Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1835
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: 17109
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Found at i:1190 original size:15 final size:15
Alignment explanation
Indices: 1170--1200 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1160 ATTTCGTTTG
*
1170 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1185 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1200 G
1 G
1201 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:3032 original size:21 final size:21
Alignment explanation
Indices: 3003--3047 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2993 AAGTTTTCAT
*
3003 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
3023 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
3045 TTT
1 TTT
3048 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:6625 original size:34 final size:34
Alignment explanation
Indices: 6580--6748 Score: 248
Period size: 34 Copynumber: 5.0 Consensus size: 34
6570 TAGGTGAAGC
*
6580 ATATTAAGTGTGTTAGGTAATGTATTTGGTGAGA
1 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAGA
* *
6614 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
1 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAGA
* *
6648 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
1 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAGA
* * *
6682 ATATTAGATGTGTTAGGCAATGTATTTGGTGAAA
1 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAGA
* *
6716 ATATTAGGTGTGTTAGGTAATGTGTTAGGTGAG
1 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAG
6749 TATGATATTT
Statistics
Matches: 122, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 122 1.00
ACGTcount: A:0.25, C:0.01, G:0.34, T:0.40
Consensus pattern (34 bp):
ATATTAGGTGTGTTAGGTAATGTATTTGGTGAGA
Found at i:11514 original size:34 final size:34
Alignment explanation
Indices: 11473--11641 Score: 248
Period size: 34 Copynumber: 5.0 Consensus size: 34
11463 TAGGTGAAGC
11473 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAGA
1 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAGA
* *
11507 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
1 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAGA
* *
11541 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
1 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAGA
* * * *
11575 ATATTAGATGTGTTAGGCAATGTATTTGGTAAAA
1 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAGA
* *
11609 ATATTAGGTGTGTTAGGTAATGTGTTAGGTGAG
1 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAG
11642 TATGATATTT
Statistics
Matches: 121, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 121 1.00
ACGTcount: A:0.25, C:0.01, G:0.34, T:0.40
Consensus pattern (34 bp):
ATATTAGGTGTGTTAGGTAATGTATTTGGTGAGA
Found at i:13701 original size:2 final size:2
Alignment explanation
Indices: 13694--13743 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
13684 AATCAATTGA
13694 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
13736 AT AT AT AT
1 AT AT AT AT
13744 GATCATGCTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13985 original size:23 final size:24
Alignment explanation
Indices: 13958--14019 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
13948 TTTTAAAAGA
13958 AATTAAAATATTAAAT-TTTTTTAT
1 AATTAAAAT-TTAAATATTTTTTAT
* *
13982 -ATTAATATTTATATATTTTTTAT
1 AATTAAAATTTAAATATTTTTTAT
14005 AATT-AAATTTAAATA
1 AATTAAAATTTAAATA
14020 AATAAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
22 5 0.16
23 24 0.75
24 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
AATTAAAATTTAAATATTTTTTAT
Found at i:14206 original size:17 final size:16
Alignment explanation
Indices: 14173--14226 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
14163 TTTTTCACAA
14173 ATTTTTATTTAAATTT
1 ATTTTTATTTAAATTT
**
14189 ATTTTTAGTTTAGCTTT
1 ATTTTTA-TTTAAATTT
**
14206 ATTTATTATAAAAATTT
1 ATTT-TTATTTAAATTT
14223 ATTT
1 ATTT
14227 ATCATAATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
16 7 0.23
17 20 0.67
18 3 0.10
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (16 bp):
ATTTTTATTTAAATTT
Found at i:14551 original size:4 final size:4
Alignment explanation
Indices: 14544--14570 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
14534 AAACAAACAA
14544 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
14571 ACATTAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Done.