Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_26930

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: 1722
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26


Found at i:360 original size:6 final size:6

Alignment explanation


    Indices: 322--373  Score: 50
    Period size: 6  Copynumber: 8.7  Consensus size: 6

        312 TATCCAAAAG

                     *      *      *    * *                  *     
        322 GATAAA GACAAA GACAAA GAAAAA AACAAA GATAAA GATAAA AATAAA
          1 GATAAA GATAAA GATAAA GATAAA GATAAA GATAAA GATAAA GATAAA

                
        370 GATA
          1 GATA

        374 GAGAGGTTGA


Statistics
Matches: 38,  Mismatches: 8, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
   6   38  1.00

ACGTcount: A:0.71, C:0.06, G:0.13, T:0.10


Consensus pattern (6 bp):   
GATAAA

Found at i:372 original size:18 final size:18

Alignment explanation


    Indices: 329--373  Score: 63
    Period size: 18  Copynumber: 2.5  Consensus size: 18

        319 AAGGATAAAG

                   *          
        329 ACAAAGACAAAGAAAAAA
          1 ACAAAGATAAAGAAAAAA

                         *    
        347 ACAAAGATAAAGATAAAA
          1 ACAAAGATAAAGAAAAAA

             *       
        365 ATAAAGATA
          1 ACAAAGATA

        374 GAGAGGTTGA


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   24  1.00

ACGTcount: A:0.73, C:0.07, G:0.11, T:0.09


Consensus pattern (18 bp):   
ACAAAGATAAAGAAAAAA
Done.