Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 163 of 163
Found at i:55380434 original size:21 final size:21
Alignment explanation
Indices: 55380404--55380443 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
55380394 TAATTGAATA
* *
55380404 AATAATAATACATGATAAAGG
1 AATAAAAATACATAATAAAGG
55380425 AATAAAAATACATAATAAA
1 AATAAAAATACATAATAAA
55380444 ATAAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.65, C:0.05, G:0.07, T:0.23
Consensus pattern (21 bp):
AATAAAAATACATAATAAAGG
Found at i:55380508 original size:12 final size:12
Alignment explanation
Indices: 55380492--55380527 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
55380482 AATAACATCT
55380492 ATAATAATAGTA
1 ATAATAATAGTA
*
55380504 GTAATAATAGTA
1 ATAATAATAGTA
55380516 ATAATAATAGTA
1 ATAATAATAGTA
55380528 TTATAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (12 bp):
ATAATAATAGTA
Found at i:55382790 original size:18 final size:18
Alignment explanation
Indices: 55382769--55382806 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
55382759 ATTCAGGTAA
55382769 AACCGAAAAAATTCGGTT
1 AACCGAAAAAATTCGGTT
**
55382787 AACCGACTAAATTCGGTT
1 AACCGAAAAAATTCGGTT
55382805 AA
1 AA
55382807 TTGGTCGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (18 bp):
AACCGAAAAAATTCGGTT
Found at i:55389477 original size:37 final size:37
Alignment explanation
Indices: 55389431--55389506 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
55389421 TGTTAATTTC
*
55389431 AAGAATTATGT-AATGTTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAAAT-TTTTTAATTACGTAGTGATTCA
*
55389468 AAGACTTATGTAAATTTTTTAATTACGTAGTGATTCA
1 AAGAATTATGTAAATTTTTTAATTACGTAGTGATTCA
55389505 AA
1 AA
55389507 TAGGTTAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 33 0.92
38 3 0.08
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.43
Consensus pattern (37 bp):
AAGAATTATGTAAATTTTTTAATTACGTAGTGATTCA
Found at i:55389530 original size:18 final size:18
Alignment explanation
Indices: 55389504--55389541 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
55389494 GTAGTGATTC
*
55389504 AAATAGGTTAAGTTGGTT
1 AAATAGGTTAAGTCGGTT
*
55389522 AAATCGGTTAAGTCGGTT
1 AAATAGGTTAAGTCGGTT
55389540 AA
1 AA
55389542 TTTTTAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.34
Consensus pattern (18 bp):
AAATAGGTTAAGTCGGTT
Found at i:55391790 original size:26 final size:26
Alignment explanation
Indices: 55391744--55391816 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 26
55391734 ACAATTGATA
* *
55391744 AAAACAACT-AAACCTTAAAAATTTAAC
1 AAAACAA-TAAAACCCT-AAAATCTAAC
* **
55391771 AAAACAATAAAATCCTAAAATCTAGT
1 AAAACAATAAAACCCTAAAATCTAAC
*
55391797 AAAACAATGAAACCCTAAAA
1 AAAACAATAAAACCCTAAAA
55391817 ATAAAAAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
26 26 0.68
27 12 0.32
ACGTcount: A:0.60, C:0.18, G:0.03, T:0.19
Consensus pattern (26 bp):
AAAACAATAAAACCCTAAAATCTAAC
Found at i:55391909 original size:28 final size:28
Alignment explanation
Indices: 55391855--55392014 Score: 125
Period size: 28 Copynumber: 5.8 Consensus size: 28
55391845 ATCTTACAAT
*
55391855 AATAACAAAACCTT-AAAAT-TCGATAAG
1 AATAGCAAAACCTTAAAAATCTC-ATAAG
* *
55391882 AATAGCAAAGCCTTAAAAATCTGATAAG
1 AATAGCAAAACCTTAAAAATCTCATAAG
* *
55391910 AATAGCAAAATCC-TAAAAAGCAT-AAAAG
1 AATAGCAAAA-CCTTAAAAATC-TCATAAG
* **
55391938 AACAGTGAAACCTTAAAAATC-CAGTAAG
1 AATAGCAAAACCTTAAAAATCTCA-TAAG
* * * *
55391966 AATAGCAAAGCCCTAAAATTCCCATAA-
1 AATAGCAAAACCTTAAAAATCTCATAAG
*
55391993 AATAACAAAACCTTAAAAATCT
1 AATAGCAAAACCTTAAAAATCT
55392015 AGTTATGTAA
Statistics
Matches: 103, Mismatches: 22, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
27 32 0.31
28 65 0.63
29 6 0.06
ACGTcount: A:0.54, C:0.17, G:0.09, T:0.19
Consensus pattern (28 bp):
AATAGCAAAACCTTAAAAATCTCATAAG
Found at i:55392176 original size:27 final size:27
Alignment explanation
Indices: 55392145--55392219 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 27
55392135 TAACGGAACT
55392145 CTAAAAATCTAATAATATAACAAAACC
1 CTAAAAATCTAATAATATAACAAAACC
* ** *
55392172 TTAAAAATCTTGTAGTAATAACAAAACC
1 CTAAAAATCTAATAAT-ATAACAAAACC
* *
55392200 CTAAAAATCCAATAAAATAA
1 CTAAAAATCTAATAATATAA
55392220 TGAAAATCAA
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
27 16 0.43
28 21 0.57
ACGTcount: A:0.57, C:0.16, G:0.03, T:0.24
Consensus pattern (27 bp):
CTAAAAATCTAATAATATAACAAAACC
Found at i:55392276 original size:29 final size:27
Alignment explanation
Indices: 55392244--55392324 Score: 99
Period size: 29 Copynumber: 2.8 Consensus size: 27
55392234 TAATATATAT
*
55392244 ATAGTGAAACCTTAAAAAGTCTAGTAGAA
1 ATAGTGAAACC-TAAAAA-TCTAGTAAAA
*
55392273 ATAGTGAAATCCTAAAAATCTGGTAAAA
1 ATAGTGAAA-CCTAAAAATCTAGTAAAA
55392301 ATAGTGAAAACCTAAAAAATCTAG
1 ATAGTG-AAACCT-AAAAATCTAG
55392325 ATTGTTTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
28 17 0.37
29 27 0.59
30 2 0.04
ACGTcount: A:0.51, C:0.11, G:0.15, T:0.23
Consensus pattern (27 bp):
ATAGTGAAACCTAAAAATCTAGTAAAA
Found at i:55392303 original size:28 final size:28
Alignment explanation
Indices: 55392244--55392324 Score: 101
Period size: 28 Copynumber: 2.8 Consensus size: 28
55392234 TAATATATAT
*
55392244 ATAGTGAAACCTTAAAAAGTCTAGTAGAA
1 ATAGTGAAACC-TAAAAAGTCTAGTAAAA
*
55392273 ATAGTGAAATCCTAAAAA-TCTGGTAAAA
1 ATAGTGAAA-CCTAAAAAGTCTAGTAAAA
*
55392301 ATAGTGAAAACCTAAAAAATCTAG
1 ATAGTG-AAACCTAAAAAGTCTAG
55392325 ATTGTTTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
28 22 0.48
29 22 0.48
30 2 0.04
ACGTcount: A:0.51, C:0.11, G:0.15, T:0.23
Consensus pattern (28 bp):
ATAGTGAAACCTAAAAAGTCTAGTAAAA
Found at i:55395646 original size:23 final size:23
Alignment explanation
Indices: 55395606--55395657 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
55395596 TTATACGAGC
* *
55395606 TTACTA-TGTAATATCCCGAAAA
1 TTACTACTATAATACCCCGAAAA
55395628 TTACTACTATAATACCCCGAAAA
1 TTACTACTATAATACCCCGAAAA
55395651 TTACTAC
1 TTACTAC
55395658 AGTAAGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (23 bp):
TTACTACTATAATACCCCGAAAA
Found at i:55396128 original size:22 final size:24
Alignment explanation
Indices: 55396101--55396147 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
55396091 TAATTAAATA
*
55396101 AATTTTA-GTTT-ATTAATATTTT
1 AATTTTATGTTTAAATAATATTTT
*
55396123 AATTTTATTTTTAAATAATATTTT
1 AATTTTATGTTTAAATAATATTTT
55396147 A
1 A
55396148 TTTAGTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 3 0.14
24 11 0.52
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
AATTTTATGTTTAAATAATATTTT
Found at i:55400695 original size:26 final size:26
Alignment explanation
Indices: 55400656--55400728 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
55400646 TATTTTCTCG
* * *
55400656 AAATTTTACCAGGGGCAAAATCGTTA
1 AAATTTTACTAGGGGTAAAATCGTCA
* *
55400682 AAATTTTACTAGGGGTAAGATTGTCA
1 AAATTTTACTAGGGGTAAAATCGTCA
**
55400708 AAATTTTGTTAGGGGTAAAAT
1 AAATTTTACTAGGGGTAAAAT
55400729 AGGGATGATA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (26 bp):
AAATTTTACTAGGGGTAAAATCGTCA
Found at i:55404692 original size:12 final size:12
Alignment explanation
Indices: 55404675--55404713 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
55404665 ATGAGTTATT
55404675 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
55404687 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
55404699 TAAGTGAGTAAG
1 TAAGTAAGCAAG
55404711 TAA
1 TAA
55404714 AGAAGTGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:55404701 original size:20 final size:20
Alignment explanation
Indices: 55404676--55404719 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
55404666 TGAGTTATTT
55404676 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
** *
55404696 AAGTAAGTGAGTAAGTAAAG
1 AAGTAAGCAAGTAAGTAAAC
55404716 AAGT
1 AAGT
55404720 GAGTAAAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.05, G:0.25, T:0.18
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:55410001 original size:24 final size:24
Alignment explanation
Indices: 55409969--55410023 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
55409959 TCCGGTGCTT
*
55409969 CCCGTTAATTACTCTTCGGAGCTA
1 CCCGTTAATTACTCTTCAGAGCTA
* *
55409993 CCCGTTAATTTCTCTTTAGAGCTA
1 CCCGTTAATTACTCTTCAGAGCTA
*
55410017 CTCGTTA
1 CCCGTTA
55410024 TAGGCTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.27, G:0.15, T:0.38
Consensus pattern (24 bp):
CCCGTTAATTACTCTTCAGAGCTA
Found at i:55415534 original size:9 final size:9
Alignment explanation
Indices: 55415522--55415567 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
55415512 TTATGTAGTA
55415522 TTTTAAATTT
1 TTTTAAA-TT
55415532 TTTTAAATT
1 TTTTAAATT
*
55415541 TTTTTAATT
1 TTTTAAATT
*
55415550 TTTTAAAAT
1 TTTTAAATT
*
55415559 TTTAAAATT
1 TTTTAAATT
55415568 AAGACTAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
9 24 0.77
10 7 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTAAATT
Found at i:55415537 original size:10 final size:10
Alignment explanation
Indices: 55415522--55415561 Score: 64
Period size: 10 Copynumber: 4.1 Consensus size: 10
55415512 TTATGTAGTA
55415522 TTTTAAATTT
1 TTTTAAATTT
55415532 TTTTAAATTT
1 TTTTAAATTT
55415542 TTTT-AATTT
1 TTTTAAATTT
*
55415551 TTTAAAATTT
1 TTTTAAATTT
55415561 T
1 T
55415562 AAAATTAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
9 8 0.29
10 20 0.71
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTAAATTT
Found at i:55415549 original size:19 final size:19
Alignment explanation
Indices: 55415522--55415561 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
55415512 TTATGTAGTA
*
55415522 TTTTAAATTTTTTTAAATT
1 TTTTAAATTTTTTAAAATT
*
55415541 TTTTTAATTTTTTAAAATT
1 TTTTAAATTTTTTAAAATT
55415560 TT
1 TT
55415562 AAAATTAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTAAATTTTTTAAAATT
Found at i:55454542 original size:97 final size:97
Alignment explanation
Indices: 55454376--55454569 Score: 370
Period size: 97 Copynumber: 2.0 Consensus size: 97
55454366 ATTAAATTAA
*
55454376 TTTGAATATAGGGAATTTCCAAAACTCAATTTTGATACTGAAGCTGTTAGCTTTATGTAAGTTCT
1 TTTGAATATAGGGAATTTCCAAAACTCAATTTTGATACCGAAGCTGTTAGCTTTATGTAAGTTCT
*
55454441 CCGATTTCTTTTTTACTTCTCTCTGTTAATTT
66 CCGATTCCTTTTTTACTTCTCTCTGTTAATTT
55454473 TTTGAATATAGGGAATTTCCAAAACTCAATTTTGATACCGAAGCTGTTAGCTTTATGTAAGTTCT
1 TTTGAATATAGGGAATTTCCAAAACTCAATTTTGATACCGAAGCTGTTAGCTTTATGTAAGTTCT
55454538 CCGATTCCTTTTTTACTTCTCTCTGTTAATTT
66 CCGATTCCTTTTTTACTTCTCTCTGTTAATTT
55454570 CCCCAAAACA
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 95 1.00
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.45
Consensus pattern (97 bp):
TTTGAATATAGGGAATTTCCAAAACTCAATTTTGATACCGAAGCTGTTAGCTTTATGTAAGTTCT
CCGATTCCTTTTTTACTTCTCTCTGTTAATTT
Found at i:55456931 original size:31 final size:32
Alignment explanation
Indices: 55456893--55456961 Score: 122
Period size: 31 Copynumber: 2.2 Consensus size: 32
55456883 TCGACGAATA
*
55456893 TCGGGGGATATCCCTGTCCGGTATAAG-TTTT
1 TCGGGGGATATCCCTGTCCGGTATAAGCTCTT
55456924 TCGGGGGATATCCCTGTCCGGTATAAGCTCTT
1 TCGGGGGATATCCCTGTCCGGTATAAGCTCTT
55456956 TCGGGG
1 TCGGGG
55456962 TATCCCCTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 27 0.75
32 9 0.25
ACGTcount: A:0.14, C:0.22, G:0.32, T:0.32
Consensus pattern (32 bp):
TCGGGGGATATCCCTGTCCGGTATAAGCTCTT
Found at i:55457395 original size:21 final size:22
Alignment explanation
Indices: 55457371--55457412 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
55457361 TTTCACTGCC
*
55457371 CGGTTCAGTTTTTTTA-GCGTA
1 CGGTTCAGATTTTTTATGCGTA
55457392 CGGTTCAGATTTTTTATGCGT
1 CGGTTCAGATTTTTTATGCGT
55457413 CCGGACCGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.14, C:0.14, G:0.24, T:0.48
Consensus pattern (22 bp):
CGGTTCAGATTTTTTATGCGTA
Found at i:55457503 original size:15 final size:15
Alignment explanation
Indices: 55457483--55457534 Score: 104
Period size: 15 Copynumber: 3.5 Consensus size: 15
55457473 CGGTTTAGGT
55457483 ATATCCCTAGGAGGG
1 ATATCCCTAGGAGGG
55457498 ATATCCCTAGGAGGG
1 ATATCCCTAGGAGGG
55457513 ATATCCCTAGGAGGG
1 ATATCCCTAGGAGGG
55457528 ATATCCC
1 ATATCCC
55457535 GGTTGCGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (15 bp):
ATATCCCTAGGAGGG
Found at i:55457547 original size:30 final size:29
Alignment explanation
Indices: 55457466--55457549 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 29
55457456 CTATTCTACA
55457466 GATATCCCGGTTTAGGTATATCCCTAGGAGG
1 GATATCCCGG-TT-GGTATATCCCTAGGAGG
* *
55457497 GATATCCCTAGG-AGGGATATCCCTAGGAGG
1 GATATCCC--GGTTGGTATATCCCTAGGAGG
55457527 GATATCCCGGTTGCGTATATCCC
1 GATATCCCGGTTG-GTATATCCC
55457550 AATCCAAGGA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
28 2 0.04
29 1 0.02
30 32 0.71
31 8 0.18
33 2 0.04
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (29 bp):
GATATCCCGGTTGGTATATCCCTAGGAGG
Done.