Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2570
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: 23066
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:911 original size:21 final size:19
Alignment explanation
Indices: 889--926 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
879 TAACTTGATA
*
889 ATAATTAAAAATA-ATTTT
1 ATAATTAAAAAAATATTTT
907 ATAATTAAAAAAATATTTT
1 ATAATTAAAAAAATATTTT
926 A
1 A
927 CGTAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAATTAAAAAAATATTTT
Found at i:1415 original size:24 final size:22
Alignment explanation
Indices: 1378--1424 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
1368 ATTAATATAA
**
1378 ATTTTTTAATATTTTTATTATT
1 ATTTTTTAATATTTAAATTATT
1400 ATTTTTTAAATAATTTAAATTATT
1 ATTTTTT-AAT-ATTTAAATTATT
1424 A
1 A
1425 ATTAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 3 0.14
24 11 0.52
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
ATTTTTTAATATTTAAATTATT
Found at i:1432 original size:22 final size:20
Alignment explanation
Indices: 1407--1465 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
1397 ATTATTTTTT
*
1407 AAATAATTTAAATTATTAATTA
1 AAATAA-TTAAATT-TAAATTA
*
1429 AAATTAATTAAATTTAAATTT
1 AAA-TAATTAAATTTAAATTA
**
1450 AAATAAAAAAATTTAA
1 AAATAATTAAATTTAA
1466 CTGTTTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 11 0.34
21 8 0.25
22 10 0.31
23 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATAATTAAATTTAAATTA
Found at i:7707 original size:2 final size:2
Alignment explanation
Indices: 7700--7732 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
7690 TGTAAATCTT
7700 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7733 TACCCTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13796 original size:2 final size:2
Alignment explanation
Indices: 13789--13814 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13779 TTTTAAAATC
13789 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
13815 TAAAGAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21245 original size:3 final size:3
Alignment explanation
Indices: 21237--21270 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
21227 AGTTCACTAG
21237 TAA TAA TAA TAA T-A TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21271 ATATATTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 25 0.86
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:21255 original size:8 final size:8
Alignment explanation
Indices: 21237--21266 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
21227 AGTTCACTAG
21237 TAATAATAA
1 TAAT-ATAA
21246 TAATATAA
1 TAATATAA
21254 TAATATAA
1 TAATATAA
21262 TAATA
1 TAATA
21267 ATAAATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
TAATATAA
Found at i:21255 original size:11 final size:10
Alignment explanation
Indices: 21238--21273 Score: 54
Period size: 11 Copynumber: 3.4 Consensus size: 10
21228 GTTCACTAGT
21238 AATAATAATA
1 AATAATAATA
21248 ATATAATAATA
1 A-ATAATAATA
21259 TAATAATAATA
1 -AATAATAATA
21270 AATA
1 AATA
21274 TATTTTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.21
11 18 0.75
12 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AATAATAATA
Found at i:21499 original size:29 final size:28
Alignment explanation
Indices: 21435--21500 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 28
21425 TACAATAATA
21435 ATATTAAATTAAAAATTATATTAATTTTT
1 ATATTAAATTAAAAATTATATT-ATTTTT
21464 ATAATTAAATTTAAATAA-TATATT-TTATTT
1 AT-ATTAAA-TTAAA-AATTATATTATT-TTT
21494 ATATTAA
1 ATATTAA
21501 TAATAATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
29 9 0.27
30 11 0.33
31 11 0.33
32 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
ATATTAAATTAAAAATTATATTATTTTT
Done.