Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5550.1
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: 21396
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:481 original size:11 final size:11
Alignment explanation
Indices: 476--502 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
466 AAAAAAAATG
476 AAAAAACGAAA
1 AAAAAACGAAA
487 AAAAAACGAAA
1 AAAAAACGAAA
498 AAAAA
1 AAAAA
503 TTTCAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.07, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAACGAAA
Found at i:1575 original size:30 final size:28
Alignment explanation
Indices: 1539--1594 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
1529 AAGCAAAAAA
* *
1539 GAAAAAGAGTGTGTGCAAGAAAGTAAAGTT
1 GAAAAAGAGAGTGAGCAA-AAAG-AAAGTT
1569 GAAAAAGAGAGTGAGCAAAAAGAAAG
1 GAAAAAGAGAGTGAGCAAAAAGAAAG
1595 CGTGGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.54, C:0.04, G:0.30, T:0.12
Consensus pattern (28 bp):
GAAAAAGAGAGTGAGCAAAAAGAAAGTT
Found at i:4876 original size:29 final size:29
Alignment explanation
Indices: 4843--4899 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
4833 ATAACCAAAC
*
4843 CTACAAAAACTTTATATCCATAAACCCAA
1 CTACAAAAACTTCATATCCATAAACCCAA
*
4872 CTACATAAACTTCATATCCATAAACCCA
1 CTACAAAAACTTCATATCCATAAACCCA
4900 TCTTTGAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.25
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAA
Found at i:5274 original size:30 final size:30
Alignment explanation
Indices: 5240--5336 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
5230 AGCTCACTCC
5240 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
5270 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
5300 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
5330 TAGCTCA
1 TAGCTCA
5337 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:7927 original size:5 final size:5
Alignment explanation
Indices: 7917--7980 Score: 51
Period size: 5 Copynumber: 12.0 Consensus size: 5
7907 AAGAGAAAAC
*
7917 AAAGA AAAGA AAACGAA AAAGCA AAAGA AGA-A AAAGA AAACGA AAATGA
1 AAAGA AAAGA AAA-G-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AAA-GA
7966 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
7981 GAGGCAAGAG
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
4 4 0.08
5 24 0.49
6 16 0.33
7 5 0.10
ACGTcount: A:0.75, C:0.05, G:0.17, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:7978 original size:27 final size:26
Alignment explanation
Indices: 7910--7980 Score: 88
Period size: 27 Copynumber: 2.7 Consensus size: 26
7900 TCTTGTAAAG
*
7910 AGAAAACAAAGAAAAGAAAACGAAAA
1 AGAAAAAAAAGAAAAGAAAACGAAAA
* *
7936 AGCAAAAGAAGAAAAAGAAAACGAAAA
1 AGAAAAAAAAG-AAAAGAAAACGAAAA
*
7963 TGAAATAAAAAGAAAAGA
1 AGAAA-AAAAAGAAAAGA
7981 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
26 8 0.22
27 24 0.65
28 5 0.14
ACGTcount: A:0.75, C:0.06, G:0.17, T:0.03
Consensus pattern (26 bp):
AGAAAAAAAAGAAAAGAAAACGAAAA
Found at i:8094 original size:30 final size:31
Alignment explanation
Indices: 8060--8130 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
8050 AAAGGAAAAT
*
8060 GAAAAAGAAA-ATGAGATTGAAAAA-AAGAAC
1 GAAAAAGAAATATGAGAGTGAAAAAGAAG-AC
* *
8090 G-AAAAGAAATTTGAGAGTGAAAAAGAAGAT
1 GAAAAAGAAATATGAGAGTGAAAAAGAAGAC
8120 GAAAAAGAAAT
1 GAAAAAGAAAT
8131 TGAAACAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 8 0.23
30 15 0.43
31 12 0.34
ACGTcount: A:0.63, C:0.01, G:0.23, T:0.13
Consensus pattern (31 bp):
GAAAAAGAAATATGAGAGTGAAAAAGAAGAC
Found at i:17585 original size:22 final size:22
Alignment explanation
Indices: 17555--17598 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
17545 TTTGGTATTT
17555 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
17577 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
17599 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:21186 original size:16 final size:16
Alignment explanation
Indices: 21165--21195 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21155 TGCGCTCACG
*
21165 CTCTCTTGCCTTTTAC
1 CTCTCTTGACTTTTAC
21181 CTCTCTTGACTTTTA
1 CTCTCTTGACTTTTA
21196 TCGTAATTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.32, G:0.06, T:0.52
Consensus pattern (16 bp):
CTCTCTTGACTTTTAC
Done.