Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold521
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: 5670
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Found at i:426 original size:21 final size:21
Alignment explanation
Indices: 402--453 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
392 ATAGAAAGTG
*
402 AAAAAGTTGAAAGAAGTTGAT
1 AAAAAGTTAAAAGAAGTTGAT
** *
423 AAAAAACTAAAAGGAGTTGAT
1 AAAAAGTTAAAAGAAGTTGAT
444 AGAAAAGTTA
1 A-AAAAGTTA
454 TAGGCGATAG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.56, C:0.02, G:0.21, T:0.21
Consensus pattern (21 bp):
AAAAAGTTAAAAGAAGTTGAT
Found at i:2578 original size:27 final size:25
Alignment explanation
Indices: 2540--2590 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 25
2530 CGCTTTTTTT
*
2540 AAATAAATTTTTATATTTTTATAATTC
1 AAATAAACTTTTA-ATTTTTA-AATTC
2567 AAATAAACTTTTAATTTTTAAATT
1 AAATAAACTTTTAATTTTTAAATT
2591 ATATTCAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.17
26 7 0.30
27 12 0.52
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (25 bp):
AAATAAACTTTTAATTTTTAAATTC
Found at i:2607 original size:30 final size:31
Alignment explanation
Indices: 2558--2617 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
2548 TTTTATATTT
*
2558 TTATAATTCAAATAAACTTTTAATTTTTAAA
1 TTATAATTCAAATAAACTTTTAAATTTTAAA
2589 TTAT-ATTC-AATAAGACTTTTAAATTTTAA
1 TTATAATTCAAATAA-ACTTTTAAATTTTAA
2618 GTGTAATCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 5 0.19
30 18 0.67
31 4 0.15
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (31 bp):
TTATAATTCAAATAAACTTTTAAATTTTAAA
Found at i:2703 original size:16 final size:16
Alignment explanation
Indices: 2682--2712 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2672 ATATTATCTC
2682 ATTTAAAATAAAAATT
1 ATTTAAAATAAAAATT
2698 ATTTAAAATAAAAAT
1 ATTTAAAATAAAAAT
2713 CAGATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATTTAAAATAAAAATT
Found at i:3932 original size:19 final size:19
Alignment explanation
Indices: 3908--3974 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
3898 AATTCAACGA
3908 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
3927 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
3942 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
3959 ATTGTATC-ATACATAA
1 TTTGTATCGATACATAA
3975 TTAGCTTACT
Statistics
Matches: 42, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
18 8 0.19
19 19 0.45
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:3946 original size:32 final size:31
Alignment explanation
Indices: 3910--3971 Score: 106
Period size: 32 Copynumber: 2.0 Consensus size: 31
3900 TTCAACGATT
*
3910 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATC-ATACAA
3942 TGTATCGATACATAAGTATTGTATCATACA
1 TGTATCGATACATAAGTATTGTATCATACA
3972 TAATTAGCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 5 0.17
32 24 0.83
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (31 bp):
TGTATCGATACATAAGTATTGTATCATACAA
Found at i:3947 original size:13 final size:13
Alignment explanation
Indices: 3929--3953 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3919 ACATAAGTTT
3929 TGTATCGATACAA
1 TGTATCGATACAA
3942 TGTATCGATACA
1 TGTATCGATACA
3954 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4032 original size:13 final size:13
Alignment explanation
Indices: 4014--4039 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4004 TACATTTTTC
4014 TGTATCGATACAT
1 TGTATCGATACAT
4027 TGTATCGATACAT
1 TGTATCGATACAT
4040 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Done.