Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g03724.F2
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: 1840
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Found at i:393 original size:27 final size:26
Alignment explanation
Indices: 363--422 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 26
353 AGGGAGAGAG
*
363 AAGAAAGGGAAAGGAAAAGGAGGAA-GA
1 AAGAAA-GGAAAAGAAAAGGA-GAAGGA
390 AAGAGAAGGAAAAGAAAAGGAGAAGGA
1 AAGA-AAGGAAAAGAAAAGGAGAAGGA
417 AAGAAA
1 AAGAAA
423 AGAGAGAGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
27 23 0.77
28 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (26 bp):
AAGAAAGGAAAAGAAAAGGAGAAGGA
Found at i:414 original size:17 final size:17
Alignment explanation
Indices: 391--429 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
381 GGAGGAAGAA
391 AGAGAAGGAAAAGAAAAG
1 AGAGAAGG-AAAGAAAAG
409 -GAGAAGGAAAGAAAAG
1 AGAGAAGGAAAGAAAAG
425 AGAGA
1 AGAGA
430 GACGAAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (17 bp):
AGAGAAGGAAAGAAAAG
Found at i:423 original size:43 final size:43
Alignment explanation
Indices: 335--449 Score: 112
Period size: 43 Copynumber: 2.6 Consensus size: 43
325 GAGGGGGAGG
* * *
335 AGGAGGAAGAGGAAGAGAAGGGAGAGAGAAGAAAGGGAAAGGAAA
1 AGGAGGAAGA--AAGAGAAGGAAAAGAAAAGAAAGGGAAAGGAAA
380 AGGAGGAAGAAAGAGAAGGAAAAGAAAAGGAGAA-GGAAA-GAAA
1 AGGAGGAAGAAAGAGAAGGAAAAGAAAA-GA-AAGGGAAAGGAAA
*
423 AGAGAGAGACG-AAGAG-AGGAAAAGAAA
1 AG-GAG-GAAGAAAGAGAAGGAAAAGAAA
450 GAAGAGAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
43 32 0.52
44 15 0.24
45 15 0.24
ACGTcount: A:0.58, C:0.01, G:0.41, T:0.00
Consensus pattern (43 bp):
AGGAGGAAGAAAGAGAAGGAAAAGAAAAGAAAGGGAAAGGAAA
Found at i:462 original size:22 final size:21
Alignment explanation
Indices: 418--470 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
408 GGAGAAGGAA
* *
418 AGAAAAGAGAGAGACGAAGAG
1 AGAAAAGAAAGAGACGAAAAG
439 AGGAAAAGAAAGAAGA-GAAAAG
1 A-GAAAAGAAAG-AGACGAAAAG
461 AG-AAAGAAAG
1 AGAAAAGAAAG
471 GAAAGCAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 8 0.29
21 2 0.07
22 15 0.54
23 3 0.11
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (21 bp):
AGAAAAGAAAGAGACGAAAAG
Found at i:468 original size:20 final size:20
Alignment explanation
Indices: 442--488 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
432 CGAAGAGAGG
442 AAAAGAAA-GAAGAGAAAAGA
1 AAAAGAAAGGAA-AGAAAAGA
* *
462 GAAAGAAAGGAAAGCAAAGA
1 AAAAGAAAGGAAAGAAAAGA
482 AAAAGAA
1 AAAAGAA
489 GGATAAGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (20 bp):
AAAAGAAAGGAAAGAAAAGA
Found at i:481 original size:27 final size:26
Alignment explanation
Indices: 371--487 Score: 82
Period size: 27 Copynumber: 4.5 Consensus size: 26
361 AGAAGAAAGG
* *
371 GAAAG-GAAAAGGAGGAAGAAAGAGAAG
1 GAAAGAGAAAA-GAGAAAGAAAG-GAAA
* *
398 GAAA-AGAAAAGGAGAAGGAAAGAAAA
1 GAAAGAGAAAA-GAGAAAGAAAGGAAA
* * * *
424 GAGAGAGACGAAGAG-AGGAAAAGAAA
1 GAAAGAGA-AAAGAGAAAGAAAGGAAA
450 G-AAGAGAAAAGAGAAAGAAAGGAAA
1 GAAAGAGAAAAGAGAAAGAAAGGAAA
475 GCAAAGA-AAAAGA
1 G-AAAGAGAAAAGA
488 AGGATAAGTT
Statistics
Matches: 72, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
24 5 0.07
25 15 0.21
26 21 0.29
27 29 0.40
28 2 0.03
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (26 bp):
GAAAGAGAAAAGAGAAAGAAAGGAAA
Done.