Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2078
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: 8641
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Found at i:3427 original size:18 final size:18
Alignment explanation
Indices: 3370--3427 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 18
3360 ATATTATTAT
*
3370 TATATTTAA-ATTTAATA
1 TATATTTAATATATAATA
* * *
3387 TA-A-ATAATTTATAAAA
1 TATATTTAATATATAATA
*
3403 TAAATTTAATATATAATA
1 TATATTTAATATATAATA
3421 TATATTT
1 TATATTT
3428 TGTTAGTAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 5
0.70 0.19 0.12
Matches are distributed among these distances:
15 3 0.10
16 8 0.27
17 3 0.10
18 16 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TATATTTAATATATAATA
Found at i:3464 original size:27 final size:29
Alignment explanation
Indices: 3419--3490 Score: 94
Period size: 28 Copynumber: 2.5 Consensus size: 29
3409 TAATATATAA
* *
3419 TATATATTTTGTTAGTAATTT-ATAATTTT
1 TATATATTATATTA-TAATTTAATAATTTT
3448 T-TATATTATATTATAATTTAATAATTTT
1 TATATATTATATTATAATTTAATAATTTT
*
3476 TATTTATTATATTAT
1 TATATATTATATTAT
3491 TTTAATTATG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 6 0.16
28 19 0.50
29 13 0.34
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (29 bp):
TATATATTATATTATAATTTAATAATTTT
Found at i:3494 original size:27 final size:27
Alignment explanation
Indices: 3436--3496 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 27
3426 TTTGTTAGTA
3436 ATTT-ATAATTTTTTATATTATATTAT
1 ATTTAATAATTTTTTATATTATATTAT
*
3462 AATTTAATAATTTTTATTTATTATATTAT
1 -ATTTAATAATTTTT-TATATTATATTAT
3491 -TTTAAT
1 ATTTAAT
3497 TATGTATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 10 0.32
28 9 0.29
29 12 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
ATTTAATAATTTTTTATATTATATTAT
Found at i:3527 original size:31 final size:30
Alignment explanation
Indices: 3451--3535 Score: 77
Period size: 31 Copynumber: 2.8 Consensus size: 30
3441 TAATTTTTTA
*
3451 TATTATATTATAATTTAATA-AT-TTTT-ATT
1 TATTAAATTA-AA-TTAATATATATTTTAATT
* ** *
3480 TATTATATTATTTTAATTATGTATTTTAATT
1 TATTAAATTAAATTAA-TATATATTTTAATT
3511 TATTAAATTAAATTAATATATATTT
1 TATTAAATTAAATTAATATATATTT
3536 ATTTAAATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
27 4 0.09
28 2 0.04
29 11 0.24
30 12 0.27
31 16 0.36
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (30 bp):
TATTAAATTAAATTAATATATATTTTAATT
Found at i:3561 original size:13 final size:13
Alignment explanation
Indices: 3545--3570 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3535 TATTTAAATT
3545 TTAATATTAATAA
1 TTAATATTAATAA
3558 TTAATATTAATAA
1 TTAATATTAATAA
3571 ATTTTAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATATTAATAA
Found at i:3607 original size:10 final size:10
Alignment explanation
Indices: 3582--3653 Score: 53
Period size: 10 Copynumber: 7.4 Consensus size: 10
3572 TTTTAACATA
*
3582 TTTATATATTT
1 TTTAT-TATAT
3593 TTTATTATAT
1 TTTATTATAT
3603 TTTATTA-AT
1 TTTATTATAT
*
3612 TTTTTTATAT
1 TTTATTATAT
** *
3622 GATATCATAT
1 TTTATTATAT
3632 TTTA--AT-T
1 TTTATTATAT
3639 TTTATTTATAT
1 TTTA-TTATAT
3650 TTTA
1 TTTA
3654 AATTATTAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
7 5 0.10
8 2 0.04
9 8 0.17
10 23 0.48
11 10 0.21
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (10 bp):
TTTATTATAT
Found at i:4160 original size:23 final size:21
Alignment explanation
Indices: 4120--4176 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
4110 ATTTTAATTT
* *
4120 TAAATTTAATTCAGATAATATAA
1 TAAATTAAATTTA-ATAATAT-A
*
4143 TTAATTAATATTTAATAATATA
1 TAAATTAA-ATTTAATAATATA
4165 TAAATTAAATTT
1 TAAATTAAATTT
4177 TAATTTCTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 4 0.14
22 8 0.28
23 13 0.45
24 4 0.14
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
TAAATTAAATTTAATAATATA
Found at i:4180 original size:22 final size:23
Alignment explanation
Indices: 4134--4176 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
4124 TTTAATTCAG
*
4134 ATAATATAATTAATTAATATTTA
1 ATAATATAATAAATTAATATTTA
4157 ATAATAT-ATAAATTAA-ATTT
1 ATAATATAATAAATTAATATTT
4177 TAATTTCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 8 0.42
23 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAATATAATAAATTAATATTTA
Done.