.02643 3.24881 3.42036 0.80789 5.11944 5.32202 5.05156 4.93798 4.31048 3.17489 3.02349 5.75701 1.84728 26 m - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00161 6.43192 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype10a.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype10a.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,88 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype11.1\n+LENG 22\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Mon Jul 27 12:46:46 2015\n+NSEQ 26\n+EFFN 26.000000\n+CKSUM 2826442667\n+STATS LOCAL MSV -6.4416 0.72805\n+STATS LOCAL VITERBI -6.8167 0.72805\n+STATS LOCAL FORWARD -4.0569 0.72805\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 3.06327 5.61197 3.20857 1.95192 3.36719 3.31898 4.59546 3.15778 2.57118 2.87003 5.21024 2.79906 2.38430 3.20490 3.59390 2.14827 2.10886 3.45134 6.69535 4.32584\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.10326 6.87243 2.33235 0.61958 0.77255 0.00000 *\n+ 1 5.65297 7.62461 6.51373 5.34808 7.37382 6.11256 5.74560 6.53337 0.88866 5.78505 6.69743 5.59873 2.55448 1.08012 2.45930 5.60677 2.93858 6.24467 7.67565 6.67931 1 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.22721 6.77088 1.59899 0.61958 0.77255 1.50497 0.25106\n+ 2 0.87973 6.95399 2.58458 2.57014 6.30997 2.89638 5.29946 5.82188 4.17049 5.28925 6.06439 4.37500 5.43263 2.61982 4.71608 4.31722 1.49401 5.36556 7.42420 5.95859 2 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00214 6.54581 7.26815 0.61958 0.77255 0.06504 2.76509\n+ 3 2.94588 8.06477 2.04308 0.38473 7.34971 5.46358 6.07652 6.92113 2.98172 6.35809 7.23195 4.90527 6.13099 5.24870 5.85218 5.15879 5.62931 3.05157 8.50078 6.90607 3 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00154 6.87243 7.59478 0.61958 0.77255 0.48576 0.95510\n+ 4 5.69418 8.66715 0.74502 0.92240 7.84815 5.57181 6.32655 7.52473 5.68531 6.90698 7.92280 2.32921 6.32124 5.53326 6.57239 5.45007 6.04516 6.99425 9.05931 7.30130 4 d - - -\n+ 2.68470 4.42348 2.77438 2.73246 3.46477 2.40636 3.72617 3.29477 2.67487 2.69478 4.24813 2.90470 2.73863 3.18269 2.89603 2.37749 2.77642 2.98641 4.58600 3.60732\n+ 0.50813 1.13221 2.57626 0.36158 1.19262 0.48576 0.95510\n+ 5 4.13408 6.06642 4.79037 4.25097 5.31519 5.01161 5.33204 4.69632 4.23324 2.87625 5.23171 1.67562 1.20866 3.00048 4.64508 2.33094 2.16901 2.35354 6.68996 5.41781 7 p - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00167 6.79387 7.51622 0.61958 0.77255 0.17588 1.82459\n+ 6 4.23507 5.61367 6.16997 2.50229 2.81150 5.40234 5.73533 2.09326 5.34895 1.06600 4.73059 5.55538 2.03096 5.48563 5.36763 2.44691 3.37854 2.57769 6.23708 5.06062 8 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00154 6.87243 7.59478 0.61958 0.77255 0.48576 0.95510\n+ 7 2.63354 6.67206 4.90081 4.39906 6.44154 5.13056 5.61159 5.91451 2.35473 5.40994 6.16299 4.86691'..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00154 6.87243 7.59478 0.61958 0.77255 0.48576 0.95510\n+ 15 1.83092 6.62267 6.03988 2.16082 7.45023 0.63167 7.18305 6.98562 6.42235 6.62902 7.36070 5.94974 6.19144 6.50114 6.65692 2.53655 2.36854 6.03254 8.74696 7.63181 18 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00154 6.87243 7.59478 0.61958 0.77255 0.48576 0.95510\n+ 16 4.22173 3.21992 5.39738 3.16881 2.55201 5.24231 5.58698 4.31908 4.76997 2.37256 4.96066 3.02838 5.64795 5.03334 5.04343 0.86329 1.71613 4.10626 6.44761 5.23830 19 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00154 6.87243 7.59478 0.61958 0.77255 0.48576 0.95510\n+ 17 4.98671 6.30702 6.80349 6.29075 0.65017 6.07936 5.87845 3.07210 6.07260 2.06693 5.34971 6.11958 2.77229 6.10058 6.03636 2.41741 5.21544 4.56795 6.12547 2.25485 20 F - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00154 6.87243 7.59478 0.61958 0.77255 0.48576 0.95510\n+ 18 4.25097 5.63142 6.18020 5.56720 4.71773 5.41572 5.75071 1.09710 5.35231 1.19087 3.08323 5.56829 3.19460 5.49526 2.78275 2.54382 2.93735 3.86935 6.25397 5.07887 21 i - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00154 6.87243 7.59478 0.61958 0.77255 0.48576 0.95510\n+ 19 4.62307 6.71355 5.20113 4.74720 6.43279 5.33061 5.84820 2.37152 1.63527 5.40711 6.22906 1.93662 5.88484 5.01058 4.77538 2.75366 0.82517 5.40137 7.58096 6.31975 22 t - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00154 6.87243 7.59478 0.61958 0.77255 0.48576 0.95510\n+ 20 4.13052 6.40564 4.46722 2.82325 5.67134 4.93536 5.13785 1.71625 3.90877 4.67723 5.47458 1.83868 5.33082 4.27283 2.55736 1.18350 2.92282 4.75456 6.89246 2.87093 23 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00154 6.87243 7.59478 0.61958 0.77255 0.48576 0.95510\n+ 21 4.30961 6.49895 4.71927 4.13967 3.29539 5.11326 2.29576 5.17155 2.19842 3.09409 5.57119 4.64088 0.98076 1.97302 4.31288 4.33828 2.42860 4.84962 6.95294 5.63795 24 p - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00154 6.87243 7.59478 0.61958 0.77255 0.48576 0.95510\n+ 22 5.97874 7.83248 7.05178 5.66150 7.66151 6.35084 5.91002 6.75778 0.42054 5.97441 6.91389 2.25427 6.61000 5.03430 1.58249 5.92833 5.97051 6.49705 7.83494 6.89157 25 K - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00104 6.87193 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype10b.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype10b.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,85 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype11.2\n+LENG 21\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Mon Jul 27 12:54:16 2015\n+NSEQ 4\n+EFFN 4.000000\n+CKSUM 2929604314\n+STATS LOCAL MSV -6.5951 0.73266\n+STATS LOCAL VITERBI -7.0599 0.73266\n+STATS LOCAL FORWARD -3.2356 0.73266\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.53878 5.63240 3.38445 1.89488 5.29210 4.00484 4.04242 4.80347 1.63923 4.30404 4.17394 3.51107 1.80774 2.74018 3.00246 2.79368 2.80467 3.73917 6.34251 5.14880\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.00000 *\n+ 1 3.22283 5.12565 4.72960 4.63185 5.58865 3.89104 5.59653 5.02640 4.68371 4.73574 5.59690 4.53027 0.59806 4.95906 4.85276 3.42630 1.36853 4.34589 6.88513 5.79956 1 P - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 2 4.10941 6.12665 4.56979 3.80220 5.72394 4.57806 4.40740 5.06368 2.53834 4.37145 5.28266 4.12541 4.93385 0.87659 1.09975 4.08121 4.22590 4.75229 6.28496 5.21153 2 q - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 3 4.81271 6.44149 5.07288 4.60759 6.17405 4.93894 5.25639 5.79217 0.13196 5.11184 6.12690 4.92115 5.45017 4.46991 3.63257 4.85607 5.02597 5.46942 6.76991 5.89471 3 K - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 4 0.13884 5.37390 5.28464 5.28248 5.84631 4.14753 6.05100 5.27079 5.34307 5.03692 5.98543 4.97628 4.98417 5.54403 5.37783 3.75834 4.11404 4.61881 7.04944 6.11806 4 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 5 3.14412 5.07634 4.56601 4.50149 5.66081 3.81102 5.55908 5.23887 4.69279 4.89093 5.68207 4.42913 0.77362 4.90433 4.88873 1.06248 3.70910 4.41426 6.95252 5.82569 5 p - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.29648 5.15864 1.38301 0.61958 0.77255 0.48576 0.95510\n+ 6 3.09193 5.22779 3.33730 3.08087 4.95727 3.69948 4.36277 4.50462 3.10531 4.04746 4.87871 3.52432 4.31906 1.37101 3.46898 1.03560 3.46313 4.02086 6.15146 4.81366 6 s - - -\n+ 2.68634 4.42241 2.77536 2.73139 3.46370 2.40529 3.72511 3.29370 2.67757 2.69371 4.24706 2.90363 2.73504 3.18162 2.89817 2.37903 2.77536 2.98534 4.58493 3.61519\n+ 0.61460 0.78652 5.59593 0.07199 2.66705 0.23757 1.55373\n+ 7 4.84589 6.68580 3.93942 0.11168 6.34286 4.72455 5.62542 6.19623 4.77114 5.59581 6.69205 4.56014 '..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 14 3.97792 5.99445 4.22139 3.79355 5.74091 4.43550 4.69452 5.17283 0.59631 4.57314 5.47017 4.17915 1.50645 3.85335 3.19752 3.99866 4.23545 4.77840 6.49517 5.39854 15 K - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 15 4.05217 6.26650 3.35146 1.33360 5.93062 4.24725 5.01284 5.54601 4.03927 5.02772 5.95938 3.91509 0.61324 4.22966 4.53013 3.99764 4.41698 5.06902 6.97884 5.68973 16 P - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 16 1.29490 5.31483 3.69525 3.24946 5.05588 3.87579 4.40205 4.47702 1.53952 4.03372 4.84003 3.67931 1.69902 3.55312 3.39597 3.23792 3.51042 4.02589 6.19039 4.90395 17 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 17 3.78614 6.21128 3.23804 0.70777 5.63988 4.13172 4.45052 5.09834 1.45673 4.50678 5.36377 3.61197 4.67390 3.59635 3.36595 3.68960 4.02308 4.69130 6.54050 5.21441 18 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 18 3.25255 5.35850 3.35014 1.59446 4.61705 3.93659 4.31069 4.00086 3.14542 3.59144 1.48759 3.53979 1.77087 3.49726 3.57039 3.30125 3.51942 3.71532 5.94233 4.62365 19 m - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 19 3.57504 5.82296 3.71610 3.22996 5.22265 4.17329 1.70595 4.68908 1.42342 4.12269 4.96036 3.69459 1.41618 3.39372 2.92305 3.54873 3.77885 4.32131 6.14470 4.88456 20 p - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 20 3.47309 5.98891 3.00343 1.48897 5.34307 3.92020 4.32051 4.84343 3.13787 4.30960 5.11686 3.39273 1.41679 1.60150 3.61712 3.39070 3.73506 4.40917 6.43353 4.99665 21 p - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 21 4.81271 6.44149 5.07288 4.60759 6.17405 4.93894 5.25639 5.79217 0.13196 5.11184 6.12690 4.92115 5.45017 4.46991 3.63257 4.85607 5.02597 5.46942 6.76991 5.89471 22 K - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00578 5.15585 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype11.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype11.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,88 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype11\n+LENG 22\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Fri Jul 24 13:28:46 2015\n+NSEQ 25\n+EFFN 25.000000\n+CKSUM 2273933145\n+STATS LOCAL MSV -6.6146 0.73033\n+STATS LOCAL VITERBI -6.8423 0.73033\n+STATS LOCAL FORWARD -3.9990 0.73033\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 3.09064 5.63016 3.22081 1.95971 3.38019 3.40352 4.92360 3.12146 2.49955 2.85583 5.22122 2.78930 2.33664 3.23004 3.54699 2.12082 2.14904 3.57935 6.87487 4.23471\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00160 6.83446 7.55680 0.61958 0.77255 0.00000 *\n+ 1 4.87588 7.28309 4.81526 2.31359 6.73428 5.44220 5.56169 6.14732 0.96102 5.54434 6.35361 4.90890 2.58477 1.17708 4.32277 4.81341 2.70152 5.74228 7.58472 6.29433 1 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00160 6.83446 7.55680 0.61958 0.77255 0.48576 0.95510\n+ 2 1.35410 6.70930 2.88926 1.34530 6.05182 3.18537 5.12735 5.54345 2.56859 5.01393 5.75529 4.36389 5.32137 2.88627 4.38797 4.13518 1.75732 5.09949 7.14084 5.71877 2 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00160 6.83446 7.55680 0.61958 0.77255 0.48576 0.95510\n+ 3 2.95845 7.84390 1.33389 0.71013 7.13798 5.37688 5.93164 6.69118 2.34047 6.13480 6.97630 4.81997 6.01012 5.09133 5.59401 5.00322 5.43694 2.97475 8.27312 6.71705 3 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.06167 6.83446 2.83483 0.61958 0.77255 0.48576 0.95510\n+ 4 2.52838 7.14110 1.03790 1.39652 6.46429 5.08976 5.44906 5.97418 4.30089 2.69531 6.20859 2.26305 5.59999 4.57218 2.57846 4.48196 4.81494 5.52393 7.56864 6.10603 4 d - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.14599 6.77449 2.00480 0.61958 0.77255 0.21042 1.66201\n+ 5 4.02813 6.18111 4.42951 3.90234 5.43118 4.84784 5.09044 4.85052 3.90337 2.59899 5.28794 1.56071 1.11437 2.84696 4.35611 2.28607 3.02418 4.53294 6.71561 2.97493 5 p - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00183 6.69941 7.42176 0.61958 0.77255 0.12682 2.12773\n+ 6 4.22283 5.59592 6.19112 5.57680 2.73674 5.39244 5.72157 1.98702 5.36070 1.13376 4.70143 5.55657 1.68327 5.48838 5.36610 2.04903 3.36043 3.83728 6.20687 3.10320 6 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00160 6.83446 7.55680 0.61958 0.77255 0.48576 0.95510\n+ 7 2.51835 6.48121 6.57071 6.40608 7.11191 5.28748 7.18547 6.56413 6.38331 6.26745 7.04220 6.05431 '..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00160 6.83446 7.55680 0.61958 0.77255 0.48576 0.95510\n+ 15 2.24178 6.59894 5.91542 2.04021 7.40464 0.58128 7.09937 6.94019 6.32355 6.57807 7.31308 5.87432 6.15072 6.40654 6.58322 2.45428 2.33138 5.99787 8.69699 7.56524 16 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00160 6.83446 7.55680 0.61958 0.77255 0.48576 0.95510\n+ 16 4.18332 3.14560 5.32426 3.14218 2.34767 5.19965 5.53441 4.29195 4.69946 2.46924 4.93027 2.87726 5.60255 4.96759 4.98283 0.95018 1.66385 4.07808 6.41628 5.20449 17 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00160 6.83446 7.55680 0.61958 0.77255 0.48576 0.95510\n+ 17 4.90255 6.22756 6.73275 6.21099 0.68740 6.00268 5.83917 3.04497 5.99312 1.99381 5.27242 6.05322 2.75386 6.02953 5.96058 2.46996 5.13151 4.48575 6.09758 2.18297 18 F - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00160 6.83446 7.55680 0.61958 0.77255 0.48576 0.95510\n+ 18 4.21457 5.59630 6.13602 5.52350 4.68412 5.37841 5.71279 1.05477 5.31036 1.31823 3.01234 5.52827 3.07825 5.45494 2.70646 2.52132 2.86929 3.83511 6.21886 5.04330 19 i - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00160 6.83446 7.55680 0.61958 0.77255 0.48576 0.95510\n+ 19 4.56162 6.64886 5.13731 4.68924 6.34993 5.27516 5.80424 2.36379 1.85808 5.33499 6.15729 1.82850 5.83025 4.96963 4.77095 2.67790 0.79564 5.32529 7.52033 6.25346 20 t - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00160 6.83446 7.55680 0.61958 0.77255 0.48576 0.95510\n+ 20 4.22221 6.59851 4.43737 2.57496 5.94460 4.96828 5.20169 1.64150 3.93811 4.92230 5.69730 1.76918 5.39007 4.32037 2.53254 1.14779 2.79514 5.00066 7.08927 5.71498 21 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00160 6.83446 7.55680 0.61958 0.77255 0.48576 0.95510\n+ 21 4.26352 6.46380 4.66702 4.08839 3.27917 5.06686 2.99811 5.13997 2.02605 3.02474 5.53489 4.59201 0.95641 1.90889 4.27842 4.28971 2.39553 4.81499 6.91956 5.60228 22 p - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00160 6.83446 7.55680 0.61958 0.77255 0.48576 0.95510\n+ 22 5.94434 7.79585 7.04607 5.63073 7.62575 6.31748 5.87302 6.72078 0.38110 5.93708 6.87664 2.98899 6.57478 4.99720 1.45886 5.89430 5.93484 6.46058 7.79735 6.85490 23 K - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00108 6.83393 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype11a.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype11a.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,94 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype12.1\n+LENG 24\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Wed Jul 29 11:54:06 2015\n+NSEQ 64\n+EFFN 64.000000\n+CKSUM 2634953749\n+STATS LOCAL MSV -6.9012 0.72285\n+STATS LOCAL VITERBI -7.0426 0.72285\n+STATS LOCAL FORWARD -3.7767 0.72285\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.58914 2.48672 3.02391 3.37037 2.97905 1.76807 4.73799 3.65499 3.46769 2.94384 5.68355 2.87127 3.73673 3.95413 3.48222 2.48301 3.00258 2.88711 5.75687 2.37571\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00064 7.75457 8.47691 0.61958 0.77255 0.00000 *\n+ 1 5.13239 6.50131 7.08484 6.48060 1.19234 2.27771 3.65701 3.66616 6.26381 2.45237 5.62157 3.52214 6.65538 6.38367 6.26566 2.31220 5.36429 3.66960 6.99986 1.28495 1 f - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00064 7.75457 8.47691 0.61958 0.77255 0.48576 0.95510\n+ 2 2.91884 6.64402 7.21752 6.63210 0.60980 4.30821 3.68330 5.08626 6.41325 2.50873 5.76914 6.56151 6.78918 6.51574 6.40586 4.14173 5.51487 2.87611 6.97864 1.68522 2 F - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00064 7.75457 8.47691 0.61958 0.77255 0.48576 0.95510\n+ 3 5.13643 6.50418 7.09953 6.49471 2.32016 6.30036 6.56913 3.30242 6.27675 3.60318 5.62347 3.51677 6.66246 6.39611 6.27655 3.82266 2.43208 3.31951 7.01702 0.44948 3 Y - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02893 7.75457 3.57255 0.61958 0.77255 0.48576 0.95510\n+ 4 7.42633 8.41472 8.81151 8.56585 2.32870 8.41244 7.31463 3.76558 8.39634 0.24829 6.29490 8.12331 8.39985 7.93066 8.14049 3.44127 7.59265 6.29506 7.31603 2.83081 4 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00066 7.72630 8.44864 0.61958 0.77255 0.18891 1.75943\n+ 5 5.69242 7.59286 8.03611 8.10862 8.45367 0.10309 8.62156 8.10574 8.10375 2.85199 8.50195 7.33511 7.26377 8.12509 8.00846 3.51819 6.29723 7.09272 9.73590 8.77802 5 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01120 7.75457 4.53639 0.61958 0.77255 0.48576 0.95510\n+ 6 4.91763 7.42766 3.28771 1.82564 6.76774 0.67856 5.87104 6.25435 4.61747 5.73089 6.47192 5.13065 6.07138 2.49662 3.90940 2.45816 5.15090 4.19335 3.86377 3.58923 6 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00064 7.74401 8.46635 0.61958 0.77255 0.30458 1.33725\n+ 7 4.83525 7.34845 3.17668 3.27190 6.69460 1.66286 5.79558 3.28065 2.79273 3.53772 6.38882 2.09518'..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00064 7.75457 8.47691 0.61958 0.77255 0.48576 0.95510\n+ 17 2.33804 7.34566 5.08495 3.16909 6.69043 1.40681 5.79679 6.17614 2.98977 3.26042 6.38642 3.74240 1.53904 2.83009 2.43987 3.80855 3.12695 2.80777 7.77852 6.36781 21 g - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01443 7.75457 4.27590 0.61958 0.77255 0.48576 0.95510\n+ 18 4.84885 7.36461 2.97171 1.84814 6.71065 1.74709 5.80643 6.19817 2.53480 5.67014 6.40557 1.68897 6.01152 2.37068 2.24211 2.28429 3.73201 5.75588 7.79602 6.38301 22 n - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.74078 8.46313 0.61958 0.77255 0.27376 1.42926\n+ 19 6.44512 9.35223 0.71926 2.63399 8.55789 2.17230 3.52801 8.19966 2.94543 7.59825 8.55843 1.69580 7.12553 6.30718 7.20117 2.92614 6.77975 7.68588 9.74821 8.04211 23 d - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00064 7.75457 8.47691 0.61958 0.77255 0.48576 0.95510\n+ 20 1.75800 6.52404 7.15569 6.54977 4.09285 3.47586 6.71474 1.37972 6.33889 3.60889 5.65756 6.52819 6.71569 6.47259 6.34738 2.94922 3.18155 0.94659 7.20072 6.02273 24 v - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00064 7.75457 8.47691 0.61958 0.77255 0.48576 0.95510\n+ 21 9.03125 0.00165 9.14496 9.23767 9.76203 8.17789 9.74534 10.18815 9.42286 9.22920 10.58721 9.54527 8.81979 9.73212 9.15741 9.42691 9.45241 9.79205 10.03768 10.01024 25 C - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00064 7.75457 8.47691 0.61958 0.77255 0.48576 0.95510\n+ 22 0.60193 7.35904 8.16282 8.11730 7.88289 6.27243 8.42864 6.53688 7.92226 3.64885 7.78377 7.22175 7.13557 7.95274 7.82133 3.50972 3.40475 1.03683 9.40099 8.35331 26 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00064 7.75457 8.47691 0.61958 0.77255 0.48576 0.95510\n+ 23 0.77215 7.17783 5.80882 5.25264 6.64845 3.12506 6.36449 6.05445 2.59395 4.14795 6.50578 5.69396 6.41904 5.54340 2.86812 2.55964 1.55099 3.47628 7.93226 6.64422 27 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00064 7.75457 8.47691 0.61958 0.77255 0.48576 0.95510\n+ 24 8.00193 3.79242 8.63289 8.70852 3.69385 8.26521 6.78266 7.54391 8.46780 6.57138 8.01610 7.75468 8.51332 7.97374 8.16552 7.71713 8.18510 7.51937 6.84314 0.05715 28 Y - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00043 7.75436 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype11b.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype11b.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,106 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype12.2\n+LENG 28\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Thu Jul 30 09:30:38 2015\n+NSEQ 11\n+EFFN 11.000000\n+CKSUM 1188814779\n+STATS LOCAL MSV -7.0433 0.72870\n+STATS LOCAL VITERBI -7.1696 0.72870\n+STATS LOCAL FORWARD -3.3150 0.72870\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.75755 2.86320 2.94237 2.92244 3.64495 1.88651 3.48503 3.32484 2.72914 2.74552 4.12302 2.90340 3.92729 3.74754 3.27942 2.59681 3.29265 2.84135 4.87562 2.66668\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.18528 6.05380 1.79110 0.61958 0.77255 0.00000 *\n+ 1 3.45162 5.80235 1.54775 3.15955 5.08886 1.96832 4.44173 4.54016 3.23229 4.09132 2.64813 1.83292 4.62201 3.56937 3.71984 3.44237 2.50475 4.16723 6.28420 2.78698 1 d - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00419 5.87271 6.59506 0.61958 0.77255 1.33581 0.30509\n+ 2 2.34073 4.85519 5.09565 4.49861 1.94941 2.45134 4.87747 3.29540 4.34346 1.82073 3.97229 4.62022 4.92771 4.52901 2.37388 2.45018 3.65979 2.31139 5.47138 2.58465 2 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00419 5.87271 6.59506 0.61958 0.77255 1.33581 0.30509\n+ 3 3.89959 5.25148 5.67736 5.13518 1.36435 5.00279 1.81431 3.70306 4.93418 2.26240 4.37498 5.04857 5.35363 5.01734 4.94348 2.69815 4.12919 2.27784 5.23374 1.74134 3 f - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00419 5.87271 6.59506 0.61958 0.77255 1.33581 0.30509\n+ 4 3.62824 5.37442 4.42685 3.85713 4.23638 4.55175 2.65057 1.99543 2.18568 3.57795 4.48265 4.24962 4.92989 4.05452 3.91871 2.28846 3.85384 3.67031 5.70648 1.07180 4 y - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00419 5.87271 6.59506 0.61958 0.77255 0.17967 1.80515\n+ 5 5.56775 6.63635 7.57461 7.02760 4.51160 7.17694 7.42463 1.74124 6.95362 0.27498 4.21004 7.42622 6.85694 6.50443 6.74864 6.73150 5.74316 3.98153 6.96553 6.15413 5 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00350 6.05380 6.77614 0.61958 0.77255 0.48576 0.95510\n+ 6 5.37902 7.34053 4.66423 1.73401 7.40575 0.24959 6.49078 7.25699 5.78769 6.63617 7.66033 5.29759 6.16788 5.78818 6.30809 5.36411 5.82913 6.61969 8.21053 7.22988 6 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00350 6.05380 6.77614 0.61958 0.77255 0.48576 0.95510\n+ 7 4.89003 7.77828 1.88730 1.20371 7.03475 0.74389 5.55484 6.70246 4.88778 6.09300 7.08942 4.2425'..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00350 6.05380 6.77614 0.61958 0.77255 0.48576 0.95510\n+ 21 4.00367 6.60204 1.60608 2.44148 5.92176 2.47015 4.88110 5.43879 2.44672 4.89758 5.67278 1.61679 5.02295 4.00734 4.30696 1.45450 4.26031 4.98337 7.02839 5.55339 24 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00350 6.05380 6.77614 0.61958 0.77255 0.48576 0.95510\n+ 22 1.98887 4.99066 5.57551 4.96511 4.09525 4.79903 5.14033 2.45274 4.75650 2.33030 2.41507 4.95806 5.16054 4.89268 4.77222 2.59373 2.41592 1.12191 5.63592 4.45871 25 v - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00350 6.05380 6.77614 0.61958 0.77255 0.48576 0.95510\n+ 23 5.49386 0.14184 6.83134 6.83247 6.24730 5.78568 2.28091 7.11933 6.60935 6.49839 7.62238 6.67311 6.53077 7.00956 6.57397 5.71502 6.03725 6.54029 7.54172 6.24565 26 C - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00350 6.05380 6.77614 0.61958 0.77255 0.48576 0.95510\n+ 24 0.71977 5.81096 6.46859 6.38297 6.03383 4.89203 6.93842 4.00276 6.28226 4.68808 5.84937 5.76673 5.71149 6.41086 6.27251 4.40579 4.60922 0.84393 7.80659 6.68572 27 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00350 6.05380 6.77614 0.61958 0.77255 0.48576 0.95510\n+ 25 1.46028 5.67266 5.78584 5.46746 6.05006 1.19047 6.22425 5.49360 5.39392 5.18836 5.99165 5.21718 5.33481 5.59252 5.57514 1.96076 1.76253 4.84425 2.38465 6.30432 28 g - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00350 6.05380 6.77614 0.61958 0.77255 0.48576 0.95510\n+ 26 5.70868 7.09001 6.01276 5.63115 4.23362 5.92965 5.42351 6.07446 1.69074 5.22287 6.48358 5.69026 6.36004 5.38916 4.65479 5.65479 5.90221 5.92010 5.83828 0.29622 29 Y - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00350 6.05380 6.77614 0.61958 0.77255 0.48576 0.95510\n+ 27 3.46173 5.82299 3.77399 2.40910 2.93078 2.52575 2.35438 4.55873 1.57647 2.67087 4.87923 3.75415 4.65203 3.57286 3.69489 1.93984 3.69288 4.18282 6.28888 2.83187 30 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00350 6.05380 6.77614 0.61958 0.77255 0.48576 0.95510\n+ 28 2.49150 5.95508 3.70318 1.86959 5.29601 1.74406 4.41652 4.77890 1.77844 4.25842 4.99707 2.77059 4.62241 2.59511 3.64398 3.41867 3.68582 2.77291 6.39003 2.98671 31 g - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00235 6.05266 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype12.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype12.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,100 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype13.3\n+LENG 26\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Wed Jul 29 15:10:18 2015\n+NSEQ 41\n+EFFN 30.216980\n+CKSUM 2444189330\n+STATS LOCAL MSV -6.2563 0.72009\n+STATS LOCAL VITERBI -6.5810 0.72009\n+STATS LOCAL FORWARD -4.0849 0.72009\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 3.13085 4.16814 2.53748 2.80871 3.61513 2.12326 2.32880 3.98863 2.72121 2.99470 4.22031 2.95070 4.09066 3.86543 2.67260 2.60940 2.70619 3.20397 4.61308 2.83857\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00133 7.01839 7.74073 0.61958 0.77255 0.00000 *\n+ 1 4.83303 7.03444 5.28131 4.61534 6.39189 5.56956 2.04820 5.77045 1.58328 3.23933 2.78040 3.10111 5.92732 4.71380 1.27421 4.83653 2.01980 5.43870 3.02189 6.14823 1 r - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00133 7.01839 7.74073 0.61958 0.77255 0.48576 0.95510\n+ 2 5.02401 7.65122 2.09690 4.28894 6.94069 5.42593 1.17480 6.48733 4.79765 5.94142 6.73735 1.61126 2.55729 1.99533 5.37110 3.45824 5.29084 6.02874 8.06601 2.63748 2 h - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00133 7.01839 7.74073 0.61958 0.77255 0.48576 0.95510\n+ 3 5.93694 7.83109 7.08968 5.77116 7.73391 6.37996 6.05982 6.86321 0.58655 6.10293 7.02877 5.95380 6.69188 5.18504 1.69269 1.99573 2.34234 6.55969 7.97812 7.01912 3 K - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00133 7.01839 7.74073 0.61958 0.77255 0.48576 0.95510\n+ 4 6.44586 7.53366 7.72613 7.46520 2.68584 7.23978 6.17654 5.69394 7.02367 0.44036 6.16692 6.93592 3.68834 6.94641 1.99579 6.63566 6.64306 5.81237 6.26580 2.25012 4 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00133 7.01839 7.74073 0.61958 0.77255 0.48576 0.95510\n+ 5 6.37446 3.13047 8.11566 8.19865 8.59908 0.05314 8.65679 8.55002 8.24715 7.97254 8.95047 7.82558 7.49360 8.40562 8.04707 6.61738 6.95732 7.67957 9.23027 8.89387 5 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00133 7.01839 7.74073 0.61958 0.77255 0.48576 0.95510\n+ 6 6.95763 8.44402 6.85139 3.64383 8.13166 0.06465 8.18689 8.70642 7.58248 7.96280 9.10318 7.34252 7.62515 7.75788 7.75470 7.08745 7.44670 8.09719 3.55749 8.13289 6 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02533 7.01839 3.72474 0.61958 0.77255 0.48576 0.95510\n+ 7 2.20122 5.74477 6.01781 5.41915 1.24873 5.45982 5.77808 4.18390 3.44919 3.20435 3.47446 5.5290'..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00133 7.01839 7.74073 0.61958 0.77255 0.48576 0.95510\n+ 19 2.22732 7.56067 4.53075 0.55199 6.95985 5.45143 5.86559 6.46714 3.42232 5.91309 6.70883 4.92559 6.00320 2.32657 5.17554 1.99073 5.27799 6.00592 8.02657 6.57465 19 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00133 7.01839 7.74073 0.61958 0.77255 0.48576 0.95510\n+ 20 4.28004 6.26352 4.84491 2.95516 3.30123 5.16265 5.37315 4.83748 1.25910 2.25853 5.35047 4.76088 5.54703 3.40619 1.88350 4.38337 3.05565 2.04218 6.80010 2.43144 20 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00133 7.01839 7.74073 0.61958 0.77255 0.48576 0.95510\n+ 21 4.93159 7.28165 5.26997 4.61925 6.75778 5.61124 1.73113 6.14681 1.92762 5.54121 6.34240 1.56729 5.97493 4.71639 2.17265 1.75726 2.04100 5.75308 7.57067 6.32190 21 n - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00133 7.01839 7.74073 0.61958 0.77255 0.48576 0.95510\n+ 22 4.75272 6.09971 6.73348 6.12440 2.04144 5.95488 6.28642 1.17557 5.91720 2.75430 1.56261 2.29268 6.27731 6.01018 5.91225 5.27644 2.01603 4.16956 6.70597 5.55610 22 i - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00133 7.01839 7.74073 0.61958 0.77255 0.48576 0.95510\n+ 23 6.51033 7.82223 7.27100 7.28197 4.63260 6.94811 0.47518 6.88156 7.05812 5.96473 7.34782 6.83286 7.45968 7.06151 7.00524 6.48252 1.40824 6.73208 6.30601 2.23840 23 H - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00133 7.01839 7.74073 0.61958 0.77255 0.48576 0.95510\n+ 24 2.99744 2.22683 7.48651 7.47795 7.30755 5.58418 7.83782 5.63330 7.29355 6.17013 7.15753 6.55007 1.98147 7.32730 7.19287 5.08916 5.40535 0.38972 8.87665 7.84637 24 V - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00133 7.01839 7.74073 0.61958 0.77255 0.48576 0.95510\n+ 25 5.54915 6.99642 7.10987 6.09512 5.27092 6.38466 0.93302 5.41185 4.65818 2.43293 5.99012 6.14353 6.68334 5.59763 1.07796 5.81157 5.70922 2.22355 3.87132 5.30891 25 h - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00133 7.01839 7.74073 0.61958 0.77255 0.48576 0.95510\n+ 26 1.95730 7.23276 6.46413 6.54009 5.30654 6.01591 6.65393 7.06594 6.96740 6.35117 7.51379 2.21978 6.80686 6.93370 7.05501 5.56828 5.97019 6.49412 6.95947 0.32593 26 Y - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00090 7.01795 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype13a.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype13a.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,79 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype14.1\n+LENG 19\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Tue Jul 28 16:27:03 2015\n+NSEQ 3\n+EFFN 3.000000\n+CKSUM 3093060998\n+STATS LOCAL MSV -6.7082 0.72505\n+STATS LOCAL VITERBI -6.8337 0.72505\n+STATS LOCAL FORWARD -3.8518 0.72505\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 3.47924 1.91926 2.83439 3.35071 4.28868 1.92877 3.84701 2.98486 3.43339 3.08189 4.99840 3.99859 4.54541 3.64707 3.34265 2.30221 3.06635 2.83915 3.27001 2.53423\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.00000 *\n+ 1 4.29855 0.10028 5.77903 5.78110 5.77175 4.59606 6.25487 5.29727 5.71123 5.04500 6.22088 5.61060 5.34072 6.00555 5.61979 4.56287 4.83824 4.91742 6.78097 6.01854 1 C - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 2 3.02268 5.23372 3.37314 2.98013 4.97088 1.63718 4.21433 4.42723 1.49394 3.95115 4.73915 3.44327 4.25097 3.35530 3.28784 1.62572 3.35373 3.94809 6.08670 4.76345 2 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 3 4.38137 5.94081 5.22664 5.27215 6.19954 0.08431 6.19771 6.15946 5.56295 5.60855 6.66681 5.39550 5.33385 5.81061 5.58400 4.59559 4.92251 5.50436 6.92319 6.36842 3 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.28833 4.92694 1.41373 0.61958 0.77255 0.48576 0.95510\n+ 4 3.34515 5.91492 1.15706 2.49930 5.20500 3.61294 4.15557 4.78205 3.14375 4.24796 5.10450 3.08457 4.23586 1.30099 3.71239 3.22651 3.63613 4.33912 6.35911 4.85778 4 d - - -\n+ 2.68628 4.42235 2.77530 2.73133 3.46364 2.40523 3.72505 3.29364 2.67751 2.69365 4.24700 2.90357 2.73750 3.18157 2.89811 2.37785 2.77530 2.98529 4.58487 3.61513\n+ 0.46354 1.00426 5.37523 0.10557 2.30072 0.26958 1.44265\n+ 5 2.89356 4.83222 4.31982 4.26018 5.47750 0.72461 5.34283 5.02710 4.51214 4.68541 5.45809 4.18579 4.40932 4.68138 4.71813 1.24546 3.46052 4.18042 6.77312 5.65434 6 g - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 6 4.75690 5.89417 5.20186 5.03953 2.56183 5.19715 1.38050 4.63093 4.78525 3.79450 5.13036 4.77208 5.53043 4.86640 4.82076 4.65566 4.97326 4.54264 4.23434 0.64196 7 Y - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 7 3.19057 5.21774 3.96099 3.49658 5.09430 3.84936 4.44950 4.57607 2.91985 4.09993 4.94280 3.81724 '..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 12 3.81074 5.18723 5.53612 5.31808 4.61167 4.79531 6.03761 2.58028 5.23451 3.17087 4.49373 5.34410 5.36627 5.55797 5.34702 4.44980 4.18522 0.27818 6.51146 5.29766 13 V - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 13 3.24875 5.69464 1.49203 2.71309 5.12157 1.63591 4.17291 4.62048 2.99362 4.10441 4.90177 3.26875 4.29391 3.31121 1.70191 3.19240 3.52336 4.17753 6.22854 4.81129 14 d - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 14 4.99618 6.06306 5.50145 5.47688 3.03415 5.14289 4.56794 4.93796 5.34433 4.11379 5.49786 5.19187 5.62424 5.36166 5.27931 4.99638 5.30063 4.85723 4.68580 0.17648 15 Y - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 15 3.07107 5.34105 1.50520 2.83353 5.02671 3.65738 4.27169 4.50284 3.16941 4.05125 4.84509 3.34557 4.25384 3.42509 3.67633 1.51135 1.67402 4.01900 6.22336 4.82847 16 d - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 16 2.89356 4.83222 4.31982 4.26018 5.47750 0.72461 5.34283 5.02710 4.51214 4.68541 5.45809 4.18579 4.40932 4.68138 4.71813 1.24546 3.46052 4.18042 6.77312 5.65434 17 g - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.28833 4.92694 1.41373 0.61958 0.77255 0.48576 0.95510\n+ 17 4.88152 5.91896 5.41569 5.34424 3.86378 4.74096 5.15629 5.04869 5.12774 4.27972 5.62529 5.38609 5.32476 5.46177 5.09546 5.08305 5.23282 4.94738 0.15640 3.83752 18 W - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01427 4.65288 5.37523 0.61958 0.77255 0.26958 1.44265\n+ 18 4.29855 0.10028 5.77903 5.78110 5.77175 4.59606 6.25487 5.29727 5.71123 5.04500 6.22088 5.61060 5.34072 6.00555 5.61979 4.56287 4.83824 4.91742 6.78097 6.01854 19 C - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 19 3.48371 5.13896 4.66925 4.42336 4.28566 1.49304 5.18896 3.62533 4.35517 0.64979 4.30932 4.56883 4.84444 4.66485 4.52342 3.76510 3.88843 3.52207 5.93830 4.75271 20 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00730 4.92341 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype13b.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype13b.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,118 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype14.2\n+LENG 32\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Tue Jul 28 16:17:39 2015\n+NSEQ 8\n+EFFN 2.628906\n+CKSUM 3760608179\n+STATS LOCAL MSV -7.4951 0.71981\n+STATS LOCAL VITERBI -7.6469 0.71981\n+STATS LOCAL FORWARD -4.1078 0.71981\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.90190 2.45101 2.86412 2.78407 4.22511 1.87795 3.37520 3.67807 2.68716 2.89926 4.42466 3.45809 3.74053 2.98260 3.20135 3.00066 2.95608 3.07760 3.03803 3.33675\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01199 4.82517 5.54752 0.61958 0.77255 0.00000 *\n+ 1 4.42099 5.64797 5.71438 5.43713 3.80975 5.19088 5.84037 3.11708 5.23212 0.23184 3.67092 5.65307 5.52016 5.34108 5.22063 5.03151 4.69423 3.37923 5.92241 4.84295 1 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01199 4.82517 5.54752 0.61958 0.77255 0.48576 0.95510\n+ 2 4.10816 0.12302 5.62020 5.60375 5.57106 4.44372 6.08514 5.03998 5.51500 4.81789 5.98886 5.42911 5.18989 5.81486 5.44300 4.37280 4.64432 4.67680 6.63136 5.82318 2 C - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01199 4.82517 5.54752 0.61958 0.77255 0.48576 0.95510\n+ 3 4.19845 5.78580 5.03570 5.07119 6.02829 0.10236 6.02432 5.95085 5.35807 5.42542 6.47157 5.20404 5.18257 5.61121 5.40357 4.40825 4.73731 5.30712 6.78906 6.18986 3 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01199 4.82517 5.54752 0.61958 0.77255 0.48576 0.95510\n+ 4 3.70660 4.90608 5.77713 5.28875 4.05122 5.29110 5.92736 1.64411 5.21380 1.66616 3.79357 5.44508 5.47859 5.38608 5.33102 4.71284 3.95744 0.75504 6.17425 5.02038 4 v - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01199 4.82517 5.54752 0.61958 0.77255 0.48576 0.95510\n+ 5 2.94048 5.21200 3.07749 1.73246 4.75551 3.60652 4.07397 4.20598 2.89530 3.76410 4.55657 3.24842 4.13577 3.21669 3.36980 1.37492 1.93670 3.77615 5.94865 4.57724 5 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01199 4.82517 5.54752 0.61958 0.77255 0.48576 0.95510\n+ 6 4.19845 5.78580 5.03570 5.07119 6.02829 0.10236 6.02432 5.95085 5.35807 5.42542 6.47157 5.20404 5.18257 5.61121 5.40357 4.40825 4.73731 5.30712 6.78906 6.18986 6 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01199 4.82517 5.54752 0.61958 0.77255 0.48576 0.95510\n+ 7 2.24217 5.78823 1.66013 1.48103 5.12369 1.95079 4.09746 4.63844 3.01708 4.11244 4.90731 3.11847 '..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01199 4.82517 5.54752 0.61958 0.77255 0.48576 0.95510\n+ 25 3.58660 5.76752 4.03927 3.26983 5.32676 4.17589 4.01798 4.62902 1.43612 3.97589 4.83316 3.65830 4.50826 1.10132 1.86870 3.54788 3.71894 4.28909 5.94928 4.81706 25 q - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01199 4.82517 5.54752 0.61958 0.77255 0.48576 0.95510\n+ 26 3.16997 5.44796 3.16920 2.80844 4.66112 3.78862 1.19349 4.26245 2.68143 3.77001 4.60068 3.32033 2.58780 2.03506 3.03873 3.15374 3.41250 3.89481 5.82982 4.45433 26 h - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01199 4.82517 5.54752 0.61958 0.77255 0.48576 0.95510\n+ 27 5.23319 6.19006 5.69763 5.66712 4.19386 4.97077 5.47080 5.46439 5.49139 4.65741 6.02203 5.71087 5.56473 5.80956 5.42261 5.44007 5.59465 5.35693 0.10933 4.16491 27 W - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01199 4.82517 5.54752 0.61958 0.77255 0.48576 0.95510\n+ 28 3.58325 6.34961 0.98907 1.35428 5.60625 3.70250 4.32391 5.19177 3.45606 4.62319 5.50326 2.12190 4.37525 3.49852 4.14727 3.41087 3.88981 4.70860 6.76658 5.15887 28 d - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01199 4.82517 5.54752 0.61958 0.77255 0.48576 0.95510\n+ 29 4.10816 0.12302 5.62020 5.60375 5.57106 4.44372 6.08514 5.03998 5.51500 4.81789 5.98886 5.42911 5.18989 5.81486 5.44300 4.37280 4.64432 4.67680 6.63136 5.82318 29 C - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01199 4.82517 5.54752 0.61958 0.77255 0.48576 0.95510\n+ 30 2.81364 4.84958 2.52976 2.79712 4.08542 2.68481 3.93381 2.75343 2.79020 3.12716 3.97122 3.28566 4.08114 3.12704 3.22924 2.36870 1.75441 2.60188 5.42150 4.12374 30 t - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01199 4.82517 5.54752 0.61958 0.77255 0.48576 0.95510\n+ 31 2.92464 5.43240 2.11671 2.53223 4.77371 1.83087 3.85533 4.25819 2.09626 3.73342 4.48555 2.41328 4.05020 2.96221 2.45110 2.87738 3.16080 3.82346 5.86298 4.44910 31 g - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01199 4.82517 5.54752 0.61958 0.77255 0.48576 0.95510\n+ 32 3.65150 5.80271 4.16288 3.33854 5.39113 4.22476 4.02849 4.67163 0.89662 4.00189 4.86760 3.70669 4.54619 1.78843 1.80896 3.61156 3.77014 4.33926 5.96003 4.85145 32 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00809 4.82127 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype13c.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype13c.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,91 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype14.3\n+LENG 23\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Tue Jul 28 15:58:32 2015\n+NSEQ 60\n+EFFN 38.909912\n+CKSUM 3233938693\n+STATS LOCAL MSV -6.6788 0.72026\n+STATS LOCAL VITERBI -6.9771 0.72026\n+STATS LOCAL FORWARD -4.0744 0.72026\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.82531 2.05809 2.83212 2.72052 4.92550 1.77574 3.19463 5.51568 2.78183 2.41318 4.82188 2.55520 4.24228 3.10702 3.14577 2.60296 3.43608 4.49851 5.62702 5.05682\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00104 7.26521 7.98755 0.61958 0.77255 0.00000 *\n+ 1 7.01107 8.01775 8.77332 8.31849 3.20015 8.32030 8.14471 5.10292 8.25414 0.06323 5.46284 8.56639 8.06829 7.70758 7.96962 8.04077 7.16390 5.59755 7.84986 6.65931 1 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00104 7.26521 7.98755 0.61958 0.77255 0.48576 0.95510\n+ 2 8.34315 0.00289 8.63533 8.72712 9.21980 7.64340 9.22864 9.61784 8.90281 8.69461 10.02758 8.98808 8.29482 9.20396 8.64220 8.70546 8.79460 9.18010 9.53267 9.46273 2 C - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00104 7.26521 7.98755 0.61958 0.77255 0.48576 0.95510\n+ 3 7.54892 8.78173 8.11156 8.19720 8.82444 0.03738 3.42029 9.28623 8.52188 8.48711 9.67952 8.39243 8.09022 8.76084 8.41245 7.79307 8.06777 8.65950 9.43200 8.95840 3 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00104 7.26521 7.98755 0.61958 0.77255 0.48576 0.95510\n+ 4 6.02769 8.04179 6.83606 5.72883 7.74637 6.52368 6.18378 6.93456 0.80333 3.41886 3.76168 3.78842 6.80350 1.69600 1.38118 5.98377 3.87397 6.63710 8.11162 7.09134 4 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00104 7.26521 7.98755 0.61958 0.77255 0.48576 0.95510\n+ 5 4.90543 7.45655 4.68111 2.40883 6.80898 2.58035 3.80172 6.31243 3.34027 5.77584 6.53805 2.03107 5.97607 4.93288 5.14828 0.60863 2.87848 5.86007 7.90261 6.45661 5 S - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00104 7.26521 7.98755 0.61958 0.77255 0.48576 0.95510\n+ 6 0.35773 7.16803 5.39593 3.66777 6.70654 5.67962 5.93377 6.11499 3.38724 5.62949 6.43818 5.31157 2.89405 5.06731 2.67458 3.87025 5.22426 2.85251 7.76193 6.48468 6 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00104 7.26521 7.98755 0.61958 0.77255 0.48576 0.95510\n+ 7 2.52999 6.91065 4.64784 4.09193 6.25691 2.80047 5.35934 5.74307 1.73079 5.21642 5.95156 3.19092'..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00111 7.19815 7.92050 0.61958 0.77255 1.50161 0.25202\n+ 16 4.34177 6.85543 2.91781 2.66240 6.20198 0.96306 5.30134 5.68878 2.44804 5.16116 3.00712 3.14882 5.50808 2.61701 2.43262 2.63976 4.57289 5.24688 3.48062 5.87546 16 g - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.09051 7.19815 2.45587 0.61958 0.77255 1.50161 0.25202\n+ 17 4.29662 6.81211 2.07484 3.97497 6.15744 2.88792 3.15924 5.64504 2.44114 5.11768 5.85385 1.13303 3.31599 4.35121 4.48818 1.91396 2.72564 5.20312 7.24432 3.23132 17 n - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00122 7.10885 7.83120 0.61958 0.77255 2.08143 0.13325\n+ 18 3.07397 7.35574 2.74829 2.12382 6.68425 0.76675 2.97445 6.19196 4.51549 5.65452 6.41767 3.19533 3.59249 4.80014 1.98865 4.70880 5.03205 5.74067 7.78344 6.32767 18 g - - -\n+ 2.69037 4.42644 2.77617 2.73326 3.46773 2.39055 3.72914 3.29773 2.67085 2.69774 4.25109 2.89229 2.74159 3.18565 2.89964 2.38227 2.77389 2.98937 4.58896 3.61922\n+ 0.75842 0.63263 7.83120 0.84359 0.56241 0.08123 2.55077\n+ 19 8.34315 0.00289 8.63533 8.72712 9.21980 7.64340 9.22864 9.61784 8.90281 8.69461 10.02758 8.98808 8.29482 9.20396 8.64220 8.70546 8.79460 9.18010 9.53267 9.46273 23 C - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00104 7.26521 7.98755 0.61958 0.77255 0.48576 0.95510\n+ 20 3.00697 7.16309 4.82097 3.19712 6.59768 2.74719 0.63565 6.06710 4.65306 2.76547 6.37395 3.89594 2.73726 4.96146 5.15349 2.12481 5.06853 5.64284 7.76643 6.36879 24 H - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00104 7.26521 7.98755 0.61958 0.77255 0.48576 0.95510\n+ 21 3.22497 6.96287 3.43872 3.06526 6.30821 1.65098 3.69053 5.79656 2.25767 5.26843 6.00479 1.68871 5.60377 4.49851 4.63808 1.44014 2.37896 5.35392 7.39468 5.97985 25 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.06917 7.26521 2.71613 0.61958 0.77255 0.48576 0.95510\n+ 22 4.56372 7.09833 1.91102 2.42129 6.43842 1.13700 5.50089 5.93248 3.19074 5.40150 6.14613 1.74525 5.68949 4.60520 3.47132 2.19242 4.80137 3.39903 7.52849 6.10130 26 g - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.07712 7.19715 2.61085 0.61958 0.77255 1.51076 0.24941\n+ 23 2.85468 6.86371 2.70768 4.00760 6.20882 3.37166 2.94906 5.69775 3.46274 5.16955 5.90709 0.69882 5.49924 2.71074 4.54070 2.38607 3.08845 5.25492 7.29610 5.87987 27 n - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00081 7.12084 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype13d.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype13d.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,82 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype14.5.1\n+LENG 20\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Tue Jul 28 15:11:41 2015\n+NSEQ 3\n+EFFN 3.000000\n+CKSUM 1974769037\n+STATS LOCAL MSV -6.2417 0.72590\n+STATS LOCAL VITERBI -6.4613 0.72590\n+STATS LOCAL FORWARD -3.8234 0.72590\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 3.09939 5.34179 3.56833 2.56615 5.15587 2.75704 3.98798 3.72583 2.63739 4.20631 5.22984 3.16584 1.72039 4.27391 2.49511 2.00840 1.88271 3.49221 6.38113 5.23487\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.00000 *\n+ 1 4.61481 6.07111 5.30731 5.32973 6.09810 4.70884 6.20185 6.06257 5.49846 5.48299 6.63431 5.51390 0.08208 5.83390 5.52536 4.83363 5.12935 5.56226 6.87226 6.25948 1 P - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 2 4.39942 6.12840 4.64246 4.17909 5.79396 4.61603 4.88629 5.35693 0.20070 4.71863 5.71531 4.51427 5.11690 4.08594 3.28682 4.43275 4.61403 5.03784 6.46104 5.51309 2 K - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 3 2.93229 4.87523 4.21430 4.09482 5.33356 3.60244 5.19534 4.88225 4.26040 4.53422 5.33819 4.12587 0.85235 4.50786 4.50678 1.15285 3.47765 4.13495 6.63303 5.46413 3 p - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 4 4.63269 6.17031 5.23627 4.65723 5.83104 4.75957 5.16203 5.57076 3.40946 4.88757 5.93594 4.90413 5.28406 4.40770 0.15346 4.72514 4.87591 5.25930 6.52707 5.64972 4 R - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 5 3.13756 4.76435 4.93159 4.57526 4.38750 4.06107 5.27808 2.73098 4.45087 3.14279 4.27350 4.53983 4.72437 4.72802 4.61863 3.51719 0.97725 1.17836 6.08623 4.88825 5 t - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 6 3.08109 5.36914 3.32462 2.87673 4.90492 3.76162 4.07678 4.36262 2.69790 3.85989 4.65119 1.54805 4.24165 3.20539 1.71503 1.68970 3.35391 3.93342 5.97504 4.64483 6 n - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 7 3.27344 5.30033 4.02344 3.51231 5.14381 3.91836 4.40301 4.60705 2.79733 4.10434 4.95627 3.83310'..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 13 4.61481 6.07111 5.30731 5.32973 6.09810 4.70884 6.20185 6.06257 5.49846 5.48299 6.63431 5.51390 0.08208 5.83390 5.52536 4.83363 5.12935 5.56226 6.87226 6.25948 13 P - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 14 3.20488 5.08928 4.55393 4.52410 5.40775 3.81848 5.51279 5.14253 4.68514 4.79455 5.67446 4.46164 4.64594 4.93377 4.83796 0.22583 3.76883 4.40181 6.67484 5.53906 14 S - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 15 3.50003 5.91709 3.10752 0.97437 5.33100 3.93150 4.20296 4.77826 1.30024 4.20360 5.04085 3.41027 4.44134 3.34032 3.10962 3.42009 3.73005 4.37545 6.25707 4.93044 15 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 16 3.31622 4.81296 4.99547 4.57967 4.15273 4.36776 5.25550 1.21591 4.43038 2.82051 4.02519 4.66967 4.90293 4.72427 4.60360 3.79818 1.03988 2.34253 5.93481 4.73045 16 t - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 17 3.58225 5.80439 3.13467 3.03424 4.53192 3.95513 1.38161 4.83099 3.27733 4.28753 5.20700 0.93310 4.56079 3.67401 3.65682 3.54143 3.89269 4.43035 5.92171 4.37378 17 n - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 18 2.97326 4.88448 4.35407 4.16776 5.17734 3.66022 5.17235 4.57145 4.19442 4.28924 5.15624 4.18536 1.26457 4.49575 4.42368 3.16924 0.81327 3.98163 6.50276 5.36060 18 t - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 19 3.42384 5.23617 4.84601 4.77568 5.39247 4.01365 5.64153 4.72950 4.75585 4.52264 5.55782 4.69647 4.81267 5.08969 4.87301 3.64217 0.20934 4.25217 6.65833 5.63018 19 T - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510\n+ 20 4.41353 6.36850 3.55766 0.17446 5.94872 4.38487 5.21442 5.70456 4.29834 5.15447 6.21155 4.15585 5.06174 4.48988 4.73891 4.34638 4.76278 5.30888 6.85038 5.78836 20 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00730 4.92341 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype14.4.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype14.4.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,91 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype14.4\n+LENG 23\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Tue Jul 28 15:21:50 2015\n+NSEQ 91\n+EFFN 91.000000\n+CKSUM 1829739437\n+STATS LOCAL MSV -6.5070 0.72748\n+STATS LOCAL VITERBI -7.1393 0.72748\n+STATS LOCAL FORWARD -3.5442 0.72748\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.81642 2.29817 2.87787 2.84232 5.21343 1.73650 3.31688 4.64076 2.86406 2.42860 4.82927 2.63024 4.04170 3.21529 3.02541 2.62503 3.19709 3.61796 4.43421 4.25618\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00045 8.10272 8.82506 0.61958 0.77255 0.00000 *\n+ 1 7.92646 8.91303 9.59873 9.18458 3.48995 9.08711 9.05082 6.02523 9.13733 0.03949 6.38238 9.44932 8.92214 8.61278 8.85014 8.95628 8.07974 6.52242 8.76318 7.59483 1 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00045 8.10272 8.82506 0.61958 0.77255 0.48576 0.95510\n+ 2 9.48546 0.00113 9.50220 9.59526 10.13392 8.54747 10.10594 10.57141 9.78463 9.59683 10.96754 9.92576 9.18472 10.09805 9.51719 9.90243 9.88813 10.19884 10.39286 10.38464 2 C - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00045 8.10272 8.82506 0.61958 0.77255 0.48576 0.95510\n+ 3 8.91575 9.81926 9.30469 9.39565 9.94112 0.02612 3.70657 10.38755 9.64278 9.49497 10.78123 9.63556 9.08426 9.91350 9.43099 9.22261 9.39636 9.87525 10.35089 10.13926 3 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00045 8.10272 8.82506 0.61958 0.77255 0.48576 0.95510\n+ 4 5.82240 7.43966 6.96891 6.22655 6.60836 6.75526 6.82196 3.22187 1.25880 3.20089 3.45934 4.27852 7.10082 2.36654 1.13560 6.07626 3.36673 2.07237 7.96151 6.79067 4 r - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02586 8.10272 3.67986 0.61958 0.77255 0.48576 0.95510\n+ 5 2.92763 7.66112 4.08423 2.33285 7.00735 3.20323 4.23060 6.49453 3.75962 5.96702 6.70195 2.08461 4.02029 5.20240 5.33552 0.67689 2.74561 3.86869 8.09318 6.68080 5 S - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00046 8.07732 8.79966 0.61958 0.77255 1.43126 0.27313\n+ 6 0.96450 7.69258 5.43833 3.35968 7.04438 1.49091 3.55874 6.52632 2.26842 5.99560 6.73391 5.42411 3.50456 3.87688 2.23323 4.29024 5.41674 3.37778 8.11690 6.71415 6 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.05781 8.07732 2.88487 0.61958 0.77255 1.43126 0.27313\n+ 7 1.96312 7.59521 2.26576 2.50800 6.94170 2.54482 6.04142 6.42867 2.24280 5.90110 6.63551 2.27554'..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00691 7.87427 5.03558 0.61958 0.77255 3.11173 0.04555\n+ 16 2.47047 7.45351 3.36381 3.12326 6.79995 1.42535 2.80205 3.26031 2.86461 5.75938 3.90498 3.65113 3.05274 3.02072 2.08748 3.15096 2.29605 5.84488 3.83976 6.47361 16 g - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.08652 7.86794 2.49490 0.61958 0.77255 2.72029 0.06812\n+ 17 4.87261 7.38703 2.41631 3.63262 6.73337 2.50100 3.32319 6.22049 2.25258 5.69286 6.42748 1.44259 2.53105 2.21736 5.06057 1.96447 3.13956 5.77837 7.81884 3.62912 17 n - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00062 7.78894 8.51128 0.61958 0.77255 1.95660 0.15238\n+ 18 3.59975 7.49063 3.19494 2.62207 6.83616 0.83629 2.59265 6.32497 4.67045 5.79667 6.53364 3.81709 3.98074 5.02480 2.49371 2.57382 2.09637 5.88202 7.92299 6.50722 18 g - - -\n+ 2.69262 4.43221 2.78281 2.73883 3.46122 2.38030 3.70619 3.30350 2.67675 2.69985 4.25685 2.89659 2.74735 3.19142 2.90518 2.37412 2.77836 2.99514 4.51548 3.60731\n+ 0.81794 0.69791 2.79628 1.05543 0.42778 0.22262 1.61155\n+ 19 3.03655 0.70561 2.34052 2.78325 6.91289 2.81942 3.89078 6.38919 4.81852 5.88238 6.62915 2.88618 6.27422 5.17581 5.31009 2.50345 4.02248 3.76847 8.02544 4.28639 23 c - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.12291 8.00728 2.16002 0.61958 0.77255 1.15114 0.38020\n+ 20 3.50400 7.44322 2.94812 3.58107 6.76491 2.81004 1.02737 6.23474 4.70702 2.66177 3.56270 4.19058 2.53669 5.06684 3.22374 1.84527 5.22112 2.90178 7.89018 6.49373 24 h - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00054 7.91436 8.63671 0.61958 0.77255 0.03322 3.42108\n+ 21 3.83963 7.67251 3.52617 3.74939 7.01889 1.45576 2.93070 6.50579 2.39119 3.12955 6.71283 1.99036 6.32559 3.50688 3.18291 1.94623 3.78621 3.66494 8.10441 2.31925 25 g - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03854 8.10272 3.28339 0.61958 0.77255 0.48576 0.95510\n+ 22 2.89749 7.63670 2.68705 2.95601 6.98305 1.62376 2.91907 2.59740 3.72806 5.94253 6.67703 1.63674 6.28988 3.06481 3.42684 2.70430 3.53463 2.33838 8.06863 6.65691 26 g - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.04702 8.06465 3.08740 0.61958 0.77255 1.69307 0.20329\n+ 23 2.35641 7.59383 3.43264 2.96958 6.94005 1.46437 3.57287 6.42687 4.04413 5.89960 6.63420 1.32919 6.24707 3.25020 5.26797 2.78150 2.77502 3.05493 2.91254 6.61410 27 n - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00033 8.01795 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype14.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype14.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,223 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype15.1\n+LENG 67\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Tue Jul 28 14:44:29 2015\n+NSEQ 13\n+EFFN 2.193115\n+CKSUM 3412623817\n+STATS LOCAL MSV -8.5592 0.71879\n+STATS LOCAL VITERBI -9.3900 0.71879\n+STATS LOCAL FORWARD -3.6891 0.71879\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.52984 5.07967 2.82451 2.25196 4.37397 3.33162 3.73315 3.14016 2.28288 3.14202 4.14584 2.83745 3.01554 2.47819 2.88911 2.36170 2.59837 3.16702 5.72363 4.43425\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01373 4.69073 5.41307 0.61958 0.77255 0.00000 *\n+ 1 2.43610 5.33073 3.07025 1.46277 4.68567 3.60515 3.77256 4.14965 2.13402 3.62122 4.37861 3.07610 4.00430 2.31453 2.41688 2.82971 3.09169 3.72878 5.73955 4.36249 1 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01373 4.69073 5.41307 0.61958 0.77255 0.48576 0.95510\n+ 2 2.34333 5.25715 2.57853 2.48120 4.59343 3.55209 3.73879 4.06722 2.27281 3.55553 4.30353 3.02519 3.94798 2.00818 2.13557 2.75116 2.43961 3.64377 5.69297 4.29554 2 q - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01373 4.69073 5.41307 0.61958 0.77255 0.48576 0.95510\n+ 3 3.48075 5.65822 3.85267 3.15721 5.20128 4.06159 3.94784 4.52027 0.74486 3.88593 4.74415 2.82919 4.41423 3.06965 1.95243 3.44630 3.62608 4.17904 5.87072 4.72527 3 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01373 4.69073 5.41307 0.61958 0.77255 0.48576 0.95510\n+ 4 3.21087 5.41404 3.57966 2.95064 4.76973 3.89808 3.90179 4.15122 1.04106 2.47913 4.47340 3.40262 4.26592 2.07127 2.54506 3.20402 3.39580 3.82889 5.73449 4.49938 4 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01373 4.69073 5.41307 0.61958 0.77255 0.48576 0.95510\n+ 5 2.76698 5.23731 3.02796 2.10872 4.56810 3.54415 2.95669 4.04186 2.13481 3.01499 4.28250 2.58195 3.93750 2.83287 2.66209 2.05979 2.56694 3.62042 5.67723 4.27834 5 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01373 4.69073 5.41307 0.61958 0.77255 0.48576 0.95510\n+ 6 2.76558 5.21387 2.58337 1.80253 4.53370 3.54408 3.73766 4.00189 2.11827 3.04829 4.26228 3.02197 3.93962 2.84340 2.97249 2.32290 2.44025 3.04640 5.66231 4.26679 6 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01373 4.69073 5.41307 0.61958 0.77255 0.48576 0.95510\n+ 7 1.44539 5.23416 2.96926 1.83177 4.59509 3.57216 3.86517 4.04697 2.33591 3.58282 4.36739 3.09504'..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01373 4.69073 5.41307 0.61958 0.77255 0.48576 0.95510\n+ 60 3.66234 4.91332 5.54600 5.02890 3.66435 5.06314 5.53941 0.75807 4.87215 2.02951 2.02997 5.20175 5.25930 4.99536 4.95159 4.46652 3.90564 2.17964 5.77355 4.67381 62 i - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01373 4.69073 5.41307 0.61958 0.77255 0.48576 0.95510\n+ 61 2.88791 4.93787 3.29618 3.09968 4.80710 3.51470 4.41032 4.25369 3.29544 3.91407 4.76066 1.09277 4.19537 3.62328 3.68132 2.99246 1.43121 3.76954 6.08968 4.77490 63 n - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01373 4.69073 5.41307 0.61958 0.77255 0.48576 0.95510\n+ 62 1.01488 4.54108 4.00782 3.54683 4.43734 2.49276 4.51619 3.82692 3.51473 3.52397 4.36206 3.71990 4.10776 3.79806 3.84528 2.17688 2.32618 2.62894 5.81460 4.60339 64 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01373 4.69073 5.41307 0.61958 0.77255 0.48576 0.95510\n+ 63 2.82838 4.86883 3.44513 3.03502 4.54002 3.55557 4.17473 3.93499 2.32332 3.56640 4.40094 3.43677 4.13369 3.36366 3.26601 2.31615 0.97317 3.53437 5.79314 4.52096 65 t - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01373 4.69073 5.41307 0.61958 0.77255 0.48576 0.95510\n+ 64 2.94445 4.79337 2.57486 2.93675 3.83662 3.75820 2.40010 1.27754 3.03728 2.98096 3.90421 3.40571 4.20138 3.34979 3.42958 3.09105 3.18992 2.99100 5.28867 3.95674 66 i - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01373 4.69073 5.41307 0.61958 0.77255 0.48576 0.95510\n+ 65 3.08403 5.49658 3.00185 1.00950 4.82146 3.69026 2.82379 4.30319 2.53356 3.77274 4.57233 3.16589 4.14190 3.03067 2.38009 3.03552 3.31078 3.90638 5.86829 4.50702 67 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01373 4.69073 5.41307 0.61958 0.77255 0.48576 0.95510\n+ 66 3.37020 5.81911 2.78029 0.70713 5.18577 3.72329 4.12507 4.66328 2.20433 4.12805 4.98144 3.20643 4.28892 3.27828 3.25357 3.27842 3.62845 4.25772 6.21649 4.83186 68 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01373 4.69073 5.41307 0.61958 0.77255 0.48576 0.95510\n+ 67 3.52902 6.29604 0.68393 2.06416 5.54937 3.61253 4.25867 5.14129 3.42090 4.57689 5.47571 2.26118 4.29918 3.44018 4.12729 3.34998 3.84331 4.65962 6.72314 5.10413 69 D - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00926 4.68626 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype15.2.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype15.2.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,97 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype15.2\n+LENG 25\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Tue Jul 28 10:24:42 2015\n+NSEQ 19\n+EFFN 19.000000\n+CKSUM 4237242158\n+STATS LOCAL MSV -6.8027 0.73800\n+STATS LOCAL VITERBI -7.1293 0.73800\n+STATS LOCAL FORWARD -3.4672 0.73800\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 3.13329 6.08575 3.15489 2.95214 3.91806 3.41639 4.00028 3.00580 2.72832 2.66038 4.08381 2.52800 2.44000 3.06229 2.86246 2.08793 1.85695 3.62279 5.42264 5.38976\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00208 6.57018 7.29252 0.61958 0.77255 0.00000 *\n+ 1 3.99923 6.49087 4.19327 3.66655 5.85449 4.73782 2.35475 5.32914 2.17688 4.79174 5.53984 1.17476 5.13965 1.95392 4.03857 2.55520 1.97910 4.89442 6.90456 5.51468 1 n - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.09669 6.57018 2.39948 0.61958 0.77255 0.48576 0.95510\n+ 2 2.17732 5.55451 4.85544 4.29102 2.42989 4.84740 5.16498 2.84592 2.72479 3.79715 4.69347 4.66108 1.79760 4.52820 4.56581 2.20100 1.32048 3.85134 6.17485 4.95005 2 t - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00229 6.47577 7.19812 0.61958 0.77255 0.19023 1.75314\n+ 3 5.16716 7.98515 2.26909 1.57613 7.24136 5.21477 5.88317 6.85127 5.08231 6.26763 7.17846 1.90984 1.64391 5.06713 5.82500 4.97559 1.18971 6.34957 8.41353 6.76296 3 t - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00208 6.57018 7.29252 0.61958 0.77255 0.48576 0.95510\n+ 4 2.39163 6.33953 2.00019 1.29312 5.68518 4.60233 4.78866 2.59277 2.26728 4.64442 5.38032 4.06980 4.99595 2.73061 2.31417 3.79192 4.06067 4.73054 3.18266 5.36123 4 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00208 6.57018 7.29252 0.61958 0.77255 0.48576 0.95510\n+ 5 3.96627 6.32873 4.23096 2.64570 5.73743 4.71798 5.00780 5.19772 3.77634 4.72634 5.49406 4.26634 2.84180 2.36107 4.25768 1.10255 1.35235 2.86458 6.89554 5.51434 5 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00208 6.57018 7.29252 0.61958 0.77255 0.48576 0.95510\n+ 6 2.34534 6.29050 4.10025 2.31516 5.61598 4.61305 4.80313 3.16601 3.54529 4.58781 5.33809 1.18954 3.39748 3.90679 2.16788 1.96894 4.06361 4.67096 3.32596 5.33929 6 n - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00208 6.57018 7.29252 0.61958 0.77255 0.48576 0.95510\n+ 7 2.25935 6.20153 2.48308 3.59339 5.49382 2.63889 4.83126 3.15152 3.59281 4.48578 5.26039 2.71612'..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00208 6.57018 7.29252 0.61958 0.77255 0.48576 0.95510\n+ 18 4.93061 7.24231 1.82125 4.34200 7.32881 5.18728 6.16390 6.93512 5.44033 6.41988 7.30453 2.69667 5.95678 5.37736 6.14195 0.46947 2.34247 6.23470 8.55796 7.00845 18 S - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00208 6.57018 7.29252 0.61958 0.77255 0.48576 0.95510\n+ 19 4.89270 7.56780 2.83113 2.23466 6.91182 0.85334 5.70658 6.47493 4.76432 5.91661 6.75675 2.68607 5.76835 4.86794 5.40798 1.58110 2.42770 5.98709 8.05562 6.49386 19 g - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00208 6.57018 7.29252 0.61958 0.77255 0.48576 0.95510\n+ 20 1.99296 6.22889 4.42353 3.88310 5.73354 4.73976 5.10184 5.18313 2.29792 4.73421 3.27444 3.10656 5.20566 4.22935 4.32596 1.21136 1.31224 4.76389 6.91706 5.56316 20 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.09579 6.57018 2.40854 0.61958 0.77255 0.48576 0.95510\n+ 21 2.24252 5.52054 4.85389 2.32610 4.65992 4.85780 5.14346 4.01171 4.23270 2.74011 2.42137 4.65752 1.35987 4.52063 4.55634 1.67827 4.09559 2.59376 6.12311 4.90072 21 p - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00229 6.47667 7.19902 0.61958 0.77255 0.19128 1.74814\n+ 22 4.22743 5.57754 2.47882 5.60294 2.44624 5.43982 5.79373 0.98818 5.40252 1.44083 4.63541 5.60233 5.78442 5.53192 5.41734 2.82237 4.46152 2.49298 6.26232 5.08943 22 i - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00208 6.57018 7.29252 0.61958 0.77255 0.48576 0.95510\n+ 23 4.86499 6.94181 2.28245 4.84820 7.42693 5.27281 6.58379 7.04770 5.92885 6.60062 7.45877 5.28447 2.33388 5.84823 6.49214 4.94577 0.28432 6.21435 8.63706 7.31754 23 T - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.10276 6.57018 2.34077 0.61958 0.77255 0.48576 0.95510\n+ 24 4.68355 6.92152 5.04828 4.38814 6.45927 5.30820 2.20284 5.81151 3.56253 5.19516 6.03014 4.81516 1.49509 1.36268 2.19566 4.65378 1.61961 5.44310 7.20217 6.01390 24 q - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00230 6.46972 7.19207 0.61958 0.77255 0.18346 1.78609\n+ 25 2.62103 5.66872 5.54584 5.02204 2.82589 5.06768 5.63202 4.24907 4.90320 2.91415 4.90069 5.19302 0.56180 2.97464 5.10249 4.41188 2.39922 4.03114 6.39263 5.19110 25 P - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00140 6.56950 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype15a.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype15a.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,139 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype16.1\n+LENG 39\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Tue Jul 28 16:37:39 2015\n+NSEQ 77\n+EFFN 17.346619\n+CKSUM 289630424\n+STATS LOCAL MSV -7.5613 0.71952\n+STATS LOCAL VITERBI -7.9564 0.71952\n+STATS LOCAL FORWARD -4.0575 0.71952\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.61130 5.79592 3.10896 1.85515 4.28921 3.41619 4.00756 2.62370 2.16343 2.73772 4.59503 3.17408 3.58881 2.49090 2.70320 2.76931 2.49708 3.91006 6.23695 4.69789\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00227 6.48314 7.20549 0.61958 0.77255 0.00000 *\n+ 1 0.13094 6.90943 5.26738 2.47376 7.46663 5.41620 6.90702 7.09957 6.18540 6.67992 7.55452 5.67750 6.23621 6.22804 6.54413 5.09362 5.50777 6.27075 8.54807 7.49492 1 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00227 6.48314 7.20549 0.61958 0.77255 0.48576 0.95510\n+ 2 5.75640 6.84729 7.83246 7.30199 3.33296 7.44337 7.80401 0.60357 7.25658 1.04485 4.67711 7.64752 7.20781 6.92014 7.12705 6.95577 5.95309 3.19772 7.42241 6.57142 2 I - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00227 6.48314 7.20549 0.61958 0.77255 0.48576 0.95510\n+ 3 3.09245 6.26700 2.91778 1.94619 5.61224 4.52968 4.71672 3.36915 2.58440 3.53517 5.30762 2.44249 2.41916 2.23019 2.25543 3.71819 2.73105 2.25851 6.69958 5.28853 3 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00227 6.48314 7.20549 0.61958 0.77255 0.48576 0.95510\n+ 4 2.62805 6.26865 2.83333 1.52637 5.61465 4.52928 4.71623 4.10861 1.59257 2.83097 5.30907 3.30348 4.92277 2.21009 3.13012 3.07260 2.78743 3.47250 6.70078 5.28927 4 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00227 6.48314 7.20549 0.61958 0.77255 0.48576 0.95510\n+ 5 5.24547 8.15250 0.75351 0.88281 7.34709 5.17960 3.77259 7.00627 5.20342 6.40696 7.38395 4.61049 5.91292 5.10519 6.02552 5.02022 5.58582 3.23371 8.55077 6.83524 5 d - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00227 6.48314 7.20549 0.61958 0.77255 0.48576 0.95510\n+ 6 3.94428 7.94177 2.46901 0.27224 7.18140 5.14401 5.80426 6.78901 3.11974 6.19828 7.11530 4.57596 5.84275 3.11123 5.69194 4.91260 5.42788 6.29194 8.33796 6.69240 6 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.05986 6.48314 2.87214 0.61958 0.77255 0.48576 0.95510\n+ 7 2.74648 6.24043 3.97916 1.36486 5.58843 3.14588 4.68609 5.07302 1.43069 4.54493 5.28136 3.96997'..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00227 6.48314 7.20549 0.61958 0.77255 0.48576 0.95510\n+ 32 3.80758 6.25531 2.95952 1.45859 3.20254 3.98257 4.77685 3.89762 3.53012 3.18104 5.30471 0.91287 4.97590 3.88444 3.15876 3.78037 4.04009 4.63093 6.70376 5.30670 40 n - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00227 6.48314 7.20549 0.61958 0.77255 0.48576 0.95510\n+ 33 3.87046 5.40646 2.15699 2.11709 4.51702 4.93864 5.22686 2.20288 4.47054 1.51914 2.59784 2.54389 5.31101 4.71998 4.71209 4.21226 2.41058 2.85157 3.57506 4.80963 41 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00227 6.48314 7.20549 0.61958 0.77255 0.48576 0.95510\n+ 34 2.08069 5.64953 5.69562 5.19019 5.00649 4.97352 5.75314 3.02361 5.07816 2.83274 5.00905 3.21710 5.54142 5.29166 5.24805 3.19412 0.49921 4.08281 6.50438 5.32207 42 T - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00227 6.48314 7.20549 0.61958 0.77255 0.48576 0.95510\n+ 35 4.12415 6.13645 5.17284 4.74461 6.14998 3.02817 5.85808 3.41026 4.72751 5.21505 6.01427 2.87230 5.54528 5.06314 3.84820 0.39216 2.39220 5.06182 7.43176 6.18058 43 S - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00227 6.48314 7.20549 0.61958 0.77255 0.48576 0.95510\n+ 36 4.61070 6.68108 3.70219 4.74273 7.22703 0.21038 6.39337 6.80408 5.56021 6.35616 7.18238 5.14037 5.89554 5.64310 3.40697 2.51911 5.13933 5.95862 8.44931 7.12194 44 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00227 6.48314 7.20549 0.61958 0.77255 0.48576 0.95510\n+ 37 2.58454 6.11906 6.76861 6.72416 6.84855 4.95391 7.13096 3.21027 6.56465 6.00862 6.79349 5.89386 5.83070 6.61662 6.50106 1.85229 0.36394 5.41976 8.23905 7.21971 45 T - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00227 6.48314 7.20549 0.61958 0.77255 0.48576 0.95510\n+ 38 3.89249 5.32816 5.52373 4.92961 3.29413 5.01953 2.97142 2.46474 4.77887 1.97523 4.44440 5.06648 0.94840 3.92884 4.90250 1.98105 3.61630 3.57915 5.94280 4.75637 46 p - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00227 6.48314 7.20549 0.61958 0.77255 0.48576 0.95510\n+ 39 4.75362 6.02352 6.87644 6.38649 5.41755 6.17162 6.88676 0.34082 6.27484 3.08284 5.22768 6.42331 6.51092 6.48479 6.36999 2.48965 2.92409 2.68095 7.30106 6.09268 47 I - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00153 6.48240 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype15b.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype15b.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,142 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype16.2\n+LENG 40\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Wed Jul 29 10:17:37 2015\n+NSEQ 12\n+EFFN 12.000000\n+CKSUM 4175376862\n+STATS LOCAL MSV -7.4821 0.72035\n+STATS LOCAL VITERBI -7.7779 0.72035\n+STATS LOCAL FORWARD -3.5291 0.72035\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.15350 5.76832 3.49627 2.54078 4.08181 3.23431 2.91975 3.21289 2.52085 2.57511 4.67123 3.24145 3.00341 2.57708 3.18522 2.25201 2.30159 3.88432 6.23066 3.84312\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00322 6.13491 6.85726 0.61958 0.77255 0.00000 *\n+ 1 0.24386 6.33525 6.28676 6.29919 4.90477 5.17708 6.18867 6.10015 6.28843 5.55706 6.66113 5.86238 5.98305 6.37586 6.27078 4.74272 5.10480 5.54980 6.52294 1.84844 1 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00322 6.13491 6.85726 0.61958 0.77255 0.48576 0.95510\n+ 2 0.16732 5.88883 6.47956 6.48655 6.48379 4.75792 6.95059 5.13136 6.36227 5.40964 6.41020 5.69817 5.62839 6.43760 6.29449 4.27515 4.61243 2.43157 7.99746 6.95716 2 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00322 6.13491 6.85726 0.61958 0.77255 0.48576 0.95510\n+ 3 5.66607 7.20310 5.27045 1.16549 5.54592 5.92783 6.68040 4.93829 5.79598 0.45553 5.40214 5.81342 6.48400 6.00183 6.06880 5.86652 5.97317 5.21426 7.50518 6.45915 3 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00322 6.13491 6.85726 0.61958 0.77255 0.48576 0.95510\n+ 4 3.67387 5.89630 4.06895 1.95181 5.16623 4.47850 4.63420 2.05757 1.99399 2.35070 4.96355 3.99808 4.86145 3.77440 1.93515 3.69548 1.72055 4.24360 6.36144 5.04321 4 t - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00322 6.13491 6.85726 0.61958 0.77255 0.48576 0.95510\n+ 5 3.92086 5.98394 4.85586 4.45985 6.22848 4.61734 5.57981 5.69607 1.84196 5.24258 6.01229 4.75250 2.25409 4.74983 4.59607 0.69876 2.00780 5.04955 7.35886 6.11619 5 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00322 6.13491 6.85726 0.61958 0.77255 0.48576 0.95510\n+ 6 1.36710 6.01924 3.78693 1.92527 5.39351 2.75261 4.52215 4.87659 3.26498 4.35945 5.09982 3.79358 3.04264 2.74317 3.75696 2.02545 2.11257 4.43592 6.49282 5.08613 6 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00322 6.13491 6.85726 0.61958 0.77255 0.48576 0.95510\n+ 7 3.70557 6.10309 3.97996 3.46527 5.57426 4.44090 4.70298 5.04126 2.48912 4.52590 5.28317 3.9865'..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00322 6.13491 6.85726 0.61958 0.77255 0.48576 0.95510\n+ 33 3.52483 6.00721 2.68769 1.84552 5.34043 4.29656 2.10164 2.17616 3.22726 4.30683 2.84661 2.05898 4.69262 3.58904 1.97935 3.49177 3.75620 4.39160 6.44602 5.04233 37 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00322 6.13491 6.85726 0.61958 0.77255 0.48576 0.95510\n+ 34 1.95833 5.81554 2.94578 1.78003 5.08049 4.33498 3.00402 2.15376 3.31437 4.08624 4.87914 3.84429 2.47139 3.66730 3.78877 2.51225 3.75651 2.10734 6.30030 4.94362 38 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00322 6.13491 6.85726 0.61958 0.77255 0.48576 0.95510\n+ 35 3.81180 6.20687 3.85485 2.35582 5.67774 4.47249 2.36640 5.15818 3.64395 4.66470 5.43314 4.02779 1.72569 3.96871 4.13639 1.59923 1.35404 4.71215 6.81550 5.41249 39 t - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.16684 6.13491 1.88719 0.61958 0.77255 0.48576 0.95510\n+ 36 4.35886 6.14267 6.16279 6.17617 1.68519 5.00943 5.86590 5.83770 6.19945 5.19612 6.35968 5.66764 5.80885 6.18665 6.15378 0.30497 4.91761 5.33778 6.13917 4.45045 40 S - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00379 5.97187 6.69422 0.61958 0.77255 0.18137 1.79654\n+ 37 4.03150 5.98667 5.17435 5.23612 6.81013 0.49118 6.52129 6.36990 5.81350 6.01622 6.76958 1.88407 5.53562 5.86255 6.03267 4.21788 1.80538 5.40911 8.10500 6.98909 41 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00322 6.13491 6.85726 0.61958 0.77255 0.48576 0.95510\n+ 38 1.11762 5.80500 6.42163 6.42510 6.75939 4.60624 6.87687 6.27974 6.30242 5.97612 6.69026 5.56291 5.49538 6.33617 6.23125 1.14647 1.16685 5.27412 8.09683 7.12197 42 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00322 6.13491 6.85726 0.61958 0.77255 0.48576 0.95510\n+ 39 1.93130 5.27159 4.53522 3.96542 4.40597 4.58199 2.43797 1.70345 3.90142 2.40568 4.37990 4.35045 2.27871 4.20333 2.52857 2.02453 3.82151 3.54406 5.86079 4.63422 43 i - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00322 6.13491 6.85726 0.61958 0.77255 0.48576 0.95510\n+ 40 3.86510 5.24455 5.72172 5.10840 4.22284 5.03290 5.35545 1.58846 4.86607 1.19662 2.45633 5.15700 5.37393 5.03917 2.05827 2.02318 4.09521 3.40580 5.85029 4.69461 44 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00217 6.13386 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype15c.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype15c.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,223 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype16.6\n+LENG 67\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Wed Jul 29 11:18:22 2015\n+NSEQ 16\n+EFFN 11.699219\n+CKSUM 4008273966\n+STATS LOCAL MSV -8.6588 0.71879\n+STATS LOCAL VITERBI -9.3642 0.71879\n+STATS LOCAL FORWARD -3.4758 0.71879\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.56428 5.56496 3.08820 2.18152 3.94471 3.58555 3.61277 3.39837 2.14967 2.71310 4.29760 2.84561 2.90502 2.70669 2.73596 2.54540 2.47996 3.41046 5.14479 4.48080\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00330 6.11120 6.83354 0.61958 0.77255 0.00000 *\n+ 1 0.14314 6.03528 6.32528 6.38336 6.91748 4.81478 7.00196 6.49129 6.42071 6.16316 6.92733 5.74181 2.54683 6.48752 6.36325 4.36367 4.74369 5.51427 8.13423 7.24560 1 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00330 6.11120 6.83354 0.61958 0.77255 0.48576 0.95510\n+ 2 5.23776 6.34757 7.35940 6.86766 4.78244 6.96958 7.52133 1.26797 6.84115 0.53208 4.46822 7.16898 6.84416 6.65343 6.80223 6.48026 5.45881 2.43595 7.21755 6.31703 2 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00330 6.11120 6.83354 0.61958 0.77255 0.48576 0.95510\n+ 3 2.02717 5.99810 3.74063 2.49153 5.34160 4.26565 4.45292 4.82604 1.72910 2.49460 5.03941 1.88639 3.02432 2.10322 3.67873 3.45524 2.90759 4.38795 6.43149 5.02204 3 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00330 6.11120 6.83354 0.61958 0.77255 0.48576 0.95510\n+ 4 2.53046 5.57580 4.03082 1.40616 4.77671 4.39369 4.60919 2.84905 2.06048 2.88283 4.65870 3.96922 2.56013 3.79765 3.89864 3.60636 2.55880 2.13337 6.10811 4.80671 4 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00330 6.11120 6.83354 0.61958 0.77255 0.48576 0.95510\n+ 5 4.94228 7.84793 1.62457 0.45555 7.07669 4.85355 5.59812 6.74253 4.92359 6.13262 7.12624 4.28949 2.35548 4.80193 5.77040 4.71249 5.28967 6.21650 8.26920 6.55121 5 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.04899 6.11120 3.08798 0.61958 0.77255 0.48576 0.95510\n+ 6 2.80105 7.20507 3.68178 0.27047 6.64613 4.79394 2.67268 6.32597 4.57251 5.76272 6.67992 4.30890 5.49830 4.68898 5.15228 4.53674 5.01811 5.81163 7.82055 6.26335 6 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00345 6.06566 6.78801 0.61958 0.77255 0.80883 0.58947\n+ 7 3.65388 6.13694 3.87686 1.17895 5.50900 4.39378 4.54426 4.97569 1.50478 4.42902 5.18065 2.5890'..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00383 5.96166 6.68401 0.61958 0.77255 1.26957 0.32983\n+ 60 3.41963 5.91575 3.67514 3.11575 5.26228 4.19132 4.37025 4.74203 1.93958 4.21740 2.98011 2.62695 4.58337 1.80291 2.59369 1.73855 2.08987 4.30760 6.34389 4.94230 63 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00383 5.96166 6.68401 0.61958 0.77255 1.26957 0.32983\n+ 61 3.49294 5.20485 2.88543 3.80254 4.33719 4.46523 2.88767 1.78476 3.72610 1.45555 4.30532 4.20397 1.74303 4.05218 2.70731 3.71981 3.72404 3.47563 5.78313 4.55086 64 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00383 5.96166 6.68401 0.61958 0.77255 1.26957 0.32983\n+ 62 3.65938 5.02320 5.60274 4.99568 2.67025 4.85032 5.19192 1.58894 2.08630 1.22338 4.07829 5.00330 5.20004 4.92583 4.81306 4.16580 2.61022 2.26338 5.67487 4.50486 65 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00383 5.96166 6.68401 0.61958 0.77255 0.66232 0.72495\n+ 63 3.51609 5.25697 4.36358 3.80665 4.40536 4.47942 2.74929 2.50428 3.76164 2.00429 4.36995 1.41043 4.86894 4.07060 4.11930 1.61457 2.74464 3.53902 5.84527 4.60701 66 n - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.06261 6.02902 2.84245 0.61958 0.77255 1.00208 0.45746\n+ 64 3.40985 3.35600 3.77225 3.21476 4.93355 4.22719 2.85264 4.36182 3.20935 3.94315 2.34659 2.69855 2.88128 2.60081 2.63645 2.44369 2.47886 4.01881 1.86270 4.81484 67 w - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00380 5.97021 6.69255 0.61958 0.77255 1.24025 0.34152\n+ 65 3.47322 5.26863 4.24399 3.67998 4.42453 4.41722 4.66301 2.67995 2.05151 1.29737 4.37282 2.74031 4.80242 3.95127 3.99031 2.44809 1.77674 3.55111 5.84382 4.59721 68 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00380 5.97021 6.69255 0.61958 0.77255 1.24025 0.34152\n+ 66 3.45774 5.19028 4.31720 3.75055 2.79259 4.43195 2.43642 3.69185 3.70678 2.40519 2.78691 2.57708 2.09200 4.01072 4.06532 1.54366 2.64953 3.46529 5.77063 4.53372 69 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00380 5.97021 6.69255 0.61958 0.77255 1.24025 0.34152\n+ 67 2.30736 5.80017 5.03126 4.67225 5.58908 0.46042 5.56564 5.23887 4.27401 4.86038 5.71601 4.84289 5.29010 4.84875 2.45930 4.04919 4.33153 4.74730 6.91864 2.71501 70 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00256 5.96897 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype2a.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype2a.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,133 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype2.1\n+LENG 37\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Thu Jul 16 13:47:44 2015\n+NSEQ 8\n+EFFN 1.011719\n+CKSUM 4013176524\n+STATS LOCAL MSV -7.3787 0.71954\n+STATS LOCAL VITERBI -7.8390 0.71954\n+STATS LOCAL FORWARD -4.2263 0.71954\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.89909 3.74986 2.77516 2.13578 3.48962 1.89953 4.37464 2.89004 2.66913 2.73220 4.34843 3.12646 4.18084 3.34570 3.21165 2.95244 3.17965 2.69553 3.85796 3.56963\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02262 4.19624 4.91858 0.61958 0.77255 0.00000 *\n+ 1 3.54028 4.91353 4.70902 4.36249 3.29315 4.38993 4.91843 2.52611 4.12791 0.55887 3.23618 4.60723 4.77723 4.41673 4.24593 4.01805 3.82390 2.64525 5.27673 4.07080 1 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02262 4.19624 4.91858 0.61958 0.77255 0.48576 0.95510\n+ 2 3.11940 4.84985 3.85836 3.80474 4.91676 0.36809 4.89265 4.60761 4.02933 4.21612 5.20329 4.02421 4.25011 4.32848 4.21794 3.30250 3.62552 4.07309 5.91373 5.03386 2 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02262 4.19624 4.91858 0.61958 0.77255 0.48576 0.95510\n+ 3 3.37471 5.51389 0.54602 2.59938 4.94310 3.48993 4.26433 4.61305 3.41669 4.16719 5.16454 3.16769 4.16619 3.51229 3.96793 3.30854 3.72416 4.22126 6.04395 4.77803 15 D - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02262 4.19624 4.91858 0.61958 0.77255 0.48576 0.95510\n+ 4 3.27549 5.41488 2.67901 0.63899 4.80866 3.51572 4.14791 4.33056 3.07344 3.90036 4.87398 3.17201 4.13983 3.36551 3.50646 3.23223 3.58665 3.98571 5.91750 4.65753 16 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02262 4.19624 4.91858 0.61958 0.77255 0.48576 0.95510\n+ 5 3.11940 4.84985 3.85836 3.80474 4.91676 0.36809 4.89265 4.60761 4.02933 4.21612 5.20329 4.02421 4.25011 4.32848 4.21794 3.30250 3.62552 4.07309 5.91373 5.03386 17 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02262 4.19624 4.91858 0.61958 0.77255 0.48576 0.95510\n+ 6 3.11940 4.84985 3.85836 3.80474 4.91676 0.36809 4.89265 4.60761 4.02933 4.21612 5.20329 4.02421 4.25011 4.32848 4.21794 3.30250 3.62552 4.07309 5.91373 5.03386 18 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02262 4.19624 4.91858 0.61958 0.77255 0.48576 0.95510\n+ 7 3.01429 0.46800 4.58839 4.41069 4.34441 3.55755 4.98838 3.55655 4.24544 3.45017 4.58606 4.31427 '..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02262 4.19624 4.91858 0.61958 0.77255 0.48576 0.95510\n+ 30 3.03207 5.01709 2.94615 2.87092 4.43628 3.43432 4.23826 4.23141 3.17780 3.84361 4.80662 0.69142 4.10735 3.52221 3.53455 3.09339 3.43100 3.81941 5.70435 4.36960 88 N - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02262 4.19624 4.91858 0.61958 0.77255 0.48576 0.95510\n+ 31 3.07366 4.54098 4.56530 4.25029 3.81078 4.04980 5.00403 2.09394 4.12388 2.44834 3.73731 4.38537 4.60101 4.46570 4.30387 3.58331 3.43271 0.69510 5.64600 4.39314 89 v - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02262 4.19624 4.91858 0.61958 0.77255 0.48576 0.95510\n+ 32 2.50742 4.42543 3.52579 3.37013 4.42066 3.15118 4.46368 3.99426 3.46687 3.69327 4.59946 3.53181 3.91930 3.79183 3.73308 0.69027 3.01412 3.45540 5.76864 4.51000 90 S - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02262 4.19624 4.91858 0.61958 0.77255 0.48576 0.95510\n+ 33 3.93082 5.17898 4.62212 4.41705 3.07595 4.12437 4.35949 3.98366 4.14122 3.31679 4.59979 4.50511 4.67111 4.51112 4.20797 4.13113 4.25042 3.88213 0.42626 3.06319 91 W - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02262 4.19624 4.91858 0.61958 0.77255 0.48576 0.95510\n+ 34 3.27549 5.41488 2.67901 0.63899 4.80866 3.51572 4.14791 4.33056 3.07344 3.90036 4.87398 3.17201 4.13983 3.36551 3.50646 3.23223 3.58665 3.98571 5.91750 4.65753 92 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02262 4.19624 4.91858 0.61958 0.77255 0.48576 0.95510\n+ 35 3.70266 5.01241 4.68674 4.47355 0.60090 4.29292 4.06562 3.19995 4.37593 2.49955 3.88807 4.40128 4.75225 4.45660 4.41479 3.94781 4.00802 3.21267 4.23894 2.57372 93 F - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02262 4.19624 4.91858 0.61958 0.77255 0.48576 0.95510\n+ 36 3.37471 5.51389 0.54602 2.59938 4.94310 3.48993 4.26433 4.61305 3.41669 4.16719 5.16454 3.16769 4.16619 3.51229 3.96793 3.30854 3.72416 4.22126 6.04395 4.77803 94 D - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02262 4.19624 4.91858 0.61958 0.77255 0.48576 0.95510\n+ 37 3.11940 4.84985 3.85836 3.80474 4.91676 0.36809 4.89265 4.60761 4.02933 4.21612 5.20329 4.02421 4.25011 4.32848 4.21794 3.30250 3.62552 4.07309 5.91373 5.03386 95 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01528 4.18890 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype2b.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype2b.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,109 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype2.2\n+LENG 29\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Thu Jul 16 13:48:31 2015\n+NSEQ 42\n+EFFN 3.186401\n+CKSUM 2149497564\n+STATS LOCAL MSV -7.0185 0.71993\n+STATS LOCAL VITERBI -7.2652 0.71993\n+STATS LOCAL FORWARD -4.4220 0.71993\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.25053 5.40393 2.90786 2.77490 3.56997 2.97518 2.59573 3.34771 2.27008 2.21710 3.32368 3.55963 4.37213 2.74568 2.54214 3.15044 3.53219 2.70921 6.01663 4.51593\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01032 4.97440 5.69675 0.61958 0.77255 0.00000 *\n+ 1 2.90292 5.41152 1.92318 2.28062 4.75155 3.65087 3.85798 4.23722 2.15500 3.71488 4.45594 1.99703 4.05793 2.95822 3.10164 2.32720 2.58119 3.43153 5.84616 4.43254 1 d - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01032 4.97440 5.69675 0.61958 0.77255 0.48576 0.95510\n+ 2 0.59633 4.72379 4.48494 4.12891 4.84056 3.08054 5.01169 4.19451 4.10041 3.93903 4.78030 4.11236 2.41403 4.34697 4.35379 3.04361 3.33345 2.66384 6.23525 5.06542 2 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01032 4.97440 5.69675 0.61958 0.77255 0.48576 0.95510\n+ 3 3.06311 5.58431 2.74877 1.04228 4.91177 3.69917 3.98380 4.40133 2.32229 3.88113 4.64230 2.27919 4.16034 3.09801 3.28438 3.00666 3.30536 3.16426 6.01826 4.58907 3 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01032 4.97440 5.69675 0.61958 0.77255 0.48576 0.95510\n+ 4 2.88554 4.52170 3.91575 3.34398 3.64590 3.90239 4.16966 2.48881 3.08602 2.72692 1.84541 2.45817 4.27887 3.56455 3.17861 2.75084 2.77314 2.54195 5.11439 2.47937 4 m - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01032 4.97440 5.69675 0.61958 0.77255 0.48576 0.95510\n+ 5 3.84317 6.63952 0.80384 1.13256 5.89282 3.85386 4.54299 5.51673 3.76530 4.93743 5.87252 3.29695 4.56244 3.73476 4.51389 3.64550 4.17005 5.02195 7.06034 5.42431 5 d - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01032 4.97440 5.69675 0.61958 0.77255 0.48576 0.95510\n+ 6 1.15281 4.75769 4.55460 4.24219 5.27453 2.35597 5.17748 4.74298 4.24105 4.40611 5.17403 4.14877 4.35126 4.46989 4.49743 1.00985 2.73758 4.00039 6.59349 5.44912 6 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01032 4.97440 5.69675 0.61958 0.77255 0.48576 0.95510\n+ 7 4.06335 5.97943 4.61700 3.82056 5.21417 4.50717 3.00090 4.93721 2.48820 4.25729 5.19378 4.10942 '..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01032 4.97440 5.69675 0.61958 0.77255 0.48576 0.95510\n+ 22 3.72491 6.49367 0.64200 1.65823 5.72897 3.82116 3.26534 5.33271 3.59781 4.76346 5.65558 3.25810 4.50117 3.63237 4.29149 3.54741 4.03450 4.85216 6.89875 5.28569 71 D - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01032 4.97440 5.69675 0.61958 0.77255 0.48576 0.95510\n+ 23 2.94828 5.44404 2.79453 2.36349 4.79574 3.39121 3.87576 4.27299 1.20083 3.74205 4.48890 2.84144 4.09269 2.97676 2.22723 2.90758 2.97122 3.83950 5.86224 4.46521 72 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01032 4.97440 5.69675 0.61958 0.77255 0.48576 0.95510\n+ 24 4.90098 6.28158 4.91869 4.86696 4.74767 4.86330 0.11602 5.83415 4.74550 5.11025 6.32065 5.19378 5.49635 5.28218 4.88159 5.00890 5.28267 5.53487 6.11860 4.69360 73 H - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01032 4.97440 5.69675 0.61958 0.77255 0.48576 0.95510\n+ 25 3.83713 5.01064 5.98357 5.56092 4.47309 5.53942 6.46578 1.10556 5.53905 2.84198 4.16787 5.72963 5.74406 5.83518 5.73728 5.01649 4.10563 0.69598 6.71052 5.45858 74 v - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01032 4.97440 5.69675 0.61958 0.77255 0.48576 0.95510\n+ 26 2.71624 5.61331 3.32699 2.52022 5.01149 3.87245 3.99831 4.44269 1.22911 3.88696 4.67453 3.34619 4.28015 1.49817 2.87473 3.16209 3.41673 4.03957 5.97059 4.64895 75 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01032 4.97440 5.69675 0.61958 0.77255 0.48576 0.95510\n+ 27 3.83502 5.92883 3.85977 3.44921 5.52428 4.26055 4.34137 4.94123 0.41325 4.31006 5.21029 3.10953 4.72442 3.48843 2.78165 3.80858 4.03295 4.58260 6.23629 5.08825 76 K - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01032 4.97440 5.69675 0.61958 0.77255 0.48576 0.95510\n+ 28 0.35767 4.78863 4.91002 4.72462 4.99201 3.68636 5.44857 3.87135 4.64189 3.92546 4.94688 4.41837 4.50611 4.86419 4.75946 3.18216 3.48186 2.73465 6.52077 5.37306 77 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01032 4.97440 5.69675 0.61958 0.77255 0.48576 0.95510\n+ 29 2.93519 5.21464 3.29113 2.72311 4.49319 3.73481 3.17327 3.91889 2.42067 1.89245 4.27824 3.24328 4.12197 1.67645 2.66659 2.62772 2.81817 3.57018 5.67894 4.33975 78 q - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00696 4.97104 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype3.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype3.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,118 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype3.3\n+LENG 32\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Thu Jul 23 10:09:15 2015\n+NSEQ 44\n+EFFN 3.510010\n+CKSUM 2184309054\n+STATS LOCAL MSV -7.1350 0.71979\n+STATS LOCAL VITERBI -7.5438 0.71979\n+STATS LOCAL FORWARD -4.6028 0.71979\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.73884 3.39915 3.50821 2.37133 4.17037 2.54244 3.37951 2.93276 3.27548 1.87451 4.20435 2.60203 2.89091 3.48600 3.84881 3.11395 2.98846 2.89114 5.77974 2.88095\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00955 5.05179 5.77414 0.61958 0.77255 0.00000 *\n+ 1 3.21372 5.51608 3.10076 2.86964 5.02936 2.34894 2.96024 4.53494 3.13851 4.06859 4.87384 2.02743 1.09600 3.44283 3.61574 3.20792 3.52323 4.09429 6.22050 4.82229 1 p - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00955 5.05179 5.77414 0.61958 0.77255 0.48576 0.95510\n+ 2 2.95349 4.38801 4.58100 3.98608 3.18379 4.08305 4.39763 1.92823 3.83421 1.31381 3.48851 4.12699 2.93394 4.02948 2.58018 3.16658 3.18565 2.35721 5.00537 3.82136 2 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00955 5.05179 5.77414 0.61958 0.77255 0.48576 0.95510\n+ 3 2.07935 4.49260 4.34534 3.77918 3.65573 2.86370 4.40678 2.13045 3.67737 2.07554 3.65146 4.00956 4.42305 3.91885 3.89613 3.30935 1.42996 2.70959 5.16428 3.96773 3 t - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00955 5.05179 5.77414 0.61958 0.77255 0.48576 0.95510\n+ 4 3.06094 4.99435 4.40342 4.33242 5.52131 3.72393 5.41478 5.09490 4.52460 4.74819 5.55040 4.30495 0.58729 4.75273 4.73557 1.48142 3.61981 4.30343 6.81668 5.67261 4 P - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00955 5.05179 5.77414 0.61958 0.77255 0.48576 0.95510\n+ 5 2.99313 5.03140 3.75399 3.48327 5.13627 3.67812 4.72794 4.60027 3.64096 4.21776 5.01339 1.63782 4.38459 3.93321 4.03523 2.04899 0.93384 4.02121 6.40394 5.12745 5 t - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00955 5.05179 5.77414 0.61958 0.77255 0.48576 0.95510\n+ 6 2.95238 4.81362 4.54596 4.27883 4.85460 3.70662 5.14568 4.07183 4.25632 3.93575 4.83178 4.24025 0.68577 4.51869 4.46970 2.41530 3.45528 1.90356 6.29405 5.11052 6 P - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00955 5.05179 5.77414 0.61958 0.77255 0.48576 0.95510\n+ 7 3.24273 5.66306 3.35218 2.60635 5.06016 3.90848 4.03892 4.49589 1.36833 3.93697 4.72179 3.37982 '..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00955 5.05179 5.77414 0.61958 0.77255 0.48576 0.95510\n+ 25 4.32051 5.54729 5.71864 5.33995 3.11993 5.31535 4.81768 3.31076 5.08371 0.47933 3.82297 5.23322 5.53109 5.08417 5.06408 4.74388 4.53933 3.50383 4.93387 1.86210 48 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00955 5.05179 5.77414 0.61958 0.77255 0.48576 0.95510\n+ 26 3.74645 6.29450 2.88679 0.50383 5.61760 3.95893 4.48638 5.18004 3.37653 4.61561 5.50002 3.43225 4.58866 2.26978 3.85443 3.61704 4.03304 4.74493 6.69869 5.23635 49 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00955 5.05179 5.77414 0.61958 0.77255 0.48576 0.95510\n+ 27 3.34510 5.61601 2.21603 2.90052 3.95378 3.94387 1.70229 4.33232 3.11495 3.83006 4.71128 3.43070 4.42070 2.88782 3.58498 3.31066 3.58923 3.99760 5.43695 1.29689 50 y - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00955 5.05179 5.77414 0.61958 0.77255 0.48576 0.95510\n+ 28 3.65971 6.38197 1.79071 1.72482 5.65962 2.57468 4.43296 5.22655 3.50886 4.66576 5.51783 0.99698 4.50080 3.59760 4.16492 3.50690 3.95547 4.75000 6.80774 5.23248 51 n - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00955 5.05179 5.77414 0.61958 0.77255 0.48576 0.95510\n+ 29 0.27511 4.85309 4.91488 4.83618 5.45726 3.66104 5.61094 4.70867 4.82496 4.56003 5.41753 4.45035 4.51761 5.01442 4.91149 3.17044 2.96757 4.03707 6.84349 5.76436 52 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00955 5.05179 5.77414 0.61958 0.77255 0.48576 0.95510\n+ 30 3.50178 5.11233 4.25552 1.47825 3.83893 4.48369 4.77075 2.57314 3.76333 0.95116 3.67956 4.23074 4.82981 4.07627 4.06951 3.80714 3.73443 2.95766 5.66221 4.49181 53 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00955 5.05179 5.77414 0.61958 0.77255 0.48576 0.95510\n+ 31 3.27139 5.37201 3.31581 1.73601 4.47785 3.95193 4.21917 3.87171 2.97356 1.10648 4.34659 3.49321 4.40436 2.30003 3.35428 3.31017 3.50667 3.65075 5.83661 4.53204 54 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00955 5.05179 5.77414 0.61958 0.77255 0.48576 0.95510\n+ 32 4.36471 5.52561 6.35019 5.77678 3.66428 5.84380 6.13710 1.35315 5.65782 0.65511 2.56031 6.02263 5.76245 5.42901 5.55864 5.27102 4.56019 2.97368 5.98601 5.09005 55 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00644 5.04868 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype4.4.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype4.4.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,145 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype4.4\n+LENG 41\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Thu Jul 23 11:10:06 2015\n+NSEQ 29\n+EFFN 5.108276\n+CKSUM 485695351\n+STATS LOCAL MSV -7.4082 0.71946\n+STATS LOCAL VITERBI -7.6560 0.71946\n+STATS LOCAL FORWARD -4.2413 0.71946\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.11233 5.54980 3.04085 1.95779 3.49784 2.77351 4.03338 2.89368 2.58091 2.26145 4.53480 3.53725 3.75428 3.39430 2.96468 2.63257 3.01560 3.39918 5.62672 3.37540\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.13476 5.36501 2.10867 0.61958 0.77255 0.00000 *\n+ 1 2.67268 5.42574 3.26557 2.70910 2.36109 3.14906 3.17259 4.20852 2.27472 3.71843 4.47430 3.25158 2.33924 2.64430 2.17449 2.37521 3.21843 3.80143 5.87501 4.48331 1 r - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00792 5.23817 5.96052 0.61958 0.77255 0.30016 1.34977\n+ 2 2.44814 5.45879 3.33656 2.35630 4.76510 3.83667 4.02842 3.27960 2.09762 3.74747 4.51019 3.32123 1.93597 2.71144 3.26519 2.39164 2.35180 2.97744 5.91573 4.52976 2 p - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00697 5.36501 6.08736 0.61958 0.77255 0.48576 0.95510\n+ 3 2.40351 5.54776 3.29818 2.02144 4.88971 2.91018 2.68108 4.37279 1.64577 3.85128 4.58943 3.28969 4.21417 2.75879 2.87443 3.01015 2.38002 3.16114 5.98192 4.57385 3 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00697 5.36501 6.08736 0.61958 0.77255 0.48576 0.95510\n+ 4 2.38692 5.03022 3.64449 2.66006 4.21131 2.92832 4.18111 2.83754 3.06415 2.17985 4.11882 3.56509 2.56763 3.39764 3.17977 2.20846 2.08334 3.32950 5.57589 3.40369 4 t - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00697 5.36501 6.08736 0.61958 0.77255 0.48576 0.95510\n+ 5 1.73421 5.34499 3.48020 2.93034 4.74930 2.33725 4.15245 4.19311 2.29226 3.75305 4.53393 3.44330 3.08326 3.28053 3.39912 1.67599 2.67909 3.08053 5.94925 4.59140 5 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00697 5.36501 6.08736 0.61958 0.77255 0.48576 0.95510\n+ 6 2.27118 5.53307 1.93480 2.51087 4.86521 3.82825 4.02293 4.34187 2.76642 2.85415 4.57988 2.81218 2.82225 3.12470 3.25781 1.87672 2.42742 3.91732 5.97607 4.57272 6 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00697 5.36501 6.08736 0.61958 0.77255 0.48576 0.95510\n+ 7 2.40214 4.86110 4.13386 3.58619 4.15662 2.91045 4.50414 2.65099 3.53996 3.23309 4.11895 3.93247 '..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00697 5.36501 6.08736 0.61958 0.77255 0.48576 0.95510\n+ 34 4.54707 6.40493 5.17179 4.29115 5.62509 4.92767 2.07897 5.41734 2.82801 4.68937 5.64084 4.54307 5.28473 3.88808 0.37585 4.53023 4.64336 5.12834 6.40835 5.24270 71 R - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00697 5.36501 6.08736 0.61958 0.77255 0.48576 0.95510\n+ 35 0.23316 5.11260 5.31291 5.30001 5.92303 3.90278 6.01146 5.41359 5.33389 5.13527 5.89280 4.76158 4.77938 5.43863 5.35975 2.44742 3.78894 4.51161 7.26785 6.22614 72 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00697 5.36501 6.08736 0.61958 0.77255 0.48576 0.95510\n+ 36 3.66372 5.93918 3.28351 0.44699 5.58851 2.54808 4.77623 5.00489 3.74513 4.61721 5.47543 3.74005 4.74071 3.95605 4.25846 3.65117 4.01992 3.11233 6.80121 5.38608 73 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00697 5.36501 6.08736 0.61958 0.77255 0.48576 0.95510\n+ 37 5.23579 6.95914 4.30455 0.07525 6.68451 5.03481 5.99737 6.62550 5.19760 5.97748 7.10821 4.93873 5.72419 5.33312 5.60796 5.17941 5.60641 6.20433 7.42419 6.56779 74 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00697 5.36501 6.08736 0.61958 0.77255 0.48576 0.95510\n+ 38 4.60002 5.81690 6.23045 6.02877 4.95293 5.57508 6.68405 0.16281 5.96316 3.41263 4.82558 6.15896 6.03949 6.24847 6.02571 5.44227 4.92310 2.94415 6.92758 5.77278 75 I - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00697 5.36501 6.08736 0.61958 0.77255 0.48576 0.95510\n+ 39 5.48271 6.40992 5.92508 5.91261 2.92904 5.77454 3.22201 5.20057 5.66019 4.27395 5.68320 5.34924 6.09131 5.52301 5.54990 5.28822 5.69513 5.14955 4.60547 0.19000 76 Y - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00697 5.36501 6.08736 0.61958 0.77255 0.48576 0.95510\n+ 40 2.51817 5.74320 3.35601 0.51937 5.51895 4.01566 4.72139 4.94576 3.64543 4.53359 5.35625 3.72930 4.65782 3.88975 4.13906 3.51546 2.41392 4.45507 6.71797 5.32231 77 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00697 5.36501 6.08736 0.61958 0.77255 0.48576 0.95510\n+ 41 3.93478 6.64189 1.63734 0.68040 5.94107 4.10634 4.71048 5.50677 3.80730 4.95322 5.81778 3.55404 4.76570 3.88051 4.47116 3.78098 2.20325 5.02881 7.09802 5.51788 78 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00470 5.36274 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype4a.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype4a.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,142 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype4.A\n+LENG 40\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Thu Jul 23 12:01:45 2015\n+NSEQ 4\n+EFFN 1.097656\n+CKSUM 1218734851\n+STATS LOCAL MSV -7.5272 0.71953\n+STATS LOCAL VITERBI -7.9356 0.71953\n+STATS LOCAL FORWARD -4.1841 0.71953\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.31203 4.92021 2.60091 1.96907 3.51270 3.55561 3.62548 2.84997 2.67282 2.43235 4.30163 3.22101 3.43428 3.30209 2.85380 2.43251 3.14859 3.27199 5.51054 3.60253\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02160 4.24172 4.96406 0.61958 0.77255 0.00000 *\n+ 1 3.35724 5.29780 3.55547 3.12746 4.77124 3.78655 4.02647 4.22914 0.62352 3.72049 4.67725 3.52926 4.27321 3.20782 2.58034 3.38410 3.59007 3.92175 5.68367 4.55893 2 K - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02160 4.24172 4.96406 0.61958 0.77255 0.48576 0.95510\n+ 2 3.26036 5.36545 3.72199 2.98566 4.88299 3.84216 3.72160 4.20429 1.01955 3.59703 4.47284 3.36277 4.19302 2.85078 1.61489 3.24293 3.40451 3.88419 5.59417 4.46310 3 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02160 4.24172 4.96406 0.61958 0.77255 0.48576 0.95510\n+ 3 3.31989 4.99760 3.96895 3.87226 4.80993 3.66510 4.90443 4.47001 3.96516 4.04775 5.12360 4.13463 0.35959 4.34147 4.15420 3.50232 3.79279 4.06930 5.87668 4.94046 4 P - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02160 4.24172 4.96406 0.61958 0.77255 0.48576 0.95510\n+ 4 2.54060 4.45729 3.57816 3.42873 4.47406 3.18281 4.51855 4.05619 3.52908 3.75262 4.65688 3.57931 3.95535 3.85044 3.79072 0.64575 3.05133 3.50601 5.81852 4.56501 5 S - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02160 4.24172 4.96406 0.61958 0.77255 0.48576 0.95510\n+ 5 2.54060 4.45729 3.57816 3.42873 4.47406 3.18281 4.51855 4.05619 3.52908 3.75262 4.65688 3.57931 3.95535 3.85044 3.79072 0.64575 3.05133 3.50601 5.81852 4.56501 6 S - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02160 4.24172 4.96406 0.61958 0.77255 0.48576 0.95510\n+ 6 2.54060 4.45729 3.57816 3.42873 4.47406 3.18281 4.51855 4.05619 3.52908 3.75262 4.65688 3.57931 3.95535 3.85044 3.79072 0.64575 3.05133 3.50601 5.81852 4.56501 7 S - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02160 4.24172 4.96406 0.61958 0.77255 0.48576 0.95510\n+ 7 2.54060 4.45729 3.57816 3.42873 4.47406 3.18281 4.51855 4.05619 3.52908 3.75262 4.65688 3.57931 '..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02160 4.24172 4.96406 0.61958 0.77255 0.48576 0.95510\n+ 33 3.47573 5.25593 4.00884 3.46147 4.70791 3.87054 4.16512 4.29040 2.48284 3.73899 4.74294 3.78558 4.36742 3.37895 0.53658 3.55076 3.72423 4.00144 5.64756 4.57038 71 R - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02160 4.24172 4.96406 0.61958 0.77255 0.48576 0.95510\n+ 34 0.59005 4.42187 3.88291 3.71116 4.46500 3.23314 4.68269 3.64962 3.73835 3.51244 4.51550 3.75286 4.00869 4.04692 3.95078 2.77530 3.07921 3.23660 5.85266 4.70160 72 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02160 4.24172 4.96406 0.61958 0.77255 0.48576 0.95510\n+ 35 3.33021 5.46741 2.71595 0.59483 4.86937 3.55673 4.19813 4.40201 3.13107 3.96555 4.94140 3.21589 4.18420 3.41740 3.56614 3.28432 3.64305 4.05375 5.96855 4.71441 73 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02160 4.24172 4.96406 0.61958 0.77255 0.48576 0.95510\n+ 36 3.33021 5.46741 2.71595 0.59483 4.86937 3.55673 4.19813 4.40201 3.13107 3.96555 4.94140 3.21589 4.18420 3.41740 3.56614 3.28432 3.64305 4.05375 5.96855 4.71441 74 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02160 4.24172 4.96406 0.61958 0.77255 0.48576 0.95510\n+ 37 3.33233 4.66957 4.83156 4.47431 3.65271 4.44507 5.14980 0.70989 4.31084 2.17908 3.54708 4.67118 4.85532 4.63081 4.46786 3.99073 3.63062 1.92870 5.60888 4.36958 75 i - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02160 4.24172 4.96406 0.61958 0.77255 0.48576 0.95510\n+ 38 3.82467 5.16175 4.40625 4.21863 2.41007 4.27822 3.85730 3.78892 4.06751 3.14321 4.42678 4.20912 4.74957 4.28012 4.16846 3.91792 4.11658 3.67855 4.06301 0.52018 76 Y - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02160 4.24172 4.96406 0.61958 0.77255 0.48576 0.95510\n+ 39 3.33021 5.46741 2.71595 0.59483 4.86937 3.55673 4.19813 4.40201 3.13107 3.96555 4.94140 3.21589 4.18420 3.41740 3.56614 3.28432 3.64305 4.05375 5.96855 4.71441 77 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02160 4.24172 4.96406 0.61958 0.77255 0.48576 0.95510\n+ 40 2.66111 4.50153 3.81181 3.60214 4.35087 3.32357 4.58402 3.52676 3.55285 3.37622 4.41487 3.73574 4.06213 3.93159 3.78166 2.86812 0.67181 3.17831 5.75283 4.57244 78 T - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01459 4.23471 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype4b.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype4b.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,121 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype4.C\n+LENG 33\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Thu Jul 23 12:04:52 2015\n+NSEQ 7\n+EFFN 4.344238\n+CKSUM 1872572733\n+STATS LOCAL MSV -7.0059 0.71975\n+STATS LOCAL VITERBI -7.1995 0.71975\n+STATS LOCAL FORWARD -4.3356 0.71975\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.83923 5.35114 3.35093 1.97049 3.01464 2.87254 3.98166 3.10722 3.21882 2.92817 4.32586 3.34457 3.55725 3.53112 2.92952 2.77914 2.68312 2.72196 4.83849 3.33635\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.18873 5.22742 1.79203 0.61958 0.77255 0.00000 *\n+ 1 4.18351 5.66422 5.10512 4.62597 0.65132 4.81577 4.52829 4.20260 3.85300 3.53516 4.76515 4.69758 5.24450 4.48849 1.43325 4.33448 4.44066 4.10565 4.91891 3.25772 1 F - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00958 5.04827 5.77062 0.61958 0.77255 0.94356 0.49305\n+ 2 3.92542 5.79774 4.56282 4.10659 5.62113 4.39965 4.89782 5.16012 3.23913 4.59919 5.52465 4.40422 0.64557 4.09831 1.31636 4.01987 4.25935 4.74064 6.48408 5.44010 2 P - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00958 5.04827 5.77062 0.61958 0.77255 0.94356 0.49305\n+ 3 3.11307 5.27097 3.57148 3.13821 4.98557 1.66847 4.30623 4.41104 1.50880 3.96040 4.76489 3.57998 4.35332 3.45495 3.30369 3.16884 1.47507 3.96356 6.11213 4.81981 3 t - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00958 5.04827 5.77062 0.61958 0.77255 0.27897 1.41289\n+ 4 3.11492 5.13580 4.01236 3.75490 5.36838 3.80233 4.97831 4.84317 3.91489 4.46186 5.24768 1.88411 4.53797 4.19387 4.29282 1.54303 0.90674 4.20973 6.63741 5.38063 4 t - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00801 5.22742 5.94976 0.61958 0.77255 0.48576 0.95510\n+ 5 1.79188 5.14772 3.92849 3.44775 5.13172 1.72315 4.60300 4.58904 3.38742 4.16428 4.93805 3.80925 4.42182 3.76378 1.73642 1.49569 3.45485 4.04367 6.33500 5.04587 5 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00801 5.22742 5.94976 0.61958 0.77255 0.48576 0.95510\n+ 6 3.18889 4.90602 4.55108 4.11865 4.26793 4.05342 4.90087 3.52319 3.99859 1.60487 4.22391 4.28609 1.63890 4.30736 4.23336 3.45716 1.18470 3.31365 5.82583 4.63285 6 t - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00801 5.22742 5.94976 0.61958 0.77255 0.48576 0.95510\n+ 7 2.18951 4.59930 4.74879 4.18402 3.79759 4.20829 4.67989 1.84598 4.05651 2.83380 3.78767 4.32129 '..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00801 5.22742 5.94976 0.61958 0.77255 0.48576 0.95510\n+ 26 4.33591 6.23454 4.90108 4.07814 5.41277 4.75352 1.50947 5.21492 2.70112 4.51099 5.45330 4.35540 5.11473 3.73557 0.58823 4.32054 4.44635 4.92130 6.24833 5.05486 50 R - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00801 5.22742 5.94976 0.61958 0.77255 0.48576 0.95510\n+ 27 0.12479 5.45933 5.39556 5.40319 5.95450 4.23084 6.15497 5.40219 5.46512 5.15692 6.10067 5.07571 5.06893 5.65789 5.48644 3.84707 4.20468 4.73084 7.13890 6.22788 51 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00801 5.22742 5.94976 0.61958 0.77255 0.48576 0.95510\n+ 28 3.72412 5.73683 3.48927 0.54183 5.12863 4.22712 4.86095 3.90549 3.79220 4.00057 5.06559 3.90768 4.83689 4.07554 4.22767 3.79713 4.05329 1.84155 6.54936 5.20452 52 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00801 5.22742 5.94976 0.61958 0.77255 0.48576 0.95510\n+ 29 4.97577 6.77802 4.05890 0.09786 6.45807 4.82754 5.74923 6.34088 4.91330 5.72475 6.83266 4.68479 5.51516 5.06437 5.33702 4.91345 5.34071 5.92656 7.24881 6.32424 53 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00801 5.22742 5.94976 0.61958 0.77255 0.48576 0.95510\n+ 30 4.05087 5.20920 6.23268 5.82534 4.71750 5.81127 6.83008 0.78466 5.82864 3.05673 4.39045 6.00579 5.99505 6.14623 6.04765 5.30744 4.32020 0.89457 7.02480 5.75704 54 i - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00801 5.22742 5.94976 0.61958 0.77255 0.48576 0.95510\n+ 31 5.47908 6.45166 5.94928 5.96885 3.39846 5.50150 4.94121 5.43505 5.86082 4.55640 5.96400 5.61826 5.98983 5.81052 5.73824 5.45439 5.78489 5.35905 5.04495 0.11283 55 Y - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00801 5.22742 5.94976 0.61958 0.77255 0.48576 0.95510\n+ 32 3.09472 5.18582 3.43408 1.75673 4.46611 2.16950 4.19994 3.85452 3.04781 1.89258 4.34002 3.48972 4.32802 3.38246 3.49234 3.16074 1.72969 3.54864 5.77999 4.46707 56 t - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00801 5.22742 5.94976 0.61958 0.77255 0.48576 0.95510\n+ 33 4.97577 6.77802 4.05890 0.09786 6.45807 4.82754 5.74923 6.34088 4.91330 5.72475 6.83266 4.68479 5.51516 5.06437 5.33702 4.91345 5.34071 5.92656 7.24881 6.32424 57 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00540 5.22481 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype4c.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype4c.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,121 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype4.D\n+LENG 33\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Thu Jul 23 11:27:39 2015\n+NSEQ 5\n+EFFN 2.866211\n+CKSUM 1725598554\n+STATS LOCAL MSV -6.9198 0.71973\n+STATS LOCAL VITERBI -7.1784 0.71973\n+STATS LOCAL FORWARD -4.3724 0.71973\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.98900 5.22413 2.89804 2.05150 3.56154 2.81632 3.98547 2.84234 3.27419 2.48715 4.58630 3.77581 3.96738 3.30865 2.68590 2.55192 2.81129 3.07995 5.80989 3.11799\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01122 4.89143 5.61378 0.61958 0.77255 0.00000 *\n+ 1 3.09843 5.47377 3.35091 2.79084 4.84961 2.27201 2.19707 4.28685 2.46249 3.75126 4.53800 3.29799 4.20434 1.75434 1.85073 3.06936 3.31027 3.89423 5.84683 4.52751 1 q - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01122 4.89143 5.61378 0.61958 0.77255 0.48576 0.95510\n+ 2 1.92353 4.58261 4.97352 4.42618 3.85854 4.42424 4.93209 1.41050 4.30318 2.70580 3.77281 4.55156 4.80712 4.51855 4.44736 3.76907 2.08110 1.46670 5.52028 4.32260 2 i - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01122 4.89143 5.61378 0.61958 0.77255 0.48576 0.95510\n+ 3 3.06977 5.02121 3.52494 3.03935 4.08554 3.87069 1.53692 3.59201 2.82329 3.24488 4.14142 3.49531 4.28988 2.10510 3.15436 3.17038 3.30646 1.78754 5.45367 4.11687 3 h - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01122 4.89143 5.61378 0.61958 0.77255 0.48576 0.95510\n+ 4 2.89354 4.90075 3.35960 1.78531 4.01932 3.74513 3.97154 3.48084 2.84602 2.08866 3.99140 3.33628 4.14581 3.18704 3.27413 1.99977 3.12817 3.20789 5.38946 2.42651 4 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01122 4.89143 5.61378 0.61958 0.77255 0.48576 0.95510\n+ 5 1.77224 4.66287 4.09918 3.62953 4.40691 3.59373 4.58183 3.74941 3.59591 3.48434 4.34476 3.83587 1.94211 3.88179 3.92388 1.52539 3.20701 1.85481 5.81014 4.59541 5 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01122 4.89143 5.61378 0.61958 0.77255 0.48576 0.95510\n+ 6 1.56329 5.10017 1.95949 2.96519 4.83430 3.61746 4.30671 4.24204 3.20179 3.86858 4.68013 3.42855 4.22373 3.47810 3.67132 3.02140 1.29880 3.79177 6.08891 4.74889 6 t - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01122 4.89143 5.61378 0.61958 0.77255 0.48576 0.95510\n+ 7 1.67335 4.74876 4.14197 3.77981 5.10806 1.72053 4.85035 4.57674 3.81614 4.21004 4.98060 3.90140 '..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01122 4.89143 5.61378 0.61958 0.77255 0.48576 0.95510\n+ 26 4.56785 6.12040 5.17002 4.58972 5.77012 4.71032 5.10255 5.49963 3.35010 4.82307 5.86873 4.83978 5.23283 4.34546 0.16410 4.65856 4.81066 5.18955 6.47750 5.58844 50 R - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01122 4.89143 5.61378 0.61958 0.77255 0.48576 0.95510\n+ 27 0.56599 4.69276 4.58997 4.42861 5.27805 3.48349 5.30517 4.72178 4.46613 4.44017 5.22857 4.19158 4.32509 4.66052 4.63352 1.53674 3.33337 3.96400 6.62751 5.51204 51 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01122 4.89143 5.61378 0.61958 0.77255 0.48576 0.95510\n+ 28 3.31564 5.34801 3.23759 0.78885 4.68033 3.91347 4.43020 3.55287 3.31128 3.57065 4.58736 3.56030 4.46873 3.62990 3.74203 3.39015 3.61523 1.83882 6.08470 4.74417 52 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01122 4.89143 5.61378 0.61958 0.77255 0.48576 0.95510\n+ 29 4.34866 6.31932 3.50251 0.18674 5.88811 4.33435 5.15293 5.62960 4.22756 5.08672 6.13801 4.09659 5.00932 4.42423 4.66916 4.28162 4.69585 5.23629 6.80236 5.72572 53 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01122 4.89143 5.61378 0.61958 0.77255 0.48576 0.95510\n+ 30 3.99112 5.24752 5.64553 5.37414 4.31829 5.09404 6.02861 0.32071 5.25293 2.78609 4.18510 5.51618 5.51900 5.54947 5.35507 4.79532 4.30180 2.38279 6.33177 5.12418 54 I - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01122 4.89143 5.61378 0.61958 0.77255 0.48576 0.95510\n+ 31 4.93728 6.01646 5.44682 5.41567 2.99380 5.09948 4.52571 4.87812 5.28075 4.06162 5.44203 5.14110 5.58011 5.30736 5.22341 4.94137 5.24136 4.79645 4.64589 0.18622 55 Y - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01122 4.89143 5.61378 0.61958 0.77255 0.48576 0.95510\n+ 32 4.34866 6.31932 3.50251 0.18674 5.88811 4.33435 5.15293 5.62960 4.22756 5.08672 6.13801 4.09659 5.00932 4.42423 4.66916 4.28162 4.69585 5.23629 6.80236 5.72572 56 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01122 4.89143 5.61378 0.61958 0.77255 0.48576 0.95510\n+ 33 4.34866 6.31932 3.50251 0.18674 5.88811 4.33435 5.15293 5.62960 4.22756 5.08672 6.13801 4.09659 5.00932 4.42423 4.66916 4.28162 4.69585 5.23629 6.80236 5.72572 57 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00757 4.88778 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype5.1.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype5.1.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,79 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype5.1\n+LENG 19\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Thu Jul 23 14:22:49 2015\n+NSEQ 63\n+EFFN 63.000000\n+CKSUM 3834339736\n+STATS LOCAL MSV -6.2724 0.72371\n+STATS LOCAL VITERBI -6.3568 0.72371\n+STATS LOCAL FORWARD -3.8078 0.72371\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.53914 6.14473 4.96223 5.80646 3.97497 3.74976 2.36174 3.97366 3.02081 2.87199 4.36966 2.63935 3.61947 4.30841 2.25059 2.91452 2.26063 4.59058 3.90709 2.36277\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.00000 *\n+ 1 0.64512 7.39058 3.59767 7.98774 8.36224 3.87895 8.47645 7.88986 7.94509 7.58346 8.29417 7.14275 7.07985 7.94265 7.85861 1.75012 1.74840 2.60301 9.70084 8.73147 1 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 2 0.44731 7.38667 8.11551 8.17847 8.39737 1.83812 8.53059 7.93376 8.02437 7.62684 8.32775 3.73279 3.26296 8.01301 7.89402 5.69479 2.14736 4.18473 9.73301 8.78425 2 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 3 7.58102 9.16548 7.50896 7.22281 9.13039 7.57427 7.99683 8.78123 0.18208 8.00004 9.01289 1.83922 8.12569 7.21885 6.39111 7.60509 7.81126 8.40091 9.53267 8.77813 3 K - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 4 7.00921 8.75739 8.14144 6.83876 7.92243 7.33700 3.35036 7.82644 5.10090 7.02218 1.77526 6.99317 7.66742 6.22020 0.25063 6.99791 7.06893 7.56392 8.69184 7.53734 4 R - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 5 7.13740 8.29676 9.13941 8.48284 6.09372 8.48107 8.79417 5.42338 7.83006 0.29528 3.00604 8.76351 8.34463 7.87879 3.28738 8.01030 1.86061 5.89886 8.52783 7.75243 5 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 6 1.69153 7.40211 8.17070 8.22354 8.30164 6.22717 8.55905 2.97846 8.03582 7.37178 8.20964 7.21765 7.11755 8.04349 7.90820 5.73550 0.28365 6.58889 9.71423 8.74685 6 T - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 7 0.23345 7.45171 8.06686 8.13666 7.57556 6.25548 8.30720 7.93712 8.02800 7.55459 8.33573 7.20786 '..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 12 5.25813 7.67489 5.56392 3.50615 7.07179 3.47775 6.07754 6.50629 3.64318 4.04172 6.72269 5.46599 6.36860 3.07864 1.40848 2.96079 1.87646 6.09771 0.98035 6.71049 12 w - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 13 6.32316 8.22709 7.76756 6.58485 8.38263 3.40903 6.89466 4.20227 3.25361 6.87300 7.77864 6.70575 7.32631 6.03030 0.32569 2.07210 2.93381 7.15940 8.77435 7.80836 13 R - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 14 5.85894 7.21093 7.42658 6.92794 3.91728 6.90258 1.03853 2.94907 6.74735 2.88334 6.34249 2.78017 7.24707 2.89783 6.79096 1.86265 6.08642 5.51299 6.89061 1.48240 14 h - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 15 5.49584 8.04996 3.83683 4.92100 7.37271 6.03070 0.91207 6.88830 5.13054 6.33967 7.11709 2.37375 2.42551 2.29482 3.25345 3.32588 5.74146 6.44468 8.44561 1.65782 15 h - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 16 4.00587 6.46810 6.43275 5.84626 3.31964 6.08618 2.24808 4.13906 5.72851 2.63749 5.58279 6.06056 1.06490 3.27446 4.45376 1.83912 1.98920 4.72213 7.07861 3.34853 16 p - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 17 3.43765 3.52132 6.97488 6.36115 3.60921 6.18814 1.47894 2.40824 6.14784 3.41770 5.51607 2.65212 4.22602 6.27990 6.15868 3.12777 5.25311 4.64422 7.00880 0.91369 17 y - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 18 1.64387 6.49035 4.16933 5.74747 3.32316 1.89679 1.45845 2.66585 5.64553 4.68781 5.60406 2.55428 4.42959 5.88301 5.86241 5.34175 2.22621 3.77865 7.09817 2.99079 18 h - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 19 5.10557 6.48423 7.04715 6.44933 1.65617 6.25926 0.97188 2.93409 6.23544 2.00610 5.60198 3.71532 6.63091 6.36334 6.24376 3.52454 1.87116 4.73559 7.03058 5.78934 19 h - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00044 7.73881 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype5.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype5.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,73 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype5.2\n+LENG 17\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Fri Jul 24 12:50:31 2015\n+NSEQ 63\n+EFFN 63.000000\n+CKSUM 1499272824\n+STATS LOCAL MSV -6.2169 0.72230\n+STATS LOCAL VITERBI -6.1259 0.72230\n+STATS LOCAL FORWARD -4.3041 0.72230\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.40242 5.95102 4.92048 5.84833 4.50325 4.76877 2.50996 4.21809 2.82338 2.82016 5.19353 2.69950 3.29337 4.20595 2.10030 3.34533 2.41821 4.54989 3.49955 2.36130\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.00000 *\n+ 1 0.43150 7.39122 3.86544 8.00906 8.36658 3.74467 8.48828 7.89232 7.97237 7.58891 8.29988 7.14796 7.08190 7.96030 7.87411 3.75835 1.65954 2.44322 9.70678 8.74052 1 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 2 0.27866 7.38806 8.09070 8.15583 8.39477 6.18891 8.52637 7.92207 8.01622 7.62227 8.32567 3.26974 3.11921 8.00764 7.88969 5.69618 2.01566 3.99702 9.73131 8.78042 2 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 3 7.15192 8.87662 8.27831 6.86962 8.74942 7.41811 7.09452 7.93226 0.08661 7.14048 8.09409 7.04120 7.71648 6.23138 2.63235 7.12013 7.15356 7.66978 8.92883 8.05259 3 K - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 4 7.00767 8.75900 8.14157 6.82970 7.95782 7.33474 3.31719 7.83399 5.08904 7.03546 3.72459 6.98502 7.66231 6.20931 0.08082 6.99420 7.06369 7.56551 8.69846 7.55484 4 R - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 5 7.36213 8.38667 9.33357 8.74332 2.68362 8.99253 8.98728 5.39170 8.64830 0.19818 2.85439 9.20178 8.50889 8.08560 3.14667 8.55010 7.50203 5.89744 8.48184 7.63907 5 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 6 3.18808 7.41119 8.16452 8.21340 8.26971 6.24384 8.56610 2.88420 8.03340 7.29157 8.17147 7.23007 7.13200 8.04878 7.91220 5.75329 0.11551 6.50430 9.70840 8.73302 6 T - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 7 0.06090 7.45532 8.16410 8.23485 8.45735 6.25328 8.58787 8.01744 8.08724 7.70140 8.40801 7.24765 '..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 10 0.14510 7.38579 8.18144 8.24920 8.40678 3.30767 8.54824 7.92945 8.04858 7.63587 8.33618 7.18980 7.08513 8.03565 7.90457 5.69523 2.67190 3.88698 9.74251 8.80002 10 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 11 0.13614 7.43156 3.25147 7.56400 8.41453 6.19966 8.40733 7.94205 7.87921 7.63811 8.35188 7.05619 7.08946 7.84013 7.87021 2.88721 6.10762 3.77760 9.74620 8.74785 11 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 12 6.37779 8.44626 7.03092 3.63943 8.11098 3.55903 6.61253 7.33237 3.62368 3.97398 7.51080 6.37893 7.19551 2.99104 1.26858 3.02362 6.45904 7.02127 0.67612 7.49386 12 W - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 13 6.33527 8.24204 7.74598 6.56315 8.37302 3.31897 6.87977 4.11809 3.10213 6.86038 7.76634 6.69382 7.32506 6.01443 0.35525 2.02886 2.85080 7.15692 8.76203 7.79335 13 R - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 14 7.50039 8.45869 8.45809 8.38109 3.98571 8.05210 0.86070 2.88782 8.12587 2.83651 7.64563 2.63586 8.30776 3.05980 7.91242 7.45173 7.69389 7.03551 6.80957 1.14024 14 h - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 15 5.43381 7.98579 3.70254 4.88550 7.32033 5.99339 0.69866 6.82396 5.07941 6.27807 7.04932 2.13467 2.33661 2.29835 3.10411 3.09746 5.67804 6.37956 8.39122 3.17301 15 h - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 16 3.94097 6.42152 6.70944 6.11005 3.28195 6.14064 2.30811 4.07243 5.94658 2.54222 5.53877 6.21432 0.89968 3.14507 4.40470 4.29369 1.86581 4.67129 7.03821 2.39222 16 p - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00065 7.73902 8.46137 0.61958 0.77255 0.48576 0.95510\n+ 17 3.64706 3.29724 6.96265 6.34966 3.60335 6.18588 1.32690 2.34863 6.13887 3.60724 5.51679 2.39217 2.58477 6.27315 6.15376 3.00556 5.25210 4.64509 7.01019 1.29190 17 y - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00044 7.73881 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype6.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype6.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,73 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype6.1\n+LENG 17\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Fri Jul 24 12:06:02 2015\n+NSEQ 60\n+EFFN 21.990967\n+CKSUM 1082650495\n+STATS LOCAL MSV -6.3464 0.72070\n+STATS LOCAL VITERBI -6.0906 0.72070\n+STATS LOCAL FORWARD -4.4150 0.72070\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.09095 6.78454 6.31059 4.94311 3.98231 2.91799 4.43568 3.77086 5.45936 2.95179 4.58366 1.80870 5.11460 3.14726 2.13216 2.10519 1.71190 3.45796 7.67295 3.63687\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00181 6.71063 7.43297 0.61958 0.77255 0.00000 *\n+ 1 4.94409 7.20602 5.26708 3.70996 6.72822 5.55509 5.47383 6.06583 3.27283 3.72635 6.26657 5.03075 2.59333 0.34366 2.78093 3.78910 5.10045 5.70318 7.42632 6.24488 1 Q - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00181 6.71063 7.43297 0.61958 0.77255 0.48576 0.95510\n+ 2 4.93341 6.88431 5.59180 5.68371 7.42714 5.47795 7.12545 7.24615 6.45227 6.82377 7.64093 0.08038 6.32264 6.48132 6.74588 3.18641 5.50415 6.31151 8.65865 7.48648 2 N - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00181 6.71063 7.43297 0.61958 0.77255 0.48576 0.95510\n+ 3 0.37075 6.32671 6.38771 3.53251 6.78301 3.19061 6.97505 6.21545 6.22897 5.92773 6.72964 5.89608 5.99623 6.37198 6.36906 2.87955 3.74490 1.99190 8.16839 7.06314 3 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00181 6.71063 7.43297 0.61958 0.77255 0.48576 0.95510\n+ 4 4.47258 6.39428 6.77929 6.76482 7.35653 3.20863 7.35492 6.88734 6.57816 6.56057 7.27554 6.08459 6.06565 6.77115 3.68806 0.37747 1.52056 5.86950 8.66026 7.67811 4 S - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00181 6.71063 7.43297 0.61958 0.77255 0.48576 0.95510\n+ 5 2.30865 6.51948 5.73555 3.10143 7.34177 0.23044 7.09528 6.81298 6.43961 6.52231 7.28737 5.79667 6.08152 6.44582 6.65074 4.75835 5.15196 3.60680 8.66422 7.55145 5 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00181 6.71063 7.43297 0.61958 0.77255 0.48576 0.95510\n+ 6 5.06842 6.98145 5.87978 5.96383 7.54452 5.60846 7.30048 7.33407 6.58291 6.91479 7.75225 0.07420 6.44804 6.68318 6.80600 5.24258 3.24162 6.42349 8.69516 7.63983 6 N - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00181 6.71063 7.43297 0.61958 0.77255 0.48576 0.95510\n+ 7 6.19942 7.25417 8.23116 7.66164 5.10635 7.87273 8.08335 3.04517 7.60732 0.21953 3.07080 8.09805 '..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00181 6.71063 7.43297 0.61958 0.77255 0.48576 0.95510\n+ 10 6.94034 7.70344 7.57939 7.62572 1.37782 7.23774 1.68280 6.45919 7.31777 3.73724 6.93668 6.69316 7.46734 6.89549 2.43997 6.66170 7.10974 6.43211 5.78782 0.83217 10 y - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00181 6.71063 7.43297 0.61958 0.77255 0.48576 0.95510\n+ 11 4.90940 6.86085 5.59751 5.68938 7.42509 5.46094 7.12450 7.22937 6.45368 6.81171 7.62378 0.09339 6.30762 6.48018 6.74274 2.94083 5.48151 6.28963 8.66146 7.49130 11 N - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00181 6.71063 7.43297 0.61958 0.77255 0.48576 0.95510\n+ 12 0.65454 6.21179 6.84029 6.60600 6.31669 5.18566 6.94888 5.61585 6.42493 5.42826 3.25941 6.01217 5.99946 6.51588 6.40785 2.52876 1.30792 2.82020 7.78689 6.67762 12 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00181 6.71063 7.43297 0.61958 0.77255 0.48576 0.95510\n+ 13 4.94589 6.79089 7.13935 7.14844 7.00050 5.60574 7.61939 6.43760 6.94422 5.88860 3.31728 6.53124 6.45583 7.15092 6.89906 5.17969 0.07291 5.95499 8.48533 7.44785 13 T - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00181 6.71063 7.43297 0.61958 0.77255 0.48576 0.95510\n+ 14 6.28811 7.87933 7.40051 6.43268 7.41063 6.51542 6.69749 7.10373 4.81972 6.26360 3.23340 6.56990 6.99290 5.90575 0.07072 6.37637 6.49711 6.88357 8.17550 7.23125 14 R - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00181 6.71063 7.43297 0.61958 0.77255 0.48576 0.95510\n+ 15 3.63641 6.22114 7.07538 6.58431 3.04197 6.32747 7.04593 1.12564 6.46810 4.21076 5.41056 6.59964 6.68210 6.66143 6.54978 5.73306 0.67437 2.93400 7.45438 6.24573 15 T - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00181 6.71063 7.43297 0.61958 0.77255 0.48576 0.95510\n+ 16 5.41190 7.24170 6.88359 6.30504 7.60945 5.92861 6.73363 7.20077 4.94212 6.56689 7.47022 6.29451 6.61237 5.94964 0.10606 2.69636 5.86001 6.55126 8.30449 7.38997 16 R - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00181 6.71063 7.43297 0.61958 0.77255 0.48576 0.95510\n+ 17 5.70838 7.43162 7.41968 7.49884 7.99041 6.15899 8.11400 7.95050 7.64098 7.43670 8.35377 7.15205 6.97204 7.77332 7.52564 0.01540 6.29617 7.04282 8.83328 8.22429 17 S - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00122 6.71003 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype7.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype7.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,154 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype7.1\n+LENG 44\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Thu Jul 23 13:40:09 2015\n+NSEQ 25\n+EFFN 4.617310\n+CKSUM 2296379995\n+STATS LOCAL MSV -7.5196 0.71935\n+STATS LOCAL VITERBI -7.8705 0.71935\n+STATS LOCAL FORWARD -3.8599 0.71935\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.59896 5.46679 2.45811 2.02908 4.50074 3.15485 3.44202 3.06015 2.64220 2.45242 4.20850 2.46220 3.07939 2.79494 3.60716 2.77517 2.70617 3.40663 4.82586 4.62528\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00760 5.27880 6.00114 0.61958 0.77255 0.00000 *\n+ 1 2.51452 5.55747 1.82476 1.75741 4.89661 3.79785 4.01152 4.38097 2.76372 3.86215 4.60570 2.15752 4.20863 3.11331 3.26099 2.29824 3.03415 2.94951 5.99649 4.58329 1 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00760 5.27880 6.00114 0.61958 0.77255 0.48576 0.95510\n+ 2 3.13561 5.66933 2.29401 2.15881 5.00822 2.24111 2.53165 4.50195 2.63796 3.97173 4.71710 2.62833 4.26045 1.59220 3.34949 3.08407 3.37334 4.05769 6.09942 4.67227 2 q - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00760 5.27880 6.00114 0.61958 0.77255 0.48576 0.95510\n+ 3 3.98466 6.16532 4.04254 3.54311 5.58669 4.46611 1.26454 5.05077 0.84522 4.39937 5.27746 3.30703 4.86774 3.55399 2.86806 3.93305 4.13892 4.70813 6.32767 5.13436 3 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00760 5.27880 6.00114 0.61958 0.77255 0.48576 0.95510\n+ 4 3.22331 4.87687 4.22511 3.61065 3.91531 4.19710 4.37299 3.33321 3.24567 1.78400 3.93405 3.96100 4.56180 1.94578 2.68472 3.47343 3.44457 2.85079 1.49672 4.13727 4 w - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00760 5.27880 6.00114 0.61958 0.77255 0.48576 0.95510\n+ 5 3.01531 5.34840 3.32807 1.68265 4.62747 3.81432 4.01400 2.77259 2.78312 3.62551 4.40878 2.97882 4.20867 2.92913 3.26106 2.00325 1.76730 3.70335 5.82391 3.88100 16 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00760 5.27880 6.00114 0.61958 0.77255 0.48576 0.95510\n+ 6 5.01389 6.46788 5.86241 5.93172 6.75866 0.04457 6.76003 6.83415 6.22126 6.19634 7.29911 6.03719 5.84283 6.45794 6.16445 5.24371 5.55680 6.16082 7.36601 6.95087 17 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00760 5.27880 6.00114 0.61958 0.77255 0.48576 0.95510\n+ 7 4.87205 5.97702 6.66616 6.18315 2.64000 6.21129 6.05787 3.17218 6.05389 0.25020 3.59300 6.34490 '..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00760 5.27880 6.00114 0.61958 0.77255 0.48576 0.95510\n+ 37 3.29161 5.76278 3.15221 2.10682 5.14183 3.89889 4.23207 4.62723 3.02785 4.11553 4.88895 3.39169 1.42253 2.14054 3.52092 1.62487 3.54772 4.19257 6.25670 4.83710 64 p - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00760 5.27880 6.00114 0.61958 0.77255 0.48576 0.95510\n+ 38 1.76065 5.24517 1.59941 2.66124 4.48981 3.85092 4.07312 3.90504 2.88052 3.51018 4.32363 3.38324 4.25235 3.22403 3.34740 3.07017 2.46540 2.80410 5.75383 2.75259 65 d - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00760 5.27880 6.00114 0.61958 0.77255 0.48576 0.95510\n+ 39 4.17549 6.47540 3.36097 0.45063 6.09046 4.33086 5.07302 5.72235 4.13252 5.17887 6.10675 3.94792 1.69763 4.28210 4.66650 4.09048 4.52913 5.23584 7.13136 5.79879 66 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00760 5.27880 6.00114 0.61958 0.77255 0.48576 0.95510\n+ 40 3.48681 5.89079 2.62211 2.96209 5.43664 3.94869 4.51262 4.94127 3.45303 4.44954 5.25563 0.74278 2.47349 3.66581 4.00031 3.44354 2.32839 4.46656 6.60734 5.15706 67 n - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00760 5.27880 6.00114 0.61958 0.77255 0.48576 0.95510\n+ 41 1.84060 5.81380 3.20649 0.61806 5.59860 2.76419 4.69945 5.09911 3.68195 4.62962 5.44939 3.64966 4.63090 3.87142 4.21564 3.51498 3.89509 4.57002 6.78235 5.35550 68 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00760 5.27880 6.00114 0.61958 0.77255 0.48576 0.95510\n+ 42 3.39669 5.62222 3.38350 3.13652 5.04246 3.98379 1.89866 4.65055 3.28339 4.19506 5.02113 1.08872 4.54967 3.65642 3.70245 3.41159 1.67552 4.22698 6.28066 4.87986 69 n - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00760 5.27880 6.00114 0.61958 0.77255 0.48576 0.95510\n+ 43 0.86316 5.09915 4.31760 4.04548 5.39164 3.83499 5.16938 4.82441 4.15228 4.49213 5.28774 1.73300 4.59814 4.41872 4.48530 3.29451 1.60092 4.19510 6.69905 5.48714 70 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00760 5.27880 6.00114 0.61958 0.77255 0.48576 0.95510\n+ 44 3.31978 5.79508 0.96595 2.31776 5.09508 3.90192 4.24166 2.60934 3.09066 4.08435 4.87087 2.59952 4.39472 3.37173 3.61561 3.26489 2.45621 4.16011 6.25287 4.82351 71 d - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00512 5.27632 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype8a.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype8a.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,109 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype8.4\n+LENG 29\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Thu Jul 30 10:01:58 2015\n+NSEQ 4\n+EFFN 4.000000\n+CKSUM 4023134057\n+STATS LOCAL MSV -6.9375 0.72459\n+STATS LOCAL VITERBI -7.2275 0.72459\n+STATS LOCAL FORWARD -3.8492 0.72459\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.04157 5.39514 3.01498 2.06409 3.29765 3.45823 2.89175 3.51583 3.73832 2.21064 4.73380 3.46250 4.09980 2.70578 3.50633 2.06130 3.16488 3.37350 4.64556 3.33410\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.00000 *\n+ 1 4.81473 6.42995 4.69044 4.60954 5.86900 4.87909 5.69420 5.93872 4.40133 5.25330 6.39254 5.02444 5.52106 0.11207 4.58815 4.89242 5.18471 5.59733 6.85761 5.82712 1 Q - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 2 1.45083 5.16890 3.72449 3.39671 4.04594 3.96659 4.44323 4.03142 3.49530 3.66688 4.56639 1.62308 4.52452 3.80596 3.87903 3.35184 3.56638 3.71140 5.54385 1.48094 2 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 3 3.39038 5.87274 1.59904 2.86399 5.24082 3.94346 4.20276 4.71484 2.86402 4.15947 4.95121 3.40917 4.42064 1.47766 1.52883 3.32331 3.62422 4.29135 6.25197 4.87111 3 q - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 4 1.38958 5.16691 5.29588 4.94059 4.07703 4.49725 5.50153 3.19410 4.77806 0.66278 3.92904 4.93982 5.07411 4.97136 4.87379 3.96413 3.97521 3.20383 6.01061 4.89652 4 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 5 1.41613 5.31985 3.38018 1.46145 4.96282 3.80134 4.37201 4.37695 3.21536 3.97939 4.78390 3.53481 4.36583 3.52799 3.67916 3.17220 1.62433 3.94330 6.18758 4.83818 5 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 6 4.22799 6.13483 4.67306 3.97976 5.15955 4.65536 0.69677 5.11951 2.74125 4.44322 5.38958 4.28483 5.04750 3.73602 1.32516 4.22185 4.37085 4.82004 6.13904 4.87511 6 h - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 7 4.91943 6.07804 6.20575 5.96913 4.17473 5.59449 6.33051 3.51589 5.80807 0.14441 4.01175 6.19412 '..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 22 3.01531 4.94217 4.81094 4.66611 5.55899 3.72357 5.55399 5.02772 4.69381 4.73337 5.51692 4.43160 4.56817 4.90606 4.85749 0.63000 1.28243 4.24050 6.89758 5.78220 22 S - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 23 1.47305 4.99757 3.91330 3.42455 4.16444 4.03063 4.42276 3.48931 3.28463 1.59429 4.08781 3.82741 4.49152 1.61536 3.61388 3.34868 3.44847 3.29707 5.64739 4.40675 23 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 24 3.15911 5.18310 3.42444 1.61552 4.48291 3.91010 4.30483 1.63962 3.18442 3.49446 4.38087 3.55829 4.39490 3.50819 3.61672 1.50727 3.43274 3.43412 5.84031 4.53103 24 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 25 0.53591 5.00108 4.96942 4.93050 5.75225 1.36260 5.77526 5.24281 5.05343 4.94766 5.71949 4.57125 4.64130 5.17840 5.13993 3.30015 3.67156 4.37764 7.05245 6.02617 25 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 26 3.27214 4.79974 4.82140 4.32828 3.71013 4.24846 4.71789 3.19286 4.12167 2.97507 3.99821 4.41921 1.51565 4.39078 4.26654 3.62933 3.57620 1.49108 1.60507 3.93283 26 v - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 27 3.54534 5.83964 3.11521 1.31571 5.57375 3.93490 4.66835 5.11962 3.65044 4.63964 5.48516 3.59890 4.60747 3.85099 4.16541 0.76147 3.91941 4.59684 6.75314 5.32189 27 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 28 3.48291 5.35395 4.92936 4.93521 5.74889 4.08558 5.87396 5.53331 5.11190 5.16623 6.03882 4.79831 4.92226 5.33069 5.21964 0.15816 4.05785 4.73385 6.97619 5.89655 28 S - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510\n+ 29 3.35366 5.82426 3.02908 1.36223 5.15518 3.87413 1.73126 4.68575 3.09379 4.17501 4.97097 3.36476 4.40093 3.39954 3.58957 1.51991 3.61835 4.25629 6.29795 4.85860 29 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00578 5.15585 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype8b.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype8b.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,130 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype8.5\n+LENG 36\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Thu Jul 30 10:18:41 2015\n+NSEQ 7\n+EFFN 7.000000\n+CKSUM 3525130470\n+STATS LOCAL MSV -7.0136 0.72467\n+STATS LOCAL VITERBI -7.5293 0.72467\n+STATS LOCAL FORWARD -3.6782 0.72467\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.82373 5.62238 2.85600 2.24629 4.38480 3.39708 4.46701 3.19464 2.81832 2.20391 3.95464 3.21745 4.18333 2.87110 2.74405 2.92929 3.03827 2.85376 4.39567 3.31130\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00529 5.64135 6.36369 0.61958 0.77255 0.00000 *\n+ 1 2.05726 5.58300 3.57351 3.01095 4.88265 4.03831 4.22578 4.32348 1.61719 2.36427 4.64949 3.54040 4.43078 3.34693 2.28850 2.16454 2.18071 3.95170 6.05294 4.69204 1 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00529 5.64135 6.36369 0.61958 0.77255 0.48576 0.95510\n+ 2 0.06646 5.99436 6.05007 6.09853 6.58762 4.75510 6.75834 6.17338 6.16271 5.85365 6.77322 5.67765 5.59464 6.31598 6.11467 4.40710 4.77091 5.39921 7.65492 6.86769 2 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00529 5.64135 6.36369 0.61958 0.77255 0.48576 0.95510\n+ 3 0.29290 5.39128 5.88195 5.79757 5.71277 4.33290 6.34233 4.19652 5.68513 4.55214 5.61800 5.19978 5.17500 5.81921 5.68555 3.84126 4.12994 2.00287 7.31362 6.21044 3 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00529 5.64135 6.36369 0.61958 0.77255 0.48576 0.95510\n+ 4 4.25277 6.57059 0.50285 3.49288 6.05675 2.11659 5.24926 5.62294 4.45388 2.04573 6.12664 4.06057 5.17276 4.47082 5.09614 4.18718 4.63099 5.19583 7.34492 5.87226 4 D - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00529 5.64135 6.36369 0.61958 0.77255 0.48576 0.95510\n+ 5 3.48791 5.74778 3.70566 0.93539 4.88660 4.22414 4.38703 4.44141 2.04505 2.26054 4.80951 3.72876 4.63081 3.53835 3.44993 3.48879 3.71101 4.10694 6.10757 2.37779 5 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00529 5.64135 6.36369 0.61958 0.77255 0.48576 0.95510\n+ 6 5.64252 6.70979 6.84485 6.66198 4.78741 6.13329 7.00633 4.16668 6.58227 0.07207 4.60446 6.91652 6.47374 6.50500 6.43145 6.35629 5.90560 4.55149 6.92085 5.99983 6 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00529 5.64135 6.36369 0.61958 0.77255 0.48576 0.95510\n+ 7 3.77868 6.37819 1.15133 1.46715 5.70129 4.22683 4.62142 5.21553 3.47688 4.66573 5.45452 3.67578 '..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00529 5.64135 6.36369 0.61958 0.77255 0.48576 0.95510\n+ 29 3.25346 5.07118 3.99792 3.43056 4.22925 4.19050 4.42825 3.59601 3.36562 1.60766 4.17188 3.87002 4.57412 2.29750 2.29514 2.23056 2.15658 2.17686 5.64030 4.38967 29 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00529 5.64135 6.36369 0.61958 0.77255 0.48576 0.95510\n+ 30 0.29735 5.36202 5.71217 5.72481 6.25578 4.15364 6.34716 5.77492 5.72565 5.47960 6.21358 5.05810 5.03782 5.79097 5.70449 1.78844 4.04382 4.80717 7.59236 6.58387 30 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00529 5.64135 6.36369 0.61958 0.77255 0.48576 0.95510\n+ 31 3.63762 5.07852 5.18558 4.54237 3.96078 4.72366 4.91272 3.33057 2.06629 1.93442 4.04389 4.69845 5.06881 4.47910 4.14448 4.04565 3.86241 2.08615 0.98723 4.29906 31 w - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00529 5.64135 6.36369 0.61958 0.77255 0.48576 0.95510\n+ 32 3.44452 5.98651 2.18657 2.00980 5.32678 2.32289 4.37181 4.82536 3.17183 4.29508 5.04836 2.19858 4.54436 3.48284 3.68960 1.55673 2.08210 4.37864 6.42540 4.98744 32 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00529 5.64135 6.36369 0.61958 0.77255 0.48576 0.95510\n+ 33 4.31402 5.54214 6.37501 5.87757 4.49820 5.79032 6.39976 0.55337 5.75809 1.72811 4.25418 5.99625 6.00442 5.87407 5.82345 5.20921 2.26796 2.69943 6.61359 5.50711 33 I - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00529 5.64135 6.36369 0.61958 0.77255 0.48576 0.95510\n+ 34 5.92010 6.68547 6.55133 6.61470 1.74911 6.20720 4.71518 5.42457 6.37424 4.46119 5.90323 5.68275 6.44608 5.89547 6.08321 5.64700 6.09737 5.40829 4.77637 0.27536 34 Y - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00529 5.64135 6.36369 0.61958 0.77255 0.48576 0.95510\n+ 35 3.36547 5.20551 3.94775 1.28781 4.32340 4.24746 4.53455 3.68619 3.49724 3.43669 4.33292 3.92922 4.66729 3.81710 3.88698 3.52726 2.07086 2.09291 5.75594 1.75822 35 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00529 5.64135 6.36369 0.61958 0.77255 0.48576 0.95510\n+ 36 1.60368 5.97710 2.14232 2.00015 5.32135 1.61897 4.37759 4.81649 3.17333 4.28990 5.04571 3.55423 4.54985 3.48970 2.21942 3.39154 3.69276 4.37307 6.42228 4.98891 36 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00356 5.63962 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype9a.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype9a.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,151 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype8.1\n+LENG 43\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Thu Jul 30 10:00:33 2015\n+NSEQ 3\n+EFFN 1.426758\n+CKSUM 2141265981\n+STATS LOCAL MSV -7.9829 0.71940\n+STATS LOCAL VITERBI -8.2346 0.71940\n+STATS LOCAL FORWARD -3.8926 0.71940\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.43923 4.91715 3.46041 2.48655 3.13209 2.43728 4.38528 2.89957 2.42908 1.87590 3.55402 2.94915 4.15209 3.71795 2.85758 3.02543 3.23017 2.73116 5.44741 4.19853\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01843 4.39895 5.12130 0.61958 0.77255 0.00000 *\n+ 1 0.46289 4.55076 4.09538 3.95013 4.67453 3.35506 4.89416 3.88887 3.98317 3.74186 4.73664 3.93541 4.14579 4.27648 4.17117 2.90812 3.22346 3.44224 6.04094 4.91748 1 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01843 4.39895 5.12130 0.61958 0.77255 0.48576 0.95510\n+ 2 3.56065 5.46878 3.76783 3.32757 4.98283 3.95133 4.18428 4.45775 0.49094 3.91958 4.88186 3.71591 4.43812 3.36657 2.69481 3.58573 3.78768 4.14671 5.83729 4.74642 2 K - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01843 4.39895 5.12130 0.61958 0.77255 0.48576 0.95510\n+ 3 0.46289 4.55076 4.09538 3.95013 4.67453 3.35506 4.89416 3.88887 3.98317 3.74186 4.73664 3.93541 4.14579 4.27648 4.17117 2.90812 3.22346 3.44224 6.04094 4.91748 3 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01843 4.39895 5.12130 0.61958 0.77255 0.48576 0.95510\n+ 4 3.11520 5.27231 3.33625 2.86368 4.71409 3.71050 3.86472 4.18246 2.26893 3.65193 4.50858 1.96912 4.16165 3.01211 1.11837 3.11795 3.34428 3.82106 5.68294 4.43750 4 r - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01843 4.39895 5.12130 0.61958 0.77255 0.48576 0.95510\n+ 5 3.10293 5.45449 2.93224 1.77360 4.85477 3.63035 3.82893 4.27312 1.12825 3.72953 4.56201 3.11872 4.09746 2.96186 2.66887 3.04939 3.32189 3.89385 5.80567 4.50401 5 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01843 4.39895 5.12130 0.61958 0.77255 0.48576 0.95510\n+ 6 3.80859 5.13189 5.03731 4.70951 3.43134 4.64831 5.20781 2.68849 4.47744 0.42188 3.34105 4.93877 5.01201 4.71163 4.55468 4.33229 4.08828 2.85655 5.46683 4.30232 6 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01843 4.39895 5.12130 0.61958 0.77255 0.48576 0.95510\n+ 7 3.80859 5.13189 5.03731 4.70951 3.43134 4.64831 5.20781 2.68849 4.47744 0.42188 3.34105 4.93877 '..b'.68648 4.42255 2.77550 2.73153 3.46384 2.40543 3.72273 3.29384 2.67771 2.69385 4.24720 2.90377 2.73676 3.18177 2.89721 2.37851 2.77550 2.98428 4.58507 3.61533\n+ 0.33802 1.26993 5.12130 1.47270 0.26046 0.48576 0.95510\n+ 36 3.80859 5.13189 5.03731 4.70951 3.43134 4.64831 5.20781 2.68849 4.47744 0.42188 3.34105 4.93877 5.01201 4.71163 4.55468 4.33229 4.08828 2.85655 5.46683 4.30232 45 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01843 4.39895 5.12130 0.61958 0.77255 0.48576 0.95510\n+ 37 3.56065 5.46878 3.76783 3.32757 4.98283 3.95133 4.18428 4.45775 0.49094 3.91958 4.88186 3.71591 4.43812 3.36657 2.69481 3.58573 3.78768 4.14671 5.83729 4.74642 46 K - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01843 4.39895 5.12130 0.61958 0.77255 0.48576 0.95510\n+ 38 2.85272 4.92622 3.43830 2.93856 4.54966 3.54061 3.94728 3.99679 2.45775 3.54386 4.38857 3.33451 4.06712 3.11187 1.33564 1.60832 3.16530 3.59659 5.65836 4.40583 47 r - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01843 4.39895 5.12130 0.61958 0.77255 0.48576 0.95510\n+ 39 3.04942 4.88319 3.61438 3.10823 1.73610 3.82920 3.91372 3.36937 1.35914 2.92608 3.95648 3.50489 4.24213 3.29317 3.02292 3.16982 3.28587 3.17344 4.91712 3.42110 48 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01843 4.39895 5.12130 0.61958 0.77255 0.48576 0.95510\n+ 40 3.44986 5.14039 4.22702 4.20557 5.27674 0.24083 5.25904 5.03797 4.45550 4.60970 5.61201 4.39417 4.54328 4.73884 4.60255 3.64133 3.96973 4.46400 6.20012 5.40715 49 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01843 4.39895 5.12130 0.61958 0.77255 0.48576 0.95510\n+ 41 3.44986 5.14039 4.22702 4.20557 5.27674 0.24083 5.25904 5.03797 4.45550 4.60970 5.61201 4.39417 4.54328 4.73884 4.60255 3.64133 3.96973 4.46400 6.20012 5.40715 50 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01843 4.39895 5.12130 0.61958 0.77255 0.48576 0.95510\n+ 42 2.89877 4.91455 3.56175 3.00617 4.45822 3.60909 3.94555 3.81098 2.42444 3.40685 4.28757 3.38923 4.10578 3.11772 1.32770 2.98488 1.67859 3.47161 5.59371 4.37125 51 r - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01843 4.39895 5.12130 0.61958 0.77255 0.48576 0.95510\n+ 43 3.44986 5.14039 4.22702 4.20557 5.27674 0.24083 5.25904 5.03797 4.45550 4.60970 5.61201 4.39417 4.54328 4.73884 4.60255 3.64133 3.96973 4.46400 6.20012 5.40715 52 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01244 4.39296 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype9b.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype9b.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,124 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype8.2\n+LENG 34\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Thu Jul 30 10:00:39 2015\n+NSEQ 4\n+EFFN 2.035156\n+CKSUM 3090411652\n+STATS LOCAL MSV -7.3255 0.71968\n+STATS LOCAL VITERBI -7.4015 0.71968\n+STATS LOCAL FORWARD -4.0363 0.71968\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.75651 5.31011 2.65808 1.71102 3.09657 2.79636 3.70526 3.23486 3.01315 2.25940 3.95578 3.24957 4.46668 2.84659 3.12179 3.01381 3.73807 2.95068 5.00897 2.92599\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01449 4.63716 5.35950 0.61958 0.77255 0.00000 *\n+ 1 4.50533 5.67950 5.04591 4.95967 2.72587 4.78231 4.23763 4.44572 4.81206 3.69074 5.03928 4.77514 5.25838 4.91037 4.81427 4.54196 4.80565 4.35505 4.38011 0.27554 1 Y - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01449 4.63716 5.35950 0.61958 0.77255 0.48576 0.95510\n+ 2 3.90476 5.96930 3.14040 0.30121 5.46201 3.99187 4.73384 5.10868 3.74557 4.61288 5.62639 3.70068 4.65014 3.97900 4.18980 3.84212 4.23709 4.73273 6.45972 5.29239 2 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01449 4.63716 5.35950 0.61958 0.77255 0.48576 0.95510\n+ 3 1.17797 5.29703 1.25685 2.71616 5.00771 3.53158 4.28177 4.43551 3.29853 4.06195 4.91745 3.23741 4.19406 3.46978 3.83258 3.08318 3.44798 3.97371 6.24981 4.84789 3 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01449 4.63716 5.35950 0.61958 0.77255 0.48576 0.95510\n+ 4 3.82466 5.03856 5.71985 5.19290 3.51016 5.25860 5.65555 1.16818 5.04691 0.88772 3.26677 5.39865 5.34883 5.05151 5.07206 4.67640 4.05099 2.34255 5.72538 4.69140 4 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01449 4.63716 5.35950 0.61958 0.77255 0.48576 0.95510\n+ 5 3.33008 5.49676 3.22613 2.91942 4.29564 3.84881 1.06144 4.32113 2.62191 3.77670 4.68144 3.40042 4.33261 1.81442 2.90533 3.30889 3.56373 3.99048 5.57967 4.12761 5 h - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01449 4.63716 5.35950 0.61958 0.77255 0.48576 0.95510\n+ 6 3.53988 5.57399 3.98183 3.29508 4.74279 4.09602 1.94937 4.43645 2.25307 3.83131 4.73241 3.65935 4.46926 3.16812 0.83928 3.53555 3.69699 4.12768 5.70034 4.45352 6 r - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01449 4.63716 5.35950 0.61958 0.77255 0.48576 0.95510\n+ 7 3.90476 5.96930 3.14040 0.30121 5.46201 3.99187 4.73384 5.10868 3.74557 4.61288 5.62639 3.70068 '..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01449 4.63716 5.35950 0.61958 0.77255 0.48576 0.95510\n+ 27 3.90476 5.96930 3.14040 0.30121 5.46201 3.99187 4.73384 5.10868 3.74557 4.61288 5.62639 3.70068 4.65014 3.97900 4.18980 3.84212 4.23709 4.73273 6.45972 5.29239 27 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01449 4.63716 5.35950 0.61958 0.77255 0.48576 0.95510\n+ 28 3.19611 5.14917 3.25254 1.27085 4.10599 3.86452 4.22318 3.38257 3.07197 1.37679 4.03779 3.48133 4.34273 3.44662 3.45252 3.28758 3.45115 3.25274 5.63747 4.34093 28 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01449 4.63716 5.35950 0.61958 0.77255 0.48576 0.95510\n+ 29 0.96601 4.50737 4.18293 3.94878 4.93778 3.29367 4.91218 4.36008 3.98792 4.07373 4.87770 3.88108 4.10494 4.22621 4.22656 1.13128 3.11465 3.68496 6.28414 5.12540 29 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01449 4.63716 5.35950 0.61958 0.77255 0.48576 0.95510\n+ 30 3.86304 5.49875 4.67836 4.69146 5.70193 0.14811 5.69263 5.55305 4.96574 5.07309 6.09831 4.84625 4.90022 5.23113 5.05706 4.06472 4.39539 4.93648 6.53397 5.84965 30 G - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01449 4.63716 5.35950 0.61958 0.77255 0.48576 0.95510\n+ 31 3.99399 5.21392 5.59441 5.13994 1.15351 5.14246 4.83370 2.77102 4.97295 0.94348 3.29269 5.13324 5.27476 4.86667 4.93212 4.55113 4.20571 3.00496 4.91007 3.41184 31 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01449 4.63716 5.35950 0.61958 0.77255 0.48576 0.95510\n+ 32 2.93989 5.30603 2.98558 2.60169 4.73974 3.59015 3.88907 4.20177 1.77447 3.70101 4.48845 1.60282 4.06371 3.01546 2.99294 1.93432 3.19698 3.78403 5.83290 4.46681 32 n - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01449 4.63716 5.35950 0.61958 0.77255 0.48576 0.95510\n+ 33 3.59973 5.31981 3.75190 3.54837 2.81003 4.17937 3.99695 4.05812 3.62591 3.49291 4.60005 1.80472 4.67743 3.91981 3.91424 3.64374 3.88636 3.83939 4.44606 0.81250 33 y - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01449 4.63716 5.35950 0.61958 0.77255 0.48576 0.95510\n+ 34 3.82552 5.67755 3.74057 3.57568 4.96574 4.11164 4.71202 4.80559 3.35708 4.21274 5.28440 4.01762 4.71429 0.33396 3.59545 3.87263 4.15382 4.49907 6.10066 4.90109 34 Q - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00978 4.63244 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Motifs/Phylotype9c.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Motifs/Phylotype9c.hmm Wed Jul 04 16:39:13 2018 -0400 |
| [ |
| b'@@ -0,0 +1,157 @@\n+HMMER3/f [hmmer3.1-snap20121016 | October 2012]\n+NAME Phylotype8.3\n+LENG 45\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Thu Jul 30 10:01:46 2015\n+NSEQ 2\n+EFFN 0.964844\n+CKSUM 2573194580\n+STATS LOCAL MSV -7.7375 0.71937\n+STATS LOCAL VITERBI -8.0923 0.71937\n+STATS LOCAL FORWARD -4.2620 0.71937\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.16699 4.73404 2.74114 2.41760 3.00810 2.35573 4.32771 3.04733 3.29014 2.79627 4.30136 3.58197 3.72181 3.39424 2.62148 2.29159 2.84776 2.86522 5.39271 3.59524\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.00000 *\n+ 1 3.37493 5.17189 3.89907 3.36034 4.60417 3.79142 4.08663 4.17613 2.41932 3.63792 4.63921 3.69244 4.28759 3.29996 0.60531 3.45037 3.62568 3.88929 5.57074 4.47670 1 R - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 2 2.60406 4.44616 3.72719 3.50681 4.26642 3.27226 4.49694 3.43188 3.45585 3.28433 4.32374 3.65800 4.00339 3.83757 3.69247 2.80976 0.75125 3.09281 5.67637 4.48635 2 t - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 3 2.48933 4.40802 3.49702 3.33804 4.39107 3.13392 4.43354 3.95999 3.43279 3.66048 4.56781 3.50576 3.89956 3.75974 3.70140 0.71658 2.99377 3.42741 5.74100 4.47959 3 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 4 2.48933 4.40802 3.49702 3.33804 4.39107 3.13392 4.43354 3.95999 3.43279 3.66048 4.56781 3.50576 3.89956 3.75974 3.70140 0.71658 2.99377 3.42741 5.74100 4.47959 4 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 5 3.24563 5.38567 2.65922 0.66497 4.77500 3.49337 4.12062 4.29101 3.04210 3.86434 4.83691 3.14832 4.11562 3.33740 3.47385 3.20393 3.55590 3.94812 5.88916 4.62627 5 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 6 3.37493 5.17189 3.89907 3.36034 4.60417 3.79142 4.08663 4.17613 2.41932 3.63792 4.63921 3.69244 4.28759 3.29996 0.60531 3.45037 3.62568 3.88929 5.57074 4.47670 6 R - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 7 2.81169 4.84036 3.29969 2.87427 4.46786 1.65012 3.92646 3.92350 2.48987 3.48298 4.34196 3.27979 '..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 38 3.50771 4.88753 4.66754 4.31907 3.27776 4.35743 4.88268 2.50779 4.08449 0.57907 3.22569 4.56607 4.74802 4.37991 4.20749 3.97946 3.79191 2.62059 5.25407 4.04279 38 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 39 3.66462 4.98158 4.65054 4.43086 0.62638 4.26463 4.04708 3.16288 4.33328 2.46788 3.85405 4.36938 4.72336 4.42081 4.37865 3.91239 3.96938 3.17397 4.22498 2.56172 39 F - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 40 0.65703 4.36951 3.79323 3.61118 4.37675 3.18379 4.59388 3.54906 3.63596 3.41585 4.42301 3.67645 3.95223 3.95096 3.85794 2.72149 3.02015 3.15009 5.77288 4.61080 40 A - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 41 3.24563 5.38567 2.65922 0.66497 4.77500 3.49337 4.12062 4.29101 3.04210 3.86434 4.83691 3.14832 4.11562 3.33740 3.47385 3.20393 3.55590 3.94812 5.88916 4.62627 41 E - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 42 3.27101 4.62091 4.73948 4.37510 3.59360 4.37404 5.05798 0.76969 4.20952 2.12940 3.49369 4.58057 4.78618 4.53357 4.37364 3.90762 3.56871 1.90165 5.53883 4.29636 42 i - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 43 3.66462 4.98158 4.65054 4.43086 0.62638 4.26463 4.04708 3.16288 4.33328 2.46788 3.85405 4.36938 4.72336 4.42081 4.37865 3.91239 3.96938 3.17397 4.22498 2.56172 43 F - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 44 3.70647 5.07328 4.29292 4.08736 2.37118 4.18885 3.80078 3.67800 3.93734 3.05218 4.32316 4.11065 4.65987 4.16910 4.05541 3.80923 3.99693 3.56378 4.02310 0.58497 44 Y - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 45 3.15873 5.13004 3.14029 2.91133 4.33717 3.59015 4.06815 4.02589 2.71355 3.49683 4.52733 3.36955 4.15488 0.78374 2.98691 3.19897 3.46067 3.74000 5.55987 4.27903 45 q - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01568 4.16300 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Reference/148_prot.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Reference/148_prot.fasta Wed Jul 04 16:39:13 2018 -0400 |
| b |
| b'@@ -0,0 +1,148003 @@\n+>Tc14800001\n+GRTGNYLFIPLRVLRTSDFVLPHMATVEELQQVIREEQEKHAQVLEELRSERESLSSLLA\n+EQQQYIQELITRLTDLRTQKCDRMLSNEQLTQRIEINTGCAVVDEALRTVENGLNSSSSK\n+RGVVLGKIWSAMMQAIVPSDGKKSSSLSTSSSATRTTNVAVITRNMIRGTNEWVKRHCKK\n+CSPCGELNKKPRPWEPAAKTEKGKSIKGCASVPNLSCVPGKNFRSVSFVLR*\n+>Tc14800002\n+AVNHRAFKAVDVLTRITRGRVMIETDTKSSPKSKSSPQEPQSAQLLSCIHSVVLGFALFG\n+TRLTFECAIPKLEEANTLKGVKRGAFDIARSFLQRLLPPKRDTAVSLHDPTVSDFVILLL\n+NAPTRLLEILNNSFSSARRLPSTSRTSVVDHLASPRLKINYALRTFADIVIDFPRPYAPN\n+SGMMTTAEKAKGEKERLGPCAPVVDLPPDLVRANVEVVQWAEEKLRNLLEKEAIDVSTGT\n+GEEIAKSLGESVMKINSVSGFLGKLQQLSVSVVDLTDVRVDVCLPCGAALCSPGGGVEEL\n+LYLRVDTVRNP*\n+>Tc14800003\n+LYYYNYYYSILSFLIHISSRLNLLGISYCIHPQVQQLFNSPTGAAKSCTTWKTNIHTDIG\n+QINNTNGQLLQLAQEARDAVDLHHTLPKALRDFLTRSSAHINGFLLEQVSELLFGPLDHL\n+DVGAHEVRGEVYNGGTGAEAFLFSLRFLRRGHHATVGRVRSRKVYDNISEGSQGVIDFQP\n+RRSKVVNNACAGRRRKPASTAEGVVEYFQKSGWGI*\n+>Tc14800004\n+FAFQALSTRVTSCNPLMYIFMRGTKCFLECPLSCHFFSFSHRTATGYERKCEMMRNDCGQ\n+TPNKNEKKAQKLGKLEVRGERGAKRYKFRHRRQYYASKRQGRKKKEARTINVDRRKTRER\n+ERNDGEMCTQQDSEKRHCDPRPQSAHNQMRAGGQPQADKQLIREVQMGWGYRRWDSPPPN\n+GLHYSESNIKAIVLITVTTREWRKEGNKEKNGIGEMTKRDKVKAVENSWRLGMPCLTNTK\n+*\n+>Tc14800005\n+AHRDHGIGASSSSSSQTMSLNLSDAIDERSYKEMEKYTVERIAGQGTFGTVQLARDKTSD\n+MLVAIKKVIQDPRFKNRELQIMQQLTKLRHPNIVSLKNFFFTAGGEGRRSDVYLNVVMEF\n+VPETLHRVCRNYYRRLVNPPLILVRVFMFQLLRSVACLHIPSINICHRDIKPHNVLVDGK\n+TGELKLCDFGSAKKLVPEEPNVAYICSRYYRAPELIFGNQYYTTAVDIWSVGCIFAEMLL\n+GEPIFCGENSAGQLREIVKVLGQPSKEELQKLNGTNMEINTNAKAMAWESVFKQPLPAEV\n+YDLCSKIFKYVPEQRITPMEALCHPLFNELREPGVKLPSGSPLPSHLFQFTPEEIDAMTD\n+SQRQHLLKK*\n+>Tc14800006\n+LTLMSTPKQFSTKQPAIKHGSLTHRCEPFTSEACHFCDIHTITIASSVLRLPLTFPLGSP\n+LCYFLCRILAMICLSPSLTWYTFHPSTYLFQNMRNAILPWPPTSSSFTRLKLANSNTKAP\n+LHTGGVADYFFSRCCRCESVMASISSGVNWNKWDGSGLPLGSFTPGSRSSLKRGWQRASM\n+GVIRCSGTYLNIFEHKSYTSAGRGCLNTDSHAIAFAFVLISILVPLSF*\n+>Tc14800007\n+RDRSCSLMRCRRTQVLCSVLFASPASQRATCHDQKKPRETHCNAVACDTTAEWVRSHVSK\n+AVEEGRQSEASAAYFASIVEDQPEFRLYVKEAERLIGNQDPRSFTRYQKMYYGERLSRFM\n+SGVASERLMRAHAENEGVRRHTQDGSSTGENYWFEAGQTLASPSVPNFIKNEVLREMREE\n+RKANSPAFEEPPAMADMAAKEEGFADHLRQQRQKLISPEDYLS*\n+>Tc14800008\n+YPKRFFFALQKMLMLLRYFMDGRCVFVALLFMIHCYVLHQCAMQGYRAVAKPLYDDISPY\n+PITASGGRVIGSPTYTLRVHFIREGLSGTGSTKAHKTPSLASPADALILHFPAVFHGDMN\n+EVLQAFSRMKRWEVVVPLNPAAERVTHRTYQLAKRSFPLPVRDSTDRSHSDMSPVIVHVS\n+DLATILRKGLPKLDSNHEGSTSDSAVVCFLIETDPSLVSTPDGMTLYDRLLNEAGGPYIS\n+SALLGLRRAHSANWALFISPCSNNHLFSWKVEPLRGLAGVSNMWWACVASDALLDINGAS\n+QWVGAHFDALM*\n+>Tc14800009\n+LGPVMETMNGVLNHICEYPISSYAVLGLVSAWLIFRIVLSLGLVLLIEIVVVIGALLYVT\n+RKEEKRTAFNILHAHRLMKDSAFLKKILEKDLPEWVTNPSASNVQWLNALIAEMWEPISQ\n+ASAKTSRACLEPLIENYKPSFIYDIKIKQCSMGSQPFVITGIQHHPSRDDQSILDVTVSW\n+DSDMDILLHLSIPGPDMHVHVRRLQLSVQMRVVLSPYASVWPCFGSMSVSIMKLWLLDFD\n+VVAGGVALDAVPAVGTFLDSFIRKTLVGMMQYPKRMIFPVVEGHITHTSLADVALGTLRI\n+HLLRADEWYPRYASDRAKTPYYVKLIMSSEDPTGKPRKSNIYNGLDAKFTDLFSFVLYDK\n+QRTLHFWMYFDVPGYDVLIGECTVPVKALLAAKNSEYTCLMSKTSGSRTTVRAKLIIMAE\n+FLPYSTGREDKASCPPQQAPPRNVSQSYTDNLSMNSENLEPPSTRSTAQSFDITEQQSPR\n+NANGSGTLFVTVHRCNGLKNKETFGVSDPYVVLRLRKQVRKSPYVSSTLDPEFNFSAALE\n+VYDMATDVLNISIIDKNSFTKDCKMGSLNLMLSRVASAPGDILREEMNLDPQGKISLELK\n+LLRH*\n+>Tc14800010\n+KVICLPLLSYIVSVVVLTGTMGKNPPKWLPGTRVKETILLQRKSVERLRADRLLRRDKLQ\n+ERRDRHRAKIDAKRKRKLSTKKFITAQTILKHAQRRERQGRLFRKIGEKVLGKRGRMGKE\n+YVKSLEDARVVLMVRARGKQIPYEVANAFQRLGLDNIYAARLLCLSPQNDPLVKQLGPFS\n+VIGHPEPAQLDELIRTRGSLWDDNTRTKRLISGNLMLEEALGQFNVLCIEDLCDVIINKT\n+EHVREVLKRIAPFDFHPPRQLYMERHRPTRQKLEVMNKDSFVEYLTQELRNSAKREKATV\n+KREKATAKRVTLGKGKSAKKSSSTSQKSA*\n+>Tc14800011\n+APRLARTPLHLRCVTRKQELGKNISQGIKLREMAQVGQQRFGCYIGNIDRSVTLEVLRQV\n+FSQCGTIIDCSLNGRDEDPYRYGFIDFATEDDRARAMKYNGFTLAGRKIKVGISKGNVGR\n+PEGYNNTATPTPPNNNGGGPGKHTHQQHQPASQTMALPQNFIPGIVPPQQQPQGAALLLQ\n+LIQQGAIDVNNLTPEQQQILMASLLPQAAPAAGGIAPMPPTAPMPYIPPPPQHPWGGPRG\n+HYQGGPMAGRAAQYTRPPANPPPPEEIVKLREVQRKQFLEVVRRDAERYERKLVERSAKE\n+NRACSVSGSEESSSEEEVDRGHPRSRRKEEEDEKEEQVSPGPREEEEQQSNNVCKPGDVG\n+DESGKHQSRSEEPYLDCSPEGEYTNVEAENVVPEVVEATSYDPEQV*\n+>Tc14800012\n+VSSDLRGMARIGEGDPRWIVNDRKDGQNVNAWHWEERDLSNDCHEELKRRLNELKLGGTD\n+DEFNLRVTEVSEIGGDVTVAQRKGRMMCYFELKLTLKWSGKMDVSGKLTVPEVDHDNFRD\n+EYDVVIASTENNEASQKAEAIVRSKGRVVVREVITKYFEELFEAYQIGKNLKNGSSLPPP\n+PPKTTQTEKGAAKSSGGSLSGSGTATNFS'..b'PSESPAVDTVSLSPSATPQEDT*\n+>Tc14817791\n+DQTRFCRSSSGALQLLLLTLFLRPLQAFARPLQFFFGIFQLFSRFLPLFSHLRLFVHIHP\n+RFPRPVQLMPPQTRLLQLLKRSPWLLVPLPHGLFARQDFLPSALPVPVFLARRCPRPRLC\n+WTWFPGFLCRGLLQALEIGPLQQARSPLKYIFPTFSRLSQDFLSALLYFVSCLVRLLQLF\n+VGLLPHFSRLHPLFSRLHQLFEHLRHPPLFSRLLPLFSRLLKLFARLIPLFMRLTRLLFR\n+LLVEPLRLLHLVFALLYVFLRHCQIFFCSLQLFLRTGECWQLAFYPRQFLGAPLLLFLPP\n+LRLLSPLVQIFLAPFPLILVQRAAEACPLKGFLARLYRRLARLLASLRA*\n+>Tc14817792\n+RASSHVFTAAWHASLRRFALDNACFPVSTSRSARCIASRIRSHPPPAASAFCNALTHSCT\n+AKSNLRLASCGARLHSSESRSICSNFSLQSSSSSSDFTNSSRPSSVKTRSTGTFVGHMSF\n+AAFNSSSHFSNRLSSASTASRAGTPPEVNSISSCMTLSHSSFALTNLSFAQSPSASSSAS\n+PARRSGSSHSSKLFHSRSSAAKQVIPSRRAFSTHSLHLSNVSCPF*\n+>Tc14817793\n+GSSATRPNHHNSSSASSHLFSHISHSSIASPNSRLAASTPCLAAARWYDPSVRVCRRSQS\n+ACLPLASANSFSASSNSDTASTQARSCRSSSNACVTLSNSGFQFSSSRRAVSNSFLRAFR\n+SISASVTRRSAVSNSCCSASTSGFATRSCSLLPNSFIACSHCSFRQSNASSTFSRPSFSF\n+CSTSRACSNFSSRSFTFFFTSSNLRLQLSHSSPSPHEDSINCPQFFRNTWAACSSSPLDR\n+FSSTSLIISRAAADTFFPRFPYSSKASRQKSSSEPRISSRDSLVAPIGSAPTAPSSSPPW\n+RPPIMSLHIFIIRKASFRKFSHCSTRSPSDCGSSCAKISKPSTTSSTHFWTSSKR*\n+>Tc14817794\n+PPPTRVWRHPLPAWLQPGGTTPPSGFAGARSPPAFLSPPPILSRPRRTRTQRAPRHVAAA\n+PPPTLASPFRILGSNSPAPAVPSPIRFCGPFDLFLHLSLVGPPFPILVAVLPHLVSPLVP\n+VRSYQTPSSPAPIVRSARATLRVLSPALPFLFVRLRVPVPTFLPGPSLFFSLPQTFASSF\n+PIRVHLPTKIRLTAPSSSATPGPLVLLRPLTGSPLLP*\n+>Tc14817795\n+QPGTVGLSSPDVILHRDCEISNWKAALSQDTHHHWIMFDVFVGTSLDAMAPSKHVRALHS\n+WNRAQWDEFRPISDKPTSQRMKRSVKGVDAVDMAIKKAIHNGIGAELLFWTPKLTKLKVM\n+VQQCRNERKRDAQIWWRRKVLLVHTAIGRWEDNVSRLAVTDPLSWNLVKSIYANRPLHSP\n+VPAVDGHTLTKLQQELALALARMYWERFTKAPEAPHMQLPSTSPGMGHLSQSRRHNWKQR\n+CVSSQEARLGGMTEFIPKGSNTWAVLAESAYFDDSIAAKFQGNGSRKLLYHC*\n+>Tc14817796\n+RYLVLVKLISQGEARITGSTTGRSAALTLANSRAIHVLGVNDFQVAGFFDPLPDLKYFPH\n+VVAKVSGCALLRVVLLRFGYLQQNNRIGSRSFHNKEAVHKREVWNERFVSTARYQHPLRT\n+VRRELRKGCGHAPCFTSTDSRFASSLRSRCSRCLTSVHQESRAMEVLGPTVPNSQWLCAC\n+LLNSAAYHISREGCCERPPLEVLPHVRGCGLVPAYQLTTYRAARHLHQLVRRTIFMPLMR\n+ITQQLRATTNAMGNQPQGTFHIFQTLLIDYLICAHVARQRTHLVSALDYFFPVIFQIDIL\n+QFNLFLRQLPVSLPHKRSFQLGILVAADAYLESVRPLWYKFFEFLLVR*\n+>Tc14817797\n+NRKQSGFISTRSSLDTLMQVTSAVRQRENGEKVTVIFIDYEWAFNSVDHGCVIELRKVFG\n+VEVHFVARIARLLQGRTEQVRASSIKSEDIETMCGVPQSPVLGPLLLLITVVDSPGKRLS\n+KIQGFMRCFFVDDLTMECPHTNILNIPETTEKAMDCITSGSEEKLMEASAGKTECMLLGS\n+GGKNTLKLEVCGIAVNETRSRKLRGLAMEPHKGLGKHVHESKSSGGCAANEAEGDRLSRM\n+GPGTDELRELYMAIVWTKA*\n+>Tc14817798\n+WFFKILQKIGSKTFSNFCKLFCKKIFFFDFFGENFFVPKMVVRDLFVPNFIENAEIRFKN\n+DSISSENGHFAIFPKFTFLGQNGQKPVFLKMVKNVKNAKNSKKRVFGTYLSFWGLFDAHS\n+GFSKFCKKLGQKLFQIFANFFVKKYFFLTFRRKFFLFQKWLCGICLSLISSKTPKSVLKM\n+IQFRARTGILRFSQNSHFWAKMAKNRFF*\n+>Tc14817799\n+WFFKILQKLGQKLFQIFANFFVKNIFFDFFGENFFVPKMVVRDLFVPNFIENAEIVLKMI\n+QFRARTGILRFSQNSHFWAKMAKNRFFLKMVKNVKNAKFEKRVFGTYLSFWGLFDAHSGF\n+SKFCKKLGQKLFQIFANFFVKKYFFLTFSAKIFLFQKWLCGICLSLISSKTPKSVLKMIQ\n+FRARTGILRFSQNSHFWAKMAKNRFF*\n+>Tc14817800\n+FTSKTPKSVLKMIQFRARTGILRFSQNSHFWAKMAKNRFFLKMVKNVKNAKIRKTRIGTY\n+LSFWGLFDAHSGFSKFCKKLGQKLFQIFANFFVKKYFFLTFSAKIFFVPKMVVRDLFVPN\n+FIENAEIRFKNDSISSENGHFAIFPKFTFWAKMAKNRFFLKMVKNVKNAKNSKNAYLARI\n+CRFGAYLTRIVVFSKILQKIGSKTFSNFCKLFCKKIFFF*\n+>Tc14817801\n+KIRRSLPSYRHKDVIIESVQRSSVVVISGGAGCGKTTQIPQMLYDEEGLFDKNLQVICTQ\n+PRRISAISVAQRVAEERGEACGDSCGYIVRFDNNTSEKTRIIYMTTGILLRLLQADPILE\n+GVACVIVDEAQERSIETDLCLLLLRDLIVEGKKYSGSYMKLVVMSAASQLEQLMSYFSPE\n+EIGSEVPVVMIRGTLHPVREYYLEDAHGWLGLPPPSIPSSYEASRPPTVDGETNVCGGGT\n+QTVYEEIMRNIGKSHQVNVCFDLVLDIVREIHRTSRGNSESILIFLPGRSEIFRMEKMIK\n+SSELCKTLFLIKLHSSITAEELSCALSVPQRDFGRLYSQLTLLKRASPLMTLFMSSTAAS\n+QESSRMTQREI*\n+>Tc14817802\n+LCFIRPPKGFRKVVLSTNIAEASITIDDIVYVIDSCLTREQSYDPEGNMMHWRTSLISRA\n+NGRQRCGLAGRCRPGVCFHLLPHGLYEKIARVSNPDILKVPLEGVCLNLKALRPNEACMN\n+ILRRCLDVPSECSVSRAVEILKNIGALTPDMEASHILEVFSRVYRFIPFWVGCSLWRHAW\n+VFWIRLRRLRRFCPPRAHFSYSMRARKRRRNL*\n+>Tc14817803\n+SMYEYPPSLLGCAIGMLRLTRGGNSQEYWCTDTRYGSLTYIGSVLSRLPLHPLLGRMLIV\n+ASCLGVLDPIATIAAFLSSKGTLFILHESQEEKEKFIKFIHSIDNSFCSDHLLILKIFDV\n+WKGSGVDANHLFHGYVSGAVLQSINQVKNELVHIVCDSVYLQGLRHPMEYASRNSKNIGL\n+VRFAALWSCYPKIASLEYSRSDDCQPQLLCWDDEFSQTLYTSVLHMKRRKDLNDFAFVFY\n+FERMLTERGFTLRDVTAVTPVEVALCLRELTLLPIKDVPPELLSSTDFRMTPLFPFTFHR\n+GERRRDMGVLFFDGGKKAFVTSMRVAETILNVRNCINYFFQLSIADGNVGCFPDSVVDII\n+VQTISHPLNDTTDRSCFIGNDPCSTWVSECGGLGGGDNND*\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Reference/IL3000.1.bt2 |
| b |
| Binary file data/Reference/IL3000.1.bt2 has changed |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Reference/IL3000.2.bt2 |
| b |
| Binary file data/Reference/IL3000.2.bt2 has changed |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Reference/IL3000.3.bt2 |
| b |
| Binary file data/Reference/IL3000.3.bt2 has changed |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Reference/IL3000.4.bt2 |
| b |
| Binary file data/Reference/IL3000.4.bt2 has changed |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Reference/IL3000.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Reference/IL3000.fasta Wed Jul 04 16:39:13 2018 -0400 |
| b |
| b'@@ -0,0 +1,693792 @@\n+>T.congo.pschr.1 | organism=Trypanosoma_congolense_IL3000 | version=2016-06-06 | length=842607 | SO=chromosome\n+GCTGAGAGAAGTTATACGCACATGGGGAGGGGAAGAAAAATAAATGGCATCCCACAGCGC\n+ATAGTGCCATACCTCGTTCGAAGGTCCGATAGGCGGCCCCGTTCCAAGTACGGACGGTAA\n+CCCCGCAGAAGAGGGGGCCCCTACGCACGCAAGCGCCCCAAAGAAAAACAAGTGAACAAG\n+TGATGAGAAGCAGATGAATAAAAAGACAAAGAGAAAGAGAAAGGATGTGGAATCGTTTGG\n+GTGCGGCTCGGAGTATCGCCCTATGCTCCTTCGGTGTGGTTAAAGTAAACGAACCTCCTC\n+CTTCACAACCACCACCACAGGTTTTCCTTACCACGCTGGAGTCCTCCACGCTCCACACCC\n+GAAATACTCTATGGCCCTAAGCCCCTTGTATTCTAATAAACCTCCTAGGGCAAAGGGTGT\n+TACCTTCCTTCTCCAAGGGACCCGAGAGGGAGCCTTGGAGAAAGGGAAGCCTGCCCCAAA\n+GCCCTAAACCACCATTAAAAAAGAAACAAACAAAAATGGGAGTGATGATGATAGGGATAT\n+GCAGGTAAATTACGAGAATAAAAATATACGCTTATCCAAAAGAGAGATGCTGGTTAAATG\n+TATCAACAAACTAACGCGGCACTCGTTTTACTGAACCAATAAAGCTGTGAGGGTGCAGGA\n+GGTGCTCCATGGTCCTCGAACCACTTCCACAGACGCCGGTAGTCCTCCTCACGGACGTGA\n+TGCACCACGACCCACTTTGGTGTGACTGCCGGGAATTGGCCGCGACCTCCAAAGTCCTCA\n+AATTTACAGCTCCCCATGTCCACCGTAATGAGACCCTCCAGTTTAAGCTTCTCCTGTAAG\n+ACACGCCCCACCATGCGGTCCTCGTTATCCGCGCTCATCGTCTTGTACTGAATAGTACGC\n+CAAATGGAGTAGGACTTACTCACCAGTGCAGCCAGTGGCTTGTAGGACACCAAGGCCTGC\n+GCCACATCTTTTGAAAGTGTGTAGCATGACCCTGCCGCAAAAACAATGTCGCGGGACTTC\n+CAAAACAAATTTAGCGGCTTTATCATGCGGCCCATGTAAAGGCCCTGCTGGGGCATGACA\n+CGAAGGTCAGCGAGGTACTGCGGCACCCGCATGAACATGTCGTCATCGCCCTTCACAAGG\n+TAAGGGGCGCTTGGGAACATGTGCAGCGCGAACTGAAACCACAAGTACGTCTTGCGGCTC\n+ATGACATACTCCACAGCGGGGCCCCAAGTGCCATCCTCACCCATCCGCTTCCGTGTCGTG\n+GGCCGCACATCGCACGTCGGTAAAAGGATCACATCGTGCGACTGAGCGGCCTCCTTCCAC\n+AGCGATTCGGAAATCTCATAGCCGTTGTCCTGGTGCGGTGCGAGGAGGTACAGTGGCAGG\n+AGCTCACCGGTGAAGTTGTTTCTTTGCCTCGCCACCTCATCGTATTGCCACCACGTCGCC\n+CGCTGAAGAGCACGCCGCCGCCGCCGGCATCTATGTCTATGGAGGGAATGCCCATTACAA\n+CGAGGTATTCACGCGCCTTCCACGTGCGGACGACATCCGGTGGAATGAAGCGGAAGTATG\n+CGCTATAGTGGATGATGGTCGTGAAGGAGCATTTTTTATGGGGTTGGATAGGCGGTGGTC\n+CATACGTGTTCCCCATAACACACACAGCATCATAATGAGCGACACGATTCCCGCACACAA\n+CCATACCCTGCCGTTCGGGCGCCCCGTCCTTCGCATAACCCACAGGAACACATTCTTTAC\n+CATCTTCAAAGAACTGCTGAGAAGACAGTTATACGCACATGGGGTGAAGCAAGGATAAAC\n+TACGGAAAGAAATAGTTTGCAGAGCAGCAAGCATCGGATGCAAGTCGGGGGGCATAAATG\n+GTGGCCCAACAGCACCGAGCTTAATTAGTTGCTGTTCGCACAGATCGTGTGTAAATTGCT\n+ACGCCCCGCTCACAGGTCCGATAGACGCCGCGGTTTAAGGTGCGGACAGTATAACGGAGT\n+AGGGGGTCTCCTGTGCAGGTATACGCCTACAGGAAAGATAAATAACAACAAGCAGCAGAG\n+GGAAACAATTAAGTACTAAGAAAACAAAGAGAAAGGGGATGGAATTATTTGTTTACTGAC\n+CGGGATGATTCTATCACCCCATCGGCTCCCCAGAGCTGAAAAGAGGTCACCTCGCGGGGC\n+ACCGGTGACAGTTACCACGACCAACGCATCCAAAATATGCACGACCGTTACGATAAAAAA\n+GAGACTACAGTGGATTAAAAAAATGAAATAATAACAGTAATGATAATAATAATACGATAA\n+ATAGTGTTCAAGTGTAATGATATGGTACGCTTTTACACTTAGGGAAGGGAGAGAGCATAT\n+AAGCTTTTCTTTACCCGTATATGGTGTCACCGTCCACCCTAGATGGCACACAACCCTCTA\n+CACCCTCATTTTGTAATGCCATTAAAACAATACGGAGTATCGTTTTATTTTGAGGATACA\n+CTCGATTGGAAATCATGTGGTAATAAATTACCTCGTGATTATATCTTCTGCCGTTTTTAA\n+CTGTCTGGAAGAGTGTTTAAAAAACTTCAAGCCGAAGCACTTCTGAAAAGCAATGTTATG\n+TGTTACCCAGTTATTATACACTCAGTTAACAACAAACACGTACCCTATGATTAAAATAAA\n+ACAATAGGTGGGGTCTTTTTATTATCATTTCAAAGGCGGGAAGTAAATGGAACGTCAACG\n+TGGGGGTGGGAGCAACCTCTGGCAGGTTTGTATTTTACAGGTCACTTAAACCAATTACTA\n+TAACATCCCTACCTGGAGTTTTAGCGGTGGCGCCAATCATAGATGCCACATGTTATTGCT\n+TGCCCTTCTGATGAGTTTGGTTTTGTGTAACATTGCCAATCCCATTAGCGCAATGTTTCC\n+CAACTCCCTATATACCCCCTAACAGCCTCCCCGACACTAGAATATTCGCCTTCTTGTTAA\n+ATATTTTGACGGGGTCAACAGACAGCCTGGCCCGCCTCTCCAAGGTGAAGACTTTTATTT\n+TTATTTTTTGGTCTGACCTCTCGAGGATGGCCGTTGCTTTTCTCAGCTGGTTCACCCAGG\n+CAACGCCTTTAGCCCTTCGGGCCTCACCGTGGTTTTCCCCTAGTTGACACAGATGAACTC\n+AGGGTTCCCACCCCGCACAGTTCACCACTTATTTTCATTAAGATGTTGGGGTAGTGATGC\n+GATAGCTTGTTGTATCGGGCGATGAGGCGAGTCATTCTCCCTCCTCTTCGGGGCACTTCT\n+GGGATGCTTCTTGAACAGGTGATGTTGATGTATTCTCGTTGATCCGCTCTCTGCCTTTGT\n+AGACAATCCAAACCCCGCAGATGCCGTTGGCATTCTTGCTGGGCGTAACCCGATACAAAC\n+ATTCCATTAAAGTGAAGCTGAAGAGCCAGTTTATCTCCCTGCCCCATTCCCTCATCCGGT\n+CCACGATGTTTCTAATCTCGCGCGGGACTCTAAGAAAGGTCCCCAAGTATTTCCGTATCC\n+TGTAACAGACAACGACCCGGTTAATCCCTCTGAGAGACGTGTGATTTCAGCGCGCGGGTT\n+GGCTTTCCGACGAGGCTAGTTAAAGTTTCCAGACCGCGGATTTTGCATTGGCAGTTCGGC\n+TGGATTATAAGCTTTCCGAATACTTCTTCGATAGGCCGTTAGGTTGCATTCATTTGCACC\n+TCTACCGTTATGTCCTAGCGTCTTGACGTTCTATCCCTAGTAAGGCGAACGTTCTACCGC\n+TGCGGGCGACGTCGTTTTAGC'..b'AATTTCCCAAAATCAAGAGAT\n+TCCGTTCAAAATAAAATTTAGTGAAAAAAGAGAATTTCGTGAAAAATGGAATTTGGCAAA\n+AAGGGGAAATTTGTAAAAAGGGGAATGTCGCAAAAAAGGGAATTTGGCAAAAAAGGGGAA\n+TTTGGCAAAAAAGGGGAATTTGGCAAAAATGGGGATTTGGCAAAAAAGGGAATTTGATAA\n+AAAAAGGGAATTTGTAAAAAGGGAATTTTGTAAAAAAGGAATTTGGCAAAAAAGGGAATT\n+TGGCAAAAAGGAGAATTTGGCAAAAAAAGGGAATTTGGCAAAAATGAAATTTTGCAAAAA\n+GGGGAATGTCGCAAAAAGAGAATTTGGCAAAAAAAGGGAATTTGGCAAAAAAGGGAATTT\n+TGGCAAAAAGGGGAATTTTGCAAAAAAGTGAAATTCGTAAAAAATAAAATTTGGCAAAAA\n+TGGAAATTTAGCGAAAAAGAGAATTTTGGCAAAAAATGGAATTTGGCAAAAAAATGAAAT\n+TTGGCAAAAAGAGAATTTGGCAAAAAAGAGAATTTGCCAAAAAATGGAATTTGGCAAAAA\n+GGGAAATTTGGCAAAAAGAGAATTTTGGCAAAAAAGGGAAATTTGGCAAAAAGGGAAATT\n+TGGCAAAAAGGGGAATTTTGCAAAAAAGTGAAATTCGTAAAAAATAAAATTTGGCAAAAA\n+TGGAAATTTAGCGAAAAAGAGAATTTTGGCAAAAAAGGGAAATTTGGCAAAAAGGGAAAT\n+TTGGCAAAAAGGGGGAATTTCGTAAAATCCCGAGATTCGCTCAAAGAGAGGGGTTTTGGA\n+AAAAAAAAAGAAAAAAAATCAAGAAGGGAATGAAATCCTGGGTATAGTAAATTTCGGATA\n+TCCCTCTTCCCCTCTTAAATAAGCCACCCAAATGTGCCGTTTCGAATTCTTAGAGAATGT\n+GTACCCCGGCTCGGCGTTCCCACCAGGGGTCGAGGGGGGGCTCCCATCCTACCGGAGTGG\n+GGGTCGTCCCATCCCCTCGACAGGTATGTTTTCGCGGTTTTAGGGTGGAAGGTGGCTAGG\n+GGTGGGTTTTGGTGGTTATATAGGGGAGGGGCGGGTTAGTCGTTGGGGCCCCTTGTATCG\n+GTGCAAGGGGTGGAGGTGATGGGTGCAGGGCCACGGGAAAGGGTGGATTTTTCGAGGAGC\n+GGACATTTTTTAAATAAAAGCCAAGTGGTGATCGAGAGGATGTCCTCCAGGGGGTTTTGT\n+TGTCAGGGGAGGTGCTGGTGCCTGTCGTGCCTTCGCTGGTGGAGGACCGTCTGCGCCGGT\n+TCTCTGGGCTTCCTTGCTGCTCTGTTGCTTTTTCCGTGAGGTGCGAGTGTTTAGCCCTTT\n+CCCCTTCCATGGTG\n+>T.congo_bin_contig_999 | organism=Trypanosoma_congolense_IL3000 | version=2016-06-06 | length=2402 | SO=contig\n+CCCTCCATTGACAATACTTCTGCAGTTGTGTGTGAACCGTATGGAGATCAACGGTTGGTG\n+CGTTGTGCCCACTGTGGACGATCTTTGGGGACTAGCGGCGCTGGCTGACACCGTTCATGG\n+CAATGGATCGTCGAGGCAGGTGACACAGTTAGTGCCAGTGCCAACGTCTGACATCACCAC\n+AAACGGTTTTTGGAGTGGTGTGTTTTGCGTACAGAACTCCTCGGAGGTGGACGTCTGTCT\n+TTACCGGATCAACCACACGTTGCCGAGTGCATCTGTGAAAAGGAAGGCGAAACTAGAGGT\n+TGTATACGGCCGCTTTTCACTGAATCTCTCGCTGTTGGAAGATGGAACCCTTTCAAGCGC\n+TTCACACCGTGTTGAGCTGCGGGAAATAACCAACACTGATCCCTCGGATGCTAATGGAAA\n+TAGCGGCTGGAATGTTGTAGGGTATGTGGATCTGTCGTGCCGCCCGCTTCTGCACTCGGG\n+TAAAGTGTACGATCCACACACTGTCTTTTTTCAGCGATGCTTGCGGGTCCAGCTGCTTCA\n+GCTCAAGGGTATTATTCGTTTCCAATCCAAGTGTTTGCGCGCCAGAGGATATGGCCGGAA\n+GTGGAGGGGGAGAAGACCGCTTGTTGGCGTACAACTGCAGTGCGGCTCTGCAATCGTGAA\n+CTCATTGCCTTTAGCTCTCCCCGCAGTACGCTCTGCAAGTGCCAAGAGGAACGAGATTTT\n+GGCTGATGACGGTAACGAGGTAAATGTTGGCAGTTGCACCACACCTCATTTTAAAGAGCC\n+ACTTGAATGCTTGCTGAGCGGTGCCGCTGATGTGCATGTGTCACTCTACATCCAGTGCAA\n+CACTACTGAATCGGAGAATAGTGCTAACGTGGCTCCTCATCTACACTTTTCTTCGGATTC\n+CCATGCGCCGCAGCACCACGAGGTGTGCGGACCCCTAACCCAGCTACGGATTGGTGAGGG\n+AACTGCCACCGTATCTCCGCAATACCACGATAACGAGAAGCTCAACGTTGAGCACATAAA\n+GTGTGAAACGCTATGGGTACAGCTCGGTGGATCGCGTCACGGGAAGACTGCATCCGCCCA\n+ACTTCAATGCCATTGGAAGCAACAAATCGTACTTGGTACGTGGCTTTCTTGCATCAGCTG\n+GTGTGGTTCCATGGTACCGGTGCACCAGCCATGGCTCATCTTCAAACTTCGTTTTCCAGG\n+TGGAGAGGCATGCTCCATATCTCTTGATTTATCGGGAAAGCCTCATTCAGGCGTGGGGCG\n+GCAGCTGGGGCAGCGCTCCGCTGTGGGCCAAGTTGCTGCCACGGTAGCCGCGGCATACAC\n+CCCATGGTGCTTTTCCTACATACACCTTCCAATAACGTGGCCGATGGGGGCTTGTATCGA\n+GTGCATCGAGCTGTATGACACAGTGGCTGATGATACACCCGTCTTACTGGGCGTTCATGA\n+ATGGGGTGTTGCAGATGCATTGTTGCTTGCTCCGACGGAGGTGCCGAGTAATGGAGATGT\n+AGAGGCATCGCTGCACTCGGTGGCTACGCGGTCCCTCTCGCTCCACCAAGTTGGACATCG\n+GCTCACATTTGGCAAGCACACGCTGCTGTTTGCAAAAAGTCGCTGCCCACCTGAGACGAC\n+AGACTCCGAGCGGTTGTGTGTTCCTTTTTCTTGGTGGCCTGAGAGTGCCGAGCTTCATTT\n+TAACCCCACTGAGAGTATCGTAGGCATCCTAGGGGCGGCAAGCTTGAGAATAAGTTGCGT\n+TCTGACAATTGGACATCGTGCTGGTGGTAGGTGGGAGTGGCAGGAGGTGACGGAGTCGTG\n+GGAAGGTCAAGCGCTACATATTTTAGCTGATACTTCTACTGCTATAGTGACAGCCTCGTG\n+GGGCAATGTTAACTTCCATTTCAAACCCTTTTCTCGGTTCTTTGCTCTTGAGGAGCTGCG\n+TAAGGGGCCAACATGTTATGCCTTACGAGCAAAAATATCGTGTCATATTCTACCGGAAAA\n+CGCGCAAGGCACAATGGAACCCCCAAGTGTGTTGCGGCGCGACGCACGACCAGCGTTCCC\n+GGAAATGGAGGCTATATTCGTGTTGGATGACCATTCCGGAAGCGTCAACGGCAAACGATC\n+ATTGGAGTTAGTGGAGTGCAAAACCACAGGGGAAGGATCACATGAAAAAGTGATAACGAA\n+AGGCTCCCTCGCCCTAGCCTGGAGTGTGAAACATGACAGCTTGGCTCTTTGTCGAACAGA\n+GGGAGGAAGTAGGATGGAGACAAGTGGTGTGAAGGGTGGAGACCTTCTCGCACAGCATGA\n+AGCGCCCATTGCCGTTAGCGATGCTGGGTGCGCAAGTCCGTCAGATGACCCTTTGCTCTT\n+TTCCTTGAGGCCTCCTGCGGTGTGGGAGGTGGCATTTGTTGAGATGTGTAACGTTTCCAT\n+TG\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Reference/IL3000.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Reference/IL3000.gtf Wed Jul 04 16:39:13 2018 -0400 |
| b |
| b'@@ -0,0 +1,23859 @@\n+BAC13h6\tEuPathDB\texon\t179\t1891\t.\t-\t.\ttranscript_id "TcIL3000_BAC13H6_001.1"; gene_id "TcIL3000_BAC13H6_001";\n+BAC13h6\tEuPathDB\tCDS\t179\t1891\t.\t-\t0\ttranscript_id "TcIL3000_BAC13H6_001.1"; gene_id "TcIL3000_BAC13H6_001";\n+BAC13h6\tEuPathDB\texon\t8057\t8959\t.\t+\t.\ttranscript_id "TcIL3000_BAC13H6_002.1"; gene_id "TcIL3000_BAC13H6_002";\n+BAC13h6\tEuPathDB\tCDS\t8057\t8959\t.\t+\t0\ttranscript_id "TcIL3000_BAC13H6_002.1"; gene_id "TcIL3000_BAC13H6_002";\n+BAC13h6\tEuPathDB\texon\t11673\t12850\t.\t+\t.\ttranscript_id "TcIL3000_BAC13H6_003.1"; gene_id "TcIL3000_BAC13H6_003";\n+BAC13h6\tEuPathDB\tCDS\t11673\t12848\t.\t+\t0\ttranscript_id "TcIL3000_BAC13H6_003.1"; gene_id "TcIL3000_BAC13H6_003";\n+BAC15b11\tEuPathDB\texon\t54\t965\t.\t+\t.\ttranscript_id "TcIL3000_BAC15B11_001.1"; gene_id "TcIL3000_BAC15B11_001";\n+BAC15b11\tEuPathDB\tCDS\t54\t965\t.\t+\t0\ttranscript_id "TcIL3000_BAC15B11_001.1"; gene_id "TcIL3000_BAC15B11_001";\n+BAC15b11\tEuPathDB\texon\t1519\t3924\t.\t+\t.\ttranscript_id "TcIL3000_BAC15B11_002.1"; gene_id "TcIL3000_BAC15B11_002";\n+BAC15b11\tEuPathDB\tCDS\t1519\t3924\t.\t+\t0\ttranscript_id "TcIL3000_BAC15B11_002.1"; gene_id "TcIL3000_BAC15B11_002";\n+BAC15b11\tEuPathDB\texon\t5740\t6795\t.\t+\t.\ttranscript_id "TcIL3000_BAC15B11_003.1"; gene_id "TcIL3000_BAC15B11_003";\n+BAC15b11\tEuPathDB\tCDS\t5740\t6795\t.\t+\t0\ttranscript_id "TcIL3000_BAC15B11_003.1"; gene_id "TcIL3000_BAC15B11_003";\n+BAC15b11\tEuPathDB\texon\t8205\t9392\t.\t+\t.\ttranscript_id "TcIL3000_BAC15B11_004.1"; gene_id "TcIL3000_BAC15B11_004";\n+BAC15b11\tEuPathDB\tCDS\t8205\t9392\t.\t+\t0\ttranscript_id "TcIL3000_BAC15B11_004.1"; gene_id "TcIL3000_BAC15B11_004";\n+BAC15b11\tEuPathDB\texon\t18274\t19650\t.\t+\t.\ttranscript_id "TcIL3000_BAC15B11_005.1"; gene_id "TcIL3000_BAC15B11_005";\n+BAC15b11\tEuPathDB\tCDS\t18274\t19650\t.\t+\t0\ttranscript_id "TcIL3000_BAC15B11_005.1"; gene_id "TcIL3000_BAC15B11_005";\n+BAC1h7\tEuPathDB\texon\t486\t1472\t.\t+\t.\ttranscript_id "TcIL3000_BAC1H7_001.1"; gene_id "TcIL3000_BAC1H7_001";\n+BAC1h7\tEuPathDB\tCDS\t486\t1472\t.\t+\t0\ttranscript_id "TcIL3000_BAC1H7_001.1"; gene_id "TcIL3000_BAC1H7_001";\n+BAC1h7\tEuPathDB\texon\t2679\t3428\t.\t+\t.\ttranscript_id "TcIL3000_BAC1H7_002.1"; gene_id "TcIL3000_BAC1H7_002";\n+BAC1h7\tEuPathDB\tCDS\t2679\t3428\t.\t+\t0\ttranscript_id "TcIL3000_BAC1H7_002.1"; gene_id "TcIL3000_BAC1H7_002";\n+BAC1h7\tEuPathDB\texon\t4138\t5217\t.\t+\t.\ttranscript_id "TcIL3000_BAC1H7_003.1"; gene_id "TcIL3000_BAC1H7_003";\n+BAC1h7\tEuPathDB\tCDS\t4138\t5217\t.\t+\t0\ttranscript_id "TcIL3000_BAC1H7_003.1"; gene_id "TcIL3000_BAC1H7_003";\n+BAC1h7\tEuPathDB\texon\t6699\t7781\t.\t+\t.\ttranscript_id "TcIL3000_BAC1H7_004.1"; gene_id "TcIL3000_BAC1H7_004";\n+BAC1h7\tEuPathDB\tCDS\t6699\t7781\t.\t+\t0\ttranscript_id "TcIL3000_BAC1H7_004.1"; gene_id "TcIL3000_BAC1H7_004";\n+BAC1h7\tEuPathDB\texon\t9612\t10373\t.\t+\t.\ttranscript_id "TcIL3000_BAC1H7_005.1"; gene_id "TcIL3000_BAC1H7_005";\n+BAC1h7\tEuPathDB\tCDS\t9612\t10373\t.\t+\t0\ttranscript_id "TcIL3000_BAC1H7_005.1"; gene_id "TcIL3000_BAC1H7_005";\n+BAC1h7\tEuPathDB\texon\t10719\t11687\t.\t+\t.\ttranscript_id "TcIL3000_BAC1H7_006.1"; gene_id "TcIL3000_BAC1H7_006";\n+BAC1h7\tEuPathDB\tCDS\t10719\t11687\t.\t+\t0\ttranscript_id "TcIL3000_BAC1H7_006.1"; gene_id "TcIL3000_BAC1H7_006";\n+BAC1h7\tEuPathDB\texon\t15961\t17019\t.\t+\t.\ttranscript_id "TcIL3000_BAC1H7_007.1"; gene_id "TcIL3000_BAC1H7_007";\n+BAC1h7\tEuPathDB\tCDS\t15961\t17019\t.\t+\t0\ttranscript_id "TcIL3000_BAC1H7_007.1"; gene_id "TcIL3000_BAC1H7_007";\n+BAC4b1\tEuPathDB\texon\t3799\t4800\t.\t+\t.\ttranscript_id "TcIL3000_BAC4B1_001.1"; gene_id "TcIL3000_BAC4B1_001";\n+BAC4b1\tEuPathDB\tCDS\t3799\t4800\t.\t+\t0\ttranscript_id "TcIL3000_BAC4B1_001.1"; gene_id "TcIL3000_BAC4B1_001";\n+BAC4b1\tEuPathDB\texon\t5065\t6078\t.\t+\t.\ttranscript_id "TcIL3000_BAC4B1_002.1"; gene_id "TcIL3000_BAC4B1_002";\n+BAC4b1\tEuPathDB\tCDS\t5065\t6078\t.\t+\t0\ttranscript_id "TcIL3000_BAC4B1_002.1"; gene_id "TcIL3000_BAC4B1_002";\n+BAC4b1\tEuPathDB\texon\t6188\t7510\t.\t+\t.\ttranscript_id "TcIL3000_BAC4B1_003.1"; gene_id "TcIL3000_BAC4B1_003";\n+BAC4b1\tEuPathDB\tCDS\t6188\t7510\t.\t+\t0\ttranscript_id "TcIL3000_BAC4B1_003.1"; gene_id "TcIL3000_BAC4B1_003";\n+T.congo.pschr.1\tEuPath'..b'25160";\n+T.congo_bin_contig_994\tEuPathDB\texon\t17809\t18264\t.\t+\t.\ttranscript_id "TcIL3000_0_25170.1"; gene_id "TcIL3000_0_25170";\n+T.congo_bin_contig_994\tEuPathDB\tCDS\t17809\t18264\t.\t+\t0\ttranscript_id "TcIL3000_0_25170.1"; gene_id "TcIL3000_0_25170";\n+T.congo_bin_contig_994\tEuPathDB\texon\t24112\t25044\t.\t+\t.\ttranscript_id "TcIL3000_0_25180.1"; gene_id "TcIL3000_0_25180";\n+T.congo_bin_contig_994\tEuPathDB\tCDS\t24112\t25044\t.\t+\t0\ttranscript_id "TcIL3000_0_25180.1"; gene_id "TcIL3000_0_25180";\n+T.congo_bin_contig_995\tEuPathDB\texon\t1\t2488\t.\t-\t.\ttranscript_id "TcIL3000_0_25190.1"; gene_id "TcIL3000_0_25190";\n+T.congo_bin_contig_995\tEuPathDB\tCDS\t2\t2488\t.\t-\t0\ttranscript_id "TcIL3000_0_25190.1"; gene_id "TcIL3000_0_25190";\n+T.congo_bin_contig_995\tEuPathDB\texon\t4866\t5486\t.\t-\t.\ttranscript_id "TcIL3000_0_25200.1"; gene_id "TcIL3000_0_25200";\n+T.congo_bin_contig_995\tEuPathDB\tCDS\t4866\t5486\t.\t-\t0\ttranscript_id "TcIL3000_0_25200.1"; gene_id "TcIL3000_0_25200";\n+T.congo_bin_contig_995\tEuPathDB\texon\t6396\t7406\t.\t-\t.\ttranscript_id "TcIL3000_0_25210.1"; gene_id "TcIL3000_0_25210";\n+T.congo_bin_contig_995\tEuPathDB\tCDS\t6396\t7406\t.\t-\t0\ttranscript_id "TcIL3000_0_25210.1"; gene_id "TcIL3000_0_25210";\n+T.congo_bin_contig_996\tEuPathDB\texon\t505\t1461\t.\t-\t.\ttranscript_id "TcIL3000_0_25220.1"; gene_id "TcIL3000_0_25220";\n+T.congo_bin_contig_996\tEuPathDB\tCDS\t505\t1461\t.\t-\t0\ttranscript_id "TcIL3000_0_25220.1"; gene_id "TcIL3000_0_25220";\n+T.congo_bin_contig_996\tEuPathDB\texon\t2825\t4060\t.\t-\t.\ttranscript_id "TcIL3000_0_25230.1"; gene_id "TcIL3000_0_25230";\n+T.congo_bin_contig_996\tEuPathDB\tCDS\t2825\t4060\t.\t-\t0\ttranscript_id "TcIL3000_0_25230.1"; gene_id "TcIL3000_0_25230";\n+T.congo_bin_contig_996\tEuPathDB\texon\t4821\t5852\t.\t-\t.\ttranscript_id "TcIL3000_0_25240.1"; gene_id "TcIL3000_0_25240";\n+T.congo_bin_contig_996\tEuPathDB\tCDS\t4821\t5852\t.\t-\t0\ttranscript_id "TcIL3000_0_25240.1"; gene_id "TcIL3000_0_25240";\n+T.congo_bin_contig_997\tEuPathDB\texon\t1693\t3033\t.\t-\t.\ttranscript_id "TcIL3000_0_25250.1"; gene_id "TcIL3000_0_25250";\n+T.congo_bin_contig_997\tEuPathDB\tCDS\t1693\t3033\t.\t-\t0\ttranscript_id "TcIL3000_0_25250.1"; gene_id "TcIL3000_0_25250";\n+T.congo_bin_contig_998\tEuPathDB\texon\t329\t1708\t.\t-\t.\ttranscript_id "TcIL3000_0_25260.1"; gene_id "TcIL3000_0_25260";\n+T.congo_bin_contig_998\tEuPathDB\tCDS\t329\t1708\t.\t-\t0\ttranscript_id "TcIL3000_0_25260.1"; gene_id "TcIL3000_0_25260";\n+T.congo_bin_contig_998\tEuPathDB\texon\t2035\t2472\t.\t-\t.\ttranscript_id "TcIL3000_0_25270.1"; gene_id "TcIL3000_0_25270";\n+T.congo_bin_contig_998\tEuPathDB\texon\t2478\t3311\t.\t-\t.\ttranscript_id "TcIL3000_0_25270.1"; gene_id "TcIL3000_0_25270";\n+T.congo_bin_contig_998\tEuPathDB\tCDS\t2035\t2472\t.\t-\t0\ttranscript_id "TcIL3000_0_25270.1"; gene_id "TcIL3000_0_25270";\n+T.congo_bin_contig_998\tEuPathDB\tCDS\t2478\t3311\t.\t-\t0\ttranscript_id "TcIL3000_0_25270.1"; gene_id "TcIL3000_0_25270";\n+T.congo_bin_contig_998\tEuPathDB\texon\t3423\t4640\t.\t-\t.\ttranscript_id "TcIL3000_0_25280.1"; gene_id "TcIL3000_0_25280";\n+T.congo_bin_contig_998\tEuPathDB\tCDS\t3423\t4640\t.\t-\t0\ttranscript_id "TcIL3000_0_25280.1"; gene_id "TcIL3000_0_25280";\n+T.congo_bin_contig_998\tEuPathDB\texon\t4734\t6071\t.\t-\t.\ttranscript_id "TcIL3000_0_25290.1"; gene_id "TcIL3000_0_25290";\n+T.congo_bin_contig_998\tEuPathDB\tCDS\t4734\t6071\t.\t-\t0\ttranscript_id "TcIL3000_0_25290.1"; gene_id "TcIL3000_0_25290";\n+T.congo_bin_contig_998\tEuPathDB\texon\t7626\t8366\t.\t-\t.\ttranscript_id "TcIL3000_0_25300.1"; gene_id "TcIL3000_0_25300";\n+T.congo_bin_contig_998\tEuPathDB\tCDS\t7626\t8366\t.\t-\t0\ttranscript_id "TcIL3000_0_25300.1"; gene_id "TcIL3000_0_25300";\n+T.congo_bin_contig_998\tEuPathDB\texon\t9061\t10806\t.\t-\t.\ttranscript_id "TcIL3000_0_25320.1"; gene_id "TcIL3000_0_25320";\n+T.congo_bin_contig_998\tEuPathDB\tCDS\t9061\t10806\t.\t-\t0\ttranscript_id "TcIL3000_0_25320.1"; gene_id "TcIL3000_0_25320";\n+T.congo_bin_contig_999\tEuPathDB\texon\t41\t2402\t.\t+\t.\ttranscript_id "TcIL3000_0_25330.1"; gene_id "TcIL3000_0_25330";\n+T.congo_bin_contig_999\tEuPathDB\tCDS\t41\t2401\t.\t+\t0\ttranscript_id "TcIL3000_0_25330.1"; gene_id "TcIL3000_0_25330";\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Reference/IL3000.rev.1.bt2 |
| b |
| Binary file data/Reference/IL3000.rev.1.bt2 has changed |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Reference/IL3000.rev.2.bt2 |
| b |
| Binary file data/Reference/IL3000.rev.2.bt2 has changed |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Reference/IL3000_prot.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Reference/IL3000_prot.fasta Wed Jul 04 16:39:13 2018 -0400 |
| b |
| b'@@ -0,0 +1,104702 @@\n+>TcIL3000_1_10\r\n+MGEDGTWGPAVEYVMSRKTYLWFQFALHMFPSAPYLVKGDDDMFMRVPQYLADLRVMPQQ\r\n+GLYMGRMIKPLNLFWKSRDIVFAAGSCYTLSKDVAQALVSYKPLAALVSKSYSIWRTIQY\r\n+KTMSADNEDRMVGRVLQEKLKLEGLITVDMGSCKFEDFGGRGQFPAVTPKWVVVHHVREE\r\n+DYRRLWKWFEDHGAPPAPSQLYWFSKTSAALVC*\r\n+>TcIL3000_1_100\r\n+MQDRKMKKSQGIVVLLVVCSVATHITSADGTETNKADFLSLGQARAVCSTSRMLKGVYVY\r\n+VASAVDEYQKKYDEVEMIRDVARLKVLGRVTLNLRCGLEAAFLLYIQDRLNVMRASLEKL\r\n+RRAATKAAGSAGIAAGRLDEFISIFKQSHGKTGHDKNCAGVQGNVVDDLKLLLKECYKGS\r\n+SSKDYFHEVDDGIVAPTFNNFDEALTSMLKTQVLEVSDAGAGGDADNSRSCHLAVINATE\r\n+SYVNESTPTNSIRWGAGVLQVNAGEPSKAVWSTNPSVEVPVFRDASTHFKEFREALNEIR\r\n+QVYIDLKEDWTMEKVSRSDIQGILSTLKRNRFEQNGTFSFRRLSSLDDATRKNWLPEWND\r\n+VKINEKVLEEELALCEGKNGVDLVSKVLFSWLVSLTLLLSLI*\r\n+>TcIL3000_1_1000\r\n+MNSFLSTFCIPRSSRLRPAPAAAGPLQVLRPFHIAEHCCHGRMRGSTVPDGGSPAFGGLS\r\n+GTRRGKRARQSNADEAGGCGVSLARDVVFKLPRGKLSKWLNSPPCCLCDVRPSSASYSNN\r\n+ALPVQCTTIPGFFAPSSASAACKPRLRCILQRALAEVRQEMGSVDNIPSDSLLVIATPSE\r\n+EQTLGLCESAGFGNARALLGLCVARELSMAYRLHCEPSLEPDKRETCGSGAPRLEEERCH\r\n+GWEKCAMRIGDTRCVGSAFCGVQLVWVAEQYRRSGVANALVDVARRHVSYGFDVPACQVA\r\n+FSEPTTLGALFARRYSGRPDFLIF*\r\n+>TcIL3000_1_1010\r\n+MLTGSSLLQELEGLSRGQRYRRVVEVGRAARAGGSECREHVVLVELSRSTVPYERLIGAL\r\n+GLWQTGSSSETLRILSDPCDRVARQAMFPAAEAIPDESLLKVFDEIPLQRLAMLCGCLER\r\n+SGRVTALVDRYVMAVSPVVRKGVGLTLLCWASAAVLAAQPATTFYLLRKSESAVLVRRNP\r\n+DFAVSLVKQCIESKDSLSPAAVSQANCVLFHLHRYHPSIGLQLLVTMIPRVCTSKGCIES\r\n+YASIYPTEVAEILIKHKMTSTLHIKRFLDKVPPELFLRMFHAGVFHEKTFREFFFEASPK\r\n+LRLFLYENSKRNLYDCDGTMDIDMIELIPKAEEREREALHALMNEKLQLDMRSWALFLSP\r\n+LPFPKAMEVAKQHLSERDVTIRAQLVGSIAYGGQYHPECLDDILDFCIKRSNENDVVRGN\r\n+FLTRLSNISHRKFEERHLPKVEAIIRAALNAKDASSCTLDTCCYMVLKLALVSDALIDSL\r\n+LLDVVRRAGLGTNLTRFALARPKLSRIWERLEPLLHEEEACDSNIYAKRGIMMMFSSCMR\r\n+DISDQSLPYLRKVCEEGGSAARSAISALLKYFPAEAMEILPGLLERKPKIICQQEVYDVV\r\n+GNNLQGEMLEKILSVESIKGTFLNEGSLPDRFRGHSWTFAKQQKYADAILKLVETNGKRW\r\n+WSLLFLTKPLDSLYSVNLADMFCAVISEDSEPTALRDCFINLLGRGENPDSLQALLETLD\r\n+DSRAPVGICAIQKRAA\r\n+>TcIL3000_1_1020\r\n+FDFLKRLHTEKKMHVDVEIAWIQALFSFLNKREVWEYLHFAAKKRKALALAAMDVPYGAL\r\n+EEQWQREAFSKLFVPLVTHAENFVVVRALERLAERALPAYDPELIKCLFNLLLTERRPEY\r\n+FPNTLRALVISTADAHEIARCLVSVKHDGLLSENVHVHCSNISSLVCRFRPIATAMVDTL\r\n+IDEGRQPAIVCKLLCWLPPAVAGEYLEKLLVKGLFHVGCATEVMKGVSNFGCDMSGAEAL\r\n+EERLRGHENPLMQRIGLEMLQWLGEKAKWGEKHRKALSEYCNASDPWVGDTAKTVMP*\r\n+>TcIL3000_1_1030\r\n+MSGDGGNGGDPPPPQLSKNSRTFMKKKLEKRAKKGSNSGAGGSGLSNGARFVPRSWQCLK\r\n+KFNCPVCRMKGSVRVEVNCKEAQAVVNCIYCIQLVPRPVDLPYPFTTSFVPRLENRADVF\r\n+FKFNELYRGLEQQAASLDATGNALQGDVKSHEGGVLSVPVLKDEGDSQKSDVCEEGEEER\r\n+ISELHDGGGVDGETVEQADEIDDVHAFFGESDQDE*\r\n+>TcIL3000_1_1040\r\n+MRNPLWLLSGCAGPRCVRKAHWQRSGCVAMWTVLRRMCSTKPLLALERVEVAHSNAYARR\r\n+GVTVGFTSCATTHAGGSRGSSLSSSSADANSGEALANYVNFVADDTSGPPATKENGAQPM\r\n+RSLRSASAVESLLFTDSAKNFCRLCMEEIQGTAKSHIVATQRASHTNHTCREVVLDSLAL\r\n+LAIRGYPIDDVFFVWADTLYQATAFQRIPSLVSPRWTVNQRSDMLAKLLSMLKRMNVLDL\r\n+SLAAQSPDTFDSATQLLHHRRRVAFERLEYIGDNSWGNHLSNRMMLLFPDRQWAYSQNAY\r\n+TFNCFRDACEMNVTLEFIFDTLRVGDLLPPGVREKLGTGKIKADVVEAVIGELHVTLWGL\r\n+EPQLYDSACYVEINGVGEARLSAVVQHCLTEIYDLIVLSYVQELSGSAIPLAKQIAAGRI\r\n+WNTVYPPVRKAKDRAVVSRKGRSTLVTVLGVGDVYQLPPTPSLFPKPTPRPTEVPHPLRR\r\n+LRSAEEIPEEMVCVGTKQDVFVHLIDSYCRLKMLDDSSTATMIVRRLCDVQFAQLKRQLV\r\n+PSLSQAALGTGEERVTRANEDNDQLDGVRSSMLTNERLLDLEEVYFRDIYFDLFPTPSRA\r\n+EEENCNENKRSRVVIAAGVKQPSEDRLSNKAQEHMAAHIIYPALEDTPTNNYIATRSKGD\r\n+RECLFSISVYVPADIKRPSAGVVTDKNLHSGEFAFLDVQVGEKGCGGAGHRELKGAKNAA\r\n+VTSDLEDSNEEKATGAEKTEKCVEAEVSATDGEEATERVHVKWLQENPYFPCKPPALCNP\r\n+VATA*\r\n+>TcIL3000_1_1050\r\n+MSSRHVQSSSVSGRKRKKSVSDIINEQFGISDARRNSADEFDDFYGDGPMIDDYYEGNES\r\n+GDENMDDNVDSRITPASKRHRAEDTSSRKKQEKRLRRRGPIDPSLSTGEYAATPVEVEAA\r\n+MDDLFGALEMDEDDMSLDEGEGLQVNEKGKHRKAETEEEYIQWLEAQQKKRQRRRGAAGL\r\n+TEEGDILQQIEALRSAQVELLQREQEGGSAADPEAKERVKAQEAIQHYVMLYSQLLRMRI\r\n+KLQPVVTRAIAFPQYYALSDFIDNGDSQIREGTTAVVQSLRGVWGKFTPL*\r\n+>TcIL3000_1_1060\r\n+MEKALFTLLNSDCTDVASTSCQRQALSRAFESSLINAVSDKKAGSSGKRKNNTPSKKREH\r\n+EDECLRRAVDSFLASPTPSPLELLFVRVATMVHCHTIMKPARPGNSEQLPQSVKETAIAL\r\n+AAALFSSRLHSPWIKSEKLASGKRKSVVCDADSEDKLNHPLWFCFLCIFLQQLSARGGDL\r\n+SLWQAFLSECSAEASARCSKEKEEADTREDTDNAMPADDSEQLGVSAWGAVSTTLFEATL\r\n+SRTRYRRSLVVCRSFCPHSVAQAPGTTFRLLDTLHEFVKDWKDQLGGNLQGEEDKGKEKN\r\n+EAKKKENALIDLYAERLGRILGDANIHALLLATAVGAVLSAMYIFPKRQGQG'..b'LLCLCAKMDS\r\n+PGGEEALGTECVGAGASAGDGWETDQKDGSTEWGHIQKGCPQSGTRTIPWLRHTLDQALR\r\n+EFIREVRVGIEAHQGGSAWVPGLLGSFGSGSKSGGCAGKLEANNGICVYYGGPEETNIDW\r\n+YMRLRNALPLLADAENASIAIRHDITHLKMLQTRAEEIYEETQASSELEAAKTATPIHNQ\r\n+SQKSNPASLLPSSTAAQDASSGVASTSRRFILPWTLLI*\r\n+>TcIL3000_BAC1H7_001\r\n+MVIGVSVGLTTVTPMHHNQKEHAALCDVLGTVVAIFESGRGGTKLQRALSRAILGNENGG\r\n+TGVRALLGTLPQEFHNPGNRHNWCGSCGHGGKDHYPGKSIPHDLLCLCTVGGDGYPFYAN\r\n+SDGAPTLCGKNAKDLLCGQAEGKHCASEARTGWSEQKFDEKVKNHLNATWGTVVKTCLGK\r\n+KMKFDLDTARNTLMEQLKPKDGYTSPIWARGHTYCGGINGDVCVSYGSCSEIPGFPQWQE\r\n+GLYEALEKADFTQTELTSAVSHNASTEDGQTDGQYGPNEDYPQGTQQENHGVQQRSKRST\r\n+NPTSHHSEQQSCSIPAQPLWLLSELFFY*\r\n+>TcIL3000_BAC1H7_002\r\n+MGNSWEARLKSVVTRETVLTQLSLYKITQRAHNIFEEMKRVNATRDVEKAKAEFNKVIFW\r\n+ENRNESDLCHATVNGLGNRSVACGKPGQEKKGTRAGKNLVMDFFCLSVQRQDGEGINQIC\r\n+GFYAGSGYKNGRIVWSKQGPWGSSTMWASIKWGCGKHMQQHPKSTAEARHILEQFLKHLK\r\n+TGGVYRWGSGNEVKGINRKEGMLGTCAGTNTGSGTDIPCDGKKGEKTGTKPGGVCLYYGP\r\n+ESEWEANID*\r\n+>TcIL3000_BAC1H7_003\r\n+MMRGVKVMMVVVGLMGIGVLAEEGGAILDASHFGLLCNITKALTGVWETVGPLGDFSERE\r\n+KELTERIDEVFFGEKEKADGMWSLPDKFTNGKQNRSLVCGSRNFPNGMPTASKSLASTIL\r\n+CLCTGITGVDEDLCGYTNFDKLKWSDSESEDIKKIFEKVWGDGFDGMFINNCVKTDTYTN\r\n+FQEAQQNLTALLKTLEETLKHKTGTLAKSNTTCNGSTPCATIRGTPTWLEKLEKIEEVSK\r\n+TILSLVQAEKDKVAKEHKEAVEEIERQAAPTTASEEAHQTTLAPVTEPVGAPAHVETHKQ\r\n+EPRRAPEEKSTQQQQRVPEQKTVETLPRQTDDSLPPPENETSGLIITSPKWLLSAAFLS*\r\n+>TcIL3000_BAC1H7_004\r\n+MIFPSF**RDRLGRMIMKMWMAMLCFVVAGVRADSAVEKEYNKRKHDALCDFLKAAVSIY\r\n+QSKGGNDAMQKALTRTIFGNEGVEDLERFKRTLPEYYSTDFGKNRANVCGQSYTAVSRTD\r\n+QHPRWPGHSAPHDLLCLCTVGKGGYPFDEASRGSIPSTTLCGKNKTTLKADNDQGWSSAG\r\n+GDGGDQMTATWTNVTGECLQEGGKARDLKMALDDFLEELEKRPWGDIPERYQLGEGDSDE\r\n+FPCSGNGKICVMYYNSTKHKHHMPWWTDLKNVLDAEEGKNKREEEPTKEESQKQKKSQRK\r\n+ENKQPQQAPRTAALKSATLDTQDGKQKNPENISAPLATIEEASGILITPPCTWFLGALLI\r\n+*\r\n+>TcIL3000_BAC1H7_005\r\n+MRKVFSTSYYCLGSGGDPAKRRDLIDCFPVGGKIEMGENNLAKIPERIADPNEPNLTAII\r\n+TKVTHSAMASYFHQKYSGDDGANCNLINGKSGILGGGLKDKLWWGGGILTIGKSFDGKME\r\n+KTKFTAGEIADAFKDREGSKAFWTEKPSEKIPHLQKTLAAFQDFKDTVSRITQKFAKIEK\r\n+IEKQIELCLSNETMEEGHTQSCFKNAVKLNAELQAANALLARYHKEKGPLPSGSASILHQ\r\n+SVVNVWFFFAFFL*\r\n+>TcIL3000_BAC1H7_006\r\n+MKLLEWQSKFIQSKSKASGSEACKITGLLFRQVRKEIDKARKEVEKLEREASRAAVFAAN\r\n+SAGRLDEFITVFANARNENSRGFYLGNDKLATSEESKDCFGGKDISIECLVDTFERASEQ\r\n+KPNLDTKIEGIKHQSLKDSFRGGSSAGCNLIKENAGGILVNTELGKSLW*SGDFLSIGGT\r\n+FGSISSIVVRVIANTTGNKAILSAYPAKHIVNLKKASNLQGSQSFPARIQSKVETIVQQI\r\n+QACLRNQGACENSAEETTTSPTSFDNVARTSADLKEKRPLPKRNVIAPVKWHIEQPHNAL\r\n+WFPANYTINRKHLNRKTQISTT*\r\n+>TcIL3000_BAC1H7_007\r\n+MATFAGVSLEVSASGDDLFDKLCNITKLSTALLSMDRNSGPLREAIYGRDDWAHFETSGR\r\n+VKIGWHCNELKLRNTLCAHYTGGRHGLGQDGCFAESLLGTFLCICAPPGGGQPSFFCHNK\r\n+SVPSGAGWSGKWEETAHQPLFKDLWRLVLQGCVATDRTLGDAFLEIDQLSRALARITGSL\r\n+KKGHQPALLYLGNTGNNCAGQIATDVCAAYPNSVGKAEIPWVKKLEAALVTLKNLGHQGR\r\n+EAKQPSAQSNQEVVLVREHQIEGADRAPEVVIEENPQPQPEDDETEPKHEKKEDKKKTSV\r\n+RHASTERSSNSSKRKTLQHSILTDLPHLATNPDDEGSVILRPTLFILAALIY*\r\n+>TcIL3000_BAC4B1_001\r\n+MEKAKDVYNRMEEELIQAKKERTLARNNLVHAIYGVQVGELPKEENITHVLQNVSRSSIF\r\n+NSQGGSKKVRYNEADPKDPTCGKTGDNGPGFTLINDFYCLCVGKENAKAVCNKAIAGPCC\r\n+CCCEKCAKGCQCGKNCNCNPKCQGCENHNKWMYLFDVNKSEIVDVPEGWKRIRKICNETV\r\n+KDEINTTAESIQEVLDDFNKLLGKNSSKKEIELKAANVESRRLFVLGYTNKMEGQGCTGK\r\n+DSESSVCVNYWSVSNLGIGIVWQNYMLKAQKHLHAMEKHIKKALQLSAMIQKLKESAEES\r\n+YRNSTHGSLLWSEDKGFRENAFFTCFIFFAFLF*\r\n+>TcIL3000_BAC4B1_002\r\n+MRRIEKVGPEIHGLVGKADQRDGSLIAKFHAIAQEAKQLMENVKDLRRKAVEKRLSAKRH\r\n+LHQVIFGDYGGDETGELDEKPETVKKIFSRDKFEESCGGKGDKPAGKSLINDFLCLCSHW\r\n+FDPKDDQSICKYKVDTSVDPKFSNWTKVWHENNHRICVNTPPLTPTPQNIQKLVALFERA\r\n+VEREQSGSQAKNVLGYVKTENKDEACNATDTGFTCVNYKYALKNGGIEWVNHLNNASQDL\r\n+QDMARYAEESESALPQLEMLEYNALLLYEEAKYSTHLPHAVPSNETDTNSSNESYQGDPT\r\n+NTSDTSEEEKLEEEDADATWKGGTPWWGILMFFLMAF*\r\n+>TcIL3000_BAC4B1_003\r\n+MLMKFALVALVFCVGALSQRPSSAEFNLFCRILAEANNMMYGPEYVYDENVDEEIIKEMT\r\n+VLYNATTGSMKDFGNSLWGTKEFLKEHPPPTDPKNREEAHRQIGNLIDKGEKKIEENKKI\r\n+ALEVNEKINEAKLSVAKGLYGEHVTVMPKDDKNLTEILNNTESTFVSSKSAAESCGHKEG\r\n+KNKPAGKTLINDLFCVCVGDADDAQGPCHQNIWSPKSWPGRGGCNGNDNCKWTQIKFGPD\r\n+DSRNPPLIQSFNESFQKIERLCREEMMQGNVKPENMAGLLREYVGMIGMGDKKTKKEKKI\r\n+FGHSERNKGGKGKNQVEKCTGEKGEWSSNDPEKKNNNICVDYTNNKSEDGKTYNITWHTK\r\n+FKNYTKIMQDAKQIEERILKNRAALLLLKSQAWVAYSREKDDETSNLDDMNVSNLFDGAR\r\n+VPPSFPFPFLFPLLYLFMIS*\r\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Reference/ORFAnnotation.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Reference/ORFAnnotation.gtf Wed Jul 04 16:39:13 2018 -0400 |
| b |
| b'@@ -0,0 +1,17803 @@\n+Tc148_allcontigs\tartemis\tCDS\t953\t1648\t.\t+\t0\ttranscript_id "Tc14800001"; gene_id "Tc14800001";\n+Tc148_allcontigs\tartemis\tCDS\t2131\t3066\t.\t+\t0\ttranscript_id "Tc14800002"; gene_id "Tc14800002";\n+Tc148_allcontigs\tartemis\tCDS\t2488\t3135\t.\t-\t0\ttranscript_id "Tc14800003"; gene_id "Tc14800003";\n+Tc148_allcontigs\tartemis\tCDS\t3655\t4377\t.\t-\t0\ttranscript_id "Tc14800004"; gene_id "Tc14800004";\n+Tc148_allcontigs\tartemis\tCDS\t4831\t5940\t.\t+\t0\ttranscript_id "Tc14800005"; gene_id "Tc14800005";\n+Tc148_allcontigs\tartemis\tCDS\t5637\t6323\t.\t-\t0\ttranscript_id "Tc14800006"; gene_id "Tc14800006";\n+Tc148_allcontigs\tartemis\tCDS\t9129\t9800\t.\t+\t0\ttranscript_id "Tc14800007"; gene_id "Tc14800007";\n+Tc148_allcontigs\tartemis\tCDS\t10112\t11047\t.\t+\t0\ttranscript_id "Tc14800008"; gene_id "Tc14800008";\n+Tc148_allcontigs\tartemis\tCDS\t11461\t13275\t.\t+\t0\ttranscript_id "Tc14800009"; gene_id "Tc14800009";\n+Tc148_allcontigs\tartemis\tCDS\t14133\t15122\t.\t+\t0\ttranscript_id "Tc14800010"; gene_id "Tc14800010";\n+Tc148_allcontigs\tartemis\tCDS\t15932\t17152\t.\t+\t0\ttranscript_id "Tc14800011"; gene_id "Tc14800011";\n+Tc148_allcontigs\tartemis\tCDS\t17770\t18786\t.\t+\t0\ttranscript_id "Tc14800012"; gene_id "Tc14800012";\n+Tc148_allcontigs\tartemis\tCDS\t20341\t21354\t.\t+\t0\ttranscript_id "Tc14800013"; gene_id "Tc14800013";\n+Tc148_allcontigs\tartemis\tCDS\t21967\t23958\t.\t+\t0\ttranscript_id "Tc14800014"; gene_id "Tc14800014";\n+Tc148_allcontigs\tartemis\tCDS\t24675\t26918\t.\t+\t0\ttranscript_id "Tc14800015"; gene_id "Tc14800015";\n+Tc148_allcontigs\tartemis\tCDS\t28052\t28684\t.\t+\t0\ttranscript_id "Tc14800016"; gene_id "Tc14800016";\n+Tc148_allcontigs\tartemis\tCDS\t29596\t30237\t.\t+\t0\ttranscript_id "Tc14800017"; gene_id "Tc14800017";\n+Tc148_allcontigs\tartemis\tCDS\t31226\t32196\t.\t-\t0\ttranscript_id "Tc14800018"; gene_id "Tc14800018";\n+Tc148_allcontigs\tartemis\tCDS\t31228\t31932\t.\t+\t0\ttranscript_id "Tc14800019"; gene_id "Tc14800019";\n+Tc148_allcontigs\tartemis\tCDS\t32922\t34304\t.\t+\t0\ttranscript_id "Tc14800020"; gene_id "Tc14800020";\n+Tc148_allcontigs\tartemis\tCDS\t33198\t34538\t.\t-\t0\ttranscript_id "Tc14800021"; gene_id "Tc14800021";\n+Tc148_allcontigs\tartemis\tCDS\t35292\t36674\t.\t+\t0\ttranscript_id "Tc14800022"; gene_id "Tc14800022";\n+Tc148_allcontigs\tartemis\tCDS\t35568\t36977\t.\t-\t0\ttranscript_id "Tc14800023"; gene_id "Tc14800023";\n+Tc148_allcontigs\tartemis\tCDS\t37664\t39046\t.\t+\t0\ttranscript_id "Tc14800024"; gene_id "Tc14800024";\n+Tc148_allcontigs\tartemis\tCDS\t37940\t39349\t.\t-\t0\ttranscript_id "Tc14800025"; gene_id "Tc14800025";\n+Tc148_allcontigs\tartemis\tCDS\t40036\t41418\t.\t+\t0\ttranscript_id "Tc14800026"; gene_id "Tc14800026";\n+Tc148_allcontigs\tartemis\tCDS\t40312\t41721\t.\t-\t0\ttranscript_id "Tc14800027"; gene_id "Tc14800027";\n+Tc148_allcontigs\tartemis\tCDS\t42409\t43791\t.\t+\t0\ttranscript_id "Tc14800028"; gene_id "Tc14800028";\n+Tc148_allcontigs\tartemis\tCDS\t42685\t44094\t.\t-\t0\ttranscript_id "Tc14800029"; gene_id "Tc14800029";\n+Tc148_allcontigs\tartemis\tCDS\t44780\t45748\t.\t+\t0\ttranscript_id "Tc14800030"; gene_id "Tc14800030";\n+Tc148_allcontigs\tartemis\tCDS\t45056\t45844\t.\t-\t0\ttranscript_id "Tc14800031"; gene_id "Tc14800031";\n+Tc148_allcontigs\tartemis\tCDS\t45705\t46466\t.\t-\t0\ttranscript_id "Tc14800032"; gene_id "Tc14800032";\n+Tc148_allcontigs\tartemis\tCDS\t47152\t48534\t.\t+\t0\ttranscript_id "Tc14800033"; gene_id "Tc14800033";\n+Tc148_allcontigs\tartemis\tCDS\t47428\t48837\t.\t-\t0\ttranscript_id "Tc14800034"; gene_id "Tc14800034";\n+Tc148_allcontigs\tartemis\tCDS\t49524\t50906\t.\t+\t0\ttranscript_id "Tc14800035"; gene_id "Tc14800035";\n+Tc148_allcontigs\tartemis\tCDS\t49800\t51209\t.\t-\t0\ttranscript_id "Tc14800036"; gene_id "Tc14800036";\n+Tc148_allcontigs\tartemis\tCDS\t51896\t53278\t.\t+\t0\ttranscript_id "Tc14800037"; gene_id "Tc14800037";\n+Tc148_allcontigs\tartemis\tCDS\t52172\t53581\t.\t-\t0\ttranscript_id "Tc14800038"; gene_id "Tc14800038";\n+Tc148_allcontigs\tartemis\tCDS\t56118\t56771\t.\t+\t0\ttranscript_id "Tc14800039"; gene_id "Tc14800039";\n+Tc148_allcontigs\tartemis\tCDS\t68225\t68887\t.\t+\t0\ttranscript_id "Tc14800040"; gene_id "Tc14800040";\n+Tc148_allcontigs\tartemis\tCDS\t73396\t74991\t.\t+\t0\ttranscript_id "Tc14800041"'..b'nscript_id "Tc14817765"; gene_id "Tc14817765";\n+Tc148_allcontigs\tartemis\tCDS\t41089272\t41091074\t.\t+\t0\ttranscript_id "Tc14817766"; gene_id "Tc14817766";\n+Tc148_allcontigs\tartemis\tCDS\t41092385\t41094133\t.\t+\t0\ttranscript_id "Tc14817767"; gene_id "Tc14817767";\n+Tc148_allcontigs\tartemis\tCDS\t41098436\t41099596\t.\t+\t0\ttranscript_id "Tc14817768"; gene_id "Tc14817768";\n+Tc148_allcontigs\tartemis\tCDS\t41100280\t41101983\t.\t+\t0\ttranscript_id "Tc14817769"; gene_id "Tc14817769";\n+Tc148_allcontigs\tartemis\tCDS\t41106832\t41107866\t.\t+\t0\ttranscript_id "Tc14817770"; gene_id "Tc14817770";\n+Tc148_allcontigs\tartemis\tCDS\t41109683\t41110357\t.\t-\t0\ttranscript_id "Tc14817771"; gene_id "Tc14817771";\n+Tc148_allcontigs\tartemis\tCDS\t41110656\t41111258\t.\t+\t0\ttranscript_id "Tc14817772"; gene_id "Tc14817772";\n+Tc148_allcontigs\tartemis\tCDS\t41110787\t41111398\t.\t-\t0\ttranscript_id "Tc14817773"; gene_id "Tc14817773";\n+Tc148_allcontigs\tartemis\tCDS\t41122619\t41123866\t.\t+\t0\ttranscript_id "Tc14817774"; gene_id "Tc14817774";\n+Tc148_allcontigs\tartemis\tCDS\t41128605\t41129687\t.\t+\t0\ttranscript_id "Tc14817775"; gene_id "Tc14817775";\n+Tc148_allcontigs\tartemis\tCDS\t41134535\t41135494\t.\t+\t0\ttranscript_id "Tc14817776"; gene_id "Tc14817776";\n+Tc148_allcontigs\tartemis\tCDS\t41137538\t41138458\t.\t+\t0\ttranscript_id "Tc14817777"; gene_id "Tc14817777";\n+Tc148_allcontigs\tartemis\tCDS\t41137564\t41138205\t.\t-\t0\ttranscript_id "Tc14817778"; gene_id "Tc14817778";\n+Tc148_allcontigs\tartemis\tCDS\t41140647\t41141840\t.\t+\t0\ttranscript_id "Tc14817779"; gene_id "Tc14817779";\n+Tc148_allcontigs\tartemis\tCDS\t41142768\t41143763\t.\t+\t0\ttranscript_id "Tc14817780"; gene_id "Tc14817780";\n+Tc148_allcontigs\tartemis\tCDS\t41145105\t41145791\t.\t-\t0\ttranscript_id "Tc14817781"; gene_id "Tc14817781";\n+Tc148_allcontigs\tartemis\tCDS\t41148402\t41149358\t.\t-\t0\ttranscript_id "Tc14817782"; gene_id "Tc14817782";\n+Tc148_allcontigs\tartemis\tCDS\t41149442\t41150137\t.\t+\t0\ttranscript_id "Tc14817783"; gene_id "Tc14817783";\n+Tc148_allcontigs\tartemis\tCDS\t41149619\t41150692\t.\t-\t0\ttranscript_id "Tc14817784"; gene_id "Tc14817784";\n+Tc148_allcontigs\tartemis\tCDS\t41150980\t41152236\t.\t-\t0\ttranscript_id "Tc14817785"; gene_id "Tc14817785";\n+Tc148_allcontigs\tartemis\tCDS\t41152518\t41153279\t.\t-\t0\ttranscript_id "Tc14817786"; gene_id "Tc14817786";\n+Tc148_allcontigs\tartemis\tCDS\t41154780\t41155499\t.\t-\t0\ttranscript_id "Tc14817787"; gene_id "Tc14817787";\n+Tc148_allcontigs\tartemis\tCDS\t41156689\t41158626\t.\t+\t0\ttranscript_id "Tc14817788"; gene_id "Tc14817788";\n+Tc148_allcontigs\tartemis\tCDS\t41156715\t41157395\t.\t-\t0\ttranscript_id "Tc14817789"; gene_id "Tc14817789";\n+Tc148_allcontigs\tartemis\tCDS\t41156960\t41159956\t.\t-\t0\ttranscript_id "Tc14817790"; gene_id "Tc14817790";\n+Tc148_allcontigs\tartemis\tCDS\t41157194\t41158243\t.\t+\t0\ttranscript_id "Tc14817791"; gene_id "Tc14817791";\n+Tc148_allcontigs\tartemis\tCDS\t41158182\t41158859\t.\t+\t0\ttranscript_id "Tc14817792"; gene_id "Tc14817792";\n+Tc148_allcontigs\tartemis\tCDS\t41158860\t41159927\t.\t+\t0\ttranscript_id "Tc14817793"; gene_id "Tc14817793";\n+Tc148_allcontigs\tartemis\tCDS\t41158945\t41159598\t.\t+\t0\ttranscript_id "Tc14817794"; gene_id "Tc14817794";\n+Tc148_allcontigs\tartemis\tCDS\t41164291\t41165169\t.\t-\t0\ttranscript_id "Tc14817795"; gene_id "Tc14817795";\n+Tc148_allcontigs\tartemis\tCDS\t41186049\t41187095\t.\t+\t0\ttranscript_id "Tc14817796"; gene_id "Tc14817796";\n+Tc148_allcontigs\tartemis\tCDS\t41199332\t41200111\t.\t+\t0\ttranscript_id "Tc14817797"; gene_id "Tc14817797";\n+Tc148_allcontigs\tartemis\tCDS\t41212550\t41213176\t.\t-\t0\ttranscript_id "Tc14817798"; gene_id "Tc14817798";\n+Tc148_allcontigs\tartemis\tCDS\t41212909\t41213529\t.\t-\t0\ttranscript_id "Tc14817799"; gene_id "Tc14817799";\n+Tc148_allcontigs\tartemis\tCDS\t41218459\t41219118\t.\t-\t0\ttranscript_id "Tc14817800"; gene_id "Tc14817800";\n+Tc148_allcontigs\tartemis\tCDS\t41227321\t41228436\t.\t+\t0\ttranscript_id "Tc14817801"; gene_id "Tc14817801";\n+Tc148_allcontigs\tartemis\tCDS\t41228289\t41228927\t.\t+\t0\ttranscript_id "Tc14817802"; gene_id "Tc14817802";\n+Tc148_allcontigs\tartemis\tCDS\t41228636\t41229838\t.\t+\t0\ttranscript_id "Tc14817803"; gene_id "Tc14817803";\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Reference/Tc148.1.bt2 |
| b |
| Binary file data/Reference/Tc148.1.bt2 has changed |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Reference/Tc148.2.bt2 |
| b |
| Binary file data/Reference/Tc148.2.bt2 has changed |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Reference/Tc148.3.bt2 |
| b |
| Binary file data/Reference/Tc148.3.bt2 has changed |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Reference/Tc148.4.bt2 |
| b |
| Binary file data/Reference/Tc148.4.bt2 has changed |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Reference/Tc148.rev.1.bt2 |
| b |
| Binary file data/Reference/Tc148.rev.1.bt2 has changed |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Reference/Tc148.rev.2.bt2 |
| b |
| Binary file data/Reference/Tc148.rev.2.bt2 has changed |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/Reference/Tc148_contigs.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Reference/Tc148_contigs.fasta Wed Jul 04 16:39:13 2018 -0400 |
| b |
| b'@@ -0,0 +1,687226 @@\n+>Tc148_allcontigs\n+tatatatgtattacaatgaaggtgtacaaaacgtttaagggagatactgttgttcttgtt\n+tttttttcttgccggctaagaatacggcttcttcgttggtcttctctccctacctcctgc\n+catcgtttatgagtggtggagggagtttgtgctgtattcggttcatcgtggggattcctt\n+gtaatcaggcaaatcttgcaaaccttgtgcaggcggatagcctgcgatgcgaaacagtgg\n+cacatgcaatgcactctgaatggtgcctgacagctttcagcgggtgtcactgaactcttt\n+tccttcttgctgtggtgtcgcgtccccttccactgcctttgaagttcacgggtctacgca\n+ggagtgggaggatgtgttgtgcaacgtggccgctatggacgtgcatgtgttagtggtact\n+gcggagaaggtggtgcagtttttttccctccttattgaaaataatgtggctgtgcatgta\n+tggttcaaggaaggcaagaagaagggagtgcaactttatctgcttacatcagatatatat\n+atgagaaaaatctaagttaaaataagcatttaggtgtgagtggtgtgcttcagcgttgat\n+caaggcgcgagtcatcaacccctctgtggttacgtgagtgcgcacgcatcagtagtgggc\n+catggggactcttgaatacgtctaattttttctataagagcattgcaaaactctatcttt\n+ctggtgcttgatatttttgttttccttttcacttttttatttatctatttatcatataca\n+agaaattgcgttgccacacgctgcacttttcttcccctactttaacactgattctttttt\n+tttcttaccttttctcgacatgtagtcttcaagccgatatctctgggtatacatctattt\n+gtaaataatagcacaaaaatacacatatttattcatatatatagccagataagggcgtac\n+aggaaattatttgttcatccccttacgcgtgttgcgcacctctgattttgtgttaccaca\n+catggcaacggttgaggagttacagcaggttatccgtgaggagcaagagaagcatgcgca\n+ggtattggaggagctgcgctccgagcgcgaatccctctcatcgcttcttgcagagcaaca\n+gcagtacatacaggaactcataacgcgactgactgacttacgtacacagaagtgtgacag\n+gatgctctccaacgaacagttaactcaacgcatcgaaattaacacgggttgtgcagtagt\n+ggatgaagcactgcgtaccgtggagaatgggctgaattcttcaagttccaaacgcggtgt\n+cgtcttgggaaaaatatggtcggccatgatgcaggctatcgtgccttctgacgggaaaaa\n+gtcatcttctctgagtacaagcagctctgcaactcgaactaccaatgtggccgtgataac\n+gcgaaacatgattcgaggcacaaacgaatgggtaaagcggcattgcaagaagtgctctcc\n+ttgtggtgaattgaacaaaaagccgcgcccgtgggagccggcggccaagacggagaaggg\n+gaagtcaatcaaaggatgcgcgtccgtgccaaacctcagttgtgttcccggtaagaactt\n+ccgctctgtgtcgtttgtacttcgctaaggagacggcgaacgaagtacttctggaactgt\n+tgcgtatttcctctgtgatcaacatacaaggaagtggcggggctgcggttgctaacccaa\n+aggatattgccacacaagtaaccggtattgttacggagttggtgcagggcaagataacgg\n+aagcacgggaggcagccaagagggccccgtgagtacggggccctcggccaacgagaaatt\n+ttcctcagcagtggagatgttgttgcacaaccttgacgtgaaggttagtgtgacggtgcc\n+tgagccgaatgaactacggagtgcggttcctcgtggtcaaacaccgctgaagattactgt\n+gttgatcactgccccgaggctcctttctatcttgcagccctttgtggaaatgtgggggga\n+ttcccagcaccgcacttacattctagattgccttctgaagcctacggtgctgcatatcgc\n+tgaattgtttggtatgacgacagtcgctgagcagtcaatcaccgtgcattcaaggcagtt\n+gacgttctgacccgcataacaaggggtcgagtaatgattgaaactgataccaaaagttcc\n+cccaaaagcaaatcaagcccccaggaaccacaatcagcccagttgctgtcttgcattcac\n+tctgttgtcctcggttttgctctttttggtactcgtctgacctttgaatgtgctattcca\n+aaattggaggaggccaacaccctgaaaggtgttaagcgtggtgcgttcgatatagcgagg\n+tcttttctccagcgtcttcttcctcctaagcgagacactgccgtttcgctgcacgacccc\n+actgtatccgatttcgtgatcctgttgctaaatgccccaacccgacttttggaaatactc\n+aacaactccttcagcagtgctcgccggcttccttcgacgtcccgcacaagcgttgttgac\n+caccttgcttcgccgcggctgaaaatcaattacgccctgagaaccttcgctgatattgtc\n+atagactttcctcgaccttacgcgcccaacagtggcatgatgaccacggcggagaaagcg\n+aagggagaaaaggaacgcctcggcccctgtgcccccgttgtagacctccccccggacctc\n+gtgcgcgccaacgtcgaggtggtccagtgggccgaagagaagctcagaaacctgctcgag\n+aaggaagccattgatgtgagcactggaacgggtgaggaaatcgcgaagagccttggggag\n+agtgtgatgaagatcaacagcgtctctggcttcttgggcaagctgcagcagttgtccgtt\n+agtgttgttgatctgaccgatgtccgtgtggatgtttgtcttccatgtggtgcagctctt\n+tgcagccccggtgggggagttgaagagctgctgtacctgcgggtggatacagtacgaaat\n+ccctagcaaattgaggcgggaagaaatatgaattaggaaagagagaatggagtaataata\n+attataataatacagttagtgatgggtgctgactgaattaatcagcaaaatgaatgaatt\n+atgggaaaataaaatgagtaagacacacgcgtattagaaacagcgataatttggactaaa\n+ataagaatattcccaattcacgccttttatatttttccttgcccaaccactttgcttcca\n+tctcatattctcgcccccctttgtttaaggatgttcgtacttcatcatcttttctgctat\n+tctacaaagcctttcctctagtttccttactttttcattcccttctcctcctcactttac\n+cttttgaactaatatttcgatactatgacttgtgacgagtgggaaatgacgcgaaagaaa\n+gagaatgggaagttgggtaggtgctgtagtttctgtcaggggtattgaggagttaagcta\n+cgctcaacgtagcgtataattattcatttttttctccacctttcttccacttccgctgct\n+tgctgctgccttctgttgctatctgcagtatgccttacaggaaggttgtcttatctactt\n+agtgttagtaagacatggcatgcctaaccgccaggagttttccactgcttttactttatc\n+tctttttgtcatttctcctattccatttttttccttatttccttccttcctccattctct\n+tgtcgtaacagtaataagtactattgctttaatgttgctctcggaataatgt'..b'ggaaaaaagcgtttgtgacatc\n+catgagggttgcagaaaccattctcaatgtacgtaactgcattaattacttctttcagct\n+ttctatcgctgacggtaatgtaggttgttttccggactctgtcgtggatattatcgtcca\n+aaccattagccaccccttgaatgacaccactgatcgcagctgctttatcggaaatgaccc\n+ttgtagcacttgggtttctgagtgtggtggactcggtggaggagacaacaacgactaact\n+gtgagattcatcctatttaacaattttgtcgatgagagaatgatcgcttggagtgtgaga\n+atataatctggaatcaaggtgaatagaagcgcagtaggctgtttgaagctgacagctact\n+ggctccgcaatccaatgtatgtttattgctttgaaataaaaaccacgagagatttatgag\n+agataagcgatactctccctagccccactcaccacaacctattgctgtttaatgtatgga\n+attcttcaataccatcatatgtgatatgatcttttcttttttcagttctcttcttatgaa\n+caaaaggtcaaagtacaaaagaaagactagaaaatctatccataacggagcccctgacac\n+ctttgctaccggggaggtttcagaaaaaagatgttgctattggaccgactgtgttcaaag\n+catgagtgaactcattcctgatccgaaagatgcagggaaatattggctcacggacatcat\n+tggcaacctcagcaaggtggtgagttcaaaatccagaggtatacacaggctgcaaaggac\n+aactgaccgtcagtgcacaggcagttttcaattttttcaaattgatttgcgactgtcatg\n+taagatcaagaaagcaaatcccttaccattctaaattatccttctatgacactttttgct\n+tatggctagaatcggagttagatttgatatttatttttagtgacacagtcaatgtaggga\n+tattcatactaattattttcagtcatatcataagctttcaaaaataactgttgactttag\n+tttatttattgttcttgtatcattgtaagtgatacaactttggaattcaatctggaacag\n+gatgctaagtaaaattatgaggccgaggatgttagtaagacaatagtagtggacaaagtt\n+tgagaattagcgctatattgaatcctttcgaaatgtgttttgagtgtttatgagaccaca\n+aaggacaatcgaatatttactcatggtcacaatggacacgtttcatttgatagcaggttg\n+aaaacaaaaagtcaaatgacaatcttattgccttatttcactaggacatgtttgtattga\n+gggatgtgtttgcattcgagtagcaatgtacaattacatttgagtcaggaaccaaataat\n+gtgcgcatatcatattcttcacaaaggagtaaagacaaccaaaatcacattacccacact\n+tcatttcaatttcatttgtctttattagttttcagaatatacatacgggaagattaatta\n+actgacgtacaaattatgatcgtgaggtgctgtgtaaaattcagaagcaggtacatgttg\n+caattttcatgtagatgcggatttttaatttctcaacgggggttgagtggtaccagcaaa\n+gttgttttagggccccacttttgcaatattaagcggctcattaagctaacaaagcgccag\n+cttacgcgcagctttgctgtggaaatgttttttttgattcgtaattctcgagggaaaaaa\n+ttaaacggtgcaagtttggctttctgtggggaattttacagcgcgcatttcccaaaaatc\n+tctgtgaaatttcattttgaaagaattttccgtgaagatataggaggaaaaaatttgcgt\n+aagcgatgagagtgaaagagctatttctagtcggcatggcggcgcttgttttttgcaaag\n+ctgggcgacgctgcacacgacccagggctggaacgcaaaacaagcgacaattctgtgccg\n+catttacaagtcgcggcgaatcctcccgaggctgtttacgacccagaagacggtaacaaa\n+aatcacttcaaaaatagacgccatcaatgcctcactcggccccgaagactggttcagcga\n+agttgaaaaaaacagtgaatgtagcgacgtctcaaaagaattatggaaagcgctacgaag\n+atagttcaaaatactgggaccgttggaaagaggccgtaaaaaaagttcagtcaaagctca\n+ccagctacccaaaaattctcgtagaaaacccgacgaccaaaattgcgcgagtcaaattgg\n+gaaaaaatcgagagccaggtggcgaaaatcctagcggacttgaagcaaacaatgcatctg\n+cagagctgcgtcacattaagacaaatttcgacgctgcaataaaagggagcaaagaagaag\n+agaataaagttgtttttgactacgacacgcgggcgaatgcgtgcggaagggcagccgggg\n+aaaagggatggatgccggtaagaatttaatcctcgatttcatgtgcctggcggcctatga\n+acacgtcacacacgggacaggaaacgcatgtggtggtgcggttgaggttaaggaaagcgc\n+caaggacttcaacgccttcaagaacgaacgttccagcataaacaaaatgtggcagtcagt\n+gaaacgccactgcaccgagcaaccccactccaagcccgcgaaggcgtccgacctgcgggc\n+ggccctcgacgcttttatccaggaagtgaaccgaccgacgggaaacagtgcgccaaaatt\n+ggtgtgttcggaaacatgcatggcacaggaaacaccggatgccgcggacagtacaacgac\n+ggtgtcactgataacaatggcgtctgcgtgatttattcgaaacacccactcaacaacgtc\n+aacatctcagcattgcctggtacagagcaatcaaagacattccacggctcctcgaaaagt\n+cgaaaacgccaccgccgctatccaaagcgacatcacggacatctcaaatgctccaaaccc\n+gtgccgaggaaattacgaggaaacgaaagcggactcttagaattcggaaccgctaacctc\n+gaaaaacacactgaagctaagcaaaacgaaatgcgacgcaacatccaaccgcagaagctg\n+caacgttgacgaacgcccacgaaacgcaactccgtgaacactgcaacccccctgcgtttc\n+attcttccgtggatcctcctcacctaaaaaacaagtcaacaaaaaggggaagaaagaaag\n+agagagaaattaagaaccaccgcacgctatgcctcccactgcctgtacggttagggttta\n+gggttagggttagggttagggttaggttagggttagggttagggttagggttagggtgtt\n+agggttagggttagggttagggttagggttagggttagggttagggttagggttagggtt\n+agggttagggttagggttagggttagggttagggttagggttagggttagggttagggtt\n+aggttagggttaggggttagggttagggttagggttagggttagggttagggttagggtt\n+agggttagggttagggttagggttagggttagggttagggttagggttagggttagggta\n+gggttagggttagggttagggttagggttagggttagggttagggttagggttaggggtt\n+agggttagggttagggttagggttagggttagggttagggttagggttaggggttagggt\n+ttagggttagggttagggtttagggttaggttagggttagggttagggttagggttaggg\n+ttagggtttagggttagggttaggttagggttagggttaggtttagggttagggttaggg\n+ttaggt\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/congodata.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/congodata.csv Wed Jul 04 16:39:13 2018 -0400 |
| b |
| b'@@ -0,0 +1,44 @@\n+Strain,P1,P2,P3,P4,P5,P6,P7,P8,P9,P10,P11,P12,P13,P14,P15,Colour\r\n+IL3578,0.06920904,0.050847458,0.039548023,0.012711864,0.066384181,0.13700565,0.103107345,0.005649718,0.019774011,0.035310734,0.107344633,0.076271186,0.080508475,0.049435028,0.146892655,Burkina Faso\r\n+IL2995,0.126126126,0.207207207,0.09009009,0.018018018,0.027027027,0.018018018,0.027027027,0,0.036036036,0.027027027,0.162162162,0.063063063,0.117117117,0.018018018,0.063063063,Burkina Faso\r\n+IL3897,0.120798319,0.108193277,0.085084034,0.011554622,0.050420168,0.053571429,0.06512605,0.015756303,0.013655462,0.028361345,0.125,0.05987395,0.066176471,0.037815126,0.158613445,Burkina Faso\r\n+IL3900,0.147826087,0.135652174,0.116521739,0.022608696,0.076521739,0.036521739,0.029565217,0.005217391,0.027826087,0.046956522,0.173913043,0.050434783,0.076521739,0.034782609,0.019130435,Forest sub-type\r\n+IL3926,0.150234742,0.126760563,0.118935837,0.023474178,0.067292645,0.03286385,0.039123631,0.010954617,0.017214397,0.045383412,0.183098592,0.048513302,0.073552426,0.026604069,0.03599374,Forest sub-type\r\n+IL274,0.102671119,0.116026711,0.08263773,0.014190317,0.08096828,0.081803005,0.050918197,0.003338898,0.016694491,0.02754591,0.126043406,0.040901503,0.063439065,0.028380634,0.164440735,Kenya\r\n+IL2992,0.112690355,0.096446701,0.078172589,0.011167513,0.050761421,0.05786802,0.070050761,0.016243655,0.012182741,0.031472081,0.12893401,0.056852792,0.064974619,0.034517766,0.177664975,Kenya\r\n+IL3000,0.073317308,0.039663462,0.049278846,0.018028846,0.060096154,0.055288462,0.054086538,0.025240385,0.012019231,0.060096154,0.141826923,0.099759615,0.061298077,0.078125,0.171875,Kenya\r\n+IL3019,0.105315948,0.099297894,0.074222668,0.011033099,0.054162487,0.056168506,0.076228686,0.016048144,0.013039117,0.029087262,0.138415246,0.058174524,0.063189569,0.034102307,0.171514544,Kenya\r\n+IL3021,0.11167002,0.10362173,0.078470825,0.011066398,0.054325956,0.056338028,0.073440644,0.016096579,0.011066398,0.028169014,0.126760563,0.058350101,0.062374245,0.03722334,0.171026157,Kenya\r\n+IL3022,0.116596639,0.101890756,0.080882353,0.010504202,0.058823529,0.06092437,0.068277311,0.007352941,0.013655462,0.029411765,0.12394958,0.05987395,0.06197479,0.036764706,0.169117647,Kenya\r\n+IL3035,0.12183908,0.113409962,0.081226054,0.018390805,0.066666667,0.06743295,0.042145594,0.008429119,0.021455939,0.031417625,0.152490421,0.042145594,0.07816092,0.022222222,0.13256705,Kenya\r\n+IL3180,0.110629067,0.09978308,0.075921909,0.013015184,0.053145336,0.055314534,0.070498915,0.013015184,0.013015184,0.018438178,0.134490239,0.05856833,0.060737527,0.035791757,0.187635575,Kenya\r\n+IL3349,0.101861993,0.100766703,0.070098576,0.007667032,0.059145674,0.061336254,0.073384447,0.008762322,0.009857612,0.036144578,0.133625411,0.053669222,0.069003286,0.038335159,0.176341731,Kenya\r\n+IL374,0.135494597,0.119700748,0.087281796,0.013300083,0.074812968,0.078969244,0.044887781,0.006650042,0.015793849,0.024937656,0.128844555,0.036575229,0.057356608,0.023275145,0.152119701,Kenya\r\n+IL3775,0.07605985,0.074812968,0.069825436,0.012468828,0.058603491,0.063591022,0.089775561,0.004987531,0.016209476,0.036159601,0.137157107,0.067331671,0.064837905,0.038653367,0.189526185,Kenya\r\n+IL3779,0.089655172,0.062068966,0.034482759,0.034482759,0.051724138,0.05862069,0.106896552,0.017241379,0.013793103,0.048275862,0.134482759,0.068965517,0.055172414,0.04137931,0.182758621,Kenya\r\n+IL3932,0.064606742,0.06741573,0.073033708,0.014044944,0.095505618,0.075842697,0.081460674,0.014044944,0.02247191,0.019662921,0.123595506,0.073033708,0.039325843,0.033707865,0.202247191,Kenya\r\n+IL3949,0.12804878,0.130081301,0.099593496,0.017276423,0.039634146,0.043699187,0.050813008,0.012195122,0.011178862,0.037601626,0.150406504,0.041666667,0.073170732,0.028455285,0.136178862,Kenya\r\n+IL396,0.129508197,0.112295082,0.089344262,0.012295082,0.081147541,0.079508197,0.048360656,0.004098361,0.013114754,0.022131148,0.119672131,0.040163934,0.058196721,0.022131148,0.168032787,Kenya\r\n+IL3978,0.068055556,0.05,0.038'..b'61773,0.010144154,0.07367859,0.068339562,0.055525894,0.005872931,0.013881474,0.027762947,0.121195942,0.044313935,0.061932728,0.025093433,0.16604378,Kenya\r\n+IL410,0.103556485,0.112970711,0.094142259,0.012552301,0.074267782,0.075313808,0.052301255,0.005230126,0.013598326,0.020920502,0.120292887,0.038702929,0.074267782,0.018828452,0.183054393,Kenya\r\n+IL438,0.09297725,0.091988131,0.050445104,0.014836795,0.098911968,0.097922849,0.055390702,0,0.014836795,0.03066271,0.139465875,0.043521266,0.070227498,0.029673591,0.169139466,Kenya\r\n+IL439,0.118078176,0.117263844,0.087947883,0.013029316,0.080618893,0.07980456,0.048045603,0.004071661,0.01465798,0.027687296,0.122149837,0.038273616,0.058631922,0.026872964,0.16286645,Kenya\r\n+ILC55,0.021834061,0.03930131,0.026200873,0.008733624,0.122270742,0.126637555,0.096069869,0,0.008733624,0.021834061,0.152838428,0.048034934,0.07860262,0.030567686,0.218340611,Kenya\r\n+ILC66,0.129460581,0.121161826,0.097095436,0.012448133,0.075518672,0.07219917,0.046473029,0.008298755,0.011618257,0.02406639,0.121991701,0.037344398,0.065560166,0.019917012,0.156846473,Kenya\r\n+IL2281,0.1484375,0.150390625,0.107421875,0.016601563,0.065429688,0.067382813,0.012695313,0.008789063,0.017578125,0.032226563,0.153320313,0.032226563,0.071289063,0.028320313,0.087890625,Nigeria\r\n+IL3304,0.118333333,0.105,0.088333333,0.016666667,0.065,0.073333333,0.013333333,0.006666667,0.021666667,0.056666667,0.206666667,0.041666667,0.058333333,0.035,0.093333333,Nigeria\r\n+IL3954,0.138586957,0.116847826,0.08423913,0.024456522,0.076086957,0.08423913,0.020380435,0.00951087,0.017663043,0.036684783,0.141304348,0.043478261,0.080163043,0.028532609,0.097826087,Nigeria\r\n+IL1180,0.134306569,0.119708029,0.100729927,0.026277372,0.072992701,0.077372263,0.020437956,0.01459854,0.02189781,0.035036496,0.118248175,0.051094891,0.081751825,0.024817518,0.100729927,Tanzania\r\n+IL1769,0.092920354,0.097345133,0.081858407,0.022123894,0.050884956,0.037610619,0.077433628,0.013274336,0.019911504,0.026548673,0.128318584,0.055309735,0.084070796,0.030973451,0.181415929,Tanzania\r\n+IL2068,0.066460587,0.051004637,0.034003091,0.027820711,0.049459042,0.061823802,0.086553323,0.00309119,0.018547141,0.040185471,0.187017002,0.066460587,0.083462133,0.041731066,0.182380216,Tanzania\r\n+IL3296,0.075409836,0.068852459,0.055737705,0.006557377,0.06557377,0.078688525,0.032786885,0,0.029508197,0.02295082,0.226229508,0.062295082,0.101639344,0.02295082,0.150819672,Tanzania\r\n+IL3686,0.122362869,0.088607595,0.067510549,0.012658228,0.046413502,0.088607595,0.080168776,0.012658228,0.016877637,0.029535865,0.105485232,0.063291139,0.080168776,0.029535865,0.156118143,Tanzania\r\n+IL3688,0.117549669,0.098509934,0.071192053,0.017384106,0.052980132,0.052980132,0.072847682,0.007450331,0.013245033,0.038907285,0.139072848,0.053807947,0.067880795,0.02897351,0.167218543,Tanzania\r\n+ILC22,0.129460581,0.121161826,0.097095436,0.012448133,0.075518672,0.07219917,0.046473029,0.008298755,0.011618257,0.02406639,0.121991701,0.037344398,0.065560166,0.019917012,0.156846473,Tanzania\r\n+IL311,0.073326249,0.078639745,0.060573858,0.018065887,0.111583422,0.106269926,0.036131775,0.004250797,0.015940489,0.052072264,0.151965994,0.044633369,0.078639745,0.044633369,0.123273114,The Gambia\r\n+IL3674,0.100110011,0.099009901,0.074807481,0.01650165,0.096809681,0.099009901,0.02970297,0.00770077,0.01650165,0.04950495,0.133113311,0.04620462,0.069306931,0.03960396,0.122112211,The Gambia\r\n+IL3675,0.117801047,0.107329843,0.098167539,0.014397906,0.096858639,0.085078534,0.030104712,0.007853403,0.018324607,0.034031414,0.113874346,0.041884817,0.077225131,0.02486911,0.132198953,The Gambia\r\n+IL2326,0.06323185,0.046838407,0.018735363,0.030444965,0.035128806,0.058548009,0.098360656,0.007025761,0.009367681,0.037470726,0.18969555,0.074941452,0.100702576,0.044496487,0.18501171,Uganda\r\n+IL588,0.097727273,0.079545455,0.029545455,0.006818182,0.081818182,0.097727273,0.045454545,0,0.009090909,0.045454545,0.156818182,0.043181818,0.052272727,0.045454545,0.209090909,Uganda\r\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/congodata_deviationfromthemean.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/congodata_deviationfromthemean.csv Wed Jul 04 16:39:13 2018 -0400 |
| b |
| b'@@ -0,0 +1,1 @@\n+Strain,P1,P2,P3,P4,P5,P6,P7,P8,P9,P10,P11,P12,P13,P14,P15,Colour\rIL2995,-0.019637186,-0.108350357,-0.01512639,-0.002392738,0.041261003,0.052742362,0.030150623,0.00831415,-0.019757856,0.006440593,-0.020610832,-0.010139913,-0.046085817,0.014763942,0.088528327,Burkina Faso\rIL3578,0.0372799,0.048009392,0.035415677,0.002913416,0.001903849,-0.06624527,-0.045929695,0.002664432,-0.003495831,-0.001843114,0.034206697,-0.023348036,-0.009477175,-0.016653068,0.004698735,Burkina Faso\rIL3897,-0.014309379,-0.009336427,-0.010120334,0.004070658,0.017867862,0.017188951,-0.0079484,-0.007442153,0.002622718,0.005106275,0.01655133,-0.0069508,0.004854829,-0.005033166,-0.007022055,Burkina Faso\rIL3900,-0.041337147,-0.036795324,-0.041558039,-0.006983416,-0.008233709,0.034238641,0.027612433,0.003096759,-0.011547907,-0.013488902,-0.032361713,0.002488367,-0.005490439,-0.002000649,0.132460955,Forest sub-type\rIL3926,-0.043745802,-0.027903713,-0.043972137,-0.007848898,0.000995385,0.03789653,0.018054019,-0.002640467,-0.000936217,-0.011915792,-0.041547262,0.004409848,-0.002521126,0.006177891,0.11559765,Forest sub-type\rIL3932,0.041882198,0.03144112,0.001929992,0.001580336,-0.027217588,-0.005082317,-0.024283024,-0.005730794,-0.00619373,0.013804699,0.017955824,-0.020110558,0.031705457,-0.000925905,-0.050655801,Kenya\rIL274,0.003817821,-0.017169861,-0.00767403,0.001434963,-0.01268025,-0.011042625,0.006259453,0.004975252,-0.000416311,0.00592171,0.015507924,0.012021647,0.007592235,0.004401326,-0.012849345,Kenya\rIL374,-0.029005657,-0.020843898,-0.012318096,0.002325197,-0.006524938,-0.008208864,0.012289869,0.001664108,0.000484331,0.008529964,0.012706775,0.016347921,0.013674692,0.009506815,-0.000528311,Kenya\rIL396,-0.023019257,-0.013438232,-0.014380562,0.003330198,-0.012859511,-0.008747817,0.008816994,0.004215789,0.003163426,0.011336472,0.021879199,0.012759216,0.012834579,0.010650812,-0.016441397,Kenya\rIL399,-0.021825859,-0.009783013,-0.019989251,0.004504664,-0.007845417,-0.007939363,0.009273458,0.002326126,0.000880404,0.006949228,0.019224555,0.01442871,0.006018469,0.012251592,-0.008374393,Kenya\rIL409,-0.015774808,-0.015932258,-0.014198073,0.005481126,-0.00539056,0.002420818,0.001651756,0.002441219,0.002396706,0.005704673,0.020355388,0.008609215,0.009098572,0.007688527,-0.01445239,Kenya\rIL410,0.002932455,-0.014113861,-0.019178559,0.003072979,-0.005979752,-0.004553428,0.004876395,0.003084024,0.002679854,0.012547118,0.021258443,0.014220221,-0.003236482,0.013953508,-0.031463003,Kenya\rIL438,0.01351169,0.006868719,0.024518596,0.000788485,-0.030623938,-0.027162469,0.001786948,0.00831415,0.001441385,0.00280491,0.002085455,0.009401884,0.000803802,0.003108369,-0.017548076,Kenya\rIL439,-0.011589236,-0.018406994,-0.012984183,0.002595964,-0.012330863,-0.00904418,0.009132047,0.004242489,0.0016202,0.005780324,0.019401493,0.014649534,0.012399378,0.005908996,-0.01127506,Kenya\rILC66,-0.022971641,-0.022304976,-0.022131736,0.003177147,-0.007230642,-0.00143879,0.010704621,1.53948E-05,0.004659923,0.00940123,0.019559629,0.015578752,0.005471134,0.012864948,-0.005255083,Kenya\rIL3035,-0.01535014,-0.014553112,-0.006262354,-0.002765525,0.001621363,0.00332743,0.015032056,-0.000114969,-0.005177759,0.002049995,-0.010939091,0.010777556,-0.00712962,0.010559738,0.01902434,Kenya\rILC55,0.084654879,0.05955554,0.048762827,0.006891656,-0.053982712,-0.055877175,-0.038892219,0.00831415,0.007544556,0.011633559,-0.011287098,0.004888216,-0.00757132,0.002214274,-0.066749221,Kenya\rIL3779,0.016833768,0.036787884,0.040480941,-0.018857479,0.016563892,0.01213969,-0.049718902,-0.008927229,0.002485077,-0.014808242,0.007068571,-0.016042367,0.015858886,-0.00859735,-0.031167231,Kenya\rIL3949,-0.02155984,-0.031224451,-0.024629796,-0.001651143,0.028653884,0.027061193,0.006364642,-0.003880972,0.005099318,-0.004134006,-0.008855174,0.011256483,-0.002139432,0.004326675,0.015412528,Kenya\rIL2992,-0.006201415,0.002410149,-0.003208889,0.004457767,0.017526609,0.01289236,-0.012873111,-0.007929505,0.004095439,0.001995539'..b'5918653,0.005121078,0.009464501,0.00983601,-0.011099661,0.000961209,0.002622718,0.004055855,0.01760175,-0.0069508,0.00905651,-0.003982746,-0.017526257,Kenya\rIL3180,-0.004140127,-0.00092623,-0.000958209,0.002610096,0.015142694,0.015445846,-0.013321265,-0.004701034,0.003262996,0.015029442,0.007061091,-0.00564518,0.010293773,-0.003009797,-0.036044185,Kenya\rIL3349,0.004626947,-0.001909853,0.004865124,0.007958248,0.009142356,0.009424126,-0.016206797,-0.000448172,0.006420568,-0.002676958,0.007925919,-0.000746072,0.002028014,-0.005553199,-0.024750341,Kenya\rIL3775,0.03042909,0.024043882,0.005138264,0.003156452,0.009684539,0.007169358,-0.032597911,0.003326619,6.87037E-05,-0.002691981,0.004394223,-0.014408521,0.006193395,-0.005871407,-0.037934795,Kenya\rIL3978,0.038433384,0.04885685,0.036074811,0.00312528,0.003010252,-0.001461842,-0.031711239,0.002758594,-0.003166264,-0.001254602,-0.019559781,-0.02207685,-0.009524256,-0.015829151,-0.027575277,Kenya\rIL2281,-0.04194856,-0.051533775,-0.032458175,-0.000976283,0.002858343,0.003377568,0.044482338,-0.000474913,-0.001299945,0.001241058,-0.011768983,0.020696588,-0.000257762,0.004461648,0.063700765,Nigeria\rIL3304,-0.011844393,-0.00614315,-0.013369633,-0.001041387,0.00328803,-0.002572953,0.043844317,0.001647483,-0.005388487,-0.023199047,-0.065115337,0.011256483,0.012697967,-0.00221804,0.058258057,Nigeria\rIL3954,-0.032098017,-0.017990976,-0.00927543,-0.008831242,-0.007798927,-0.01347875,0.036797215,-0.00119672,-0.001384863,-0.003217163,0.000246982,0.009444889,-0.009131743,0.004249351,0.053765303,Nigeria\rIL1180,-0.027817629,-0.020851179,-0.025766227,-0.010652092,-0.004704671,-0.006611883,0.036739694,-0.00628439,-0.00561963,-0.001568876,0.023303155,0.001828259,-0.010720525,0.007964442,0.050861463,Tanzania\rIL1769,0.013568586,0.001511717,-0.006894707,-0.006498614,0.017403074,0.033149761,-0.020255978,-0.004960186,-0.003633324,0.006918947,0.013232746,-0.002386585,-0.013039496,0.001808509,-0.029824539,Tanzania\rIL2068,0.040028353,0.047852213,0.040960609,-0.012195431,0.018828988,0.008936578,-0.029375673,0.00522296,-0.002268961,-0.006717851,-0.045465672,-0.013537437,-0.012430833,-0.008949106,-0.030788826,Tanzania\rIL3296,0.031079104,0.030004391,0.019225995,0.009067903,0.00271426,-0.007928145,0.024390765,0.00831415,-0.013230017,0.0105168,-0.084678178,-0.009371932,-0.030608044,0.00983114,0.000771718,Tanzania\rIL3686,-0.015873929,0.010249255,0.007453151,0.002967052,0.021874528,-0.017847215,-0.022991126,-0.004344078,-0.000599457,0.003931755,0.036066098,-0.010367989,-0.009137476,0.003246095,-0.004526753,Tanzania\rIL3688,-0.011060729,0.000346916,0.003771647,-0.001758826,0.015307898,0.017780248,-0.015670032,0.000863819,0.003033147,-0.005439665,0.002478482,-0.000884797,0.003150505,0.00380845,-0.015627153,Tanzania\rILC22,-0.022971641,-0.022304976,-0.022131736,0.003177147,-0.007230642,-0.00143879,0.010704621,1.53948E-05,0.004659923,0.00940123,0.019559629,0.015578752,0.005471134,0.012864948,-0.005255083,Tanzania\rIL311,0.033162691,0.020217105,0.014389842,-0.002440607,-0.043295392,-0.035509546,0.021045875,0.004063353,0.000337691,-0.018604644,-0.010414664,0.008289781,-0.007608445,-0.011851409,0.028318276,The Gambia\rIL3674,0.006378929,-0.000153051,0.000156219,-0.00087637,-0.028521651,-0.028249521,0.02747468,0.00061338,-0.00022347,-0.01603733,0.008438019,0.00671853,0.001724369,-0.006822,0.029479179,The Gambia\rIL3675,-0.011312107,-0.008472993,-0.023203839,0.001227374,-0.028570609,-0.014318154,0.027072938,0.000460747,-0.002046427,-0.000563794,0.027676984,0.011038333,-0.006193831,0.00791285,0.019392437,The Gambia\rIL2326,0.04325709,0.052018443,0.056228337,-0.014819685,0.033159224,0.012212371,-0.041183006,0.001288389,0.006910499,-0.004003106,-0.04814422,-0.022018302,-0.029671276,-0.011714527,-0.03342032,Uganda\rIL588,0.008761667,0.019311395,0.045418245,0.008807098,-0.013530152,-0.026966893,0.011723105,0.00831415,0.007187271,-0.011986925,-0.015266852,0.009741332,0.018758573,-0.012672585,-0.057499519,Uganda\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/geoTv.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/geoTv.csv Wed Jul 04 16:39:13 2018 -0400 |
| b |
| @@ -0,0 +1,22 @@ +Strain,Location,colour +TvY486,Nigeria,b +Tv11,Nigeria,b +Tv306,Nigeria,b +Tv319,Nigeria,b +Tv338,Nigeria,b +Tv340,Nigeria,b +Tv462,Nigeria,b +Tv465,Nigeria,b +Tv493,Nigeria,b +Tv596,Nigeria,b +Tv684,Nigeria,b +Tv1392,Nigeria,b +Tv2005,Uganda,g +Tv2323,Uganda,g +Tv2714,Uganda,g +TvILV-21,Uganda,g +Tv3171,Gambia,c +Tv3638,Ivory Coast,r +Tv3651,Ivory Coast,r +Tv3658,Ivory Coast,r +TvLins,Brazil,m |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/vivax/Database/Bin_2.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/vivax/Database/Bin_2.fas Wed Jul 04 16:39:13 2018 -0400 |
| b |
| b'@@ -0,0 +1,10148 @@\n+>Tv0000010\r\n+GCGTCGGGGGCGAACGCGGTGAAGGCAGGCCTTCTGCTGGCCAGGGCGAAGGAGATATGC\r\n+GCGCTGTCCACCGCATTCAAAAAGCTGGCGACGGACATGGAGGCATGGCAACCACGCATC\r\n+GTGACACGGGACTCAGGGCGCATTGGGGACGCAGTGGACGAGAGAGAGGAGATTGACCGA\r\n+AAAATGGACGCCGCGCTGGCTGCCTACGACACAGCTGTGCAGCTGCTTCCTGCCGAAAGG\r\n+CGAGACGACGCCAACACGACGCGCGCACACGCGCTGAGCCGGCGGCTGACAGTCCTTAGG\r\n+CACGCGGCGCTGAGGAACGCGCTCGCAAGGCAACAGTGCAGCACTGCCGCCGCAGTTGCG\r\n+CGCGGACTCGCAGCGCAAATTGACGACTTCATCACCGTGTTCGGCAGCTACACGACAAGC\r\n+AGCACACATGGTGGGTGCATACCGTCCGGTGCCAGCGCACAAGACGGCAAGACGGCACAG\r\n+GACGCGCAGTGCGTCGCGTACAACCAGGACGGAAAGTTTGCAGAAGGCACGCTCGACGCA\r\n+CTGAACACTGCACTGAAAAAGTTCGACAGCGGCTGGGACAAGGAAGGCAACGACAACACT\r\n+TTCTTCGGAGGTGGCGGGACCCAGTCGTGCACTCTCACCGACGGCCCAGGATCCGACACA\r\n+GCAGCGAAACTTCCAACAACCGGCGTGCCGTGGGCAGGCGGCCTCTGGACAATCAGCGCC\r\n+GACAGCGGAAATAGCAACAAGCCAAAAATCACGTGGAACGGCGGCAGCACGCAAAAACCC\r\n+GCCAGCGCCAATGAACCAGCACAAAAAAAACTGGCCGCACTTAAAGAAGCAGTCAAGCAG\r\n+TGCCACACGCAGGCGCAAGAAGCAGAAAAGTTGTGCGCACACACCGGAGACACAGCCGTC\r\n+ACAGCCGCCGAAACGCAGCAGCTGTGCGCGAGCAAAGCCGTCGCGTACAAGCAGCACGTC\r\n+GAAGTCATAAGCGCCCGGCTGCACGCGTGGGCAAACAGCGTGCTCAAAGCAGTCGACACA\r\n+AAAAGAAGCACAAACAGCGCCAGCTCGCAACGCGGCAACGCACAAGGCGCACGCGCACCT\r\n+GCAAGCGCACCGCACAACGCCGAAAGCGACAGCACACCCACACAAGAAAAGGACACTGCA\r\n+GCACAGCACGACAACAAGAAGACACAAGCAAGCTCAGTGGCACAGGGACACACACTCGCA\r\n+CTGGCACACGCAACCAGCGCGGCGACCGCAGCAGCATTCGCACACCAACTCTTGGCGCAC\r\n+ACACCACGCCTCAACACC\r\n+>Tv0033920 \r\n+AGCAACGCGAGCGCGGCGGACAACAAGGGACTTCAGTTTGACGACGCGAAGGCGGCGTGC\r\n+GAGGTGGCAGCGGTGCTGGAGGCGATGGCGGTCGCCGCAACGATGGCAGCGGAGGAGGCC\r\n+GCCACGATCGGCGAGGCAGCTAGGGCGTGGGGGAAGACCGCTGCGGAGGTCGCGGCGGCA\r\n+ACCGGTAACACGACCGTGCTCGACCACGTGCCCGCGCCATGGGAGGTAGCAGAGAAGGTC\r\n+GAGAACGTGAGGCGCGACGCCACGCACATAACAGCAGAAGCAGGCACACAGGCTCAGCGC\r\n+GTAAAGGACTTTATTCAGCTTTTCGCACAATACAGCGGAGGCGACGGCACATCAACCAAC\r\n+GCGAGGATGTGCATCGGCAAAACCACAGGAAGCGCGGGAAGCGACACCATGAGCGGCACA\r\n+ATGGACGGCGCAGAATACATATACGCCCGGCTGGGGTGCACACGCTCGCCGGAAAACATC\r\n+AACGCCTCAGCAAGGCGGCTTCTCAACGACGCAACGCTGCAAGCACTCGACGAGAACGGC\r\n+ACACCTTTGCGGTCAGGAAGCACACTGAGCGCCCAACTGGCAGTGCCGACATTTACACTG\r\n+TCGACGGGGGTGACGGTCGGCGACGACTCGAAGGGATGCCCGCTCACCGTCATGCGCGGA\r\n+AAGAACACAAAGAAACCAGCAGGCGTCATCGAATTAGCGACAAACAAGGCCAGGCAGGTC\r\n+GACTGGGCCGGAATCTGGCGAATGACACCAGCGGGCGACAGCACGAACAGCGCCAGCGGC\r\n+AGCGGAAGTAATGCTGCCACTTCATTTTCGACGATAGACGGCGCCCAGGACCGACTGAAC\r\n+ACACTGGCAGACCGCATGGCGCGCATGCGAGAAGCCCGGAAGGCGCTGACGAAATTGAGC\r\n+ACAGAAAGCACGAAAAGCATGCCCCCGACCGCTGGCCAGGCCAGAAACATATGCACAAAA\r\n+CCGACAACGCAAGACACGGAAACACTCAAGCAGGCATACACAAAACAGCCACGGCCCACA\r\n+GAAACAAGCACCGGTGAAACGCGCCTCGGAGAAACAAAGCACGCAAACAAAAGGACAGAG\r\n+AAGGCGACGAGCGCAGCTAGCGCACACTGCCCCGACGGCACAAAGTGGGACGAAACCAGC\r\n+AAGCAGTGCCGCGCAAACAAAACGCCCAGCGACAGCACAAGGAACCTCAACACGCTCAGG\r\n+ACAGCTGCGTCTCTCTTTTTGGCAGCGGCAGGCAGCACCATGCACTTGCGCTAG\r\n+>Tv0041110 \r\n+ATGAAGCGGCGGCGCGGCTTTTTGAGCAGCTGGAGGCGCGTGGCCAGCGAGGTGAGCGAG\r\n+GAGACACAGAACTTGACGGTGGCGGGCGAAGCAGAGAAACTGGAGCGCGTCGCGGAGGGC\r\n+ATGGGCGACATTGAGCACGAGGCACTCGCAGTCGCGGGGGACGCGGCACGCACAAGCGTG\r\n+CGCCTGACAGACTTCGTCAAGCTCTTCGCGACATTCTCAGGCAGCGTCAACGGCGGCGGG\r\n+AAAACATGCATCGGTAAAGCAACAGGCTCGGGCCAAGATGCCGCAACGACGAACGGTCCC\r\n+GCAGACTACATCTACGCCGACCTGGGGTGCGACGTTTCGCCGGAGGAAATGGCAACAATG\r\n+AAAGCGCACATCATCCAGCATTGTGCCGCACCTGCGCAGGTGGGCGGACGAACGATCAAG\r\n+GGCGCCACTCTCAGCGACCAGGTTCAACAGCCCGCAAGCATTGCAATGGAGACGGGCGTC\r\n+AACACCGCAGACGACGGGAAAGGATGCCCACTCGTAATGCACAGGGCACACAAAAGTGTC\r\n+GGCATCGCAGGCGTCATCGAGGCAGCGAACAACGGGGGAACGGCGCGCAAGGTCGACTGG\r\n+GCAGGCCTCATCGAAATGACACCAAGCAGCACCAGCACCGCCAGCGGCACAAACGCCGAC\r\n+TTCGCCACAACGATGGAATGGAAAAATGACGCGCTAGCTGCACTCGGCACTATAGCAACA\r\n+CGCTACGCGAAAGTGCGCCAGAAAGCAATCGACGCCACCAAAGCGTGCGAGGCAACGAAG\r\n+CGGTGCACAGAAGCCCGGGCACAGGACAGGAACGACATGGTGCAAGAGACAAGGCAGCGG\r\n+GCCCAACAGCAAAAGAAACACACAGAAAAACGGGACGGAACCGAGAAAGGAGAAGATGAC\r\n+GCACAGACGTGCGCGAACAGCGGCGAGGTGTTCGACGCACAGCGCGGAAGGTGCGTCGTA\r\n+TCAGCGGAAACCCACAGCGGAAAAACCAAAGCAGCAACGAACGCAGAAAGAGAGAGAGCG\r\n+TCGGCGGAAAGAATGGGCACAGCGTGGCCGCGCGTGGCCGCGACCATGGCTTTGGCAATG\r\n+ACAACGAAGCAGGCGGACTGA\r\n+>V5266253_5\r\n+gcagcgaaggcagtaaaggattcggcggagcaggtgcgcgacggaatcgaaagctttgca\r\n+ccagttggaagagagggaaatgtggtcgaagagacaggagg'..b'caaagcagctcgatgggctagcgacggctatc\r\n+gccaggggaccaaacaacggctggggccaggaggcaaggaaagtttgggacaatggtctc\r\n+gaaaccgccatgatatacctgtgcaacaacgctaacggaggcagcaacgggtgcggaacc\r\n+aacgacggaacccactgcccgtgcgtgccgaaaggcttcactgcgaagacaggaacagga\r\n+actcgatcgtcgatcgaaacaacgggaaaaataatccacacaggcagcccgaagacggac\r\n+ggaaaagagggaacaggacagtggcgagtggacaaaaacaacgccgcggtgagtgaggcc\r\n+gagctgaaaactaacctcaacgccgccatgcgaatctgcgaggccctagaaggcaccaca\r\n+gcacaccacctcaacactgcagacacaatcgaacaaacaatcagcaccctgctcagagcg\r\n+atgaaacgcacagccgaaagcccgaggagagatgcctggggcgcatgcacacggacgaag\r\n+gatgcgacgggtcgtccggcgaaaaaggagcgtgcatatgctacaaaccgacacgcggaa\r\n+acacaacagaaatatcgtgggccagcaaagcactcaccgcagtgcacgcactacgcagtt\r\n+tgctgcgcacagagaaacaagctgcgcagctcaaca\r\n+>V6305207_6\r\n+gcagcgcaggcagtaaaggattcggcggagcaaatgcgcgacgaaatcgaacgctttgca\r\n+gcagttggacgagaagaacatgtgctcgaagagacaggacaaccaggcacaggtgcggga\r\n+attggcccgcgaacggaagtcggcgaagcggggacacgaagcccaagggcgcttgcaacc\r\n+agtctagccgagatggccgagagctacgcgatgcaggcaatttacggcagcaagcaggcg\r\n+ggagctgacggccagcaggggacggacgcagaaaacgcgacaaacaagctgctcacaatg\r\n+ctccgcggagaggagaccacaaacgggggatttgacgcggacggcaacgacgcggggctc\r\n+atcctgccgatgatcctgctgtgcaacgacgcaagaacaagcagcgcgtgcggaacggga\r\n+gatggcaccacgtgcccatgcagcaccgcagccgtgcccgccagtggactcgaacaaaca\r\n+aacgccaagggctgggtgtggagcgtgctgaaagcaacgagcggtaccaacatgggctca\r\n+gccaagacctgatcgtcggcaactggctcatcagcaagcacatctgcgaaaaccacacga\r\n+cacacgtgaggtcgctggggactgcggccgacctggcaggccagctcgaagctgctgccc\r\n+acgcaatcgtgcacgccatgaagccaagcggccaggccgagggttacagccagcaaaaga\r\n+tgtgcctggggcaggttgtgtcgagtaaggcctgcgacggcgacacaagcagcagcgcgt\r\n+acgcctgcgcctgcttcgataaggcagccgcagctaacagagggcagggcatcaagttca\r\n+tcaatcacctgctcaccgccgcgaacgcactccgcagactgcagagactgcgcgacgacg\r\n+tgacgcgccacaacgacacagtcaccgcaatcgaaaagcacaggctcagcgcgaaagaga\r\n+agcgcgctgacacaggaaacacagggaagataaacaccagcgcaagagccggcaaggggg\r\n+aacaagaacagcaaactaacgtggcagcaggcaaaggggccgccgcgacaacagaaagcg\r\n+catgcgaaaagatgggaggccaatgggacgcgcacaggcaggcgtgcgcacagcaggaga\r\n+agaggcgcacgccg\r\n+>V9448499_9\r\n+ttggagggcgcggcaacaaagcacgcggggccgcttgtgcgcgcggcggcagcgtggcac\r\n+acgtgcgcagcgagcggggcagagaagtgcagcactttgagggagaagtcagcgaccgca\r\n+ggcacgctggcacaagcaacagacaaggccgcgaaggcgacggcactcgcagggcagctg\r\n+tccgcgcaagcactggggcacgcaaggcgcatcgacgacgccaccaggctttttgcggcg\r\n+cacagcggcaccacggcgttgactagcagcagcagcaacaaggcatgcctggtgtttaag\r\n+gcaaacgcgggggcgaacgaaaacatacgcttcgcgaacggcaagtttgtctcgggcgcg\r\n+ggcgcgggggcagcggttaaggacctcgcggggtgcgaagaaacttcggcagaggatgag\r\n+tcagaggaatcgagcttgagtttgaccttggaacagcttgtcgaaaaggtgacccaagca\r\n+gtcaacgaggccggagacgcacagctcggggcgcacgctttcggcgccggtgacggcaca\r\n+aacatcgccacagcaccgtgcgacacgctcacgaacttcgcaacagccgcgacatcctcg\r\n+ccgctcaaggacagcacggaagtgcccattggaccgtggtggaaaatgacaggcgcgcag\r\n+ggaggcagcccggcccttggcataacacttttgtcgccagcaaagcacgaaacggacatc\r\n+gccgcaatggccgctatcgcgcgagccgcggacacagagaaaaaaactctcttggacgcg\r\n+tgcaccaccgcactcagcaaacataaaggcccaaagaccacacagtgcgacgcaaacagc\r\n+gcggaaatggcactgacaacgctggctaacgagacaccggcggaagcgcacaaaatacag\r\n+gaggcacgaacactgacacaagaagcagaagaaaagggcatagaaggtcaggcacaggag\r\n+agcgaagcagaaggaacaaaacccaaaggcacaacaacaaaaaatagcgcaggaaccagc\r\n+accgcgctcacaaaagacataagggcagaggaaagcacatgcagcgaaagaaacggaaag\r\n+tggaacagcaaaacagggaagtgcgaaacaacagacggtgccgctgcgttgcgcgccgca\r\n+ctggccacaacgtggtgggcactggcacagcactga\r\n+>V9943350_9\r\n+gcattggcgagcaacgggcaggggaaggcactctctgaggacaaggtggcagtggtctgc\r\n+aagctttcggcactgctgaagaagatgagcttggaggccaaaaaactggggagtgtggcg\r\n+acactggccacgggcttcgaggcaagcgcggcggaggaagacatgcacgtgatgcgggag\r\n+gcgctgggcagcgcggcacggctactaagacgacgagccaggagaggcgcagccacacgg\r\n+aacgagacgcagcagggacggctagcgcagcggattgtgcgcctgcacgaagcggagcaa\r\n+cagaaagcactcgcggcaaagctgtcagaaaacgtcaggcagcgcacggcactcagcgcg\r\n+gcgcagatagacagctggataaaaacattcgcggctaattaccagggtccaaacgtggcg\r\n+tgcatcgtcgcggatggggggacgggaaacgggaaagcccaggaagtaaggttcgccaca\r\n+gcggacaaacaagcaggagggtgcgccgccagagcagcagaagtgaaagacgaaatgctg\r\n+ccacagcaaaagatgccgacacaagataatgaatggcagcaggcaatcgcagaggcccaa\r\n+gcatcgaaacgtgacatgctagtcggcaccgagggcaatacgaaatgcactctcacggca\r\n+ggcactggaggaagctacgccggcgccgccgcggacaacacacacacgtggggcttcttc\r\n+tggcaactcactggacacggagacgcgcgcggcgtcagcctcaag\r\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/vivax/Database/Bin_2.fas.nhr |
| b |
| Binary file data/vivax/Database/Bin_2.fas.nhr has changed |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/vivax/Database/Bin_2.fas.nin |
| b |
| Binary file data/vivax/Database/Bin_2.fas.nin has changed |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/vivax/Database/Bin_2.fas.nsq |
| b |
| Binary file data/vivax/Database/Bin_2.fas.nsq has changed |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/vivax/Database/COGlist.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/vivax/Database/COGlist.txt Wed Jul 04 16:39:13 2018 -0400 |
| b |
| @@ -0,0 +1,385 @@ +COG1 +COG10 +COG11 +COG12 +COG13 +COG14 +COG15 +COG16 +COG17 +COG18 +COG19 +COG2 +COG20 +COG21 +COG22 +COG23 +COG231 +COG24 +COG25 +COG26 +COG27 +COG28 +COG29 +COG3 +COG30 +COG31 +COG32 +COG33 +COG34 +COG35 +COG36 +COG37 +COG38 +COG39 +COG4 +COG40 +COG41 +COG42 +COG43 +COG44 +COG45 +COG46 +COG47 +COG48 +COG49 +COG5 +COG50 +COG51 +COG52 +COG53 +COG54 +COG55 +COG56 +COG57 +COG58 +COG59 +COG6 +COG60 +COG61 +COG62 +COG63 +COG64 +COG65 +COG66 +COG67 +COG68 +COG69 +COG7 +COG70 +COG71 +COG72 +COG73 +COG74 +COG75 +COG76 +COG77 +COG78 +COG79 +COG8 +COG80 +COG81 +COG82 +COG83 +COG84 +COG85 +COG86 +COG87 +COG88 +COG89 +COG9 +COG90 +COG91 +COG92 +COG93 +COG94 +COG95 +COG96 +COGP1 +COGP10 +COGP100 +COGP101 +COGP102 +COGP103 +COGP104 +COGP105 +COGP106 +COGP107 +COGP108 +COGP109 +COGP11 +COGP110 +COGP111 +COGP112 +COGP113 +COGP114 +COGP115 +COGP116 +COGP117 +COGP118 +COGP119 +COGP12 +COGP120 +COGP121 +COGP122 +COGP123 +COGP124 +COGP125 +COGP126 +COGP127 +COGP128 +COGP129 +COGP13 +COGP130 +COGP131 +COGP132 +COGP133 +COGP134 +COGP135 +COGP136 +COGP137 +COGP138 +COGP139 +COGP14 +COGP140 +COGP141 +COGP142 +COGP143 +COGP144 +COGP145 +COGP146 +COGP147 +COGP148 +COGP149 +COGP15 +COGP150 +COGP151 +COGP152 +COGP153 +COGP154 +COGP155 +COGP156 +COGP157 +COGP158 +COGP159 +COGP16 +COGP160 +COGP161 +COGP162 +COGP163 +COGP164 +COGP165 +COGP166 +COGP167 +COGP168 +COGP169 +COGP17 +COGP170 +COGP171 +COGP172 +COGP173 +COGP174 +COGP175 +COGP176 +COGP177 +COGP178 +COGP179 +COGP18 +COGP180 +COGP181 +COGP182 +COGP183 +COGP184 +COGP185 +COGP186 +COGP187 +COGP188 +COGP189 +COGP19 +COGP190 +COGP191 +COGP192 +COGP193 +COGP194 +COGP195 +COGP196 +COGP197 +COGP198 +COGP199 +COGP2 +COGP20 +COGP200 +COGP201 +COGP202 +COGP203 +COGP204 +COGP205 +COGP206 +COGP207 +COGP208 +COGP209 +COGP21 +COGP210 +COGP211 +COGP212 +COGP213 +COGP214 +COGP215 +COGP216 +COGP217 +COGP218 +COGP219 +COGP22 +COGP220 +COGP221 +COGP222 +COGP223 +COGP224 +COGP225 +COGP226 +COGP227 +COGP228 +COGP229 +COGP23 +COGP230 +COGP232 +COGP233 +COGP234 +COGP235 +COGP236 +COGP237 +COGP238 +COGP239 +COGP24 +COGP240 +COGP241 +COGP242 +COGP243 +COGP244 +COGP245 +COGP246 +COGP247 +COGP248 +COGP249 +COGP25 +COGP250 +COGP251 +COGP252 +COGP253 +COGP254 +COGP255 +COGP256 +COGP257 +COGP258 +COGP259 +COGP26 +COGP260 +COGP261 +COGP262 +COGP263 +COGP264 +COGP265 +COGP266 +COGP267 +COGP268 +COGP269 +COGP27 +COGP270 +COGP271 +COGP272 +COGP273 +COGP274 +COGP275 +COGP276 +COGP277 +COGP278 +COGP279 +COGP28 +COGP280 +COGP281 +COGP282 +COGP283 +COGP284 +COGP285 +COGP286 +COGP287 +COGP288 +COGP289 +COGP29 +COGP3 +COGP30 +COGP31 +COGP32 +COGP33 +COGP34 +COGP35 +COGP36 +COGP37 +COGP38 +COGP39 +COGP4 +COGP40 +COGP41 +COGP42 +COGP43 +COGP44 +COGP45 +COGP46 +COGP47 +COGP48 +COGP49 +COGP5 +COGP50 +COGP51 +COGP52 +COGP53 +COGP54 +COGP55 +COGP56 +COGP57 +COGP58 +COGP59 +COGP6 +COGP60 +COGP61 +COGP62 +COGP63 +COGP64 +COGP65 +COGP66 +COGP67 +COGP68 +COGP69 +COGP7 +COGP70 +COGP71 +COGP72 +COGP73 +COGP74 +COGP75 +COGP76 +COGP77 +COGP78 +COGP79 +COGP80 +COGP80 +COGP81 +COGP82 +COGP83 +COGP84 +COGP85 +COGP86 +COGP87 +COGP88 +COGP89 +COGP9 +COGP90 +COGP91 +COGP92 +COGP93 +COGP94 +COGP95 +COGP96 +COGP97 +COGP98 +COGP99 |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/vivax/Database/COGs.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/vivax/Database/COGs.fas Wed Jul 04 16:39:13 2018 -0400 |
| b |
| b'@@ -0,0 +1,6877 @@\n+>COG1\r\n+GAGCAAGAGGGAGGACGGGGCGATAGGATGAAGTGTTTGCTGCTGACATGGTGCGCCGTG\r\n+CTTCTGCAGGCATGTGCGCTGGGGGATAATGAGATTGGGAAAAACGGCATCACAGATGCT\r\n+GGGGCAGAGGACATGTGCGACACAGCTGTGCGGCTGAGGCAGGGAGCTCTGGCTGCCATG\r\n+GGGGTGGCGGACGCAGCAGCCGAAAAAGCACAGGCGGTCGCGGCGGCGGTGCAAATCGCA\r\n+TCCGAGGAGGCAGCGGCGGCAGACCTGAAGCGGGGAAATGAAATCAGCGCAGCACTTCCG\r\n+AACAGCACGCGCGCCGAAGAGGCACTCGCTAAGGCGAGGCACATCGCCAAGCAGGCGGCA\r\n+AAAACCGCACTGCTTTGCGGCAGCCTGGCAGGTCAAATCAGCCAGTGGATAATGGACATG\r\n+GGCAGCGCCGCGTCAAAGCCGGACAGCGGCGCGGGGTACATCAAGCACAGCGGTGAAACA\r\n+TTCAGTGGCGGAACCATCACAAGCGCTAACACCGCAGGAGAATGGCAGAAGGAAGTGCCT\r\n+AGCGCGTACGGCGCCATTCCAGAAAACTGCAACCCAACCGACACACAAGACGTGGCCGAC\r\n+GCCTTGAGCACACTGGACACGCTCAAGGAAGCAAGTCTCACGTCGAAGGTGGACCCAGAC\r\n+GACACCACGCAGAGCAGCAACGAAGTAGCCACAGGCACAACATGCCCGCTCACGAGCGGC\r\n+GACGCGACAAGCCACGCAGGCATTTACAGGAAGTCGGTAGAATGGGCAGGACTTTGGACA\r\n+GTCAAAGACATCACGCAGCTCAGCTCGGGGTCAAGCGTCACGATCACAGTCTCTAAAACA\r\n+CGAAAACTCGAGGAAGCGAAAACTGCGGCGGGCGCGCTCGCAGAGCTCGCAAAGAACGAA\r\n+AGCGACACCGAACGCAGCAACAAACAGGAAAAATCATGGAAAACCATTTGCGCGTGGAAG\r\n+AAGCTCGACATGTGATCTCGGTCGAAAGACGCTATGCGAAAAGAAGTGAGGAGAGCGATA\r\n+GAAGAGCTGGTCGCAGCACTGCGCGACGCGGGAAAAGCGCAAACAGCCGAAACTGATGCA\r\n+GATAAGGCCGAAGACGCTGACGCCGAATCGAAAGGCACTACAGAAGGGCGAAAAACACGC\r\n+AGCCTTGCAAGCGGCACACACAGCGCAAGCACGGGACCACGCAGCACAGCATCACAGGAA\r\n+CACTTACCGGCGAACACAGAAAGCTCAGCGAGCGAACGCAACAAGGGGGCCACTATGCTC\r\n+TGCGCTCTGGCCGCCGTGCTGCACCACTGA\r\n+>COG10\r\n+TTGCACACAAAGTTTCTCTTTTCACTTTCACCTGATATGAGAACAGCGTCAATGCGTACG\r\n+ACTCTCGTTGGCGTGTTCCTCGCAATCACTTTAAGTGGCACTGCGCCGGACATTTTTGTG\r\n+CGCTGCGCTGCAAGAGGGAGACCTGGAGGTGCGTTGCTCGTTGAAGGGGGCGCTGAGTTG\r\n+ATTTGTGACCTTTCCGGAGCGCTGAAAAAAGTTAGGCATTACGCTGAAAATTTTTACAAG\r\n+AACCATGGCTTTTCGTGCTTGAGAAACGTTGTCGAACGTGTAAAAAGTAATGCCGAAACG\r\n+CTGGCCAACAAAATAGACGCATTCATTGATAAATTTGAAAAGGGTAACAAGGGAGATGTC\r\n+ATTTGTTTAGCAGAAGTTGACGGGCGTAACAGAAAAGCTACATCTACAAAAAATAATGTC\r\n+AAGCTCTACGGATGTAACAATCATTGGTATAATATTAATGATTTTACCAGTGATGTTCAA\r\n+AAGGAGCTGAATCAAAAACTTGAGAAGTTTACAGATAGTCTTGCGTCTGGCAAAGGAGGA\r\n+TGGAAAAATGGTGTGGTAGGTGTTTTTGATGAAAATAAACATGGTGATGGGTGTCCGTTG\r\n+ACACAGCACTTTTCCCATTGGGAGTACGGATGCACAGGGGAACTCAGTCAACACGGCACA\r\n+ACGTATGACGGTTTGTGGTTTATTGAGGGTGTGGATTATGATAGATGCTATTCATACGAT\r\n+TGCTCATGTTCAGGTGATTACTTGTCTGCACACCCTAAAATTTACTGGATTGGTGACGGT\r\n+GACAGTAGCGAGGCGAAAACGTTGAAGACTTTACGTGAGGATCTAAAGACATTAAAAGAG\r\n+TCAGACGAGTCAAAGTGCGCAAAGCAAGATGTGGATCGTTCAACAGCCCCCAAAACTCAG\r\n+CTCCATGGAAACAGTGATGACGACAATTCTCATGCGGATACAAGCGATGGTGTACGCGAG\r\n+AATGCGGATAACATTGAAACTGAGCAGCAGACTGGCGATTCCTTTGGCGCGGCTGACACC\r\n+AACGCCACTGTTGTCTCGAAGAACCACGGCGAACCACGTGCGCGCAGAGAGACAAGCACC\r\n+CGCAACAGTCGTAATAATGACAGCAACTCGATGCGAGCGAGCACAGACAACAATGCGTCA\r\n+ACCGTGCCAGCGCAAAACAGTCCCCTT\r\n+>COG11\r\n+GCGCACAAAGTTTCTCTTTTCACTCTTTCACCAGATATGAGAACAGCTTCACTGCGTACG\r\n+ACTCTCGTTGGCGTGTTCCTCGCAGTCACTTTAAGCAGCATCGGACCGGACATTTTTGTG\r\n+CGCTGCGCTGCAAGAGGGAGACCAGGAGGTGCGTTGCTCGTTGAGGGTGGCGCGCAGTTG\r\n+ATTTGCGACCTTTCCGGAGCGCTGAAAAAAGTTAGGCATTACGCTGAAAATTTTTACAAG\r\n+AACCATGGCTCTTCGTGTTTGAGAGATCTTGTTCAACATGTAAAGAATAGTGCTGACACG\r\n+TTGACCAACCAAATAGATGCGTTCGTTGATAAATTTGAAAAGGGGAATGAGGGAGGTGCC\r\n+GTTTGTTTGGCAGAAATTAATGCCCGTCACCATGAAGCTCCATCCACCAAAGGTGATGCC\r\n+AGGCTATCCGGATGCTACGAAGATTGGCGCGGTATTGATGGTTTCACACGCGATGTTGAA\r\n+AAGGAGTTGAACGAAACCATTAAAATGTTCTATGGTGTTGCTGACAGAGAAAGTTGGAAA\r\n+AACGGAGTGTCGAGTGTTTTCGGTACAAATGCACGTGGACCAGGATGTCCGTTGACACTA\r\n+CATGAAGCCAGTATGGGAGCTGGTTGTAAAGGAAAACTCCATCAATATGGCACGACATAT\r\n+GGCGGCTTGTGGGAAATTAAAGGCGTGGATTATGAAAGATGTGATGAATACGATTGTTCA\r\n+TGCACGGGGCATTACTCACCCGAACCGAGAATTTACTGGATTGGTGATGATGACAATGAC\r\n+TATGCAAATATGTTGAAAACTCTACGTGAGGATCTGAGGACATTGAAAAAGGCTGAGGAG\r\n+TCAAAGTGCACAAACCTACATATGGCACTTTCAACACACACCCAAACTCAGTTCCATGGA\r\n+AACAATGATAACGACAATTCCGGTGCGGATAGAAGGGACGATGTGGGCGGGAATGCGGAT\r\n+GGCATTGAAACTGAGCAGCAGACTGGCGATTCCTTTGGCGCGGCTGACACTAACGCCACT\r\n+GTTGTCTCGGAGAACCACGGCGACTCACGTGCGCGCAGAGAGACAAGCGACCGCAACAGT\r\n+CGTAATAATGACAGCAACTCGGTGCGAGCGAGCACTGACAACAATGCATCAACCGTGTCG\r\n+GCGCAAAACAGTCCCCTTCACGCCGACATCCACATCAGCTCAAGCTGCCATGTGGGTGGT\r\n+GTAATTTTTATGTTCGCAGGCGTCTTTTTTGGAAAAACTTTTATTTTGTCCCCCATGCGA\r\n+\r\n+>COG12\r\n+CGACTCTCGTTGGCGTGTTCCTCGCAGCCACTTTA'..b'TCAAAGTTGTCAGATATGTCCTTTTTTGCTAGATGATTTCGTGCGCAAAGGT\r\n+GGTACCCCAATGAACTGGGGCGGGTTCTGTGTCGCGGAGCAGTCGAGTAGTGGCACCGTC\r\n+ATCAGGTTCAACAGAGAGAAGCGTCATGTTCTCTTAGGCGTGGCACGTGAGCTTGGTGAG\r\n+TTGGAGTGGCTGCTCTCGAACGGTAGTAGGCGCGATGGGAGGTGGCTGCGCGCCGGTCGG\r\n+AGGACAGCCAAAACGATTCCCCAGCTCGCAGCCGATGTTGATAAATCTCTACTAATTCCC\r\n+CACCATGGCGCCAGCTCCACAGGTGGGGTCAAGGACGTTGTGAACGCGATTTTGAAGGAG\r\n+GCTGAGGGAGTTCAGACGTTCCCTAACATGTCAGAACTGAAGAACTTTCCTTTCAAGAGG\r\n+CCAGAGAGACGACGTCGCGAAAGAAAAAACACCTCATCGTCTGTGGCAGAAAGTAAAAGA\r\n+GCTAACACGCTTGCATATTTCCCTCTCTTGCTTATGTCTTTTTTTTCGCACCATAGTTTA\r\n+GTGACCCGGTGTTGCGCTATATCTTGCCCC\r\n+>COGP96\r\n+GTGCCCCTTCACGTGTGTGCAATTGTGGCACTAAGGACTGGCGACACGATGCAAATATGC\r\n+GGCCTATCTGCCTCCCTCAAGCTGACTGCGAGGACTTTCGAGGGCCTTGTGGAGCAGGCT\r\n+CTGCGGATTGAGAAGGATGCGTTTGCGAAAATCATGGTCACGGAGGAAGCACTGCGCACT\r\n+GCATCGAGGAAAGTGACAGAGATGGACACGAAACTAACAATGCTGCCCGCTGCGCTTCGC\r\n+AGGCTACAGGCGGATGTAATGGCCGCAGAGAGGTCTGTGGACGACGCGTGGAGCAGGTAT\r\n+TACGCACTTCGTGCGGGTGTCAGGGCGTTGGTGCGACGGGTTGCTGCTGTCGTGCCGAAG\r\n+GCTGCCTCTTCTTGTGGTAAAATTGACAACTTCGTCGCTGCTTTTGCCACCGCTGAATCC\r\n+CGTGAAAATTTCAAGTCCGTCACAGAGTTAGGTGATCCGTTCATTTTGCAGTATGAAGAT\r\n+CACAGAGGTCTTGGAATGGGAAAAAATCCTGCCCCATCACTGCTTAGCAACTCGACCGGT\r\n+TGCACGTATGAAAACTACACTTTGGCGCGTCCACAAAATATCACCACCACAATCGTGGAC\r\n+GATGTTGTCGTACTAGGGGAAGATGGAATGCTTTGCATGACTAATATTATCACCACTTTT\r\n+GAGAAATCTCAAAGTTGTCAGATATGTCCTTTTTTGCTAGATGATTTCGTGCGCAAAGGT\r\n+GGTACCCCAATGAACTGGGGCGGGTTCTGTGTCGCGGAGCAGTCGAGTAGTGGCACCGTC\r\n+ATCAGGTTCAACAGAGAGAAGCGTCATGTTCTCTTAGGCGTGGCACGTGAGCTTGGTGAG\r\n+TTGGAGTGGCTGCTCTCGAACGGTAGTAGGCGCGATGGGGGGTTGCTGCGCGCTGGGCGG\r\n+AGGACAGACAAAACGATTCCCCAGCTCGCAGCCGATGTTGATAAAGCTCTACTAATTTTC\r\n+CACCAGAGCCCCAGCTCTACATGTGGGGTCAAGGACGTTGTGGACGCGATTTTGAAGGAG\r\n+GATGAGGGAGTTCAAACGTTCGCCAACATGTCAGAACCGAAGAACTTTCCTTTCAAGAGG\r\n+CCAGAGAGACGACACCGCGAAAGAAAAAACACCTCATCGTCTGTGGCAGAAAGTAAAAGA\r\n+GCTAACACGCTTGCATATTTCCCTCTCTTGGTTATGTTTTTTCCCACCATAGTCTAGTGA\r\n+CCAGTGCTGTGCTATATCTTCCCCCTGATT\r\n+>COGP97\r\n+tATTTTGGAGTTTGCAGATCGGCGAAATCTAAATGCGGGAAGAAACTACCCTGCGTCACT\r\n+GCTCAGCAACTTGACCGGTTGCACATATGAAAACTACACACTATCATATCCTCAAAATAC\r\n+CACCACCACAATCGTGGACAATGTTGTCGTACTAGGGGAAGATGGAATGCTTTGCATGAG\r\n+CAACAGCTTGGTAAGTTTTAAAAGTCCTCAAAATTGTCAGATATGCCCTTTTTTGCTAAA\r\n+TGATTTCGTGCACAAAGGTGGTACCCCAATGAACTGGGGCGGGTTCTGGGTCGCGGAGCA\r\n+GTCGAGTAGCGGCACCGTTATCAGGTTCAACAGAGAGAAGCGTCATGTTCTCTTAGGCGT\r\n+GGCACGTGAGCTTGGTGAGTTGGAGTGGCTGCTCTCGAACGGTAGTAGGCGCGATGGGAG\r\n+GTGGCTGCGCGCCGGTCGGAGGACAGCCAAAACGATTCCCCAGCTCGCAGCCGATGTTGA\r\n+TAAATCTCTACTAATACCCCACCATGGCGCCAGCTCCACAGGTGGGGTCAAGGACGTTGT\r\n+GAACGCGATTTTGAAGGAGGCTGAGGGAGTTCAGACGTTCCCTAACATGTCAGAACTGAA\r\n+GAACTTTCCTTTCAAGAGGCCAGAGAGACGACGTCGCGAAAGAAAAAACACCTCATCGTC\r\n+TGTGGCAGAAAGTAAAAGAGCTAACACGCTTGCATATT\r\n+>COGP98\r\n+GTCGCCGGAGGCATCGACGCCTTCATGCTCACTCTGGCCACGTACTCAGCAGGCGCTCAC\r\n+ACAGGCGAACGCAACGCACGCTGCCTCAATAACGACGCCGAAGGCACGACTGCTGAAAAG\r\n+TACGAGGCGGGAGAAGGAAGTGGAAAGAGCGAGGATACAGTCAACGCCATGCTCGACCTC\r\n+ATCGCGGACTGCAGGAACGCGCAGCCAACAAACAAAACAGTCGCGGCAGCCAAGGCAGCC\r\n+ATCGAAGAACGTGGATTCGTCAAACCGTTCGACAGCACGTCAGATAGGGGAGGCATTGCA\r\n+CCAGGACACGCCAGTCAAGACGACGGTGGCTGCGCCCTCCTCGCCGGACACGCACGCAGC\r\n+AGCGGAAATCAAGCTCTTTTTCAAACAGCCAGCGGCAGCTTCCCGTTCGCGGTTTACGGC\r\n+GGCATTTGGACAGTACAGTCACCAGGCACAAACGACAATGGCATCAAACTGCAAATCACA\r\n+CAAGACCAAGACGGAACACGCAACGGAACAGGCATGACCGCTGAAAGACAGGCACTCATC\r\n+AGGAGACAGGGCACGGCCGGTGACGAGATGACCGACATTAGCCAAGTGAAACTGCTAGCA\r\n+GACGGGTTCGCACACGGAGACAAGGCAAGTAGCATC\r\n+>COGP99\r\n+GTCGCCGGAGGCATCGATGCCTTCATGCTCACTTTGGCCACGTACTCAGCAGGCGCTCAC\r\n+ACAGGAAAACGAAACGCACGCTGCCTCAATAACGCCGCCGAAGGCACGACTGCTGAAAAG\r\n+TACGAGGCGGGAGAAGGAAATGGAAAGAGCGAGGATACAGTCAACGCCATGCTCACCCTC\r\n+ATCGAGGCCTGCAGGAACGCGCAGCCAACAAACAAAACAGTCGGGCAAGCCAAGGCAGCC\r\n+ATCGAAGAACAGGGATTCGTCAAACCGTTCGACAGCACGGAAGATAGGGGAGGCATTGCA\r\n+CCAGGACACGACAGTCAAGACGACGGTGGTTGCGCCCTCCTCGCCGGACACGCACGCACC\r\n+GGCGGAAATCAAGCTCTTTTTCAAACAGCCAGCGGCAGCTACCCGTTCGCGGTTTACGGC\r\n+GGCATTTGGACAGTACAGTCACCAGGCACAAACAACGCTGGCATCAAACTGCAAATCACA\r\n+CAGGACCAAGACGGAGGCAAAGGGAACACAACGGGCATGACACATGGCGGGAAGGCAATC\r\n+ATCAGGAAACAGGGCACGGCCGGAGACGAGATGACCGACATTAGCCAAGTGAAACTGCTA\r\n+GCAAACGGGTTCGCACACGGAGAAAAGGCAAGTAGCATC\r\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/vivax/Database/COGs.fas.nhr |
| b |
| Binary file data/vivax/Database/COGs.fas.nhr has changed |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/vivax/Database/COGs.fas.nin |
| b |
| Binary file data/vivax/Database/COGs.fas.nin has changed |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/vivax/Database/COGs.fas.nsq |
| b |
| Binary file data/vivax/Database/COGs.fas.nsq has changed |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/vivax/Database/binlist.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/vivax/Database/binlist.txt Wed Jul 04 16:39:13 2018 -0400 |
| b |
| b'@@ -0,0 +1,698 @@\n+Tv0000010\n+Tv0000300\n+Tv0000360\n+Tv0001110 \n+Tv0001380\n+Tv0001830 \n+Tv0002130\n+Tv0002620\n+Tv0002700 \n+Tv0002740 \n+Tv0002900\n+Tv0003020 \n+Tv0003520 \n+Tv0003710\n+Tv0004750 \n+Tv0005010\n+Tv0005140\n+Tv0005680 \n+Tv0005950 \n+Tv0006120\n+Tv0006500 \n+Tv0006800 \n+Tv0007070 \n+Tv0007490 \n+Tv0007510 \n+Tv0008100 \n+Tv0008150 \n+Tv0008160\n+Tv0008840 \n+Tv0008950 \n+Tv0009290 \n+Tv0009650 \n+Tv0009860\n+Tv0010070 \n+Tv0010080 \n+Tv0010270\n+Tv0010770 \n+Tv0011440 \n+Tv0011860\n+Tv0012000 \n+Tv0012050 \n+Tv0012450 \n+Tv0012660 \n+Tv0012860 \n+Tv0013450 \n+Tv0013480 \n+Tv0013780\n+Tv0013960 \n+Tv0014100\n+Tv0014340 \n+Tv0014600\n+Tv0014620 \n+Tv0014810 \n+Tv0015020 \n+Tv0015120\n+Tv0015650 \n+Tv0015670\n+Tv0015930 \n+Tv0016330 \n+Tv0016410\n+Tv0016680\n+Tv0017020 \n+Tv0017060 \n+Tv0017470 \n+Tv0018540\n+Tv0018570\n+Tv0018590\n+Tv0020050 \n+Tv0020100 \n+Tv0020290\n+Tv0020380 \n+Tv0020720 \n+Tv0021450 \n+Tv0021610\n+Tv0021620 \n+Tv0021700 \n+Tv0021780\n+Tv0022010 \n+Tv0022050\n+Tv0022060 \n+Tv0022180 \n+Tv0022350\n+Tv0022520\n+Tv0022590\n+Tv0022610 \n+Tv0022730 \n+Tv0023350 \n+Tv0023520 \n+Tv0023580 \n+Tv0023740 \n+Tv0023960 \n+Tv0024270\n+Tv0024370\n+Tv0024560 \n+Tv0024600 \n+Tv0024840 \n+Tv0024850 \n+Tv0024870 \n+Tv0025350 \n+Tv0025420\n+Tv0025610\n+Tv0026230\n+Tv0027540 \n+Tv0027830 \n+Tv0027880 \n+Tv0028240\n+Tv0028410\n+Tv0028750\n+Tv0029140\n+Tv0029650 \n+Tv0029800\n+Tv0030520 \n+Tv0030620\n+Tv0030670 \n+Tv0030760\n+Tv0030770\n+Tv0031500 \n+Tv0031530 \n+Tv0031660 \n+Tv0031670 \n+Tv0031980 \n+Tv0032700 \n+Tv0033060 \n+Tv0033140 \n+Tv0033370 \n+Tv0033440\n+Tv0033920 \n+Tv0033960\n+Tv0034390 \n+Tv0034520 \n+Tv0034520 \n+Tv0034760 \n+Tv0035240 \n+Tv0035350 \n+Tv0035360 \n+Tv0035540 \n+Tv0035620 \n+Tv0035910 \n+Tv0036050 \n+Tv0036080 \n+Tv0036240 \n+Tv0036570\n+Tv0037040 \n+Tv0037300 \n+Tv0037340 \n+Tv0037850 \n+Tv0037860 \n+Tv0037880 \n+Tv0038830\n+Tv0039980 \n+Tv0040080\n+Tv0040200 \n+Tv0040490 \n+Tv0040590\n+Tv0040620\n+Tv0041110 \n+Tv0041360 \n+Tv0041550 \n+Tv0041680\n+Tv0042300 \n+Tv0042310\n+Tv0042320 \n+Tv0042480 \n+Tv0042560\n+Tv0042590 \n+Tv0042610 \n+Tv0043130\n+Tv0043150\n+Tv0043200\n+Tv0043340 \n+Tv0043460 \n+Tv0043480\n+Tv0044240 \n+Tv0044550\n+Tv0044560\n+Tv0044950\n+Tv0045350 \n+Tv0045760 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493_448427\n+Tv493_486566\n+Tv493_509356\n+Tv493_667234\n+Tv493_66782\n+Tv493_69625\n+Tv493_751854\n+Tv493_754408\n+Tv596_1165132\n+Tv596_123623\n+Tv596_134646\n+Tv596_147267\n+Tv596_148195\n+Tv596_170702\n+Tv596_210268\n+Tv596_213218\n+Tv596_221391\n+Tv596_250473\n+Tv596_285896\n+Tv596_314781\n+Tv596_321660\n+Tv596_323433\n+Tv596_343488\n+Tv596_370840\n+Tv596_378298\n+Tv596_405781\n+Tv596_42241\n+Tv596_527836\n+Tv596_551764\n+Tv596_583339\n+Tv596_704691\n+Tv596_729466\n+Tv596_742870\n+Tv596_883510\n+Tv596_883612\n+Tv596_899423\n+Tv596_915061\n+Tv596_974457\n+Tv684_227971\n+Tv684_248614\n+Tv684_268302\n+Tv684_290561\n+Tv684_327831\n+Tv684_351198\n+Tv684_354168\n+Tv684_376947\n+Tv684_411795\n+Tv684_431639\n+Tv684_435080\n+Tv684_450384\n+Tv684_586663\n+Tv684_606588\n+Tv684_623247\n+Tv684_655177\n+Tv684_689900\n+Tv684_699420\n+Tv684_99701\n+TvILV21_1164675\n+TvILV21_1230725\n+TvILV21_1388321\n+TvILV21_1587320\n+TvILV21_1602413\n+TvILV21_1674410\n+TvILV21_1744972\n+TvILV21_1787888\n+TvILV21_1849707\n+TvILV21_28996\n+TvILV21_312538\n+TvILV21_319579\n+TvILV21_33104\n+TvILV21_350747\n+TvILV21_436697\n+TvILV21_585092\n+TvILV21_588596\n+TvILV21_633588\n+TvILV21_891189\n+TvILV21_995752\n+V10066347_\n+V10125969_\n+V18222530_\n+V22967852_\n+V2901728_2\n+V4824126_4\n+V5266253_5\n+V6305207_6\n+V9448499_9\n+V9943350_9\n' |
| b |
| diff -r 000000000000 -r 36cb22bd911d data/vivax/TvDatabase.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/vivax/TvDatabase.csv Wed Jul 04 16:39:13 2018 -0400 |
| b |
| b'@@ -0,0 +1,1084 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|
| b |
| diff -r 000000000000 -r 36cb22bd911d data/vivax/geoTv.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/vivax/geoTv.csv Wed Jul 04 16:39:13 2018 -0400 |
| b |
| @@ -0,0 +1,22 @@ +Strain,Location,colour +TvY486,Nigeria,b +Tv11,Nigeria,b +Tv306,Nigeria,b +Tv319,Nigeria,b +Tv338,Nigeria,b +Tv340,Nigeria,b +Tv462,Nigeria,b +Tv465,Nigeria,b +Tv493,Nigeria,b +Tv596,Nigeria,b +Tv684,Nigeria,b +Tv1392,Nigeria,b +Tv2005,Uganda,g +Tv2323,Uganda,g +Tv2714,Uganda,g +TvILV-21,Uganda,g +Tv3171,Gambia,c +Tv3638,Ivory Coast,r +Tv3651,Ivory Coast,r +Tv3658,Ivory Coast,r +TvLins,Brazil,m |