Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_026890
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: 106746
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:1003 original size:2 final size:2
Alignment explanation
Indices: 996--1020 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
986 TAGTATAGAC
996 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
1021 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 496 -- 995
TTTTGGGTGTATAGCTTAATTGGTAGAGCATTAGGCTTTTAACTTAATGGTCGCAGGTTCAAGTC
CTGCTATACCCAAATGTTTTTATAGAAGTTCTCCAGGCAGTTCATATGCACATCAAAATATACAT
TGTACGTTGACTCGTCGAGTACGATTAATTACGTTAAACTAAAATATATATATATTTTTAATGTC
TTTATGGCCGCTCACGCCCTTTTTTTTTCTTTGCGAAAAAAGGCCGCGGGCCTCTAAGCTTAGAG
TGGGTGAATAGAACGTCGCAGCGTTTGATGCGGCTCTGAAAAGATAGAAGTTAAGTAGGTGTTAC
CAACTACTTAACTATTTAACTTATCTATATTATACAATCTGCAGCAATCCTGCATTCTGCAATTA
AGGAGTTGTTTGATAGCAACTGTGAATAACAATATAGATATAGATATTTTCATAAAATAAATAAA
TAGCTTATTTATTATTGGCCAAATACATAATATTTTAGTATAGAC
Right flanking sequence: Indices 1021 -- 1520
TGGCTAATAATGCCGTATTGATTGTTGTTTCATTAAAGCTAATTGCTGTTGGAATAAAAGCTCTA
GTAAACTAGAAGTCTCGATTACATGTGCCGCGTTTTGCGCTTTTCGGACAGCATTGCTGGAGCTG
GCAACATGAAGAGCGGATTCCCGTTATTTTCAAATTCCTAAGTAATCTACGTCACCGTCAACCTT
AATTCATGAGATATGCGTCTCTTTCATTAATTATCTAAATTATGCCAACCTATCTTATGAAAGCC
AGCCCGGCAGTATAATATAATAAATACTGGCTCGCTCGCGTATATTCCCACATTCATTCGTCAAA
TCAGGCAATCTCTATTGAATAAAAGAGAAGATATGATAATAAATTGAATAAGAAGCTTCCGAGTA
CGCAAATGGTAGGAATACACCAGAAGTATTGGCAACCTAGAAATAGGCCGGCAAAAGGTACAAGA
ATAGCATGTCGCCACTAGCTGTGTTATGGCATTGGCCGCCTCCAA
Found at i:19063 original size:19 final size:20
Alignment explanation
Indices: 19021--19063 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
19011 GGATGTTGGT
* *
19021 CATGACTTTCGAAAAGTTCC
1 CATGACTATCGAAAAGTTCA
*
19041 CATGACTAT-GAAAATTTCA
1 CATGACTATCGAAAAGTTCA
19060 CATG
1 CATG
19064 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 18521 -- 19020
GAGTTAAAAATGCATTTTTTTTCTTTTTTATTTTCATTTTCAATTTTTTTATTTTCAAATTTATG
GGAGACTTGTCATATTTAGAATCTTTCTGTGGTGTGCTTTGTTTTTTATTATTTTGTACTTTTTT
TTTATCATCTAAATATAGGCGCGATACGTGGGCAAACAAGGAGCGTAGGCTTGAAATAAAAAAAA
AAATAAAACCGCGTAAGCGGGCACAGAGAACAAAGCGCCAAGCGCTTTGTTGGCCTAACGAAAAA
AAGAAACAAAGAAATAAAAATAAAGAAAATTTTTCCTTTTTATTTCTTTCAAATAAATCAAAAAT
ATTTTTGATTTATTTGCTGCAATTTTTAAAAACCTTCGGCTTCAACGAAAAAGCAAAAATTTTGA
CTTTTTATTCTCTGCTTGCTTTTTCGCAAGCTTATTCTTCCGTCCCTGAAAATATTTGGAATAGA
TTTTTTATTGTTCGCGCCTTACCAAAAAGACTGATGGATGTTGGT
Right flanking sequence: Indices 19064 -- 19563
GAGGAGTTTGCATCTTTATTATGGGTGTTATTTTGTCGTGCGACCCTGCAGCTTATGCGCGACTA
TCTCGTGTTTAAGCTCACGCCATGTAGGCGTGAACTCTGGTTGAATTCGGGTTCTCAATCCCGCC
GCTGAAATGCTCAGTCGACTCTTGAACCTTGATAGGAAGACGGCTTCTTCCTAAATTAGTGCAAA
AGGTTCAAGGACTTAGGATGAACTTAATGTGAATGGGTATAAGCTTCGCTGCTCAAAAACACCCA
GTATTGACCACACTGAGAGACTTGCCAATGGCAAGAAAGGCCGCGGGTAACGCTAGTTGGCGAAA
TGGCGTTAAGCATTCCTAGCGATACGGAAAGAGAGGTCGTGATGATATCATCTACGTTCGTACTG
TTCTTCGTGGAGTAAATCTCACATCCAAAAATCTAACCAGGGAACGGGATAATTCCCATTAAGTT
CCAGTAAAACTGGCAGGCCAGCCGGGCCGTAAGCTAGTGGGAACA
Found at i:30524 original size:18 final size:18
Alignment explanation
Indices: 30501--30537 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
30491 TTAGGCTTTT
30501 ATTAAGCAACATACAAAA
1 ATTAAGCAACATACAAAA
30519 ATTAAGCAACATACAAAA
1 ATTAAGCAACATACAAAA
30537 A
1 A
30538 AAACTAAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.16, G:0.05, T:0.16
Consensus pattern (18 bp):
ATTAAGCAACATACAAAA
Left flanking sequence: Indices 30001 -- 30500
GGGCAGGCTGACCCGAAAAGAACTGCGATTCTGCTTTATCATCTCATGCTAAATGAAATATATAT
ATATATATTTCATTTAGCAAGCGCCAGCGGACTCGCGGAGGATTATTGAGCAGGCCGATAGACTA
GCCGACGAATATCTCCTTTTTTATTGCTGCTTTTGTGGCATGCTTCCTTTGCTTTGCTATCGGGT
AAGCCCTGAGCCCCTCGAGCAGTAGTGCCTTGGTTGTAATCACAAGTGATCTAACGGCCGCCCCT
AAGAAAGCCCCAGAAATTCTATGGAAAATAGAAAAAGTAGAAGTAAGCTGTGGCTTATAAATGGT
AAGATGAGGTGATAACGGTCGATTAATTTTCATGTTTTTAGTTGACTTTGATTTTAACTCAAGGT
GACAGGATTTGAACCTATGACCCTCTGTACCCAAAACAGATGCGCTACCAGACTGCGCTACACCT
TGGCTGACGTTCCCTAATGAATATTTGATAAATGTTTAGGCTTTT
Right flanking sequence: Indices 30538 -- 31037
AAACTAAGACTAATAAAAACTCTATTTTTAACGCCACTGAAAAAAAGCACTATCATCTCGTTCAG
TTTCTTTTTTGCTTGAAAATACTTTTTTTGGTGGACGTTTATTATTGTTTCAGCCTTTTAATGCT
CGCTCGAAGAAGGGCAAGTCGATCATTGTCTGCCTTATTTATAAAGCTTTATAATGCAATTACAT
GTAATTGCATTATAAAGTCAAATATTCAAATAAGATATTATTAATCTTTCAGTTATGTTATTAAT
TAAGTAATTCCATGAGAAATAGCCATGAATAATCATAGATAAATAAAAGGGCCCAGATCTAAAGG
TATTCCATAGAATATAGCATACTTACAATTTGCAATCACTACGTAATTCCATAATGCGAAAGAAG
CGTAGCAAGTTTATTGGGCCAAAGGTTCTACATAGTGAATGCATTTTGGTCTATGGGTAGTAAAC
CTTAGTATGATGATAATTTAGTTAGTGATACGCAGAGGTTTTCTA
Found at i:37913 original size:24 final size:24
Alignment explanation
Indices: 37886--37931 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
37876 TGCTAATACG
*
37886 AAAAATAAAAAGA-AGACTAAAGA
1 AAAAAAAAAAAGAGAGACTAAAGA
* *
37909 AAAAAAAAATAGAGATACTAAAG
1 AAAAAAAAAAAGAGAGACTAAAG
37932 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 37386 -- 37885
CTCAGTGAAATTGAACTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGTAAGACCCCGTGC
ACCTTTACTATAGCTTTGCAGTGACAACCTTGATTGAATGTGTAGGATAGGTGGGAGGTGGTGAC
GTTGCACGTCACCACCAATCTTGAAATACCACTCTTTCGTCTAAGGATGTCTAACTGCCGAAACA
GAGGCGGGACACTGCATGGTGGTTAGTTTATCTGGGGCGGATGCCTTTAAGTAAGGGGCGCTTGG
ATGGTAACATCCCAGGCCAATCTGGCTATATGCTGAAATCTCCATTTCTTGGACAATCAGCAGGG
AAGGCTGAAAAAAGCCACTGCGAAAAATTTATTTGGCTCCCTCAACGACTGCATGCCAGGTATCC
AACAATGCAATAATGATTGGATAATGATACAGTCTGAACTTCCAGTAAACTGGAAGCCTAAAGTA
CTGTTCACTACGAAACAGTGATAGGACATTCAAACTGCTAATACG
Right flanking sequence: Indices 37932 -- 38431
TGAGCACTTCAATTGAATCAAATACAACGACAAGTATGTTGCAGAGTGAATGAACATAATTGCCC
AAAGAGTAACGGAGGTGTGCGAAGGTAGGCTCGAGCTAATATTATGACAGCTTTAGAGCGTAATG
GTAGAAGCCTGCCTGACTGTGAGACTTACCAGTCGAACAGAGACGAAAGTCGGCCATAGTGATCC
GGGAGTCCCGTGTGGAAGGGCTCTCGCTCAACGGATCAAAGGTACGCCGGGGATAACAGGCTGAT
GACTCCCAAGAGCTCTTATCGACGGAGTCGTTTGGCACCTCGATGTCGACTCATCACATCCTGGG
GTTGAAGAAGGTCCCAAGGGTTCGGTTGTTCGCCGATGAAAGTGGTACGTGAGTTGGGTTTAGAA
CGTCGTGAGACAGTTCGGTTCCTATCTACCGTTGGTGTTTAAGAGAGAACTGCGAGAAGCCAACC
CTAGTACGAGAGGACTGGGTTGGGTCAACCTATGGTGTACCGGTT
Found at i:41619 original size:81 final size:81
Alignment explanation
Indices: 41484--41632 Score: 255
Period size: 81 Copynumber: 1.8 Consensus size: 81
41474 TAAATACTCG
*
41484 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
41549 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* *
41565 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA
41629 CCAA
65 CCAA
41633 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 40984 -- 41483
AACTTCAATCTACTTTAGTCAATCATATGGATATAAAAAAAGCGGCTAATTTAGAAATAACATCA
GTATTTCAACAACTTTTTGAGCTCATTTTTTACCCATATAATTCTTTATGCTCTTGTTTGAACAA
GCCAATTTGTGCTTCATCCACTATACAAGAAAAGACGCAAGGAGGGTTACTTAGTCACCAGAGGA
TAACCACTTAGTAACTTGGGTCCCCACTTTGCCAATTAAAGCCTGCGGCTTTATTGACAGAACTG
GGGACCCAAGTTTGTAGCGAACCTTTTTTTTTAATATTTCGGGAACCCCCCAAAAATATTAAAAA
TATTTTTTGCTGCGAAAAACAGCGTCCTCAAAAATTAGAAAGATTTAAACTAATGGATGATTTGT
TTTTTTGGCGAATAACGGGATTCGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTAT
TAAGTTATACTCGCCCTTTTTCCAATTTAGACATTTAAATACTCG
Right flanking sequence: Indices 41633 -- 42132
ATGAGCTTAGGGAAGCGAAGCGCAGAGTGGAAACACAATCTTTTTGTTTCGTTTTATTTTCGCCA
TTTTATTTTATAGACATCCCCGGCTTATTCCGGCTCGGCTGGACCTGCGGCATTTTTTCAAATAT
TTGAAAAATCTATAGTCCCTTGTCTTAAGGCGTGTAGAGACTCCTTTTTTATTGATTTATACTAG
TCTATCTTAGATCCGAGATAGTGCCGAAAAAATGATTCAATTTCATCTAACCACGGTTGCCTTGG
CAATGGCAATTACTCTTATACGATATGCAGAATACTCCAAAACCTCTATTTATTCTATTTAGAAC
TAAAAGAAGATAATGCTTTTTTATAAAAAAATCATAAAGTGCAAAGATTCAAATTTTGAGCTTTG
TTTTACGTAGTTTTGCCATCTATATAATATAATATAGTAAGAAATAATAAGTTGGCGAGGAATTA
AAAAAAAATATATATATATATATTTTTTTTTTATTCTGTGGTCCT
Found at i:77989 original size:16 final size:16
Alignment explanation
Indices: 77968--77999 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
77958 AATTATCATT
77968 ATATATTATGGTGTTG
1 ATATATTATGGTGTTG
77984 ATATATTATGGTGTTG
1 ATATATTATGGTGTTG
78000 GCATGGCAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (16 bp):
ATATATTATGGTGTTG
Left flanking sequence: Indices 77468 -- 77967
TGGATCAAACGAAGTTTATCTGGCTATAGTTTACAAGAGATTTTGACCAACAGATTAAAATATAA
AATAAAAAGGAGAGGTTTTGCGCTGTGGTATCTTTGTACTAAATTTATTGGAGCTTCCGCCCTGA
CTAAATAAGTTGTAGTAGAAGAGGTTATTATGGCCCAGGCGTGCCGCCGTCTTCTCTGTTTTATC
AATTTTGTTTCGTTTATCTCTTTATGAATCTGCTGATATTTTGCTGATTCCACATCAGATCCAGC
TACGGCGCAAAAAACGTCTATGCCTAGAACGTATCAATTAGCTACTTTTATGCGCAGATTTATTA
TACTGGGAATTTTTCTAGCGGGCATATCTAATAGTTTTTTTGGTTTCGCTGGTCTTATTATAGCA
AGCGCGTAATCATCCGAACAGTTGTCGTCTACTGTTTCCATTAAATTTGATGATTTACCACATTG
CAAAATTTAATTGACTTCGTTAAGTCTTCCCTAAAAATTATCATT
Right flanking sequence: Indices 78000 -- 78499
GCATGGCAGCGGCTATCAAAAAAGTTGTTTCTGGTATTAGAACCCCAGTCATCGGGGCTTTTGTA
GCTTCTACAGCAATGACGGCCTATAGCAAAATAAAGTAAGTCATAGAGGCGTCTCGAAGCTTAAT
AAGTACAGCAATGCCCGGGCGACCGGCCTGCCCAATATCGTGCCCACATATATGCGCGGAAATAA
TATGATATGAGCTGTTGGTGTACCGCCCAGCGAAGAAGCTTATCCCGGCCGAGTAACCGCTCCTG
TAGACAGCCAGGATGAGTTAGCAATAGCACGGCGCGCCTCCGGCTTTACTTGATAACAAATCGGT
TAGAGCTTTACACGTATAGCGCCTTCGGCCCTTGGCGAGTTCACGGAATATATACTGTTTTTTCA
GCTTATTTCAGTTTTTCGTATATTTCTATTTTACTTAATTGACGGTTTAGAAGAGATGCCATGAA
AAAGTTTCATAGCATAGTCTCAAGATACAATATAACACGTAGAAG
Done.