Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_31744

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, 526

Length: 878
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.25


Found at i:404 original size:21 final size:21

Alignment explanation


    Indices: 338--407  Score: 59
    Period size: 21  Copynumber: 3.3  Consensus size: 21

        328 TATTTCCAGG

                  *              
        338 CCCACCCGGAATAGTCCCGAA
          1 CCCACCTGGAATAGTCCCGAA

                   * *  ** * * **
        359 CCCACCTAGTATTTTTCAGGG
          1 CCCACCTGGAATAGTCCCGAA

                                 
        380 CCCACCTGGAATAGTCCCGAA
          1 CCCACCTGGAATAGTCCCGAA

                   
        401 CCCACCT
          1 CCCACCT

        408 AGTATTTTTC


Statistics
Matches: 32,  Mismatches: 17, Indels: 0
        0.65            0.35        0.00

Matches are distributed among these distances:
  21   32  1.00

ACGTcount: A:0.24, C:0.40, G:0.17, T:0.19


Consensus pattern (21 bp):   
CCCACCTGGAATAGTCCCGAA

Found at i:416 original size:42 final size:41

Alignment explanation


    Indices: 295--417  Score: 165
    Period size: 42  Copynumber: 3.0  Consensus size: 41

        285 CCACCACCAA

                            *  *     *  * *       *   
        295 GCCCACCCGGAATAGTTCCAAACCCGCCGATTATATTTCCAG
          1 GCCCACCCGGAATAGTCCCGAACCCACCTAGTAT-TTTTCAG

                                                      
        337 GCCCACCCGGAATAGTCCCGAACCCACCTAGTATTTTTCAGG
          1 GCCCACCCGGAATAGTCCCGAACCCACCTAGTATTTTTCA-G

                   *                               
        379 GCCCACCTGGAATAGTCCCGAACCCACCTAGTATTTTTC
          1 GCCCACCCGGAATAGTCCCGAACCCACCTAGTATTTTTC

        418 CAAGCCCTCC


Statistics
Matches: 73,  Mismatches: 7, Indels: 2
        0.89            0.09        0.02

Matches are distributed among these distances:
  41    5  0.07
  42   68  0.93

ACGTcount: A:0.24, C:0.36, G:0.17, T:0.23


Consensus pattern (41 bp):   
GCCCACCCGGAATAGTCCCGAACCCACCTAGTATTTTTCAG
Done.