Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold770
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: 12267
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Found at i:2225 original size:82 final size:81
Alignment explanation
Indices: 2109--2264 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
2099 AAATTGTACA
* * * *
2109 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
2173 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
2190 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
2255 TGCGAGTTGA
65 TGCGAATTGA
2265 TTATAGCACT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:2232 original size:55 final size:52
Alignment explanation
Indices: 2108--2283 Score: 185
Period size: 55 Copynumber: 3.3 Consensus size: 52
2098 TAAATTGTAC
* *
2108 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCG-AGTGAATATG
* * *
2161 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-GAA-TATG
* * * *
2216 TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGTTGATTAT-
1 -AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAG-TGAATATG
*
2269 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2284 GGCTCAATAT
Statistics
Matches: 104, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
52 14 0.13
53 3 0.03
54 39 0.38
55 46 0.44
56 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.28
Consensus pattern (52 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTGAATATG
Found at i:2265 original size:27 final size:27
Alignment explanation
Indices: 2108--2283 Score: 162
Period size: 27 Copynumber: 6.6 Consensus size: 27
2098 TAAATTGTAC
2108 AGCACTAAGTGTGCG-ATTCGACTATGT
1 AGCACTAAGTGTGCGAATT-GACTATGT
* * *
2135 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
2161 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* * *
2189 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGAAT-TGACTATGT
* * *
2217 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
2244 GGCACTAAGTGTGCGAGTTGA-T-TAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
2269 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2284 GGCTCAATAT
Statistics
Matches: 122, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
25 14 0.11
26 1 0.01
27 83 0.68
28 24 0.20
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:10301 original size:82 final size:81
Alignment explanation
Indices: 10185--10340 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
10175 AAATTGTACA
* * * *
10185 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
10249 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
10266 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
10331 TGCGAGTTGA
65 TGCGAATTGA
10341 TGTATAGCAC
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:10308 original size:55 final size:52
Alignment explanation
Indices: 10184--10360 Score: 178
Period size: 55 Copynumber: 3.3 Consensus size: 52
10174 TAAATTGTAC
* *
10184 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCG-AGTGAATATG
* * *
10237 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-GAA-TATG
* * * *
10292 TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGTTGATGTAT-
1 -AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAG-TGA-ATATG
*
10346 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
10361 GGCTCAATAT
Statistics
Matches: 104, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
53 17 0.16
54 36 0.35
55 49 0.47
56 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (52 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTGAATATG
Found at i:10341 original size:27 final size:27
Alignment explanation
Indices: 10185--10340 Score: 163
Period size: 27 Copynumber: 5.7 Consensus size: 27
10175 AAATTGTACA
*
10185 GCACTAAGTGTGCG-ATTCGACTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
* *
10212 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
10239 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
10266 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * *
10294 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
10321 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
10341 TGTATAGCAC
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
27 83 0.77
28 25 0.23
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:10357 original size:26 final size:26
Alignment explanation
Indices: 10266--10360 Score: 93
Period size: 27 Copynumber: 3.5 Consensus size: 26
10256 TGACCATGCG
* * *
10266 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAGT-TGATTA-CTA
* *
10294 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAGTTGATTAC-TA
10321 GCACTAAGTGTGCGAGTTGATGTA-TA
1 GCACTAAGTGTGCGAGTTGAT-TACTA
*
10347 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
10361 GGCTCAATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
26 14 0.25
27 25 0.44
28 18 0.32
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (26 bp):
GCACTAAGTGTGCGAGTTGATTACTA
Found at i:12219 original size:22 final size:22
Alignment explanation
Indices: 12191--12255 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
12181 GCAAATACTT
*
12191 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
12213 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
* *
12235 TTGGCGCAAAGTCATAATCAG
1 TTGGCACAAAGCCATAATCAG
12256 AATAATTGGA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.06
22 31 0.89
23 2 0.06
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.22
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Done.