Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_22569

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: 2724
ACGTcount: A:0.37, C:0.14, G:0.29, T:0.20


Found at i:493 original size:18 final size:18

Alignment explanation


    Indices: 466--512  Score: 58
    Period size: 18  Copynumber: 2.6  Consensus size: 18

        456 AGATAGGGAC

                              
        466 AGAGAAAAGGAAAAGGAA
          1 AGAGAAAAGGAAAAGGAA

                 *    **      
        484 AGAGACAAGGCCAAGGAA
          1 AGAGAAAAGGAAAAGGAA

              *        
        502 AGGGAAAAGGA
          1 AGAGAAAAGGA

        513 GAGAGACAAA


Statistics
Matches: 23,  Mismatches: 6, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  18   23  1.00

ACGTcount: A:0.57, C:0.06, G:0.36, T:0.00


Consensus pattern (18 bp):   
AGAGAAAAGGAAAAGGAA

Found at i:572 original size:18 final size:18

Alignment explanation


    Indices: 533--577  Score: 56
    Period size: 18  Copynumber: 2.5  Consensus size: 18

        523 CTTAAGGATC

                         *    
        533 GAGAGAAGGAGAGGGAAG
          1 GAGAGAAGGAGAGAGAAG

                      *        
        551 GAGAGAAGGATAGAGATA-
          1 GAGAGAAGGAGAGAGA-AG

                     
        569 GAGAGAAGG
          1 GAGAGAAGG

        578 GAAAAGATAG


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  18   23  0.96
  19    1  0.04

ACGTcount: A:0.47, C:0.00, G:0.49, T:0.04


Consensus pattern (18 bp):   
GAGAGAAGGAGAGAGAAG

Found at i:585 original size:18 final size:18

Alignment explanation


    Indices: 551--588  Score: 51
    Period size: 18  Copynumber: 2.1  Consensus size: 18

        541 GAGAGGGAAG

                        *     
        551 GAGAGAAGGATAGAGATA
          1 GAGAGAAGGATAAAGATA

                               
        569 GAGAGAAGGGA-AAAGATA
          1 GAGAGAA-GGATAAAGATA

              
        587 GA
          1 GA

        589 AGTAAACAGA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  18   15  0.83
  19    3  0.17

ACGTcount: A:0.53, C:0.00, G:0.39, T:0.08


Consensus pattern (18 bp):   
GAGAGAAGGATAAAGATA
Done.