Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_24623

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, 331

Length: 552
ACGTcount: A:0.33, C:0.16, G:0.33, T:0.18


Found at i:405 original size:6 final size:6

Alignment explanation


    Indices: 396--461  Score: 53
    Period size: 6  Copynumber: 10.5  Consensus size: 6

        386 GTGAAGACCC

                                    *   *                *  *          
        396 TGAGGA TGAGGA TGAGGA TGACGA CGAGGA TGACGACGA CGACGA TGATGGA
          1 TGAGGA TGAGGA TGAGGA TGAGGA TGAGGA TGA-G--GA TGAGGA TGA-GGA

                             
        448 -GAGGA TGAGGA TGA
          1 TGAGGA TGAGGA TGA

        462 AGAGGATGTT


Statistics
Matches: 47,  Mismatches: 8, Indels: 10
        0.72            0.12        0.15

Matches are distributed among these distances:
   5    3  0.06
   6   37  0.79
   7    3  0.06
   9    4  0.09

ACGTcount: A:0.33, C:0.09, G:0.44, T:0.14


Consensus pattern (6 bp):   
TGAGGA

Found at i:426 original size:18 final size:18

Alignment explanation


    Indices: 403--445  Score: 59
    Period size: 18  Copynumber: 2.4  Consensus size: 18

        393 CCCTGAGGAT

                    *  *      
        403 GAGGATGAGGATGACGAC
          1 GAGGATGACGACGACGAC

                              
        421 GAGGATGACGACGACGAC
          1 GAGGATGACGACGACGAC

              *    
        439 GATGATG
          1 GAGGATG

        446 GAGAGGATGA


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   22  1.00

ACGTcount: A:0.33, C:0.14, G:0.42, T:0.12


Consensus pattern (18 bp):   
GAGGATGACGACGACGAC

Found at i:501 original size:21 final size:21

Alignment explanation


    Indices: 475--520  Score: 83
    Period size: 21  Copynumber: 2.2  Consensus size: 21

        465 GGATGTTGAA

                                 
        475 GAAGAAGAAAATGAAGATGAG
          1 GAAGAAGAAAATGAAGATGAG

                     *           
        496 GAAGAAGAAGATGAAGATGAG
          1 GAAGAAGAAAATGAAGATGAG

                
        517 GAAG
          1 GAAG

        521 CCCTGCAGCC


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.54, C:0.00, G:0.37, T:0.09


Consensus pattern (21 bp):   
GAAGAAGAAAATGAAGATGAG

Found at i:520 original size:15 final size:15

Alignment explanation


    Indices: 471--512  Score: 50
    Period size: 15  Copynumber: 2.8  Consensus size: 15

        461 AAGAGGATGT

                  *        
        471 TGAAGAAGAAGAAAA
          1 TGAAGATGAAGAAAA

                     *      
        486 TGAAGATGAGGAAGAA
          1 TGAAGATGAAGAA-AA

                        
        502 -GAAGATGAAGA
          1 TGAAGATGAAGA

        513 TGAGGAAGCC


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  15   21  0.91
  16    2  0.09

ACGTcount: A:0.57, C:0.00, G:0.33, T:0.10


Consensus pattern (15 bp):   
TGAAGATGAAGAAAA
Done.