Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_34919

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: 3785
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26


Found at i:1559 original size:21 final size:20

Alignment explanation


    Indices: 1521--1579  Score: 59
    Period size: 21  Copynumber: 3.0  Consensus size: 20

       1511 AGCTTCTCGA

                          *       
       1521 AGAAGAAG-AGAAGGAAAAGCG
          1 AGAAGAAGAAGAA-CAAAAG-G

            *                   
       1542 TGAAGAAGAAGAACAAAAGG
          1 AGAAGAAGAAGAACAAAAGG

               *               
       1562 AGAGGAA-AAGAACAAAAG
          1 AGAAGAAGAAGAACAAAAG

       1580 AACGAGAGAA


Statistics
Matches: 33,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  19   11  0.33
  20    6  0.18
  21   12  0.36
  22    4  0.12

ACGTcount: A:0.61, C:0.05, G:0.32, T:0.02


Consensus pattern (20 bp):   
AGAAGAAGAAGAACAAAAGG

Found at i:1586 original size:22 final size:19

Alignment explanation


    Indices: 1545--1593  Score: 53
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       1535 AAAAGCGTGA

                *              
       1545 AGAAGAAGAACAAAAGGAG
          1 AGAAAAAGAACAAAAGGAG

              *                   
       1564 AGGAAAAGAACAAAAGAACGAG
          1 AGAAAAAGAACAAAAG---GAG

                    
       1586 AGAAAAAG
          1 AGAAAAAG

       1594 CTCAGGAGAA


Statistics
Matches: 24,  Mismatches: 3, Indels: 3
        0.80            0.10        0.10

Matches are distributed among these distances:
  19   14  0.58
  22   10  0.42

ACGTcount: A:0.65, C:0.06, G:0.29, T:0.00


Consensus pattern (19 bp):   
AGAAAAAGAACAAAAGGAG
Done.