Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1368
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: 22253
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:1651 original size:82 final size:81
Alignment explanation
Indices: 1535--1690 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
1525 AAATTGTACA
* * * *
1535 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
1599 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
1616 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
1681 TGCGAGTTGA
65 TGCGAATTGA
1691 TTGTATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:1658 original size:55 final size:52
Alignment explanation
Indices: 1534--1687 Score: 175
Period size: 55 Copynumber: 2.9 Consensus size: 52
1524 TAAATTGTAC
* *
1534 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCG-AGTGAATATG
* * *
1587 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-GAA-TATG
* * *
1642 TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGT
1 -AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT
1688 TGATTGTATA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
53 3 0.03
54 36 0.42
55 46 0.53
56 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (52 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTGAATATG
Found at i:1692 original size:27 final size:27
Alignment explanation
Indices: 1535--1690 Score: 163
Period size: 27 Copynumber: 5.7 Consensus size: 27
1525 AAATTGTACA
*
1535 GCACTAAGTGTGCG-ATTCGACTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
* *
1562 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
1589 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
1616 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * *
1644 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
1671 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
1691 TTGTATAGCA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
27 83 0.77
28 25 0.23
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:1701 original size:27 final size:27
Alignment explanation
Indices: 1527--1711 Score: 101
Period size: 27 Copynumber: 6.8 Consensus size: 27
1517 GCGGGATTAA
*
1527 ATTGTACAGCACTAAGTGTGCG-ATTCG
1 ATTGTATAGCACTAAGTGTGCGAATT-G
*
1554 ACTATGT-T-GCACTAAGTGTGCGAAATG
1 A-T-TGTATAGCACTAAGTGTGCGAATTG
1581 AATATG-AT-GCACTAAGTGTGCGAATTG
1 -AT-TGTATAGCACTAAGTGTGCGAATTG
*** *** * *
1608 ACCATGCGGCACTAAGTGTGCGAGTCTA
1 ATTGTATAGCACTAAGTGTGCGAAT-TG
* * * *
1636 ACTATGTAGCACTAAGTGTGCGATTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*** * *
1663 ATTACGTGGCACTAAGTGTGCGAGTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*
1690 ATTGTATAGCACTGAGTGTGCG
1 ATTGTATAGCACTAAGTGTGCG
1712 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 24, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.01
27 96 0.76
28 26 0.21
29 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
ATTGTATAGCACTAAGTGTGCGAATTG
Found at i:1702 original size:82 final size:81
Alignment explanation
Indices: 1527--1711 Score: 210
Period size: 82 Copynumber: 2.3 Consensus size: 81
1517 GCGGGATTAA
* * * *
1527 ATTGTACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCA
1 ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
1592 CTAAGTGTGCGAATTG
66 CTAAGTGTGCGAATTG
*** * * ** *
1608 ACCATGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGG
1 ATTGTACAGCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-G
*
1672 CACTAAGTGTGCGAGTTG
64 CACTAAGTGTGCGAATTG
* *
1690 ATTGTATAGCACTGAGTGTGCG
1 ATTGTACAGCACTAAGTGTGCG
1712 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
81 21 0.26
82 61 0.74
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
CTAAGTGTGCGAATTG
Found at i:9559 original size:82 final size:81
Alignment explanation
Indices: 9443--9598 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
9433 AAATTGTACA
* * * *
9443 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
9507 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
9524 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
9589 TGCGAGTTGA
65 TGCGAATTGA
9599 TTGTATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:9566 original size:55 final size:52
Alignment explanation
Indices: 9442--9595 Score: 175
Period size: 55 Copynumber: 2.9 Consensus size: 52
9432 TAAATTGTAC
* *
9442 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCG-AGTGAATATG
* * *
9495 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-GAA-TATG
* * *
9550 TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGT
1 -AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT
9596 TGATTGTATA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
53 3 0.03
54 36 0.42
55 46 0.53
56 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (52 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTGAATATG
Found at i:9600 original size:27 final size:27
Alignment explanation
Indices: 9443--9598 Score: 163
Period size: 27 Copynumber: 5.7 Consensus size: 27
9433 AAATTGTACA
*
9443 GCACTAAGTGTGCG-ATTCGACTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
* *
9470 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
9497 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
9524 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * *
9552 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
9579 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
9599 TTGTATAGCA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
27 83 0.77
28 25 0.23
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:9609 original size:27 final size:27
Alignment explanation
Indices: 9435--9619 Score: 101
Period size: 27 Copynumber: 6.8 Consensus size: 27
9425 GCGGGATTAA
*
9435 ATTGTACAGCACTAAGTGTGCG-ATTCG
1 ATTGTATAGCACTAAGTGTGCGAATT-G
*
9462 ACTATGT-T-GCACTAAGTGTGCGAAATG
1 A-T-TGTATAGCACTAAGTGTGCGAATTG
9489 AATATG-AT-GCACTAAGTGTGCGAATTG
1 -AT-TGTATAGCACTAAGTGTGCGAATTG
*** *** * *
9516 ACCATGCGGCACTAAGTGTGCGAGTCTA
1 ATTGTATAGCACTAAGTGTGCGAAT-TG
* * * *
9544 ACTATGTAGCACTAAGTGTGCGATTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*** * *
9571 ATTACGTGGCACTAAGTGTGCGAGTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*
9598 ATTGTATAGCACTGAGTGTGCG
1 ATTGTATAGCACTAAGTGTGCG
9620 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 24, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.01
27 96 0.76
28 26 0.21
29 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
ATTGTATAGCACTAAGTGTGCGAATTG
Found at i:9610 original size:82 final size:81
Alignment explanation
Indices: 9435--9619 Score: 210
Period size: 82 Copynumber: 2.3 Consensus size: 81
9425 GCGGGATTAA
* * * *
9435 ATTGTACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCA
1 ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
9500 CTAAGTGTGCGAATTG
66 CTAAGTGTGCGAATTG
*** * * ** *
9516 ACCATGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGG
1 ATTGTACAGCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-G
*
9580 CACTAAGTGTGCGAGTTG
64 CACTAAGTGTGCGAATTG
* *
9598 ATTGTATAGCACTGAGTGTGCG
1 ATTGTACAGCACTAAGTGTGCG
9620 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
81 21 0.26
82 61 0.74
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
CTAAGTGTGCGAATTG
Found at i:20551 original size:50 final size:49
Alignment explanation
Indices: 20378--20566 Score: 236
Period size: 49 Copynumber: 3.8 Consensus size: 49
20368 TAGCCAAAGC
* * * *
20378 TATCTGGTACACATAGTAGCCTGCACATAGTACTACACATGCGACCAAT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
* * *
20427 TATCCGGTACACGTAGTAGCTTGCACTTAGTACTACACATGTGACCAAT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
* *
20476 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCATAGT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCA-A-T
** **
20527 T-TTGGGTACGTATAGTAGCCTGCACTTAGTACTACACACG
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACG
20567 CTACCTCACA
Statistics
Matches: 125, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
49 88 0.70
50 35 0.28
51 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.28
Consensus pattern (49 bp):
TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
Done.