Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_07476

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, 419

Length: 699
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29


Found at i:62 original size:15 final size:16

Alignment explanation


    Indices: 42--71  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

         32 AATCACTGAG

                            
         42 TCAGTT-CATAGAAAC
          1 TCAGTTCCATAGAAAC

                           
         57 TCAGTTCCATAGAAA
          1 TCAGTTCCATAGAAA

         72 GCTGACTCAG


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    6  0.43
  16    8  0.57

ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27


Consensus pattern (16 bp):   
TCAGTTCCATAGAAAC

Found at i:524 original size:51 final size:51

Alignment explanation


    Indices: 469--575  Score: 171
    Period size: 51  Copynumber: 2.1  Consensus size: 51

        459 ACCTTTTGTT

                                        *                       
        469 GAAGACAATGAAGAAAGTG-AAACTTATGAACCAGAAGAAGAAGAAGAAGAA
          1 GAAGACAATGAAGAAAGTGAAAAC-TATCAACCAGAAGAAGAAGAAGAAGAA

                 * *                                           
        520 GAAGATATTGAAGAAAGTGAAAACTATCAACCAGAAGAAGAAGAAGAAGAA
          1 GAAGACAATGAAGAAAGTGAAAACTATCAACCAGAAGAAGAAGAAGAAGAA

                 
        571 GAAGA
          1 GAAGA

        576 AGAATTAATG


Statistics
Matches: 52,  Mismatches: 3, Indels: 2
        0.91            0.05        0.04

Matches are distributed among these distances:
  51   48  0.92
  52    4  0.08

ACGTcount: A:0.57, C:0.07, G:0.25, T:0.10


Consensus pattern (51 bp):   
GAAGACAATGAAGAAAGTGAAAACTATCAACCAGAAGAAGAAGAAGAAGAA

Found at i:560 original size:3 final size:3

Alignment explanation


    Indices: 552--579  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

        542 ACTATCAACC

                                                 
        552 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
          1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A

        580 TTAATGGAAG


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00


Consensus pattern (3 bp):   
AGA

Done.