Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g01426.M1
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: 2930
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Found at i:402 original size:33 final size:32
Alignment explanation
Indices: 365--469 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 32
355 GAAGGAAAGG
* * *
365 GAGAGAGAAAGAAGAGAAAAAGATAAGGAGAAA
1 GAGAG-GAAAGAAGAGAGAAGGAAAAGGAGAAA
* * *
398 GAGAGGGATAGGAGAGAGAAGGAAAAGGAGAGA
1 GAGA-GGAAAGAAGAGAGAAGGAAAAGGAGAAA
**
431 GAGAGGAGGGAAAGAGAGAAGGAAAAGGAGAAA
1 GAGAGGAAAG-AAGAGAGAAGGAAAAGGAGAAA
464 GAGAGG
1 GAGAGG
470 GAGGTAGACC
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
32 4 0.07
33 55 0.92
34 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.44, T:0.02
Consensus pattern (32 bp):
GAGAGGAAAGAAGAGAGAAGGAAAAGGAGAAA
Found at i:426 original size:66 final size:66
Alignment explanation
Indices: 334--471 Score: 161
Period size: 66 Copynumber: 2.1 Consensus size: 66
324 ATTTAGAGAG
* * * * *
334 GAGGGGTAGCAGAGAGAGGGAGAAGGAAAGGGAGAGAGAAAG-AAGAGAAAAAGATAAGGAGAAA
1 GAGGGATAGCAGAGAGAAGGAAAAGGAAAGAGAGAG-GAAAGAAAGAGAAAAAGAAAAGGAGAAA
398 GA
65 GA
* * ** * *
400 GAGGGATAGGAGAGAGAAGGAAAAGGAGAGAGAGAGGAGGGAAAGAGAGAAGGAAAAGGAGAAAG
1 GAGGGATAGCAGAGAGAAGGAAAAGGAAAGAGAGAGGAAAGAAAGAGAAAAAGAAAAGGAGAAAG
465 A
66 A
466 GAGGGA
1 GAGGGA
472 GGTAGACCGG
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 3 0.05
66 57 0.95
ACGTcount: A:0.51, C:0.01, G:0.46, T:0.02
Consensus pattern (66 bp):
GAGGGATAGCAGAGAGAAGGAAAAGGAAAGAGAGAGGAAAGAAAGAGAAAAAGAAAAGGAGAAAG
A
Found at i:463 original size:20 final size:20
Alignment explanation
Indices: 410--468 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
400 GAGGGATAGG
410 AGAGAGAAGGAAAAGGAG--
1 AGAGAGAAGGAAAAGGAGAA
428 AGAGAG-AGG---AGG-GAA
1 AGAGAGAAGGAAAAGGAGAA
443 AGAGAGAAGGAAAAGGAGAA
1 AGAGAGAAGGAAAAGGAGAA
463 AGAGAG
1 AGAGAG
469 GGAGGTAGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
13 1 0.03
14 3 0.09
15 6 0.18
16 3 0.09
17 3 0.09
18 6 0.18
19 3 0.09
20 9 0.26
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (20 bp):
AGAGAGAAGGAAAAGGAGAA
Found at i:560 original size:75 final size:75
Alignment explanation
Indices: 480--672 Score: 323
Period size: 75 Copynumber: 2.6 Consensus size: 75
470 GAGGTAGACC
* *
480 GGAGAGAGAGAAGCAGTAGTAGGTCGAGGAGGCACGAAAGTGATCGTGAGATTGAGAGGGAACGG
1 GGAGAGAGAGAAGCAGTAGTAGGTCGAGGAGGCACGAGAGTGATCGTGAGATAGAGAGGGAACGG
545 GAGAGAGATA
66 GAGAGAGATA
* * *
555 GGAGAGAGAGGAGCAGTAGTAGGTCGAGGAGGCACGAGAGTGATCGTGAGCTAGAGAGGGAGCGG
1 GGAGAGAGAGAAGCAGTAGTAGGTCGAGGAGGCACGAGAGTGATCGTGAGATAGAGAGGGAACGG
620 GAGAGAGATA
66 GAGAGAGATA
* *
630 GGAGAGAGAGAAGCAGTAGTAGGTTGAGGAGACACGAGAGTGA
1 GGAGAGAGAGAAGCAGTAGTAGGTCGAGGAGGCACGAGAGTGA
673 ACGCGATCAA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 110 1.00
ACGTcount: A:0.35, C:0.08, G:0.46, T:0.11
Consensus pattern (75 bp):
GGAGAGAGAGAAGCAGTAGTAGGTCGAGGAGGCACGAGAGTGATCGTGAGATAGAGAGGGAACGG
GAGAGAGATA
Done.