Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1598
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: 30124
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:3269 original size:15 final size:15
Alignment explanation
Indices: 3249--3315 Score: 82
Period size: 16 Copynumber: 4.3 Consensus size: 15
3239 ACGGTATTGT
*
3249 AAAAAAAATAT-ATAA
1 AAAAAAAAT-TCAAAA
3264 AAAAAAAATTCGAAAA
1 AAAAAAAATTC-AAAA
*
3280 AAAAAAAATTTGAAAA
1 AAAAAAAA-TTCAAAA
3296 AAAAAAAATTCAAAA
1 AAAAAAAATTCAAAA
3311 AAAAA
1 AAAAA
3316 GTTTGTATTC
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
14 1 0.02
15 20 0.43
16 23 0.50
17 2 0.04
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (15 bp):
AAAAAAAATTCAAAA
Found at i:3420 original size:20 final size:20
Alignment explanation
Indices: 3396--3434 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3386 AATTAAAACA
*
3396 AAAAAAGAAGAAAAAAAAATC
1 AAAATAGAA-AAAAAAAAATC
*
3417 AAAATTGAAAAAAAAAAA
1 AAAATAGAAAAAAAAAAA
3435 GTGATTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08
Consensus pattern (20 bp):
AAAATAGAAAAAAAAAAATC
Found at i:3432 original size:33 final size:34
Alignment explanation
Indices: 3353--3435 Score: 116
Period size: 34 Copynumber: 2.5 Consensus size: 34
3343 TGTATTTAGT
* **
3353 ATTGAAGAAAAAAAAGAAGAAAAAAAAATTCGGA
1 ATTGAAAAAAAAAAAGAAGAAAAAAAAATTCAAA
3387 ATT-AAAACAAAAAAAGAAGAAAAAAAAA-TCAAA
1 ATTGAAAA-AAAAAAAGAAGAAAAAAAAATTCAAA
3420 ATTGAAAAAAAAAAAG
1 ATTGAAAAAAAAAAAG
3436 TGATTGAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
33 17 0.39
34 27 0.61
ACGTcount: A:0.73, C:0.04, G:0.12, T:0.11
Consensus pattern (34 bp):
ATTGAAAAAAAAAAAGAAGAAAAAAAAATTCAAA
Found at i:4344 original size:21 final size:20
Alignment explanation
Indices: 4319--4363 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
4309 AATCTTGAAT
*
4319 GAAATTGAGAGA-AGAAAAAA
1 GAAAATGAGAGAGAG-AAAAA
*
4339 GAAAATGAGAGTGAGAAAAA
1 GAAAATGAGAGAGAGAAAAA
4359 GAAAA
1 GAAAA
4364 AAGAATTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (20 bp):
GAAAATGAGAGAGAGAAAAA
Found at i:4380 original size:27 final size:27
Alignment explanation
Indices: 4316--4381 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
4306 ACGAATCTTG
* *
4316 AATGAAATTGAG-AGAAGAAAAAAGAA
1 AATGAGATTGAGAAAAAGAAAAAAGAA
*
4342 AATGAGAGTGAGAAAAAGAAAAAAGAA
1 AATGAGATTGAGAAAAAGAAAAAAGAA
**
4369 TTTGAGATTGAGA
1 AATGAGATTGAGA
4382 TTGATATTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 10 0.30
27 23 0.70
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (27 bp):
AATGAGATTGAGAAAAAGAAAAAAGAA
Found at i:4390 original size:12 final size:12
Alignment explanation
Indices: 4370--4405 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
4360 AAAAAAGAAT
*
4370 TTGAGATTGAGA
1 TTGATATTGAGA
*
4382 TTGATATTGATA
1 TTGATATTGAGA
4394 TTGATATTGAGA
1 TTGATATTGAGA
4406 AAAAAATTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (12 bp):
TTGATATTGAGA
Found at i:9498 original size:30 final size:28
Alignment explanation
Indices: 9445--9500 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
9435 TTCTTCCACG
* *
9445 CTTTCTTTTTGCTCACTCTCTTTTTCAA
1 CTTTCTTTTTGCACACACTCTTTTTCAA
9473 CTTTACTTTCTTGCACACACTCTTTTTC
1 CTTT-CTTT-TTGCACACACTCTTTTTC
9501 TTTTTCGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.12, C:0.30, G:0.04, T:0.54
Consensus pattern (28 bp):
CTTTCTTTTTGCACACACTCTTTTTCAA
Found at i:12377 original size:15 final size:15
Alignment explanation
Indices: 12357--12404 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
12347 TCAAAGATGG
12357 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
12372 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
12387 -TTTATGGATATAAA
1 GTTTATGGATATGAA
12401 GTTT
1 GTTT
12405 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:12384 original size:29 final size:29
Alignment explanation
Indices: 12351--12410 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
12341 AAGGATTCAA
* *
12351 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
12380 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
12409 AG
1 AG
12411 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:15579 original size:27 final size:27
Alignment explanation
Indices: 15517--15579 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
15507 GCCGAATTTC
*
15517 ATGTGTCTTAGTTCCAGCATGATTTTA
1 ATGTGTCTTAGTTCCAGCATGATTTAA
* * **
15544 ATTTCTCTTAGTTATTA-CATGATTTAA
1 ATGTGTCTTAGTT-CCAGCATGATTTAA
15571 ATGTGTCTT
1 ATGTGTCTT
15580 TGAGCCGAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
27 27 0.96
28 1 0.04
ACGTcount: A:0.24, C:0.13, G:0.14, T:0.49
Consensus pattern (27 bp):
ATGTGTCTTAGTTCCAGCATGATTTAA
Found at i:16681 original size:30 final size:30
Alignment explanation
Indices: 16647--16743 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
16637 AGCTCAGTCC
*
16647 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * * *
16677 TAGCTCAACTTTAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
16707 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
16737 TAGCTCA
1 TAGCTCA
16744 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
30 47 0.90
31 5 0.10
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:19659 original size:63 final size:65
Alignment explanation
Indices: 19590--19724 Score: 154
Period size: 67 Copynumber: 2.1 Consensus size: 65
19580 CTAACTTAAA
*
19590 TAAATGAAC-TAACACTTATGCATCA-T-TTAATCC-AGAAACTAGTTTAATTAATAGAAGCAT-
1 TAAATGAACTTAA-ACTCATGCATCACTATT-ATCCTAGAAACTAGTTTAATTAA-AGAAGCATC
19650 TAT
63 TAT
* * *
19653 TAAATGAACTTTAACTCATGCATCACTAAATTATCCTAGTAACTAGTTTATTTAAAGAAGCATCT
1 TAAATGAACTTAAACTCATGCATCACT--ATTATCCTAGAAACTAGTTTAATTAAAGAAGCATCT
19718 AT
64 AT
19720 TAAAT
1 TAAAT
19725 CAAGTTCATA
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
63 20 0.33
64 3 0.05
66 12 0.20
67 26 0.43
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (65 bp):
TAAATGAACTTAAACTCATGCATCACTATTATCCTAGAAACTAGTTTAATTAAAGAAGCATCTAT
Found at i:27723 original size:31 final size:28
Alignment explanation
Indices: 27657--27724 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
27647 GTGCTAATTT
* *
27657 GTGTGTTTGGGCGGACTATGTGATTCTG
1 GTGTGTTTGGGAGGACTATATGATTCTG
*
27685 GTGGTGTTTGGGAGGATTATATGACATTCTTG
1 GT-GTGTTTGGGAGGACTATATG--ATTC-TG
27717 GTGTGTTT
1 GTGTGTTT
27725 TGGTTGGATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 2 0.06
29 17 0.52
31 10 0.30
32 4 0.12
ACGTcount: A:0.13, C:0.07, G:0.37, T:0.43
Consensus pattern (28 bp):
GTGTGTTTGGGAGGACTATATGATTCTG
Done.