Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_13690
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, 589
Length: 983
ACGTcount: A:0.41, C:0.16, G:0.28, T:0.16
Found at i:356 original size:27 final size:26
Alignment explanation
Indices: 326--385 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 26
316 AGGGAGAGAG
*
326 AAGAAAGGGAAAGGAAAAGGAGGAA-GA
1 AAGAAA-GGAAAAGAAAAGGA-GAAGGA
353 AAGAGAAGGAAAAGAAAAGGAGAAGGA
1 AAGA-AAGGAAAAGAAAAGGAGAAGGA
380 AAGAAA
1 AAGAAA
386 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:377 original size:17 final size:17
Alignment explanation
Indices: 354--392 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
344 GGAGGAAGAA
354 AGAGAAGGAAAAGAAAAG
1 AGAGAAGG-AAAGAAAAG
372 -GAGAAGGAAAGAAAAG
1 AGAGAAGGAAAGAAAAG
388 AGAGA
1 AGAGA
393 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:386 original size:43 final size:43
Alignment explanation
Indices: 298--412 Score: 112
Period size: 43 Copynumber: 2.6 Consensus size: 43
288 GAGGGGGAGG
* * *
298 AGGAGGAAGAGGAAGAGAAGGGAGAGAGAAGAAAGGGAAAGGAAA
1 AGGAGGAAGA--AAGAGAAGGAAAAGAAAAGAAAGGGAAAGGAAA
343 AGGAGGAAGAAAGAGAAGGAAAAGAAAAGGAGAA-GGAAA-GAAA
1 AGGAGGAAGAAAGAGAAGGAAAAGAAAA-GA-AAGGGAAAGGAAA
*
386 AGAGAGAGACG-AAGAG-AGGAAAAGAAA
1 AG-GAG-GAAGAAAGAGAAGGAAAAGAAA
413 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:425 original size:22 final size:21
Alignment explanation
Indices: 381--433 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
371 GGAGAAGGAA
* *
381 AGAAAAGAGAGAGACGAAGAG
1 AGAAAAGAAAGAGACGAAAAG
402 AGGAAAAGAAAGAAGA-GAAAAG
1 A-GAAAAGAAAG-AGACGAAAAG
424 AG-AAAGAAAG
1 AGAAAAGAAAG
434 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:431 original size:20 final size:20
Alignment explanation
Indices: 405--451 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
395 CGAAGAGAGG
405 AAAAGAAA-GAAGAGAAAAGA
1 AAAAGAAAGGAA-AGAAAAGA
* *
425 GAAAGAAAGGAAAGCAAAGA
1 AAAAGAAAGGAAAGAAAAGA
445 AAAAGAA
1 AAAAGAA
452 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:444 original size:27 final size:26
Alignment explanation
Indices: 334--450 Score: 82
Period size: 27 Copynumber: 4.5 Consensus size: 26
324 AGAAGAAAGG
* *
334 GAAAG-GAAAAGGAGGAAGAAAGAGAAG
1 GAAAGAGAAAA-GAGAAAGAAAG-GAAA
* *
361 GAAA-AGAAAAGGAGAAGGAAAGAAAA
1 GAAAGAGAAAA-GAGAAAGAAAGGAAA
* * * *
387 GAGAGAGACGAAGAG-AGGAAAAGAAA
1 GAAAGAGA-AAAGAGAAAGAAAGGAAA
413 G-AAGAGAAAAGAGAAAGAAAGGAAA
1 GAAAGAGAAAAGAGAAAGAAAGGAAA
438 GCAAAGA-AAAAGA
1 G-AAAGAGAAAAGA
451 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.