Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_39773
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: 1905
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:484 original size:9 final size:10
Alignment explanation
Indices: 477--533 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
467 AAGAGAAAAC
477 AAAGAAAAGA
1 AAAGAAAAGA
487 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
499 AAAGAAGA-A
1 AAAGAAAAGA
508 AAAGAAAATGA
1 AAAGAAAA-GA
519 AATA-AAAAGA
1 AA-AGAAAAGA
529 AAAGA
1 AAAGA
534 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:500 original size:21 final size:20
Alignment explanation
Indices: 466--533 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
456 ACATTCTTGT
466 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
487 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
508 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
529 AAAGA
1 AAAGA
534 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:501 original size:6 final size:5
Alignment explanation
Indices: 477--533 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
467 AAGAGAAAAC
*
477 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
524 AAAGA AAAGA
1 AAAGA AAAGA
534 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:508 original size:15 final size:14
Alignment explanation
Indices: 477--533 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
467 AAGAGAAAAC
477 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
493 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
508 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
524 AAAGAAAAGA
1 AAAGAAAAGA
534 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:625 original size:12 final size:12
Alignment explanation
Indices: 595--626 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
585 AAAAGCCTTT
*
595 GAAAATCAAAAA
1 GAAAATGAAAAA
607 GAAAATGAAAAA
1 GAAAATGAAAAA
619 GAAAATGA
1 GAAAATGA
627 GATTGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.72, C:0.03, G:0.16, T:0.09
Consensus pattern (12 bp):
GAAAATGAAAAA
Found at i:636 original size:30 final size:30
Alignment explanation
Indices: 602--669 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
592 TTTGAAAATC
* *
602 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAACG-AAAAGAAATATGAGAGTG
* * *
632 AAAAAGAGAACGAAACGAAATTTGAGAGTG
1 AAAAAGAAAACGAAAAGAAATATGAGAGTG
662 AAAAAGAA
1 AAAAAGAA
670 TCCAGTGAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.63, C:0.03, G:0.22, T:0.12
Consensus pattern (30 bp):
AAAAAGAAAACGAAAAGAAATATGAGAGTG
Done.