Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1550
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: 29812
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Found at i:996 original size:2 final size:2
Alignment explanation
Indices: 989--1015 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
979 TGACGTTAGC
989 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1016 AATGAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4524 original size:16 final size:17
Alignment explanation
Indices: 4503--4535 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4493 ATATTGTGTA
4503 TTTTATTATAT-ATAAT
1 TTTTATTATATCATAAT
*
4519 TTTTATTCTATCATAAT
1 TTTTATTATATCATAAT
4536 ATATACTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTATTATATCATAAT
Found at i:4603 original size:24 final size:23
Alignment explanation
Indices: 4566--4654 Score: 76
Period size: 22 Copynumber: 3.9 Consensus size: 23
4556 AACATTATCA
*
4566 TTATA-TAAATTTTAAAATATTTAT
1 TTATATTAAA-TTTAAATTATTT-T
*
4590 TTATATTAAATTTATATTA-TTT
1 TTATATTAAATTTAAATTATTTT
* *
4612 TTATATTATATTTTAATTA-TTT
1 TTATATTAAATTTAAATTATTTT
* *
4634 TTATATCATATTTAATATTAT
1 TTATATTAAATTTAA-ATTAT
4655 CGAATCGGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
22 33 0.60
23 6 0.11
24 12 0.22
25 4 0.07
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (23 bp):
TTATATTAAATTTAAATTATTTT
Found at i:4604 original size:11 final size:11
Alignment explanation
Indices: 4582--4654 Score: 78
Period size: 11 Copynumber: 6.6 Consensus size: 11
4572 AAATTTTAAA
4582 ATATT-TATTT
1 ATATTATATTT
*
4592 ATATTAAATTT
1 ATATTATATTT
*
4603 ATATTATTTTT
1 ATATTATATTT
4614 ATATTATATTT
1 ATATTATATTT
*
4625 -TAATTATTTTT
1 AT-ATTATATTT
*
4636 ATATCATATTT
1 ATATTATATTT
4647 AATATTAT
1 -ATATTAT
4655 CGAATCGGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
10 6 0.12
11 38 0.75
12 7 0.14
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (11 bp):
ATATTATATTT
Found at i:4614 original size:22 final size:22
Alignment explanation
Indices: 4589--4654 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
4579 AAAATATTTA
*
4589 TTTATATTAAATTTATATTATT
1 TTTATATTATATTTATATTATT
4611 TTTATATTATATTT-TAATTATT
1 TTTATATTATATTTAT-ATTATT
*
4633 TTTATATCATATTTAATATTAT
1 TTTATATTATATTT-ATATTAT
4655 CGAATCGGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
21 1 0.03
22 32 0.82
23 5 0.13
24 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTATATTATATTTATATTATT
Found at i:5249 original size:17 final size:18
Alignment explanation
Indices: 5215--5263 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
5205 ATTATTTAAA
5215 ATATTAAATATTATTTTT
1 ATATTAAATATTATTTTT
5233 ATATT-AATATATATTTTT
1 ATATTAAATAT-TATTTTT
5251 ATAATTAAA-ATTA
1 AT-ATTAAATATTA
5264 AATAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.18
18 16 0.57
19 5 0.18
20 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATTAAATATTATTTTT
Found at i:5660 original size:16 final size:18
Alignment explanation
Indices: 5639--5671 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5629 TTTTTTATTA
5639 TTTTT-ATT-TAAAATAT
1 TTTTTAATTATAAAATAT
5655 TTTTTAATTATAAAATA
1 TTTTTAATTATAAAATA
5672 ATGAATTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 3 0.20
18 7 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTTAATTATAAAATAT
Found at i:8035 original size:18 final size:19
Alignment explanation
Indices: 8012--8052 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
8002 ATATAATTAT
*
8012 AAATATAT-ATTAAAATAA
1 AAATATATAATAAAAATAA
8030 AAATATATACATAAAAATAA
1 AAATATATA-ATAAAAATAA
8050 AAA
1 AAA
8053 CACCATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
20 12 0.60
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (19 bp):
AAATATATAATAAAAATAA
Found at i:14591 original size:2 final size:2
Alignment explanation
Indices: 14580--14612 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
14570 ATATTTTGTA
14580 AT AT -T AT 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 AT AT AT AT
14613 TGCCAATGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:16034 original size:30 final size:28
Alignment explanation
Indices: 15964--16035 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 28
15954 TCAAAAAAAT
* *
15964 ATTAATATTTTATATTTTAATTAAATTTAA
1 ATTAAT-TTTT-TATTTTAAATAAAATTAA
*
15994 ATAAAATTTTTTATTATTAAATAATAATTAA
1 AT-TAATTTTTTATT-TTAAATAA-AATTAA
16025 ATTAATTTTTT
1 ATTAATTTTTT
16036 TAAAATATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
29 4 0.11
30 21 0.60
31 10 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTAATTTTTTATTTTAAATAAAATTAA
Found at i:16644 original size:21 final size:21
Alignment explanation
Indices: 16618--16657 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
16608 ATTAAAATAT
16618 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
16639 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
16658 AATAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:22789 original size:16 final size:16
Alignment explanation
Indices: 22768--22817 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 16
22758 AAAAATATTA
22768 ATTAATATATAATTTT
1 ATTAATATATAATTTT
22784 ATTAATAATATAATATTT
1 ATTAAT-ATATAAT-TTT
**
22802 AAAAATTATATAATTT
1 ATTAA-TATATAATTT
22818 ATTTATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 6 0.21
17 9 0.31
18 13 0.45
19 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTAATATATAATTTT
Found at i:23141 original size:5 final size:5
Alignment explanation
Indices: 23131--23177 Score: 66
Period size: 5 Copynumber: 10.2 Consensus size: 5
23121 AATCATGTTA
23131 AATAT AATAT AA-A- AATA- AATAT AATAT AATAT AA-AT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
23177 A
1 A
23178 TAATAAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
3 2 0.05
4 10 0.26
5 27 0.69
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (5 bp):
AATAT
Found at i:23151 original size:17 final size:19
Alignment explanation
Indices: 23129--23177 Score: 68
Period size: 17 Copynumber: 2.7 Consensus size: 19
23119 AGAATCATGT
23129 TAAATATAATATAA-A-AA
1 TAAATATAATATAATATAA
23146 TAAATATAATATAATATAA
1 TAAATATAATATAATATAA
23165 -ATAATATAATATA
1 TA-AATATAATATA
23178 TAATAAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.48
18 2 0.07
19 13 0.45
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAATATAATATAATATAA
Found at i:23183 original size:19 final size:20
Alignment explanation
Indices: 23129--23184 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
23119 AGAATCATGT
23129 TAAATAT-A-ATATAA-AAA
1 TAAATATAATATATAATAAA
23146 TAAATATAATATA-ATATAAA
1 TAAATATAATATATA-ATAAA
23166 T-AATATAATATATAATAAA
1 TAAATATAATATATAATAAA
23185 ATTATTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
17 7 0.21
18 2 0.06
19 20 0.59
20 5 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAATATAATATATAATAAA
Found at i:23335 original size:10 final size:9
Alignment explanation
Indices: 23283--23426 Score: 56
Period size: 8 Copynumber: 16.0 Consensus size: 9
23273 TCAAAATTTA
23283 TATAAATA-
1 TATAAATAT
23291 TA-AAATATT
1 TATAAATA-T
*
23300 TTTAATATAAT
1 TATAA-AT-AT
23311 TAT-AATAT
1 TATAAATAT
*
23319 AATAAATAAT
1 TATAAAT-AT
23329 TATAAATAT
1 TATAAATAT
*
23338 TATTAA-AT
1 TATAAATAT
*
23346 TATAGGCATAT
1 TATA--AATAT
23357 TAATAATATAT
1 T-ATAA-ATAT
*
23368 TA-AAATTT
1 TATAAATAT
23376 TAT-AATA-
1 TATAAATAT
*
23383 TA-AAATTT
1 TATAAATAT
*
23391 TTTAATATAAT
1 TATAA-AT-AT
23402 TAT-AATAT
1 TATAAATAT
*
23410 AATAAATAT
1 TATAAATAT
23419 T-TAAATAT
1 TATAAATAT
23427 ATTACTAGGA
Statistics
Matches: 101, Mismatches: 16, Indels: 38
0.65 0.10 0.25
Matches are distributed among these distances:
7 10 0.10
8 31 0.31
9 24 0.24
10 16 0.16
11 16 0.16
12 4 0.04
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (9 bp):
TATAAATAT
Found at i:23344 original size:20 final size:20
Alignment explanation
Indices: 23293--23345 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
23283 TATAAATATA
*
23293 AAATATTTTTAATATAATTAT
1 AAATATTATTAA-ATAATTAT
*
23314 -AATA-TAATAAATAATTAT
1 AAATATTATTAAATAATTAT
23332 AAATATTATTAAAT
1 AAATATTATTAAAT
23346 TATAGGCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 8 0.30
19 8 0.30
20 11 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATATTATTAAATAATTAT
Found at i:23388 original size:15 final size:15
Alignment explanation
Indices: 23368--23400 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
23358 AATAATATAT
23368 TAAAATTTTATAATA
1 TAAAATTTTATAATA
*
23383 TAAAATTTTTTAATA
1 TAAAATTTTATAATA
23398 TAA
1 TAA
23401 TTATAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAAATTTTATAATA
Found at i:23425 original size:28 final size:26
Alignment explanation
Indices: 23375--23427 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
23365 TATTAAAATT
* *
23375 TTATAATATAAAATTTTTTAATATAA
1 TTATAATATAAAATATTTAAATATAA
23401 TTATAATATAATAAATATTTAAATATA
1 TTATAATAT-A-AAATATTTAAATATA
23428 TTACTAGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 9 0.39
27 1 0.04
28 13 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TTATAATATAAAATATTTAAATATAA
Found at i:23746 original size:16 final size:16
Alignment explanation
Indices: 23725--23763 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
23715 TATAATAATA
*
23725 TTTTATATTTTTTTAC
1 TTTTATAATTTTTTAC
*
23741 TTTTATTAATTTTTTAT
1 TTTTA-TAATTTTTTAC
23758 TTTTAT
1 TTTTAT
23764 TCTTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATAATTTTTTAC
Found at i:24169 original size:3 final size:3
Alignment explanation
Indices: 24163--24192 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
24153 GATGATCATG
24163 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
24193 GCTCAAAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:25615 original size:16 final size:16
Alignment explanation
Indices: 25594--25648 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
25584 ATAGCTTAAG
25594 TTTTAAATTTAGATAC
1 TTTTAAATTTAGATAC
* *
25610 TTTTAAA-TTA-TTAG
1 TTTTAAATTTAGATAC
25624 TTTTAAATTTAGATAC
1 TTTTAAATTTAGATAC
25640 TTTTAAATT
1 TTTTAAATT
25649 ATTAGGCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 9 0.27
15 6 0.18
16 18 0.55
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (16 bp):
TTTTAAATTTAGATAC
Found at i:25626 original size:30 final size:30
Alignment explanation
Indices: 25592--25653 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
25582 CGATAGCTTA
25592 AGTTTTAAATTTAGATACTTTTAAATTATT
1 AGTTTTAAATTTAGATACTTTTAAATTATT
25622 AGTTTTAAATTTAGATACTTTTAAATTATT
1 AGTTTTAAATTTAGATACTTTTAAATTATT
25652 AG
1 AG
25654 GCTTTGAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.52
Consensus pattern (30 bp):
AGTTTTAAATTTAGATACTTTTAAATTATT
Found at i:28627 original size:21 final size:22
Alignment explanation
Indices: 28603--28660 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
28593 ATTTTTATTT
28603 TATATTAATATTAAATAAA-AA
1 TATATTAATATTAAATAAATAA
** **
28624 TATATTTTTATTATTTAAATAA
1 TATATTAATATTAAATAAATAA
*
28646 TAAATTAA-ATTAAAT
1 TATATTAATATTAAAT
28661 CAATTTGAAT
Statistics
Matches: 27, Mismatches: 9, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TATATTAATATTAAATAAATAA
Found at i:28629 original size:28 final size:27
Alignment explanation
Indices: 28580--28650 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
28570 ATACTATTAA
** *
28580 AATATTAAAATAAATTTTTATTTTATATT
1 AATATT-AAATAAAAATATATTTT-TATT
28609 AATATTAAATAAAAATATATTTTTATT
1 AATATTAAATAAAAATATATTTTTATT
28636 -AT-TTAAATAATAAAT
1 AATATTAAATAA-AAAT
28651 TAAATTAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
25 8 0.21
26 6 0.16
27 4 0.11
28 14 0.37
29 6 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
AATATTAAATAAAAATATATTTTTATT
Found at i:29125 original size:20 final size:20
Alignment explanation
Indices: 29100--29151 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
29090 ATAAATTATT
29100 AATATATATAAAAATAATAC
1 AATATATATAAAAATAATAC
*
29120 AATATATAATAAATATAATAC
1 AATATAT-ATAAAAATAATAC
29141 -ATATTATATAA
1 AATA-TATATAA
29152 CCATATTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (20 bp):
AATATATATAAAAATAATAC
Found at i:29292 original size:18 final size:18
Alignment explanation
Indices: 29250--29294 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
29240 TTTATTATTT
29250 TTTAAA-AATTTTTTAAA
1 TTTAAATAATTTTTTAAA
* *
29267 TATCAAATAATTTTTTTAA
1 T-TTAAATAATTTTTTAAA
29286 TTTAAATAA
1 TTTAAATAA
29295 GTAACTCGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 1 0.04
18 11 0.48
19 11 0.48
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTAAATAATTTTTTAAA
Done.