Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2833
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: 38804
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:5477 original size:19 final size:21
Alignment explanation
Indices: 5452--5501 Score: 86
Period size: 19 Copynumber: 2.5 Consensus size: 21
5442 TAGTAGTTTC
5452 TTCAAAAAAATTC-AAAAAAA
1 TTCAAAAAAATTCAAAAAAAA
5472 -TCAAAAAAATTCAAAAAAAA
1 TTCAAAAAAATTCAAAAAAAA
5492 TTCAAAAAAA
1 TTCAAAAAAA
5502 AATTTGGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 12 0.43
20 7 0.25
21 9 0.32
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18
Consensus pattern (21 bp):
TTCAAAAAAATTCAAAAAAAA
Found at i:5502 original size:11 final size:10
Alignment explanation
Indices: 5452--5501 Score: 84
Period size: 10 Copynumber: 5.0 Consensus size: 10
5442 TAGTAGTTTC
5452 TTCAAAAAAA
1 TTCAAAAAAA
5462 TTCAAAAAAA
1 TTCAAAAAAA
5472 -TCAAAAAAA
1 TTCAAAAAAA
5481 TTCAAAAAAAA
1 TTC-AAAAAAA
5492 TTCAAAAAAA
1 TTCAAAAAAA
5502 AATTTGGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.24
10 19 0.50
11 10 0.26
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18
Consensus pattern (10 bp):
TTCAAAAAAA
Found at i:5567 original size:17 final size:16
Alignment explanation
Indices: 5543--5583 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
5533 GATATCAAGT
*
5543 TGAAAAAAAAATTTCG
1 TGAAAAAAAAAATTCG
5559 TGAAAAAAAAAATTCG
1 TGAAAAAAAAAATTCG
5575 TGAAAAAAA
1 TGAAAAAAA
5584 GAAGAAGCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.63, C:0.05, G:0.12, T:0.20
Consensus pattern (16 bp):
TGAAAAAAAAAATTCG
Found at i:21888 original size:19 final size:18
Alignment explanation
Indices: 21852--21891 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
21842 TTTCCACTCG
*
21852 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
21870 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
21889 TTT
1 TTT
21892 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:22969 original size:13 final size:13
Alignment explanation
Indices: 22951--23003 Score: 79
Period size: 14 Copynumber: 3.9 Consensus size: 13
22941 TAGCTCTCTC
22951 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
22964 TTTTTTTTTTCACAA
1 -TTTTTTTTTCA-AA
22979 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
*
22992 ATTTTTTTTCAA
1 TTTTTTTTTCAA
23004 CTTGATATCC
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
13 13 0.35
14 22 0.59
15 2 0.05
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:25290 original size:79 final size:81
Alignment explanation
Indices: 25166--25349 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
25156 GCTACTCGTT
* *
25166 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAATGCCTTC-GGATCTTAACCCG
* *
25229 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
25245 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCAC-AATGCCTTCGGATCTTAACCCG
* *
25308 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
25325 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
25350 CATCATTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 24 0.26
79 48 0.53
80 19 0.21
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:25349 original size:40 final size:40
Alignment explanation
Indices: 25147--25349 Score: 229
Period size: 39 Copynumber: 5.1 Consensus size: 40
25137 CGGAATTTAA
** *
25147 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
25187 CCGGTTATAGTAACTCGCAC-AATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
25226 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
25265 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
25305 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
25345 CCGGA
1 CCGGA
25350 CATCATTCAA
Statistics
Matches: 139, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
38 2 0.01
39 68 0.49
40 57 0.41
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:35552 original size:19 final size:20
Alignment explanation
Indices: 35507--35554 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
35497 TTCAAATTTT
35507 TCTCTTTCTTTCCTCTTCCAA
1 TCTCTTT-TTTCCTCTTCCAA
*
35528 TTTCTTTTTTCACTC-T-CAA
1 TCTCTTTTTTC-CTCTTCCAA
35547 TCTCTTTT
1 TCTCTTTT
35555 GGCTCTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 10 0.42
20 5 0.21
21 9 0.38
ACGTcount: A:0.10, C:0.31, G:0.00, T:0.58
Consensus pattern (20 bp):
TCTCTTTTTTCCTCTTCCAA
Done.