Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold768
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: 8582
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Found at i:999 original size:2 final size:2
Alignment explanation
Indices: 986--1024 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
976 AGTTTAAGAC
* *
986 TA TA TC TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1025 TGGGAAGTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1305 original size:12 final size:13
Alignment explanation
Indices: 1276--1317 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
1266 TTTTTAGATA
*
1276 TTATTATATTTATG
1 TTATTAT-TTTATT
1290 TTATT-TTTTATT
1 TTATTATTTTATT
1302 TTATTATTTT-TT
1 TTATTATTTTATT
1314 TTAT
1 TTAT
1318 CATGTAATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 16 0.62
13 5 0.19
14 5 0.19
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (13 bp):
TTATTATTTTATT
Found at i:1512 original size:21 final size:24
Alignment explanation
Indices: 1469--1525 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 24
1459 GATTGATCTG
1469 ATATAAAATTATTGTTTAAATATTA
1 ATATAAAA-TATTGTTTAAATATTA
*
1494 ATATAAAA-ATT-TTTAATATTTTA
1 ATATAAAATATTGTTTAA-ATATTA
1517 A-ATAAAATA
1 ATATAAAATA
1526 ATTTTCGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 11 0.38
23 10 0.34
25 8 0.28
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
ATATAAAATATTGTTTAAATATTA
Found at i:2773 original size:27 final size:25
Alignment explanation
Indices: 2704--2774 Score: 63
Period size: 27 Copynumber: 2.7 Consensus size: 25
2694 GTTTAAGTAA
*
2704 ATTAAAAATATTAAAAATATTTAACT
1 ATTAAATATATTAAAAA-ATTTAACT
* * *
2730 ATT-TATTTAATATAAAAACTTTCAACT
1 ATTAAATAT-AT-TAAAAAATTT-AACT
2757 ATTAAATATATTAAAAAA
1 ATTAAATATATTAAAAAA
2775 ATAATATTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
25 2 0.06
26 14 0.41
27 15 0.44
28 3 0.09
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (25 bp):
ATTAAATATATTAAAAAATTTAACT
Found at i:3118 original size:26 final size:26
Alignment explanation
Indices: 3084--3141 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
3074 TTTTAAATAA
*
3084 AATTAATAAAATATATTAT-TCAATTT
1 AATTAATAAAATATAATATATCAA-TT
* *
3110 AATTAATAATATATAATATATGAATT
1 AATTAATAAAATATAATATATCAATT
3136 AATTAA
1 AATTAA
3142 ATTAAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 25 0.89
27 3 0.11
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (26 bp):
AATTAATAAAATATAATATATCAATT
Found at i:3288 original size:6 final size:6
Alignment explanation
Indices: 3277--3305 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3267 TAAATAAAGT
3277 GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
3306 GCAGAGTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:4706 original size:11 final size:11
Alignment explanation
Indices: 4692--4730 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
4682 AAATATTTTA
4692 ATATTTATATT
1 ATATTTATATT
4703 ATATTT-TAATT
1 ATATTTAT-ATT
*
4714 ATTTTTATATT
1 ATATTTATATT
4725 ATATTT
1 ATATTT
4731 TTATAATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 1 0.04
11 22 0.92
12 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
ATATTTATATT
Found at i:4723 original size:22 final size:19
Alignment explanation
Indices: 4684--4731 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 19
4674 GTTTTTTAAA
4684 ATATTTTAATATTTATATT
1 ATATTTTAATATTTATATT
4703 ATATTTTAATTATTTTTATATT
1 ATATTTTAA-TA--TTTATATT
4725 ATATTTT
1 ATATTTT
4732 TATAATTACG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.35
20 2 0.08
22 15 0.58
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATATTTTAATATTTATATT
Found at i:5205 original size:21 final size:21
Alignment explanation
Indices: 5163--5203 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5153 AAAGGAACTG
*
5163 TAATTGTAAAATATATAAAAA
1 TAATTATAAAATATATAAAAA
5184 TAATTATAAAAT-TATAAAAA
1 TAATTATAAAATATATAAAAA
5204 ATGTTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
TAATTATAAAATATATAAAAA
Found at i:5505 original size:20 final size:18
Alignment explanation
Indices: 5482--5519 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
5472 ATATTAATAA
5482 ATTTATTTATAAATTAAATT
1 ATTTATTTA-AAA-TAAATT
5502 ATTTATTTAAAATAAATT
1 ATTTATTTAAAATAAATT
5520 TAAAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 3 0.17
20 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTATTTAAAATAAATT
Found at i:5522 original size:11 final size:11
Alignment explanation
Indices: 5506--5531 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5496 TAAATTATTT
5506 ATTTAAAATAA
1 ATTTAAAATAA
5517 ATTTAAAATAA
1 ATTTAAAATAA
5528 ATTT
1 ATTT
5532 TTTATTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATTTAAAATAA
Found at i:5540 original size:52 final size:55
Alignment explanation
Indices: 5484--5605 Score: 143
Period size: 52 Copynumber: 2.3 Consensus size: 55
5474 ATTAATAAAT
* *
5484 TTATTTATAAATTAAATTATTTATTTAAAATA-AATTTAA-AA-TAAATTTT-TTA
1 TTATTTATAAATT-AATTATTAATTTAAAATATAATTTAATAAGAAAATTTTATTA
* *
5536 TTATTT-TAAATTAA-T-TTAATTTAAATTATAATTTAATAAGAAAATTTTATTT
1 TTATTTATAAATTAATTATTAATTTAAAATATAATTTAATAAGAAAATTTTATTA
5588 TTATTTA-AAATTAATTAT
1 TTATTTATAAATTAATTAT
5606 AAAAATATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
48 11 0.19
49 8 0.14
50 4 0.07
51 13 0.22
52 21 0.36
53 1 0.02
54 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (55 bp):
TTATTTATAAATTAATTATTAATTTAAAATATAATTTAATAAGAAAATTTTATTA
Found at i:5581 original size:51 final size:50
Alignment explanation
Indices: 5495--5654 Score: 136
Period size: 52 Copynumber: 3.1 Consensus size: 50
5485 TATTTATAAA
* *
5495 TTAAATT-ATTT-ATTTAAAATA-AATTTAA-AATAAATTTTTTATTATT
1 TTAAATTAATTTAATTTAAATTATAATTTAATAAAAAATTTTTTATTATT
*
5541 TTAAATTAATTTAATTTAAATTATAATTTAATAAGAAAATTTTATTTTTATT
1 TTAAATTAATTTAATTTAAATTATAATTTAATAA-AAAATTTT-TTATTATT
*
5593 TAAAATTAATTATAA---AAATATATAAATATTAATATAAATAAATTTTTTATTAAATT
1 TTAAATTAATT-TAATTTAAAT-TAT-AAT-TT-A-ATAAA-AAATTTTTTATT--ATT
5649 TTAAAT
1 TTAAAT
5655 AATAATTTCA
Statistics
Matches: 93, Mismatches: 6, Indels: 20
0.78 0.05 0.17
Matches are distributed among these distances:
46 7 0.08
47 4 0.04
48 9 0.10
49 7 0.08
50 6 0.06
51 10 0.11
52 20 0.22
53 5 0.05
54 6 0.06
55 11 0.12
56 8 0.09
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.51
Consensus pattern (50 bp):
TTAAATTAATTTAATTTAAATTATAATTTAATAAAAAATTTTTTATTATT
Found at i:6007 original size:15 final size:15
Alignment explanation
Indices: 5956--6013 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
5946 ATTATATTTT
5956 TAATTTAATTATTT-A
1 TAATTTAATT-TTTAA
*
5971 TAATTT--TTTTAAA
1 TAATTTAATTTTTAA
*
5984 AATATTTAATTTTTAA
1 TA-ATTTAATTTTTAA
6000 TAATTTAATATTTT
1 TAATTTAAT-TTTT
6014 TTTATAAAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
12 2 0.06
13 4 0.12
14 4 0.12
15 13 0.38
16 11 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TAATTTAATTTTTAA
Found at i:6105 original size:32 final size:30
Alignment explanation
Indices: 6042--6108 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
6032 AAATAATTTA
* **
6042 ATATATATTTAATTTTTATATTATAGTATT
1 ATATATATTTAATTTTTATATAATAAAATT
*
6072 ATATATATTTTTATTTTTATATAATAAAAATT
1 ATATATA-TTTAATTTTTATATAAT-AAAATT
6104 ATATA
1 ATATA
6109 ATATAAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 7 0.23
31 15 0.48
32 9 0.29
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (30 bp):
ATATATATTTAATTTTTATATAATAAAATT
Found at i:6198 original size:18 final size:18
Alignment explanation
Indices: 6177--6237 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 18
6167 TATATTAAAA
*
6177 TTAAAATTTAATTTATTT
1 TTAAAATTAAATTTATTT
* * *
6195 TT-AAATAAAAATAATTT
1 TTAAAATTAAATTTATTT
*
6212 TTAACA-TAAATTTATTTT
1 TTAAAATTAAATTTA-TTT
6230 TTAAAATT
1 TTAAAATT
6238 TAATATTTTA
Statistics
Matches: 31, Mismatches: 9, Indels: 5
0.69 0.20 0.11
Matches are distributed among these distances:
17 18 0.58
18 12 0.39
19 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TTAAAATTAAATTTATTT
Found at i:6228 original size:17 final size:17
Alignment explanation
Indices: 6186--6230 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
6176 ATTAAAATTT
6186 AATTTATTTTTAAATAA
1 AATTTATTTTTAAATAA
* *
6203 AAATAATTTTTAACAT-A
1 AATTTATTTTTAA-ATAA
6220 AATTTATTTTT
1 AATTTATTTTT
6231 TAAAATTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 21 0.91
18 2 0.09
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTATTTTTAAATAA
Done.