Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021987.1 Corchorus olitorius cultivar O-4 contig22020, whole genome shotgun sequence

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: 16111
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:13218 original size:15 final size:13

Alignment explanation


    Indices: 13189--13236  Score: 51
    Period size: 13  Copynumber: 3.5  Consensus size: 13

      13179 TACTCTGGGG

                     **  
      13189 TCTCTCTCTTCAC
          1 TCTCTCTCTAAAC

                           
      13202 TCTCTCTCTAAGAAC
          1 TCTCTCTCT-A-AAC

                  *      
      13217 TCTCTCCCTAAAC
          1 TCTCTCTCTAAAC

                   
      13230 TCTCTCT
          1 TCTCTCT

      13237 TCCCTGAAGA


Statistics
Matches: 29,  Mismatches: 4, Indels: 4
        0.78            0.11        0.11

Matches are distributed among these distances:
  13   18  0.62
  14    1  0.03
  15   10  0.34

ACGTcount: A:0.17, C:0.42, G:0.02, T:0.40


Consensus pattern (13 bp):   
TCTCTCTCTAAAC

Found at i:15034 original size:38 final size:38

Alignment explanation


    Indices: 14987--15093  Score: 162
    Period size: 39  Copynumber: 2.8  Consensus size: 38

      14977 ATGTTTTTAA

                                                  
      14987 TTAAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGT
          1 TTAAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGT

               *         *                         
      15025 TTAGGTAATTCCAGAAGAAGATTTTGGAAAAATAAAAGT
          1 TTAAGTAATTCCAAAAGAAGATTTTGG-AAAATAAAAGT

                      *                    
      15064 TTAAG-ATATCCCAAAAGAAGATTTTGGAAA
          1 TTAAGTA-ATTCCAAAAGAAGATTTTGGAAA

      15094 TTAATAAAAT


Statistics
Matches: 62,  Mismatches: 5, Indels: 4
        0.87            0.07        0.06

Matches are distributed among these distances:
  38   29  0.47
  39   33  0.53

ACGTcount: A:0.48, C:0.07, G:0.18, T:0.28


Consensus pattern (38 bp):   
TTAAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGT

Done.