Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2177
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: 24944
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:11506 original size:9 final size:9
Alignment explanation
Indices: 11456--11532 Score: 68
Period size: 9 Copynumber: 8.6 Consensus size: 9
11446 ATCCAAAGTT
11456 TTATGTAAG
1 TTATGTAAG
*
11465 TTATGATATG
1 TTATG-TAAG
* * *
11475 ATATATATAT
1 TTATGTA-AG
11485 TTATGT-A-
1 TTATGTAAG
11492 TTATGTAAG
1 TTATGTAAG
11501 TTATGTAAG
1 TTATGTAAG
*
11510 TTATATAAG
1 TTATGTAAG
*
11519 TTATGTAAC
1 TTATGTAAG
11528 TTATG
1 TTATG
11533 ATCCAAAGTT
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
7 6 0.11
8 2 0.04
9 36 0.67
10 10 0.19
ACGTcount: A:0.35, C:0.01, G:0.16, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:11532 original size:36 final size:36
Alignment explanation
Indices: 11456--11525 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
11446 ATCCAAAGTT
* *
11456 TTATGTAAGTTATGATATGATATATATATTTATGTA
1 TTATGTAAGTTATGATAAGATATATATAGTTATGTA
*
11492 TTATGTAAGTTATG-TAAGTTATATA-AGTTATGTA
1 TTATGTAAGTTATGATAAGATATATATAGTTATGTA
11526 ACTTATGATC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 8 0.26
35 9 0.29
36 14 0.45
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (36 bp):
TTATGTAAGTTATGATAAGATATATATAGTTATGTA
Found at i:11601 original size:13 final size:13
Alignment explanation
Indices: 11583--11609 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11573 TGATTATCAT
11583 CTTTAAATTTTAA
1 CTTTAAATTTTAA
11596 CTTTAAATTTTAA
1 CTTTAAATTTTAA
11609 C
1 C
11610 CCTTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (13 bp):
CTTTAAATTTTAA
Found at i:11993 original size:25 final size:27
Alignment explanation
Indices: 11968--12023 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 27
11958 TTAAACTATA
11968 TACTT-TTAAGTATAAATAAAAAATAT
1 TACTTATTAAGTATAAATAAAAAATAT
*
11994 TATTTAAATTAAGTATAAAT-AAAAATAT
1 TACTT--ATTAAGTATAAATAAAAAATAT
12022 TA
1 TA
12024 TTTAAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 4 0.15
28 10 0.38
29 12 0.46
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (27 bp):
TACTTATTAAGTATAAATAAAAAATAT
Found at i:12026 original size:28 final size:29
Alignment explanation
Indices: 11973--12033 Score: 115
Period size: 28 Copynumber: 2.1 Consensus size: 29
11963 CTATATACTT
11973 TTAAGTATAAATAAAAAATATTATTTAAA
1 TTAAGTATAAATAAAAAATATTATTTAAA
12002 TTAAGTATAAAT-AAAAATATTATTTAAA
1 TTAAGTATAAATAAAAAATATTATTTAAA
12030 TTAA
1 TTAA
12034 ATTTTCTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 20 0.62
29 12 0.38
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (29 bp):
TTAAGTATAAATAAAAAATATTATTTAAA
Found at i:18676 original size:38 final size:38
Alignment explanation
Indices: 18634--18732 Score: 128
Period size: 38 Copynumber: 2.6 Consensus size: 38
18624 CGAATATAAT
* *
18634 AATTATAATTACCATAATTATAATAATGTTTGA-CCAAA
1 AATTATAATTACAATAATTATAATAATATTTGATCC-AA
* * * *
18672 AATTACAATTAGAATAATTATGATAATATTTGATCCTA
1 AATTATAATTACAATAATTATAATAATATTTGATCCAA
18710 AATTATAATTACAATAATTATAA
1 AATTATAATTACAATAATTATAA
18733 CAAGGATTTC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 49 0.96
39 2 0.04
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.38
Consensus pattern (38 bp):
AATTATAATTACAATAATTATAATAATATTTGATCCAA
Done.