ISEScan initial version on github

pythseq · Oct 19, 2016 · d2c4afe · d2c4afe
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diff --git a/NC_012624.fna b/NC_012624.fna
diff --git a/__pycache__/constants.cpython-33.pyc b/__pycache__/constants.cpython-33.pyc
diff --git a/__pycache__/isPredict.cpython-33.pyc b/__pycache__/isPredict.cpython-33.pyc
diff --git a/__pycache__/is_analysis.cpython-33.pyc b/__pycache__/is_analysis.cpython-33.pyc
diff --git a/__pycache__/pred.cpython-33.pyc b/__pycache__/pred.cpython-33.pyc
diff --git a/__pycache__/ssw_wrap.cpython-33.pyc b/__pycache__/ssw_wrap.cpython-33.pyc
diff --git a/__pycache__/tools.cpython-33.pyc b/__pycache__/tools.cpython-33.pyc
diff --git a/clusters.faa.hmm b/clusters.faa.hmm
diff --git a/clusters.single.faa b/clusters.single.faa
diff --git a/hmm/clusters.faa.hmm.NC_012624.fna.faa b/hmm/clusters.faa.hmm.NC_012624.fna.faa
diff --git a/hmm/clusters.single.faa.NC_012624.fna.faa b/hmm/clusters.single.faa.NC_012624.fna.faa
diff --git a/license.ssw.txt b/license.ssw.txt
@@ -0,0 +1,12 @@
+SSW Library: An SIMD Smith-Waterman C/C++/Python/Java Library for Use in Genomic Applications
+
+License: MIT
+
+Copyright (c) 2012-2015 Boston College
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
diff --git a/prediction/NC_012624.fna.gff b/prediction/NC_012624.fna.gff
@@ -0,0 +1,10 @@
+##gff-version 3
+gi|228288719|ref|NC_012624.1|	ISEScan	insertion_sequence	8950	11399	.	+	.	ID=gi|228288719|ref|NC_012624.1|_IS_1;family=IS607;cluster=IS607_8
+gi|228288719|ref|NC_012624.1|	ISEScan	terminal_inverted_repeat	8950	9013	.	+	.	ID=gi|228288719|ref|NC_012624.1|_IS_1_TIR;parent=gi|228288719|ref|NC_012624.1|_IS_1
+gi|228288719|ref|NC_012624.1|	ISEScan	terminal_inverted_repeat	11338	11399	.	+	.	ID=gi|228288719|ref|NC_012624.1|_IS_1_TIR;parent=gi|228288719|ref|NC_012624.1|_IS_1
+gi|228288719|ref|NC_012624.1|	ISEScan	insertion_sequence	30355	31343	.	+	.	ID=gi|228288719|ref|NC_012624.1|_IS_2;family=IS5;cluster=IS5_25
+gi|228288719|ref|NC_012624.1|	ISEScan	terminal_inverted_repeat	30355	30382	.	+	.	ID=gi|228288719|ref|NC_012624.1|_IS_2_TIR;parent=gi|228288719|ref|NC_012624.1|_IS_2
+gi|228288719|ref|NC_012624.1|	ISEScan	terminal_inverted_repeat	31316	31343	.	+	.	ID=gi|228288719|ref|NC_012624.1|_IS_2_TIR;parent=gi|228288719|ref|NC_012624.1|_IS_2
+gi|228288719|ref|NC_012624.1|	ISEScan	insertion_sequence	32413	33650	.	-	.	ID=gi|228288719|ref|NC_012624.1|_IS_3;family=ISH3;cluster=ISH3_0
+gi|228288719|ref|NC_012624.1|	ISEScan	terminal_inverted_repeat	32413	32456	.	-	.	ID=gi|228288719|ref|NC_012624.1|_IS_3_TIR;parent=gi|228288719|ref|NC_012624.1|_IS_3
+gi|228288719|ref|NC_012624.1|	ISEScan	terminal_inverted_repeat	33607	33650	.	-	.	ID=gi|228288719|ref|NC_012624.1|_IS_3_TIR;parent=gi|228288719|ref|NC_012624.1|_IS_3
diff --git a/prediction/NC_012624.fna.is.fna b/prediction/NC_012624.fna.is.fna
@@ -0,0 +1,82 @@
+>gi|228288719|ref|NC_012624.1|_8950_11399_+ IS607_8
+TTTCTTCATTCTACATAGTATGCAGAGAGATATTTAAACTTTTGCATTCAACATAGAGTG
+CAGAGAATCTCAAATAAAAAAATGTTATTTACCAATCTCTTTTAGAGTATCGTTTAATTC
+TAATAATTTTTCAACTACAACCTTGCCAGTCTCCGTTAACTTCACTACCTTCTTAGCAGT
+TCCTACTGAAGTTTTTTCTTCTCTCACCACTATTAACCCATTCTCTTCTAAAATCGGTAT
+CCATTTCTGGATTGTATGCCGTCGTCAACAGTTTCCGATAAACCGTGAAGTTTATATACT
+TTGTATGTAAGTTTAACTACAATGCTGAAACCTAAGGAAGTGTGCCAAAAACTAGGAATA
+TCATACCGCACACTACAGAGCTATGTTAAGAAGGGTTACATAAAACCCGTGATACTACAG
+AGTGGAAAATGGAGGTTTAAAGAAGAGGATGTCGAAAGACTCATGGGGGTTGTTAGGAAG
+AGGAAAGTAGTATTATACGCTAGGGTATCATCAAACACACAGAAAGACGACTTAATAAAC
+CAAGTTAAGTACCTGGAGGAGAACGTTAAGGACTACGACCAAGTAATAACAGACATTGGT
+TCTGGGTTGAACATGAAGAGAAAAGGATTCCTCAAGCTATTGAGAATGATACTAAACAAC
+GAAGTATCGAAAGTTGTCATAGCCTACCCAGACAGACTAGTTAGGTTCGGCTTTGAAATA
+ATAGAGGAGGCATGCAAAGCACACAACTGCGAGCTCGTGGTATTAAATAAGGAGGACAAA
+ACACCAGAGCAGGAACTAATCGAAGATTTGATCTCTATACTGGTATCATTTAGCGGAAAG
+TTGTATGGTATGAGGAGCCATAAATATGAGAAGGTGAAGAAGTGTGTCGAAGAGCTTAAG
+GCTTAAATCATTCCAACCGGAGGAGGAATACGTTTACCTAACTTACTCCCTGAAGAATAA
+TAAGAAGGTGAAGAGCAAGATATTACTAGAGAACTATAAACACCTACTACAGAAGGCTTT
+AGACTGGTTATGGGAGAGGACTAAGATAGAGAGGAAGGAGGTCAAGAAGGGCAAGAAAAT
+TTTCGCTAAGGTTAAAGTAACCTTGCCAAAGAAAAAGGAAGTTTACAAGGTGTTGAGGGA
+TGAGTTAGAGAAGGTTAACAATCTAGCTTCACATTACGTTGACAAAGCAATAAATGATGC
+TTACTCAATCTTGAATAGTTGGAGGAGGAGGGCTGAAAAAGGACAAGCGTCATTAAGGAA
+ACCTAGATTGAAGAAGGTTTACGTTAGGGTAAAGTCGACACTTAGAAAGGTTGAGGGTGA
+GAGTGTAAGGATTACAGTAAGACCTTACGAATACGTCACCTTCTCATGGTCTCACAAATG
+GTTTTCAAGGAGGGTTGAAGGGCTTGAGTTGGGTGAGCCAGTAATAAAGGAGGATAAAGT
+TCACCTACCATTTCGTTATAAGTTACCTTGGTTTACTCCCCTTGACTTTCTATCTATTGA
+TAGTAACTTGTACACATTAGACGCTTACGATGGGGAGAAGTTCGTCACATTTTCTTTGAA
+GGAGTTGTATAGTTTGAAGTTCGGTATGGAGTTGAAGAGGAGTAAAATACAGTCCTTCGC
+TTCTAAACACGGTAGGAAGGGGAAGGTATTGTTGAGGAAGTACTCCCACCGTGAAAGGAA
+CCGCGTGCTTGATTATGTTCACAAGTTTGTGAACAAACTGTTGGGAATGTATCCTCTCAC
+TATGTTTGCTGTCGAGAAGTTGAATAAGCAGTCAATGTTCCAAGACGCTGATGATAAGCT
+GTCTAAGAAGGTTTCAAGGACTGTATGGAGGACTATACACCGCGTGCTTAAATACAAGGC
+TCCCCTTTATGGTTCTTTCGTTAAGGAGGTGAACCCACACCTCACATCTAAGTCCTGCCC
+CAGATGTGGATGGGTTTCCCGAAAGGTCGGCAGGATTTTCAAGTGTGAGAGGTGTGGGTT
+CACTCTAGATAGGCAACTAAACGCATCTCTCAATATTTACCTCAAGATGTGCGGGTTTCC
+CCACCTCTTTCTTACTCCCACTGGGAGTAGGTGGATTGGGGTTATCCCGCTAAAGGGGCG
+GAGGGGTATGAACGGGGCGTTGCCCCGCGACTCTGGTGAAGCCCAAGGGCTGAGGATTGG
+ATACAAATTCATGAAAATTCAATGAAGCCCAAACCCCAACTCATTTGGCTAATTTTTACC
+AGATCCATTAAGGATCCCTCACCCATCATGTTAATATATAGTAATATTTGCATAGGAGTT
+GACAAAATATCGAGAAGCTTTTTATTTATAACAAGTTCACTCATTCTACTCTCACTACAT
+AATATAGAGAGTAAAATTTTAATAGTTTCGCTTACCAGTGCCCTCTGTTCTGCAGTCTAC
+ACAGAAAGCAAACTTTTAATACTTTCTGCACATAGTATAGAGTGATGAAA
+>gi|228288719|ref|NC_012624.1|_30355_31343_+ IS5_25
+AGAATTATACAAAAATTTATAAATAATTATACCGAGTATTACTCATGGGAAAGAGTAAGT
+ACAAGAGGGATTGGAGCAAGTACGACGAGAACGTTATAACTAGATACGAGCTAATGTTCC
+CCTTCTACGTCTTCCAACACTGGTGGGAATTACTAGCAGAAGAGAATAGGAATGCCAAGA
+AAACCTACAAGGCGCCAAAGGAGTTCAACGACTTCCTAGCGTTCCTGCACTTGTTCCTAC
+CTTATAGGGCCATAGAAGGAGTATTGAGAGCATTAGAAAGACTGAAAATCATCCCAACAA
+GCCTAGACTACTCAACAATATGGGAAAGAGTAAGAAACATGAACATAAAATTCCCAGAGG
+CAAATGACCAACTTGAAGTAATAGCAGACGCAACGGGAATAAGCACAAACAAGGGAGGAC
+AATACATTATAGCAAAATGGGGAAAAACCAAGGACTCAAAATTCCTCAAGATCGAAATAG
+TAATGGATAAGGACCAATTCAACGTAATAAACGCTGAAGTAACCAGCAACGAGGTTCAGA
+CTGCAGTTAAGACGGTTAAGGATTTACAAGATAAGGGAAAGAAGGTCAAGAAGTTTTATG
+GAGATAAAGCTTATGATGCTAATGAGGTTTACAAGACTGGGGTTGAGGTTGTTGTTCCAC
+CTAGGGAGAACGCCTCCACTAGACGCGGTCATCCTGCTAGGAGAAAGGCTGTAAGGGAGT
+TCAAGAGGTTGGGTTATAATCGTTGGAGGGAGGAGAGGGGTTACGGTGTTAGGTGGAGGA
+TTGAGTCCTTATTCTCTGCTGTGAAGCGTACTTTTGGGGAATCTGTTAGGGCTACAAGTT
+TTTTAGGACAAGTGGTTGAGGCTAAGCTCAAGTTCTGGGCTTATGCATGGATGGTCCACT
+TGGCTAATTCTTTAGTTGGTAGAGCTCCGGGTATTAGGGTGTGAGCTTGCGAATAACGTT
+GAAATAAATATTAATTACTGAAAAATTCT
+>gi|228288719|ref|NC_012624.1|_32413_33650_- ISH3_0
+CCCTAATACGGTAGACCCAAAATCGTATTATGAAAAATAATTCTGACAGAATAATATCGA
+TTCATGATAGATAACAGGATTTATATGAGTATTAAGAATTCAGTTGAAGAAAGGTTTAAG
+CTGAGGGAGATGTGGTATTACCACGTGAGTAAGTGAGATGGTAACACCGGTACTCCCTCA
+CCAAAATAACATTCAACAAATAGGATATAAATTACTTTCCATGCTGAACTTCAAGGGAAA
+GAAAGGGGAAGAGGTGGCGAGAACCCTCATCTCAGCGTGTTTATGGAACGATTCGGTGGA
+AAGCAAGTCGAGGGCGTATGGCGTGTCCCCACAGACCGTGAGGAATTACGTGGAGGAGCA
+AGGGATGGAAGTTATTGAGAAACTCTTGGAAAGCGCCAGGAAGATATCCTTGAAGGTACT
+GAAGGGAGTCAAGGAGATAGACGTCTCAATAGACTGGACAACCAAGACCTGGTACGGGAG
+ACCGGTGGGAGGGCTCGGGAGTTCGGAGGAGGGAAACTCTTGGAACTACGCAACTGCGAC
+GACAAAGTTTAATGGGAAAGTGCTCCTACTGGCCTTCGTCACTCAAGTCAAGGGGATGAC
+TAAGGAAGAGATCGTGAAGGCCCTCGTGGAGCAAGTCGTCGCGATGGGGTTCAAGATAAG
+GTTGATAACTCTTGACGCAGGTTTCTATACTGTTGATGTGCTCAACTTCATTTCACAGTT
+TAAGTATATAGTTGCTGTGCCTGTTGGGGATGTTAAGGTTTATGAGGAGTTTGACGGGGA
+TTACGCAACTAATAGTAAGAGGCATAGGAGGGATGAGCAGGTCAAGTTCAGGCTTCTCGT
+GTACAGCAAGGAAAAAGTGAGGAGAAAGAAGAAGAGTGTTGTTTATTTTGCTAGGGCTAC
+TAATCTAGACCTACCGAAGGGGGAGGTGTTGGATTTGTACAATAAGGTAAGGGGTCCCAT
+AGAGACCTCTTATAGGAACATTAAGGCTTTTCTTCCATTTACTAGTTCTACTAAGTTTGT
+TTTCCGCACGTTGATCTTCGTGCTGGCCGTGGCCTTCTACTCCCTGTACACCGTGTTCAA
+GGGGGAGGTGAGGAGGGAGCAGTTCAGGATACTCCTAATACTCTTGTTTTCTGATGATTT
+ATTCTATCTAAAAGATTTTCTATTTAAATCAATAGAACCGCTTATTAATAATATAGATTT
+ATTTTCAAGGAGGTGATTTTGGGTCTACCGAATAAGGG
diff --git a/prediction/NC_012624.fna.orf.faa b/prediction/NC_012624.fna.orf.faa
@@ -0,0 +1,25 @@
+>gi|228288719|ref|NC_012624.1|_9271_10937_+
+LKPKEVCQKLGISYRTLQSYVKKGYIKPVILQSGKWRFKEEDVERLMGVVRKRKVVLYAR
+VSSNTQKDDLINQVKYLEENVKDYDQVITDIGSGLNMKRKGFLKLLRMILNNEVSKVVIA
+YPDRLVRFGFEIIEEACKAHNCELVVLNKEDKTPEQELIEDLISILVSFSGKLYGMRSHK
+YEKVKKCVEELKLKSFQPEEEYVYLTYSLKNNKKVKSKILLENYKHLLQKALDWLWERTK
+IERKEVKKGKKIFAKVKVTLPKKKEVYKVLRDELEKVNNLASHYVDKAINDAYSILNSWR
+RRAEKGQASLRKPRLKKVYVRVKSTLRKVEGESVRITVRPYEYVTFSWSHKWFSRRVEGL
+ELGEPVIKEDKVHLPFRYKLPWFTPLDFLSIDSNLYTLDAYDGEKFVTFSLKELYSLKFG
+MELKRSKIQSFASKHGRKGKVLLRKYSHRERNRVLDYVHKFVNKLLGMYPLTMFAVEKLN
+KQSMFQDADDKLSKKVSRTVWRTIHRVLKYKAPLYGSFVKEVNPHSHLSPAPDVDGFPER
+SAGFSSVRGVGSL
+>gi|228288719|ref|NC_012624.1|_30399_31335_+
+GKSKYKRDWSKYDENVITRYELMFPFYVFQHWWELLAEENRNAKKTYKAPKEFNDFLAFL
+HLFLPYRAIEGVLRALERLKIIPTSLDYSTIWERVRNMNIKFPEANDQLEVIADATGIST
+NKGGQYIIAKWGKTKDSKFLKIEIVMDKDQFNVINAEVTSNEVQTAVKTVKDLQDKGKKV
+KKFYGDKAYDANEVYKTGVEVVVPPRENASTRRGHPARRKAVREFKRLGYNRWREERGYG
+VRWRIESLFSAVKRTFGESVRATSFLGQVVEAKLKFWAYAWMVHLANSLVGRAPVLGCEL
+ANNVEININY
+>gi|228288719|ref|NC_012624.1|_32517_33587_-
+IDNRIYMSIKNSVEERFKLREMWYYHVRSEMVTPVLPHQNNIQQIGYKLLSMLNFKGKKG
+EEVARTLISACLWNDSVESKSRAYGVSPQTVRNYVEEQGMEVIEKLLESARKISLKVLKG
+VKEIDVSIDWTTKTWYGRPVGGLGSSEEGNSWNYATATTKFNGKVLLLAFVTQVKGMTKE
+EIVKALVEQVVAMGFKIRLITLDAGFYTVDVLNFISQFKYIVAVPVGDVKVYEEFDGDYA
+TNSKRHRRDXAGQVQASRVQQGKSEEKEEDVVYFARATNLDLPKGEVLDLYNKVRGPIET
+SYRNIKAFLPFTSSTKFVXPHVDLRAGRGLLLPVHRVQGGGEEGAVQDTPNTLVF
diff --git a/prediction/NC_012624.fna.orf.fna b/prediction/NC_012624.fna.orf.fna
@@ -0,0 +1,65 @@
+>gi|228288719|ref|NC_012624.1|_9271_10937_+
+ATGCTGAAACCTAAGGAAGTGTGCCAAAAACTAGGAATATCATACCGCACACTACAGAGC
+TATGTTAAGAAGGGTTACATAAAACCCGTGATACTACAGAGTGGAAAATGGAGGTTTAAA
+GAAGAGGATGTCGAAAGACTCATGGGGGTTGTTAGGAAGAGGAAAGTAGTATTATACGCT
+AGGGTATCATCAAACACACAGAAAGACGACTTAATAAACCAAGTTAAGTACCTGGAGGAG
+AACGTTAAGGACTACGACCAAGTAATAACAGACATTGGTTCTGGGTTGAACATGAAGAGA
+AAAGGATTCCTCAAGCTATTGAGAATGATACTAAACAACGAAGTATCGAAAGTTGTCATA
+GCCTACCCAGACAGACTAGTTAGGTTCGGCTTTGAAATAATAGAGGAGGCATGCAAAGCA
+CACAACTGCGAGCTCGTGGTATTAAATAAGGAGGACAAAACACCAGAGCAGGAACTAATC
+GAAGATTTGATCTCTATACTGGTATCATTTAGCGGAAAGTTGTATGGTATGAGGAGCCAT
+AAATATGAGAAGGTGAAGAAGTGTGTCGAAGAGCTTAAGGCTTAAATCATTCCAACCGGA
+GGAGGAATACGTTTACCTAACTTACTCCCTGAAGAATAATAAGAAGGTGAAGAGCAAGAT
+ATTACTAGAGAACTATAAACACCTACTACAGAAGGCTTTAGACTGGTTATGGGAGAGGAC
+TAAGATAGAGAGGAAGGAGGTCAAGAAGGGCAAGAAAATTTTCGCTAAGGTTAAAGTAAC
+CTTGCCAAAGAAAAAGGAAGTTTACAAGGTGTTGAGGGATGAGTTAGAGAAGGTTAACAA
+TCTAGCTTCACATTACGTTGACAAAGCAATAAATGATGCTTACTCAATCTTGAATAGTTG
+GAGGAGGAGGGCTGAAAAAGGACAAGCGTCATTAAGGAAACCTAGATTGAAGAAGGTTTA
+CGTTAGGGTAAAGTCGACACTTAGAAAGGTTGAGGGTGAGAGTGTAAGGATTACAGTAAG
+ACCTTACGAATACGTCACCTTCTCATGGTCTCACAAATGGTTTTCAAGGAGGGTTGAAGG
+GCTTGAGTTGGGTGAGCCAGTAATAAAGGAGGATAAAGTTCACCTACCATTTCGTTATAA
+GTTACCTTGGTTTACTCCCCTTGACTTTCTATCTATTGATAGTAACTTGTACACATTAGA
+CGCTTACGATGGGGAGAAGTTCGTCACATTTTCTTTGAAGGAGTTGTATAGTTTGAAGTT
+CGGTATGGAGTTGAAGAGGAGTAAAATACAGTCCTTCGCTTCTAAACACGGTAGGAAGGG
+GAAGGTATTGTTGAGGAAGTACTCCCACCGTGAAAGGAACCGCGTGCTTGATTATGTTCA
+CAAGTTTGTGAACAAACTGTTGGGAATGTATCCTCTCACTATGTTTGCTGTCGAGAAGTT
+GAATAAGCAGTCAATGTTCCAAGACGCTGATGATAAGCTGTCTAAGAAGGTTTCAAGGAC
+TGTATGGAGGACTATACACCGCGTGCTTAAATACAAGGCTCCCCTTTATGGTTCTTTCGT
+TAAGGAGGTGAACCCACACCTCACATCTAAGTCCTGCCCCAGATGTGGATGGGTTTCCCG
+AAAGGTCGGCAGGATTTTCAAGTGTGAGAGGTGTGGGTTCACTCTAG
+>gi|228288719|ref|NC_012624.1|_30399_31335_+
+ATGGGAAAGAGTAAGTACAAGAGGGATTGGAGCAAGTACGACGAGAACGTTATAACTAGA
+TACGAGCTAATGTTCCCCTTCTACGTCTTCCAACACTGGTGGGAATTACTAGCAGAAGAG
+AATAGGAATGCCAAGAAAACCTACAAGGCGCCAAAGGAGTTCAACGACTTCCTAGCGTTC
+CTGCACTTGTTCCTACCTTATAGGGCCATAGAAGGAGTATTGAGAGCATTAGAAAGACTG
+AAAATCATCCCAACAAGCCTAGACTACTCAACAATATGGGAAAGAGTAAGAAACATGAAC
+ATAAAATTCCCAGAGGCAAATGACCAACTTGAAGTAATAGCAGACGCAACGGGAATAAGC
+ACAAACAAGGGAGGACAATACATTATAGCAAAATGGGGAAAAACCAAGGACTCAAAATTC
+CTCAAGATCGAAATAGTAATGGATAAGGACCAATTCAACGTAATAAACGCTGAAGTAACC
+AGCAACGAGGTTCAGACTGCAGTTAAGACGGTTAAGGATTTACAAGATAAGGGAAAGAAG
+GTCAAGAAGTTTTATGGAGATAAAGCTTATGATGCTAATGAGGTTTACAAGACTGGGGTT
+GAGGTTGTTGTTCCACCTAGGGAGAACGCCTCCACTAGACGCGGTCATCCTGCTAGGAGA
+AAGGCTGTAAGGGAGTTCAAGAGGTTGGGTTATAATCGTTGGAGGGAGGAGAGGGGTTAC
+GGTGTTAGGTGGAGGATTGAGTCCTTATTCTCTGCTGTGAAGCGTACTTTTGGGGAATCT
+GTTAGGGCTACAAGTTTTTTAGGACAAGTGGTTGAGGCTAAGCTCAAGTTCTGGGCTTAT
+GCATGGATGGTCCACTTGGCTAATTCTTTAGTTGGTAGAGCTCCGGGTATTAGGGTGTGA
+GCTTGCGAATAACGTTGAAATAAATATTAATTACTGA
+>gi|228288719|ref|NC_012624.1|_32517_33587_-
+ATGATAGATAACAGGATTTATATGAGTATTAAGAATTCAGTTGAAGAAAGGTTTAAGCTG
+AGGGAGATGTGGTATTACCACGTGAGTAAGTGAGATGGTAACACCGGTACTCCCTCACCA
+AAATAACATTCAACAAATAGGATATAAATTACTTTCCATGCTGAACTTCAAGGGAAAGAA
+AGGGGAAGAGGTGGCGAGAACCCTCATCTCAGCGTGTTTATGGAACGATTCGGTGGAAAG
+CAAGTCGAGGGCGTATGGCGTGTCCCCACAGACCGTGAGGAATTACGTGGAGGAGCAAGG
+GATGGAAGTTATTGAGAAACTCTTGGAAAGCGCCAGGAAGATATCCTTGAAGGTACTGAA
+GGGAGTCAAGGAGATAGACGTCTCAATAGACTGGACAACCAAGACCTGGTACGGGAGACC
+GGTGGGAGGGCTCGGGAGTTCGGAGGAGGGAAACTCTTGGAACTACGCAACTGCGACGAC
+AAAGTTTAATGGGAAAGTGCTCCTACTGGCCTTCGTCACTCAAGTCAAGGGGATGACTAA
+GGAAGAGATCGTGAAGGCCCTCGTGGAGCAAGTCGTCGCGATGGGGTTCAAGATAAGGTT
+GATAACTCTTGACGCAGGTTTCTATACTGTTGATGTGCTCAACTTCATTTCACAGTTTAA
+GTATATAGTTGCTGTGCCTGTTGGGGATGTTAAGGTTTATGAGGAGTTTGACGGGGATTA
+CGCAACTAATAGTAAGAGGCATAGGAGGGATGAGCAGGTCAAGTTCAGGCTTCTCGTGTA
+CAGCAAGGAAAAAGTGAGGAGAAAGAAGAAGAGTGTTGTTTATTTTGCTAGGGCTACTAA
+TCTAGACCTACCGAAGGGGGAGGTGTTGGATTTGTACAATAAGGTAAGGGGTCCCATAGA
+GACCTCTTATAGGAACATTAAGGCTTTTCTTCCATTTACTAGTTCTACTAAGTTTGTTTT
+CCGCACGTTGATCTTCGTGCTGGCCGTGGCCTTCTACTCCCTGTACACCGTGTTCAAGGG
+GGAGGTGAGGAGGGAGCAGTTCAGGATACTCCTAATACTCTTGTTTTCTGA
diff --git a/prediction/NC_012624.fna.out b/prediction/NC_012624.fna.out
@@ -0,0 +1,5 @@
+seqID                                                        family      cluster                                                          isBegin        isEnd len4is ncopy4is       start1         end1       start2         end2 score irId irLen nGaps     orfBegin       orfEnd strand len4orf   E-value ov
+# -------------------------------------------------------------------------------------------------------------------------------------------
+gi|228288719|ref|NC_012624.1|                                IS607       IS607_8                                                             8950        11399   2450        1         8950         9013        11338        11399    44   46    64     2         9271        10937      +    1667  3.2e-174  0
+gi|228288719|ref|NC_012624.1|                                IS5         IS5_25                                                             30355        31343    989        1        30355        30382        31316        31343    24   20    28     0        30399        31335      +     937  2.8e-140  0
+gi|228288719|ref|NC_012624.1|                                ISH3        ISH3_0                                                             32413        33650   1238        1        32413        32456        33607        33650    48   34    44     0        32517        33587      -    1071  7.4e-144  0
diff --git a/prediction/NC_012624.fna.sum b/prediction/NC_012624.fna.sum
@@ -0,0 +1,5 @@
+# seqid                                                      family         nIS %Genome     bps4IS     dnaLen
+gi|228288719|ref|NC_012624.1|                                IS5              1    2.34        989      42245
+gi|228288719|ref|NC_012624.1|                                IS607            1    5.80       2450      42245
+gi|228288719|ref|NC_012624.1|                                ISH3             1    2.93       1238      42245
+NC_012624.fna                                                total            3   11.07       4677      42245