Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold949
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: 28394
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:6610 original size:10 final size:10
Alignment explanation
Indices: 6597--6627 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
6587 TTTTCAAATT
6597 TTTTTTTTGA
1 TTTTTTTTGA
6607 TTTTTTTTCGA
1 TTTTTTTT-GA
6618 TTTTTTTTGA
1 TTTTTTTTGA
6628 ATCTACAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.10, C:0.03, G:0.10, T:0.77
Consensus pattern (10 bp):
TTTTTTTTGA
Found at i:6610 original size:11 final size:11
Alignment explanation
Indices: 6596--6625 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
6586 TTTTTCAAAT
*
6596 TTTTTTTTTGA
1 TTTTTTTTCGA
6607 TTTTTTTTCGA
1 TTTTTTTTCGA
6618 TTTTTTTT
1 TTTTTTTT
6626 GAATCTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTCGA
Found at i:8614 original size:14 final size:14
Alignment explanation
Indices: 8597--8636 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
8587 CGAATGGAAT
*
8597 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
8611 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
8625 GATATGAACAAA
1 GGTAGGAACAAA
8637 TTGGTCAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:10987 original size:23 final size:22
Alignment explanation
Indices: 10935--10987 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
10925 TCCACGTCTT
*
10935 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
10957 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
10980 TTTCTTTT
1 TTTCTTTT
10988 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:14653 original size:18 final size:18
Alignment explanation
Indices: 14632--14675 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
14622 ATACTCACTC
14632 TCTTTTTCAATTT-TCTTT
1 TCTTTTTCAATTTCT-TTT
**
14650 TCTTGATCAATTTCTTTT
1 TCTTTTTCAATTTCTTTT
14668 TCTTTTTC
1 TCTTTTTC
14676 TCATTCTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.11, C:0.18, G:0.02, T:0.68
Consensus pattern (18 bp):
TCTTTTTCAATTTCTTTT
Found at i:15675 original size:30 final size:31
Alignment explanation
Indices: 15641--15737 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
15631 AGCTCACTTC
*
15641 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
15671 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
15701 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
15731 TAGCTCA
1 TAGCTCA
15738 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:19527 original size:17 final size:18
Alignment explanation
Indices: 19490--19527 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
19480 GATTGAGAGT
* *
19490 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
19508 GAAAAGAAAT-TGAAAAA
1 GAAAAGAAATGTGAAAAA
19525 GAA
1 GAA
19528 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.63, C:0.03, G:0.24, T:0.11
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:19540 original size:13 final size:12
Alignment explanation
Indices: 19509--19563 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
19499 TGTGAAACAG
*
19509 AAAAGAAATTGA
1 AAAAGAAGTTGA
19521 AAAAGAAGTTGA
1 AAAAGAAGTTGA
*
19533 AGAAAGAAG-AGA
1 A-AAAGAAGTTGA
*
19545 AAATG-AGTTAGA
1 AAAAGAAGTT-GA
19557 AAAAGAA
1 AAAAGAA
19564 ACAAAAGGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 21 0.62
13 8 0.24
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.13
Consensus pattern (12 bp):
AAAAGAAGTTGA
Found at i:20784 original size:11 final size:10
Alignment explanation
Indices: 20759--20819 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
20749 ACCAATAAAA
20759 TAAA-TGAGC
1 TAAATTGAGC
*
20768 TGAATTGTAGC
1 TAAATTG-AGC
20779 TAAATTGAGC
1 TAAATTGAGC
**
20789 TCGATTGAGC
1 TAAATTGAGC
20799 TGAAA-TGAGC
1 T-AAATTGAGC
*
20809 TCAATTGAGC
1 TAAATTGAGC
20819 T
1 T
20820 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:20820 original size:20 final size:20
Alignment explanation
Indices: 20760--20820 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
20750 CCAATAAAAT
*
20760 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
20780 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
20801 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
20821 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Done.