Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold966
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: 30887
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1572 original size:20 final size:18
Alignment explanation
Indices: 1548--1605 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 18
1538 TATACAAGTC
*
1548 AAAAAAATTTGAAAATAA
1 AAAAAAATTTGAAAAGAA
*
1566 ATTAAAAAAATTGAAAAGAA
1 A--AAAAAATTTGAAAAGAA
*
1586 AAAAAAATCTGAAAA-AA
1 AAAAAAATTTGAAAAGAA
1603 AAA
1 AAA
1606 GTGTTTAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
17 5 0.15
18 13 0.38
20 16 0.47
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (18 bp):
AAAAAAATTTGAAAAGAA
Found at i:1591 original size:17 final size:17
Alignment explanation
Indices: 1569--1605 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1559 AAAATAAATT
1569 AAAAAAAT-TGAAAAGAA
1 AAAAAAATCTGAAAA-AA
1586 AAAAAAATCTGAAAAAA
1 AAAAAAATCTGAAAAAA
1603 AAA
1 AAA
1606 GTGTTTAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.78, C:0.03, G:0.08, T:0.11
Consensus pattern (17 bp):
AAAAAAATCTGAAAAAA
Found at i:2678 original size:30 final size:31
Alignment explanation
Indices: 2644--2725 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
2634 TTTGAAAAGA
*
2644 AAAAAGAAAAAGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
* * *
2674 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
* *
2704 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAAAGAAAAAGAAAT
2726 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:0.66, C:0.01, G:0.22, T:0.11
Consensus pattern (31 bp):
AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
Found at i:2698 original size:24 final size:24
Alignment explanation
Indices: 2649--2718 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
2639 AAAGAAAAAA
*
2649 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAATGAAATT
* *
2673 GAAAAAGAGAACGAAAA-GAAATTT
1 GAAAAAGAAAAAGAAAATGAAA-TT
* ** *
2697 GAGAGTGAAAAAGAAGATGAAA
1 GAAAAAGAAAAAGAAAATGAAA
2719 AAGAAATTGA
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
23 3 0.09
24 28 0.80
25 4 0.11
ACGTcount: A:0.63, C:0.01, G:0.24, T:0.11
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAATGAAATT
Found at i:13928 original size:23 final size:22
Alignment explanation
Indices: 13876--13928 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
13866 TCCACGTCTT
*
13876 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
13898 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
13921 TTTCTTTT
1 TTTCTTTT
13929 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:15369 original size:11 final size:12
Alignment explanation
Indices: 15353--15471 Score: 57
Period size: 12 Copynumber: 9.6 Consensus size: 12
15343 AAAGAAATTG
15353 AAAGAAAAC-AA
1 AAAGAAAACGAA
15364 AAAGAAAACGAA
1 AAAGAAAACGAA
* *
15376 GAAGAAAAAGAA
1 AAAGAAAACGAA
**
15388 ATTGCAAAA-GAA
1 AAAG-AAAACGAA
*
15400 AAA-AAATCGAA
1 AAAGAAAACGAA
* *
15411 AAAGTGAGA-GAA
1 AAAG-AAAACGAA
*
15423 AAAGAAAATGAAGA
1 AAAGAAAACG-A-A
*
15437 AAAGAAAATTGAA
1 AAAGAAAA-CGAA
15450 AAAGAAAAAGCGAAA
1 AAAG-AAAA-CG-AA
15465 AAAGAAA
1 AAAGAAA
15472 TTGAAAGAGA
Statistics
Matches: 82, Mismatches: 15, Indels: 19
0.71 0.13 0.16
Matches are distributed among these distances:
10 3 0.04
11 17 0.21
12 25 0.30
13 11 0.13
14 18 0.22
15 8 0.10
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.06
Consensus pattern (12 bp):
AAAGAAAACGAA
Found at i:15383 original size:39 final size:39
Alignment explanation
Indices: 15340--15479 Score: 133
Period size: 41 Copynumber: 3.5 Consensus size: 39
15330 GAAAGAGATT
*
15340 GAAAAAGAAATTGAAAGAAAACAAAA-AGAAAACGAAGAA
1 GAAAAAGAAATTGAAAGAAAA-AAAATAGAAAAAGAAGAA
* *
15379 GAAAAAGAAATTGCAAAAGAAAAAAAATCGAAAAAG-TGAGA
1 GAAAAAGAAATTG--AAAGAAAAAAAATAGAAAAAGAAGA-A
* * *
15420 GAAAAAGAAAATG-AAGAAAAGAAAATTGAAAAAGAAAAA
1 GAAAAAGAAATTGAAAGAAAA-AAAATAGAAAAAGAAGAA
15459 GCGAAAAAAGAAATTGAAAGA
1 --G-AAAAAGAAATTGAAAGA
15480 GAGCTTGAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
38 7 0.08
39 26 0.31
40 7 0.08
41 28 0.34
42 11 0.13
43 4 0.05
ACGTcount: A:0.69, C:0.04, G:0.19, T:0.08
Consensus pattern (39 bp):
GAAAAAGAAATTGAAAGAAAAAAAATAGAAAAAGAAGAA
Found at i:15386 original size:6 final size:6
Alignment explanation
Indices: 15353--15459 Score: 56
Period size: 6 Copynumber: 17.7 Consensus size: 6
15343 AAAGAAATTG
* * * ** *
15353 AAAG-A AAACAA AAAGAA AACGAA GAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
15400 AAA-AA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
15450 AAAGAA AAAG
1 AAAGAA AAAG
15460 CGAAAAAAGA
Statistics
Matches: 71, Mismatches: 26, Indels: 9
0.67 0.25 0.08
Matches are distributed among these distances:
5 6 0.08
6 54 0.76
7 7 0.10
8 4 0.06
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:15441 original size:14 final size:13
Alignment explanation
Indices: 15420--15457 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
15410 AAAAGTGAGA
15420 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
15432 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
15447 GAAAAAGAAAA
1 GAAAAAGAAAA
15458 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:15454 original size:13 final size:12
Alignment explanation
Indices: 15339--15457 Score: 54
Period size: 12 Copynumber: 10.0 Consensus size: 12
15329 AGAAAGAGAT
*
15339 TGAAAAAGAAAT
1 TGAAAAAGAAAA
15351 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
15361 -CAAAAAGAAAA
1 TGAAAAAGAAAA
* *
15372 CGAAGAAGAAAA
1 TGAAAAAGAAAA
* **
15384 AGAAATTGCAAAA
1 TGAAAAAG-AAAA
15397 -G-AAAA-AAAA
1 TGAAAAAGAAAA
* *
15406 TCGAAAAAGTGAGA
1 T-GAAAAAG-AAAA
15420 -GAAAAAGAAAA
1 TGAAAAAGAAAA
15431 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
15445 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
15458 AGCGAAAAAA
Statistics
Matches: 80, Mismatches: 14, Indels: 25
0.67 0.12 0.21
Matches are distributed among these distances:
9 4 0.05
10 7 0.09
11 13 0.16
12 28 0.35
13 14 0.17
14 12 0.15
15 2 0.03
ACGTcount: A:0.70, C:0.03, G:0.18, T:0.08
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:15471 original size:21 final size:21
Alignment explanation
Indices: 15421--15471 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
15411 AAAGTGAGAG
*
15421 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
15442 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
15463 AAAAAGAAA
1 AAAAAGAAA
15472 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:15511 original size:33 final size:33
Alignment explanation
Indices: 15474--15536 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
15464 AAAAGAAATT
15474 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
15507 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
15537 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:17335 original size:20 final size:20
Alignment explanation
Indices: 17312--17365 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
17302 AGTTTTTCCC
*
17312 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
17332 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
17352 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
17366 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:17347 original size:30 final size:30
Alignment explanation
Indices: 17312--17385 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
17302 AGTTTTTCCC
17312 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
17342 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
17372 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
17386 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:17375 original size:20 final size:20
Alignment explanation
Indices: 17312--17376 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
17302 AGTTTTTCCC
* * * *
17312 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
17332 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
17351 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
17372 AGCTC
1 AGCTC
17377 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:22652 original size:13 final size:13
Alignment explanation
Indices: 22634--22662 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
22624 AATAGTTGTG
22634 TGTTATTTAATTA
1 TGTTATTTAATTA
22647 TGTTATTTAATTA
1 TGTTATTTAATTA
22660 TGT
1 TGT
22663 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:24692 original size:13 final size:13
Alignment explanation
Indices: 24674--24699 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24664 ACCTGAAAGC
24674 AATTTAATTCATA
1 AATTTAATTCATA
24687 AATTTAATTCATA
1 AATTTAATTCATA
24700 TTAGGACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTAATTCATA
Done.