Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_00115

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: 2541
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28


Found at i:1375 original size:51 final size:52

Alignment explanation


    Indices: 1307--1409  Score: 133
    Period size: 51  Copynumber: 2.0  Consensus size: 52

       1297 GAGCAGGCTG

                                                                  
       1307 CTGAATTAAGAAAAGAAGTTGGAA-TATCT-GAGAGAAGTTTGG-AGCAAGTCA
          1 CTGAATTAAGAAAAGAAGTTGGAATTA-CTGGA-AGAAGTTTGGAAGCAAGTCA

                         *                               *       
       1358 CTGAATCT-AGAAGAGAAGTTGGAATTACTGGAAGAAGTTTGGAATCAAGTCA
          1 CTGAAT-TAAGAAAAGAAGTTGGAATTACTGGAAGAAGTTTGGAAGCAAGTCA

       1410 GTCGGCTGCT


Statistics
Matches: 46,  Mismatches: 2, Indels: 7
        0.84            0.04        0.13

Matches are distributed among these distances:
  51   33  0.72
  52   13  0.28

ACGTcount: A:0.40, C:0.09, G:0.27, T:0.24


Consensus pattern (52 bp):   
CTGAATTAAGAAAAGAAGTTGGAATTACTGGAAGAAGTTTGGAAGCAAGTCA

Found at i:1500 original size:111 final size:111

Alignment explanation


    Indices: 1302--1504  Score: 266
    Period size: 111  Copynumber: 1.8  Consensus size: 111

       1292 GGTCGGAGCA

                       *           *                 *           *         * 
       1302 GGCTGCTGAATTAAGAAAAGAAGTTGGAATATCTGAGAGAAGTTTGGAGCAAGTCACTGAATCTA
          1 GGCTGCTGAATCAAGAAAAGAAGCTGGAATATCTGAGAGAACTTTGGAGCAAGGCACTGAATCGA

               *    *                                     
       1367 GAAGAGAAGTTGGAATTACTGGAAGAAGTTTGGAATCAAGTCAGTC
         66 GAAAAGAACTTGGAATTACTGGAAGAAGTTTGGAATCAAGTCAGTC

                                                *                  *      *  
       1413 GGCTGCTGAATCAAGAAAAGAAGCTGGAATAGT-TGGGAGAACTTTGGAGC-AGGGAGCTGATTC
          1 GGCTGCTGAATCAAGAAAAGAAGCTGGAATA-TCTGAGAGAACTTTGGAGCAAGGCA-CTGAATC

                           *   *         
       1476 GAGAAAAGAACTTGGTATTGCTGGAAGAA
         64 GAGAAAAGAACTTGGAATTACTGGAAGAA

       1505 CAATGCCATT


Statistics
Matches: 78,  Mismatches: 12, Indels: 4
        0.83            0.13        0.04

Matches are distributed among these distances:
 110    3  0.04
 111   74  0.95
 112    1  0.01

ACGTcount: A:0.36, C:0.10, G:0.31, T:0.23


Consensus pattern (111 bp):   
GGCTGCTGAATCAAGAAAAGAAGCTGGAATATCTGAGAGAACTTTGGAGCAAGGCACTGAATCGA
GAAAAGAACTTGGAATTACTGGAAGAAGTTTGGAATCAAGTCAGTC
Done.