Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3643
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: 20436
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:1238 original size:21 final size:23
Alignment explanation
Indices: 1193--1239 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1183 TCACCTGCAA
* *
1193 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
1216 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
1237 TAA
1 TAA
1240 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:6415 original size:18 final size:18
Alignment explanation
Indices: 6381--6418 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
6371 AGTTGTAAAG
*
6381 TTTTATTTTTCTTTTTAT
1 TTTTATTTTTCTATTTAT
6399 TTTTATTTATT-TATTTAT
1 TTTTATTT-TTCTATTTAT
6417 TT
1 TT
6419 ATTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTATTTTTCTATTTAT
Found at i:8782 original size:17 final size:18
Alignment explanation
Indices: 8745--8782 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
8735 GATTGAGAGT
* *
8745 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
8763 GAAAAGAAAT-TGAAAAA
1 GAAAAGAAATGTGAAAAA
8780 GAA
1 GAA
8783 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.63, C:0.03, G:0.24, T:0.11
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:8795 original size:13 final size:12
Alignment explanation
Indices: 8764--8818 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
8754 TGTGAAACAG
*
8764 AAAAGAAATTGA
1 AAAAGAAGTTGA
8776 AAAAGAAGTTGA
1 AAAAGAAGTTGA
*
8788 AGAAAGAAG-AGA
1 A-AAAGAAGTTGA
*
8800 AAATGAA-TTAGA
1 AAAAGAAGTT-GA
8812 AAAAGAA
1 AAAAGAA
8819 ACAAAAGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
11 5 0.14
12 23 0.66
13 7 0.20
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.13
Consensus pattern (12 bp):
AAAAGAAGTTGA
Found at i:10189 original size:4 final size:4
Alignment explanation
Indices: 10180--10210 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
10170 AAGTTTTATT
10180 TTTA TTTA -TTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
10211 CTTAGTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:10205 original size:12 final size:11
Alignment explanation
Indices: 10174--10210 Score: 58
Period size: 12 Copynumber: 3.4 Consensus size: 11
10164 GTTGTAAAGT
10174 TTTATT-TTTA
1 TTTATTATTTA
10184 TTTATTATTTA
1 TTTATTATTTA
10195 TTTATTTATTTA
1 TTTA-TTATTTA
10207 TTTA
1 TTTA
10211 CTTAGTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 6 0.24
11 8 0.32
12 11 0.44
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:11914 original size:20 final size:20
Alignment explanation
Indices: 11891--11936 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
11881 GGGTTAAGAT
*
11891 TGAGCTAAATTGAGCTTGAG
1 TGAGCTAAATTGAGCTCGAG
* * *
11911 TGAGTTGACTTGAGCTCGAG
1 TGAGCTAAATTGAGCTCGAG
11931 TGAGCT
1 TGAGCT
11937 GGAAACGAGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.13, G:0.33, T:0.30
Consensus pattern (20 bp):
TGAGCTAAATTGAGCTCGAG
Found at i:13232 original size:21 final size:23
Alignment explanation
Indices: 13187--13233 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
13177 TCACCTGCAA
* *
13187 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
13210 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
13231 TAA
1 TAA
13234 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Done.