Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga02g00464.F1
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: 2277
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Found at i:539 original size:6 final size:6
Alignment explanation
Indices: 502--590 Score: 54
Period size: 6 Copynumber: 14.2 Consensus size: 6
492 GAGGAAGGGA
* * * * * *
502 AAAG-G AAAAAG ATAGAG AAAGGG ATAGGG AAAGAG AAAGGAG AGATAGGG
1 AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG AAA-GAG A-A-AGAG
* *
552 ATAAGGAG AAAGAG AAAGAG AAAGAG AGAGAG AAGGAG A
1 A-AA-GAG AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG A
591 GGAGAGAGAG
Statistics
Matches: 65, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
5 3 0.05
6 46 0.71
7 7 0.11
8 8 0.12
9 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.39, T:0.04
Consensus pattern (6 bp):
AAAGAG
Found at i:551 original size:27 final size:29
Alignment explanation
Indices: 515--652 Score: 104
Period size: 27 Copynumber: 5.2 Consensus size: 29
505 GGAAAAAGAT
515 AGAGAAAGGGAT-AGG-GAAAGAGAAAGG
1 AGAGAAAGGGATAAGGAGAAAGAGAAAGG
*
542 AGAGATAGGGATAAGGAGAAAGAG-AA--
1 AGAGAAAGGGATAAGGAGAAAGAGAAAGG
* * *
568 AGAGAAAGAGA-GA-GAG-AAG-GAGAGG
1 AGAGAAAGGGATAAGGAGAAAGAGAAAGG
* * *
593 AGAGAGAGGGAAAAGGAG--AGAGAGAGG
1 AGAGAAAGGGATAAGGAGAAAGAGAAAGG
*
620 AGAGAAAGGGAGAAGGAG-AAG-GAAAGGG
1 AGAGAAAGGGATAAGGAGAAAGAGAAA-GG
648 AGAGA
1 AGAGA
653 GAGAGGAGAG
Statistics
Matches: 90, Mismatches: 11, Indels: 19
0.75 0.09 0.16
Matches are distributed among these distances:
22 1 0.01
23 4 0.04
24 3 0.03
25 10 0.11
26 12 0.13
27 39 0.43
28 14 0.16
29 7 0.08
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.02
Consensus pattern (29 bp):
AGAGAAAGGGATAAGGAGAAAGAGAAAGG
Found at i:558 original size:51 final size:51
Alignment explanation
Indices: 497--655 Score: 160
Period size: 51 Copynumber: 3.0 Consensus size: 51
487 CAGTAGAGGA
* * * * *
497 AGGGAAAAGGA-AAA-AGATAGAGAAAGGGATAGGGAAAGAGAAAGGAGAGAT
1 AGGGAAAAGGAGAAAGAGAAAGAGAAAGAGAGAGAG-AAG-GAAAGGAGAGAG
* *
548 AGGGATAAGGAGAAAGAGAAAGAGAAAGAGAGAGAGAAGGAGAGGAGAGAG
1 AGGGAAAAGGAGAAAGAGAAAGAGAAAGAGAGAGAGAAGGAAAGGAGAGAG
* * *
599 AGGGAAAAGGAGAGAGAGAGGAGAGAAAGGGAGAAGGAGAAGGAAAGGGAGAGAG
1 AGGGAAAAGGAGAAAGAGA-AAGAGAAAGAGAG-A-GAGAAGGAAA-GGAGAGAG
654 AG
1 AG
656 AGGAGAGAGA
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
51 37 0.41
52 17 0.19
53 17 0.19
54 9 0.10
55 10 0.11
ACGTcount: A:0.52, C:0.00, G:0.45, T:0.03
Consensus pattern (51 bp):
AGGGAAAAGGAGAAAGAGAAAGAGAAAGAGAGAGAGAAGGAAAGGAGAGAG
Found at i:581 original size:2 final size:2
Alignment explanation
Indices: 557--666 Score: 62
Period size: 2 Copynumber: 60.5 Consensus size: 2
547 TAGGGATAAG
* * *
557 GA GA AA GA GA AA GA GA AA GA GA GA GA GA -A G- GA GA G- GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * * *
596 GA GA GG GA -A AA G- GA GA GA GA GA G- GA GA GA AA GG GA GA -A
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* *
634 G- GA GA -A G- GA AA GG GA GA GA GA GA G- GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
667 GAGCAGCAGT
Statistics
Matches: 80, Mismatches: 17, Indels: 22
0.67 0.14 0.18
Matches are distributed among these distances:
1 11 0.14
2 69 0.86
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:615 original size:78 final size:75
Alignment explanation
Indices: 515--669 Score: 186
Period size: 78 Copynumber: 2.0 Consensus size: 75
505 GGAAAAAGAT
* * * *
515 AGAGAAAGGGATAGGGAAAGAGAAAGGAGAGATAGGGATAAGGAGAAAGAGAAAGAGAAAGAGAG
1 AGAGAAAGGGAAAAGGAAAGAGAAAGGAGAGAAAGGGAGAAGGAG-AAG-GAAAG-G-AAGAGAG
580 AGAGAAG-GAGAGG
62 AGAGAAGAGAGAGG
* * * *
593 AGAGAGAGGGAAAAGGAGAGAGAGAGGAGAGAAAGGGAGAAGGAGAAGGAAAGGGAGAGAGAGAG
1 AGAGAAAGGGAAAAGGAAAGAGAAAGGAGAGAAAGGGAGAAGGAGAAGGAAAGGAAGAGAGAGAG
*
658 GAGAGAGAGG
66 AAGAGAGAGG
668 AG
1 AG
670 CAGCAGTAGG
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
74 12 0.18
75 9 0.13
76 5 0.07
77 3 0.04
78 38 0.57
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.02
Consensus pattern (75 bp):
AGAGAAAGGGAAAAGGAAAGAGAAAGGAGAGAAAGGGAGAAGGAGAAGGAAAGGAAGAGAGAGAG
AAGAGAGAGG
Done.