Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_05796

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: 1767
ACGTcount: A:0.39, C:0.11, G:0.29, T:0.21


Found at i:1121 original size:6 final size:6

Alignment explanation


    Indices: 1110--1166  Score: 78
    Period size: 6  Copynumber: 9.5  Consensus size: 6

       1100 AGGATGATGT

                                          *               *      * 
       1110 TGAAGA TGAAGA TGAAGA TGAAGA TGGAGA TGAAGA TGAAAA TGAAAA
          1 TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA

            *         
       1158 AGAAGA TGA
          1 TGAAGA TGA

       1167 TGGTGATGGT


Statistics
Matches: 45,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   6   45  1.00

ACGTcount: A:0.53, C:0.00, G:0.32, T:0.16


Consensus pattern (6 bp):   
TGAAGA

Found at i:1246 original size:24 final size:24

Alignment explanation


    Indices: 1219--1266  Score: 62
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       1209 TGATGATAAT

                                     
       1219 GAAGAAGATGAC-GAGGAAAGTAAG
          1 GAAGAAGA-GACTGAGGAAAGTAAG

                 *            *     
       1243 GAAGAGGAGACTGAGGAAGGTAAG
          1 GAAGAAGAGACTGAGGAAAGTAAG

       1267 CGGAAGAGGA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  23    3  0.14
  24   18  0.86

ACGTcount: A:0.46, C:0.04, G:0.42, T:0.08


Consensus pattern (24 bp):   
GAAGAAGAGACTGAGGAAAGTAAG
Done.