Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013612.1 Corchorus olitorius cultivar O-4 contig13645, 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: 14258
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:86 original size:31 final size:31

Alignment explanation


    Indices: 48--108  Score: 113
    Period size: 31  Copynumber: 2.0  Consensus size: 31

         38 TATTTTGACA

                                           
         48 TATTGTAAATTTAAATTTACAAACCTTGAAG
          1 TATTGTAAATTTAAATTTACAAACCTTGAAG

                        *                 
         79 TATTGTAAATTTTAATTTACAAACCTTGAA
          1 TATTGTAAATTTAAATTTACAAACCTTGAA

        109 TTTCAATATA


Statistics
Matches: 29,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  31   29  1.00

ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41


Consensus pattern (31 bp):   
TATTGTAAATTTAAATTTACAAACCTTGAAG

Found at i:848 original size:24 final size:24

Alignment explanation


    Indices: 821--886  Score: 71
    Period size: 24  Copynumber: 2.7  Consensus size: 24

        811 TGAAAATTGG

                              *     
        821 AAGCCCAAAATAATTAAATTTTAA
          1 AAGCCCAAAATAATTAAAATTTAA

                          **          
        845 AAGCCCAAAAGTAAAAAGAAATTTAA
          1 AAGCCCAAAA-TAATTA-AAATTTAA

             *               
        871 ATG-CCAAAATAATTAA
          1 AAGCCCAAAATAATTAA

        887 GAAGCCCAAA


Statistics
Matches: 34,  Mismatches: 6, Indels: 5
        0.76            0.13        0.11

Matches are distributed among these distances:
  23    1  0.03
  24   14  0.41
  25   10  0.29
  26    9  0.26

ACGTcount: A:0.58, C:0.12, G:0.08, T:0.23


Consensus pattern (24 bp):   
AAGCCCAAAATAATTAAAATTTAA

Found at i:888 original size:25 final size:26

Alignment explanation


    Indices: 821--889  Score: 74
    Period size: 25  Copynumber: 2.8  Consensus size: 26

        811 TGAAAATTGG

                                *     
        821 AAGCCCAAAATAATT-A-AATTTTAA
          1 AAGCCCAAAATAATTAAGAAATTTAA

                           *           
        845 AAGCCCAAAAGTAA-AAAGAAATTTAA
          1 AAGCCCAAAA-TAATTAAGAAATTTAA

             *                  
        871 ATG-CCAAAATAATTAAGAA
          1 AAGCCCAAAATAATTAAGAA

        890 GCCCAAAGTT


Statistics
Matches: 37,  Mismatches: 4, Indels: 7
        0.77            0.08        0.15

Matches are distributed among these distances:
  24   13  0.35
  25   15  0.41
  26    9  0.24

ACGTcount: A:0.58, C:0.12, G:0.09, T:0.22


Consensus pattern (26 bp):   
AAGCCCAAAATAATTAAGAAATTTAA
Done.