Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_28659

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, 700

Length: 1167
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25


Found at i:160 original size:6 final size:6

Alignment explanation


    Indices: 154--205  Score: 77
    Period size: 6  Copynumber: 8.7  Consensus size: 6

        144 ATCTCCTCCT

                 *      *      *                                   
        154 TCACCT TCACCT TCACCT TCACCC TCACCC TCACCC TCACCC TCACCC
          1 TCACCC TCACCC TCACCC TCACCC TCACCC TCACCC TCACCC TCACCC

                
        202 TCAC
          1 TCAC

        206 ACTCGCCTTC


Statistics
Matches: 45,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
   6   45  1.00

ACGTcount: A:0.17, C:0.60, G:0.00, T:0.23


Consensus pattern (6 bp):   
TCACCC

Found at i:161 original size:18 final size:18

Alignment explanation


    Indices: 140--200  Score: 52
    Period size: 18  Copynumber: 3.4  Consensus size: 18

        130 GCTTCTTCCT

                 *    *       
        140 CTTCATCTCCTCCTTCAC
          1 CTTCACCTCCACCTTCAC

                    *         
        158 CTTCACCTTCACCTTCAC
          1 CTTCACCTCCACCTTCAC

             *            *    
        176 CCTCACC-CTCACCCTCAC
          1 CTTCACCTC-CACCTTCAC

             *     
        194 CCTCACC
          1 CTTCACC

        201 CTCACACTCG


Statistics
Matches: 36,  Mismatches: 6, Indels: 2
        0.82            0.14        0.05

Matches are distributed among these distances:
  18   36  1.00

ACGTcount: A:0.15, C:0.57, G:0.00, T:0.28


Consensus pattern (18 bp):   
CTTCACCTCCACCTTCAC

Done.