Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_11160

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: 1950
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25


Found at i:169 original size:24 final size:24

Alignment explanation


    Indices: 142--200  Score: 66
    Period size: 24  Copynumber: 2.5  Consensus size: 24

        132 CCCATCAGCT

                                    *
        142 CCTCCTCCTTCTACCA-CTCCATCC
          1 CCTCCTCCTTCTACCACCT-CATCA

                     *  *           
        166 CCTCCTCCTCCTTCCACCTCATCA
          1 CCTCCTCCTTCTACCACCTCATCA

                 *     
        190 CCTCCGCCTTC
          1 CCTCCTCCTTC

        201 ATCCTCTGCC


Statistics
Matches: 29,  Mismatches: 5, Indels: 2
        0.81            0.14        0.06

Matches are distributed among these distances:
  24   27  0.93
  25    2  0.07

ACGTcount: A:0.10, C:0.59, G:0.02, T:0.29


Consensus pattern (24 bp):   
CCTCCTCCTTCTACCACCTCATCA

Found at i:378 original size:36 final size:36

Alignment explanation


    Indices: 289--380  Score: 103
    Period size: 36  Copynumber: 2.6  Consensus size: 36

        279 CTCATCAACA

                    *  *     *       *      *   
        289 CCATCTCCGCCGCCGCCACCGAGGAGTCCCGGTACT
          1 CCATCTCCACCACCGCCTCCGAGGAATCCCGGGACT

            *                          *        
        325 GCATCTCCACCACCGCCTCCGAGGAATTCCGGGACT
          1 CCATCTCCACCACCGCCTCCGAGGAATCCCGGGACT

                    *  *        
        361 CCATCTCCTCCTCCGCCTCC
          1 CCATCTCCACCACCGCCTCC

        381 TTCTGATTCC


Statistics
Matches: 46,  Mismatches: 10, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  36   46  1.00

ACGTcount: A:0.14, C:0.49, G:0.20, T:0.17


Consensus pattern (36 bp):   
CCATCTCCACCACCGCCTCCGAGGAATCCCGGGACT
Done.