Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_17537

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, 558

Length: 930
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.25


Found at i:602 original size:3 final size:3

Alignment explanation


    Indices: 587--620  Score: 50
    Period size: 3  Copynumber: 11.3  Consensus size: 3

        577 AGGAACTATT

                    *                *                   
        587 CTG CTG TTG CTG CTG CTG CGG CTG CTG CTG CTG C
          1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG C

        621 GGAAAGTGAT


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
   3   27  1.00

ACGTcount: A:0.00, C:0.32, G:0.35, T:0.32


Consensus pattern (3 bp):   
CTG

Found at i:621 original size:15 final size:15

Alignment explanation


    Indices: 594--622  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

        584 ATTCTGCTGT

                           
        594 TGCTGCTGCTGCGGC
          1 TGCTGCTGCTGCGGC

                          
        609 TGCTGCTGCTGCGG
          1 TGCTGCTGCTGCGG

        623 AAAGTGATGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.00, C:0.31, G:0.41, T:0.28


Consensus pattern (15 bp):   
TGCTGCTGCTGCGGC

Found at i:655 original size:15 final size:15

Alignment explanation


    Indices: 637--676  Score: 53
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        627 TGATGAGGAG

                 *         
        637 GAGGGTGAGGAAAGC
          1 GAGGGAGAGGAAAGC

                          *
        652 GAGGGAGAGGAAAGT
          1 GAGGGAGAGGAAAGC

              *       
        667 GAAGGAGAGG
          1 GAGGGAGAGG

        677 GAGAGGAGAG


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  15   22  1.00

ACGTcount: A:0.38, C:0.03, G:0.55, T:0.05


Consensus pattern (15 bp):   
GAGGGAGAGGAAAGC

Found at i:676 original size:21 final size:21

Alignment explanation


    Indices: 652--692  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        642 TGAGGAAAGC

                          *      
        652 GAGGGAGAGGAAAGTGAAGGA
          1 GAGGGAGAGGAAAGGGAAGGA

                       *        
        673 GAGGGAGAGGAGAGGGAAGG
          1 GAGGGAGAGGAAAGGGAAGG

        693 GATGAAGAGA


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

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.39, C:0.00, G:0.59, T:0.02


Consensus pattern (21 bp):   
GAGGGAGAGGAAAGGGAAGGA
Done.