Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gohir.A13G206200.5.v1.1
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: 3410
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Found at i:479 original size:6 final size:6
Alignment explanation
Indices: 468--526 Score: 55
Period size: 6 Copynumber: 9.8 Consensus size: 6
458 GGAGCAGCAA
* * ** * *
468 CAACAG CAACAG CAGCAG CAGCCT CAACAT CAACAT CAACAG CAACAG
1 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG
*
516 CAGCAG CAACA
1 CAACAG CAACA
527 ACTGCAGATG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.44, C:0.36, G:0.15, T:0.05
Consensus pattern (6 bp):
CAACAG
Found at i:486 original size:12 final size:12
Alignment explanation
Indices: 460--526 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
450 AAAGCACGGG
460 AGCAGCAACA--
1 AGCAGCAACAGC
470 A-CAGCAACAGC
1 AGCAGCAACAGC
* **
481 AGCAGCAGCCTC
1 AGCAGCAACAGC
* * *
493 AACATCAACATC
1 AGCAGCAACAGC
*
505 AACAGCAACAGC
1 AGCAGCAACAGC
517 AGCAGCAACA
1 AGCAGCAACA
527 ACTGCAGATG
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
9 8 0.18
10 1 0.02
11 1 0.02
12 34 0.77
ACGTcount: A:0.45, C:0.34, G:0.16, T:0.04
Consensus pattern (12 bp):
AGCAGCAACAGC
Found at i:578 original size:9 final size:9
Alignment explanation
Indices: 564--715 Score: 127
Period size: 9 Copynumber: 17.6 Consensus size: 9
554 GAGGCATGCC
564 CAACAACAG
1 CAACAACAG
573 CAACAACAG
1 CAACAACAG
*
582 CAGC-A-A-
1 CAACAACAG
*
588 CAACAGCAG
1 CAACAACAG
597 CAACAACAG
1 CAACAACAG
* *
606 CAACAGCAA
1 CAACAACAG
*
615 CAGCAACAG
1 CAACAACAG
* *
624 CAGCAGCAG
1 CAACAACAG
* *
633 CAACAGCAA
1 CAACAACAG
642 CAACAACAG
1 CAACAACAG
* *
651 CAACAGCAA
1 CAACAACAG
*
660 CAGCAACAG
1 CAACAACAG
669 CAACAACAG
1 CAACAACAG
*
678 CAGCAACAG
1 CAACAACAG
*
687 CAGC-A-A-
1 CAACAACAG
*
693 CAACAGCAG
1 CAACAACAG
702 CAACAACAG
1 CAACAACAG
711 CAACA
1 CAACA
716 GCAACAGCAG
Statistics
Matches: 113, Mismatches: 24, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
6 6 0.05
7 2 0.02
8 4 0.04
9 101 0.89
ACGTcount: A:0.51, C:0.34, G:0.16, T:0.00
Consensus pattern (9 bp):
CAACAACAG
Found at i:590 original size:21 final size:21
Alignment explanation
Indices: 564--742 Score: 166
Period size: 21 Copynumber: 8.5 Consensus size: 21
554 GAGGCATGCC
564 CAACAACAGCAACAACAGCAG
1 CAACAACAGCAACAACAGCAG
*
585 CAACAACAGCAGCAACAACAGCAA
1 CAAC-A-A-CAGCAACAACAGCAG
* *
609 CAGCAACAGCAACAGCAGCAG
1 CAACAACAGCAACAACAGCAG
*
630 CAGCAACAGCAACAACA--A-
1 CAACAACAGCAACAACAGCAG
* * *
648 CAGCAACAGCAACAGCAACAG
1 CAACAACAGCAACAACAGCAG
*
669 CAACAACAGCAGCAACAGCAG
1 CAACAACAGCAACAACAGCAG
* *
690 CAACAACAGCAGCAACAACAG
1 CAACAACAGCAACAACAGCAG
* * * *
711 CAACAGCAACAGCAGCAGCAG
1 CAACAACAGCAACAACAGCAG
* *
732 CCACCACAGCA
1 CAACAACAGCA
743 GTCCCAGCAG
Statistics
Matches: 133, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
18 16 0.12
19 1 0.01
20 1 0.01
21 94 0.71
22 2 0.02
23 2 0.02
24 17 0.13
ACGTcount: A:0.49, C:0.35, G:0.17, T:0.00
Consensus pattern (21 bp):
CAACAACAGCAACAACAGCAG
Found at i:732 original size:6 final size:6
Alignment explanation
Indices: 576--730 Score: 175
Period size: 6 Copynumber: 25.3 Consensus size: 6
566 ACAACAGCAA
* * * *
576 CAACAG CAGCAA CAACAG CAGCAA CAACAG CAACAG CAACAG CAACAG
1 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG
* *
624 CAGCAGCAG CAACAG CAACAA CAACAG CAACAG CAACAG CAACAG CAACAA
1 CA--A-CAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG
* * * * *
675 CAGCAG CAACAG CAGCAA CAACAG CAGCAA CAACAG CAACAG CAACAG
1 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG
*
723 CAGCAG CA
1 CAACAG CA
731 GCCACCACAG
Statistics
Matches: 123, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
6 116 0.94
7 1 0.01
8 1 0.01
9 5 0.04
ACGTcount: A:0.49, C:0.34, G:0.17, T:0.00
Consensus pattern (6 bp):
CAACAG
Found at i:1583 original size:15 final size:15
Alignment explanation
Indices: 1563--1597 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1553 TCAGTTGCAT
*
1563 CAGCAGCAACAGCAG
1 CAGCAGCAACAGCAA
*
1578 CAGCAGCAACTGCAA
1 CAGCAGCAACAGCAA
1593 CAGCA
1 CAGCA
1598 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:1592 original size:6 final size:6
Alignment explanation
Indices: 1575--1612 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1565 GCAGCAACAG
* *
1575 CAGCAG CAGCAA CTGCAA CAGCAA CAGCAA CAG-AA CAG
1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAG
1613 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.