Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_12155

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, 208

Length: 348
ACGTcount: A:0.14, C:0.09, G:0.44, T:0.32


Found at i:306 original size:18 final size:18

Alignment explanation


    Indices: 243--307  Score: 60
    Period size: 18  Copynumber: 3.6  Consensus size: 18

        233 GTGCTGGATT

                     *        
        243 TGGGTTTGGAGCTGGTGG
          1 TGGGTTTGGTGCTGGTGG

                  * *  *      
        261 TGGGTTCGTTGGTGGTGG
          1 TGGGTTTGGTGCTGGTGG

                  *      *     
        279 TGGAG-CTGGTGCCGGTGG
          1 TGG-GTTTGGTGCTGGTGG

                       
        297 TGGGTTTGGTG
          1 TGGGTTTGGTG

        308 GAGGAGCCGG


Statistics
Matches: 35,  Mismatches: 10, Indels: 4
        0.71            0.20        0.08

Matches are distributed among these distances:
  17    1  0.03
  18   33  0.94
  19    1  0.03

ACGTcount: A:0.03, C:0.08, G:0.55, T:0.34


Consensus pattern (18 bp):   
TGGGTTTGGTGCTGGTGG

Found at i:307 original size:30 final size:30

Alignment explanation


    Indices: 273--332  Score: 75
    Period size: 30  Copynumber: 2.0  Consensus size: 30

        263 GGTTCGTTGG

                  *     *  *  *           
        273 TGGTGGTGGAGCTGGTGCCGGTGGTGGGTT
          1 TGGTGGAGGAGCCGGCGCAGGTGGTGGGTT

                             *            
        303 TGGTGGAGGAGCCGGCGGAGGTGGTGGGTT
          1 TGGTGGAGGAGCCGGCGCAGGTGGTGGGTT

        333 AGGAGGTTTC


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

Matches are distributed among these distances:
  30   25  1.00

ACGTcount: A:0.07, C:0.10, G:0.58, T:0.25


Consensus pattern (30 bp):   
TGGTGGAGGAGCCGGCGCAGGTGGTGGGTT
Done.