Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_14516

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: 2094
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27


Found at i:277 original size:21 final size:21

Alignment explanation


    Indices: 251--290  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        241 GATGGTGATA

                                  
        251 AAAAG-AGTAAAAAGAAGAAAG
          1 AAAAGAAG-AAAAAGAAGAAAG

                      *        
        272 AAAAGAAGAATAAGAAGAA
          1 AAAAGAAGAAAAAGAAGAA

        291 TAAGAAGGAG


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  21   15  0.88
  22    2  0.12

ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05


Consensus pattern (21 bp):   
AAAAGAAGAAAAAGAAGAAAG

Found at i:311 original size:21 final size:21

Alignment explanation


    Indices: 287--335  Score: 64
    Period size: 21  Copynumber: 2.3  Consensus size: 21

        277 AAGAATAAGA

                *                 
        287 AGAATAAGAAGGAG-AAAAAAG
          1 AGAAAAAGAA-GAGCAAAAAAG

                                 
        308 AGAAAAAGAAGAGCAAAAAAG
          1 AGAAAAAGAAGAGCAAAAAAG

             *     
        329 AAAAAAA
          1 AGAAAAA

        336 ATACGATGAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  20    3  0.12
  21   22  0.88

ACGTcount: A:0.73, C:0.02, G:0.22, T:0.02


Consensus pattern (21 bp):   
AGAAAAAGAAGAGCAAAAAAG

Found at i:335 original size:30 final size:31

Alignment explanation


    Indices: 260--336  Score: 75
    Period size: 30  Copynumber: 2.5  Consensus size: 31

        250 AAAAAGAGTA

                       *          *        *
        260 AAAAGAAGAAAGAAAAGAAGAATAAGAAGAAT
          1 AAAA-AAGAAAAAAAAGAAGAAAAAGAAGAAC

              *  *  *                    * 
        292 AAGAAGGAGAAAAAAG-AGAAAAAGAAGAGC
          1 AAAAAAGAAAAAAAAGAAGAAAAAGAAGAAC

                           
        322 AAAAAAGAAAAAAAA
          1 AAAAAAGAAAAAAAA

        337 TACGATGAAA


Statistics
Matches: 35,  Mismatches: 10, Indels: 2
        0.74            0.21        0.04

Matches are distributed among these distances:
  30   23  0.66
  31    9  0.26
  32    3  0.09

ACGTcount: A:0.74, C:0.01, G:0.22, T:0.03


Consensus pattern (31 bp):   
AAAAAAGAAAAAAAAGAAGAAAAAGAAGAAC
Done.