Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_29258

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, 244

Length: 408
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.20


Found at i:58 original size:21 final size:22

Alignment explanation


    Indices: 32--76  Score: 65
    Period size: 21  Copynumber: 2.1  Consensus size: 22

         22 ATTAGTCAGC

                      *      *    
         32 AAGAAATGAATAA-AAATGAGG
          1 AAGAAATGAAGAAGAAAAGAGG

                                  
         53 AAGAAATGAAGAAGAAAAGAGG
          1 AAGAAATGAAGAAGAAAAGAGG

              
         75 AA
          1 AA

         77 ATTTCAATGA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  21   12  0.57
  22    9  0.43

ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09


Consensus pattern (22 bp):   
AAGAAATGAAGAAGAAAAGAGG

Found at i:61 original size:11 final size:11

Alignment explanation


    Indices: 32--69  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

         22 ATTAGTCAGC

                      *
         32 AAGAAATGAAT
          1 AAGAAATGAAG

                     * 
         43 AA-AAATGAGG
          1 AAGAAATGAAG

                       
         53 AAGAAATGAAG
          1 AAGAAATGAAG

                  
         64 AAGAAA
          1 AAGAAA

         70 AGAGGAAATT


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  10    8  0.35
  11   15  0.65

ACGTcount: A:0.66, C:0.00, G:0.24, T:0.11


Consensus pattern (11 bp):   
AAGAAATGAAG

Found at i:190 original size:3 final size:3

Alignment explanation


    Indices: 184--219  Score: 72
    Period size: 3  Copynumber: 12.0  Consensus size: 3

        174 AGTGGTGGTT

                                                           
        184 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
          1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA

        220 AATATTGAGA


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   33  1.00

ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00


Consensus pattern (3 bp):   
GAA

Done.