Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1752
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: 21200
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:64 original size:23 final size:24
Alignment explanation
Indices: 32--93 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
22 AGTTTATTAA
*
32 TAATATAAATTTAAAAA-TATTATT
1 TAATA-AAATTTAAAAATTATAATT
**
56 TAATAAAATAAAAAAATTATAATT
1 TAATAAAATTTAAAAATTATAATT
*
80 TATATAAAAATTAA
1 TA-ATAAAATTTAA
94 TATTAAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
23 9 0.30
24 13 0.43
25 8 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
TAATAAAATTTAAAAATTATAATT
Found at i:5686 original size:27 final size:28
Alignment explanation
Indices: 5651--5718 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 28
5641 TTTTATTTTA
5651 TTATAATTATATTTAAAATA-TAATATA-T
1 TTAT-ATTATATTTAAAATATTAATA-ACT
*
5679 TTATATTA-ATTTTAATATATTAATAACT
1 TTATATTATA-TTTAAAATATTAATAACT
5707 TATATATTATAT
1 T-TATATTATAT
5719 AAATTTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
26 1 0.03
27 13 0.38
28 11 0.32
29 8 0.24
30 1 0.03
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (28 bp):
TTATATTATATTTAAAATATTAATAACT
Found at i:5696 original size:20 final size:20
Alignment explanation
Indices: 5671--5761 Score: 70
Period size: 20 Copynumber: 4.8 Consensus size: 20
5661 ATTTAAAATA
5671 TAATATATTTATATTAATTT
1 TAATATATTTATATTAATTT
*
5691 TAATATA-TTA-A-TAA-CT
1 TAATATATTTATATTAATTT
*
5707 T-ATATA-TTATATAAATTT
1 TAATATATTTATATTAATTT
* *
5725 TAAAAATATTAATATTATATTT
1 T-AATATATTTATATTA-ATTT
5747 TAAT-TATTTAATATT
1 TAATATATTT-ATATT
5762 TATTATATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
15 8 0.15
16 3 0.05
17 5 0.09
18 3 0.05
19 3 0.05
20 15 0.27
21 13 0.24
22 5 0.09
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (20 bp):
TAATATATTTATATTAATTT
Found at i:5746 original size:22 final size:20
Alignment explanation
Indices: 5721--5765 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
5711 TATTATATAA
5721 ATTTTAAAAATATTAATATTAT
1 ATTTTAAAAAT-TTAATATT-T
**
5743 ATTTTAATTATTTAATATTT
1 ATTTTAAAAATTTAATATTT
5763 ATT
1 ATT
5766 ATATTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 8 0.38
22 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTTAAAAATTTAATATTT
Found at i:5765 original size:20 final size:21
Alignment explanation
Indices: 5733--5779 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
5723 TTTAAAAATA
*
5733 TTAATATTATATTTTAATTAT
1 TTAATATTATATTATAATTAT
*
5754 TTAATATT-TATTATATTTAT
1 TTAATATTATATTATAATTAT
*
5774 ATAATA
1 TTAATA
5780 ATATTTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTAATATTATATTATAATTAT
Found at i:6764 original size:36 final size:33
Alignment explanation
Indices: 6693--6765 Score: 83
Period size: 35 Copynumber: 2.1 Consensus size: 33
6683 TTAAAACAGG
* * *
6693 AAACAACACCATAAAATAAGAAATAAAAAACAA
1 AAACAACACCAAAAAAAAAGAAAAAAAAAACAA
*
6726 AAACAACGACCAAAAAAAAAAGAAAAAGAAAAAGAA
1 AAACAAC-ACC-AAAAAAAAAGAAAAA-AAAAACAA
6762 AAAC
1 AAAC
6766 TATAAACATC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 7 0.21
34 3 0.09
35 12 0.36
36 11 0.33
ACGTcount: A:0.75, C:0.14, G:0.07, T:0.04
Consensus pattern (33 bp):
AAACAACACCAAAAAAAAAGAAAAAAAAAACAA
Found at i:9048 original size:2 final size:2
Alignment explanation
Indices: 9041--9070 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9031 GGCTCGCTAC
9041 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
9071 TTATTGCCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:10526 original size:2 final size:2
Alignment explanation
Indices: 10519--10546 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10509 AAAGGAAACT
10519 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
10547 GAAGGGAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13164 original size:14 final size:14
Alignment explanation
Indices: 13116--13156 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
13106 ATATTTTCAC
13116 TTTTTTTTATTTTAA
1 TTTTTTTT-TTTTAA
* *
13131 TTTATCTTTTTTAA
1 TTTTTTTTTTTTAA
13145 TTTTTTTTTTTT
1 TTTTTTTTTTTT
13157 TTAATTTTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTTTTTTTAA
Found at i:18739 original size:3 final size:3
Alignment explanation
Indices: 18733--18781 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
18723 AAAAAAAAGG
18733 TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
18779 TAT
1 TAT
18782 CTATCTAAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 40 0.91
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:18795 original size:29 final size:28
Alignment explanation
Indices: 18734--18795 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 28
18724 AAAAAAAGGT
**
18734 ATTATTATTATTATATTATTATTATTATT
1 ATTATTATTATTATATTATTATTA-TAAC
18763 ATTATTATTATTATATTATCTATCTA-AAC
1 ATTATTATTATTATATTAT-TAT-TATAAC
18792 ATTA
1 ATTA
18796 ATCTATTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 24 0.83
30 3 0.10
31 2 0.07
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (28 bp):
ATTATTATTATTATATTATTATTATAAC
Found at i:18842 original size:4 final size:4
Alignment explanation
Indices: 18833--18901 Score: 54
Period size: 4 Copynumber: 18.0 Consensus size: 4
18823 GTTTGGCTGG
* * * * *
18833 GAAA GAAA GAAA GAAA GTAA GAAA AAAA AAAA GAAT GAAT G-AA G-AA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
* *
18879 GAAA -AAA GAAA AAAA GACA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA
18902 AAAAAAAATT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
3 8 0.15
4 45 0.85
ACGTcount: A:0.74, C:0.01, G:0.20, T:0.04
Consensus pattern (4 bp):
GAAA
Found at i:18904 original size:21 final size:20
Alignment explanation
Indices: 18838--18906 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 20
18828 GCTGGGAAAG
*
18838 AAAGAAAGAAAGTAAGAAAAA
1 AAAGAAAAAAAG-AAGAAAAA
18859 AAA-AAAGAATGAATGAAGAAGAAA
1 AAAGAAA-AA--AA-GAAGAA-AAA
18883 AAAGAAAAAAAGACAGAAAAA
1 AAAGAAAAAAAGA-AGAAAAA
18904 AAA
1 AAA
18907 AAATTATCGA
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
20 3 0.08
21 12 0.30
22 6 0.15
23 7 0.17
24 9 0.22
25 3 0.08
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.04
Consensus pattern (20 bp):
AAAGAAAAAAAGAAGAAAAA
Found at i:19636 original size:15 final size:16
Alignment explanation
Indices: 19612--19647 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
19602 TACATAAAAT
19612 TTTTTCCTTTT-TTTC
1 TTTTTCCTTTTGTTTC
*
19627 TTTTTGCTTTTGTTTC
1 TTTTTCCTTTTGTTTC
19643 TTTTT
1 TTTTT
19648 TTTCTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.81
Consensus pattern (16 bp):
TTTTTCCTTTTGTTTC
Done.