Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_28925

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: 1800
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21


Found at i:1289 original size:9 final size:9

Alignment explanation


    Indices: 1275--1313  Score: 51
    Period size: 9  Copynumber: 4.3  Consensus size: 9

       1265 GGGGTGATTT

                     
       1275 GGAGGAAGA
          1 GGAGGAAGA

                  *  
       1284 GGAGGAGGA
          1 GGAGGAAGA

                     
       1293 GGAGGAAGA
          1 GGAGGAAGA

            *  *     
       1302 AGAAGAAGA
          1 GGAGGAAGA

               
       1311 GGA
          1 GGA

       1314 AGAGGAAGAG


Statistics
Matches: 25,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
   9   25  1.00

ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00


Consensus pattern (9 bp):   
GGAGGAAGA

Found at i:1323 original size:6 final size:6

Alignment explanation


    Indices: 1276--1323  Score: 51
    Period size: 6  Copynumber: 7.5  Consensus size: 6

       1266 GGGTGATTTG

                        *      *                                   
       1276 GAGGAA GAGGAG GAGGAG GAGGAA GAAGAAGAA GAGGAA GAGGAA GAG
          1 GAGGAA GAGGAA GAGGAA GAGGAA G-AG--GAA GAGGAA GAGGAA GAG

       1324 CAGATTGAAG


Statistics
Matches: 37,  Mismatches: 2, Indels: 6
        0.82            0.04        0.13

Matches are distributed among these distances:
   6   29  0.78
   7    2  0.05
   8    2  0.05
   9    4  0.11

ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00


Consensus pattern (6 bp):   
GAGGAA
Done.