Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_19157

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, 780

Length: 1301
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.24


Found at i:134 original size:21 final size:21

Alignment explanation


    Indices: 110--151  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        100 AAGGACTTGG

                                 
        110 GGAGAAAAAGGAAGAAGAAGA
          1 GGAGAAAAAGGAAGAAGAAGA

                *  *    *        
        131 GGAGCAAGAGGAGGAAGAAGA
          1 GGAGAAAAAGGAAGAAGAAGA

        152 TGATGATGAT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.55, C:0.02, G:0.43, T:0.00


Consensus pattern (21 bp):   
GGAGAAAAAGGAAGAAGAAGA

Found at i:174 original size:3 final size:3

Alignment explanation


    Indices: 168--215  Score: 62
    Period size: 3  Copynumber: 16.0  Consensus size: 3

        158 TGATGAGGAT

                                      *                               * 
        168 GAA GAA GAA GAA GAA GAA GAG GAA GAA GAA GAA GGAA -AA GAA GGA
          1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA GAA GAA

               
        213 GAA
          1 GAA

        216 AATGGGGAAA


Statistics
Matches: 39,  Mismatches: 4, Indels: 4
        0.83            0.09        0.09

Matches are distributed among these distances:
   2    2  0.05
   3   34  0.87
   4    3  0.08

ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00


Consensus pattern (3 bp):   
GAA

Done.