Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold783
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: 163167
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
File 2 of 2
Found at i:152694 original size:11 final size:11
Alignment explanation
Indices: 152665--152698 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
152655 TTGGCCTAAT
152665 AAATGATTTTTC
1 AAAT-ATTTTTC
152677 AAA-ATTTTTC
1 AAATATTTTTC
152687 AAATATTTTTC
1 AAATATTTTTC
152698 A
1 A
152699 TAAAACTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.48
11 8 0.38
12 3 0.14
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (11 bp):
AAATATTTTTC
Found at i:155170 original size:20 final size:18
Alignment explanation
Indices: 155125--155187 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 18
155115 TTGAAGTCAT
155125 TAAAAT-ATTAAAATATA
1 TAAAATAATTAAAATATA
* *
155142 TATAATAATTATAATAATAA
1 TAAAATAATTAAAAT-AT-A
155162 TAAAATAATTAAAATTATA
1 TAAAATAATTAAAA-TATA
*
155181 TATAATA
1 TAAAATA
155188 TATATGATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
17 5 0.14
18 7 0.19
19 9 0.24
20 15 0.41
21 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATAATTAAAATATA
Found at i:155370 original size:6 final size:6
Alignment explanation
Indices: 155361--155387 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
155351 ATTATTATAT
155361 TATTTA TATTTA TATTTA TATTTA TAT
1 TATTTA TATTTA TATTTA TATTTA TAT
155388 CATATATCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:155504 original size:25 final size:26
Alignment explanation
Indices: 155460--155518 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
155450 CTTCATTAAA
155460 AAATTAAAAAAATAAAAATTTAAA-TT
1 AAATTAAAAAAATAAAAA-TTAAATTT
* * *
155486 -AATTAAAATAATTATAATTAAATTT
1 AAATTAAAAAAATAAAAATTAAATTT
155511 AAATTAAA
1 AAATTAAA
155519 TTATATGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 5 0.18
25 16 0.57
26 7 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
AAATTAAAAAAATAAAAATTAAATTT
Found at i:156517 original size:24 final size:24
Alignment explanation
Indices: 156458--156517 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
156448 TAATTTATTT
156458 TTAAA-TAACAAATAACATAATATA
1 TTAAATTAA-AAATAACATAATATA
* *
156482 TTAATATCAAAAATAATAT-ATATAA
1 TTAA-ATTAAAAATAACATAATAT-A
156507 TTAAATTAAAA
1 TTAAATTAAAA
156518 TATTTTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 14 0.47
25 14 0.47
26 2 0.07
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (24 bp):
TTAAATTAAAAATAACATAATATA
Found at i:157679 original size:17 final size:17
Alignment explanation
Indices: 157659--157717 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
157649 TATAATTGAT
157659 TTAAATA-ATAATATTTA
1 TTAAATATATAA-ATTTA
*
157676 TTAAATATCTAAATTTA
1 TTAAATATATAAATTTA
* *
157693 TTATATATATTTAAATTTT
1 TTA-A-ATATATAAATTTA
157712 TTAAAT
1 TTAAAT
157718 TAATTTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 17 0.47
18 5 0.14
19 14 0.39
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAATATATAAATTTA
Found at i:157707 original size:19 final size:17
Alignment explanation
Indices: 157671--157717 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
157661 AAATAATAAT
157671 ATTTATTAAATATCTAA
1 ATTTATTAAATATCTAA
*
157688 ATTTATTATATATATTTAA
1 ATTTATTA-A-ATATCTAA
*
157707 ATTTTTTAAAT
1 ATTTATTAAAT
157718 TAATTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 10 0.38
18 2 0.08
19 14 0.54
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTATTAAATATCTAA
Found at i:158658 original size:8 final size:8
Alignment explanation
Indices: 158645--158673 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
158635 ATTTTTAAAT
158645 TAAAAAAA
1 TAAAAAAA
158653 TAAAAAAA
1 TAAAAAAA
158661 TAAAAAAA
1 TAAAAAAA
158669 TAAAA
1 TAAAA
158674 TAAAAAGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (8 bp):
TAAAAAAA
Found at i:160344 original size:28 final size:29
Alignment explanation
Indices: 160313--160367 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
160303 TAATGGTTTC
* *
160313 TATTTATT-TATCATTAAATAAAATTTAT
1 TATTTATTAAATCATTAAAAAAAATTTAT
*
160341 TATTTATTAAATTATTAAAAAAAATTT
1 TATTTATTAAATCATTAAAAAAAATTT
160368 TAAGTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (29 bp):
TATTTATTAAATCATTAAAAAAAATTTAT
Done.