Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5801.1
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: 17599
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:462 original size:15 final size:15
Alignment explanation
Indices: 442--496 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
432 ACTCTCCTCA
*
442 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
457 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
472 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
486 TTCTTTT-TCTC
1 TTCTTTTCTCTC
497 GATCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:2915 original size:20 final size:20
Alignment explanation
Indices: 2892--2956 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
2882 CTATCCTAGA
2892 TTTTACCCAACTATAATATC
1 TTTTACCCAACTATAATATC
** * ** **
2912 TTTTTACAAAATTATCCTAGA
1 -TTTTACCCAACTATAATATC
2933 TTTTACCCAACTATAATATC
1 TTTTACCCAACTATAATATC
2953 TTTT
1 TTTT
2957 TTTCAAAACT
Statistics
Matches: 30, Mismatches: 14, Indels: 1
0.67 0.31 0.02
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.34, C:0.20, G:0.02, T:0.45
Consensus pattern (20 bp):
TTTTACCCAACTATAATATC
Found at i:2918 original size:21 final size:21
Alignment explanation
Indices: 2892--2957 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
2882 CTATCCTAGA
2892 TTTTACCCAACTATAATATCT
1 TTTTACCCAACTATAATATCT
** * ** **
2913 TTTTACAAAATTATCCTA-GA
1 TTTTACCCAACTATAATATCT
2933 TTTTACCCAACTATAATATCT
1 TTTTACCCAACTATAATATCT
2954 TTTT
1 TTTT
2958 TTCAAAACTG
Statistics
Matches: 30, Mismatches: 14, Indels: 2
0.65 0.30 0.04
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.45
Consensus pattern (21 bp):
TTTTACCCAACTATAATATCT
Found at i:3374 original size:10 final size:11
Alignment explanation
Indices: 3352--3388 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
3342 AAAGGAGAAG
3352 AAATTCAAAAA
1 AAATTCAAAAA
3363 AAATTCAAAAA
1 AAATTCAAAAA
*
3374 AAAATCGAAAAA
1 AAATTC-AAAAA
3386 AAA
1 AAA
3389 GGAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.14
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:3375 original size:12 final size:12
Alignment explanation
Indices: 3352--3388 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3342 AAAGGAGAAG
3352 AAATTC-AAAAA
1 AAATTCAAAAAA
3363 AAATTCAAAAAA
1 AAATTCAAAAAA
3375 AAA-TCGAAAAAA
1 AAATTC-AAAAAA
3387 AA
1 AA
3389 GGAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.14
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:3394 original size:22 final size:21
Alignment explanation
Indices: 3337--3398 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
3327 TATTGGATTT
* * *
3337 AAAAAAAAGGAGAAGAAATTC
1 AAAAAAAAGGAAAAAAAAATC
**
3358 AAAAAAAATTCAAAAAAAAATC
1 AAAAAAAA-GGAAAAAAAAATC
3380 GAAAAAAAAGGAAAAAAAA
1 -AAAAAAAAGGAAAAAAAA
3399 GTGACAAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 8 0.25
22 16 0.50
23 8 0.25
ACGTcount: A:0.76, C:0.05, G:0.11, T:0.08
Consensus pattern (21 bp):
AAAAAAAAGGAAAAAAAAATC
Found at i:4380 original size:37 final size:37
Alignment explanation
Indices: 4329--4399 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
4319 CATTCTTGTA
4329 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
4366 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
4400 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:4399 original size:6 final size:6
Alignment explanation
Indices: 4339--4388 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
4329 AAGAGAAAAC
*
4339 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
4388 A
1 A
4389 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:4478 original size:12 final size:12
Alignment explanation
Indices: 4470--4494 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4460 TTTGAAAAGC
4470 AAAAAGAAAATG
1 AAAAAGAAAATG
4482 AAAAAGAAAATG
1 AAAAAGAAAATG
4494 A
1 A
4495 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:4491 original size:18 final size:18
Alignment explanation
Indices: 4464--4519 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
4454 AAAGCCTTTG
4464 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
4483 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
4501 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
4518 AA
1 AA
4520 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:4504 original size:30 final size:31
Alignment explanation
Indices: 4470--4551 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
4460 TTTGAAAAGC
*
4470 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
4500 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
4530 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
4552 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:7290 original size:147 final size:147
Alignment explanation
Indices: 7023--7317 Score: 590
Period size: 147 Copynumber: 2.0 Consensus size: 147
7013 TGCTGAATTT
7023 ATGTGTGTTCACATGATGTCTTATGAATTGTTTTATTTCTTGTAGGTACAATGCTCATGGACGGC
1 ATGTGTGTTCACATGATGTCTTATGAATTGTTTTATTTCTTGTAGGTACAATGCTCATGGACGGC
7088 GCAATGAATGCTTGAAGAAACATCTCTTTTGGACATCCCACATGCATGAATGAACAACATTTAAT
66 GCAATGAATGCTTGAAGAAACATCTCTTTTGGACATCCCACATGCATGAATGAACAACATTTAAT
7153 TAGGTGCATGTATGACC
131 TAGGTGCATGTATGACC
7170 ATGTGTGTTCACATGATGTCTTATGAATTGTTTTATTTCTTGTAGGTACAATGCTCATGGACGGC
1 ATGTGTGTTCACATGATGTCTTATGAATTGTTTTATTTCTTGTAGGTACAATGCTCATGGACGGC
7235 GCAATGAATGCTTGAAGAAACATCTCTTTTGGACATCCCACATGCATGAATGAACAACATTTAAT
66 GCAATGAATGCTTGAAGAAACATCTCTTTTGGACATCCCACATGCATGAATGAACAACATTTAAT
7300 TAGGTGCATGTATGACC
131 TAGGTGCATGTATGACC
7317 A
1 A
7318 GATTCAAGGT
Statistics
Matches: 148, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 148 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (147 bp):
ATGTGTGTTCACATGATGTCTTATGAATTGTTTTATTTCTTGTAGGTACAATGCTCATGGACGGC
GCAATGAATGCTTGAAGAAACATCTCTTTTGGACATCCCACATGCATGAATGAACAACATTTAAT
TAGGTGCATGTATGACC
Found at i:10505 original size:14 final size:14
Alignment explanation
Indices: 10456--10505 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
10446 TCGTAGCTTC
*
10456 AAAAAAAAAGTT--
1 AAAAAAAAAATTCG
*
10468 AAAAAAAAAGTTTCG
1 AAAAAAAAA-ATTCG
10483 AAAAAAAAAATTCG
1 AAAAAAAAAATTCG
10497 AAAAAAAAA
1 AAAAAAAAA
10506 GAAGGAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 9 0.27
13 2 0.06
14 13 0.39
15 9 0.27
ACGTcount: A:0.74, C:0.04, G:0.08, T:0.14
Consensus pattern (14 bp):
AAAAAAAAAATTCG
Found at i:10528 original size:14 final size:14
Alignment explanation
Indices: 10455--10537 Score: 61
Period size: 13 Copynumber: 6.1 Consensus size: 14
10445 ATCGTAGCTT
*
10455 CAAAAAAAAAGTT-
1 CAAAAAAAAAATTG
* *
10468 -AAAAAAAAAGTTT
1 CAAAAAAAAAATTG
10481 CGAAAAAAAAAATT-
1 C-AAAAAAAAAATTG
*
10495 CGAAAAAAAAA--G
1 CAAAAAAAAAATTG
10507 -AAGGAAAAAAAATTG
1 CAA--AAAAAAAATTG
10522 CAAAAAAAAAATTG
1 CAAAAAAAAAATTG
10536 CA
1 CA
10538 TACGGTCTAG
Statistics
Matches: 58, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
11 1 0.02
12 12 0.21
13 17 0.29
14 14 0.24
15 12 0.21
16 2 0.03
ACGTcount: A:0.70, C:0.06, G:0.11, T:0.13
Consensus pattern (14 bp):
CAAAAAAAAAATTG
Found at i:12815 original size:24 final size:25
Alignment explanation
Indices: 12788--12841 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
12778 ATGAGTGATA
*
12788 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
12812 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
12836 AAAAAA
1 AAAAAA
12842 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
Done.