Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold860
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: 20803
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:700 original size:17 final size:17
Alignment explanation
Indices: 653--700 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
643 ATAAATATTA
*
653 AATATAGTAAAGTTAATT
1 AATATA-TAAATTTAATT
*
671 AATATATATATTTAACTT
1 AATATATAAATTTAA-TT
689 AATA-ATAAATTT
1 AATATATAAATTT
701 TAATGTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (17 bp):
AATATATAAATTTAATT
Found at i:1249 original size:2 final size:2
Alignment explanation
Indices: 1244--1274 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1234 TATAATATAC
1244 AG AG 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 AG AG A
1275 ATTGTGTACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2518 original size:31 final size:32
Alignment explanation
Indices: 2452--2510 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
2442 TTATTTAAAT
**
2452 TTAATTATAAAAATATAAAATATTTTTAATAA
1 TTAATTATAAAAATATAAAATATTTCAAATAA
2484 TTAA-TATAAAAA-ATAAAAT-TTTCAAAT
1 TTAATTATAAAAATATAAAATATTTCAAAT
2511 CAAATTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.24
30 7 0.28
31 8 0.32
32 4 0.16
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (32 bp):
TTAATTATAAAAATATAAAATATTTCAAATAA
Found at i:3703 original size:2 final size:2
Alignment explanation
Indices: 3698--3729 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3688 ATTACTTGTG
3698 TA TA TA 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
3730 ATGCGTATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8681 original size:3 final size:3
Alignment explanation
Indices: 8675--8719 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
8665 TTTGAAACAA
8675 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AGAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A-AG AA
8720 CAAGGCTTGG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:9955 original size:13 final size:13
Alignment explanation
Indices: 9923--9963 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
9913 TATTAAAATT
9923 ATTTATAAATTAA
1 ATTTATAAATTAA
9936 A---ATAAATTAA
1 ATTTATAAATTAA
*
9946 ATTTATAAATAAA
1 ATTTATAAATTAA
9959 ATTTA
1 ATTTA
9964 ATCAAATTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
10 10 0.42
13 14 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATTTATAAATTAA
Found at i:9970 original size:23 final size:23
Alignment explanation
Indices: 9923--9971 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
9913 TATTAAAATT
*
9923 ATTTATAAATTAAAATAAATTAA
1 ATTTATAAATTAAAATAAATCAA
*
9946 ATTTATAAA-TAAAATTTAATCAA
1 ATTTATAAATTAAAA-TAAATCAA
9969 ATT
1 ATT
9972 CGATCTCGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
ATTTATAAATTAAAATAAATCAA
Found at i:10451 original size:30 final size:31
Alignment explanation
Indices: 10414--10484 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
10404 ATAGACATAT
10414 ATTTAAATTTAATTTA-A-TTTAAAAT-ATAA
1 ATTTAAATTTAATTTATATTTTAAAATAAT-A
*
10443 ATTTTAAATTT-ATTTATATTTTTAAATAATA
1 A-TTTAAATTTAATTTATATTTTAAAATAATA
10474 ATTTAAATTTA
1 ATTTAAATTTA
10485 GTTAGATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
29 6 0.17
30 19 0.53
31 9 0.25
32 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
ATTTAAATTTAATTTATATTTTAAAATAATA
Found at i:10494 original size:60 final size:58
Alignment explanation
Indices: 10414--10526 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 58
10404 ATAGACATAT
* *
10414 ATTTAAATTTAATTTAATTTAAAATATAAATTTTAAAT-TTA-TTTATATTTTTAAATAATA
1 ATTTAAATTTAAGTTAATTT---ATA-AAATTTTAAATATTATTTTAAATTTTTAAATAATA
10474 ATTTAAATTT-AGTTAGATTTATAAAATTTTAAATATTATTTTAAATTTTTAAA
1 ATTTAAATTTAAGTTA-ATTTATAAAATTTTAAATATTATTTTAAATTTTTAAA
10527 AAAATATATT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
56 11 0.23
57 6 0.12
58 13 0.27
59 4 0.08
60 14 0.29
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (58 bp):
ATTTAAATTTAAGTTAATTTATAAAATTTTAAATATTATTTTAAATTTTTAAATAATA
Found at i:10890 original size:16 final size:15
Alignment explanation
Indices: 10866--10904 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
10856 ATAAAAAATA
10866 ATATAAATACGATAC
1 ATATAAATACGATAC
*
10881 ATATATAATACGATAA
1 ATATA-AATACGATAC
10897 ATA-AAATA
1 ATATAAATA
10905 AAAAGAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 4 0.18
15 6 0.27
16 12 0.55
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.28
Consensus pattern (15 bp):
ATATAAATACGATAC
Found at i:12245 original size:17 final size:18
Alignment explanation
Indices: 12209--12247 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
12199 TTATTTTTTG
*
12209 TATTATATTATATTTAAA
1 TATTATATTAAATTTAAA
*
12227 TATTATA-TAAATTTTAA
1 TATTATATTAAATTTAAA
12244 TATT
1 TATT
12248 TTAATAATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTATATTAAATTTAAA
Found at i:12272 original size:26 final size:27
Alignment explanation
Indices: 12243--12301 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
12233 ATAAATTTTA
*
12243 ATATTTTAATA-ATACATATA-ATAT-
1 ATATTTTAAAATATACATATATATATC
*
12267 ATATATTTAAAATATACATATTTATATC
1 ATAT-TTTAAAATATACATATATATATC
12295 ATATTTT
1 ATATTTT
12302 TATTATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 4 0.14
25 6 0.21
26 8 0.28
27 7 0.24
28 4 0.14
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAATATACATATATATATC
Found at i:12311 original size:10 final size:10
Alignment explanation
Indices: 12284--12352 Score: 68
Period size: 10 Copynumber: 6.6 Consensus size: 10
12274 TAAAATATAC
*
12284 ATATTTATATC
1 ATATTT-TATT
12295 ATATTTTTATT
1 ATA-TTTTATT
12306 AT-TTTTATTTT
1 ATATTTTA--TT
*
12317 ATATTATATT
1 ATATTTTATT
*
12327 ATATTATATT
1 ATATTTTATT
12337 ATATTTTATT
1 ATATTTTATT
12347 ATATTT
1 ATATTT
12353 ACATTATGTA
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
9 5 0.10
10 27 0.53
11 12 0.24
12 7 0.14
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (10 bp):
ATATTTTATT
Found at i:12316 original size:15 final size:15
Alignment explanation
Indices: 12296--12346 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
12286 ATTTATATCA
12296 TATTTTTATTATTTT
1 TATTTTTATTATTTT
*
12311 TATTTTATATTA-TAT
1 TATTTT-TATTATTTT
*
12326 TATATTATATTATATTT
1 TAT-TTTTATTAT-TTT
12343 TATT
1 TATT
12347 ATATTTACAT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 16 0.55
16 8 0.28
17 5 0.17
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTTTTATTATTTT
Found at i:12347 original size:15 final size:15
Alignment explanation
Indices: 12302--12351 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
12292 ATCATATTTT
12302 TATTAT-TTTTATTTTA
1 TATTATATTTTA--TTA
*
12318 TATTATATTATATTA
1 TATTATATTTTATTA
12333 TATTATATTTTATTA
1 TATTATATTTTATTA
12348 TATT
1 TATT
12352 TACATTATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
15 21 0.68
16 6 0.19
17 4 0.13
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTATATTTTATTA
Found at i:13727 original size:10 final size:10
Alignment explanation
Indices: 13709--13805 Score: 60
Period size: 9 Copynumber: 10.1 Consensus size: 10
13699 ATCATATTAT
13709 TATTAAAAAA
1 TATTAAAAAA
*
13719 TATT-TAAAA
1 TATTAAAAAA
*
13728 -GTTAAAAAA
1 TATTAAAAAA
**
13737 -ATTATTAAA
1 TATTAAAAAA
*
13746 TTTTAAAATAA
1 TATTAAAA-AA
* *
13757 AAATAAAAAA
1 TATTAAAAAA
*
13767 TATTTAAAAA
1 TATTAAAAAA
* *
13777 TTTTATAAAA
1 TATTAAAAAA
13787 -ATTAAAAAA
1 TATTAAAAAA
13796 T-TTAAAAAA
1 TATTAAAAAA
13805 T
1 T
13806 GAAATCTGGG
Statistics
Matches: 63, Mismatches: 20, Indels: 9
0.68 0.22 0.10
Matches are distributed among these distances:
8 2 0.03
9 30 0.48
10 24 0.38
11 7 0.11
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (10 bp):
TATTAAAAAA
Found at i:15621 original size:13 final size:12
Alignment explanation
Indices: 15572--15622 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
15562 ACCTTCACTG
15572 TTTCAAATTGAA
1 TTTCAAATTGAA
*
15584 TTTCAACATTTACTA
1 TTTCAA-ATTGA--A
15599 TTTCAAATTGAA
1 TTTCAAATTGAA
15611 TTTCAAAATTGA
1 TTTC-AAATTGA
15623 CGACACAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 11 0.33
13 11 0.33
14 4 0.12
15 7 0.21
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (12 bp):
TTTCAAATTGAA
Found at i:20233 original size:27 final size:27
Alignment explanation
Indices: 20203--20255 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
20193 GTGTCGCTTG
20203 AAATTCAATTTAAAATAATAAATGTTT
1 AAATTCAATTTAAAATAATAAATGTTT
*
20230 AAATTCAATTTAAAATAGTAAATGTT
1 AAATTCAATTTAAAATAATAAATGTT
20256 ATACAGTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.40
Consensus pattern (27 bp):
AAATTCAATTTAAAATAATAAATGTTT
Done.