Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3084
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: 18562
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Found at i:6140 original size:27 final size:27
Alignment explanation
Indices: 6109--6286 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
6099 TAAATTGTAC
6109 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
6136 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
6162 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
6190 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
6218 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
6245 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
6272 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
6287 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:6223 original size:82 final size:81
Alignment explanation
Indices: 6110--6265 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
6100 AAATTGTACA
* *
6110 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
6174 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
6191 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
6256 TGCGAGTTGA
65 TGCGAATTGA
6266 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:6277 original size:82 final size:81
Alignment explanation
Indices: 6106--6286 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
6096 GATTAAATTG
* *
6106 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
6171 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
6187 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
6251 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
6269 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
6287 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:9133 original size:24 final size:24
Alignment explanation
Indices: 9083--9136 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
9073 AATCGAATTT
*
9083 GCACACATAGTGCTCGTCACACTC
1 GCACACATAGTGCTAGTCACACTC
9107 GCACACATAGTGCCATAGT-ACAC-C
1 GCACACATAGTG-C-TAGTCACACTC
9131 GCACAC
1 GCACAC
9137 TCAGTGCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 19 0.70
25 5 0.19
26 3 0.11
ACGTcount: A:0.30, C:0.37, G:0.17, T:0.17
Consensus pattern (24 bp):
GCACACATAGTGCTAGTCACACTC
Found at i:17052 original size:24 final size:24
Alignment explanation
Indices: 17002--17055 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
16992 AATCGAATTT
*
17002 GCACACATAGTGCTCGTCACACTC
1 GCACACATAGTGCTAGTCACACTC
17026 GCACACATAGTGCCATAG-CACAC-C
1 GCACACATAGTG-C-TAGTCACACTC
17050 GCACAC
1 GCACAC
17056 TCAGTGCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 19 0.70
25 6 0.22
26 2 0.07
ACGTcount: A:0.30, C:0.39, G:0.17, T:0.15
Consensus pattern (24 bp):
GCACACATAGTGCTAGTCACACTC
Found at i:18372 original size:17 final size:18
Alignment explanation
Indices: 18345--18383 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
18335 TTTCATCACA
*
18345 TTTTCATTCTTTTTTTTC
1 TTTTCATTCTTTTCTTTC
18363 TTTT-ATTCTTTTCTTTC
1 TTTTCATTCTTTTCTTTC
18380 TTTT
1 TTTT
18384 TACATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTCATTCTTTTCTTTC
Done.