Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_38161
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: 1839
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.21
Found at i:356 original size:33 final size:32
Alignment explanation
Indices: 319--423 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 32
309 GAAGGAAAGG
* * *
319 GAGAGAGAAAGAAGAGAAAAAGATAAGGAGAAA
1 GAGAG-GAAAGAAGAGAGAAGGAAAAGGAGAAA
* * *
352 GAGAGGGATAGGAGAGAGAAGGAAAAGGAGAGA
1 GAGA-GGAAAGAAGAGAGAAGGAAAAGGAGAAA
**
385 GAGAGGAGGGAAAGAGAGAAGGAAAAGGAGAAA
1 GAGAGGAAAG-AAGAGAGAAGGAAAAGGAGAAA
418 GAGAGG
1 GAGAGG
424 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:380 original size:66 final size:66
Alignment explanation
Indices: 288--425 Score: 161
Period size: 66 Copynumber: 2.1 Consensus size: 66
278 ATTTAGAGAG
* * * * *
288 GAGGGGTAGCAGAGAGAGGGAGAAGGAAAGGGAGAGAGAAAG-AAGAGAAAAAGATAAGGAGAAA
1 GAGGGATAGCAGAGAGAAGGAAAAGGAAAGAGAGAG-GAAAGAAAGAGAAAAAGAAAAGGAGAAA
352 GA
65 GA
* * ** * *
354 GAGGGATAGGAGAGAGAAGGAAAAGGAGAGAGAGAGGAGGGAAAGAGAGAAGGAAAAGGAGAAAG
1 GAGGGATAGCAGAGAGAAGGAAAAGGAAAGAGAGAGGAAAGAAAGAGAAAAAGAAAAGGAGAAAG
419 A
66 A
420 GAGGGA
1 GAGGGA
426 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:417 original size:20 final size:20
Alignment explanation
Indices: 364--422 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
354 GAGGGATAGG
364 AGAGAGAAGGAAAAGGAG--
1 AGAGAGAAGGAAAAGGAGAA
382 AGAGAG-AGG---AGG-GAA
1 AGAGAGAAGGAAAAGGAGAA
397 AGAGAGAAGGAAAAGGAGAA
1 AGAGAGAAGGAAAAGGAGAA
417 AGAGAG
1 AGAGAG
423 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:514 original size:75 final size:75
Alignment explanation
Indices: 434--626 Score: 323
Period size: 75 Copynumber: 2.6 Consensus size: 75
424 GAGGTAGACC
* *
434 GGAGAGAGAGAAGCAGTAGTAGGTCGAGGAGGCACGAAAGTGATCGTGAGATTGAGAGGGAACGG
1 GGAGAGAGAGAAGCAGTAGTAGGTCGAGGAGGCACGAGAGTGATCGTGAGATAGAGAGGGAACGG
499 GAGAGAGATA
66 GAGAGAGATA
* * *
509 GGAGAGAGAGGAGCAGTAGTAGGTCGAGGAGGCACGAGAGTGATCGTGAGCTAGAGAGGGAGCGG
1 GGAGAGAGAGAAGCAGTAGTAGGTCGAGGAGGCACGAGAGTGATCGTGAGATAGAGAGGGAACGG
574 GAGAGAGATA
66 GAGAGAGATA
* *
584 GGAGAGAGAGAAGCAGTAGTAGGTTGAGGAGACACGAGAGTGA
1 GGAGAGAGAGAAGCAGTAGTAGGTCGAGGAGGCACGAGAGTGA
627 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.