Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2183
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: 13846
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:2491 original size:27 final size:27
Alignment explanation
Indices: 2460--2638 Score: 216
Period size: 27 Copynumber: 6.6 Consensus size: 27
2450 TAAATTGTAC
2460 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
2487 TGCACTAAGTGTGCGAATATGAATATG-
1 AGCACTAAGTGTGCG-ATTTGACTATGT
* * *
2514 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
2542 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
2570 AGCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
2597 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
2624 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2639 GACTAATATA
Statistics
Matches: 131, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
27 85 0.65
28 46 0.35
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:2522 original size:55 final size:55
Alignment explanation
Indices: 2460--2638 Score: 229
Period size: 55 Copynumber: 3.3 Consensus size: 55
2450 TAAATTGTAC
* *
2460 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAATATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGT-TGAATATGAT
* * ** *
2516 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATG-T
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAG-TTGAATATGAT
* *
2570 AGCACTAAGTGTGCGATTTGATTATGTAGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
*
2624 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2639 GACTAATATA
Statistics
Matches: 107, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
54 23 0.21
55 83 0.78
56 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
Found at i:2629 original size:82 final size:82
Alignment explanation
Indices: 2457--2638 Score: 242
Period size: 82 Copynumber: 2.2 Consensus size: 82
2447 GATTAAATTG
*
2457 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAATATGAATATGATGCACTA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAATATGAATATGATGCACTA
2522 AGTGTGCGAATTGACCA
66 AGTGTGCGAATTGACCA
* * * *
2539 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCG-ATTTGATTATG-TAGCAC
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAATATGAATATGAT-GCAC
* **
2602 TAAGTGTGCGAGTTGATTA
64 TAAGTGTGCGAATTGACCA
* *
2621 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
2639 GACTAATATA
Statistics
Matches: 86, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
81 1 0.01
82 60 0.70
83 25 0.29
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (82 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAATATGAATATGATGCACTA
AGTGTGCGAATTGACCA
Found at i:4024 original size:40 final size:40
Alignment explanation
Indices: 3980--4056 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
3970 GGGTGTTACA
* *
3980 CGGAATTAGTAACTCGCGCAAATGCCTTCGGGACTTAGCC
1 CGGAATTAATAACTAGCGCAAATGCCTTCGGGACTTAGCC
* *
4020 CGGAATTAATCACTAGCGCAAATGTCTTCGGGACTTA
1 CGGAATTAATAACTAGCGCAAATGCCTTCGGGACTTA
4057 ACCCCGTTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (40 bp):
CGGAATTAATAACTAGCGCAAATGCCTTCGGGACTTAGCC
Found at i:8892 original size:27 final size:27
Alignment explanation
Indices: 8861--9038 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
8851 TAAATTGTAC
8861 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
8888 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * * *
8914 ATGCACTAAGTGTGTGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
8942 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
8970 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
8997 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
9024 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
9039 GACTCAATAT
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 104 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:9029 original size:82 final size:81
Alignment explanation
Indices: 8858--9038 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
8848 GATTAAATTG
* *
8858 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
*
8923 GTGTGTGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
8939 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
9003 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
9021 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
9039 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:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.