Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2754
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: 22121
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Found at i:518 original size:20 final size:20
Alignment explanation
Indices: 495--548 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
485 AGTTTTTCCC
*
495 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
515 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
535 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
549 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:530 original size:30 final size:30
Alignment explanation
Indices: 495--568 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
485 AGTTTTTCCC
495 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
525 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
555 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
569 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:558 original size:20 final size:20
Alignment explanation
Indices: 495--559 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
485 AGTTTTTCCC
* * * *
495 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
515 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
534 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
555 AGCTC
1 AGCTC
560 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:2237 original size:39 final size:36
Alignment explanation
Indices: 2182--2256 Score: 98
Period size: 40 Copynumber: 2.0 Consensus size: 36
2172 AAAAAAAATT
2182 CAAAAAAATCG-AAAAAAAAGAAAAAAAAAGAAGTGA
1 CAAAAAAATCGAAAAAAAAAGAAAAAAAAA-AAGTGA
*
2218 CAAAAAAATCGAGTTAAAAAAAAGAAGAAAAAAAAGTGA
1 CAAAAAAATCGA---AAAAAAAAGAAAAAAAAAAAGTGA
2257 AAAGTCTTGC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 11 0.32
39 6 0.18
40 17 0.50
ACGTcount: A:0.72, C:0.05, G:0.15, T:0.08
Consensus pattern (36 bp):
CAAAAAAATCGAAAAAAAAAGAAAAAAAAAAAGTGA
Found at i:3319 original size:16 final size:14
Alignment explanation
Indices: 3279--3339 Score: 54
Period size: 15 Copynumber: 4.2 Consensus size: 14
3269 AGAGAAAAAG
3279 AAAATGAAGAAA-AGA
1 AAAATGAA-AAAGA-A
*
3294 AAATTGAAAAAGAA
1 AAAATGAAAAAGAA
3308 AGAGAATGAAAAA-AA
1 A-A-AATGAAAAAGAA
*
3323 AAATTGAAAAAGAA
1 AAAATGAAAAAGAA
3337 AAA
1 AAA
3340 GCGAAAAAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
13 8 0.21
14 11 0.28
15 12 0.31
16 8 0.21
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATGAAAAAGAA
Found at i:3392 original size:33 final size:33
Alignment explanation
Indices: 3355--3417 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
3345 AAAAGAAATT
3355 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
3388 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
3418 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:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:5760 original size:77 final size:78
Alignment explanation
Indices: 5626--5816 Score: 282
Period size: 78 Copynumber: 2.5 Consensus size: 78
5616 TCTTCGAAAT
* * * * * *
5626 TTAG-CCGGATATAACCACAAGCACAA-TGCCTTCGGGTCTTAGCGGATATATCAACTCGCACAA
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTAACCGGATATAGCAACTCGCACAA
5689 ATGCCTTC-GGTC
66 ATGCCTTCGGGTC
5701 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTAACCCGG-TATAGCAACTCGCACA
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTAA-CCGGATATAGCAACTCGCACA
5765 AATGCCTTCGGGTC
65 AATGCCTTCGGGTC
*
5779 TTAGCCCGAATAAAATCACTAGCACAATTGCCTTCGGG
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGG
5817 ACTTAGCCCG
Statistics
Matches: 105, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
75 4 0.04
76 19 0.18
77 38 0.36
78 44 0.42
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (78 bp):
TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTAACCGGATATAGCAACTCGCACAA
ATGCCTTCGGGTC
Found at i:5813 original size:40 final size:40
Alignment explanation
Indices: 5645--5830 Score: 208
Period size: 40 Copynumber: 4.8 Consensus size: 40
5635 TATAACCACA
*
5645 AGCAC-AATGCCTTCGGGTCTTAG--CGGATATATCAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAATCAACT
*
5682 CGCACAAATGCCTTC-GGTCTTAGCCCGGATAAAATC-ACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGAT-AAATCAACT
* * * *
5721 AGCACAATTGCCTTCGGGTC-TAACCCGG-TATAGCAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAATCAACT
* *
5759 CGCACAAATGCCTTCGGGTCTTAGCCCGAATAAAATC-ACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGAT-AAATCAACT
* *
5799 AGCACAATTGCCTTCGGGACTTAGCCCGGATA
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATA
5831 TCATTCAAAT
Statistics
Matches: 123, Mismatches: 17, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
37 15 0.12
38 31 0.25
39 35 0.28
40 39 0.32
41 3 0.02
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAATCAACT
Found at i:6795 original size:29 final size:30
Alignment explanation
Indices: 6734--6806 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 30
6724 AGTTTTTCCC
6734 AGCTCGATTT-AGCTCACATGAGCTTAATTT
1 AGCTCG-TTTGAGCTCACATGAGCTTAATTT
* *
6764 AGCTCGTTTGAGCTCA-ATTAGCTTACTTT
1 AGCTCGTTTGAGCTCACATGAGCTTAATTT
6793 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
6807 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
29 28 0.70
30 12 0.30
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCACATGAGCTTAATTT
Found at i:8477 original size:13 final size:13
Alignment explanation
Indices: 8424--8477 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
8414 AAAAAAATTC
*
8424 AAAAAAAG-AAAA
1 AAAAAAAGTGAAA
8436 AAAAAAAGTGAAA
1 AAAAAAAGTGAAA
* *
8449 AAAAATCGAGTTAAA
1 AAAAA--AAGTGAAA
8464 AAAAAAAGTGAAA
1 AAAAAAAGTGAAA
8477 A
1 A
8478 GTCTTGCGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
12 8 0.24
13 15 0.44
15 11 0.32
ACGTcount: A:0.76, C:0.02, G:0.13, T:0.09
Consensus pattern (13 bp):
AAAAAAAGTGAAA
Found at i:9482 original size:6 final size:6
Alignment explanation
Indices: 9473--9559 Score: 52
Period size: 6 Copynumber: 14.2 Consensus size: 6
9463 GAAAGAGATT
* * *
9473 GAAAAA GAAAAAA AAAAAA GAAAAA GAAAAT GAAGAAAA GAAAATT GAAAAA
1 GAAAAA G-AAAAA GAAAAA GAAAAA GAAAAA G-A-AAAA GAAAA-A GAAAAA
* * * **
9525 G-AAAT GAGAAT GAAAAA -AAATT GAAAAA GAAAAA G
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA G
9560 CGAAAAAAGA
Statistics
Matches: 61, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
5 7 0.11
6 38 0.62
7 12 0.20
8 4 0.07
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (6 bp):
GAAAAA
Found at i:9495 original size:19 final size:20
Alignment explanation
Indices: 9473--9516 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
9463 GAAAGAGATT
9473 GAAAAAGAAAA-AAAAAAAA
1 GAAAAAGAAAATAAAAAAAA
* *
9492 GAAAAAGAAAATGAAGAAAA
1 GAAAAAGAAAATAAAAAAAA
9512 GAAAA
1 GAAAA
9517 TTGAAAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (20 bp):
GAAAAAGAAAATAAAAAAAA
Found at i:9509 original size:28 final size:28
Alignment explanation
Indices: 9477--9577 Score: 102
Period size: 27 Copynumber: 3.7 Consensus size: 28
9467 GAGATTGAAA
**
9477 AAGAAAAAAAAAAAAGAAAAAGAAAATG
1 AAGAAAAAAAAAATTGAAAAAGAAAATG
*
9505 AAG-AAAAGAAAATTGAAAAAG-AAATG
1 AAGAAAAAAAAAATTGAAAAAGAAAATG
*
9531 -AGAATGAAAAAAAATTGAAAAAGAAAAAG
1 AAGAA--AAAAAAAATTGAAAAAGAAAATG
* *
9560 -CGAAAAAAGAAATTGAAA
1 AAGAAAAAAAAAATTGAAA
9578 GAGAGCTTGA
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
25 2 0.03
26 6 0.10
27 28 0.45
28 19 0.31
29 7 0.11
ACGTcount: A:0.73, C:0.01, G:0.17, T:0.09
Consensus pattern (28 bp):
AAGAAAAAAAAAATTGAAAAAGAAAATG
Found at i:9528 original size:18 final size:17
Alignment explanation
Indices: 9472--9559 Score: 57
Period size: 17 Copynumber: 5.5 Consensus size: 17
9462 AGAAAGAGAT
9472 TGAAAAAG-AAA-AAAA
1 TGAAAAAGAAAAGAAAA
9487 --AAAAAGAAAAAGAAAA
1 TGAAAAAG-AAAAGAAAA
9503 TG---AAGAAAAGAAAA
1 TGAAAAAGAAAAGAAAA
* *
9517 TTGAAAAAGAAATGAGAA
1 -TGAAAAAGAAAAGAAAA
*
9535 TGAAAAA-AAATTGAAAA
1 TGAAAAAGAAA-AGAAAA
*
9552 AGAAAAAG
1 TGAAAAAG
9560 CGAAAAAAGA
Statistics
Matches: 58, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
13 6 0.10
14 9 0.16
15 8 0.14
16 7 0.12
17 18 0.31
18 10 0.17
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (17 bp):
TGAAAAAGAAAAGAAAA
Found at i:9611 original size:33 final size:33
Alignment explanation
Indices: 9574--9636 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
9564 AAAAGAAATT
9574 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
9607 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
9637 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:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:11434 original size:20 final size:20
Alignment explanation
Indices: 11411--11464 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
11401 AGTTTTTCCC
*
11411 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
11431 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
11451 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
11465 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:11446 original size:30 final size:30
Alignment explanation
Indices: 11411--11484 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
11401 AGTTTTTCCC
11411 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
11441 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
11471 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
11485 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:11474 original size:20 final size:20
Alignment explanation
Indices: 11411--11475 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
11401 AGTTTTTCCC
* * * *
11411 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
11431 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
11450 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
11471 AGCTC
1 AGCTC
11476 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:20067 original size:39 final size:39
Alignment explanation
Indices: 19989--20198 Score: 255
Period size: 40 Copynumber: 5.3 Consensus size: 39
19979 TCTTCGGAAT
* *
19989 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATAT-ATCACTAGCACAAATGCCTTCGGGTC
*
20028 TTAGCCCGGATATATCAACTCGCACAAATGCCTTC-GGTC
1 TTAGCCCGGATATATC-ACTAGCACAAATGCCTTCGGGTC
* *
20067 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGAT-ATATCACTAGCACAAATGCCTTCGGGTC
* * *
20107 TTAACCCGG-TATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATATC-ACTAGCACAAATGCCTTCGGGTC
* * *
20146 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGAC
1 TTAGCCCGGAT-ATATCACTAGCACAAATGCCTTCGGGTC
20186 TTAGCCCGGATAT
1 TTAGCCCGGATAT
20199 CATTCAAATG
Statistics
Matches: 146, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
38 3 0.02
39 68 0.47
40 72 0.49
41 3 0.02
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.24
Consensus pattern (39 bp):
TTAGCCCGGATATATCACTAGCACAAATGCCTTCGGGTC
Found at i:20115 original size:79 final size:80
Alignment explanation
Indices: 19989--20198 Score: 336
Period size: 79 Copynumber: 2.7 Consensus size: 80
19979 TCTTCGGAAT
* * * * *
19989 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCAC
20053 AAATGCCTTC-GGTC
66 AAATGCCTTCGGGTC
*
20067 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGG-TATAGCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCAC
20131 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
*
20146 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGCCCGGATAT
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATAT
20199 CATTCAAATG
Statistics
Matches: 121, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
78 28 0.23
79 90 0.74
80 3 0.02
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.24
Consensus pattern (80 bp):
TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCAC
AAATGCCTTCGGGTC
Done.