Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_02754

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, 743

Length: 1239
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26


Found at i:376 original size:3 final size:3

Alignment explanation


    Indices: 370--401  Score: 55
    Period size: 3  Copynumber: 10.7  Consensus size: 3

        360 AAAGAAAACA

                                                *     
        370 CAG CAG CAG CAG CAG CAG CAG CAG CAG GAG CA
          1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA

        402 AGAAAAGAAG


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   27  1.00

ACGTcount: A:0.34, C:0.31, G:0.34, T:0.00


Consensus pattern (3 bp):   
CAG

Found at i:418 original size:9 final size:8

Alignment explanation


    Indices: 401--434  Score: 50
    Period size: 9  Copynumber: 4.0  Consensus size: 8

        391 CAGCAGGAGC

                    
        401 AAGAAAAG
          1 AAGAAAAG

                     
        409 AAGAAGAAG
          1 AAGAA-AAG

                     
        418 AAGAAAAAG
          1 AAG-AAAAG

                    
        427 AAGAAAAG
          1 AAGAAAAG

        435 TAGTAAACTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
   8   10  0.42
   9   12  0.50
  10    2  0.08

ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00


Consensus pattern (8 bp):   
AAGAAAAG
Done.