Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1384
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: 14628
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.38
Found at i:5721 original size:15 final size:15
Alignment explanation
Indices: 5701--5761 Score: 63
Period size: 15 Copynumber: 4.1 Consensus size: 15
5691 AGGAAAAGAG
5701 TTAAATATTAATATT
1 TTAAATATTAATATT
* * *
5716 TTAAATCTTAAAATGA
1 TTAAATATTAATAT-T
5732 TTAAATATTAA-ATT
1 TTAAATATTAATATT
*
5746 TTAAA-AATAATATT
1 TTAAATATTAATATT
5760 TT
1 TT
5762 TCAATTCTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
13 4 0.11
14 10 0.26
15 14 0.37
16 10 0.26
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (15 bp):
TTAAATATTAATATT
Found at i:5742 original size:23 final size:23
Alignment explanation
Indices: 5703--5758 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
5693 GAAAAGAGTT
*
5703 AAATATTAATATTTTAAATCTTA
1 AAATATTAATATATTAAATCTTA
*
5726 AAATGATTAA-ATATTAAATTTTA
1 AAAT-ATTAATATATTAAATCTTA
5749 AAA-A-TAATAT
1 AAATATTAATAT
5759 TTTTCAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 3 0.10
21 3 0.10
23 18 0.62
24 5 0.17
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
AAATATTAATATATTAAATCTTA
Found at i:6466 original size:14 final size:14
Alignment explanation
Indices: 6422--6470 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
6412 TTATTCAAAC
6422 TTAAAAATAAATAT
1 TTAAAAATAAATAT
*
6436 TAAATATAAATAAATAT
1 T---TAAAAATAAATAT
*
6453 TTAAAAATATATAT
1 TTAAAAATAAATAT
6467 TTAA
1 TTAA
6471 TTTTTTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 16 0.55
17 13 0.45
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TTAAAAATAAATAT
Found at i:7680 original size:13 final size:13
Alignment explanation
Indices: 7662--7686 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7652 CAACAGCTTT
7662 TAAAAATAAAAAA
1 TAAAAATAAAAAA
7675 TAAAAATAAAAA
1 TAAAAATAAAAA
7687 GTTTGTCACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:9569 original size:23 final size:21
Alignment explanation
Indices: 9543--9595 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 21
9533 TAAAAATATT
9543 AATAATTATTTATAAAAATAAAA
1 AATAATT-TTT-TAAAAATAAAA
*
9566 AAT-A-TTTTTAAATATAAAA
1 AATAATTTTTTAAAAATAAAA
*
9585 CATAATTTTTT
1 AATAATTTTTT
9596 TTAAAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 12 0.46
20 4 0.15
21 6 0.23
22 1 0.04
23 3 0.12
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AATAATTTTTTAAAAATAAAA
Found at i:10475 original size:7 final size:6
Alignment explanation
Indices: 10454--10483 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
10444 TATAAATGGC
10454 TTTTCT TTTTCT TTTTCTT TTTTCT TTTTC
1 TTTTCT TTTTCT TTTTC-T TTTTCT TTTTC
10484 ATTATAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:10477 original size:13 final size:12
Alignment explanation
Indices: 10454--10483 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
10444 TATAAATGGC
10454 TTTTCTTTTTCT
1 TTTTCTTTTTCT
10466 TTTTCTTTTTTCT
1 TTTTC-TTTTTCT
10479 TTTTC
1 TTTTC
10484 ATTATAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:10568 original size:16 final size:14
Alignment explanation
Indices: 10551--10593 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
10541 TTTATGTAAT
*
10551 ATATAATAAATTTA
1 ATATTATAAATTTA
10565 ATATT-TAAATTTTA
1 ATATTATAAA-TTTA
10579 ATATTTATAAATTTA
1 ATA-TTATAAATTTA
10594 TCTTTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 4 0.16
14 11 0.44
15 6 0.24
16 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATTATAAATTTA
Found at i:10794 original size:18 final size:17
Alignment explanation
Indices: 10740--10815 Score: 63
Period size: 18 Copynumber: 4.6 Consensus size: 17
10730 TTTTTATTTA
10740 ATTATAAA-ATAATATT
1 ATTATAAATATAATATT
* *
10756 -TT-T-AATTTAATTATA
1 ATTATAAATATAA-TATT
10771 ATTATAAATATAAATATT
1 ATTATAAATAT-AATATT
*
10789 ATTATAAAAATAATATT
1 ATTATAAATATAATATT
*
10806 -TTATTAATAT
1 ATTATAAATAT
10816 TATAATAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
13 2 0.04
14 4 0.09
15 5 0.11
16 10 0.21
17 7 0.15
18 17 0.36
19 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTATAAATATAATATT
Found at i:11189 original size:2 final size:2
Alignment explanation
Indices: 11182--11223 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
11172 TTAATGTGTT
11182 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA 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
11223 T
1 T
11224 TCTTTTGTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12637 original size:13 final size:12
Alignment explanation
Indices: 12604--12651 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
12594 TTAAAAATAA
12604 AAAATTATTTTT
1 AAAATTATTTTT
*
12616 AATAGTTATTTTTT
1 AA-AATTA-TTTTT
*
12630 AAAATTATCTTT
1 AAAATTATTTTT
12642 AAAA-TATTTT
1 AAAATTATTTT
12652 AAAGATGATA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
11 5 0.17
12 10 0.33
13 8 0.27
14 7 0.23
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (12 bp):
AAAATTATTTTT
Found at i:13517 original size:3 final size:3
Alignment explanation
Indices: 13509--13547 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
13499 GGCTAAAGGA
13509 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
13548 GTGGAGAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Done.