Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_03990

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: 3141
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26


Found at i:551 original size:54 final size:54

Alignment explanation


    Indices: 465--570  Score: 176
    Period size: 54  Copynumber: 2.0  Consensus size: 54

        455 ATGAAGAAAC

                   *                            *                 
        465 TGGACGTTTCCAAGAATCCCAGTTCAACGAAACTCCGTTTCAGGAGATCAACGG
          1 TGGACGTGTCCAAGAATCCCAGTTCAACGAAACTCCATTTCAGGAGATCAACGG

                                     * *                        
        519 TGGACGTGTCCAAGAATCCCAGTTCCAGGAAACTCCATTTCAGGAGATCAAC
          1 TGGACGTGTCCAAGAATCCCAGTTCAACGAAACTCCATTTCAGGAGATCAAC

        571 AACGTCAACA


Statistics
Matches: 48,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  54   48  1.00

ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22


Consensus pattern (54 bp):   
TGGACGTGTCCAAGAATCCCAGTTCAACGAAACTCCATTTCAGGAGATCAACGG

Found at i:616 original size:3 final size:3

Alignment explanation


    Indices: 603--632  Score: 53
    Period size: 3  Copynumber: 10.3  Consensus size: 3

        593 AGATCAAGGT

                                                     
        603 AGA AGA A-A AGA AGA AGA AGA AGA AGA AGA A
          1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A

        633 TGAACCAGAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   2    2  0.08
   3   24  0.92

ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00


Consensus pattern (3 bp):   
AGA

Found at i:674 original size:36 final size:36

Alignment explanation


    Indices: 634--703  Score: 122
    Period size: 36  Copynumber: 1.9  Consensus size: 36

        624 GAAGAAGAAT

                                   *            
        634 GAACCAGAAGTGAGGACTTTTCATTCTATAGGGAAA
          1 GAACCAGAAGTGAGGACTTTTCACTCTATAGGGAAA

                                       *      
        670 GAACCAGAAGTGAGGACTTTTCACTCTGTAGGGA
          1 GAACCAGAAGTGAGGACTTTTCACTCTATAGGGA

        704 CTGGAACTGG


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  36   32  1.00

ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24


Consensus pattern (36 bp):   
GAACCAGAAGTGAGGACTTTTCACTCTATAGGGAAA
Done.