Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1174
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: 20996
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:592 original size:18 final size:17
Alignment explanation
Indices: 557--604 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
547 TATCGTATGC
* *
557 TAATAATAATATTATAA
1 TAATAATAATTTTTTAA
*
574 TAATTATTAATTTTTTAA
1 TAA-TAATAATTTTTTAA
592 TAATAATAATTTT
1 TAATAATAATTTT
605 AAAAATAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TAATAATAATTTTTTAA
Found at i:617 original size:17 final size:17
Alignment explanation
Indices: 590--636 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
580 TTAATTTTTT
590 AATAATAATAATTTTAAA
1 AATAAT-ATAATTTTAAA
*
608 AATAATATAATGTTAAA
1 AATAATATAATTTTAAA
*
625 AATAATAAAATT
1 AATAATATAATT
637 AAATATATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 20 0.77
18 6 0.23
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
AATAATATAATTTTAAA
Found at i:638 original size:15 final size:15
Alignment explanation
Indices: 588--653 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
578 TATTAATTTT
* **
588 TTAATAATAATAATT
1 TTAAAAATAATAAAA
*
603 TTAAAAATAATATAATG
1 TTAAAAATAATA-AA-A
620 TTAAAAATAATAAAA
1 TTAAAAATAATAAAA
* *
635 TTAAATATATTAAAA
1 TTAAAAATAATAAAA
650 TTAA
1 TTAA
654 TTCTTAATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
15 28 0.65
16 3 0.07
17 12 0.28
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
TTAAAAATAATAAAA
Found at i:1706 original size:24 final size:23
Alignment explanation
Indices: 1679--1724 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
1669 TTTTTTATTT
* *
1679 TAAATTTTACTCAAATTTTAAAAA
1 TAAAATTTAATCAAA-TTTAAAAA
*
1703 TAAAATTTAATTAAATTTAAAA
1 TAAAATTTAATCAAATTTAAAA
1725 TTTTAAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (23 bp):
TAAAATTTAATCAAATTTAAAAA
Found at i:1735 original size:30 final size:31
Alignment explanation
Indices: 1691--1753 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
1681 AATTTTACTC
*
1691 AAATTTTAAAAATAAAATTTAATTAAATTTA
1 AAATTTTAAAAATAAAATATAATTAAATTTA
1722 AAATTTT-AAAATAAAATATAATTAAATTTA
1 AAATTTTAAAAATAAAATATAATTAAATTTA
1752 AA
1 AA
1754 TTAAATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 24 0.77
31 7 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (31 bp):
AAATTTTAAAAATAAAATATAATTAAATTTA
Found at i:1738 original size:35 final size:34
Alignment explanation
Indices: 1699--1770 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
1689 TCAAATTTTA
*
1699 AAAATAAAATTTAA-TTAAATTTAAAATTTTAAAAT
1 AAAATAAAATTAAATTTAAA-TT-AAATTTTAAAAT
* *
1734 AAAATATAATTAAATTTAAATTAAATTTTAAATT
1 AAAATAAAATTAAATTTAAATTAAATTTTAAAAT
1768 AAA
1 AAA
1771 CTTTTGCTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 14 0.42
35 14 0.42
36 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATAAAATTAAATTTAAATTAAATTTTAAAAT
Found at i:1765 original size:12 final size:12
Alignment explanation
Indices: 1722--1775 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
1712 ATTAAATTTA
*
1722 AAATTTTAAAAT
1 AAATTTTAAATT
* *
1734 AAAATAT-AATT
1 AAATTTTAAATT
1745 AAA-TTTAAATT
1 AAATTTTAAATT
1756 AAATTTTAAATT
1 AAATTTTAAATT
1768 AAACTTTT
1 AAA-TTTT
1776 GCTGATTAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 2 0.06
11 13 0.37
12 16 0.46
13 4 0.11
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (12 bp):
AAATTTTAAATT
Found at i:2848 original size:24 final size:22
Alignment explanation
Indices: 2821--2876 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
2811 TTATTAAAGG
2821 TATATTTTTAATAAATTTTAAAAA
1 TATATTTTT-AT-AATTTTAAAAA
* *
2845 TATATTAATTATATTTTTAAAAA
1 TATATT-TTTATAATTTTAAAAA
2868 TATTATTTT
1 TA-TATTTT
2877 AATTAATATC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
23 13 0.48
24 12 0.44
25 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TATATTTTTATAATTTTAAAAA
Found at i:14581 original size:21 final size:22
Alignment explanation
Indices: 14557--14620 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
14547 AAATAAAGTA
* *
14557 AATGAATTAGAA-AAGAAAATT
1 AATGAATTACAAGAAGAAAAAT
*
14578 AATGAGTTACAAGAAGAAAAAT
1 AATGAATTACAAGAAGAAAAAT
*
14600 AAAGAATTGACTAAGAA-AAAA
1 AATGAATT-AC-AAGAAGAAAA
14621 CAAAAACTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 10 0.29
22 14 0.40
23 6 0.17
24 5 0.14
ACGTcount: A:0.62, C:0.03, G:0.16, T:0.19
Consensus pattern (22 bp):
AATGAATTACAAGAAGAAAAAT
Done.