Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_21362

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: 2793
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27


Found at i:529 original size:6 final size:6

Alignment explanation


    Indices: 520--602  Score: 85
    Period size: 6  Copynumber: 13.8  Consensus size: 6

        510 GGACTTAGGC

                                 *             *    *        *    *
        520 CCATCA CCATCA CCATCA TCATCA CCATCA TCATCC CCATCA TCATCC
          1 CCATCA CCATCA CCATCA CCATCA CCATCA CCATCA CCATCA CCATCA

                 *      *        *             *    
        568 CCATCT CCATCT CCATCA TCATCA CCATCA TCATC
          1 CCATCA CCATCA CCATCA CCATCA CCATCA CCATC

        603 CCCAAATCTG


Statistics
Matches: 63,  Mismatches: 14, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
   6   63  1.00

ACGTcount: A:0.28, C:0.47, G:0.00, T:0.25


Consensus pattern (6 bp):   
CCATCA

Found at i:537 original size:12 final size:12

Alignment explanation


    Indices: 520--602  Score: 114
    Period size: 12  Copynumber: 6.9  Consensus size: 12

        510 GGACTTAGGC

                  *     
        520 CCATCACCATCA
          1 CCATCATCATCA

                        
        532 CCATCATCATCA
          1 CCATCATCATCA

                       *
        544 CCATCATCATCC
          1 CCATCATCATCA

                       *
        556 CCATCATCATCC
          1 CCATCATCATCA

                        *
        568 CCATC-TCCATCT
          1 CCATCAT-CATCA

                        
        580 CCATCATCATCA
          1 CCATCATCATCA

                       
        592 CCATCATCATC
          1 CCATCATCATC

        603 CCCAAATCTG


Statistics
Matches: 65,  Mismatches: 4, Indels: 4
        0.89            0.05        0.05

Matches are distributed among these distances:
  11    1  0.02
  12   63  0.97
  13    1  0.02

ACGTcount: A:0.28, C:0.47, G:0.00, T:0.25


Consensus pattern (12 bp):   
CCATCATCATCA

Done.