Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_11485

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, 315

Length: 525
ACGTcount: A:0.32, C:0.13, G:0.31, T:0.24


Found at i:415 original size:18 final size:18

Alignment explanation


    Indices: 384--464  Score: 72
    Period size: 18  Copynumber: 4.5  Consensus size: 18

        374 ATGGTGGGAG

                     *     *  
        384 TGACGAAGAAGATGACGA
          1 TGACGAAGATGATGATGA

                  *          *
        402 TGACGATGATGATGATGG
          1 TGACGAAGATGATGATGA

            *                 
        420 GGACGAAGATGATGATGA
          1 TGACGAAGATGATGATGA

            *     *    *   *  
        438 CGACGATGATGGTGAGGA
          1 TGACGAAGATGATGATGA

               *     
        456 TGAAGAAGA
          1 TGACGAAGA

        465 GGAGGACGAA


Statistics
Matches: 49,  Mismatches: 14, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
  18   49  1.00

ACGTcount: A:0.37, C:0.07, G:0.38, T:0.17


Consensus pattern (18 bp):   
TGACGAAGATGATGATGA

Found at i:418 original size:15 final size:15

Alignment explanation


    Indices: 394--458  Score: 58
    Period size: 15  Copynumber: 4.1  Consensus size: 15

        384 TGACGAAGAA

                 *         
        394 GATGACGATGACGAT
          1 GATGATGATGACGAT

                             *
        409 GATGATGATGGGGACGAA
          1 GATGATGAT---GACGAT

                          *
        427 GATGATGATGACGAC
          1 GATGATGATGACGAT

                   *   *   
        442 GATGATGGTGAGGAT
          1 GATGATGATGACGAT

              
        457 GA
          1 GA

        459 AGAAGAGGAG


Statistics
Matches: 41,  Mismatches: 6, Indels: 6
        0.77            0.11        0.11

Matches are distributed among these distances:
  15   27  0.66
  18   14  0.34

ACGTcount: A:0.32, C:0.08, G:0.40, T:0.20


Consensus pattern (15 bp):   
GATGATGATGACGAT

Found at i:475 original size:15 final size:15

Alignment explanation


    Indices: 451--485  Score: 52
    Period size: 15  Copynumber: 2.3  Consensus size: 15

        441 CGATGATGGT

                 *         
        451 GAGGATGAAGAAGAG
          1 GAGGACGAAGAAGAG

                          *
        466 GAGGACGAAGAAGAT
          1 GAGGACGAAGAAGAG

                 
        481 GAGGA
          1 GAGGA

        486 TGATGAGGTT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.46, C:0.03, G:0.46, T:0.06


Consensus pattern (15 bp):   
GAGGACGAAGAAGAG
Done.