Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_026784
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: 106818
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
TACCCAAATGTTTTTATAGGAGTTCTCCAGGCAGTTCATATGCACATCAAAATATACATTGTACG
TTGACTCGTCTAGTACGATTAATTACGTTAAACTAAAATATATATATATTTTTAATGTCTTTATG
GCCGCTCACGCCCTTTTCTTTTTCTTTGCGAAAAAAGGCCGCGGGCCTCTAATCTAAGCTTAGAG
TGGGTGAAGAGAACGTCGCAGCGTTTGATGCGGCTCTGAAAAGATAGAAGTTAAGTAGGTGTTAC
CAACTACTTAACTATTTAACTTCTCTATATTATACAATCTGCAGCAATCCTGCATTCTGCGATTA
AGGAGTTGTTTGATAGCAACTGTGAATAACAGTATAGATATAGATATTTTCATAAAATAAATAAA
TAGCTTATTTATTATTGGCCAAATACATAATATTTTAGTATAGAC
Right flanking sequence: Indices 1027 -- 1526
TGGCTAATAATGCCGTATTGATTGTTGTTTCATTAAAGCTAATTGCTGTTGGAATAAAGGCTCTA
GTAAACTAGAAGTCTCGATTACATGTGCCGCGTTTTGCGCTTTTCGGACAGCATTGCTGGAGCTG
GCAACATGAAGAGCGGATTCCCGTTATTTTCAAATTCCTAAGTAATCTACGTCACCGTCAACATT
AATTAATGAGATATGCGTCTCTTTCATTAATTATCTAAATTATGCCAACCTATCTTATGAAAGCC
AGCCCGGCAGTATAATATAATAAATACTGGCTCGCTCGCGTATATTCCCACATTCATTCGTCAAA
TCAGGCAATCTCTATTGAATAAAAGAGAAGATATGATAATAAATTGAATAAGAAGCTTCCGAGTA
CGCAAATGGTAGGAATACGCCAGAAGTATTGGCAACCTAGAAATAGGCCGGCAAAAGGTACAAGA
ATAGCATGTCGCCACTAGCTGTGTTATGGCATTGGCCGCCTCCAA
Found at i:19058 original size:19 final size:20
Alignment explanation
Indices: 19016--19058 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
19006 GGATGTTGGT
* *
19016 CATGACTTTCGAAAAGTTCC
1 CATGACTATCGAAAAGTTCA
*
19036 CATGACTAT-GAAAATTTCA
1 CATGACTATCGAAAAGTTCA
19055 CATG
1 CATG
19059 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 18516 -- 19015
GGGCTAAAAATGCATTTTTTTTCTTTTTTATTTTCATTTTCAATTTTTTTATTTTCAAATTTATG
GGAGACTTGTCATATTTAGAATCTTTCTGTGGTGTGCTTTGTTTTTTATTATTTTGTACTTTTTT
TTTATCATCTAAATATAGGCGCGATACGTGGGCAAACAAGGAGCGTAGGCTTGAAATAAAAAAAA
AAATAAAACCGCGTAAGCGGGCACAGAGAACAAAGCGCCAAGCGCTTTGTTGGCCTAACGAAAAA
AAGAAACAAAGAAATAAAAATAAAGAAAATTTTTACTTTTTATTTCTTTCAAATAAATCAAAAAT
ATTTTTGATTTATTTGCTGCAATTTTTAAAAACCTTCGGCTTCAACGAAAAAGCAAAAATTTTGA
CTTTTTATTTTCTGCTTGCTTTTTCGCAAGCTTATTCTTCCGTCCCTGAAAATATTTGGAATAGA
TTTTTTATTGTTCGCGCCTTACCAAAAAGACTGATGGATGTTGGT
Right flanking sequence: Indices 19059 -- 19558
GAGGAGTTTGCATCTTTATTATGGGTGTTATTTTGTCGTGCGACCCTGCAGCTTATGCGCGACTA
TCTCGTGTTTAAGCTCACGCCATGTAGGCGTGAACTCTGGTTGAATTCGGGTTCTCAATCCCGCC
GCTGAAATGCTCAGTCGACTCTTGAACCTTGATAGGAAGACGGCTTCTTCCTAAATTAGTGCAAA
AGGTTCAAGGACTTAGGATGAACTTAATGTGAATGGGTATAAGCTTCGCTGCTCAAAAACACCCA
GTATTGACCACACTGAGAGACTTGCCAATGGCAAGAAAGGCCGCGGGTAACGCTAGTTGGCGAAA
TGGCGTTAAGCATTCCTAGCGATACGGAAAGAGAGGTCGTGATGATATCATCTACGTTCGTACTG
TTCTTCGTGGAGTAAATCTCACATCCAAAAATCTAACCAGGGAACGGGATAATTCCCATTAAGTT
CCAGTAAAACTGGCAGGCCAGCCGGGCCGTAAGCTAGTGGGAACA
Found at i:41613 original size:81 final size:81
Alignment explanation
Indices: 41478--41626 Score: 255
Period size: 81 Copynumber: 1.8 Consensus size: 81
41468 TAAATACTCG
*
41478 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
41543 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* *
41559 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA
41623 CCAA
65 CCAA
41627 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 40978 -- 41477
AACTTCAATCTACTTTAGTCAATCATATGGATATAAAAAAAGCGGCTAATTTAGAAATAACATCA
GTATTTCAACAACTTTTTGAGCTCATTTTTTACCCATATAATTCTTTATGCTCTTGTTTGAACAA
GCCAATTTGTGCTTCATCCACTATACAAGAAAAGACGCAAGGAGGGTTACTTAGTCACCAGAGGA
TAACCACTTAGTAACTTGGGTCCCCACTTTGCCAATTAAAGCCTGCGGCTTTATTGACAGAACTG
GGGACCCAAGTTTGTAGCGAACCTTTTTTTTTCATATTTCGGGAACCCCCCAAAAATATTAAAAA
TATTTTTTGCTGCGAAAAACAGCGTCCTCAAAAATTGTAAAGATTTAAACTAATGGATGATTTGT
TTTTTTGGCGAATAACGGGATTCGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTAT
TAAGTTATACTCGCCCTTTTCCCAATTTAGACATTTAAATACTCG
Right flanking sequence: Indices 41627 -- 42126
ATGAGCTTAGGGAAGCGAAGCGCAGAGTGGAAACACAATCTTTTTGTTTCGTTTTATTTTCGCCA
TTTTATTTTATAGACATCCCCGGCTTATTCCGGCTCGGCTGGACCTGCGGCATTTTTTCAAATAT
TTGAAAAATCTATAGTCCCTTGTCTTAAGGCGTGTAGAGACTCCTTTTTTATTGATTTATACTAG
TCTATCTTAGATCCGAGATAGTGCCGAAAAAATGATTCAATTTCATCTAACCACGGTTGCCTTGG
CAATGGCAATTACTCTTATACGATATGCAGAATACTCCAAAACCTCTATTTATTCTATTTAGAAC
TAAACGAAGATAATGCTTTTTTATAAAAAAATCATAAAGTGCAAAGATTCAAATTTTGAGCTTTG
TTTTACGTAGTTTTGCCATCTATATAATATAATAAGAAATAATAAGTTGGCGAGGAATTAAAAAA
AATATATATATATATATTTTTTTTTTATTCTGTGGTCCTGCAATT
Found at i:85435 original size:22 final size:22
Alignment explanation
Indices: 85407--85450 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
85397 GGCGCTTAGA
*
85407 GGCTGCAAGTGATGAATGTGTG
1 GGCTGCAAATGATGAATGTGTG
* *
85429 GGCTGCAAATTATGCATGTGTG
1 GGCTGCAAATGATGAATGTGTG
85451 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 84907 -- 85406
TTGTCAAAAATTTACACAGAGCTTCTTAGCAACTCATTCAGTTTAAAAAAATTCAACTAAAAAAA
AATTTTCAGGCCGCTGGTTTTGTTTCCGTGCTTCCGGGTGGAGGGTGAAAGCGGCCAGGGCGCAG
CCAATTTTTTTTTTTTTCGCCCTCTGGCTACGCCCCTAGTAAGGCTTCGTCATACGAGCGGAGCT
CAAACCCCTCCATCCCCACATTAACAACATGTAGATTTGGAGAAAACAGGAACGCAACAAAACAT
TAACAAAATCGGGCCAGGAACGCTTATTTGTAGAATGTACTATTTGTAGGTTCTGTAGGTTTTTA
CTGCGTAGACGATATTATTAGATATTATTTACGTATGGCGTAGCCGGCAAAGATAACTGGGTGAC
CCAGATTAACTATGGCCTTCGCCTCTAATGCATCTGGCCCTAATCTATTAATCTCGCGCTTAGAT
AGATTAATGCATCAGTCTGGCGCTTTTCACTTTCTGGCGCTTAGA
Right flanking sequence: Indices 85451 -- 85950
AGCGTTAACAAAAACAATATATATTACATGGCTCCAGTCGTCTCAAGTCTATTGCTCCGCAACAA
TTTTTAAAATGAATCAATCATCGAAAATGATTGATAGCTACCTGCACCAAATTATGGCTGGTGTA
ATCAGGAGAAAAGGGATTCGAACCCTTAACCTGTGGTTTTGGAGACCATTGTTCTACCATTGGAA
CTATTCTCCTAAAAAAAAGTGGTTCTTGGTTTATGGAATTTGCACCTATTTGTGTCTATTTAGTA
ATAAGTTTGCTATTTTCTTTGATCTTAATCGGCGTTTCCTTTCTATTTGCTTCTTCTTCTAATTT
GGCTTATCCAGAGAAATTGTCAGCTTACGAATGCGGTTTTGATCCTTTTGATGATGCCAGAAGTC
GTTTTGATATACGATTTTATCTCGTTTCTATTTTATTTATTATATTTGATTTGGAAGTCACCTTT
TTATTTCCTTGGGCAGTTTCTCTTAACAAGATTGGTTTGTTCGGA
Found at i:97516 original size:20 final size:20
Alignment explanation
Indices: 97491--97531 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
97481 TGTTACTACG
97491 TCCCTTTACGCTTTTGTTTT
1 TCCCTTTACGCTTTTGTTTT
97511 TCCCTTTACGCTTTTGTTTT
1 TCCCTTTACGCTTTTGTTTT
97531 T
1 T
97532 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 96991 -- 97490
TATAGCCCAAAGGTTAGAAAAAAAGCCTAAAAAAATAAATAAATATCTATATACCGCTCTTTGCT
GCGCCTTTTGGAATGAAGGAACGGCGCAACTTACAATTTATTTGCAATGCGAATAAAGTGATTTT
AGCCCGTAAAACAGAATAAAATGGCTTGAGGCCGAAGGCCTCGAGTCCAAGACGATTATTTTGTT
CGTAGCCTTCCAGGTGAACAATGTAATAGATTAAATTGCGTAGCGGAGTTTTGTCCTACACAGCA
CTTTTTTTGTTTTCATGGACTTTGCTAGGCCCGGCTCTTCAGCAAGTGGCTAAAAGAGGAAGAAA
ATAAATTTTTTTTCTGAGCTTTCCCGAATGAATATAATAAAGCGCATGGCGTTAAGGTCGAAGAC
CCCCGAGTGAAGCGCTAAGGCTTCCGGGCTAAAATATTTGCTGCGAAAAGTTAAAAAACATTTTT
TTCGCTTTCTTGGGGCGCGAAGCTAATCAAGAGCTTGTTACTACG
Right flanking sequence: Indices 97532 -- 98031
ATTATGTAAAAGGAAGGCATAACAGCCCGCTATTTATAAATCAGATAGGGGACAGTGCTTCTATT
CGTTTTTATTTTAAATAAAAAAAAAGCAGCCAACTTATGTTTACTCCAAATAGACTCCGTTTTCA
TTACGAAAATTTATTACGTCAAGATTTGTTGTTAAAATTGAATTATGCCAACATTATGGAAGTTC
CTAGATTGTGTAAAATAATAATAGTTCCAAAGGCGCCCTCTAATTTAATAAAAAATGTAAAATTA
GCTATGGAGATTGTTTGTGGTCAAAAATTCATACGAACACGAAGCAGAGATTCGGCAGGAAAGTC
GTTTCGATTTAATAAATTTATATTAAATCAAGAGTCAAAAAAAGACACAGGATATGTCACTTACC
TAGCACAAAGCACTCTACGAGGGCATACCATGTATAATTTCTTGGAAAAACTTATTACGATAATA
TCTTTTTACGATTACCCAGTTAAAGTACAACAAAACTCCATTCAA
Done.