Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold560
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: 18573
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Found at i:2692 original size:26 final size:27
Alignment explanation
Indices: 2576--2724 Score: 156
Period size: 27 Copynumber: 5.5 Consensus size: 27
2566 ATATTGAGTC
* * * * *
2576 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCAACATAGTCAATT
* *
2603 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCAACATAGTC-AATT
** *
2631 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAACATAGTCAATT
* * *
2658 CGCACACTTAGTGCATCAT-TTCATTT
1 CGCACACTTAGTGCAACATAGTCAATT
*
2684 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCAACATAGTCAATT
2711 CGCACACTTAGTGC
1 CGCACACTTAGTGC
2725 TGTACAATTT
Statistics
Matches: 105, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
26 23 0.22
27 58 0.55
28 24 0.23
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCAACATAGTCAATT
Found at i:2708 original size:53 final size:55
Alignment explanation
Indices: 2576--2725 Score: 162
Period size: 53 Copynumber: 2.8 Consensus size: 55
2566 ATATTGAGTC
* * * * *
2576 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCTACATAGTCAAACT
** * * * **
2631 CGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGC-ATCAT-TTC-ATTT
1 CGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCTA-CATAGTCAAACT
2684 CGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCT
1 CGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCT
2726 GTACAATTTA
Statistics
Matches: 79, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
53 39 0.49
54 3 0.04
55 37 0.47
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCTACATAGTCAAACT
Found at i:7402 original size:27 final size:27
Alignment explanation
Indices: 7371--7544 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
7361 TTAAATTGTC
7371 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
7398 TGCACTAAGTGTGCGAAATGAAT-TG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
7423 ATGCA--AAGTGTGCGAATTGACCATG-
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
7448 CGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
7476 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
7503 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
7530 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
7545 GACTCAAATG
Statistics
Matches: 123, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
24 17 0.14
25 2 0.02
26 15 0.12
27 74 0.60
28 15 0.12
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:15469 original size:27 final size:27
Alignment explanation
Indices: 15438--15611 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
15428 TAAATTGTAC
*
15438 AGCACTAAGTGTGCGATTTGACTATTT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
15465 TGCACTAAGTGTGCGA-ATGA-AATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
15489 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
15517 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
15545 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
15572 AGCACTAAGTGTGCGA-TTGATTA-AT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
15597 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
15612 GAAAATCATT
Statistics
Matches: 126, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
25 32 0.25
26 13 0.10
27 58 0.46
28 23 0.18
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:15499 original size:52 final size:54
Alignment explanation
Indices: 15438--15587 Score: 171
Period size: 55 Copynumber: 2.8 Consensus size: 54
15428 TAAATTGTAC
* *
15438 AGCACTAAGTGTGCGATTTGACTATTTTGCACTAAGTGTGCGA-ATGA-AATG-
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGATGACAATGT
* * ** * *
15489 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATGT
1 A-GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAG-ATGACAATGT
* *
15545 AGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGA
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGA
15588 TTGATTAATA
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
51 1 0.01
52 37 0.46
54 3 0.04
55 39 0.48
56 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.29
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGATGACAATGT
Done.