Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_26576

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: 1740
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30


Found at i:1219 original size:6 final size:6

Alignment explanation


    Indices: 1208--1263  Score: 58
    Period size: 6  Copynumber: 9.3  Consensus size: 6

       1198 GTAACCAGTG

                                        **      *      *      *    
       1208 CACCAT CACCAT CACCAT CACCAT TTCCAT CTCCAT CTCCAT CTCCAT
          1 CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT

             *       
       1256 CTCCAT CA
          1 CACCAT CA

       1264 TCTTCAAGTG


Statistics
Matches: 46,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   6   46  1.00

ACGTcount: A:0.25, C:0.48, G:0.00, T:0.27


Consensus pattern (6 bp):   
CACCAT

Found at i:1225 original size:12 final size:12

Alignment explanation


    Indices: 1210--1263  Score: 72
    Period size: 12  Copynumber: 4.5  Consensus size: 12

       1200 AACCAGTGCA

                       *
       1210 CCATCACCATCA
          1 CCATCACCATCT

                      * 
       1222 CCATCACCATTT
          1 CCATCACCATCT

                 *      
       1234 CCATCTCCATCT
          1 CCATCACCATCT

                 *      
       1246 CCATCTCCATCT
          1 CCATCACCATCT

                  
       1258 CCATCA
          1 CCATCA

       1264 TCTTCAAGTG


Statistics
Matches: 37,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  12   37  1.00

ACGTcount: A:0.24, C:0.48, G:0.00, T:0.28


Consensus pattern (12 bp):   
CCATCACCATCT

Found at i:1231 original size:18 final size:18

Alignment explanation


    Indices: 1208--1263  Score: 76
    Period size: 18  Copynumber: 3.1  Consensus size: 18

       1198 GTAACCAGTG

                   *     *    
       1208 CACCATCACCATCACCAT
          1 CACCATCTCCATCTCCAT

                  *           
       1226 CACCATTTCCATCTCCAT
          1 CACCATCTCCATCTCCAT

             *                
       1244 CTCCATCTCCATCTCCAT
          1 CACCATCTCCATCTCCAT

              
       1262 CA
          1 CA

       1264 TCTTCAAGTG


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

Matches are distributed among these distances:
  18   32  1.00

ACGTcount: A:0.25, C:0.48, G:0.00, T:0.27


Consensus pattern (18 bp):   
CACCATCTCCATCTCCAT
Done.