Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold509
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: 31081
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:9500 original size:52 final size:52
Alignment explanation
Indices: 9439--9539 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
9429 CATGCACATA
* *
9439 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
9491 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
9540 CGTTTCCTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.33
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
Found at i:14619 original size:52 final size:52
Alignment explanation
Indices: 14558--14658 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
14548 CATGCACATA
* *
14558 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
14610 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
14659 CGTTTCCTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.33
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
Found at i:19880 original size:29 final size:30
Alignment explanation
Indices: 19815--19870 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
19805 TTAGAGAGAA
19815 AAAAT-AAATAAACAAAGGGAAAGGATAAG
1 AAAATAAAATAAACAAAGGGAAAGGATAAG
*
19844 AAAATAAAATAAACAAGGGGAAAGGAT
1 AAAATAAAATAAACAAAGGGAAAGGAT
19871 GGAATTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.64, C:0.04, G:0.21, T:0.11
Consensus pattern (30 bp):
AAAATAAAATAAACAAAGGGAAAGGATAAG
Found at i:22625 original size:11 final size:11
Alignment explanation
Indices: 22609--22649 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
22599 AGAAGTGACC
22609 AAAAAAAGAAA
1 AAAAAAAGAAA
*
22620 AAAAAAAGTAA
1 AAAAAAAGAAA
*
22631 AAGAAAAGAACA
1 AAAAAAAGAA-A
22643 AAAAAAA
1 AAAAAAA
22650 AGTGAAAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 18 0.72
12 7 0.28
ACGTcount: A:0.85, C:0.02, G:0.10, T:0.02
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:22657 original size:25 final size:23
Alignment explanation
Indices: 22588--22658 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 23
22578 AACGAAATTC
22588 AAAA-AAAAAAAAGAAGTGACCAAA-
1 AAAAGAAAAAAAA-AAGTGA--AAAG
22612 AAAAGAAAAAAAAAAGT-AAAAG
1 AAAAGAAAAAAAAAAGTGAAAAG
22634 AAAAGAACAAAAAAAAAGTGAAAAG
1 AAAAG-A-AAAAAAAAAGTGAAAAG
22659 TATTGCGAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
21 3 0.07
22 5 0.12
23 2 0.05
24 19 0.45
25 13 0.31
ACGTcount: A:0.77, C:0.04, G:0.14, T:0.04
Consensus pattern (23 bp):
AAAAGAAAAAAAAAAGTGAAAAG
Found at i:25469 original size:20 final size:20
Alignment explanation
Indices: 25423--25469 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
25413 AGCTTGTTTC
*
25423 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
25443 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
25463 CAGCTCA
1 CAGCTCA
25470 ATCTTAACCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:27110 original size:52 final size:52
Alignment explanation
Indices: 27032--27132 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
27022 CATGCACATA
* *
27032 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCCGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCCGCTGTCCATTATTG
*
27084 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCCGCTGTCCATTA
27133 CGTTTCCTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCCGCTGTCCATTATTG
Found at i:29309 original size:21 final size:21
Alignment explanation
Indices: 29264--29326 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
29254 TTTGAACCAT
* * *
29264 TACCAATTCGTACCAAATACCA
1 TACCATTTCATACC-AATTCCA
*
29286 TACCATTTTATACCAATTCCA
1 TACCATTTCATACCAATTCCA
*
29307 TACCATTTCGTACCAATTCC
1 TACCATTTCATACCAATTCC
29327 CAAATACCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 24 0.69
22 11 0.31
ACGTcount: A:0.33, C:0.32, G:0.03, T:0.32
Consensus pattern (21 bp):
TACCATTTCATACCAATTCCA
Found at i:30550 original size:12 final size:12
Alignment explanation
Indices: 30533--30583 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
30523 AGACCGTATA
30533 CAATTTTTTTTT
1 CAATTTTTTTTT
30545 CAATTTTTTTTCTTTT
1 CAA---TTTTT-TTTT
*
30561 CGATTTTTTTTT
1 CAATTTTTTTTT
30573 CAATTTTTTTT
1 CAATTTTTTTT
30584 CGAAACTACA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
12 17 0.52
13 5 0.15
15 5 0.15
16 6 0.18
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.75
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:30567 original size:15 final size:15
Alignment explanation
Indices: 30536--30583 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
30526 CCGTATACAA
30536 TTTTTTTTTCAATTT
1 TTTTTTTTTCAATTT
*
30551 TTTTTCTTTTCGA---
1 TTTTT-TTTTCAATTT
30564 TTTTTTTTTCAATTT
1 TTTTTTTTTCAATTT
30579 TTTTT
1 TTTTT
30584 CGAAACTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
12 6 0.22
13 5 0.19
15 10 0.37
16 6 0.22
ACGTcount: A:0.10, C:0.08, G:0.02, T:0.79
Consensus pattern (15 bp):
TTTTTTTTTCAATTT
Done.