Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gorai.004G160000.2-JGI_221_v2.1
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, 687
Length: 1145
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.28
Found at i:555 original size:15 final size:15
Alignment explanation
Indices: 532--600 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
522 CAGCAAAACC
*
532 GCCGGAGAAGGAGGA
1 GCCGAAGAAGGAGGA
*
547 GCCGAAGAAGGAAGA
1 GCCGAAGAAGGAGGA
* * *
562 ACCCAAGAAAGAGGA
1 GCCGAAGAAGGAGGA
*
577 GCCCAAGAAGGAGGA
1 GCCGAAGAAGGAGGA
592 GCCGAAGAA
1 GCCGAAGAA
601 AGAAGAACCC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.43, C:0.17, G:0.39, T:0.00
Consensus pattern (15 bp):
GCCGAAGAAGGAGGA
Found at i:614 original size:15 final size:15
Alignment explanation
Indices: 551--691 Score: 93
Period size: 15 Copynumber: 8.8 Consensus size: 15
541 GGAGGAGCCG
*
551 AAGAAGGAAGAACCC
1 AAGAAAGAAGAACCC
* *
566 AAGAAAGAGGAGCCC
1 AAGAAAGAAGAACCC
* * * *
581 AAGAAGGAGGAGCCG
1 AAGAAAGAAGAACCC
596 AAGAAAGAAGAACCC
1 AAGAAAGAAGAACCC
* *
611 AAGAAGGAAGAGGAGCCA
1 AAGAAAGAAGA--A-CCC
629 AAGAAAGAAGAACCC
1 AAGAAAGAAGAACCC
*
644 AAGAAGGAAGAGGAACCC
1 AAG-A--AAGAAGAACCC
* *
662 AAGAAGGAAGAGGAGCCA
1 AAGAAAGAAGA--A-CCC
680 AAGAAAGAAGAA
1 AAGAAAGAAGAA
692 GAGAAACAGC
Statistics
Matches: 99, Mismatches: 18, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
15 56 0.57
16 3 0.03
17 3 0.03
18 37 0.37
ACGTcount: A:0.53, C:0.15, G:0.32, T:0.00
Consensus pattern (15 bp):
AAGAAAGAAGAACCC
Found at i:621 original size:18 final size:18
Alignment explanation
Indices: 595--693 Score: 96
Period size: 18 Copynumber: 5.7 Consensus size: 18
585 AGGAGGAGCC
*
595 GAAGAAAGAAGAACCCAA
1 GAAGGAAGAAGAACCCAA
* *
613 GAAGGAAG-AGGAGCC-A
1 GAAGGAAGAAGAACCCAA
*
629 -AAGAAAGAAGAACCCAA
1 GAAGGAAGAAGAACCCAA
*
646 GAAGGAAGAGGAACCCAA
1 GAAGGAAGAAGAACCCAA
* * *
664 GAAGGAAGAGGAGCCAAA
1 GAAGGAAGAAGAACCCAA
*
682 GAAAGAAGAAGA
1 GAAGGAAGAAGA
694 GAAACAGCCA
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
15 6 0.09
16 6 0.09
17 6 0.09
18 48 0.73
ACGTcount: A:0.56, C:0.13, G:0.31, T:0.00
Consensus pattern (18 bp):
GAAGGAAGAAGAACCCAA
Found at i:633 original size:33 final size:33
Alignment explanation
Indices: 551--672 Score: 148
Period size: 33 Copynumber: 3.9 Consensus size: 33
541 GGAGGAGCCG
* *
551 AAGAAGGAAGA--A-CCCAAGAAAGAGGAGCCC
1 AAGAAGGAAGAGGAGCCCAAGAAAGAAGAACCC
*
581 AAGAA-G--GAGGAGCCGAAGAAAGAAGAACCC
1 AAGAAGGAAGAGGAGCCCAAGAAAGAAGAACCC
*
611 AAGAAGGAAGAGGAGCCAAAGAAAGAAGAACCC
1 AAGAAGGAAGAGGAGCCCAAGAAAGAAGAACCC
* *
644 AAGAAGGAAGAGGAACCCAAGAAGGAAGA
1 AAGAAGGAAGAGGAGCCCAAGAAAGAAGA
673 GGAGCCAAAG
Statistics
Matches: 79, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
27 2 0.03
29 2 0.03
30 25 0.32
31 1 0.01
33 49 0.62
ACGTcount: A:0.52, C:0.16, G:0.32, T:0.00
Consensus pattern (33 bp):
AAGAAGGAAGAGGAGCCCAAGAAAGAAGAACCC
Found at i:675 original size:51 final size:51
Alignment explanation
Indices: 550--691 Score: 179
Period size: 51 Copynumber: 2.9 Consensus size: 51
540 AGGAGGAGCC
* * * * *
550 GAAGAAGGAAGAACCCAAG-A--AAGAGGAGCCCAAG-AAGGAGGAGCC--
1 GAAGAAAGAAGAACCCAAGAAGGAAGAGGAGCCAAAGAAAGAAGAACCCAA
595 GAAGAAAGAAGAACCCAAGAAGGAAGAGGAGCCAAAGAAAGAAGAACCCAA
1 GAAGAAAGAAGAACCCAAGAAGGAAGAGGAGCCAAAGAAAGAAGAACCCAA
* *
646 GAAGGAAGAGGAACCCAAGAAGGAAGAGGAGCCAAAGAAAGAAGAA
1 GAAGAAAGAAGAACCCAAGAAGGAAGAGGAGCCAAAGAAAGAAGAA
692 GAGAAACAGC
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
45 18 0.21
46 1 0.01
48 13 0.15
49 8 0.10
51 44 0.52
ACGTcount: A:0.53, C:0.15, G:0.32, T:0.00
Consensus pattern (51 bp):
GAAGAAAGAAGAACCCAAGAAGGAAGAGGAGCCAAAGAAAGAAGAACCCAA
Done.