Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_04152

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: 3105
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29


Found at i:194 original size:6 final size:6

Alignment explanation


    Indices: 186--295  Score: 51
    Period size: 6  Copynumber: 17.8  Consensus size: 6

        176 AGACTGAGCC

                 *                                 * *   **     **  
        186 TGAAGC TGAAGA TGAAGA TGAA-A GTGAAGA TGAGGT TGGGGA TGGGGA
          1 TGAAGA TGAAGA TGAAGA TGAAGA -TGAAGA TGAAGA TGAAGA TGAAGA

                               *    *      *      *      *      *     
        234 TGAAGA TGAGGATGA TGGAGA AGAAGA CGAAGA AGAAGA AGAAGA CGAAGA
          1 TGAAGA TGA--A-GA TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA

            *           
        285 CGAAGA TGAAG
          1 TGAAGA TGAAG

        296 CCGACGCCGA


Statistics
Matches: 85,  Mismatches: 14, Indels: 10
        0.78            0.13        0.09

Matches are distributed among these distances:
   5    1  0.01
   6   77  0.91
   7    2  0.02
   8    1  0.01
   9    4  0.05

ACGTcount: A:0.44, C:0.04, G:0.40, T:0.13


Consensus pattern (6 bp):   
TGAAGA

Found at i:258 original size:3 final size:3

Alignment explanation


    Indices: 252--295  Score: 52
    Period size: 3  Copynumber: 14.7  Consensus size: 3

        242 AGGATGATGG

                        *                       *       *       *     
        252 AGA AGA AGA CGA AGA AGA AGA AGA AGA CGA AGA CGA AGA TGA AG
          1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG

        296 CCGACGCCGA


Statistics
Matches: 33,  Mismatches: 8, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
   3   33  1.00

ACGTcount: A:0.57, C:0.07, G:0.34, T:0.02


Consensus pattern (3 bp):   
AGA

Found at i:267 original size:12 final size:12

Alignment explanation


    Indices: 252--295  Score: 61
    Period size: 12  Copynumber: 3.7  Consensus size: 12

        242 AGGATGATGG

                        
        252 AGAAGAAGACGA
          1 AGAAGAAGACGA

                     *  
        264 AGAAGAAGAAGA
          1 AGAAGAAGACGA

               *        
        276 AGACGAAGACGA
          1 AGAAGAAGACGA

               *    
        288 AGATGAAG
          1 AGAAGAAG

        296 CCGACGCCGA


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  12   28  1.00

ACGTcount: A:0.57, C:0.07, G:0.34, T:0.02


Consensus pattern (12 bp):   
AGAAGAAGACGA
Done.