Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2773
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: 36846
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:7046 original size:12 final size:12
Alignment explanation
Indices: 7029--7086 Score: 82
Period size: 12 Copynumber: 4.8 Consensus size: 12
7019 TCGGTATTGT
7029 AAAAAAAAATTC
1 AAAAAAAAATTC
*
7041 AAAAAAAATTTC
1 AAAAAAAAATTC
7053 AAAAAAAAAATTTC
1 -AAAAAAAAA-TTC
7067 -AAAAAAAATTC
1 AAAAAAAAATTC
7078 AAAAAAAAA
1 AAAAAAAAA
7087 GTTTGTATTC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
11 3 0.07
12 27 0.66
13 8 0.20
14 3 0.07
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:7062 original size:25 final size:25
Alignment explanation
Indices: 7029--7086 Score: 100
Period size: 25 Copynumber: 2.3 Consensus size: 25
7019 TCGGTATTGT
7029 AAAAAAAAA-TTCAAAAAAAATTTCA
1 AAAAAAAAATTTCAAAAAAAA-TTCA
7054 AAAAAAAAATTTCAAAAAAAATTCA
1 AAAAAAAAATTTCAAAAAAAATTCA
7079 AAAAAAAA
1 AAAAAAAA
7087 GTTTGTATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 21 0.66
26 11 0.34
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (25 bp):
AAAAAAAAATTTCAAAAAAAATTCA
Found at i:7173 original size:27 final size:28
Alignment explanation
Indices: 7130--7198 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
7120 TAGTATTGAA
* * *
7130 GAAAAAAAGAAGAAAAAAAATTTGGAATT
1 GAAAAAAAAAAGAAAAAAAA-TCGAAATT
7159 -AAAAAAAAAAGAAAAAAAATCGAAATT
1 GAAAAAAAAAAGAAAAAAAATCGAAATT
7186 GAAAAAAAAAAGA
1 GAAAAAAAAAAGA
7199 GTGATTGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.17
28 30 0.83
ACGTcount: A:0.74, C:0.01, G:0.13, T:0.12
Consensus pattern (28 bp):
GAAAAAAAAAAGAAAAAAAATCGAAATT
Found at i:8117 original size:17 final size:15
Alignment explanation
Indices: 8097--8135 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
8087 GCGAGCGAGA
8097 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
8114 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
8129 AAGATGA
1 AA-ATGA
8136 GTGGGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:23574 original size:23 final size:22
Alignment explanation
Indices: 23522--23574 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
23512 TCCACGTCTT
*
23522 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
23544 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
23567 TTTCTTTT
1 TTTCTTTT
23575 TTCACTCTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:31756 original size:13 final size:12
Alignment explanation
Indices: 31724--31759 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
31714 GTGAAAGATG
*
31724 TGAAAAAGAAAT
1 TGAAAAAGAAGT
31736 TGAAAAAGAAGT
1 TGAAAAAGAAGT
31748 TGAAGAAAGAAG
1 TGAA-AAAGAAG
31760 AGAAAATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 15 0.68
13 7 0.32
ACGTcount: A:0.61, C:0.00, G:0.25, T:0.14
Consensus pattern (12 bp):
TGAAAAAGAAGT
Found at i:33149 original size:4 final size:4
Alignment explanation
Indices: 33130--33163 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
33120 GTTGTAAAGT
33130 TTTA TTTTA TTTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA -TTTA -TTTA TTTA TTTA TTTA TTTA TTTA
33164 CTTAGTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 20 0.69
5 9 0.31
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Done.