Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold397
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: 433447
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
File 4 of 4
Found at i:425494 original size:20 final size:20
Alignment explanation
Indices: 425464--425516 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
425454 TTTAGAAATT
425464 ATAAA-ATAATTGTATG-AA
1 ATAAATATAATTGTATGAAA
*
425482 ATAAAATATAATT-TATTAAA
1 AT-AAATATAATTGTATGAAA
*
425502 ATAAATATAAGTGTA
1 ATAAATATAATTGTA
425517 AAAATTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 2 0.07
19 15 0.52
20 12 0.41
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.36
Consensus pattern (20 bp):
ATAAATATAATTGTATGAAA
Found at i:426927 original size:32 final size:32
Alignment explanation
Indices: 426888--426951 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
426878 AAAAAATTAT
* * *
426888 AATATTAAAT-TTATAATTTTTGATATTAAATA
1 AATATTAAATATAATAAATTTTGA-ATAAAATA
426920 AATATTAAATATAATAAATTTTGAATAAAATA
1 AATATTAAATATAATAAATTTTGAATAAAATA
426952 TGTATTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (32 bp):
AATATTAAATATAATAAATTTTGAATAAAATA
Found at i:427060 original size:19 final size:20
Alignment explanation
Indices: 427023--427061 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
427013 ATATCTTAAA
427023 ATTGGTTTAATATGTATTTT
1 ATTGGTTTAATATGTATTTT
* *
427043 ATTGTTTTAGTATG-ATTTT
1 ATTGGTTTAATATGTATTTT
427062 TATTAATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (20 bp):
ATTGGTTTAATATGTATTTT
Found at i:429479 original size:25 final size:25
Alignment explanation
Indices: 429448--429521 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 25
429438 TTATAAAAAA
429448 TAAATTTAAATTTTATATTTATTTT
1 TAAATTTAAATTTTATATTTATTTT
* ** *
429473 TAAATTT-AATTATATAAATATAATT
1 TAAATTTAAATTTTATATTTAT-TTT
*
429498 TAAAATTAAACTTTTATATTTATT
1 TAAATTTAAA-TTTTATATTTATT
429522 ATAAATAAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
24 11 0.30
25 15 0.41
26 2 0.05
27 9 0.24
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (25 bp):
TAAATTTAAATTTTATATTTATTTT
Found at i:429526 original size:25 final size:24
Alignment explanation
Indices: 429447--429526 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
429437 TTTATAAAAA
*
429447 ATAAATTTAAATTTTATATTTATT
1 ATAAAATTAAATTTTATATTTATT
* * * * *
429471 TTTAAATTTAATTATATAAATATAATT
1 ATAAAATTAAATT-T-TATAT-TTATT
429498 -TAAAATTAAACTTTTATATTTATT
1 ATAAAATTAAA-TTTTATATTTATT
429522 ATAAA
1 ATAAA
429527 TAAATATTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 9
0.68 0.17 0.15
Matches are distributed among these distances:
24 13 0.32
25 9 0.22
26 13 0.32
27 6 0.15
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (24 bp):
ATAAAATTAAATTTTATATTTATT
Found at i:431428 original size:32 final size:31
Alignment explanation
Indices: 431386--431447 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
431376 TTATAAATTT
431386 ATATAAATTTTAAAAT-TTTAATGATTTATATG
1 ATATAAATTTTAAAATATTT-AT-ATTTATATG
* *
431418 ATATATATTTTAATATATTTATATTTATAT
1 ATATAAATTTTAAAATATTTATATTTATAT
431448 TTTTTATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 8 0.30
32 16 0.59
33 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (31 bp):
ATATAAATTTTAAAATATTTATATTTATATG
Found at i:431442 original size:6 final size:6
Alignment explanation
Indices: 431431--431469 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
431421 TATATTTTAA
*
431431 TATATT TATATT TATATTT TTTATAT TATATT TATATT T
1 TATATT TATATT TATA-TT TATAT-T TATATT TATATT T
431470 TTTATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 19 0.66
7 10 0.34
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TATATT
Found at i:431459 original size:20 final size:21
Alignment explanation
Indices: 431421--431479 Score: 84
Period size: 20 Copynumber: 2.8 Consensus size: 21
431411 TTATATGATA
*
431421 TATATTTTAATATATTTATATT
1 TATATTTT-TTATATTTATATT
431443 TATATTTTTTATA-TTATATT
1 TATATTTTTTATATTTATATT
431463 TATATTTTTTATTATTT
1 TATATTTTTTA-TATTT
431480 TTTAATTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 18 0.53
21 6 0.18
22 10 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TATATTTTTTATATTTATATT
Found at i:431460 original size:26 final size:24
Alignment explanation
Indices: 431400--431469 Score: 79
Period size: 24 Copynumber: 2.8 Consensus size: 24
431390 AAATTTTAAA
* *
431400 ATTTTAAT-GATTTATATGATATAT
1 ATTTTAATATATTTATAT-TTATAT
431424 ATTTTAATATATTTATATTTATAT
1 ATTTTAATATATTTATATTTATAT
*
431448 TTTTTATATTATATTTATATTT
1 ATTTTA-A-TATATTTATATTT
431470 TTTATTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
24 18 0.45
25 9 0.22
26 13 0.32
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (24 bp):
ATTTTAATATATTTATATTTATAT
Found at i:431473 original size:9 final size:9
Alignment explanation
Indices: 431441--431483 Score: 59
Period size: 9 Copynumber: 4.4 Consensus size: 9
431431 TATATTTATA
431441 TTTATATTT
1 TTTATATTT
431450 TTTATATTAT
1 TTTATATT-T
431460 ATTTATATTT
1 -TTTATATTT
431470 TTTATTATTT
1 TTTA-TATTT
431480 TTTA
1 TTTA
431484 ATTATGTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 12 0.39
10 11 0.35
11 8 0.26
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTATATTT
Found at i:431474 original size:15 final size:14
Alignment explanation
Indices: 431435--431495 Score: 54
Period size: 14 Copynumber: 4.2 Consensus size: 14
431425 TTTTAATATA
431435 TTTATATTTATATTT
1 TTTATA-TTATATTT
431450 TTTATATTATATTT
1 TTTATATTATATTT
*
431464 ATATT-TTTTATTATTT
1 -T-TTATATTA-TATTT
*
431480 TTTA-ATTATGTTT
1 TTTATATTATATTT
431493 TTT
1 TTT
431496 TTTTTTTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
13 7 0.18
14 13 0.33
15 12 0.31
16 7 0.18
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTATATTATATTT
Found at i:431503 original size:30 final size:29
Alignment explanation
Indices: 431419--431488 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 29
431409 ATTTATATGA
*
431419 TATATATTTTA-A-TATATTTATA---TT
1 TATATTTTTTATATTATATTTATATTTTT
431443 TATATTTTTTATATTATATTTATATTTTT
1 TATATTTTTTATATTATATTTATATTTTT
431472 TATTATTTTTTA-ATTAT
1 TA-TATTTTTTATATTAT
431489 GTTTTTTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
24 10 0.26
25 1 0.03
26 10 0.26
29 9 0.23
30 9 0.23
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (29 bp):
TATATTTTTTATATTATATTTATATTTTT
Found at i:432901 original size:51 final size:51
Alignment explanation
Indices: 432825--432926 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
432815 GGAAAAAGGA
432825 AAGAGAAATCGCTTTGGATGAGCATATTCTATGAATTAATACTGTATGTAT
1 AAGAGAAATCGCTTTGGATGAGCATATTCTATGAATTAATACTGTATGTAT
432876 AAGAGAAATCGCTTTGGATGAGCATATTCTATGAATTAATACTGTATGTAT
1 AAGAGAAATCGCTTTGGATGAGCATATTCTATGAATTAATACTGTATGTAT
432927 CTTTCACAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (51 bp):
AAGAGAAATCGCTTTGGATGAGCATATTCTATGAATTAATACTGTATGTAT
Done.