Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1219
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: 16348
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:2372 original size:8 final size:8
Alignment explanation
Indices: 2355--2392 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
2345 GTCAGCATTA
*
2355 TTTTTATT
1 TTTTTCTT
2363 TTTTTC-T
1 TTTTTCTT
2370 TTTTTCTT
1 TTTTTCTT
2378 TTTTTCTT
1 TTTTTCTT
*
2386 TCTTTCT
1 TTTTTCT
2393 CTCCTTTGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTCTT
Found at i:2379 original size:15 final size:15
Alignment explanation
Indices: 2355--2392 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2345 GTCAGCATTA
*
2355 TTTTTATTTTTTTCT
1 TTTTTCTTTTTTTCT
2370 TTTTTCTTTTTTTCT
1 TTTTTCTTTTTTTCT
2385 TTCTTTCT
1 TT-TTTCT
2393 CTCCTTTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTCTTTTTTTCT
Found at i:3638 original size:136 final size:136
Alignment explanation
Indices: 3389--3642 Score: 431
Period size: 136 Copynumber: 1.9 Consensus size: 136
3379 CTCTTCTTCT
* *
3389 TTCATATGCATCATCCATGACGCATGTGAATGGAAATAAAATCAACCACAGGCAACGAAAATCAA
1 TTCAGATGCATCATCCATGACGCATGTGAATGGAAATAAAATCAACAACAGGCAACGAAAATCAA
* *
3454 TTAAACAAGTAATATAGCTGATCTGCAATCTATTTAATTTGTACTACACAATTTTGCAACAAGCA
66 TTAAACAAGTAATATAGCTGATCTACAATCTATTTAATATGTACTACACAATTTTGCAACAAGCA
3519 TACTCA
131 TACTCA
3525 TTCAGATGCATCATCCATGACGCATGTG-ATGGGAAATAAAATCAACAACAGGCAACGAAAA-CA
1 TTCAGATGCATCATCCATGACGCATGTGAAT-GGAAATAAAATCAACAACAGGCAACGAAAATC-
*
3588 AATTAAACAAGTACTATAGCTGATCTACAATCTATTTAATATGTACTACACAATT
64 AATTAAACAAGTAATATAGCTGATCTACAATCTATTTAATATGTACTACACAATT
3643 GCAAATTGCA
Statistics
Matches: 111, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
135 3 0.03
136 108 0.97
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.26
Consensus pattern (136 bp):
TTCAGATGCATCATCCATGACGCATGTGAATGGAAATAAAATCAACAACAGGCAACGAAAATCAA
TTAAACAAGTAATATAGCTGATCTACAATCTATTTAATATGTACTACACAATTTTGCAACAAGCA
TACTCA
Found at i:6220 original size:12 final size:12
Alignment explanation
Indices: 6203--6231 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
6193 AAAGAAACAC
6203 AGTAGAAGCAAA
1 AGTAGAAGCAAA
6215 AGTAGAAGCAAA
1 AGTAGAAGCAAA
6227 A-TAGA
1 AGTAGA
6232 GAAGAAACGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.59, C:0.07, G:0.24, T:0.10
Consensus pattern (12 bp):
AGTAGAAGCAAA
Found at i:6267 original size:22 final size:22
Alignment explanation
Indices: 6220--6272 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
6210 GCAAAAGTAG
*
6220 AAGCAAAA-TAGAGAAGAAACG
1 AAGCAAAAGTAGAGAAGAAACA
*
6241 CAGCAAAAGTAGAGAA-AAATCA
1 AAGCAAAAGTAGAGAAGAAA-CA
*
6263 AAGCAGAAGT
1 AAGCAAAAGT
6273 GAAGTAGAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.58, C:0.11, G:0.23, T:0.08
Consensus pattern (22 bp):
AAGCAAAAGTAGAGAAGAAACA
Found at i:8127 original size:23 final size:22
Alignment explanation
Indices: 8066--8111 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
8056 AAATTAAGAG
8066 TAATAA-AAT-AAATAAATATA
1 TAATAACAATAAAATAAATATA
8086 TAATAACAATTAAAATAAATATA
1 TAATAACAA-TAAAATAAATATA
8109 TAA
1 TAA
8112 GTACACAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.26
21 2 0.09
22 1 0.04
23 14 0.61
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATAACAATAAAATAAATATA
Found at i:8812 original size:1 final size:1
Alignment explanation
Indices: 8806--8872 Score: 53
Period size: 1 Copynumber: 67.0 Consensus size: 1
8796 TGCTTCAGAG
* * ** * * * * *
8806 AAAAAAAAGAAAAACAAAAAAAAAAAAAGGAAAAATAGAAAAAAAAAGAAAAAAAGAAAAAATAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8871 AA
1 AA
8873 GGGAAGAAAA
Statistics
Matches: 50, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.87, C:0.01, G:0.09, T:0.03
Consensus pattern (1 bp):
A
Found at i:8826 original size:8 final size:8
Alignment explanation
Indices: 8804--8867 Score: 60
Period size: 8 Copynumber: 8.0 Consensus size: 8
8794 ACTGCTTCAG
8804 AGAAAAAA
1 AGAAAAAA
*
8812 A-AGAAAA
1 AGAAAAAA
*
8819 ACAAAAAA
1 AGAAAAAA
8827 A-AAAAAA
1 AGAAAAAA
*
8834 GGAAAAATA
1 AGAAAAA-A
*
8843 GAAAAAAAA
1 -AGAAAAAA
8852 AGAAAAAA
1 AGAAAAAA
8860 AGAAAAAA
1 AGAAAAAA
8868 TAAAAGGGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
7 12 0.26
8 27 0.59
9 2 0.04
10 5 0.11
ACGTcount: A:0.86, C:0.02, G:0.11, T:0.02
Consensus pattern (8 bp):
AGAAAAAA
Found at i:8831 original size:20 final size:19
Alignment explanation
Indices: 8806--8873 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
8796 TGCTTCAGAG
8806 AAAAAAAAGAAAAACAAAAA
1 AAAAAAAAGAAAAA-AAAAA
* * *
8826 AAAAAAAAGGAAAAATAGA
1 AAAAAAAAGAAAAAAAAAA
8845 AAAAAAAAGAAAAAAAGAAA
1 AAAAAAAAGAAAAAAA-AAA
*
8865 AAATAAAAG
1 AAAAAAAAG
8874 GGAAGAAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 17 0.43
20 23 0.57
ACGTcount: A:0.85, C:0.01, G:0.10, T:0.03
Consensus pattern (19 bp):
AAAAAAAAGAAAAAAAAAA
Found at i:12202 original size:20 final size:20
Alignment explanation
Indices: 12164--12203 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
12154 TAAGATTTAA
12164 TCAAATTAAAATGATAAAAT
1 TCAAATTAAAATGATAAAAT
12184 TCAACATTAAAATGA-AAAAT
1 TCAA-ATTAAAATGATAAAAT
12204 AATGACAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (20 bp):
TCAAATTAAAATGATAAAAT
Found at i:12327 original size:20 final size:20
Alignment explanation
Indices: 12302--12341 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
12292 TTATAAATCA
*
12302 ATTTAATTTAAATTATTTTT
1 ATTTAATTAAAATTATTTTT
12322 ATTTAATTAAAATTATTTTT
1 ATTTAATTAAAATTATTTTT
12342 TTATTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTAATTAAAATTATTTTT
Found at i:12375 original size:17 final size:18
Alignment explanation
Indices: 12347--12381 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
12337 TTTTTTTATT
12347 TAAAAATATAAAAATTTA
1 TAAAAATATAAAAATTTA
12365 TAAAAAT-TAAAAATTTA
1 TAAAAATATAAAAATTTA
12382 ATATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAAAATATAAAAATTTA
Found at i:12382 original size:8 final size:8
Alignment explanation
Indices: 12344--12382 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
12334 TTATTTTTTT
12344 ATTTAAAA
1 ATTTAAAA
*
12352 ATATAAAA
1 ATTTAAAA
12360 ATTTATAAA
1 ATTTA-AAA
*
12369 AATTAAAA
1 ATTTAAAA
12377 ATTTAA
1 ATTTAA
12383 TATTTTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATTTAAAA
Found at i:13255 original size:21 final size:20
Alignment explanation
Indices: 13218--13257 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
13208 TGATAACTAG
**
13218 TAATTTTTTAGGAAAAAATT
1 TAATTTTTTAAAAAAAAATT
13238 TAATTTTTTAAAAGAAAAAT
1 TAATTTTTTAAAA-AAAAAT
13258 GAAGGAATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (20 bp):
TAATTTTTTAAAAAAAAATT
Found at i:15003 original size:23 final size:23
Alignment explanation
Indices: 14973--15018 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
14963 AAAAGAGAGT
*
14973 TTGATCATACAGCCTTTATCCTA
1 TTGATCATACACCCTTTATCCTA
14996 TTGATCATACACCCTTTATCCTA
1 TTGATCATACACCCTTTATCCTA
15019 CCTACCTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.28, G:0.07, T:0.39
Consensus pattern (23 bp):
TTGATCATACACCCTTTATCCTA
Done.