Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2615
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: 22533
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Found at i:526 original size:5 final size:6
Alignment explanation
Indices: 503--537 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
493 TGAAAACCCA
503 AAAAAGT AAAGAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAA-T AAA-AAT AAAAAT AAAAAT AAAAAT AAA
538 TGAAAAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 18 0.67
7 7 0.26
8 2 0.07
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:7190 original size:4 final size:4
Alignment explanation
Indices: 7181--7217 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
7171 TTAATACTAA
7181 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
7218 TTTAAGAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:11533 original size:27 final size:28
Alignment explanation
Indices: 11478--11569 Score: 159
Period size: 28 Copynumber: 3.3 Consensus size: 28
11468 ATGTACTAGA
11478 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
11506 ATACCCCTATGTATGC-AAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
* *
11533 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATTACCATT
11561 ATACCCCTA
1 ATACCCCTA
11570 GGGTTAATTT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
27 27 0.44
28 34 0.56
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATTACCATT
Found at i:11733 original size:27 final size:27
Alignment explanation
Indices: 11675--11764 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 27
11665 AGGAAGCGTC
11675 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
11703 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
11730 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
11759 CTGGTG
1 CTGGTG
11765 ACTCTGTCAC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 23 0.42
28 25 0.45
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:11783 original size:55 final size:56
Alignment explanation
Indices: 11675--11789 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 56
11665 AGGAAGCGTC
* *
11675 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
11730 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
11786 CTGG
1 CTGG
11790 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.58
56 21 0.40
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:19411 original size:26 final size:28
Alignment explanation
Indices: 19358--19432 Score: 129
Period size: 26 Copynumber: 2.8 Consensus size: 28
19348 AGATGTACTA
19358 AATACCCCTATGTATGCAAAATTACCAT
1 AATACCCCTATGTATGCAAAATTACCAT
19386 AATA-CCCTATGTATG-AAAATTACCAT
1 AATACCCCTATGTATGCAAAATTACCAT
19412 -ATACCCCTATGTATGCAAAAT
1 AATACCCCTATGTATGCAAAAT
19433 GACCTTTATA
Statistics
Matches: 45, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
25 3 0.07
26 22 0.49
27 16 0.36
28 4 0.09
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.29
Consensus pattern (28 bp):
AATACCCCTATGTATGCAAAATTACCAT
Found at i:19446 original size:27 final size:26
Alignment explanation
Indices: 19363--19447 Score: 109
Period size: 27 Copynumber: 3.2 Consensus size: 26
19353 TACTAAATAC
*
19363 CCCTATGTATGCAAAATTACCATAATA
1 CCCTATGTATGCAAAATTACC-TTATA
*
19390 CCCTATGTATG-AAAATTACCATATA
1 CCCTATGTATGCAAAATTACCTTATA
*
19415 CCCCTATGTATGCAAAATGACCTTTATA
1 -CCCTATGTATGCAAAATTACC-TTATA
19443 CCCTA
1 CCCTA
19448 GGGTTAATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
25 3 0.06
26 20 0.39
27 24 0.47
28 4 0.08
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.31
Consensus pattern (26 bp):
CCCTATGTATGCAAAATTACCTTATA
Found at i:19594 original size:26 final size:26
Alignment explanation
Indices: 19563--19640 Score: 95
Period size: 26 Copynumber: 2.9 Consensus size: 26
19553 CTGGTGGCTA
*
19563 TGCCACAAATTAT-TGTTCTGGTGCCC
1 TGCCACAAA-TATCTGTTCTGGTGCAC
*
19589 TGCCACATATATCTGTTCTGGTGGCAC
1 TGCCACAAATATCTGTTCTGGT-GCAC
19616 TGCCACAAAATATCTGTATCTGGTG
1 TGCCAC-AAATATCTGT-TCTGGTG
19641 ACTCTGTCAC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
25 3 0.07
26 17 0.38
27 9 0.20
28 10 0.22
29 6 0.13
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (26 bp):
TGCCACAAATATCTGTTCTGGTGCAC
Found at i:19651 original size:29 final size:28
Alignment explanation
Indices: 19563--19651 Score: 94
Period size: 26 Copynumber: 3.2 Consensus size: 28
19553 CTGGTGGCTA
* *
19563 TGCCACAAATTAT-TGTTCTGGTG-CCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
* *
19589 TGCCAC-ATATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
19616 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
19645 TGTCACA
1 TGCCACA
19652 TTTTCTGTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
25 4 0.08
26 16 0.31
27 8 0.15
28 9 0.17
29 15 0.29
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Done.