Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold859
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: 41548
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:8652 original size:24 final size:25
Alignment explanation
Indices: 8625--8678 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
8615 ATGAGTGATA
*
8625 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
8649 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
8673 AAAAAA
1 AAAAAA
8679 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:13789 original size:20 final size:20
Alignment explanation
Indices: 13764--13818 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
13754 TGTGGTTCAA
*
13764 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
13784 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
13804 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
13819 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:14086 original size:17 final size:17
Alignment explanation
Indices: 14066--14106 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
14056 CTAAGCTGTT
14066 ATTTAATGTTCAGCCAA
1 ATTTAATGTTCAGCCAA
14083 ATTTAATGTTCAGCCAA
1 ATTTAATGTTCAGCCAA
14100 ATTTAAT
1 ATTTAAT
14107 TAACTTGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.39
Consensus pattern (17 bp):
ATTTAATGTTCAGCCAA
Found at i:14807 original size:20 final size:20
Alignment explanation
Indices: 14761--14807 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
14751 AGCTCGTTTC
*
14761 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
14781 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
14801 CAGCTCA
1 CAGCTCA
14808 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:16360 original size:20 final size:20
Alignment explanation
Indices: 16314--16360 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
16304 AGCTCGTTTC
*
16314 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
16334 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
16354 CAGCTCA
1 CAGCTCA
16361 ATTTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:17335 original size:11 final size:10
Alignment explanation
Indices: 17319--17348 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
17309 CACGTAACGT
17319 AAAAAAAAGTC
1 AAAAAAAA-TC
17330 AAAAAAAATC
1 AAAAAAAATC
17340 AAAAAAAAT
1 AAAAAAAAT
17349 TGAGTTGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:18605 original size:48 final size:47
Alignment explanation
Indices: 18526--18631 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
18516 GAGTGTCATG
*
18526 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
18574 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
18622 GAAAAAGAAA
1 GAAAAAGAAA
18632 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:20347 original size:20 final size:20
Alignment explanation
Indices: 20301--20347 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
20291 AGCTCGTTTC
*
20301 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
20321 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
20341 CAGCTCA
1 CAGCTCA
20348 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:35722 original size:11 final size:11
Alignment explanation
Indices: 35706--35740 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
35696 AAAAGAGAAT
35706 AAATTCAAAAA
1 AAATTCAAAAA
35717 AAATTC-AAAA
1 AAATTCAAAAA
*
35727 AAATTGAAAAA
1 AAATTCAAAAA
35738 AAA
1 AAA
35741 GAAGTGACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.17
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:35728 original size:10 final size:10
Alignment explanation
Indices: 35706--35739 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
35696 AAAAGAGAAT
35706 AAATTCAAAAA
1 AAATTC-AAAA
35717 AAATTCAAAA
1 AAATTCAAAA
*
35727 AAATTGAAAA
1 AAATTCAAAA
35737 AAA
1 AAA
35740 AGAAGTGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 16 0.73
11 6 0.27
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.18
Consensus pattern (10 bp):
AAATTCAAAA
Found at i:38732 original size:20 final size:19
Alignment explanation
Indices: 38709--38773 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
38699 AAGCTCAAAC
38709 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
38729 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
38749 AAGCTTATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
38769 GAGCT
1 GAGCT
38774 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:40629 original size:14 final size:13
Alignment explanation
Indices: 40592--40666 Score: 53
Period size: 14 Copynumber: 5.4 Consensus size: 13
40582 TTTCAAGCTC
*
40592 TTTTCAATTTCTT
1 TTTTCAATTTTTT
**
40605 TTTTCGCTTTTTCT
1 TTTTCAATTTTT-T
40619 TTTTCAATTTTTT
1 TTTTCAATTTTTT
40632 TCATTCTCAATTTTCTT
1 T--TT-TCAATTTT-TT
*
40649 TTCTTC-ATTTTCT
1 TT-TTCAATTTTTT
40662 TTTTC
1 TTTTC
40667 TCTCACTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
12 3 0.06
13 14 0.28
14 16 0.32
15 5 0.10
16 9 0.18
17 3 0.06
ACGTcount: A:0.11, C:0.19, G:0.01, T:0.69
Consensus pattern (13 bp):
TTTTCAATTTTTT
Found at i:40631 original size:16 final size:16
Alignment explanation
Indices: 40612--40645 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40602 CTTTTTTCGC
* *
40612 TTTTTCTTTTTCAATT
1 TTTTTCATTCTCAATT
40628 TTTTTCATTCTCAATT
1 TTTTTCATTCTCAATT
40644 TT
1 TT
40646 CTTTTCTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTCATTCTCAATT
Found at i:40693 original size:18 final size:17
Alignment explanation
Indices: 40672--40730 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 17
40662 TTTTCTCTCA
40672 CTTTTTCGATTTCTTTTT
1 CTTTTTC-ATTTCTTTTT
*
40690 CTTTTGCAATTTCTTTTT
1 CTTTTTC-ATTTCTTTTT
40708 CTTTTTCATTTTCTTTTT
1 CTTTTTCA-TTTCTTTTT
*
40726 GTTTT
1 CTTTT
40731 CTTTCAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
17 1 0.03
18 35 0.97
ACGTcount: A:0.07, C:0.15, G:0.05, T:0.73
Consensus pattern (17 bp):
CTTTTTCATTTCTTTTT
Found at i:40719 original size:7 final size:6
Alignment explanation
Indices: 40642--40734 Score: 62
Period size: 6 Copynumber: 15.3 Consensus size: 6
40632 TCATTCTCAA
* * ** * *
40642 TTTTCTT TTCTTCA TTTTCT TTTTCT CTCACT TTTTCG ATTTCT TTTTCT
1 TTTTC-T TT-TTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
* * * * *
40692 TTTGCA ATTTCT TTTTCT TTTTCA TTTTCT TTTT-G TTTTCT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TT
40735 CAATTTCTTT
Statistics
Matches: 62, Mismatches: 22, Indels: 5
0.70 0.25 0.06
Matches are distributed among these distances:
5 4 0.06
6 51 0.82
7 4 0.06
8 3 0.05
ACGTcount: A:0.06, C:0.18, G:0.03, T:0.72
Consensus pattern (6 bp):
TTTTCT
Found at i:40730 original size:11 final size:12
Alignment explanation
Indices: 40613--40734 Score: 63
Period size: 12 Copynumber: 9.7 Consensus size: 12
40603 TTTTTTCGCT
40613 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
*
40626 TTTTTTTCATTCTCAA
1 TTTTCTT--TT-TC-A
40642 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
40656 TTTTCTTTTTC-
1 TTTTCTTTTTCA
**
40667 TCTCACTTTTTCGA
1 T-TTTCTTTTTC-A
40681 -TTTCTTTTTC-
1 TTTTCTTTTTCA
** *
40691 TTTTGCAATTTCT
1 TTTT-CTTTTTCA
40704 TTTTCTTTTTCA
1 TTTTCTTTTTCA
*
40716 TTTTCTTTTT-G
1 TTTTCTTTTTCA
40727 TTTTCTTT
1 TTTTCTTT
40735 CAATTTCTTT
Statistics
Matches: 86, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
11 12 0.14
12 39 0.45
13 13 0.15
14 6 0.07
15 5 0.06
16 9 0.10
17 2 0.02
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.70
Consensus pattern (12 bp):
TTTTCTTTTTCA
Done.