Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_025931
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: 106809
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:1009 original size:2 final size:2
Alignment explanation
Indices: 1002--1026 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
992 TAGTATAGAC
1002 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1027 TGGCTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Left flanking sequence: Indices 502 -- 1001
GTGTATAGCTTAATTGGTAGAGCATTAGGCTTTTAACTTAATGGTCGCAGGTTCAAGTCCTGCTA
TACCCAAATGTTTTTATAGAAGTTCTCCAGGCAGTTCATATGCACATCAAAATATACATTGTACG
TTGACTCGTCTAGTACGATTAATTACGTTAAACTAAAATATATATATATTTTTAATGTCTTTATG
GCCGCTCACGCCCTTTTTTTTTTTTTTGCGAAAAAAGGCCGCGGGCCTCTAATCTAAGCTTAGAG
TGGGTGAATAGAACGTCGCAGCGTTTGATGCGGCTCTGAAAAGATAGAAGTTAAGTAGGTGTTAC
CAACTACTTAACTATTTAACTTATCTATATTATACAATCTGCAGCAATCCTGCATTCTGCAATTA
AGGAGTTGTTTGATAGCAACTGTGAATAACAGTATAGATATAGATATTTTCATAAAATAAATAAA
TAGCTTATTTATTATTGGCCAAATACATAATATTTTAGTATAGAC
Right flanking sequence: Indices 1027 -- 1526
TGGCTAATAATGCCGTATTGATTGTTGTTTCATTAAAGCTAATTGCTGTTGGAATAAAGGCTCTA
GTAAACTAGAAGTCTCGATTATATGTGCCGCGTTTTGCGCTTTTCGGACAGCATTGCTGGAGCTG
GCAACATGAAGAGCGGATTCCCGTTATTTTCAAATTCCTAAGTAATCTACGTCACCGTCAACATT
AATTCATGAGATATGCGTCTCTTTCATTAATTATCTAAATTATGCCAACCTATCTTATGAAAGCC
AGCCCGGCAGTATAATATAATAAATACTGGTTCGCTCGCGTATATTCCCACATTCATTCGTCAAA
TCAGGCAATCTCTATTGAATAAAAGAGAAGATATGATAATAAATTGAATAAGAAGCTTCCGAGTA
CGCAAATGGTAGGAATACGCCAGAAGTATTGGCAACCTAGAAATAGGCCGGCAAAAGGTACAAGA
ATAGCATGTCGCCACTAGCTGTGTTATGGCATTGGCCGCCTCCAA
Found at i:19045 original size:19 final size:20
Alignment explanation
Indices: 19003--19045 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
18993 GGATGTTGGT
* *
19003 CATGACTTTCGAAAAGTTCC
1 CATGACTATCGAAAAGTTCA
*
19023 CATGACTAT-GAAAATTTCA
1 CATGACTATCGAAAAGTTCA
19042 CATG
1 CATG
19046 GAGGAGTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
CATGACTATCGAAAAGTTCA
Left flanking sequence: Indices 18503 -- 19002
GAGCTAAAAATGCATTTTTTTTCTTTTTTATTTTCATTTTCAATTTTTTTATTTTCAAATTTATG
GGAGACTTGTCATATTTAGAATCTTTCTGTGGTGTGCTTTGTTTTTTATTATTTTGTACTTTTTT
TTTATCATCTAAATATAGGCGCGATACGTGGGCAAACAAGGAGCGTAGGCTTGAAATAAAAAAAA
AAATAAAACCGCGTAAGCGGGCACAGAGAACAAAGCGCCAAGCGCTTTGTTGGCCTAACGAAAAA
AAGAAACAAAGAAATAAAAATAAAGAAAATTTTTACTTTTTATTTCTTTCAAATAAATCAAAAAT
ATTTTTGATTTATTTGCTGCAATTTTTAAAAACCTTCGGCTTCAACGAAAAAGCAAAAATTTTGA
CTTTTTATTCTCTGCTTGCTTTTTCGCAAGCTTATTCTTCCGTCCCTGAAAATATTTGGAATAGA
TTTTTTATTGTTCGCGCCTTACCAAAAAGACTGATGGATGTTGGT
Right flanking sequence: Indices 19046 -- 19545
GAGGAGTTTGCATCTTTATTATGGGTGTTATTTTGTCGTGCGACCCTGCAGCTTATGCGCGACTA
TCTCGTGTTTAAGCTCACGCCATGTAGGCGTGAACTCTGGTTGAATTCGGGTTCTCAATCCCGCC
GCTGAAATGCTCAGTCGACTCTTGAACCTTGATAGGAAGACGGCTTCTTCCTAAATTAGTGCAAA
AGGTTCAAGGATTTAGGATGAACTTAATGTGAATGGGTATAAGCTTCGCTGCTCAAAAACACCCA
GTATTGACCACACTGAGAGACTTGCCAATGGCAAGAAAGGCCGCGGGTAACGCTAGTTGGCGAAA
TGGCGTTAAGCATTCCTAGCGATACGGAAAGAGAGGTCGTGATGATATCATCTACGTTCGTACTG
TTCTTCGTGGAGTAAATCTCACATCCAAAAATCTAACCAGGGAACGGGATAATTCCCATTAAGTT
CCAGTAAAACTGGCAGGCCAGCCGGGCCGTAAGCTAGTGGGAACA
Found at i:37896 original size:24 final size:24
Alignment explanation
Indices: 37869--37914 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
37859 TGCTAATATG
*
37869 AAAAATAAAAAGA-AGACTAAAGA
1 AAAAAAAAAAAGAGAGACTAAAGA
* *
37892 AAAAAAAAATAGAGATACTAAAG
1 AAAAAAAAAAAGAGAGACTAAAG
37915 TGAGCACTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.72, C:0.04, G:0.13, T:0.11
Consensus pattern (24 bp):
AAAAAAAAAAAGAGAGACTAAAGA
Left flanking sequence: Indices 37369 -- 37868
CTCAGTGAAATTGAACTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGTAAGACCCCGTGC
ACCTTTACTATAGCTTTGCAGTGACAACCTTGATTGAATGTGTAGGATAGGTGGGAGGTGGTGAC
GTTGCACGTCACCACCAATCTTGAAATACCACTCTTTCGTCTAAGGATGTCTAACTGCCGAAACA
GAGGCGGGACACTGCATGGTGGTTAGTTTATCTGGGGCGGATGCCTTTAAGTAAGGGGCGCTTGG
ATGGTAACATCCCAGGCCAATCTGGCTATATGCTGAAATCTCCATTTCTTGGACAATCAGCAGGG
AAGGCTGAAAAAAGCCACTGCGAAAAATTTATTTGGCTCCCTCAACGACTGCATGCCAGGTATCC
AACAATGCAATAATGATTGGATAATGATACAGTCTGAACTTCCAGTAAACTGGAAGCCTAAAGTA
CTGTTCACTACGAAACAGTGATAGGACATTCAAACTGCTAATATG
Right flanking sequence: Indices 37915 -- 38414
TGAGCACTTCAATTGAATCAAATACAACGACAAGTATGTTGCAGAGTGAATGAACATAATTGCCC
AAAGAGTAACGGAGGTGTGCGAAGGTAGGCTCGAGCTAATATTATGACAGCTTTAGAGCGTAATG
GTAGAAGCCTGCCTGACTGTGAGACTTACCAGTCGAACAGAGACGAAAGTCGGCCATAGTGATCC
GGGAGTCCCGTGTGGAAGGGCTCTCGCTCAACGGATCAAAGGTACGCCGGGGATAACAGGCTGAT
GACTCCCAAGAGCTCTTATCGACGGAGTCGTTTGGCACCTCGATGTCGACTCATCACATCCTGGG
GTTGAAGAAGGTCCCAAGGGTTCGGTTGTTCGCCGATGAAAGTGGTACGTGAGTTGGGTTTAGAA
CGTCGTGAGACAGTTCGGTTCCTATCTACCGTTGGTGTTTAAGAGAGAACTGCGAGAAGCCAACC
CTAGTACGAGAGGACTGGGTTGGGTCAACCTATGGTGTACCGGTT
Found at i:41602 original size:81 final size:81
Alignment explanation
Indices: 41467--41615 Score: 255
Period size: 81 Copynumber: 1.8 Consensus size: 81
41457 TAAATACTCG
*
41467 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
41532 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* *
41548 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA
41612 CCAA
65 CCAA
41616 ATGAGCTTAG
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
81 62 0.97
82 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (81 bp):
CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
CAAGCGAGTATGCTCA
Left flanking sequence: Indices 40967 -- 41466
ACTTCAATCTACTTTAGTCAATCATATGGATATAAAAAAAGCGGCTAATTTAGAAATAACATCAG
TATTTCAACAACTTTTTGAGCTCATTTTTTACCCATATAATTCTTTATGCTCTTGTTTGAACAAG
CCAATTTGTGCTTCATCCACTATACAAGAAAAGACGCAAGGAGGGTTACTTAGTCACCAGAGGAT
AACCACTTAGTAACTTGGGTCCCCACTTTGCCAATTAAAGCCTGCGGCTTTATTGACAGAACTGG
GGACCCAAGTTTGTAGCGAACCTTTTTTTTTTAATATTTCGGGAACCCCCCAAAAATATTAAAAA
TATTTTTTGCTGCGAAAAACAGCGTCCTCAAAAATTGTAAAGATTTAAACTAATGGATGATTTGT
TTTTTTGGCGAATAACGGGATTCGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTAT
TAAGTTATACTCGCCCTTTTTCCAATTTAGACATTTAAATACTCG
Right flanking sequence: Indices 41616 -- 42115
ATGAGCTTAGGGAAGCGAAGCGCAGAGTGGAAACACAATCTTTTTGTTTCGTTTTATTTTCGCCA
TTTTATTTTATAGACATCCCCGGCTTATTCCGGCTCGGCTGGACCTGCGGCATTTTTTCAAATAT
TTGAAAAATCTATAGTCCCTTGTCTTAAGGCGTGTAGAGACTCCTTTTTTATTGATTTATACTAG
TCTATCTTAGATCCGAGATAGTGCCGAAAAAATGATTCAATTTCATCTAACCACGGTTGCCTTGG
CAATGGCAATTACTCTTATACGATATGCAGAATACTCCAAAACCTCTATTTATTCTATTTAGAAC
TAAAAGAAGATAATGCTTTTTTATAAAAAAATCATAAAGTGCAAAGATTCAAATTTTGAGCTTTG
TTTTACGTAGTTTTGCCATCTATATAATATAATATAGTAAGAAATAATAAGTTGGCGAGGAATTA
AAAAAAATATATATATATATATTTTTTTTTTATTCTGTGGTCCTG
Found at i:85432 original size:22 final size:22
Alignment explanation
Indices: 85404--85447 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
85394 GGCGCTTAGA
*
85404 GGCTGCAAGTGATGAATGTGTG
1 GGCTGCAAATGATGAATGTGTG
* *
85426 GGCTGCAAATTATGCATGTGTG
1 GGCTGCAAATGATGAATGTGTG
85448 AGCGTTAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.11, G:0.36, T:0.30
Consensus pattern (22 bp):
GGCTGCAAATGATGAATGTGTG
Left flanking sequence: Indices 84904 -- 85403
TTGTCAAAAATTTACACAGAGCTTCTTAGCAACTCATTCAGTTTAAAAAAATTCAACTAAAAAAA
AATTTTCAGGCCGCTGGTTTTGTTTCCGTGCTTCCGGGTGGAGGGTGAAAGCGGCCAGGGCGCAG
CCAATTTTTTTTTTTTTCGCCCTCTGGCTACGCCCCTAGTAAGGCTTCGTCATACGAGCGGAGCT
CAAACCCCTCCATCCCCACATTAACAACATGTAGATTTGGAGAAAACAGGAACGCAACAAAACAT
TAACAAAATCGGGCCAGGAACGCTTATTTGTAGAATGTACTATTTGTAGGTTCTGTAGGTTTTTA
CTGCGTAGACGATATTATTAGATATTATTTACGTATGGCGTAGCCGGCAAAGATAACTGGGTGAC
CCAGATTAACTATGGCCTTCGCCTCTAATGCATCTGGCCCTAATCTATTAATCTCGCGCTTAGAT
AGATTAATGCATCAGTCTGGCGCTTTTCACTTTCTGGCGCTTAGA
Right flanking sequence: Indices 85448 -- 85947
AGCGTTAACAAAAACAATATATATTACATGGCTCCAGTCGTCTCAAGTCTATTGCTCCGCAACAA
TTTTTAAAATGAATCAATCATCGAAAATGATTGATAGCTACCTGCACCAAATTATGGCTGGTGTA
ATCAGGAGAAAAGGGATTCGAACCCTTAACCTGTGGTTTTGGAGACCATTGTTCTACCATTGGAA
CTATTCTCCTAAAAAAAAGTGGTTCTTGGTTTATGGAATTTGCACCTATTTGTGTCTATTTAGTA
ATAAGTTTGCTATTTTCTTTGATCTTAATCGGCGTTTCTTTTCTATTTGCTTCTTCTTCTAATTT
GGCTTATCCAGAAAAATTGTCAGCTTACGAATGCGGTTTTGATCCTTTTGATGATGCCAGAAGTC
GTTTTGATATACGATTTTATCTCGTTTCTATTTTATTTATTATATTTGATTTGGAAGTCACCTTT
TTATTTCCTTGGGCAGTTTCTCTTAACAAGATTGGTTTGTTCGGA
Found at i:97511 original size:20 final size:20
Alignment explanation
Indices: 97486--97526 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
97476 TGTTACTACG
97486 TCCCTTTACGCTTTTGTTTT
1 TCCCTTTACGCTTTTGTTTT
97506 TCCCTTTACGCTTTTGTTTT
1 TCCCTTTACGCTTTTGTTTT
97526 T
1 T
97527 ATTATGTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.05, C:0.24, G:0.10, T:0.61
Consensus pattern (20 bp):
TCCCTTTACGCTTTTGTTTT
Left flanking sequence: Indices 96986 -- 97485
TATAGCCCAAAGGTTAGAAAAAAAGCCTAAAAAAATAAATAAATATCTATATACCGCTCTTTGCT
GCGCCTTTTGGAATGAAGGAACGGCGCAACTTACAATTTATTTGCAATGCGAATAAAGTGATTTT
AGCCCGCAAAACAGAATAAAATGCCTTGAGGCCGAAGGCCTCGAGTCCAAGACGATTATTTTGTT
CGTAGCCTTCCAGGTGAACAATGTAATAGATTAAATAGCGTAGCGGAGTTTTGTCCTACACAGCA
CTTTTTTTGTTTTCATGGACTTTGCTAGGCCCGGCTCTTCAGCAAGTGGCTAAAAGAGGAAGAAA
ATAAATTTTTTTTCTGAGCTTTCCCGAATGAATATAATAAAGCGCATGGCGTTAAGGTCGAAGAC
CCCCGAGTGAAGCGCTAAGGCTTCCGGGCTAAAATATTTGCTGCGAAAAGTTAAAAAACATTTTT
TTCGCTTTCTTGGGGCGCGAAGCTAATCAAGAGCTTGTTACTACG
Right flanking sequence: Indices 97527 -- 98026
ATTATGTAAAAGGAAGGCATAACAGCCCGCTATTTATAAATCAGATAGGGGACAGTGCTTCTATT
CGTTTTTATTTTAAATAAAAAAAAAGCAGCCAACTTATGTTTACTCCAAATAGACTCCGTTTTCA
TTACGAAAATTTATTACGTCAAGATTTGTTGTTAAAATTGAATTATGCCAACATTATGGAAGTTC
CTAGATTGTGTAAAATAATAATAGTTCCAAAGGCGCCCTCTAATTTAATAAAAAATGTAAAATTA
GCTATGGAGATTGTTTGTGGTCAAAAATTCATACGAACACGAAGCAGAGATTCGGCAGGAAAGTC
GTTTCGATTTAATAAATTTATATTAAATCAAGAGTCAAAAAAAGACACAGGATATGTCACTTACC
TAGCACAAAGCACTCTACGAGGGCATACCATGTATAATTTCTTGGAAAAACTTATTACGATAATA
TCTTTTTACGATTACCCAGTTAAAGTACAACAAAACTCCATTCAA
Done.