Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_30973
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: 3678
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Found at i:3511 original size:273 final size:272
Alignment explanation
Indices: 3013--3662 Score: 890
Period size: 273 Copynumber: 2.3 Consensus size: 272
3003 CAAGGTAAAT
* * *
3013 CATGGAGATAACAAATCAAAATTACCTATTGTCGAGGCAAGATCTCTGGAGGATATACATAAAGC
1 CATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATAGACAAAGC
* * * *
3078 TGTTCGACAACTTCCAGAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTTAAGGAATGAAT
66 TATTCAACAACTTCGA-AATCTAAT-C--C--A---G-CACATTCTTCAGGCTCAAGGAATGAAT
* * * * ** * **
3143 CATTAACAGATAAGGATACTGAGACTAATGTGGTGCTTCCAGTTCTTGAAACAAGGTCAGCAGAA
121 CATCAAAAGATAAGAAGACCAAGACTAATGTGGTGCTGCCAGTTCTTGAAACAAGACCAGCAGAA
3208 GATATTGATTTGGCTTTTAAGCAACTTCATGAAGGAG-TCA-ATGTCGAGGAAGTAATTGTTCCG
186 GATATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTTCACAT-T-GAGGAAGTAATTGTTCCG
*
3271 AGTATGATTGAGAAACTGCCAGAT
249 AGTATGATTGAGAAACTGCCAGAC
* * *
3295 CTTGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATTTAGACAAAGC
1 CATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATAGACAAAGC
* * *
3360 TATTCAACAACTTGTGAAATCTAATCCAGCATATTCTTCAGGCTCAAGGATTGAATCATCAAAAG
66 TATTCAACAACTT-CGAAATCTAATCCAGCACATTCTTCAGGCTCAAGGAATGAATCATCAAAAG
** * * *
3425 ATGCGAAGACCAAGACTAATGTGGTGCTGCCAGTTTTTGAAGCAAGACCAGCCGAAGATATTGAT
130 ATAAGAAGACCAAGACTAATGTGGTGCTGCCAGTTCTTGAAACAAGACCAGCAGAAGATATTGAT
*
3490 TTGGCTTTTAAGCAACTTCATGAAGGAGTTGACATTGAGGAAGTAATTGTTCCGAGTATGATTGA
195 TTGGCTTTTAAGCAACTTCATGAAGGAGTTCACATTGAGGAAGTAATTGTTCCGAGTATGATTGA
3555 GAAACTGCCAGAC
260 GAAACTGCCAGAC
*
3568 CATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGACATAGACAAAGC
1 CATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATAGACAAAGC
3633 TATTCAACAACTTCCGAAATCTAATCCAGC
66 TATTCAACAACTT-CGAAATCTAATCCAGC
3663 TGAGCTGCCA
Statistics
Matches: 330, Mismatches: 35, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
273 242 0.73
274 4 0.01
275 2 0.01
277 1 0.00
279 1 0.00
281 1 0.00
282 78 0.24
283 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (272 bp):
CATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATAGACAAAGC
TATTCAACAACTTCGAAATCTAATCCAGCACATTCTTCAGGCTCAAGGAATGAATCATCAAAAGA
TAAGAAGACCAAGACTAATGTGGTGCTGCCAGTTCTTGAAACAAGACCAGCAGAAGATATTGATT
TGGCTTTTAAGCAACTTCATGAAGGAGTTCACATTGAGGAAGTAATTGTTCCGAGTATGATTGAG
AAACTGCCAGAC
Done.