Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_10335

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: 1982
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.29


Found at i:1355 original size:42 final size:42

Alignment explanation


    Indices: 1308--1437  Score: 134
    Period size: 42  Copynumber: 3.1  Consensus size: 42

       1298 ACCTCCGCCG

                    *           *     *        *      
       1308 CCACCTGTGTACTCTCCTCCTCCACCGCCACCATCTCCACCT
          1 CCACCTGTTTACTCTCCTCCACCACCACCACCATCACCACCT

                       *  *        *         *       *
       1350 CCACCTGTTTATTCACCTCCACCTCCACCACCACCACCACCA
          1 CCACCTGTTTACTCTCCTCCACCACCACCACCATCACCACCT

               * *           *           *     *      
       1392 CCAGCAGTTTACTCTCCACCACCACCACCTCCATCCCCACCT
          1 CCACCTGTTTACTCTCCTCCACCACCACCACCATCACCACCT

                
       1434 CCAC
          1 CCAC

       1438 TATCACCCCC


Statistics
Matches: 68,  Mismatches: 20, Indels: 0
        0.77            0.23        0.00

Matches are distributed among these distances:
  42   68  1.00

ACGTcount: A:0.20, C:0.55, G:0.05, T:0.20


Consensus pattern (42 bp):   
CCACCTGTTTACTCTCCTCCACCACCACCACCATCACCACCT

Found at i:1886 original size:45 final size:44

Alignment explanation


    Indices: 1800--1906  Score: 121
    Period size: 45  Copynumber: 2.5  Consensus size: 44

       1790 ACCGCCGCCA

                                        *               
       1800 CCATCACCATCACCCCCA--CCCCCAATTCATTACAAACCACCT
          1 CCATCACCATCACCCCCACCCCCCCAATCCATTACAAACCACCT

                    *                              **     
       1842 CCATCACCTTCACCCCCACCCCCACCAATCCATTATC-ATTCACCT
          1 CCATCACCATCACCCCCACCCCC-CCAATCCATTA-CAAACCACCT

               *          *     
       1887 CCACCACCATCACCTCCACC
          1 CCATCACCATCACCCCCACC

       1907 GGCTCCCGTA


Statistics
Matches: 54,  Mismatches: 7, Indels: 5
        0.82            0.11        0.08

Matches are distributed among these distances:
  42   17  0.31
  44    3  0.06
  45   33  0.61
  46    1  0.02

ACGTcount: A:0.27, C:0.55, G:0.00, T:0.18


Consensus pattern (44 bp):   
CCATCACCATCACCCCCACCCCCCCAATCCATTACAAACCACCT
Done.