Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_37740

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, 651

Length: 1086
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23


Found at i:918 original size:15 final size:15

Alignment explanation


    Indices: 900--998  Score: 63
    Period size: 15  Copynumber: 6.6  Consensus size: 15

        890 AGCTTGATAT

                           
        900 AGATGACGATGAAGA
          1 AGATGACGATGAAGA

                        *  
        915 AGATGACGATGATGA
          1 AGATGACGATGAAGA

            *     *  *     
        930 TGATGAGGAGGAAGA
          1 AGATGACGATGAAGA

            *     *  *     
        945 GGATGATGAGGAAGA
          1 AGATGACGATGAAGA

            *     *    **  
        960 GGATGAGGATGCTGA
          1 AGATGACGATGAAGA

            *     *     *  
        975 CGATGAGGATGAGGA
          1 AGATGACGATGAAGA

            *        
        990 TGATGACGA
          1 AGATGACGA

        999 AGGAAGTAAG


Statistics
Matches: 68,  Mismatches: 16, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  15   68  1.00

ACGTcount: A:0.37, C:0.05, G:0.41, T:0.16


Consensus pattern (15 bp):   
AGATGACGATGAAGA

Found at i:949 original size:21 final size:21

Alignment explanation


    Indices: 907--1000  Score: 98
    Period size: 21  Copynumber: 4.5  Consensus size: 21

        897 TATAGATGAC

                 *     *  *  *   
        907 GATGAAGAAGATGACGATGAT
          1 GATGACGAAGAGGATGAGGAT

                 *  *     *      
        928 GATGATGAGGAGGAAGAGGAT
          1 GATGACGAAGAGGATGAGGAT

                 *               
        949 GATGAGGAAGAGGATGAGGAT
          1 GATGACGAAGAGGATGAGGAT

             *      *            
        970 GCTGACGATGAGGATGAGGAT
          1 GATGACGAAGAGGATGAGGAT

                      
        991 GATGACGAAG
          1 GATGACGAAG

       1001 GAAGTAAGAC


Statistics
Matches: 60,  Mismatches: 13, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  21   60  1.00

ACGTcount: A:0.37, C:0.04, G:0.43, T:0.16


Consensus pattern (21 bp):   
GATGACGAAGAGGATGAGGAT
Done.