Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2104
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: 18250
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Found at i:4644 original size:2 final size:2
Alignment explanation
Indices: 4637--4671 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4627 AAGAAGAAAA
4637 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4672 TTGCATTAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7114 original size:41 final size:41
Alignment explanation
Indices: 7034--7113 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 41
7024 TTATTTTATT
*
7034 ATTTAAAATAATATTAAAAAATATTTATTATATAAAAAATA
1 ATTTAAAATAATATTAAAAAAAATTTATTATATAAAAAATA
* * *
7075 ATTTAAATTAAT-TTAAATAAAAAATTTATTTTATCAAAA
1 ATTTAAAATAATATT-AA-AAAAAATTTATTATATAAAAA
7114 TTCGATCTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 2 0.06
41 13 0.39
42 18 0.55
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (41 bp):
ATTTAAAATAATATTAAAAAAAATTTATTATATAAAAAATA
Found at i:7237 original size:11 final size:11
Alignment explanation
Indices: 7223--7247 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
7213 ACTTTGATTA
7223 AAAAATAAAAT
1 AAAAATAAAAT
7234 AAAAATAAAAT
1 AAAAATAAAAT
7245 AAA
1 AAA
7248 TCTCTAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:7911 original size:17 final size:17
Alignment explanation
Indices: 7887--7939 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 17
7877 TAGATATTTA
7887 AAAT-TTTATATAATAT
1 AAATATTTATATAATAT
7903 AAATATTTA-AT-ATAT
1 AAATATTTATATAATAT
* *
7918 CAAA-ATTAATAAAATAT
1 -AAATATTTATATAATAT
7935 AAATA
1 AAATA
7940 ACATTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
15 8 0.27
16 13 0.43
17 9 0.30
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATTTATATAATAT
Found at i:11879 original size:26 final size:25
Alignment explanation
Indices: 11832--11884 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
11822 AAAAATATTT
*
11832 AATATATTTATAAATATAATATTAA
1 AATATATTTATAAATATAATATAAA
* * *
11857 AATATAATTTTTAAATTTTATATAAA
1 AATAT-ATTTATAAATATAATATAAA
11883 AA
1 AA
11885 AATTAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
AATATATTTATAAATATAATATAAA
Found at i:12259 original size:30 final size:28
Alignment explanation
Indices: 12190--12293 Score: 88
Period size: 30 Copynumber: 3.7 Consensus size: 28
12180 GAAATATTAT
* * * *
12190 AATTATATTTAAAGATATTTTATATTTA
1 AATTATATTTTAATAAATTATATATTTA
* *
12218 TATT-TATTTTAATAAATTA-ATCATTTT
1 AATTATATTTTAATAAATTATAT-ATTTA
*
12245 TATTATAAATTTTAA-AATATTATATATTTA
1 AATTAT--ATTTTAATAA-ATTATATATTTA
12275 AATTATATTTTAATAAATT
1 AATTATATTTTAATAAATT
12294 TTTGTATTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
26 2 0.03
27 19 0.31
28 14 0.23
29 4 0.07
30 20 0.33
31 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (28 bp):
AATTATATTTTAATAAATTATATATTTA
Found at i:12707 original size:15 final size:15
Alignment explanation
Indices: 12687--12717 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12677 ATAAATAAAT
*
12687 TAAAATATATTTATA
1 TAAAATATATTCATA
12702 TAAAATATATTCATA
1 TAAAATATATTCATA
12717 T
1 T
12718 CAATACTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAAATATATTCATA
Found at i:13351 original size:2 final size:2
Alignment explanation
Indices: 13344--13381 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
13334 AACAAAGATA
*
13344 AT AT AT AT AG AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13382 AAAGAAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13807 original size:2 final size:2
Alignment explanation
Indices: 13800--13830 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13790 AAGATTTTTA
13800 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
13831 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:13835 original size:2 final size:2
Alignment explanation
Indices: 13830--13860 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13820 TCTCTCTCTC
13830 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 T
13861 CATTTCTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17105 original size:23 final size:21
Alignment explanation
Indices: 17074--17125 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 21
17064 ATTTATTTAA
*
17074 TAAATAATAAATTTAATATTTTT
1 TAAA-AATAAATTT-ATAATTTT
*
17097 TATAAAATATATTTATAATTTT
1 TA-AAAATAAATTTATAATTTT
17119 TAAAAAT
1 TAAAAAT
17126 TATAAATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 5 0.19
22 9 0.35
23 10 0.38
24 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAAAATAAATTTATAATTTT
Found at i:17129 original size:22 final size:23
Alignment explanation
Indices: 17079--17125 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
17069 TTTAATAAAT
* *
17079 AATAAATTTAATATTTTTTATAA
1 AATATATTTAATAATTTTTATAA
17102 AATATATTT-ATAATTTTTA-AA
1 AATATATTTAATAATTTTTATAA
17123 AAT
1 AAT
17126 TATAAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 9 0.41
23 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AATATATTTAATAATTTTTATAA
Done.