Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1372
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: 21556
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Found at i:2139 original size:27 final size:27
Alignment explanation
Indices: 2108--2285 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
2098 TAAATTGTAC
2108 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
2135 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
2161 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
2189 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
2217 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
2244 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
2271 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2286 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:2222 original size:82 final size:81
Alignment explanation
Indices: 2109--2264 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
2099 AAATTGTACA
* *
2109 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
2173 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
2190 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
2255 TGCGAGTTGA
65 TGCGAATTGA
2265 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:2276 original size:82 final size:81
Alignment explanation
Indices: 2105--2285 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
2095 GATTAAATTG
* *
2105 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
2170 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
2186 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
2250 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
2268 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
2286 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
Found at i:10169 original size:27 final size:27
Alignment explanation
Indices: 10138--10315 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
10128 TAAATTGTAC
10138 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
10165 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
10191 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
10219 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
10247 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
10274 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
10301 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
10316 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:10252 original size:82 final size:81
Alignment explanation
Indices: 10139--10294 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
10129 AAATTGTACA
* *
10139 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
10203 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
10220 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
10285 TGCGAGTTGA
65 TGCGAATTGA
10295 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:10306 original size:82 final size:81
Alignment explanation
Indices: 10135--10315 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
10125 GATTAAATTG
* *
10135 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
10200 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
10216 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
10280 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
10298 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
10316 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
Found at i:15676 original size:26 final size:26
Alignment explanation
Indices: 15645--15750 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
15635 TGAAATGCCC
15645 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
15671 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
*
15697 ATCAT-GAATATTTACCT-AACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
15721 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
15747 ATCA
1 ATCA
15751 ATTTTATCAA
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
24 11 0.15
25 22 0.30
26 40 0.55
ACGTcount: A:0.37, C:0.25, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:15723 original size:50 final size:52
Alignment explanation
Indices: 15645--15750 Score: 189
Period size: 50 Copynumber: 2.1 Consensus size: 52
15635 TGAAATGCCC
15645 ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
*
15697 ATCAT-GAATATTTACCT-AACCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
15747 ATCA
1 ATCA
15751 ATTTTATCAA
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
50 37 0.70
51 11 0.21
52 5 0.09
ACGTcount: A:0.37, C:0.25, G:0.07, T:0.32
Consensus pattern (52 bp):
ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
Done.