Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1282
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: 23362
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Found at i:585 original size:14 final size:14
Alignment explanation
Indices: 543--585 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
533 TTAAATTATT
543 ATTTAATTATAAAA
1 ATTTAATTATAAAA
* *
557 ATATT-TTTATTAAA
1 AT-TTAATTATAAAA
571 ATTTAATTATAAAA
1 ATTTAATTATAAAA
585 A
1 A
586 ATATTAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
13 2 0.09
14 19 0.83
15 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTTAATTATAAAA
Found at i:1176 original size:23 final size:23
Alignment explanation
Indices: 1150--1199 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
1140 TTTATTTTAT
*
1150 AATTATAAAT-ATTTTTATAAATA
1 AATTATAAATAATATTT-TAAATA
*
1173 AATT-TAAATAATATTTTAAATT
1 AATTATAAATAATATTTTAAATA
1195 AATTA
1 AATTA
1200 AATTCAAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AATTATAAATAATATTTTAAATA
Found at i:2373 original size:23 final size:23
Alignment explanation
Indices: 2347--2393 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2337 ATCGATTTAT
2347 AATTGTTTAAAATAATATTAAAA
1 AATTGTTTAAAATAATATTAAAA
* * * *
2370 AATTTTTTATATTAATATTTAAA
1 AATTGTTTAAAATAATATTAAAA
2393 A
1 A
2394 TTAAATTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AATTGTTTAAAATAATATTAAAA
Found at i:3017 original size:25 final size:25
Alignment explanation
Indices: 2980--3028 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2970 TTACATATTC
2980 AATTATATCTAATACAAATATATTAT
1 AATTATATCTAATACAAAT-TATTAT
* *
3006 AATT-TATTTAATATAAATTATTA
1 AATTATATCTAATACAAATTATTA
3029 ATATATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 12 0.57
26 4 0.19
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (25 bp):
AATTATATCTAATACAAATTATTAT
Found at i:3061 original size:47 final size:48
Alignment explanation
Indices: 3010--3111 Score: 115
Period size: 47 Copynumber: 2.2 Consensus size: 48
3000 TATTATAATT
* *
3010 TATTTAATATA-AATTATTAATATATAAAA-ATTTATAT-A-GATAAATAA
1 TATTTAATATACAA-TAATAATATATAAAATATTTA-ATCACAATAAA-AA
*
3057 TATTTAA-ATACGATAATAATATATAAAATATTTAATCACAATAAAAA
1 TATTTAATATACAATAATAATATATAAAATATTTAATCACAATAAAAA
3104 TATTTAAT
1 TATTTAAT
3112 TGAAAGAGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
46 19 0.40
47 23 0.49
48 5 0.11
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (48 bp):
TATTTAATATACAATAATAATATATAAAATATTTAATCACAATAAAAA
Found at i:3074 original size:19 final size:19
Alignment explanation
Indices: 3039--3083 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3029 ATATATAAAA
*
3039 ATTTATATAGATAAATAAT
1 ATTTAAATAGATAAATAAT
3058 ATTTAAATACGAT-AATAAT
1 ATTTAAATA-GATAAATAAT
*
3077 ATATAAA
1 ATTTAAA
3084 ATATTTAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (19 bp):
ATTTAAATAGATAAATAAT
Found at i:3383 original size:26 final size:26
Alignment explanation
Indices: 3352--3401 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3342 TAATTTTGTT
* *
3352 TATTTT-ATAATTTTTTATATAATTTA
1 TATTTTGATAAATTATTAT-TAATTTA
3378 TATTTTGATAAATTATTATTAATT
1 TATTTTGATAAATTATTATTAATT
3402 AATAAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 11 0.52
27 10 0.48
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
TATTTTGATAAATTATTATTAATTTA
Found at i:3620 original size:9 final size:9
Alignment explanation
Indices: 3607--3641 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
3597 AATTAAATAA
3607 ATATAAAAT
1 ATATAAAAT
* *
3616 TTATAAAAA
1 ATATAAAAT
3625 ATATAAAAT
1 ATATAAAAT
3634 ATATAAAA
1 ATATAAAA
3642 ATTACATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
ATATAAAAT
Found at i:3628 original size:18 final size:18
Alignment explanation
Indices: 3581--3642 Score: 70
Period size: 18 Copynumber: 3.2 Consensus size: 18
3571 AATAAAACAT
*
3581 AAAAATATAAGAATTAAATTA
1 AAAAATATAA-AATT-TA-TA
3602 AATAAATATAAAATTTATA
1 AA-AAATATAAAATTTATA
*
3621 AAAAATATAAAATATATA
1 AAAAATATAAAATTTATA
3639 AAAA
1 AAAA
3643 TTACATTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
18 19 0.50
19 4 0.11
20 1 0.03
21 6 0.16
22 8 0.21
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (18 bp):
AAAAATATAAAATTTATA
Found at i:3641 original size:16 final size:16
Alignment explanation
Indices: 3572--3641 Score: 56
Period size: 15 Copynumber: 4.4 Consensus size: 16
3562 ACTTATAGAA
*
3572 ATAAAACATAAAA-AT
1 ATAAAATATAAAATAT
* *
3587 ATAAGAAT-TAAATTAA
1 ATAA-AATATAAAATAT
3603 AT-AAATATAAAATTTAT
1 ATAAAATATAAAA--TAT
*
3620 AAAAAATATAAAATAT
1 ATAAAATATAAAATAT
3636 ATAAAA
1 ATAAAA
3642 ATTACATTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 11
0.70 0.12 0.18
Matches are distributed among these distances:
14 3 0.07
15 13 0.31
16 13 0.31
17 3 0.07
18 10 0.24
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (16 bp):
ATAAAATATAAAATAT
Found at i:3944 original size:15 final size:15
Alignment explanation
Indices: 3924--3956 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3914 TAATAAACTA
3924 TTTAATTTTTTTAAT
1 TTTAATTTTTTTAAT
3939 TTTAATTTTTTTAAT
1 TTTAATTTTTTTAAT
3954 TTT
1 TTT
3957 TGAAGGTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTAATTTTTTTAAT
Found at i:4061 original size:2 final size:2
Alignment explanation
Indices: 4054--4086 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4044 TCTCATTTAA
4054 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4087 CTTTATTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4803 original size:7 final size:7
Alignment explanation
Indices: 4791--4816 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4781 ATTAGTGATT
4791 TAATTAA
1 TAATTAA
4798 TAATTAA
1 TAATTAA
4805 TAATTAA
1 TAATTAA
4812 TAATT
1 TAATT
4817 TATCTTTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TAATTAA
Found at i:5263 original size:22 final size:21
Alignment explanation
Indices: 5222--5266 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
5212 AAAAATATTT
*
5222 TATATAAATTTAATATAAAAA
1 TATAAAAATTTAATATAAAAA
*
5243 TATAAAAATATTAGTATAAAAA
1 TATAAAAAT-TTAATATAAAAA
5265 TA
1 TA
5267 ATATTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
TATAAAAATTTAATATAAAAA
Found at i:5491 original size:20 final size:20
Alignment explanation
Indices: 5468--5527 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
5458 ATTTTTTGTT
5468 TATTTAAATAGAATTTTAAA
1 TATTTAAATAGAATTTTAAA
5488 TATTTTAAA-AGAATTTT-AA
1 TA-TTTAAATAGAATTTTAAA
* *
5507 TA-TCAAATA-AATATTAAA
1 TATTTAAATAGAATTTTAAA
5525 TAT
1 TAT
5528 ACTAAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 9 0.26
18 5 0.15
19 4 0.12
20 10 0.29
21 6 0.18
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (20 bp):
TATTTAAATAGAATTTTAAA
Found at i:6415 original size:19 final size:19
Alignment explanation
Indices: 6378--6421 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
6368 TGAAACTTAA
6378 TTAAATTAAATAAAATTTAT
1 TTAAATTAAAT-AAATTTAT
6398 TTAAATATAAAT-AATTTAT
1 TTAAAT-TAAATAAATTTAT
*
6417 ATAAA
1 TTAAA
6422 AAATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 11 0.50
20 6 0.27
21 5 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAAATTAAATAAATTTAT
Found at i:6420 original size:13 final size:13
Alignment explanation
Indices: 6402--6449 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
6392 ATTTATTTAA
*
6402 ATATAAATAATTT
1 ATATAAATAATAT
*
6415 ATATAAAAAATAT
1 ATATAAATAATAT
*
6428 ATATTAATAA-AT
1 ATATAAATAATAT
*
6440 ATAGAAATAA
1 ATATAAATAA
6450 ACAAACATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (13 bp):
ATATAAATAATAT
Found at i:6703 original size:16 final size:16
Alignment explanation
Indices: 6682--6716 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
6672 TAATAAAACC
*
6682 GAACTTGAAATGATTT
1 GAACTTAAAATGATTT
6698 GAACTTAAAATGATTT
1 GAACTTAAAATGATTT
6714 GAA
1 GAA
6717 TTCGAATCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (16 bp):
GAACTTAAAATGATTT
Found at i:7736 original size:18 final size:20
Alignment explanation
Indices: 7710--7749 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
7700 ATTTATATTC
*
7710 ATTGTGTAT-TAAAT-TTTA
1 ATTGAGTATATAAATATTTA
7728 ATTGAGTATATAAATATTTA
1 ATTGAGTATATAAATATTTA
7748 AT
1 AT
7750 AGATCTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 5 0.26
20 6 0.32
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (20 bp):
ATTGAGTATATAAATATTTA
Found at i:8030 original size:19 final size:18
Alignment explanation
Indices: 8008--8043 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7998 TTTGATATTA
*
8008 TTTTTAATTATAAAATGTC
1 TTTTTAAATA-AAAATGTC
8027 TTTTTAAATAAAAATGT
1 TTTTTAAATAAAAATGT
8044 AAGACTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (18 bp):
TTTTTAAATAAAAATGTC
Found at i:9216 original size:29 final size:31
Alignment explanation
Indices: 9167--9225 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 31
9157 TTTATATTTT
*
9167 TATATATTAAGTAATATTTATCATATAAAAA
1 TATATATTAAGTAATATTTATAATATAAAAA
* *
9198 TATATA-TATGTAATA-TTATAATGTAAAA
1 TATATATTAAGTAATATTTATAATATAAAA
9226 CATTAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 11 0.44
30 8 0.32
31 6 0.24
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (31 bp):
TATATATTAAGTAATATTTATAATATAAAAA
Found at i:10730 original size:2 final size:2
Alignment explanation
Indices: 10723--10753 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
10713 ATCATGTCGA
10723 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
10754 TTGGAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11753 original size:13 final size:13
Alignment explanation
Indices: 11737--11800 Score: 53
Period size: 13 Copynumber: 5.0 Consensus size: 13
11727 ATGATTAATT
11737 ATTATAAATATAA
1 ATTATAAATATAA
**
11750 ATTATAAATATTG
1 ATTATAAATATAA
*
11763 ATAATAAA-A-AA
1 ATTATAAATATAA
11774 ATTA-AAATTATAAA
1 ATTATAAA-TAT-AA
*
11788 ATTATAATTATAA
1 ATTATAAATATAA
11801 TATTTGTTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
10 3 0.08
11 3 0.08
12 2 0.05
13 20 0.51
14 9 0.23
15 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (13 bp):
ATTATAAATATAA
Found at i:11790 original size:14 final size:14
Alignment explanation
Indices: 11748--11800 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
11738 TTATAAATAT
11748 AAATTATAAATATTGA
1 AAATTATAAA-ATT-A
* * *
11764 TAATAAAAAAATTA
1 AAATTATAAAATTA
11778 AAATTATAAAATTA
1 AAATTATAAAATTA
*
11792 TAATTATAA
1 AAATTATAA
11801 TATTTGTTAT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
14 20 0.67
15 3 0.10
16 7 0.23
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
AAATTATAAAATTA
Found at i:12466 original size:2 final size:2
Alignment explanation
Indices: 12459--12491 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12449 ATTAACTCTT
12459 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12492 TAAAAATAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12881 original size:17 final size:17
Alignment explanation
Indices: 12849--12882 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12839 CCTCAGCAAA
* *
12849 TGATTTTTTTATTATTT
1 TGATTTTTTAAGTATTT
12866 TGATTTTTTAAGTATTT
1 TGATTTTTTAAGTATTT
12883 ATATCTAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.71
Consensus pattern (17 bp):
TGATTTTTTAAGTATTT
Found at i:17442 original size:17 final size:17
Alignment explanation
Indices: 17403--17460 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
17393 TTAATTGTAT
*
17403 TATAATAAAAATTTTAA
1 TATAATAAAAATATTAA
17420 TAATAA-AAAAATATTAA
1 T-ATAATAAAAATATTAA
*
17437 CTATAATAAATAT-TTAA
1 -TATAATAAAAATATTAA
*
17454 TAAAATA
1 TATAATA
17461 TGTATTTGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
16 6 0.17
17 19 0.54
18 10 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
TATAATAAAAATATTAA
Found at i:21503 original size:23 final size:25
Alignment explanation
Indices: 21453--21503 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 25
21443 TATTTTTTTA
* * *
21453 TTTTTTAAAACAAATAAAGATCATT
1 TTTTTTAAAACAAATAAACATAAAT
21478 TTTTTTAAAA-AAA-AAACATAAAT
1 TTTTTTAAAACAAATAAACATAAAT
21501 TTT
1 TTT
21504 GAACTTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 10 0.43
24 3 0.13
25 10 0.43
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (25 bp):
TTTTTTAAAACAAATAAACATAAAT
Found at i:23324 original size:21 final size:21
Alignment explanation
Indices: 23298--23339 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
23288 GTGATTTGAA
*
23298 AAGGGTTGCCATGACTTGCGT
1 AAGGGTTGCCACGACTTGCGT
23319 AAGGGTTGCCACGACTTGCGT
1 AAGGGTTGCCACGACTTGCGT
23340 GGGCTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.21, G:0.33, T:0.26
Consensus pattern (21 bp):
AAGGGTTGCCACGACTTGCGT
Done.