Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold862
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: 12116
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Found at i:4607 original size:21 final size:20
Alignment explanation
Indices: 4577--4617 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4567 TATGATATGC
4577 ATTTAAGTAAAATAAAAAATA
1 ATTTAAGT-AAATAAAAAATA
* *
4598 ATTTAGGTAAATAATAAATA
1 ATTTAAGTAAATAAAAAATA
4618 CTGATAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (20 bp):
ATTTAAGTAAATAAAAAATA
Found at i:4948 original size:7 final size:7
Alignment explanation
Indices: 4936--5005 Score: 56
Period size: 7 Copynumber: 9.9 Consensus size: 7
4926 CATATCAAAT
4936 TTTAAAA
1 TTTAAAA
4943 TTTAAAA
1 TTTAAAA
4950 TTT-AAA
1 TTTAAAA
4956 TTT-AAA
1 TTTAAAA
*
4962 TTATGAAA
1 TT-TAAAA
4970 TTTGGATAAA
1 TTT--A-AAA
*
4980 TTCAAAA
1 TTTAAAA
4987 TTT-AAA
1 TTTAAAA
*
4993 TATAAAA
1 TTTAAAA
5000 TTTAAA
1 TTTAAA
5006 TTTTTATTAC
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
6 16 0.31
7 25 0.48
8 6 0.12
10 5 0.10
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.41
Consensus pattern (7 bp):
TTTAAAA
Found at i:4958 original size:13 final size:13
Alignment explanation
Indices: 4936--5008 Score: 58
Period size: 13 Copynumber: 5.2 Consensus size: 13
4926 CATATCAAAT
4936 TTTAAAATTTAAAA
1 TTTAAAATTT-AAA
4950 TTT-AAATTTAAA
1 TTTAAAATTTAAA
*
4962 TTATGAAATTTGGATAAA
1 TT-T-AAAATT---TAAA
*
4980 TTCAAAATTTAAA
1 TTTAAAATTTAAA
*
4993 TATAAAATTTAAA
1 TTTAAAATTTAAA
5006 TTT
1 TTT
5009 TTATTACAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
12 5 0.11
13 24 0.51
14 3 0.06
15 4 0.09
16 5 0.11
18 6 0.13
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (13 bp):
TTTAAAATTTAAA
Found at i:6533 original size:2 final size:2
Alignment explanation
Indices: 6526--6555 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6516 AATGTCAAAC
6526 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6556 ATCAGACTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6703 original size:2 final size:2
Alignment explanation
Indices: 6698--6722 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6688 TGTGTGTGTG
6698 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 T
6723 TAAAAACTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7324 original size:24 final size:25
Alignment explanation
Indices: 7271--7325 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
7261 GGATCTTAAT
**
7271 ATTTATAATCTATTTTTATTTTTAA
1 ATTTATAATCTATTTTTATTTAAAA
7296 A-TTATAAT-T-TTTTTATATTAAAA
1 ATTTATAATCTATTTTTAT-TTAAAA
7319 ATTTATA
1 ATTTATA
7326 TATTAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 7 0.27
23 6 0.23
24 12 0.46
25 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTTATAATCTATTTTTATTTAAAA
Found at i:7753 original size:2 final size:2
Alignment explanation
Indices: 7746--7802 Score: 69
Period size: 2 Copynumber: 28.5 Consensus size: 2
7736 TTCTGGAGTC
* * * *
7746 AT AT AT AT AT AT AT AT AT AT AT TT AT TT AT TT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
7788 AT AT TT AT AT AT AT A
1 AT AT AT AT AT AT AT A
7803 AATTCAAATC
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (2 bp):
AT
Found at i:7782 original size:20 final size:20
Alignment explanation
Indices: 7746--7802 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
7736 TTCTGGAGTC
*
7746 ATATATATATATATATATAT
1 ATATATTTATATATATATAT
* *
7766 ATTTATTTATTTATATATAT
1 ATATATTTATATATATATAT
*
7786 GTATATTTATATATATA
1 ATATATTTATATATATA
7803 AATTCAAATC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
ATATATTTATATATATATAT
Found at i:8883 original size:21 final size:22
Alignment explanation
Indices: 8859--8899 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
8849 CAAAGAAAAA
*
8859 TTTATTTAAATATG-AATAATT
1 TTTATATAAATATGTAATAATT
*
8880 TTTATATAATTATGTAATAA
1 TTTATATAAATATGTAATAA
8900 ATATAAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTATATAAATATGTAATAATT
Found at i:8969 original size:17 final size:19
Alignment explanation
Indices: 8949--8987 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
8939 TTTTGATATC
8949 TTTGTTA-TTTAAGTT-TT
1 TTTGTTATTTTAAGTTATT
8966 TTTGTTATTTTAAGTTATT
1 TTTGTTATTTTAAGTTATT
8985 TTT
1 TTT
8988 ATAAGATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.35
18 8 0.40
19 5 0.25
ACGTcount: A:0.18, C:0.00, G:0.10, T:0.72
Consensus pattern (19 bp):
TTTGTTATTTTAAGTTATT
Found at i:10522 original size:19 final size:19
Alignment explanation
Indices: 10495--10537 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
10485 TAATTATATG
*
10495 ATTTTATTTA-AAATAAAAT
1 ATTTAATTTATAAA-AAAAT
*
10514 ATTTAATTTATAAAAATAT
1 ATTTAATTTATAAAAAAAT
10533 ATTTA
1 ATTTA
10538 TAATTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTAATTTATAAAAAAAT
Found at i:11611 original size:17 final size:17
Alignment explanation
Indices: 11589--11646 Score: 71
Period size: 17 Copynumber: 3.2 Consensus size: 17
11579 AAATATGGAG
11589 TAAATTTATTAATAATA
1 TAAATTTATTAATAATA
*
11606 TAAATTTACTAATAATAA
1 TAAATTTATTAATAAT-A
11624 TTAATATTTATATAATAATA
1 -TAA-ATTTAT-TAATAATA
11644 TAA
1 TAA
11647 TAACACAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 15 0.43
18 1 0.03
19 6 0.17
20 6 0.17
21 7 0.20
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATTTATTAATAATA
Found at i:11796 original size:128 final size:130
Alignment explanation
Indices: 11587--11822 Score: 289
Period size: 128 Copynumber: 1.8 Consensus size: 130
11577 CTAAATATGG
* * * * * *
11587 AGTAAATTTATTAATAATATAAATTTACTAATAATAATTAATATTTATATAATAATATAATAACA
1 AGTAAATGTACTAATAATATAAATTTAATAATAATAATCAATATTTATATAACAATACAATAACA
* * * *
11652 CAAATTATATGATAACTTTATAAACTTAAATAGTAAT-ATATAGTATGACATGTACTAAATAAAA
66 CAAAGTATATGATAACTATATAAAATTAAATACTAATAATATAGTATGACATGTACTAAATAAAA
* * * *
11716 AGTAAATGTACTAATAATAT-AATTTAATAATATTAATCAATATTTATATAGCAATACAGTAGCA
1 AGTAAATGTACTAATAATATAAATTTAATAATAATAATCAATATTTATATAACAATACAATAACA
** *
11780 TGACGTATAT-AGTAACTATATAAAATTAAATACTAATAATATA
66 CAAAGTATATGA-TAACTATATAAAATTAAATACTAATAATATA
11823 CATCAATAAT
Statistics
Matches: 88, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
127 1 0.01
128 64 0.73
129 23 0.26
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (130 bp):
AGTAAATGTACTAATAATATAAATTTAATAATAATAATCAATATTTATATAACAATACAATAACA
CAAAGTATATGATAACTATATAAAATTAAATACTAATAATATAGTATGACATGTACTAAATAAAA
Done.