Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga13g02316.F12
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: 3348
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Found at i:434 original size:6 final size:6
Alignment explanation
Indices: 423--481 Score: 73
Period size: 6 Copynumber: 9.8 Consensus size: 6
413 GGAGCAGCAA
* ** * *
423 CAACAG CAACAG CAGCAG CAACCT CAACAT CAACAT CAACAG CAACAG
1 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG
471 CAACAG CAACA
1 CAACAG CAACA
482 ACTGCAGATG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.47, C:0.36, G:0.12, T:0.05
Consensus pattern (6 bp):
CAACAG
Found at i:438 original size:18 final size:18
Alignment explanation
Indices: 415--472 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
405 AAAGCACGGG
415 AGCAGCAACAACAGCAAC
1 AGCAGCAACAACAGCAAC
* **
433 AGCAGCAGCAACCTCAAC
1 AGCAGCAACAACAGCAAC
* * *
451 ATCAACATCAACAGCAAC
1 AGCAGCAACAACAGCAAC
469 AGCA
1 AGCA
473 ACAGCAACAA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.47, C:0.34, G:0.14, T:0.05
Consensus pattern (18 bp):
AGCAGCAACAACAGCAAC
Found at i:533 original size:9 final size:9
Alignment explanation
Indices: 519--682 Score: 136
Period size: 9 Copynumber: 18.2 Consensus size: 9
509 GAGGCATGCC
519 CAACAACAG
1 CAACAACAG
528 CAACAACAG
1 CAACAACAG
* *
537 CAGCAACAA
1 CAACAACAG
* * *
546 CAGCAGCAA
1 CAACAACAG
*
555 CAACAGCAG
1 CAACAACAG
*
564 CAGCAACAG
1 CAACAACAG
573 CAACAGCAGCAG
1 CAACA--A-CAG
*
585 CAGCAACAG
1 CAACAACAG
594 CAACAACAG
1 CAACAACAG
603 CAACAACAG
1 CAACAACAG
*
612 CAGCAACAG
1 CAACAACAG
*
621 CAGC-A-A-
1 CAACAACAG
*
627 CAACAGCAG
1 CAACAACAG
*
636 CAACAGCAG
1 CAACAACAG
645 CAACAACAG
1 CAACAACAG
* *
654 CAGCAACAA
1 CAACAACAG
*
663 CAGCAACAG
1 CAACAACAG
*
672 CAACAGCAG
1 CAACAACAG
681 CA
1 CA
683 GCAGCCACCA
Statistics
Matches: 130, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
6 3 0.02
7 1 0.01
8 2 0.02
9 115 0.88
10 1 0.01
11 1 0.01
12 7 0.05
ACGTcount: A:0.49, C:0.34, G:0.18, T:0.00
Consensus pattern (9 bp):
CAACAACAG
Found at i:540 original size:12 final size:12
Alignment explanation
Indices: 519--682 Score: 190
Period size: 12 Copynumber: 13.9 Consensus size: 12
509 GAGGCATGCC
*
519 CAACAACAGCAA
1 CAACAGCAGCAA
531 CAACAGCAGCAA
1 CAACAGCAGCAA
543 CAACAGCAGCAA
1 CAACAGCAGCAA
*
555 CAACAGCAGCAG
1 CAACAGCAGCAA
* *
567 CAACAGCAACAG
1 CAACAGCAGCAA
*
579 CAGCAGCAGCAA
1 CAACAGCAGCAA
* * * *
591 CAGCAACAACAG
1 CAACAGCAGCAA
* *
603 CAACAACAGCAG
1 CAACAGCAGCAA
615 CAACAGCAGCAA
1 CAACAGCAGCAA
627 CAACAGCAG---
1 CAACAGCAGCAA
636 CAACAGCAGCAA
1 CAACAGCAGCAA
648 CAACAGCAGCAA
1 CAACAGCAGCAA
* *
660 CAACAGCAACAG
1 CAACAGCAGCAA
672 CAACAGCAGCA
1 CAACAGCAGCA
683 GCAGCCACCA
Statistics
Matches: 133, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
9 9 0.07
12 124 0.93
ACGTcount: A:0.49, C:0.34, G:0.18, T:0.00
Consensus pattern (12 bp):
CAACAGCAGCAA
Found at i:545 original size:21 final size:21
Alignment explanation
Indices: 519--697 Score: 193
Period size: 21 Copynumber: 8.5 Consensus size: 21
509 GAGGCATGCC
519 CAACAACAGCAACAACAGCAG
1 CAACAACAGCAACAACAGCAG
540 CAACAACAGCAGCAACAACAGCAG
1 CAAC-A-A-CAGCAACAACAGCAG
* *
564 CAGCAACAGCAACAGCAGCAG
1 CAACAACAGCAACAACAGCAG
*
585 CAGCAACAGCAAC-A-A-CAG
1 CAACAACAGCAACAACAGCAG
*
603 CAACAACAGCAGCAACAGCAG
1 CAACAACAGCAACAACAGCAG
*
624 CAACAACAGCAGCAACAGCAG
1 CAACAACAGCAACAACAGCAG
* *
645 CAACAACAGCAGCAACAACAG
1 CAACAACAGCAACAACAGCAG
* * * *
666 CAACAGCAACAGCAGCAGCAG
1 CAACAACAGCAACAACAGCAG
* *
687 CCACCACAGCA
1 CAACAACAGCA
698 GTCCCAGCAG
Statistics
Matches: 138, Mismatches: 14, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
18 14 0.10
19 2 0.01
20 1 0.01
21 99 0.72
22 2 0.01
23 2 0.01
24 18 0.13
ACGTcount: A:0.47, C:0.35, G:0.18, T:0.00
Consensus pattern (21 bp):
CAACAACAGCAACAACAGCAG
Found at i:1538 original size:15 final size:15
Alignment explanation
Indices: 1518--1552 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1508 TCAGTTGCAT
*
1518 CAGCAGCAACAGCAG
1 CAGCAGCAACAGCAA
*
1533 CAGCAGCAACTGCAA
1 CAGCAGCAACAGCAA
1548 CAGCA
1 CAGCA
1553 ACAGCAACAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.34, G:0.23, T:0.03
Consensus pattern (15 bp):
CAGCAGCAACAGCAA
Found at i:1547 original size:6 final size:6
Alignment explanation
Indices: 1530--1567 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1520 GCAGCAACAG
* *
1530 CAGCAG CAGCAA CTGCAA CAGCAA CAGCAA CAG-AA CAG
1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAG
1568 TAACTCACAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.45, C:0.32, G:0.21, T:0.03
Consensus pattern (6 bp):
CAGCAA
Done.