Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1474
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: 7790
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Found at i:551 original size:2 final size:2
Alignment explanation
Indices: 546--571 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
536 AAAGAGAGAG
546 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
572 TTCTATGACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1389 original size:11 final size:11
Alignment explanation
Indices: 1373--1402 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
1363 TTAATTTTGT
1373 ATTTTAATTTA
1 ATTTTAATTTA
1384 ATTTTAATTTA
1 ATTTTAATTTA
1395 ATATTTAA
1 AT-TTTAA
1403 AAAATTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATTTTAATTTA
Found at i:1400 original size:18 final size:19
Alignment explanation
Indices: 1360--1402 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1350 GTTAAATATT
* *
1360 TATTTAATTTTGTATTTTA
1 TATTTAATTTTGAATTTAA
1379 -ATTTAATTTT-AATTTAA
1 TATTTAATTTTGAATTTAA
1396 TATTTAA
1 TATTTAA
1403 AAAATTACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TATTTAATTTTGAATTTAA
Found at i:1608 original size:16 final size:17
Alignment explanation
Indices: 1589--1624 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1579 TGATATGACA
1589 TTTATAACATATTAT-T
1 TTTATAACATATTATGT
*
1605 TTTATCACATATTATGT
1 TTTATAACATATTATGT
1622 TTT
1 TTT
1625 CATTTACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (17 bp):
TTTATAACATATTATGT
Found at i:2511 original size:23 final size:24
Alignment explanation
Indices: 2470--2516 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
2460 AAATACATGA
* * *
2470 ATTTAATATATATTTTTAA-ATTT
1 ATTTAATAAAAATTATTAATATTT
2493 ATTTAATAAAAATTATTAATATTT
1 ATTTAATAAAAATTATTAATATTT
2517 TAAAATTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTAATAAAAATTATTAATATTT
Found at i:3820 original size:21 final size:21
Alignment explanation
Indices: 3778--3841 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
3768 GCTTTTCTAA
* * * *
3778 TTAATAGTTATAAATTATTAT
1 TTAATAATAATAAATAAATAT
3799 TTAATAATAATAAATAAATA-
1 TTAATAATAATAAATAAATAT
3819 TTAAT-ATAA-AAATAAA-AT
1 TTAATAATAATAAATAAATAT
3837 TTAAT
1 TTAAT
3842 TTTTATTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
17 1 0.03
18 12 0.32
19 4 0.11
20 5 0.13
21 16 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
TTAATAATAATAAATAAATAT
Found at i:3848 original size:28 final size:28
Alignment explanation
Indices: 3817--3873 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
3807 AATAAATAAA
3817 TATTAATATAAAAATAA-AATTTAATTTT
1 TATTAAT-TAAAAATAATAATTTAATTTT
**
3845 TATTAATTATGAATAATAATTTAATTTT
1 TATTAATTAAAAATAATAATTTAATTTT
3873 T
1 T
3874 TTATCTAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (28 bp):
TATTAATTAAAAATAATAATTTAATTTT
Found at i:4365 original size:26 final size:27
Alignment explanation
Indices: 4295--4365 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 27
4285 TATTTATACA
* *
4295 ATATAATATAAATCTTT-TTAAATTAT
1 ATATAATATAAATATTTAATAAATTAT
* * * *
4321 CTATAATAT-AATATATAATAATTTTT
1 ATATAATATAAATATTTAATAAATTAT
4347 ATATAATATAAAT-TTTAAT
1 ATATAATATAAATATTTAAT
4366 TTTTAAATTA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
25 5 0.14
26 27 0.77
27 3 0.09
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (27 bp):
ATATAATATAAATATTTAATAAATTAT
Found at i:5403 original size:2 final size:2
Alignment explanation
Indices: 5396--5424 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5386 ATGGCTTCAA
5396 CT CT CT CT CT CT CT CT CT CT CT -T CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5425 ATATATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:5429 original size:2 final size:2
Alignment explanation
Indices: 5424--5466 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
5414 CTCTTCTCTC
5424 TA TA TA TA TA -A TA TA TA TA TA TA -A TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5463 TA TA
1 TA TA
5467 ATGGATCTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5437 original size:9 final size:9
Alignment explanation
Indices: 5424--5464 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
5414 CTCTTCTCTC
5424 TATATAT-A
1 TATATATAA
5432 TA-ATAT-A
1 TATATATAA
5439 TATATATAA
1 TATATATAA
5448 TATATATAA
1 TATATATAA
5457 TATATATA
1 TATATATA
5465 TAATGGATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.23
8 6 0.19
9 18 0.58
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TATATATAA
Found at i:5438 original size:11 final size:11
Alignment explanation
Indices: 5424--5468 Score: 74
Period size: 11 Copynumber: 4.1 Consensus size: 11
5414 CTCTTCTCTC
5424 TATATATATAA
1 TATATATATAA
5435 TATATATAT-A
1 TATATATATAA
5445 TAATATATATAA
1 T-ATATATATAA
5457 TATATATATAA
1 TATATATATAA
5468 T
1 T
5469 GGATCTTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 2 0.06
11 28 0.88
12 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TATATATATAA
Found at i:5440 original size:13 final size:13
Alignment explanation
Indices: 5424--5466 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
5414 CTCTTCTCTC
5424 TATATATATAATA
1 TATATATATAATA
5437 TATATATATAATA
1 TATATATATAATA
5450 TATATA-AT-ATA
1 TATATATATAATA
5461 TATATA
1 TATATA
5467 ATGGATCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.30
12 2 0.07
13 19 0.63
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TATATATATAATA
Found at i:5542 original size:22 final size:22
Alignment explanation
Indices: 5514--5557 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5504 TCCAAGCCAT
5514 ACCTTTAAGACATAGAACGGAA
1 ACCTTTAAGACATAGAACGGAA
*
5536 ACCTTTAAGACATAGAATGGAA
1 ACCTTTAAGACATAGAACGGAA
5558 GAAGCAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.20
Consensus pattern (22 bp):
ACCTTTAAGACATAGAACGGAA
Done.