Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2421
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: 40726
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:582 original size:30 final size:30
Alignment explanation
Indices: 548--644 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
538 AGCTCACTCC
548 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
578 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
608 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
638 TAGCTCA
1 TAGCTCA
645 TTTTAGTTTT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:2398 original size:12 final size:13
Alignment explanation
Indices: 2363--2399 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
2353 AAAAAAGAAG
2363 AAATTCAGAAAAAA
1 AAATTC-GAAAAAA
2377 AAATTC-AAAAAA
1 AAATTCGAAAAAA
2389 AAA-TCGAAAAA
1 AAATTCGAAAAA
2400 GGAAAAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 2 0.09
12 14 0.64
14 6 0.27
ACGTcount: A:0.73, C:0.08, G:0.05, T:0.14
Consensus pattern (13 bp):
AAATTCGAAAAAA
Found at i:3348 original size:21 final size:20
Alignment explanation
Indices: 3318--3387 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 20
3308 ACATTCTTGT
*
3318 AAAGAGAAAACAAAGAAAAGA
1 AAAGA-AAAAAAAAGAAAAGA
*
3339 AAAGAAAAAAGAAA-AGCAAGA
1 AAAGAAAAAA-AAAGA-AAAGA
*
3360 GAAGAAAAAAAAATGAAATA-A
1 AAAGAAAAAAAAA-GAAA-AGA
3381 AAAGAAA
1 AAAGAAA
3388 GAGAGGCAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
20 8 0.21
21 29 0.74
22 2 0.05
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAAAAAGAAAAGA
Found at i:3359 original size:26 final size:25
Alignment explanation
Indices: 3322--3387 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
3312 TCTTGTAAAG
3322 AGAAAACAAAGAAAAGAAAAGAAAAA
1 AGAAAACAAAGAAAAGAAAA-AAAAA
*
3348 AGAAAAGC-AAGAGAAGAAAAAAAAA
1 AGAAAA-CAAAGAAAAGAAAAAAAAA
* *
3373 TGAAATAAAAAGAAA
1 AGAAA-ACAAAGAAA
3388 GAGAGGCAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 9 0.27
26 23 0.70
27 1 0.03
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (25 bp):
AGAAAACAAAGAAAAGAAAAAAAAA
Found at i:3469 original size:11 final size:12
Alignment explanation
Indices: 3437--3467 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3427 TTGAGAGAAC
3437 TTGAAAAAGCCT
1 TTGAAAAAGCCT
3449 TTGAAAAAGCCT
1 TTGAAAAAGCCT
3461 TTGAAAA
1 TTGAAAA
3468 GCAAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:6332 original size:23 final size:22
Alignment explanation
Indices: 6280--6332 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
6270 TCCACGTCTT
*
6280 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
6302 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
6325 TTTCTTTT
1 TTTCTTTT
6333 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:9716 original size:11 final size:11
Alignment explanation
Indices: 9700--9750 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
9690 AATACAAACT
9700 TTTTTTTTGAA
1 TTTTTTTTGAA
9711 TTTTTTTTGAA
1 TTTTTTTTGAA
*
9722 TTTTTTTTTCAA
1 -TTTTTTTTGAA
*
9734 GTTTTTTT--A
1 TTTTTTTTGAA
9743 TTTTTTTT
1 TTTTTTTT
9751 TACAATACCG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
9 8 0.22
11 18 0.50
12 10 0.28
ACGTcount: A:0.14, C:0.02, G:0.06, T:0.78
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:9725 original size:23 final size:21
Alignment explanation
Indices: 9699--9751 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 21
9689 GAATACAAAC
* *
9699 TTTTTTTTTGAATTTTTTTTGAA
1 TTTTTTTTTCAAGTTTTTTT--A
9722 TTTTTTTTTCAAGTTTTTTTA
1 TTTTTTTTTCAAGTTTTTTTA
9743 TTTTTTTTT
1 TTTTTTTTT
9752 ACAATACCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 10 0.36
23 18 0.64
ACGTcount: A:0.13, C:0.02, G:0.06, T:0.79
Consensus pattern (21 bp):
TTTTTTTTTCAAGTTTTTTTA
Found at i:15137 original size:18 final size:18
Alignment explanation
Indices: 15116--15173 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
15106 ACCTCACTCT
15116 TTTTTTGATTTCTTTTTC
1 TTTTTTGATTTCTTTTTC
** *
15134 TTTTTCAATCTCTTTTTC
1 TTTTTTGATTTCTTTTTC
15152 TTTTCTTTTGATTTCTTTTTC
1 --TT-TTTTGATTTCTTTTTC
15173 T
1 T
15174 CGCTCGCACT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
18 15 0.48
19 1 0.03
20 2 0.06
21 13 0.42
ACGTcount: A:0.07, C:0.16, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTTTGATTTCTTTTTC
Found at i:16128 original size:12 final size:13
Alignment explanation
Indices: 16104--16131 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
16094 CAAAAAAAAA
16104 TTTGAATTTTTTT
1 TTTGAATTTTTTT
16117 TTTGAATTTTTTT
1 TTTGAATTTTTTT
16130 TT
1 TT
16132 CAAATTTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTGAATTTTTTT
Found at i:22549 original size:17 final size:18
Alignment explanation
Indices: 22527--22563 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
22517 TGGAATAAAC
22527 TTAGTTAA-TTAAATAAG
1 TTAGTTAATTTAAATAAG
*
22544 TTAGTTAATTTAATTAAG
1 TTAGTTAATTTAAATAAG
22562 TT
1 TT
22564 CAGCTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAGTTAATTTAAATAAG
Found at i:27338 original size:33 final size:33
Alignment explanation
Indices: 27300--27362 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
27290 GATTACTCAC
27300 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
27333 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
27363 AATTTCTTTT
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:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:27389 original size:21 final size:21
Alignment explanation
Indices: 27360--27415 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
27350 CAAGCTCTCT
*
27360 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
27381 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
27402 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
27416 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:27402 original size:18 final size:17
Alignment explanation
Indices: 27379--27514 Score: 64
Period size: 18 Copynumber: 7.6 Consensus size: 17
27369 TTTTTTCGCT
27379 TTTTCTTTTTCAATTTTC
1 TTTTCTTTTTC-ATTTTC
*
27397 TTTTCTTCATTTTCTTTTTC
1 TTTTC-T--TTTTCATTTTC
**
27417 TCTCACTTTTTCGA-TTTC
1 T-TTTCTTTTTC-ATTTTC
* *
27435 TTTTTCTTTTGCAATTTC
1 -TTTTCTTTTTCATTTTC
*
27453 TTTTTCTTTTTCGTTTTC
1 -TTTTCTTTTTCATTTTC
27471 TTTT-TGTTTTC--TTTC
1 TTTTCT-TTTTCATTTTC
* * *
27486 AATTTCTTTTTCAATCTC
1 -TTTTCTTTTTCATTTTC
*
27504 TTTTCCTTTTC
1 TTTTCTTTTTC
27515 TCGCTCAATG
Statistics
Matches: 92, Mismatches: 14, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
15 4 0.04
16 9 0.10
17 20 0.22
18 43 0.47
19 2 0.02
20 7 0.08
21 7 0.08
ACGTcount: A:0.08, C:0.20, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTCTTTTTCATTTTC
Found at i:27408 original size:14 final size:14
Alignment explanation
Indices: 27359--27415 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
27349 TCAAGCTCTC
27359 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
27372 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
27386 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
27400 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
27414 TT
1 TT
27416 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:27497 original size:6 final size:6
Alignment explanation
Indices: 27377--27484 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
27367 TCTTTTTTCG
* * * **
27377 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
27428 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
27476 -GTTTT CTTT
1 CTTTTT CTTT
27485 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:28542 original size:13 final size:13
Alignment explanation
Indices: 28524--28567 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
28514 TTCAAAAAAA
28524 AAATTTTTTTTTG
1 AAATTTTTTTTTG
28537 AAA-TTTTTTTTG
1 AAATTTTTTTTTG
*
28549 AAATTTTTTTTTC
1 AAATTTTTTTTTG
28562 AAATTT
1 AAATTT
28568 CCTCTTCCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 12 0.41
13 17 0.59
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (13 bp):
AAATTTTTTTTTG
Found at i:28545 original size:12 final size:12
Alignment explanation
Indices: 28528--28559 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
28518 AAAAAAAAAT
28528 TTTTTTTTGAAA
1 TTTTTTTTGAAA
28540 TTTTTTTTGAAA
1 TTTTTTTTGAAA
28552 TTTTTTTT
1 TTTTTTTT
28560 TCAAATTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (12 bp):
TTTTTTTTGAAA
Found at i:30401 original size:15 final size:15
Alignment explanation
Indices: 30381--30418 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
30371 CAAAAAAATC
30381 AAAAAAAATTGATTG
1 AAAAAAAATTGATTG
30396 AAAAAAAATTGATTG
1 AAAAAAAATTGATTG
30411 AAAAAAAA
1 AAAAAAAA
30419 AATTCAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (15 bp):
AAAAAAAATTGATTG
Found at i:30510 original size:42 final size:40
Alignment explanation
Indices: 30394--30510 Score: 112
Period size: 42 Copynumber: 2.9 Consensus size: 40
30384 AAAAATTGAT
* * * *
30394 TGAAAAAAAATTGA-TTGAAAAAAAAAATTCAAAAAAAAG
1 TGAAAAAAAAATGAGTTAAAAAAAAAAAATGAAAAAAAAG
* *
30433 TGAAAAAAAAATCGAG-CAAAAAAAAAGAAAAGAAAAAAAAGG
1 TGAAAAAAAAAT-GAGTTAAAAAAAAA-AAATGAAAAAAAA-G
* *
30475 TGAAAAAAAAATGAAGTTTAAAAAAAAAAGTGAAAA
1 TGAAAAAAAAATG-AGTTAAAAAAAAAAAATGAAAA
30511 GTCTTGCGAG
Statistics
Matches: 62, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
39 11 0.18
40 10 0.16
41 11 0.18
42 22 0.35
43 8 0.13
ACGTcount: A:0.71, C:0.03, G:0.14, T:0.13
Consensus pattern (40 bp):
TGAAAAAAAAATGAGTTAAAAAAAAAAAATGAAAAAAAAG
Found at i:33299 original size:17 final size:18
Alignment explanation
Indices: 33277--33313 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
33267 TGGAATAAAC
33277 TTAGTTAA-TTAAATAAG
1 TTAGTTAATTTAAATAAG
*
33294 TTAGTTAATTTAATTAAG
1 TTAGTTAATTTAAATAAG
33312 TT
1 TT
33314 CAGCTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAGTTAATTTAAATAAG
Done.