Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_29677

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: 1779
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29


Found at i:582 original size:21 final size:20

Alignment explanation


    Indices: 532--585  Score: 74
    Period size: 21  Copynumber: 2.6  Consensus size: 20

        522 TGTTCTAATT

                                
        532 AAAAA-AGAAGCTGAATGGA
          1 AAAAAGAGAAGCTGAATGGA

                *                 
        551 AAAAGGAAGAAGCTGAATGGAA
          1 AAAAAG-AGAAGCTGAATGG-A

                         
        573 AAAAAGAGAAGCT
          1 AAAAAGAGAAGCT

        586 TTGTTGCAAC


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  19    4  0.13
  21   20  0.67
  22    6  0.20

ACGTcount: A:0.57, C:0.06, G:0.28, T:0.09


Consensus pattern (20 bp):   
AAAAAGAGAAGCTGAATGGA

Found at i:583 original size:24 final size:21

Alignment explanation


    Indices: 536--575  Score: 80
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        526 CTAATTAAAA

                                 
        536 AAGAAGCTGAATGGAAAAAGG
          1 AAGAAGCTGAATGGAAAAAGG

                               
        557 AAGAAGCTGAATGGAAAAA
          1 AAGAAGCTGAATGGAAAAA

        576 AAGAGAAGCT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.55, C:0.05, G:0.30, T:0.10


Consensus pattern (21 bp):   
AAGAAGCTGAATGGAAAAAGG
Done.