Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold233
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: 44625
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:4639 original size:23 final size:22
Alignment explanation
Indices: 4609--4651 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
4599 CTTAGTTAAC
4609 ATTTATGT-TACTATTAATGTAAA
1 ATTTATGTATA-TATT-ATGTAAA
4632 ATTTATGTATATATTATGTA
1 ATTTATGTATATATTATGTA
4652 TTTTGAGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 12 0.63
24 2 0.11
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (22 bp):
ATTTATGTATATATTATGTAAA
Found at i:12431 original size:27 final size:27
Alignment explanation
Indices: 12400--12577 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
12390 TAAATTGTAC
12400 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
12427 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
12453 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
12481 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
12509 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
12536 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
12563 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
12578 GACTCAGTAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:12514 original size:82 final size:81
Alignment explanation
Indices: 12401--12556 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
12391 AAATTGTACA
* *
12401 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
12465 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
12482 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
12547 TGCGAGTTGA
65 TGCGAATTGA
12557 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:12568 original size:82 final size:81
Alignment explanation
Indices: 12397--12577 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
12387 GATTAAATTG
* *
12397 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
12462 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
12478 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
12542 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
12560 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
12578 GACTCAGTAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:24867 original size:23 final size:22
Alignment explanation
Indices: 24837--24879 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
24827 CTTAGTTAAC
24837 ATTTATGT-TACTATTAATGTAAA
1 ATTTATGTATA-TATT-ATGTAAA
24860 ATTTATGTATATATTATGTA
1 ATTTATGTATATATTATGTA
24880 TTTTGAGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 12 0.63
24 2 0.11
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (22 bp):
ATTTATGTATATATTATGTAAA
Found at i:32662 original size:27 final size:27
Alignment explanation
Indices: 32631--32808 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
32621 TAAATTGTAC
32631 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
32658 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
32684 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
32712 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
32740 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
32767 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
32794 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
32809 GACTCAGTAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:32745 original size:82 final size:81
Alignment explanation
Indices: 32632--32787 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
32622 AAATTGTACA
* *
32632 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
32696 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
32713 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
32778 TGCGAGTTGA
65 TGCGAATTGA
32788 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:32799 original size:82 final size:81
Alignment explanation
Indices: 32628--32808 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
32618 GATTAAATTG
* *
32628 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
32693 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
32709 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
32773 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
32791 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
32809 GACTCAGTAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.