Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3546
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: 37422
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Found at i:15548 original size:13 final size:13
Alignment explanation
Indices: 15530--15554 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15520 TGACCGTGTG
15530 AAAGGACACGGGC
1 AAAGGACACGGGC
15543 AAAGGACACGGG
1 AAAGGACACGGG
15555 TGTGTGTCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.40, T:0.00
Consensus pattern (13 bp):
AAAGGACACGGGC
Found at i:21455 original size:46 final size:46
Alignment explanation
Indices: 21320--21492 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
21310 GTAATTTGTG
*
21320 TGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-ATTGAGACGA
1 TGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTA-CGAGAC-A
* * *
21367 GTGCTAGTGTAAGA-CATGT-TCGGGGCAT-GCATTGGCCT-CGAGACA
1 -TGCCAGTGTAAGACCATGTCT-GGGACATGGCATCGG-CTACGAGACA
*
21412 TAAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCTACGAGACA
1 T--GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTACGAGACA
*
21458 TGTCAGTGTAAGACCATGTCTGGGACATGGCATCG
1 TGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
21493 ACATGGATAC
Statistics
Matches: 106, Mismatches: 10, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
44 12 0.11
45 17 0.16
46 52 0.49
47 13 0.12
48 12 0.11
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.23
Consensus pattern (46 bp):
TGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTACGAGACA
Found at i:29495 original size:16 final size:16
Alignment explanation
Indices: 29471--29521 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
29461 AGTAATCGGC
*
29471 AAATCCCGAAAAGCCG
1 AAATGCCGAAAAGCCG
*
29487 AAATGCCGAAAAGTCG
1 AAATGCCGAAAAGCCG
* *
29503 AAATGCCAAAAAGCTG
1 AAATGCCGAAAAGCCG
29519 AAA
1 AAA
29522 GTTTGGCTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.49, C:0.22, G:0.20, T:0.10
Consensus pattern (16 bp):
AAATGCCGAAAAGCCG
Found at i:29783 original size:28 final size:28
Alignment explanation
Indices: 29734--29817 Score: 150
Period size: 28 Copynumber: 3.0 Consensus size: 28
29724 GAGCATGACT
*
29734 GTAAATGTGATTTGGGCCTAATGGGCCAC
1 GTAAATGTGA-ATGGGCCTAATGGGCCAC
29763 GTAAATGTGAATGGGCCTAATGGGCCAC
1 GTAAATGTGAATGGGCCTAATGGGCCAC
29791 GTAAATGTGAATGGGCCTAATGGGCCA
1 GTAAATGTGAATGGGCCTAATGGGCCA
29818 TATGAAAGAG
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 44 0.81
29 10 0.19
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
GTAAATGTGAATGGGCCTAATGGGCCAC
Found at i:29836 original size:56 final size:56
Alignment explanation
Indices: 29734--29844 Score: 127
Period size: 56 Copynumber: 2.0 Consensus size: 56
29724 GAGCATGACT
* * * *
29734 GTAAATGTGATTTGGGCCTAATGGGCCACGTAAATGTGAATGGGCCTAATGGGCCAC
1 GTAAATGTGATATGGGCCTAATGGGCCACATAAATGAGAATAGGCCT-ATGGGCCAC
* * *
29791 GTAAATGTGA-ATGGGCCTAATGGGCCATATGAAA-GAGATTAGGCCTGTGGGCCA
1 GTAAATGTGATATGGGCCTAATGGGCCACAT-AAATGAGAATAGGCCTATGGGCCA
29845 TATATAGGTA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
55 7 0.15
56 26 0.57
57 13 0.28
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.23
Consensus pattern (56 bp):
GTAAATGTGATATGGGCCTAATGGGCCACATAAATGAGAATAGGCCTATGGGCCAC
Found at i:31526 original size:40 final size:40
Alignment explanation
Indices: 31437--31531 Score: 106
Period size: 40 Copynumber: 2.4 Consensus size: 40
31427 TATCTGGGTA
*
31437 TCGCACACTTAGTGCCTCA--TATAGCCGAAACCATTCTAAT
1 TCGCACACTTAGTG-CT-ATTTATAGCCGAAACCATTCGAAT
* *
31477 TGGCACACTTAGTGCTATTTATAGCCGAAACTATTTCGAA-
1 TCGCACACTTAGTGCTATTTATAGCCGAAACCA-TTCGAAT
*
31517 TCGCTCACTTAGTGC
1 TCGCACACTTAGTGC
31532 CGAACACAGT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
38 1 0.02
39 2 0.04
40 39 0.83
41 5 0.11
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (40 bp):
TCGCACACTTAGTGCTATTTATAGCCGAAACCATTCGAAT
Found at i:33407 original size:27 final size:26
Alignment explanation
Indices: 33376--33553 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 26
33366 TAAATTGTAC
33376 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
33403 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
33429 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
33457 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA--TTGACTATGT
* *
33485 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
33512 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
33539 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
33554 GACTCAATAT
Statistics
Matches: 129, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.01
27 103 0.80
28 25 0.19
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:33492 original size:82 final size:81
Alignment explanation
Indices: 33377--33532 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
33367 AAATTGTACA
* *
33377 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
33441 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
33458 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
33523 TGCGAGTTGA
65 TGCGAATTGA
33533 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:33544 original size:82 final size:81
Alignment explanation
Indices: 33373--33553 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
33363 GATTAAATTG
* *
33373 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
33438 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
33454 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
33518 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
33536 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
33554 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.