Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5772.1
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: 18062
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Found at i:1503 original size:29 final size:29
Alignment explanation
Indices: 1470--1526 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1460 TGGTTGTTAA
* *
1470 AGCCACACGGCCGTTTGCCAAGCCGTGTG
1 AGCCACACGGCAGTGTGCCAAGCCGTGTG
* *
1499 AGCCACATGGCAGTGTGGCAAGCCGTGT
1 AGCCACACGGCAGTGTGCCAAGCCGTGT
1527 AACTCACTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.19, C:0.30, G:0.33, T:0.18
Consensus pattern (29 bp):
AGCCACACGGCAGTGTGCCAAGCCGTGTG
Found at i:1623 original size:63 final size:63
Alignment explanation
Indices: 1521--1683 Score: 197
Period size: 63 Copynumber: 2.6 Consensus size: 63
1511 GTGTGGCAAG
*
1521 CCGTGTAACTCACTATTTTGAATTTAAAGTCACACGGGCTAGAGACACGA-GCGTGTGTCTAGA
1 CCGTGTAACTCACTATTTTGAATTTAAAGTCACACGGGCTAGAGACA-GAGGCGTGTGTCCAGA
* * * *
1584 CCGTGTAACTCACTATTTGTGAA-TTAAGGTCACATGGGCTAGAGACATAGGCGTGTGTCCAGG
1 CCGTGTAACTCACTATTT-TGAATTTAAAGTCACACGGGCTAGAGACAGAGGCGTGTGTCCAGA
* * *
1647 CTGTGTAACTCACTGTTTTTGGAATTT-GAGTCACACG
1 CCGTGTAACTCACT-ATTTT-GAATTTAAAGTCACACG
1684 ACTGTGTGTA
Statistics
Matches: 85, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
62 1 0.01
63 65 0.76
64 17 0.20
65 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (63 bp):
CCGTGTAACTCACTATTTTGAATTTAAAGTCACACGGGCTAGAGACAGAGGCGTGTGTCCAGA
Found at i:2307 original size:28 final size:28
Alignment explanation
Indices: 2271--2333 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
2261 TGCATTTGTA
* * *
2271 TCTGAATTTGTAGCTGTATTTAATATGT
1 TCTGTATTTGTAACTGTATCTAATATGT
*
2299 TCTGTATTTGTAACTGTATCTGATATGT
1 TCTGTATTTGTAACTGTATCTAATATGT
2327 TCTGTAT
1 TCTGTAT
2334 CTGTTTCTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.22, C:0.10, G:0.17, T:0.51
Consensus pattern (28 bp):
TCTGTATTTGTAACTGTATCTAATATGT
Found at i:4009 original size:18 final size:18
Alignment explanation
Indices: 3988--4051 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
3978 GATATTTAGT
*
3988 TTATTTGAATTATTCGAG
1 TTATTTGAATTATTAGAG
* *
4006 TTATTTGAATTCA--AAAT
1 TTATTTGAATT-ATTAGAG
* *
4023 TTATTTGAATCATTTGAG
1 TTATTTGAATTATTAGAG
4041 TTATTTGAATT
1 TTATTTGAATT
4052 TAAAAATTCA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
16 1 0.03
17 11 0.31
18 22 0.63
19 1 0.03
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (18 bp):
TTATTTGAATTATTAGAG
Found at i:4026 original size:35 final size:35
Alignment explanation
Indices: 3987--4056 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
3977 TGATATTTAG
*
3987 TTTATTTGAATTATTCGAGTTATTTGAATTCAAAA
1 TTTATTTGAATCATTCGAGTTATTTGAATTCAAAA
* *
4022 TTTATTTGAATCATTTGAGTTATTTGAATTTAAAA
1 TTTATTTGAATCATTCGAGTTATTTGAATTCAAAA
4057 ATTCAACTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.50
Consensus pattern (35 bp):
TTTATTTGAATCATTCGAGTTATTTGAATTCAAAA
Found at i:4754 original size:30 final size:30
Alignment explanation
Indices: 4720--4779 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
4710 ACTTAACAAG
*
4720 CAAATACCTCTAAAATAATAATAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* *
4750 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
4780 TAATAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:9104 original size:30 final size:30
Alignment explanation
Indices: 9068--9128 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
9058 CACGGGCTGG
*
9068 CACATGGGTGTGTGGCTTGCCCGTGTGGAT
1 CACATGGGCGTGTGGCTTGCCCGTGTGGAT
9098 CACATGGGCGTGTGGCTTGCCCGTGTGGAT
1 CACATGGGCGTGTGGCTTGCCCGTGTGGAT
9128 C
1 C
9129 TTGAAAACTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.10, C:0.23, G:0.39, T:0.28
Consensus pattern (30 bp):
CACATGGGCGTGTGGCTTGCCCGTGTGGAT
Found at i:10935 original size:48 final size:48
Alignment explanation
Indices: 10870--10965 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
10860 TTGAATATTA
10870 CGAATATTGGAATGTAAGTATAGGTGTGATCGGTCATAGGAATTTGAT
1 CGAATATTGGAATGTAAGTATAGGTGTGATCGGTCATAGGAATTTGAT
* *
10918 CGAATATTGGATTGTAAGTATATGTGTGATCGGTCATAGGAATTTGAT
1 CGAATATTGGAATGTAAGTATAGGTGTGATCGGTCATAGGAATTTGAT
10966 ATGAAGTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.30, C:0.06, G:0.28, T:0.35
Consensus pattern (48 bp):
CGAATATTGGAATGTAAGTATAGGTGTGATCGGTCATAGGAATTTGAT
Found at i:11969 original size:51 final size:51
Alignment explanation
Indices: 11893--11997 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 51
11883 AGCTTGGAAA
*
11893 TTTAAGAGCAAATTGTAATAATCTGCTTAGGACAGCAGCAGTAGCGTGATT
1 TTTAAGAGCAAATTGTAATAATCTGCTTAGGACAGCAGCAGTAGCATGATT
*
11944 TTTAAGAGCAAATTGTAATAATCTGCTTAGGACAGCAGCAGTGGCATGATT
1 TTTAAGAGCAAATTGTAATAATCTGCTTAGGACAGCAGCAGTAGCATGATT
11995 TTT
1 TTT
11998 GAAAATCACC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.31
Consensus pattern (51 bp):
TTTAAGAGCAAATTGTAATAATCTGCTTAGGACAGCAGCAGTAGCATGATT
Found at i:16277 original size:22 final size:21
Alignment explanation
Indices: 16246--16296 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
16236 AAACATTTGC
* *
16246 TTCTTCTTATTTTTCTTTTTCT
1 TTCTTCTTATCTTTC-CTTTCT
*
16268 TTCTTTTTATCTTTCCTTTCT
1 TTCTTCTTATCTTTCCTTTCT
16289 TTCTTCTT
1 TTCTTCTT
16297 TTTACTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.75
Consensus pattern (21 bp):
TTCTTCTTATCTTTCCTTTCT
Done.