Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2142
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: 36823
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:4042 original size:4 final size:4
Alignment explanation
Indices: 4033--4060 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
4023 AAGTTTTATT
4033 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
4061 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:16673 original size:22 final size:21
Alignment explanation
Indices: 16639--16681 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
16629 GGCTGTTAAA
*
16639 AAAAGGAGCTTAAAGATCATT
1 AAAAGGAGCTTAAAGAGCATT
*
16660 AAAAGGAGTTTTAAAGAGCATT
1 AAAAGGAG-CTTAAAGAGCATT
16682 TTATGCCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.26
Consensus pattern (21 bp):
AAAAGGAGCTTAAAGAGCATT
Found at i:17538 original size:13 final size:13
Alignment explanation
Indices: 17520--17583 Score: 83
Period size: 13 Copynumber: 4.8 Consensus size: 13
17510 TAGTTTCTCG
*
17520 AAAAAAAACTCGA
1 AAAAAAAATTCGA
*
17533 AAAAAAAATTCAA
1 AAAAAAAATTCGA
17546 AAAAAAAATTTTCGA
1 AAAAAAAA--TTCGA
*
17561 AAAAAAAATTCAA
1 AAAAAAAATTCGA
17574 AAAAAAAATT
1 AAAAAAAATT
17584 GGTTTATATT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
13 33 0.73
15 12 0.27
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.17
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:17560 original size:28 final size:28
Alignment explanation
Indices: 17529--17583 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
17519 GAAAAAAAAC
17529 TCGAAAAAAAAATTCAAAAAAAAAATTT
1 TCGAAAAAAAAATTCAAAAAAAAAATTT
17557 TCGAAAAAAAAATTCAAAAAAAAAATT
1 TCGAAAAAAAAATTCAAAAAAAAAATT
17584 GGTTTATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.69, C:0.07, G:0.04, T:0.20
Consensus pattern (28 bp):
TCGAAAAAAAAATTCAAAAAAAAAATTT
Found at i:17643 original size:16 final size:16
Alignment explanation
Indices: 17622--17676 Score: 101
Period size: 16 Copynumber: 3.4 Consensus size: 16
17612 TATCAAGTTG
*
17622 AAAAAAAATTTCGTGA
1 AAAAAAAAATTCGTGA
17638 AAAAAAAAATTCGTGA
1 AAAAAAAAATTCGTGA
17654 AAAAAAAAATTCGTGA
1 AAAAAAAAATTCGTGA
17670 AAAAAAA
1 AAAAAAA
17677 GAAGAAGAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.65, C:0.05, G:0.11, T:0.18
Consensus pattern (16 bp):
AAAAAAAAATTCGTGA
Found at i:25723 original size:22 final size:21
Alignment explanation
Indices: 25689--25731 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
25679 GGCTGTTAAA
*
25689 AAAAGGAGCTTAAAGATCATT
1 AAAAGGAGCTTAAAGAGCATT
*
25710 AAAAGGAGTTTTAAAGAGCATT
1 AAAAGGAG-CTTAAAGAGCATT
25732 TTATGCCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.26
Consensus pattern (21 bp):
AAAAGGAGCTTAAAGAGCATT
Found at i:29595 original size:23 final size:22
Alignment explanation
Indices: 29544--29596 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
29534 CCTCGTCTAT
*
29544 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTTTTTCTTTTTCTAAC
29566 -TCATTTTTTCTTCTTTCTTC-AAC
1 TTC-TTTTTT-TTCTTT-TTCTAAC
29589 TTCTTTTT
1 TTCTTTTT
29597 CAATTTTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.19
23 14 0.54
24 5 0.19
ACGTcount: A:0.09, C:0.21, G:0.02, T:0.68
Consensus pattern (22 bp):
TTCTTTTTTTTCTTTTTCTAAC
Found at i:29596 original size:24 final size:21
Alignment explanation
Indices: 29544--29596 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
29534 CCTCGTCTAT
29544 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTT-TTTCTTTTTCTAAC
*
29566 -TCATTTTTTCTTCTTTCTTCAAC
1 TTCTTTTTTTCTT-TTTC-T-AAC
29589 TTCTTTTT
1 TTCTTTTT
29597 CAATTTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 6 0.24
21 9 0.36
22 1 0.04
23 3 0.12
24 6 0.24
ACGTcount: A:0.09, C:0.21, G:0.02, T:0.68
Consensus pattern (21 bp):
TTCTTTTTTTCTTTTTCTAAC
Found at i:33183 original size:14 final size:14
Alignment explanation
Indices: 33164--33210 Score: 71
Period size: 13 Copynumber: 3.5 Consensus size: 14
33154 ACGAGATTGT
33164 AAAAAAAA-TCGAA
1 AAAAAAAATTCGAA
33177 AAAAAAAATTCGAA
1 AAAAAAAATTCGAA
*
33191 AAAAGAAATTC-AA
1 AAAAAAAATTCGAA
33204 AAAAAAA
1 AAAAAAA
33211 GTTTGTATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
13 16 0.52
14 15 0.48
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.11
Consensus pattern (14 bp):
AAAAAAAATTCGAA
Found at i:35312 original size:14 final size:14
Alignment explanation
Indices: 35293--35345 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
35283 TCTATTGAGC
35293 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
* *
35307 GAGAAAAACAAAGA
1 GAGAAAAAGAAAAA
*
35321 GTG-AAAAGAAAAA
1 GAGAAAAAGAAAAA
*
35334 GAAAGAAAAGAA
1 GAGA-AAAAGAA
35346 TGAGGAGAGT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
13 9 0.30
14 14 0.47
15 7 0.23
ACGTcount: A:0.74, C:0.02, G:0.23, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:36403 original size:21 final size:19
Alignment explanation
Indices: 36378--36419 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
36368 TTTGGTATTG
*
36378 GGAATTGGTTCGAAATAGTAT
1 GGAATT-GTACGAAAT-GTAT
36399 GGAATTGTACGAAATGTAT
1 GGAATTGTACGAAATGTAT
36418 GG
1 GG
36420 TATTTGGTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 8 0.40
21 6 0.30
ACGTcount: A:0.33, C:0.05, G:0.31, T:0.31
Consensus pattern (19 bp):
GGAATTGTACGAAATGTAT
Found at i:36431 original size:21 final size:21
Alignment explanation
Indices: 36378--36432 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
36368 TTTGGTATTG
*
36378 GGAATTGGTTCGAAATAGTAT
1 GGAATTGGTACGAAATAGTAT
36399 GGAATT-GTACGAAAT-GTAT
1 GGAATTGGTACGAAATAGTAT
*
36418 GGTATTTGGTACGAA
1 GG-AATTGGTACGAA
36433 TTGGTAATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 6 0.20
20 11 0.37
21 13 0.43
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATAGTAT
Done.