Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_19387

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: 2025
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24


Found at i:200 original size:3 final size:3

Alignment explanation


    Indices: 194--234  Score: 55
    Period size: 3  Copynumber: 13.7  Consensus size: 3

        184 TCAACTTCTT

                                  *       *      *                
        194 CAC CAC CAC CAC CAC CAT CAC CAT CAC CCC CAC CAC CAC CA
          1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA

        235 GCAGAGTCAA


Statistics
Matches: 32,  Mismatches: 6, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
   3   32  1.00

ACGTcount: A:0.32, C:0.63, G:0.00, T:0.05


Consensus pattern (3 bp):   
CAC

Found at i:280 original size:18 final size:18

Alignment explanation


    Indices: 193--281  Score: 54
    Period size: 18  Copynumber: 4.9  Consensus size: 18

        183 GTCAACTTCT

                  *    *      
        193 TCACCACCACCACCACCA
          1 TCACCATCACCGCCACCA

                       *      
        211 TCACCATCACCCCCACCA
          1 TCACCATCACCGCCACCA

            *     *  ** *  *  
        229 CCACCAGCAGAGTCAAC-
          1 TCACCATCACCGCCACCA

                *  *  *        
        246 TCCATCAACATCGCCACCA
          1 T-CACCATCACCGCCACCA

                             
        265 TCACCATCACCGCCACC
          1 TCACCATCACCGCCACC

        282 GCCACCGTCA


Statistics
Matches: 50,  Mismatches: 19, Indels: 4
        0.68            0.26        0.05

Matches are distributed among these distances:
  18   49  0.98
  19    1  0.02

ACGTcount: A:0.30, C:0.54, G:0.06, T:0.10


Consensus pattern (18 bp):   
TCACCATCACCGCCACCA
Done.