Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold792
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: 52899
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:4182 original size:22 final size:24
Alignment explanation
Indices: 4136--4182 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
4126 CACCTGCAAT
* *
4136 AAACACATTAAAATGAGTTTATTA
1 AAACACATTAAAATCAGCTTATTA
4160 AAACACATTAAAA-CA-CTTATTA
1 AAACACATTAAAATCAGCTTATTA
4182 A
1 A
4183 TCATAACACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 1 0.05
24 13 0.62
ACGTcount: A:0.53, C:0.13, G:0.04, T:0.30
Consensus pattern (24 bp):
AAACACATTAAAATCAGCTTATTA
Found at i:6934 original size:48 final size:47
Alignment explanation
Indices: 6855--6960 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
6845 GAGTGTCATG
*
6855 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
6903 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
6951 GAAAAAGAAA
1 GAAAAAGAAA
6961 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:8674 original size:20 final size:20
Alignment explanation
Indices: 8628--8674 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
8618 AGCTCGTTTC
*
8628 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
8648 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
8668 CAGCTCA
1 CAGCTCA
8675 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:14473 original size:15 final size:14
Alignment explanation
Indices: 14453--14488 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 14
14443 CTTCTTCTTC
14453 TTTTTTTTCACGAAT
1 TTTTTTTTCAC-AAT
14468 TTTTTTTTCACAAT
1 TTTTTTTTCACAAT
14482 TTTTTTT
1 TTTTTTT
14489 CAACTTGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.17, C:0.11, G:0.03, T:0.69
Consensus pattern (14 bp):
TTTTTTTTCACAAT
Found at i:14548 original size:12 final size:12
Alignment explanation
Indices: 14531--14575 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
14521 GAAACCAATT
14531 TTTTTTTTTGAA
1 TTTTTTTTTGAA
14543 TTTTTTTTTTGAA
1 -TTTTTTTTTGAA
**
14556 TTTTTTTTCAAA
1 TTTTTTTTTGAA
14568 TTTTTTTT
1 TTTTTTTT
14576 GAAGAAACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 18 0.60
13 12 0.40
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:14575 original size:13 final size:13
Alignment explanation
Indices: 14530--14563 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
14520 GGAAACCAAT
14530 TTTTTTTTTTGAA
1 TTTTTTTTTTGAA
14543 TTTTTTTTTTGAA
1 TTTTTTTTTTGAA
14556 TTTTTTTT
1 TTTTTTTT
14564 CAAATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (13 bp):
TTTTTTTTTTGAA
Found at i:15592 original size:21 final size:23
Alignment explanation
Indices: 15547--15593 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
15537 TCACCTGCAA
* *
15547 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
15570 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
15591 TAA
1 TAA
15594 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:28232 original size:11 final size:12
Alignment explanation
Indices: 28201--28231 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
28191 TTGTAGATTC
28201 AAAAAAAATCGA
1 AAAAAAAATCGA
28213 AAAAAAAATCGA
1 AAAAAAAATCGA
28225 AAAAAAA
1 AAAAAAA
28232 TTGCATACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.81, C:0.06, G:0.06, T:0.06
Consensus pattern (12 bp):
AAAAAAAATCGA
Found at i:30506 original size:16 final size:17
Alignment explanation
Indices: 30468--30506 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
30458 AAGAAGAAAA
30468 ACAAAAAGATGAGTGAT
1 ACAAAAAGATGAGTGAT
*
30485 AAAAAAAGA-GAGTGAT
1 ACAAAAAGATGAGTGAT
*
30501 TCAAAA
1 ACAAAA
30507 GAAAAAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.59, C:0.05, G:0.21, T:0.15
Consensus pattern (17 bp):
ACAAAAAGATGAGTGAT
Found at i:36267 original size:29 final size:29
Alignment explanation
Indices: 36233--36292 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
36223 ATGTATTAGT
* *
36233 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
36262 TTAGGACATATTTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
36291 TT
1 TT
36293 TTCTGTTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:41616 original size:20 final size:19
Alignment explanation
Indices: 41593--41657 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
41583 AAGCTCAAAC
41593 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
41613 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
41633 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
41653 GAGCT
1 GAGCT
41658 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:46907 original size:29 final size:29
Alignment explanation
Indices: 46873--46945 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
46863 ATGTATTAGT
* *
46873 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
46902 TTAGGACATATTTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
46931 TTAGGACATATTTAA
1 TTAGGACATATTTAA
46946 TAATATCTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.32
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:49633 original size:14 final size:15
Alignment explanation
Indices: 49614--49650 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
49604 TTATTGATGC
49614 TTAAATTAAG-TTCT
1 TTAAATTAAGCTTCT
*
49628 TTAAATTATGCTTCT
1 TTAAATTAAGCTTCT
49643 TT-AATTAA
1 TTAAATTAA
49651 ACTAGTTGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.51
Consensus pattern (15 bp):
TTAAATTAAGCTTCT
Found at i:50559 original size:11 final size:11
Alignment explanation
Indices: 50543--50599 Score: 87
Period size: 11 Copynumber: 5.0 Consensus size: 11
50533 TAGTAGTTTC
50543 TTCAAAAAAAA
1 TTCAAAAAAAA
50554 TTCAAAAAAAAA
1 TTC-AAAAAAAA
*
50566 ATCAAAAAAAAA
1 TTC-AAAAAAAA
50578 TTCAAAAAAAA
1 TTCAAAAAAAA
50589 TTCAAAAAAAA
1 TTCAAAAAAAA
50600 AATTGGTTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
11 22 0.51
12 21 0.49
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.16
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:50563 original size:12 final size:12
Alignment explanation
Indices: 50546--50600 Score: 94
Period size: 12 Copynumber: 4.7 Consensus size: 12
50536 TAGTTTCTTC
50546 AAAAAAAATTCA
1 AAAAAAAATTCA
*
50558 AAAAAAAAATCA
1 AAAAAAAATTCA
50570 AAAAAAAATTC-
1 AAAAAAAATTCA
50581 AAAAAAAATTCA
1 AAAAAAAATTCA
50593 AAAAAAAA
1 AAAAAAAA
50601 ATTGGTTTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
11 11 0.28
12 29 0.73
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:50603 original size:24 final size:24
Alignment explanation
Indices: 50546--50600 Score: 94
Period size: 23 Copynumber: 2.3 Consensus size: 24
50536 TAGTTTCTTC
50546 AAAAAAAATTCAAAAAAAAAATCA
1 AAAAAAAATTCAAAAAAAAAATCA
*
50570 AAAAAAAATTC-AAAAAAAATTCA
1 AAAAAAAATTCAAAAAAAAAATCA
50593 AAAAAAAA
1 AAAAAAAA
50601 ATTGGTTTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 19 0.63
24 11 0.37
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (24 bp):
AAAAAAAATTCAAAAAAAAAATCA
Found at i:50664 original size:17 final size:18
Alignment explanation
Indices: 50642--50681 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
50632 TATCAAGTTG
50642 AAAAAAAAA-TTCGTGAA
1 AAAAAAAAATTTCGTGAA
50659 AAAAAAAAATTTCGTGAA
1 AAAAAAAAATTTCGTGAA
50677 AAAAA
1 AAAAA
50682 GAAGAAGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.68, C:0.05, G:0.10, T:0.17
Consensus pattern (18 bp):
AAAAAAAAATTTCGTGAA
Found at i:52593 original size:20 final size:20
Alignment explanation
Indices: 52568--52621 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
52558 AACGAGTTAA
*
52568 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTTGAATGAGCTAAC
*
52588 TTGAGCATGAATGAGCTAAC
1 TTGAGCTTGAATGAGCTAAC
*
52608 -TGAGCTCGAATGAG
1 TTGAGCTTGAATGAG
52622 TTGAACACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.26
Consensus pattern (20 bp):
TTGAGCTTGAATGAGCTAAC
Done.