Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_20973
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, 432
Length: 720
ACGTcount: A:0.19, C:0.41, G:0.16, T:0.25
Found at i:344 original size:45 final size:45
Alignment explanation
Indices: 295--438 Score: 128
Period size: 45 Copynumber: 3.2 Consensus size: 45
285 TAGCTCCCCA
* * *
295 CCACCAGCTTCTCCTCCCCCGGCTACTCCACCTCCCGCAACTCCC
1 CCACCAGCTTCTCCTCCACCGGCTACTCCACCTCCAGCTACTCCC
* * * * * * *
340 CCACCGGCTTCTCCACCGCCGGCTACCCCACCACCTGCTTCTCCC
1 CCACCAGCTTCTCCTCCACCGGCTACTCCACCTCCAGCTACTCCC
* * * * * *
385 CCTCCTGCTACTCCTCCACCAGCAACTCCTCCTCCAGCTAC-CCC
1 CCACCAGCTTCTCCTCCACCGGCTACTCCACCTCCAGCTACTCCC
429 ACCACCAGCT
1 -CCACCAGCT
439 CCTTTGGCTT
Statistics
Matches: 76, Mismatches: 22, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
44 3 0.04
45 73 0.96
ACGTcount: A:0.15, C:0.58, G:0.10, T:0.18
Consensus pattern (45 bp):
CCACCAGCTTCTCCTCCACCGGCTACTCCACCTCCAGCTACTCCC
Found at i:347 original size:30 final size:30
Alignment explanation
Indices: 305--434 Score: 95
Period size: 30 Copynumber: 4.3 Consensus size: 30
295 CCACCAGCTT
*
305 CTCCTCCC-CCGGCTACTCCACCTCCCGCAA
1 CTCC-CCCACCGGCTACTCCACCTCCCGCTA
* * *
335 CTCCCCCACCGGCTTCTCCACCGCCGGCTA
1 CTCCCCCACCGGCTACTCCACCTCCCGCTA
* * * *
365 C-CCCACCACCTGCTTCTCCCCCTCCTGCTA
1 CTCCC-CCACCGGCTACTCCACCTCCCGCTA
* * * * *
395 CTCCTCCACCAGCAACTCCTCCTCCAGCTA
1 CTCCCCCACCGGCTACTCCACCTCCCGCTA
425 C-CCCACCACC
1 CTCCC-CCACC
435 AGCTCCTTTG
Statistics
Matches: 81, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
29 8 0.10
30 71 0.88
31 2 0.02
ACGTcount: A:0.14, C:0.59, G:0.09, T:0.18
Consensus pattern (30 bp):
CTCCCCCACCGGCTACTCCACCTCCCGCTA
Found at i:353 original size:15 final size:15
Alignment explanation
Indices: 295--404 Score: 62
Period size: 15 Copynumber: 7.3 Consensus size: 15
285 TAGCTCCCCA
* *
295 CCACCAGCTTCTCCTC
1 CCACCGGCTACTCC-C
*
311 CC-CCGGCTACTCCA
1 CCACCGGCTACTCCC
* * *
325 CCTCCCGCAACTCCC
1 CCACCGGCTACTCCC
* *
340 CCACCGGCTTCTCCA
1 CCACCGGCTACTCCC
*
355 CCGCCGGCTAC-CCC
1 CCACCGGCTACTCCC
* *
369 ACCACCTGCTTCTCCC
1 -CCACCGGCTACTCCC
* * *
385 CCTCCTGCTACTCCT
1 CCACCGGCTACTCCC
400 CCACC
1 CCACC
405 AGCAACTCCT
Statistics
Matches: 70, Mismatches: 21, Indels: 7
0.71 0.21 0.07
Matches are distributed among these distances:
14 4 0.06
15 61 0.87
16 5 0.07
ACGTcount: A:0.12, C:0.59, G:0.10, T:0.19
Consensus pattern (15 bp):
CCACCGGCTACTCCC
Found at i:398 original size:60 final size:60
Alignment explanation
Indices: 320--434 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
310 CCCCCGGCTA
* ** *
320 CTCCACCTCCCGCAACTCCCCCACCGGCTTCTCCACCGCCGGCTACCCCACCACCTGCTT
1 CTCCACCTCCCGCAACTCCCCCACCAGCAACTCCACCGCCAGCTACCCCACCACCTGCTT
* * * * * *
380 CTCCCCCTCCTGCTACTCCTCCACCAGCAACTCCTCCTCCAGCTACCCCACCACC
1 CTCCACCTCCCGCAACTCCCCCACCAGCAACTCCACCGCCAGCTACCCCACCACC
435 AGCTCCTTTG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.15, C:0.59, G:0.09, T:0.17
Consensus pattern (60 bp):
CTCCACCTCCCGCAACTCCCCCACCAGCAACTCCACCGCCAGCTACCCCACCACCTGCTT
Found at i:412 original size:15 final size:15
Alignment explanation
Indices: 394--437 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
384 CCCTCCTGCT
394 ACTCCTCCACCAGCA
1 ACTCCTCCACCAGCA
* *
409 ACTCCTCCTCCAGCT
1 ACTCCTCCACCAGCA
* *
424 ACCCCACCACCAGC
1 ACTCCTCCACCAGC
438 TCCTTTGGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.23, C:0.57, G:0.07, T:0.14
Consensus pattern (15 bp):
ACTCCTCCACCAGCA
Found at i:438 original size:15 final size:15
Alignment explanation
Indices: 286--438 Score: 51
Period size: 15 Copynumber: 10.3 Consensus size: 15
276 CCCGTCCGTT
286 AGCT-CCCCACCACC
1 AGCTACCCCACCACC
* * * *
300 AGCTTCTCCTCCCCC
1 AGCTACCCCACCACC
* * *
315 GGCTACTCCACCTCC
1 AGCTACCCCACCACC
* *
330 CGCAACTCCC-CCACC
1 AGCTAC-CCCACCACC
* * * *
345 GGCTTCTCCACCGCC
1 AGCTACCCCACCACC
*
360 GGCTACCCCACCACC
1 AGCTACCCCACCACC
* * *
375 TGCTTCTCCC-CCTCC
1 AGCTAC-CCCACCACC
* * *
390 TGCTACTCCTCCACC
1 AGCTACCCCACCACC
* * * *
405 AGCAACTCCTCCTCC
1 AGCTACCCCACCACC
420 AGCTACCCCACCACC
1 AGCTACCCCACCACC
435 AGCT
1 AGCT
439 CCTTTGGCTT
Statistics
Matches: 102, Mismatches: 32, Indels: 9
0.71 0.22 0.06
Matches are distributed among these distances:
14 8 0.08
15 89 0.87
16 5 0.05
ACGTcount: A:0.15, C:0.58, G:0.10, T:0.18
Consensus pattern (15 bp):
AGCTACCCCACCACC
Done.