Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2560
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: 13636
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Found at i:1726 original size:35 final size:35
Alignment explanation
Indices: 1687--1759 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
1677 ACACATTCTT
1687 TATTCTCGTAAGATCAATCTCACATAAATAATATA
1 TATTCTCGTAAGATCAATCTCACATAAATAATATA
*
1722 TATTCTCGTCAGATCAATCTCACATAAATAATATA
1 TATTCTCGTAAGATCAATCTCACATAAATAATATA
1757 TAT
1 TAT
1760 CACATACTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (35 bp):
TATTCTCGTAAGATCAATCTCACATAAATAATATA
Found at i:3937 original size:27 final size:26
Alignment explanation
Indices: 3906--4083 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 26
3896 TAAATTGTAC
3906 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
3933 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
3959 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
3987 GGCACTAAGTGTGCGAGTCTGACTATGT
1 AGCACTAAGTGTGCGA-T-TGACTATGT
* *
4015 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* * *
4042 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
4069 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
4084 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
26 1 0.01
27 100 0.79
28 25 0.20
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:4022 original size:82 final size:81
Alignment explanation
Indices: 3907--4062 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
3897 AAATTGTACA
* * *
3907 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
3971 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
3988 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
4053 TGCGAGTTGA
65 TGCGAATTGA
4063 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 18 0.27
82 48 0.73
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:4074 original size:82 final size:81
Alignment explanation
Indices: 3903--4083 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
3893 GATTAAATTG
* * *
3903 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
3968 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
3984 TGCGGCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
4048 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
4066 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
4084 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 20 0.24
82 63 0.76
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:12093 original size:27 final size:27
Alignment explanation
Indices: 12062--12239 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
12052 TAAATTGTAC
12062 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
12089 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
12115 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
12143 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
12171 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
12198 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
12225 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
12240 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:12176 original size:82 final size:81
Alignment explanation
Indices: 12063--12218 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
12053 AAATTGTACA
* *
12063 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
12127 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
12144 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
12209 TGCGAGTTGA
65 TGCGAATTGA
12219 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:12230 original size:82 final size:81
Alignment explanation
Indices: 12059--12239 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
12049 GATTAAATTG
* *
12059 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
12124 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
12140 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
12204 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
12222 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
12240 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.