Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2321
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: 10514
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.34
Found at i:5226 original size:28 final size:28
Alignment explanation
Indices: 5195--5268 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 28
5185 TTAAATATTT
5195 AATATTAGTATAAA-AAT-AAAAAAATAAA
1 AATATT-GTA-AAATAATAAAAAAAATAAA
* *
5223 AATATTTTAAAATAATAAAAAAAATTAA
1 AATATTGTAAAATAATAAAAAAAATAAA
*
5251 AATA-T-AAAAATAATAAAA
1 AATATTGTAAAATAATAAAA
5269 TTATTTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 15 0.37
27 6 0.15
28 20 0.49
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.27
Consensus pattern (28 bp):
AATATTGTAAAATAATAAAAAAAATAAA
Found at i:5260 original size:26 final size:27
Alignment explanation
Indices: 5212--5268 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
5202 GTATAAAAAT
*
5212 AAAAAAATAAAAATATTTTAAAATAATA
1 AAAAAAATAAAAATA-TTAAAAATAATA
*
5240 AAAAAAATTAAAATA-TAAAAATAATA
1 AAAAAAATAAAAATATTAAAAATAATA
5266 AAA
1 AAA
5269 TTATTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 13 0.48
28 14 0.52
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (27 bp):
AAAAAAATAAAAATATTAAAAATAATA
Found at i:6586 original size:28 final size:28
Alignment explanation
Indices: 6545--6602 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
6535 GTAATTAATT
6545 ATTATATAATAATTATATATTTAAT-AAA
1 ATTATATAATAATTAT-TATTTAATGAAA
*
6573 ATTATAATAA-AATTATTATTTTATGAAA
1 ATTAT-ATAATAATTATTATTTAATGAAA
6601 AT
1 AT
6603 AAAATATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 7 0.26
28 16 0.59
29 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
ATTATATAATAATTATTATTTAATGAAA
Found at i:6608 original size:27 final size:28
Alignment explanation
Indices: 6550--6663 Score: 71
Period size: 27 Copynumber: 4.2 Consensus size: 28
6540 TAATTATTAT
*
6550 ATAATAATTATATATTTAATAAAATTATA
1 ATAA-AATTATATATTTAATAAAATTAAA
*
6579 ATAAAATTAT-TATTTTATGAAAA-TAAA
1 ATAAAATTATATATTTAAT-AAAATTAAA
* * ** *
6606 ATATAATTGTA-ATAAAAT-AAATTAAT
1 ATAAAATTATATATTTAATAAAATTAAA
* * *
6632 CT-TAATAATA-ATTTAATAAAA-TAAA
1 ATAAAATTATATATTTAATAAAATTAAA
6657 ATAAAAT
1 ATAAAAT
6664 ATTATGAAAT
Statistics
Matches: 64, Mismatches: 16, Indels: 13
0.69 0.17 0.14
Matches are distributed among these distances:
25 18 0.28
26 10 0.16
27 22 0.34
28 10 0.16
29 4 0.06
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (28 bp):
ATAAAATTATATATTTAATAAAATTAAA
Found at i:6627 original size:25 final size:25
Alignment explanation
Indices: 6598--6665 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 25
6588 TTATTTTATG
6598 AAAATAAAATATAATTGTAATAAAAT
1 AAAATAAAATATAATT-TAATAAAAT
*
6624 AAATTAATCTTAATAATAATTTAATAAAAT
1 AAAATAA----AAT-ATAATTTAATAAAAT
6654 AAAATAAAATAT
1 AAAATAAAATAT
6666 TATGAAATTG
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
25 2 0.06
26 9 0.26
30 18 0.51
31 6 0.17
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (25 bp):
AAAATAAAATATAATTTAATAAAAT
Found at i:6655 original size:16 final size:15
Alignment explanation
Indices: 6600--6654 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 15
6590 ATTTTATGAA
6600 AATAAAATATAATTGT
1 AATAAAATATAATT-T
6616 AATAAAATA-AA-TT
1 AATAAAATATAATTT
**
6629 AATCTTAATAATAATTT
1 AAT-AAAAT-ATAATTT
6646 AATAAAATA
1 AATAAAATA
6655 AAATAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
13 4 0.13
14 4 0.13
15 4 0.13
16 14 0.45
17 5 0.16
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
AATAAAATATAATTT
Found at i:8349 original size:14 final size:15
Alignment explanation
Indices: 8330--8359 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
8320 CAGTTTTATT
8330 AAATAAATT-AAATA
1 AAATAAATTCAAATA
8344 AAATAAATTCAAATA
1 AAATAAATTCAAATA
8359 A
1 A
8360 TTAAACTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATAAATTCAAATA
Found at i:8508 original size:3 final size:3
Alignment explanation
Indices: 8500--8531 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
8490 ATTAATATAG
8500 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
8532 AGAAAACACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:10207 original size:13 final size:14
Alignment explanation
Indices: 10189--10217 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10179 TCACTTTCGA
10189 TAATTC-AAATCAC
1 TAATTCAAAATCAC
10202 TAATTCAAAATCAC
1 TAATTCAAAATCAC
10216 TA
1 TA
10218 TCACCTGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (14 bp):
TAATTCAAAATCAC
Done.