Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001215.1 Corchorus olitorius cultivar O-4 contig01215, 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, 633

Length: 1056
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33


Found at i:277 original size:42 final size:42

Alignment explanation


    Indices: 218--298  Score: 144
    Period size: 42  Copynumber: 1.9  Consensus size: 42

        208 GCTAAGTCTT

                                                      
        218 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
          1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA

                     *                     *       
        260 GAAAATTCTTTGTAAATTAAGAAATACTCAATTCAAATC
          1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC

        299 CTGATCCTTA


Statistics
Matches: 37,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  42   37  1.00

ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31


Consensus pattern (42 bp):   
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA

Found at i:876 original size:29 final size:31

Alignment explanation


    Indices: 836--915  Score: 94
    Period size: 31  Copynumber: 2.6  Consensus size: 31

        826 CCTCCCGAAT

                               *  *        
        836 AGGTTTAGGCTCAATTTGGTGCTGA-GT-AA
          1 AGGTTTAGGCTCAATTTGGAGCAGACGTGAA

                          *                 
        865 AGGTTTAGGCTCAAATT-GAGCAGATCGTGAA
          1 AGGTTTAGGCTCAATTTGGAGCAGA-CGTGAA

                      *         
        896 AGGTTTAGGCCCAATTTGGA
          1 AGGTTTAGGCTCAATTTGGA

        916 TATTTAGCCT


Statistics
Matches: 42,  Mismatches: 5, Indels: 5
        0.81            0.10        0.10

Matches are distributed among these distances:
  28    5  0.12
  29   16  0.38
  30    2  0.05
  31   17  0.40
  32    2  0.05

ACGTcount: A:0.28, C:0.12, G:0.30, T:0.30


Consensus pattern (31 bp):   
AGGTTTAGGCTCAATTTGGAGCAGACGTGAA
Done.