Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_22228

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, 757

Length: 1263
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.29


Found at i:728 original size:18 final size:18

Alignment explanation


    Indices: 705--763  Score: 68
    Period size: 18  Copynumber: 3.3  Consensus size: 18

        695 GTGCACATCA

                               
        705 TCATGATCAT-GATCATGG
          1 TCATGATCATGGA-CATGG

                   *          
        723 TCATGATGATGGACATGG
          1 TCATGATCATGGACATGG

                               
        741 TCAT-AGTCATGGACATGG
          1 TCATGA-TCATGGACATGG

            *    
        759 GCATG
          1 TCATG

        764 GAGGTGAGGA


Statistics
Matches: 35,  Mismatches: 3, Indels: 5
        0.81            0.07        0.12

Matches are distributed among these distances:
  17    1  0.03
  18   32  0.91
  19    2  0.06

ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29


Consensus pattern (18 bp):   
TCATGATCATGGACATGG

Found at i:734 original size:12 final size:12

Alignment explanation


    Indices: 704--751  Score: 51
    Period size: 12  Copynumber: 4.0  Consensus size: 12

        694 CGTGCACATC

                  *     
        704 ATCATGATCATG
          1 ATCATGGTCATG

                        
        716 ATCATGGTCATG
          1 ATCATGGTCATG

              *    *    
        728 ATGATGGACATG
          1 ATCATGGTCATG

            *    *      
        740 GTCATAGTCATG
          1 ATCATGGTCATG

        752 GACATGGGCA


Statistics
Matches: 29,  Mismatches: 7, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  12   29  1.00

ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31


Consensus pattern (12 bp):   
ATCATGGTCATG
Done.