Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2012
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: 56367
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:5063 original size:2 final size:2
Alignment explanation
Indices: 5056--5098 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5046 ATTTTTAATG
5056 AT AT AT AT AT AT AT 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 AT AT AT AT
5098 A
1 A
5099 CATCATCAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5648 original size:3 final size:3
Alignment explanation
Indices: 5635--5665 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
5625 CTTATGCTTT
*
5635 TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5666 CCAAGAGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:5907 original size:13 final size:13
Alignment explanation
Indices: 5889--5913 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5879 AAATTAAGAT
5889 TTAATTTATTTAA
1 TTAATTTATTTAA
5902 TTAATTTATTTA
1 TTAATTTATTTA
5914 TTTTTAAAAA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTAATTTATTTAA
Found at i:5973 original size:77 final size:77
Alignment explanation
Indices: 5850--6006 Score: 296
Period size: 77 Copynumber: 2.0 Consensus size: 77
5840 AACTGAAAAG
* *
5850 TATAATAAGGTAATAATAAATGATAAAATAAATTAAGATTTAATTTATTTAATTAATTTATTTAT
1 TATAATAAGGTAATAATAAATGATAAAATAAATTAAGATTTAATTTAATTAATTAATTTAATTAT
5915 TTTTAAAAATAA
66 TTTTAAAAATAA
5927 TATAATAAGGTAATAATAAATGATAAAATAAATTAAGATTTAATTTAATTAATTAATTTAATTAT
1 TATAATAAGGTAATAATAAATGATAAAATAAATTAAGATTTAATTTAATTAATTAATTTAATTAT
5992 TTTTAAAAATAA
66 TTTTAAAAATAA
6004 TAT
1 TAT
6007 TTAGTAGATT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (77 bp):
TATAATAAGGTAATAATAAATGATAAAATAAATTAAGATTTAATTTAATTAATTAATTTAATTAT
TTTTAAAAATAA
Found at i:5984 original size:13 final size:13
Alignment explanation
Indices: 5966--5990 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5956 AAATTAAGAT
5966 TTAATTTAATTAA
1 TTAATTTAATTAA
5979 TTAATTTAATTA
1 TTAATTTAATTA
5991 TTTTTAAAAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAATTTAATTAA
Found at i:6167 original size:3 final size:3
Alignment explanation
Indices: 6159--6202 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
6149 AAAGATTAAT
6159 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
6203 CAATAACTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12854 original size:2 final size:2
Alignment explanation
Indices: 12843--12889 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
12833 AAAGGATTAA
12843 AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12884 AG AG AG
1 AG AG AG
12890 CAGTGGTTGG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16065 original size:17 final size:16
Alignment explanation
Indices: 16018--16065 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
16008 TATAATATTT
*
16018 AATTAAATTTATTTATA
1 AATTAAA-TAATTTATA
*
16035 AATTAAATAATTTATC
1 AATTAAATAATTTATA
*
16051 AATTCAATAAATTTA
1 AATTAAAT-AATTTA
16066 ATTTATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTAAATAATTTATA
Found at i:18059 original size:2 final size:2
Alignment explanation
Indices: 18052--18079 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18042 TTTGTTTACC
18052 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
18080 AAAGATTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25876 original size:51 final size:52
Alignment explanation
Indices: 25777--25887 Score: 142
Period size: 50 Copynumber: 2.2 Consensus size: 52
25767 AATTGACTTA
25777 AATTT-AA-TAAAATTAAATTATTATATAATTTTAAAAAAATTATTTAAATTT
1 AATTTAAATTAAAATTAAATTATTATATAATTTTAAAAAAATTATTTAAA-TT
* *
25828 AATTTAAATTAAAATTATATTATTAT-T-A-TTTAAAAATATTAATTTAAATT
1 AATTTAAATTAAAATTAAATTATTATATAATTTTAAAAAAATT-ATTTAAATT
*
25878 AAATTAAATT
1 AATTTAAATT
25888 TATTTGAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
50 22 0.41
51 13 0.24
52 3 0.06
53 16 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (52 bp):
AATTTAAATTAAAATTAAATTATTATATAATTTTAAAAAAATTATTTAAATT
Found at i:25891 original size:40 final size:37
Alignment explanation
Indices: 25815--25887 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 37
25805 TTTTAAAAAA
*
25815 ATTATTTAAATTTAATTTAAATTAAAATTATATTATT
1 ATTATTTAAATTTAATTTAAATTAAAATTAAATTATT
25852 ATTATTTAAAAATATTAATTTAAATT-AAATTAAATT
1 ATTATTT--AAAT-TTAATTTAAATTAAAATTAAATT
25888 TATTTGAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 7 0.22
39 13 0.41
40 12 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (37 bp):
ATTATTTAAATTTAATTTAAATTAAAATTAAATTATT
Found at i:27096 original size:100 final size:100
Alignment explanation
Indices: 26923--27223 Score: 548
Period size: 100 Copynumber: 3.0 Consensus size: 100
26913 CCAAAGAACC
*
26923 GTTTGTAAATTGGTGAGGAGCTGACTAAGGGTCTCGGTTCTGGTGGGAAACCAGAAAACGGCGTG
1 GTTTGTAAATTGGTGAGGAGCTGACTAAGGGTCTCGGTTCTGGTGGGAAACCAGAAACCGGCGTG
26988 AATGCTGCCAGTGAAAGCAGAGCAGCAATCGAGGA
66 AATGCTGCCAGTGAAAGCAGAGCAGCAATCGAGGA
* *
27023 GTTTGTAAATTTGTGAGGAGCTGACTAAGGGTCTCGGTTCTGGTGGGAAACCAGAAGCCGGCGTG
1 GTTTGTAAATTGGTGAGGAGCTGACTAAGGGTCTCGGTTCTGGTGGGAAACCAGAAACCGGCGTG
* *
27088 AATGCTGCCAGTGAAAGCAGAGCAGCAATAGTGGA
66 AATGCTGCCAGTGAAAGCAGAGCAGCAATCGAGGA
*
27123 GTCTGTAAATTGGTGAGGAGCTGACTAAGGGTCTCGGTTCTGGTGGGAAACCAGAAACCGGCGTG
1 GTTTGTAAATTGGTGAGGAGCTGACTAAGGGTCTCGGTTCTGGTGGGAAACCAGAAACCGGCGTG
27188 AATGCTGCCAGTGAAAGCAGAGCAGCAATCGAGGA
66 AATGCTGCCAGTGAAAGCAGAGCAGCAATCGAGGA
27223 G
1 G
27224 GTGGTTCATG
Statistics
Matches: 191, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 191 1.00
ACGTcount: A:0.28, C:0.17, G:0.35, T:0.20
Consensus pattern (100 bp):
GTTTGTAAATTGGTGAGGAGCTGACTAAGGGTCTCGGTTCTGGTGGGAAACCAGAAACCGGCGTG
AATGCTGCCAGTGAAAGCAGAGCAGCAATCGAGGA
Found at i:28244 original size:60 final size:60
Alignment explanation
Indices: 28146--28266 Score: 197
Period size: 60 Copynumber: 2.0 Consensus size: 60
28136 TGCTAGAGGG
*
28146 CATGCTAGTGATAGAAATCATGAGGTTAATAATGAAGCATTGAAAAAGGATTATTCGGGA
1 CATGCTAGTGATAGAAATCATGACGTTAATAATGAAGCATTGAAAAAGGATTATTCGGGA
* * * *
28206 CATGTTAGTGATAGAAATCTTGACTTTAATAATGAAGCATTGAAAAAGGATTATTTGGGA
1 CATGCTAGTGATAGAAATCATGACGTTAATAATGAAGCATTGAAAAAGGATTATTCGGGA
28266 C
1 C
28267 GTGAAAGGCT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (60 bp):
CATGCTAGTGATAGAAATCATGACGTTAATAATGAAGCATTGAAAAAGGATTATTCGGGA
Found at i:31704 original size:18 final size:18
Alignment explanation
Indices: 31681--31717 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
31671 CGCAGGGAGA
31681 CTAAGTTTATGCACATCG
1 CTAAGTTTATGCACATCG
31699 CTAAGTTTATGCACATCG
1 CTAAGTTTATGCACATCG
31717 C
1 C
31718 ATTTATCAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.32
Consensus pattern (18 bp):
CTAAGTTTATGCACATCG
Found at i:37197 original size:18 final size:18
Alignment explanation
Indices: 37174--37209 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
37164 TAACACAAAA
37174 AATGTTACAATAACTAGG
1 AATGTTACAATAACTAGG
37192 AATGTTACAATAACTAGG
1 AATGTTACAATAACTAGG
37210 CATAGGCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (18 bp):
AATGTTACAATAACTAGG
Found at i:46220 original size:33 final size:34
Alignment explanation
Indices: 46183--46262 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 34
46173 AATTTAATTT
* *
46183 ATTTAAATTTAAATTACTATTTATCT-TATTAAA
1 ATTTAAATTTAAATTAATATTTATATATATTAAA
** * * *
46216 ATTTATTTTTATATTAATATTTATATATTTTATA
1 ATTTAAATTTAAATTAATATTTATATATATTAAA
46250 A-TTAAATTTAAAT
1 ATTTAAATTTAAAT
46263 AAAAAATATA
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
33 30 0.83
34 6 0.17
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (34 bp):
ATTTAAATTTAAATTAATATTTATATATATTAAA
Found at i:46245 original size:22 final size:21
Alignment explanation
Indices: 46210--46259 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
46200 TATTTATCTT
*
46210 ATTAAAATT-TAT-TTTTAT-
1 ATTAAATTTATATATTTTATA
46228 ATTAATATTTATATATTTTATA
1 ATTAA-ATTTATATATTTTATA
46250 ATTAAATTTA
1 ATTAAATTTA
46260 AATAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 5 0.19
19 3 0.11
20 3 0.11
21 11 0.41
22 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTAAATTTATATATTTTATA
Found at i:52361 original size:19 final size:19
Alignment explanation
Indices: 52330--52367 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
52320 AATTCAAATT
52330 AAATTATTATTTATTTAAA
1 AAATTATTATTTATTTAAA
52349 AAATATATT-TTTATTTAAA
1 AAAT-TATTATTTATTTAAA
52368 TTTAATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATTATTATTTATTTAAA
Found at i:52635 original size:22 final size:21
Alignment explanation
Indices: 52609--52661 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
52599 AAATAAAAAA
*
52609 TTTATAAATATTGAAATTTAAT
1 TTTATAAATATT-AAATATAAT
*
52631 TTTATATATATTAAATATAAT
1 TTTATAAATATTAAATATAAT
52652 TATTA-AAATA
1 T-TTATAAATA
52662 ATTATATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
TTTATAAATATTAAATATAAT
Found at i:52655 original size:13 final size:13
Alignment explanation
Indices: 52639--52677 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
52629 ATTTTATATA
52639 TATTAAATATAAT
1 TATTAAATATAAT
52652 TATTAAA-ATAAT
1 TATTAAATATAAT
52664 TATATAAAT-TAAT
1 TAT-TAAATATAAT
52677 T
1 T
52678 TAATTAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATTAAATATAAT
Found at i:55224 original size:28 final size:26
Alignment explanation
Indices: 55190--55259 Score: 76
Period size: 24 Copynumber: 2.8 Consensus size: 26
55180 ATTGAATAAG
55190 AAAAAT-ATAT-TAAATATAATTTTTT
1 AAAAATAATATATAAATATAA-TTTTT
*
55215 AAAAATAATAAAT-AA-ATAATTTTT
1 AAAAATAATATATAAATATAATTTTT
* *
55239 AAGAATCATATATAAATATAA
1 AAAAATAATATATAAATATAA
55260 ATGTAAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
24 15 0.41
25 12 0.32
26 9 0.24
27 1 0.03
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (26 bp):
AAAAATAATATATAAATATAATTTTT
Done.