Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2433
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: 20505
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Found at i:437 original size:14 final size:14
Alignment explanation
Indices: 418--447 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
408 AATAAAATAA
418 AAAAAATTTCATCC
1 AAAAAATTTCATCC
432 AAAAAATTTCATCC
1 AAAAAATTTCATCC
446 AA
1 AA
448 GTCTAACGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAAAATTTCATCC
Found at i:11231 original size:32 final size:34
Alignment explanation
Indices: 11191--11256 Score: 109
Period size: 32 Copynumber: 2.0 Consensus size: 34
11181 AAAATCATAT
11191 ATTAAAATTTATAT-AATATA-AATTATTAAAAA
1 ATTAAAATTTATATAAATATATAATTATTAAAAA
*
11223 ATTAAAATTTATATAAATATATAATTTTTAAAAA
1 ATTAAAATTTATATAAATATATAATTATTAAAAA
11257 CAATTATAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 14 0.45
33 6 0.19
34 11 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (34 bp):
ATTAAAATTTATATAAATATATAATTATTAAAAA
Found at i:12027 original size:18 final size:18
Alignment explanation
Indices: 12004--12056 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
11994 ATTTATTAAA
12004 ATATTAAAATATTAATTT
1 ATATTAAAATATTAATTT
* *
12022 ATATTAATATATT-TTTT
1 ATATTAAAATATTAATTT
*
12039 ATTAATAAAATATTAATT
1 A-TATTAAAATATTAATT
12057 CAAATCATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 4 0.14
18 22 0.79
19 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTAAAATATTAATTT
Found at i:12259 original size:14 final size:14
Alignment explanation
Indices: 12242--12287 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
12232 TATAATTATT
*
12242 TTTAAAAAATAATA
1 TTTAAAAATTAATA
*
12256 TTTAAAAATTTAAAA
1 TTTAAAAA-TTAATA
*
12271 TTTAAATATTAATA
1 TTTAAAAATTAATA
12285 TTT
1 TTT
12288 TTATCTCTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TTTAAAAATTAATA
Found at i:12508 original size:7 final size:7
Alignment explanation
Indices: 12496--12524 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
12486 TATTTGGTCA
12496 TCATAAT
1 TCATAAT
12503 TCATAAT
1 TCATAAT
12510 TCATAAT
1 TCATAAT
12517 TCATAAT
1 TCATAAT
12524 T
1 T
12525 ATATGTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (7 bp):
TCATAAT
Found at i:13064 original size:18 final size:17
Alignment explanation
Indices: 13036--13071 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
13026 AAATTAATTG
*
13036 ATTTTTTATATTTTATA
1 ATTTTTTATATTTAATA
13053 ATTTTATTATATTTAATA
1 ATTTT-TTATATTTAATA
13071 A
1 A
13072 ATTAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTTTATATTTAATA
Found at i:13079 original size:18 final size:18
Alignment explanation
Indices: 13041--13080 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
13031 AATTGATTTT
* * *
13041 TTATATTTTATAATTTTA
1 TTATATTTAATAAATTAA
13059 TTATATTTAATAAATTAA
1 TTATATTTAATAAATTAA
13077 TTAT
1 TTAT
13081 TAAATTTAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATATTTAATAAATTAA
Found at i:13082 original size:21 final size:21
Alignment explanation
Indices: 13041--13100 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
13031 AATTGATTTT
*
13041 TTATATTTTAT-AATT--TTA
1 TTATATTTAATAAATTAATTA
13059 TTATATTTAATAAATTAATTA
1 TTATATTTAATAAATTAATTA
* * *
13080 TTAAATTTAACAAAATAATTA
1 TTATATTTAATAAATTAATTA
13101 CATTCATTAC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.29
19 4 0.11
21 21 0.60
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATATTTAATAAATTAATTA
Found at i:13700 original size:6 final size:7
Alignment explanation
Indices: 13683--13709 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
13673 CGCCGGAAGG
13683 GGGGGGT
1 GGGGGGT
13690 GGGGGGT
1 GGGGGGT
13697 GGGGGGT
1 GGGGGGT
13704 GGGGGG
1 GGGGGG
13710 AAGGTTAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.89, T:0.11
Consensus pattern (7 bp):
GGGGGGT
Found at i:15537 original size:21 final size:22
Alignment explanation
Indices: 15511--15555 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
15501 AAATAAATAT
*
15511 AAATAAATTA-AAATTTATAAA
1 AAATAAATTATAAATGTATAAA
*
15532 AAATAAATTATTAATGTATAAA
1 AAATAAATTATAAATGTATAAA
15554 AA
1 AA
15556 TTTATTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AAATAAATTATAAATGTATAAA
Found at i:16569 original size:5 final size:5
Alignment explanation
Indices: 16559--16590 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
16549 TTCTTGTATA
16559 TTATT TTATT TTATTT TTATT TTATT TTATT T
1 TTATT TTATT TTA-TT TTATT TTATT TTATT T
16591 GTGGTTGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:16580 original size:16 final size:16
Alignment explanation
Indices: 16559--16590 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
16549 TTCTTGTATA
16559 TTATTTTATTTTATTT
1 TTATTTTATTTTATTT
16575 TTATTTTATTTTATTT
1 TTATTTTATTTTATTT
16591 GTGGTTGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (16 bp):
TTATTTTATTTTATTT
Found at i:18920 original size:22 final size:24
Alignment explanation
Indices: 18894--18945 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
18884 TTAAATATAA
18894 ATAATACAAAAAAAAT-TAAA-AC
1 ATAATACAAAAAAAATATAAACAC
* *
18916 ATAATATAAAAAAAATATAAACAG
1 ATAATACAAAAAAAATATAAACAC
18940 ATAATA
1 ATAATA
18946 ATATACGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 15 0.58
23 4 0.15
24 7 0.27
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.21
Consensus pattern (24 bp):
ATAATACAAAAAAAATATAAACAC
Done.