Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3674
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: 112541
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Found at i:8141 original size:19 final size:19
Alignment explanation
Indices: 8117--8153 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
8107 TCGAGACTAT
*
8117 GCTGTTGGAATTTTATCTA
1 GCTGTTGGAATTTCATCTA
*
8136 GCTGTTGGTATTTCATCT
1 GCTGTTGGAATTTCATCT
8154 GATTAGGGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.14, G:0.22, T:0.49
Consensus pattern (19 bp):
GCTGTTGGAATTTCATCTA
Found at i:53649 original size:21 final size:21
Alignment explanation
Indices: 53623--53669 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
53613 GTCCATCGAT
53623 TGTTAGTTCTCTTGAAACTTC
1 TGTTAGTTCTCTTGAAACTTC
53644 TGTTAGTTCTCTTGAAACTTC
1 TGTTAGTTCTCTTGAAACTTC
53665 TGTTA
1 TGTTA
53670 CATCCCTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (21 bp):
TGTTAGTTCTCTTGAAACTTC
Found at i:99481 original size:15 final size:15
Alignment explanation
Indices: 99461--99490 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
99451 CCAGTATATT
99461 ATTTTATTTCACTTA
1 ATTTTATTTCACTTA
99476 ATTTTATTTCACTTA
1 ATTTTATTTCACTTA
99491 GCCTGCCTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTATTTCACTTA
Found at i:109857 original size:5 final size:5
Alignment explanation
Indices: 109847--109881 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
109837 AAGAGGGAAG
*
109847 GAAAA GAAAA GAAGAG GAAAA GAAAA GAAAA GAAA
1 GAAAA GAAAA GAA-AA GAAAA GAAAA GAAAA GAAA
109882 TGAGAGAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:109858 original size:21 final size:21
Alignment explanation
Indices: 109834--109880 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
109824 AAGAAAGGGG
* *
109834 AAGAAGAGGGAAGGAAAAGAA
1 AAGAAGAGGAAAAGAAAAGAA
109855 AAGAAGAGGAAAAGAAAAGAA
1 AAGAAGAGGAAAAGAAAAGAA
109876 AAGAA
1 AAGAA
109881 ATGAGAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (21 bp):
AAGAAGAGGAAAAGAAAAGAA
Found at i:109864 original size:16 final size:16
Alignment explanation
Indices: 109845--109875 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
109835 AGAAGAGGGA
109845 AGGAAAAGAAAAGAAG
1 AGGAAAAGAAAAGAAG
109861 AGGAAAAGAAAAGAA
1 AGGAAAAGAAAAGAA
109876 AAGAAATGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (16 bp):
AGGAAAAGAAAAGAAG
Found at i:110171 original size:14 final size:14
Alignment explanation
Indices: 110133--110162 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
110123 AGAAGGGGGG
110133 AAAAAAAAAAGAAA
1 AAAAAAAAAAGAAA
110147 AAAAAAAAAAGAAA
1 AAAAAAAAAAGAAA
110161 AA
1 AA
110163 GAGAGAAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGAAA
Found at i:110310 original size:21 final size:22
Alignment explanation
Indices: 110286--110369 Score: 61
Period size: 21 Copynumber: 3.9 Consensus size: 22
110276 AAAAACGGAA
110286 GAAAAGAAGAAG-GAGAGAGGG
1 GAAAAGAAGAAGAGAGAGAGGG
* *
110307 GAAAA-AAGGAAGGGAG-GATGG
1 GAAAAGAA-GAAGAGAGAGAGGG
* * *
110328 GAAGAAG-GGAAGTGAGAAAGGG
1 GAA-AAGAAGAAGAGAGAGAGGG
110350 G-AAAGAAGAAGAGAAGAGAG
1 GAAAAGAAGAAGAG-AGAGAG
110370 AAGAAAACAA
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
20 5 0.10
21 29 0.60
22 14 0.29
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.02
Consensus pattern (22 bp):
GAAAAGAAGAAGAGAGAGAGGG
Found at i:110373 original size:15 final size:15
Alignment explanation
Indices: 110353--110391 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
110343 GAAAGGGGAA
* *
110353 AGAAGAAGAGAAGAG
1 AGAAGAAAACAAGAG
110368 AGAAGAAAACAAGAG
1 AGAAGAAAACAAGAG
*
110383 AGACGAAAA
1 AGAAGAAAA
110392 AAAAAGACGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.64, C:0.05, G:0.31, T:0.00
Consensus pattern (15 bp):
AGAAGAAAACAAGAG
Found at i:110421 original size:18 final size:19
Alignment explanation
Indices: 110387--110422 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
110377 CAAGAGAGAC
*
110387 GAAAAAAAAAGACGGGAAG
1 GAAAAAAAAAGAAGGGAAG
110406 GAAAAAAAAA-AAGGGAA
1 GAAAAAAAAAGAAGGGAA
110423 AAGGAAGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.69, C:0.03, G:0.28, T:0.00
Consensus pattern (19 bp):
GAAAAAAAAAGAAGGGAAG
Found at i:110447 original size:24 final size:23
Alignment explanation
Indices: 110388--110451 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 23
110378 AAGAGAGACG
**
110388 AAAAAAAAAGACGGGAAGGAAAA
1 AAAAAAAAAGAAAGGAAGGAAAA
**
110411 AAAAAAAGGGAAAAGGAAGGAAAA
1 AAAAAAAAAG-AAAGGAAGGAAAA
110435 AAAAAAAAAGAAAGGAA
1 AAAAAAAAAGAAAGGAA
110452 AAAAAGAGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 15 0.44
24 19 0.56
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAGAAAGGAAGGAAAA
Found at i:110470 original size:15 final size:15
Alignment explanation
Indices: 110403--110462 Score: 52
Period size: 14 Copynumber: 4.1 Consensus size: 15
110393 AAAAGACGGG
110403 AAGGAAAAAAAAA-A
1 AAGGAAAAAAAAAGA
* ** *
110417 AGGGAAAAGGAAGGA
1 AAGGAAAAAAAAAGA
*
110432 AA-AAAAAAAAAAGA
1 AAGGAAAAAAAAAGA
*
110446 AAGGAAAAAAAGAGA
1 AAGGAAAAAAAAAGA
110461 AA
1 AA
110463 TGAGAAAAGA
Statistics
Matches: 33, Mismatches: 11, Indels: 3
0.70 0.23 0.06
Matches are distributed among these distances:
14 19 0.58
15 14 0.42
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAGGAAAAAAAAAGA
Found at i:110598 original size:21 final size:20
Alignment explanation
Indices: 110547--110590 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
110537 AAAAGGGGGG
110547 AAAAAAAGGAGAAGAAAAGGA
1 AAAAAAAGGAGAAGAAAA-GA
*
110568 AAAAAAAGGAGGAGAAAA-A
1 AAAAAAAGGAGAAGAAAAGA
110587 AAAA
1 AAAA
110591 GGAAAGGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
21 17 0.77
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (20 bp):
AAAAAAAGGAGAAGAAAAGA
Found at i:110626 original size:32 final size:32
Alignment explanation
Indices: 110584--110659 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
110574 AGGAGGAGAA
* *
110584 AAAAAAAGGAAAG-GAAAAGGGAAGAGAAATAG
1 AAAAAGAGGAAAGTGAAAAGGGAAAAGAAA-AG
110616 AAAAAGAGGAAAGTGAAAAGGGAAAAGAAAAG
1 AAAAAGAGGAAAGTGAAAAGGGAAAAGAAAAG
**
110648 AAGGAGAGGAAA
1 AAAAAGAGGAAA
110660 AGAGAAGGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 24 0.62
33 15 0.38
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (32 bp):
AAAAAGAGGAAAGTGAAAAGGGAAAAGAAAAG
Found at i:110634 original size:14 final size:13
Alignment explanation
Indices: 110617--110671 Score: 53
Period size: 14 Copynumber: 4.3 Consensus size: 13
110607 GAGAAATAGA
110617 AAAAGAGGAAAGTG
1 AAAAGAGGAAAG-G
*
110631 AAAAG-GGAAAAG
1 AAAAGAGGAAAGG
*
110643 AAAAGAAGGAGAGG
1 AAAAG-AGGAAAGG
110657 AAAAGA-G-AAGG
1 AAAAGAGGAAAGG
110668 AAAA
1 AAAA
110672 ACAAGCGGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
11 7 0.20
12 7 0.20
13 6 0.17
14 15 0.43
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.02
Consensus pattern (13 bp):
AAAAGAGGAAAGG
Found at i:110894 original size:22 final size:22
Alignment explanation
Indices: 110844--110915 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
110834 ATGGAGGAAA
110844 AAAGAAA-AAGAGAAAAAAGAG
1 AAAGAAAGAAGAGAAAAAAGAG
* * * *
110865 GAACAAAGAAGGGAAAAGAGAG
1 AAAGAAAGAAGAGAAAAAAGAG
110887 AAAGAAAGGAA-A-AAAAAAGA-
1 AAAGAAA-GAAGAGAAAAAAGAG
110907 AAAGGAAAG
1 AAA-GAAAG
110916 GAAGGAGGGA
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
20 4 0.10
21 16 0.40
22 17 0.43
23 3 0.08
ACGTcount: A:0.71, C:0.01, G:0.28, T:0.00
Consensus pattern (22 bp):
AAAGAAAGAAGAGAAAAAAGAG
Done.