Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_24827

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: 11069
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.30


Found at i:6571 original size:9 final size:9

Alignment explanation


    Indices: 6505--6579  Score: 55
    Period size: 9  Copynumber: 8.3  Consensus size: 9

       6495 AAACCTTGAT

                     
       6505 GATGACGAG
          1 GATGACGAG

                 *   
       6514 GATGAGGA-
          1 GATGACGAG

                *     
       6522 GATGTCTG-G
          1 GATGAC-GAG

                    * 
       6531 AGATGACGGG
          1 -GATGACGAG

                 * * 
       6541 GATGAAGTG
          1 GATGACGAG

                 *  *
       6550 GATGAAGAT
          1 GATGACGAG

                     
       6559 GATGACGAG
          1 GATGACGAG

                     
       6568 GATGACGAG
          1 GATGACGAG

               
       6577 GAT
          1 GAT

       6580 CATAATGATT


Statistics
Matches: 52,  Mismatches: 10, Indels: 8
        0.74            0.14        0.11

Matches are distributed among these distances:
   8    4  0.08
   9   42  0.81
  10    6  0.12

ACGTcount: A:0.32, C:0.07, G:0.44, T:0.17


Consensus pattern (9 bp):   
GATGACGAG

Found at i:6579 original size:27 final size:28

Alignment explanation


    Indices: 6502--6579  Score: 72
    Period size: 27  Copynumber: 2.9  Consensus size: 28

       6492 AGAAAACCTT

                             *         **
       6502 GATGATGACGAGGATGAGGA-GATGTCTG
          1 GATGATGACGAGGATGAAGAGGATG-CAA

                      *        *        
       6530 GA-GATGACGGGGATGAAGTGGATG-AA
          1 GATGATGACGAGGATGAAGAGGATGCAA

                             *      
       6556 GATGATGACGAGGATGACGAGGAT
          1 GATGATGACGAGGATGAAGAGGAT

       6580 CATAATGATT


Statistics
Matches: 40,  Mismatches: 8, Indels: 5
        0.75            0.15        0.09

Matches are distributed among these distances:
  26    2  0.05
  27   32  0.80
  28    6  0.15

ACGTcount: A:0.32, C:0.06, G:0.44, T:0.18


Consensus pattern (28 bp):   
GATGATGACGAGGATGAAGAGGATGCAA
Done.