Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_09088

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, 318

Length: 531
ACGTcount: A:0.31, C:0.18, G:0.32, T:0.19


Found at i:421 original size:9 final size:9

Alignment explanation


    Indices: 403--440  Score: 58
    Period size: 9  Copynumber: 4.2  Consensus size: 9

        393 TGGCACTGGA

                 *   
        403 GACGAGGAT
          1 GACGACGAT

                 *   
        412 GACGATGAT
          1 GACGACGAT

                     
        421 GACGACGAT
          1 GACGACGAT

                     
        430 GACGACGAT
          1 GACGACGAT

              
        439 GA
          1 GA

        441 TGAGGGTGAG


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   9   27  1.00

ACGTcount: A:0.34, C:0.16, G:0.37, T:0.13


Consensus pattern (9 bp):   
GACGACGAT

Found at i:457 original size:6 final size:6

Alignment explanation


    Indices: 448--497  Score: 55
    Period size: 6  Copynumber: 8.3  Consensus size: 6

        438 TGATGAGGGT

                               *   *             *  *      *       
        448 GAGGAA GAGGAA GAGGAG GAAGAA GAGGAA GAAGAT GAGGAG GAGGAA
          1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA

              
        496 GA
          1 GA

        498 AGAACTTCAG


Statistics
Matches: 35,  Mismatches: 9, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
   6   35  1.00

ACGTcount: A:0.48, C:0.00, G:0.50, T:0.02


Consensus pattern (6 bp):   
GAGGAA

Found at i:468 original size:9 final size:9

Alignment explanation


    Indices: 451--500  Score: 64
    Period size: 9  Copynumber: 5.6  Consensus size: 9

        441 TGAGGGTGAG

                     
        451 GAAGAGGAA
          1 GAAGAGGAA

              *      
        460 GAGGAGGAA
          1 GAAGAGGAA

                     
        469 GAAGAGGAA
          1 GAAGAGGAA

                 *  *
        478 GAAGATGAG
          1 GAAGAGGAA

              *      
        487 GAGGAGGAA
          1 GAAGAGGAA

                 
        496 GAAGA
          1 GAAGA

        501 ACTTCAGCCC


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

Matches are distributed among these distances:
   9   33  1.00

ACGTcount: A:0.50, C:0.00, G:0.48, T:0.02


Consensus pattern (9 bp):   
GAAGAGGAA

Found at i:493 original size:18 final size:18

Alignment explanation


    Indices: 447--500  Score: 72
    Period size: 18  Copynumber: 3.0  Consensus size: 18

        437 ATGATGAGGG

                           *  
        447 TGAGGAAGAGGAAGAGGA
          1 TGAGGAAGAGGAAGAAGA

            *  *              
        465 GGAAGAAGAGGAAGAAGA
          1 TGAGGAAGAGGAAGAAGA

                  *           
        483 TGAGGAGGAGGAAGAAGA
          1 TGAGGAAGAGGAAGAAGA

        501 ACTTCAGCCC


Statistics
Matches: 30,  Mismatches: 6, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  18   30  1.00

ACGTcount: A:0.48, C:0.00, G:0.48, T:0.04


Consensus pattern (18 bp):   
TGAGGAAGAGGAAGAAGA
Done.