Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_041093
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 315003
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:60261 original size:39 final size:39
Alignment explanation
Indices: 60206--60281 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
60196 CCCATCCTTC
*
60206 AATATCATGATTGGGTCAACCAGGCCAGATCATGAGTCA
1 AATATCATGATCGGGTCAACCAGGCCAGATCATGAGTCA
*
60245 AATATCATGATCGGGTCGACCAGGCCAGATCATGAGT
1 AATATCATGATCGGGTCAACCAGGCCAGATCATGAGT
60282 GAATAGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (39 bp):
AATATCATGATCGGGTCAACCAGGCCAGATCATGAGTCA
Left flanking sequence: Indices 59706 -- 60205
ATAGAGGTTACTTTAGCCTGTTGTACTGGAGTGCTTCATCGTCAAAAGAACAACAATGGGTTGTA
GCATTTTATATTGATTTGTCTAGAGGATGTAAAAGAGGGCTTTCTCATCTAAAGGGAGGGGTGAG
CTTTCTCACTATAGAATTCGCACTACGAACGAAAGACCAACGAGGATTCAGGAGGAGAAGGAGTA
GGGGCTAGCTTTCATTGAAGTAGAGGCACGAAGTAGCAAAGAATTTCGATTAAAAGAAAGGTGTG
AAGAACTCAAATGGAAAATCCTTTCCATCCCACGAATCCAAAACGCATTTTTGAAAGCCGAGGGA
ACCGTAAGGTAACCACGCCACCGATTTCTCCAACGAAAGCAATCGACATGATGATTCCTAGCGAA
AACTCGCGAAAAGGAATCAAGCCGGAAGCTTCGATTGAAGAGATTCGATCTTGCATCATCTTCCG
CTTTTTTCGAGATCCGGAGTTTTTCGAGAAAAGGTCCCATCCTTC
Right flanking sequence: Indices 60282 -- 60781
GAATAGAAAATCGAAAACGTACATAGCTGTTCCAGCTGAAATACTTGGAATAATTCTACCACTTC
TACTAGGAGTAGCCTTTTTAGTGCTAGCTGAACGTAAAGTAATGGCTTTTGTGCAACGTCGAAAG
GGTCCTGATGTAGTGGGATCGTTCGGATTGTTACAACCTCTAGCAGATGGTTCGAAATTGATTCT
AAAAGAACCTATTTCACCAAGTAGTGCTAATTTCTCCCTTTTTAGAATGGCTCCAGTCACTACAT
TTATGCTAAGTCTGGTTGCTCGGGCCGTTGTACCTTTTGATTATGGTATGGTATTGTCAGATCCG
AACATAGGGCTACTTTATTTGTTTGCCATATCTTCGCTAGGTGTTTATGGAATTATTATAGCAGG
TTGGTCTAGTAATTATAGGGGGCGGCCGTTCGGTCGCCTATGATACTAGGACCAATAGGTAAAAA
ATTTCTTTGTGCCGCAGGTGTTGAACGATCTACTCTACACAGGTG
Found at i:74806 original size:22 final size:21
Alignment explanation
Indices: 74755--74807 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
74745 CTTGGACTTG
* *
74755 GAGCTCACAAATGCGCCGTTT
1 GAGCTAACGAATGCGCCGTTT
*
74776 GAG-TGAACGAATGCGCTGTTAT
1 GAGCT-AACGAATGCGCCGTT-T
74798 GAGCTAACGA
1 GAGCTAACGA
74808 GTTTTCCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.04
21 15 0.58
22 9 0.35
23 1 0.04
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (21 bp):
GAGCTAACGAATGCGCCGTTT
Left flanking sequence: Indices 74255 -- 74754
CACTTGAGGGAGGGCAAAATCAATCAGATTCTGACCTGAAAAGAATGAATTTCTCTTGAACTTCT
CCACTTCCCACCTAGAGCAGCTTCGCTCGCGGTGATCTAATTATTGGACTAGCTGAACTAAGACT
AAGTAGATCTTCTAGAACGACTGCCGGACCATTCCATTCATTGTCTTCTTCTCAACCTCTCCTCT
CCTCGGTGACTCTGAACTACCAAGCCAATCTCTAGTCGAAGGTAGTTTACTTGCTTACTCAAGAG
AGTCAAAAAAGAGGGACTGCTACTCTTTTTTACCTACTTATCTAACCACCCTTTTTTGCAAGAGA
CGCTTTGTCCACTTCCTAGCCAAAGCCCAATTCACCACGTGAAAGTTCGTCACTATCAATAGCTC
CTTACTTAGACCCTTCCTTCCCCATAGCCACTGGCTCACGACCTTTCGACTCTCGCTAAAGAAGA
GAAATTAACCCTTAACTTCTCATACCGGATAGGCTCTTGGACTTG
Right flanking sequence: Indices 74808 -- 75307
GTTTTCCTTTTTTTCTGCTGAACTCGGAGAAGAGGAGGTAGCGGTTCGTGCTTGAGTTGAATCAC
TTGACTTTGGCCCTATCTTTCTATTTAGATAAGTAGTAGATCCCCTTACCAGGAAATGAACTAGG
TAAAAGCTATAGGCAGCTACCTGGTAGGCAACTCGTCAGGAAGAGTCTATATCACCGATAGGCCA
ATTAGATGGAATTACAGAAAGCTGTATAAGTTAGAAGAAGGAGCAAAGGGTTGAAAGCGGACAGA
TGCCATCGAATCGGATGTCTTCCTTCAATCCGCTCTTAGAGTTCGAGAATCCAAGCGCAGTCAAG
TCAGTACGTACCAATGCCTTCGGTCGGTAAGTCATTAAGGCCTGCTCTAGGTGACTTGGAAGTGC
CTGAAGCTAAGAAGTAAGTCTACTTTTACTTCTTAGTCTAGGTCTTAGAAGCACAAGCGGGAGCC
AGGGGGAAGGCCTTCAGGCCGCTGGTGGAACTCCCAGGGAATGGC
Found at i:105864 original size:29 final size:29
Alignment explanation
Indices: 105830--105906 Score: 154
Period size: 29 Copynumber: 2.7 Consensus size: 29
105820 GGTTGTAATA
105830 GCTTAAGCTATGCTTTTGGTTGTTTACAT
1 GCTTAAGCTATGCTTTTGGTTGTTTACAT
105859 GCTTAAGCTATGCTTTTGGTTGTTTACAT
1 GCTTAAGCTATGCTTTTGGTTGTTTACAT
105888 GCTTAAGCTATGCTTTTGG
1 GCTTAAGCTATGCTTTTGG
105907 AAGAGAGTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.17, C:0.14, G:0.22, T:0.47
Consensus pattern (29 bp):
GCTTAAGCTATGCTTTTGGTTGTTTACAT
Left flanking sequence: Indices 105330 -- 105829
TGAAGTAAGGAATGAATCAAGGGATTCTCACTCCAAATAGGGAATTGTGTCAGTAATAGGATAGA
TGAATCTCAGAAGTCAGAACAAGGCCCTGGCATCTATGCCATGTGAAGCCTCAAGAATAAGTATA
AGGAATAAGGGATGAAAGCCTAGTAAGTAGCTGCAGTCGCAGGTGTCTTTTCAGCAGGTTTTGTT
TTAGGAGTTCTTCTTCGTTTAGTTTCGGAATCAGGTTAGGGAGTTTCACTCTGGGATGGGACAAA
TGCAGCAAAGGCCTCGCCGATTGAGAAGAAAGAGTGTAAAGCACTAAACAAGAGGGAAAACCCTA
TCTATCAGGAGCTATACCTGAATGAAAGCAAGGAAGTGCATCACGGGTGTGGGGCACTACCGCTT
ATCCTTTCACACAACAGTAACACGGGCTCCTCAAGTATCCGCTCTAGTAAGGAAATAGGTGAACA
AGTCTGCTATTCCTGACTTTCAAATAGGTATATCAGGTTGTAATA
Right flanking sequence: Indices 105907 -- 106406
AAGAGAGTATGGACATGACCTTTTTTAGAAAGGGTACTTGCTTAAAGGATTCCCTGTTCTGTCAT
AGAGGGGTGTTGCTATAGCTGTCTTTCTTGTAAGTGGTATCAGTAGTAGTATGTTACCGGTTCAA
CAGGAGTTGGATCCTAAGAAGTTAGGTAAATAGCCATTCTCACCACAGCATATACCTCCACTGCT
TATGTCACTGGTGATGAACTCAATATGACTATTTAAGCTAGCGTGGTAACGCGAGAGTGAGTGAA
AGTGAATCGATTAACGAGACTGAGTTAGAATACCTTAAGCTTGTGGTATGTAATCGCTTATGCGA
AGCTTAAGGGAATTAACAGCTTTCTTCATTCTATTCTCTGGTTTAGTCTCAGAATCAGTTGTAGT
TGAAAGGAAGTTAGCTCAATCAGTTGGAGTTTCCGAATCAGGTTGGGTATTCTGGGATAAGTGCC
ATATAAAGAGTATTCTCACTCTAAGTCAGTAAGTAACTGTCTACT
Found at i:148009 original size:15 final size:15
Alignment explanation
Indices: 147989--148018 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
147979 CTTTGAACTC
*
147989 TTCCTATCCGAGTAG
1 TTCCTATCCCAGTAG
148004 TTCCTATCCCAGTAG
1 TTCCTATCCCAGTAG
148019 GTAGTAGGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.30, G:0.17, T:0.33
Consensus pattern (15 bp):
TTCCTATCCCAGTAG
Left flanking sequence: Indices 147489 -- 147988
CATAAATCTCTTTTCAAGTTGTTTCCAAATCTCAGCAGCAGTACTAATAAAAAGTCTATCCTTTT
TAATAGATTCAGAGACATTGTTATGAAGCCAAGAGATTACCAGGTCATTGCAGACATCCCACTGT
GTTGCATTTGTTTCATCCTCCTTGCTTCTTGTCACTGTTCCATTGAGAAATCCCAGTTTTCTCTT
GGATGAGATCTTTATTTCAAGAGCCCTTCTCCAAGATCTGTAATCAGTTGCACCTTCTAGCTTAG
TAACACTGACTGAATGAGGTCCATCAGATGGGTGAACAAACAGAGGATTTTGCATATCAGCAAAT
GTGAACTTAGACATGGTTGCAGAAAAGAAGAAAAAATACGCGGTTTCATAGCTCGATTTTACTAT
GGGACTTTCTGGATGTTTAAGTATCCCACTAATCTATTCCTACAGTAAACAACAAGCAGTCTGCT
AGCCCAGAGTGGAGGAGAGAGATCCAATTAGCTTACTTTGAACTC
Right flanking sequence: Indices 148019 -- 148518
GTAGTAGGAAGCCAAGCAAGGATAAGAGAGAGATCCTATGGTTAGGCCAGTTAGTTAATGCTGGA
AGGTTATAGAAGACGAAAACGATGGATGTCCTAAGTGACAATGCCATCGGAAAATAGACTCTTTA
TTCGGACTAGCACACGAGGGCGTTAAGCTTACTAACACTAATAAGAAGAAGAACCCTTATTATTA
GAGAAAGGGGATAGAGAATATCAATGCTATATGATTGACCATGAACTTTCTTACCTCACTTGCGG
TTCTCTAAGGTCTTCCAAAAGGCTGATTGAAGGTTAGGTTAGATAAAGAAAGATAAGAATAGAAT
GGATGAGGTAGTTCTTTCTTCCTACTGGTAGGGTTAGATCAAGATAGACTGCGTTAGAAGCCATT
AGAAGTAGCCCTCTCTTGCTATTAGCTCCTGTAGCTAAGCGAACCCAAGCTAATCTCTTTCCTGT
AGGACTCAGCATTCCCTGTGCTGGTAGTGGCATAAGGACTAGCAT
Found at i:175393 original size:24 final size:24
Alignment explanation
Indices: 175361--175408 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
175351 AATCTGAAAC
* *
175361 ATCATTTAATACAGATTTTCCTTT
1 ATCAATTAATACAGATTTACCTTT
* *
175385 ATCAATTAATGCTGATTTACCTTT
1 ATCAATTAATACAGATTTACCTTT
175409 CATTGATATG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.48
Consensus pattern (24 bp):
ATCAATTAATACAGATTTACCTTT
Left flanking sequence: Indices 174861 -- 175360
ATAAGGATTATTATCATAATATAAAAAGAAAAATGGTCATTCAATAGGGGCTCGAGGGGGGAAGG
GACCAAACTACCGAATTTATTAACATACCAATCATGGTTGGACCTACTTCCTCCTATATTATTCT
AATAAAAGTTATACCAATAGTCGTATTCTCGAGTAAGCATGTGGCTTAGCTTAGACGAGAGTAAA
CCCGGACAAGTTTTGTCCAATTCCCGTTGGAGGGATTGGATATAGTCCGGTTGTATGACCCCTTT
AAAAAAATCATGCCGCATAATGACCAAGAATTTTTTTAAATTAGTTAGCCTGGAGATAGTAAGCG
GGTCATCAATATCACCAGGGATCCAAACCGATGTGCTAAAGAAAAAAGGAGATGAGTATACTGAG
GATAGATCTATATCCGGAGGAACCGGAATCCCCTGAAGAATAACTGAAGGCATTTCCGATCCAGA
CGCTCCGGATGGATCCATCATATTGAGTTGGTTGGAATCTGAAAC
Right flanking sequence: Indices 175409 -- 175908
CATTGATATGAAAATTTTTTTGTTTTTTCGCTCCTTCTTGTCTTTGTTCGTTCCTGAGTCCGGAG
AGTTCCTGGAAGTAATACTTGTTCGGAAGTTGCTCCGATAAGAGAAAGAACCTATATTATTAATA
TATCTTGTACGGCTATCTAATCCATCCCACTTGCTGATCGATAAGATGTATCCTAAAGGACTTTA
TTCCGCCCTCTTATGTTATGTCTGCGGCACTGTAGCTCCCGCTCATTGCCCTTTGCTATCGCCTG
GCCTCGGACTCGACTAAGACTTCTTTCAATTGCTTACCCAGCTTCGGGCGGATCATCCTTTAGAA
GTAGAAGTGGAATGGAGGAATGATAGCAAGAAAGAAGAAGATCAATAGTCGAGATAAGAGCGGTC
AGAATAGCTTTTACAATGACAAGAACAATCAACTATTTACTTCCTTAAGAACGTTAATAAAAAAA
CAGAGTTCTGTGGAGCAACCCTCCACTGACGGTCTTGCCCCTATA
Found at i:182197 original size:18 final size:18
Alignment explanation
Indices: 182157--182199 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
182147 CAGAACCTAC
182157 CATAGTCGCGAGTCTGTTT
1 CATAGTCGCGAG-CTGTTT
182176 -ATAGTCGCGA-CTGTTGT
1 CATAGTCGCGAGCTGTT-T
182193 CATAGTC
1 CATAGTC
182200 AACAAGGGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 16 0.73
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.35
Consensus pattern (18 bp):
CATAGTCGCGAGCTGTTT
Left flanking sequence: Indices 181657 -- 182156
TGAGTCATCAAAGCCTTTCTGACTTGGCCTGGCCCGGTCGCCCTACGCGACTGGCGCTTCAAAAG
GTAGTTTCTACTTGCTTACTTGTTAGAGTAAGGCGAAACTCTCGTCGTAGTTTGGCGATCTAAGG
GGCGGACACTTTTTGTTATCTAAAGGCGAAGACTGATCAGTGGGCGAACACTCGGCCCAGCGGGC
GAACATGCCGGGCTCCGGCTCCGCGCACCTGCTGACACCTTTCGAAGCACTTTCTAGTGTGCGCT
TTAGTTTTAGAATGTGTCGTTCATCCTTACTTGTTCCAAGTAAGCAAATAGGAATTACCTTACTT
TAACGAGTAAGTGAATTGGCATTACCTTACTCATTCAAGTAAGCAAGTAGTCGAGTTCCTTCGCC
TTACGAGTCTACAAGCCTTTCTCATTTCAGTGCTCGAGCTTGAGCTGATGTCAGCTCAAGGGGCC
TTTAGTCTTTTGATTAGAGTAGAGGTTTCAGCAAGCAGAACCTAC
Right flanking sequence: Indices 182200 -- 182699
AACAAGGGCGTTTAGGCTTCCAGGAAAAAACTTCGAATTGGGAGGGCGATCCTCCCGGTGAACTG
ACCGTACCCCAAACCGACACAGGTGAACAAGTAGAGTATACTAGGGCGCTTGAGAGAACCATGTC
GAAGGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCCTATCTTTTGATTAG
GAAAGCGGCACATACCAGGGGGTAGCGACTGTTTATTAAAAACACAGGACTCTGCTAAGTGGTAA
CACGATGTATAGAGTCTGACACCTGCCCGGTGCTGGAAGGTCGGAAGGAAAAGTGTTATAAGCTT
TGAATGGAAGCCCCAGTAAACGGCGGCAGTAACTCTAACTGTCCTAAGGTAGCGAAATTCCTTGT
CGCATAAGTAGCGACCTGCACGAATGGTGTAACGACTGCCCCGCTGTCTCCGACATGGACCCGGT
GAAATTGAATTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACG
Found at i:233925 original size:24 final size:21
Alignment explanation
Indices: 233898--233941 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
233888 TATGAAAGCT
233898 TTCCTATTCAAGACATACTACCAA
1 TTCCT-TTCAAG-C-TACTACCAA
*
233922 TTCCTTTGAAGCTACTACCA
1 TTCCTTTCAAGCTACTACCA
233942 CTACCGAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 1 0.05
23 5 0.26
24 5 0.26
ACGTcount: A:0.32, C:0.30, G:0.07, T:0.32
Consensus pattern (21 bp):
TTCCTTTCAAGCTACTACCAA
Left flanking sequence: Indices 233398 -- 233897
GCTTTCTGTGGAAGGTTCGATTACGGGAAGGAAATAGAGGTCACAAGGTAAGGGACCGCTTTCCA
AAAGCATAGCTTTAGCTATTACAACCCTTTTATGCGTGGAAAATGAATCAAAGCAGTTCTCCCTT
ACTCTAAGAAGTAAGCAAGTAGAAACTACCTCGACCTGCGGGTCTTCTAAATAAATGGTTCTTGT
TTATGCTCGTATAGCATAAAAAGGATTCATTGGGGGGGCCATGAGAAATCCACTTTGTACCTTCG
TATCTATAATCTAAACACTTCTCACCTCTGTGCCTTCTTTACTTCCCGGCTCAAGCAAGAGCCAC
AGTGACTGCAACAAGAGGAAAGCCACCTTAATCAGTCAAGCAAGTAATTTGAATAGGGATTATGA
ACAGGCCCTTACCTTGGCCTTAGCCGTTCGATTGATTGTTCTAAAGTCAAGCCTTTCACTTCATT
GTTCAAGCTCTTGAACATGGGTTGAGTTCATACATTATGAAAGCT
Right flanking sequence: Indices 233942 -- 234441
CTACCGAAGCCGGCTTGCTTCTTTTGGTTACCGGTTGGGCTTTCTACCGATGGGAGATTAGTCAG
CGGAAGACTTGCAGGCTAGCTCGTGCAATCAACGAAAAAAGCCTTCTCCATACTCTATCTTCTAA
GTGAATTGGCATTACCTTAGTAAGCTAGCTTTCTAAGCTAAGCAAGCCCGGTTCTCCGGGCACTA
CGGTAGGACGTGGATCGATCATGACGAGAATGGACTTTTCCGTAATGTAATAGAAGAGTCACAGT
CCAGTTCCCCCGGCTATCTCTTTTTTCTTACTAGTAATAATAAGAGATATGAATGAAAGCGGGTA
AGGGCTTGGCTTAACCCTGTGTTCTCTCCTAATCAGGTCGGGGGCGGAGACCGGCTTCATCATTC
AGTGGTAGAGTGTTCATAGAAAAGAAGGCGTCGCCCAACGAGTGGCAGATTTTGGTGGTGGATGC
TAAGGCAGTTCCTTTTTTCTGGTTTCTGGAGAGAATCTCGCTCAT
Found at i:237070 original size:17 final size:17
Alignment explanation
Indices: 237045--237079 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
237035 ACTATTTATG
237045 TTGAACTTTATTCATAC
1 TTGAACTTTATTCATAC
* *
237062 TTGAGCTTTCTTCATAC
1 TTGAACTTTATTCATAC
237079 T
1 T
237080 GAAGTTGCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.09, T:0.49
Consensus pattern (17 bp):
TTGAACTTTATTCATAC
Left flanking sequence: Indices 236545 -- 237044
TGCCGGAAAATCGAAATATACGAGATCACAAACGTGGATTGCTCGCAGCTAAAACAAAAAAGACG
TTAGAAAGCTTTTTGTAAAGATCCCGATACCGGTTTTTCCGGCTCCGTGACCGAAAAAACCTAAC
ATACTAGTAACAGACCGAAAAGGTTTGTGAGGTTCCTGCTAGAGTGACTCTCACTCTAGTGGGGA
GAAGGCAGGTGGGAACGAGCGGAGCGAGAGCAAGTTCCAGTGGCGGGCTGTCTTCATGGTTCCCA
GATCATGGTATAGAACTCGATGTAGCCCTTTTGATGCGGTGCTTTCTCGATCAACTATCTGACTT
TAATGAAGAAAGACAGCTCAACGAAGTGTTTTCAGCTTTGTTTTAGCCGCTGGACATGCCCTTAC
CCTCGAAGGAAGGAAGGGAAAGTTTAAGGGCATGTTCATATCGTTCTAAGGCAAAGGGAAGGTGG
GTCTTTATAGGGTATCAGACTGATAATTTGCTCATACTATTTATG
Right flanking sequence: Indices 237080 -- 237579
GAAGTTGCTCATACTGATCATTTGCTCATACTGATGGTTCGTTAGGCTACTGCTGTCTCTGGTTG
GTTATGCTACTGCTGTGTCTGGTCAGCCTATTACGATCTAGCATTGGCCCCAACAAATTGTCTAG
CCACAGCGAATGAATCAAGCTGGGAAGTAAGGGATCGGAGCTGCTAGCACTGAGTGGTTTGTCTG
AAAATAGGAGATGATTCAATATCAACCTATATCAACTGAACACCCCATAATAGATAGACAATAAG
AAAATCTGAATGATGATTTAGATTAATACCTTCTTGAGATTTTATTACATCTACTCTAAAGGGTA
TCAGAATTGATATATGTACTTTTTTCTTGCTTTTCCCCCATAATGCAAGCATGTAAGCATGTAAA
CAACCTTAATGCTTTGCAAGCACTAAGTAAGTAAACTACCTTTTGTACGATATCAGAAATGACCT
ATGACCCGAAAGAAAAAAGATGTTCAAAACTTCCCTTTAGGAATA
Found at i:237093 original size:15 final size:16
Alignment explanation
Indices: 237073--237113 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
237063 TGAGCTTTCT
237073 TCATACTGA-AGTTGC
1 TCATACTGACAGTTGC
*
237088 TCATACTGATCATTTGC
1 TCATACTGA-CAGTTGC
237105 TCATACTGA
1 TCATACTGA
237114 TGGTTCGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
17 14 0.61
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.37
Consensus pattern (16 bp):
TCATACTGACAGTTGC
Left flanking sequence: Indices 236573 -- 237072
CAAACGTGGATTGCTCGCAGCTAAAACAAAAAAGACGTTAGAAAGCTTTTTGTAAAGATCCCGAT
ACCGGTTTTTCCGGCTCCGTGACCGAAAAAACCTAACATACTAGTAACAGACCGAAAAGGTTTGT
GAGGTTCCTGCTAGAGTGACTCTCACTCTAGTGGGGAGAAGGCAGGTGGGAACGAGCGGAGCGAG
AGCAAGTTCCAGTGGCGGGCTGTCTTCATGGTTCCCAGATCATGGTATAGAACTCGATGTAGCCC
TTTTGATGCGGTGCTTTCTCGATCAACTATCTGACTTTAATGAAGAAAGACAGCTCAACGAAGTG
TTTTCAGCTTTGTTTTAGCCGCTGGACATGCCCTTACCCTCGAAGGAAGGAAGGGAAAGTTTAAG
GGCATGTTCATATCGTTCTAAGGCAAAGGGAAGGTGGGTCTTTATAGGGTATCAGACTGATAATT
TGCTCATACTATTTATGTTGAACTTTATTCATACTTGAGCTTTCT
Right flanking sequence: Indices 237114 -- 237613
TGGTTCGTTAGGCTACTGCTGTCTCTGGTTGGTTATGCTACTGCTGTGTCTGGTCAGCCTATTAC
GATCTAGCATTGGCCCCAACAAATTGTCTAGCCACAGCGAATGAATCAAGCTGGGAAGTAAGGGA
TCGGAGCTGCTAGCACTGAGTGGTTTGTCTGAAAATAGGAGATGATTCAATATCAACCTATATCA
ACTGAACACCCCATAATAGATAGACAATAAGAAAATCTGAATGATGATTTAGATTAATACCTTCT
TGAGATTTTATTACATCTACTCTAAAGGGTATCAGAATTGATATATGTACTTTTTTCTTGCTTTT
CCCCCATAATGCAAGCATGTAAGCATGTAAACAACCTTAATGCTTTGCAAGCACTAAGTAAGTAA
ACTACCTTTTGTACGATATCAGAAATGACCTATGACCCGAAAGAAAAAAGATGTTCAAAACTTCC
CTTTAGGAATAGGCAGTTAAGTCATACCAGACATGAAATCCTCAG
Found at i:237142 original size:25 final size:25
Alignment explanation
Indices: 237114--237167 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
237104 CTCATACTGA
237114 TGGTTCGTTAGGCTACTGCTGTCTC
1 TGGTTCGTTAGGCTACTGCTGTCTC
* * *
237139 TGGTTGGTTATGCTACTGCTGTGTC
1 TGGTTCGTTAGGCTACTGCTGTCTC
237164 TGGT
1 TGGT
237168 CAGCCTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.07, C:0.19, G:0.31, T:0.43
Consensus pattern (25 bp):
TGGTTCGTTAGGCTACTGCTGTCTC
Left flanking sequence: Indices 236614 -- 237113
AAAGCTTTTTGTAAAGATCCCGATACCGGTTTTTCCGGCTCCGTGACCGAAAAAACCTAACATAC
TAGTAACAGACCGAAAAGGTTTGTGAGGTTCCTGCTAGAGTGACTCTCACTCTAGTGGGGAGAAG
GCAGGTGGGAACGAGCGGAGCGAGAGCAAGTTCCAGTGGCGGGCTGTCTTCATGGTTCCCAGATC
ATGGTATAGAACTCGATGTAGCCCTTTTGATGCGGTGCTTTCTCGATCAACTATCTGACTTTAAT
GAAGAAAGACAGCTCAACGAAGTGTTTTCAGCTTTGTTTTAGCCGCTGGACATGCCCTTACCCTC
GAAGGAAGGAAGGGAAAGTTTAAGGGCATGTTCATATCGTTCTAAGGCAAAGGGAAGGTGGGTCT
TTATAGGGTATCAGACTGATAATTTGCTCATACTATTTATGTTGAACTTTATTCATACTTGAGCT
TTCTTCATACTGAAGTTGCTCATACTGATCATTTGCTCATACTGA
Right flanking sequence: Indices 237168 -- 237667
CAGCCTATTACGATCTAGCATTGGCCCCAACAAATTGTCTAGCCACAGCGAATGAATCAAGCTGG
GAAGTAAGGGATCGGAGCTGCTAGCACTGAGTGGTTTGTCTGAAAATAGGAGATGATTCAATATC
AACCTATATCAACTGAACACCCCATAATAGATAGACAATAAGAAAATCTGAATGATGATTTAGAT
TAATACCTTCTTGAGATTTTATTACATCTACTCTAAAGGGTATCAGAATTGATATATGTACTTTT
TTCTTGCTTTTCCCCCATAATGCAAGCATGTAAGCATGTAAACAACCTTAATGCTTTGCAAGCAC
TAAGTAAGTAAACTACCTTTTGTACGATATCAGAAATGACCTATGACCCGAAAGAAAAAAGATGT
TCAAAACTTCCCTTTAGGAATAGGCAGTTAAGTCATACCAGACATGAAATCCTCAGCCTCGAATG
AAAGATATGAGGAATTTCATTGCCTCTCTTTTCTGGCTAAGGGGG
Found at i:243498 original size:15 final size:15
Alignment explanation
Indices: 243480--243513 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
243470 CTTATAACCT
243480 TTTGCATTATCATCA
1 TTTGCATTATCATCA
243495 TTTGCATTATCATCA
1 TTTGCATTATCATCA
243510 TTTG
1 TTTG
243514 ATTTAGGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.50
Consensus pattern (15 bp):
TTTGCATTATCATCA
Left flanking sequence: Indices 242980 -- 243479
CACCCGATAAACAAAATATGCTCAATAATCGGGAATTATCGCTTTTTGATTCAACAATTCCCCAT
TGTTTGGGCTTATACACCATTGGTAGATGGAGTTTTATTGGAAGAAGAGAAGTGTCGAATTTACA
CTCAACGTAGACACCGCTGGAACGATAGTGATAACCCTTCTTTTTTTTTACATCGGTATTATTTT
TAACTGAAGTATCCAAAACCTTAAGGTCTATCAGACCTCGTTCAATCAAAAATTCGATCAAAGCA
GTACCAAAAGGATAACTTATAAGATTTTTTGATTTCTTTTTATTGGCAGCTTTTTCCATCATTTT
ATTACCGTTATGACGAACCAGAGATTCAATCCTTTCGATAACACTAGCACACCTTACACTACTTT
CAATGCTGAACAAACTACTTAAAACATTAATTAAAATCCATTCAATGGTATAAGGTCCAAAAACA
GAAAGCATCTCCATATCTTCAGGAGAAAGTATATTCTTATAACCT
Right flanking sequence: Indices 243514 -- 244013
ATTTAGGGATGATCTTAATCCTTGAAGGTGTATCACTACTCTTATCCACTTTAAATTTACCTTGA
AGATACTCTTTAGCACTAGGTAATTCGCTGTTAATGAACATCTTCATCAGCCCAGGCTGACATTG
ATAGACAGATTTCTCTTCGTATGATAAACAAAGATTTTCTATCTCATTTTGTAAGTCCTTCAAGC
TATTTTCGGTGTGTTCTTTACCAACACGCGCTCTATATTCCTTCCATTTTTTTTTTTTCAATTAA
AGAATTCTGCTATAAGTGGGTTTGATTTTCCAACTATTGTTGTGTCTCTACCCTGGACTATCATC
CCTCTTCAATTTTGCGTAGTCTAACAATAGATCTGATATGATCATTGTGTAGGATAGCTATCGCA
AGATCTCAAGGGTATCAGTAAGAATAGAAGCCATTTCTACTATATCTACCCTGGTTATGAGAGGA
AATCCGCGTTGAAGCATTAATTTCGTACAACCAGAGTATGGCTTC
Found at i:271712 original size:21 final size:21
Alignment explanation
Indices: 271669--271725 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
271659 AAGTTCCCCC
* *
271669 TCTTCTGCATCAAGTTCATCT
1 TCTTCTGCATCAAGATCACCT
* *
271690 TCTTCTTCATCATGATCACCT
1 TCTTCTGCATCAAGATCACCT
*
271711 TCCATCT-CATCAAGA
1 T-CTTCTGCATCAAGA
271726 GCATAAAAGG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.23, C:0.32, G:0.07, T:0.39
Consensus pattern (21 bp):
TCTTCTGCATCAAGATCACCT
Left flanking sequence: Indices 271169 -- 271668
TTAGGTTGTAATAGCTAAAGCTATGCTTTTGGAAGGAGCTATGGAATTTTATTTCTAGTGCTGCT
AGACAGAGCAACACTCCTCTTCTTGTTGGAGGGGATTTCCATTCTATTCTTGAAGCTGAACAAGC
AACGGCTGAGTTAACGCTATAGGCTTTCGCGTCATCCAGCAAGAAAACGGCTGCGCCTTCCGGCG
ATAGAAGGCGCAACGGCTTTCGCGCTAGCGCGCTCACCCGCTGCTTTTATGTTTCTACCCCTATC
ATTCATTTGGTAATTATTCACCCATTGGAAACAATTACCAAACTTTCTGCTAACTTTATTGAAAT
TATGCATTTTAACTCTAGTCTCAACTAAAGCTATAATTTGAATATTATTACTAGAAATAAGCTTT
CTAATTTCACCTATCTTGAGAGGATCATTCAAACCTCTCACATTCCAAGTGCAAATGTTGTGCTT
CATTTATCGGGAGGGATAGTATCTTCAGTAGGGTTAAGTTCCCCC
Right flanking sequence: Indices 271726 -- 272225
GCATAAAAGGTATTGTTTGGACTGGTGGCTCGTTTAGCTTGATTGTGATTTCTTGCTCTTCTGGT
AACCACTTTCCACCCTACATCAGCTCCTGAATTCACCACAGTTGGAGCATGCTCAGGTGTGTTAA
CAGTAGCATTTGTCACTACAACAGGCTGTTTAGGAACCCACACTTTTTTTGGTTTTAGGCAGAGC
TTTTGCTTTTGGTGGATTCCTAACTGTTGGAGCAACTTTGTTGCAGTCATGCCCAGGCATATTAC
AAATCTGACAGTAACTCGGCTTCCAATCATAAAGGACATCCTGCTTGAACACATTACCTTGAGCA
TCTTCAACCCAAACATGATCAGGCAAAGGCATAGTAACATCCATCTCGATTAAAAGCCTAGCAAA
GGAGACTCTACTTTGTTCAGAGGTGCAAGCATCAGCATATAGGGGTACACTCCCATCAAGCTTCC
AATTCTACTCAGTGAATCACTACTCCAACAATGCAAAGGCAGATT
Found at i:307260 original size:18 final size:18
Alignment explanation
Indices: 307220--307262 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
307210 CAGAACCTAC
307220 CATAGTCGCGAGTCTGTTT
1 CATAGTCGCGAG-CTGTTT
307239 -ATAGTCGCGA-CTGTTGT
1 CATAGTCGCGAGCTGTT-T
307256 CATAGTC
1 CATAGTC
307263 AACAAGGGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 16 0.73
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.35
Consensus pattern (18 bp):
CATAGTCGCGAGCTGTTT
Left flanking sequence: Indices 306720 -- 307219
TATGAACCTTGAGTCATCAAAGCCTTTCTGACTTGGCCTGGCCCGGTCGCCCTACGCGACTGGCG
CTTCAAAAGGTAGTTTCTACTTGCTTACTTGTTAGAGTAAGGCGAAACTCTCGTCGTAGTTTGGC
GATCTAAGGGGCGGACACTTTTTGTTATCTAAAGGCGAAGACTGATCAGTGGGCGAACACTCGGC
CCAGCGGGCGAACATGCCGGGCTCCGGCTCCGCGCACCTGCTGACACCTTTCGAAGCACTTTCTA
GTGTGCGCTTTAGTTTTAGAATGTGTCGTTCATCCTTACTTGTTCCAAGTAAGCAAATAGGAATT
ACCTTACTTTAACGAGTAAGTGAATTGGCATTACCTTAGTAAGCAAGTAGTCGAGTTCCTTCGCC
TTACGAGTCTACAAGCCTTTCTCATTTCAGTGCTCGAGCTTGAGCTGATGTCAGCTCAAGGGGCC
TTTAGTCTTTTGATTAGAGTAGAGGTTTCAGCAAGCAGAACCTAC
Right flanking sequence: Indices 307263 -- 307762
AACAAGGGCGTTTAGGCTTCCAGGAAAAAACTTCGAATTGGGAGGGCGATCCTCCCGGTGAACTG
ACCGTACCCCAAACCGACACAGGTGAACAAGTAGAGTATACTAGGGCGCTTGAGAGAACCATGTC
GAAGGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCCTATCTTTTGATTAG
GAAAGCGGCACATACCAGGGGGTAGCGACTGTTTATTAAAAACACAGGACTCTGCTAAGTGGTAA
CACGATGTATAGAGTCTGACACCTGCCCGGTGCTGGAAGGTCGGAAGGAAAAGTGTTATAAGCTT
TGAATGGAAGCCCCAGTAAACGGCGGCAGTAACTCTAACTGTCCTAAGGTAGCGAAATTCCTTGT
CGCATAAGTAGCGACCTGCACGAATGGTGTAACGACTGCCCCGCTGTCTCCGACATGGACCCGGT
GAAATTGAATTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACG
Done.