Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3075
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: 21451
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Found at i:4457 original size:39 final size:39
Alignment explanation
Indices: 4400--4720 Score: 490
Period size: 39 Copynumber: 8.3 Consensus size: 39
4390 CGAGACTTTA
* * *
4400 AGCCCGGATATAATACCAGCAC-AAAGCCTACGGGACTTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGAC-TT
*
4439 AGCCCGGATATAACACCAGCACAAATGCCTTCGGG-C-T
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
*
4476 AGCCCGGATATAACACCAGCACGACTGCCTT--GGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
* *
4513 AGCCCGGATATAACACCAACGCGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
* *
4552 AGCCCGGATATAACACCAGCACGAATTCCTTTGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
*
4591 AGCCCGGATATAACACTAGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
4630 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
* *
4669 AACCCAGATATAACACCAGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
4708 AGCCCGGATATAA
1 AGCCCGGATATAA
4721 TTCTCCATTA
Statistics
Matches: 257, Mismatches: 20, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
35 2 0.01
36 1 0.00
37 59 0.23
39 185 0.72
40 10 0.04
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (39 bp):
AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
Found at i:6612 original size:27 final size:27
Alignment explanation
Indices: 6575--6779 Score: 223
Period size: 27 Copynumber: 7.6 Consensus size: 27
6565 TAAATTGTAC
*
6575 AGCACTAAGTGTGCGATTTGGCTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
6602 AGCACTAAGTGTGCGATTTGACCATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** **
6629 TGCACTAAGTGTGCGAAATGAAAATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
6655 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
6683 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
6710 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * * *
6738 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
6765 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
6780 GACTTAATAT
Statistics
Matches: 152, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
27 128 0.84
28 24 0.16
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:6636 original size:54 final size:54
Alignment explanation
Indices: 6576--6779 Score: 257
Period size: 54 Copynumber: 3.8 Consensus size: 54
6566 AAATTGTACA
* * *
6576 GCACTAAGTGTGCGATTTGGCTATGTAGCACTAAGTGTGCGATTTGACCATGTT
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
** ** * *
6630 GCACTAAGTGTGCGAAATGAAAATG-ATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGTTGACTATGTA-GCACTAAGTGTGCGATTTGACCATGTG
**
6684 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGTG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGA-TTTGACCATGTG
* * *
6739 GCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
6780 GACTTAATAT
Statistics
Matches: 128, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 80 0.62
55 47 0.37
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
Found at i:12155 original size:28 final size:27
Alignment explanation
Indices: 12088--12157 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 27
12078 GGAATATGAT
* *
12088 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTAACCATGCA
* *
12115 GCACTAAGTGTGCGAATCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TAACCATGCA
*
12143 GCACTAAGGGTGCGA
1 GCACTAAGTGTGCGA
12158 TTTGATTACG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 17 0.46
28 20 0.54
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTAACCATGCA
Found at i:12173 original size:55 final size:53
Alignment explanation
Indices: 12033--12184 Score: 178
Period size: 55 Copynumber: 2.8 Consensus size: 53
12023 TAAATTGTAC
* * *
12033 AGCACTAAGTGTGCGATTCGATTATGTTGCACTAAGTGTGCGAAAGGAATATG
1 AGCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGAAACGAATATG
* ** * * *
12086 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAATCTAACTATG
1 A-GCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGAAACGAA-TATG
* *
12141 TAGCACTAAGGGTGCGATTTGATTACGTGGCACTAAGTGTGCGA
1 -AGCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGA
12185 GTTGAGTGAA
Statistics
Matches: 81, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
53 1 0.01
54 39 0.48
55 40 0.49
56 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.27
Consensus pattern (53 bp):
AGCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGAAACGAATATG
Found at i:12189 original size:27 final size:27
Alignment explanation
Indices: 12034--12189 Score: 145
Period size: 27 Copynumber: 5.7 Consensus size: 27
12024 AAATTGTACA
* *
12034 GCACTAAGTGTGCG-ATTCGATTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
** *
12061 GCACTAAGTGTGCGAAAGGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
12088 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* *
12115 GCACTAAGTGTGCGAATCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * * *
12143 GCACTAAGGGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
12170 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
12190 GTGAATAGCA
Statistics
Matches: 105, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
27 82 0.78
28 23 0.22
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:18044 original size:27 final size:27
Alignment explanation
Indices: 18007--18211 Score: 223
Period size: 27 Copynumber: 7.6 Consensus size: 27
17997 TAAATTGTAC
*
18007 AGCACTAAGTGTGCGATTTGGCTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
18034 AGCACTAAGTGTGCGATTTGACCATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** **
18061 TGCACTAAGTGTGCGAAATGAAAATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
18087 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
18115 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
18142 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * * *
18170 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
18197 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
18212 GACTTAATAT
Statistics
Matches: 152, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
27 128 0.84
28 24 0.16
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:18068 original size:54 final size:54
Alignment explanation
Indices: 18008--18211 Score: 257
Period size: 54 Copynumber: 3.8 Consensus size: 54
17998 AAATTGTACA
* * *
18008 GCACTAAGTGTGCGATTTGGCTATGTAGCACTAAGTGTGCGATTTGACCATGTT
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
** ** * *
18062 GCACTAAGTGTGCGAAATGAAAATG-ATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGTTGACTATGTA-GCACTAAGTGTGCGATTTGACCATGTG
**
18116 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGTG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGA-TTTGACCATGTG
* * *
18171 GCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
18212 GACTTAATAT
Statistics
Matches: 128, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 80 0.62
55 47 0.37
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
Done.