Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_16968

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: 4362
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.25


Found at i:416 original size:18 final size:18

Alignment explanation


    Indices: 389--430  Score: 75
    Period size: 18  Copynumber: 2.3  Consensus size: 18

        379 GATGTGCAGA

                 *            
        389 GAAAGGTGGGTAAGATGG
          1 GAAAGCTGGGTAAGATGG

                              
        407 GAAAGCTGGGTAAGATGG
          1 GAAAGCTGGGTAAGATGG

                  
        425 GAAAGC
          1 GAAAGC

        431 GTAAGCGTGG


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  18   23  1.00

ACGTcount: A:0.36, C:0.05, G:0.45, T:0.14


Consensus pattern (18 bp):   
GAAAGCTGGGTAAGATGG

Found at i:584 original size:99 final size:99

Alignment explanation


    Indices: 413--604  Score: 366
    Period size: 99  Copynumber: 1.9  Consensus size: 99

        403 ATGGGAAAGC

                            *                           *                    
        413 TGGGTAAGATGGGAAAGCGTAAGCGTGGGAGACCGCCCAAGTTGGTGGATAAGGGGAATGATCAG
          1 TGGGTAAGATGGGAAAACGTAAGCGTGGGAGACCGCCCAAGTTGCTGGATAAGGGGAATGATCAG

                                              
        478 TCTCATAGTGAAGTGAAGGATGTGCAGAGTAAGG
         66 TCTCATAGTGAAGTGAAGGATGTGCAGAGTAAGG

                                                                             
        512 TGGGTAAGATGGGAAAACGTAAGCGTGGGAGACCGCCCAAGTTGCTGGATAAGGGGAATGATCAG
          1 TGGGTAAGATGGGAAAACGTAAGCGTGGGAGACCGCCCAAGTTGCTGGATAAGGGGAATGATCAG

                                        
        577 TCTCATAGTGAAGTGAAGGATGTGCAGA
         66 TCTCATAGTGAAGTGAAGGATGTGCAGA

        605 TGAAGGATGT


Statistics
Matches: 91,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  99   91  1.00

ACGTcount: A:0.31, C:0.12, G:0.38, T:0.19


Consensus pattern (99 bp):   
TGGGTAAGATGGGAAAACGTAAGCGTGGGAGACCGCCCAAGTTGCTGGATAAGGGGAATGATCAG
TCTCATAGTGAAGTGAAGGATGTGCAGAGTAAGG

Found at i:625 original size:15 final size:15

Alignment explanation


    Indices: 590--619  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

        580 CATAGTGAAG

                           
        590 TGAAGGATGTGCAGA
          1 TGAAGGATGTGCAGA

                           
        605 TGAAGGATGTGCAGA
          1 TGAAGGATGTGCAGA

        620 GTAAGGTGGG


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.33, C:0.07, G:0.40, T:0.20


Consensus pattern (15 bp):   
TGAAGGATGTGCAGA
Done.