Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007245.1 Corchorus olitorius cultivar O-4 contig07270, 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: 3001
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37


Found at i:16 original size:2 final size:2

Alignment explanation


    Indices: 10--65  Score: 112
    Period size: 2  Copynumber: 28.0  Consensus size: 2

          1 TCTACTTCA

                                                                          
         10 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                                
         52 TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC

         66 GTTCTCTTTT


Statistics
Matches: 54,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   54  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
TC

Found at i:760 original size:43 final size:43

Alignment explanation


    Indices: 699--789  Score: 173
    Period size: 43  Copynumber: 2.1  Consensus size: 43

        689 AGATGCTTAG

                        *                              
        699 TTATAGTCCAATTGAAATGATTAATATATATTAAAACAACATA
          1 TTATAGTCCAATGGAAATGATTAATATATATTAAAACAACATA

                                                       
        742 TTATAGTCCAATGGAAATGATTAATATATATTAAAACAACATA
          1 TTATAGTCCAATGGAAATGATTAATATATATTAAAACAACATA

                 
        785 TTATA
          1 TTATA

        790 TGTTTATACG


Statistics
Matches: 47,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  43   47  1.00

ACGTcount: A:0.48, C:0.09, G:0.08, T:0.35


Consensus pattern (43 bp):   
TTATAGTCCAATGGAAATGATTAATATATATTAAAACAACATA

Found at i:2292 original size:2 final size:2

Alignment explanation


    Indices: 2285--2336  Score: 77
    Period size: 2  Copynumber: 26.0  Consensus size: 2

       2275 TCAAATTTGG

                           *     *                 *                      
       2285 TA TA TA TA TA CA TA CA TA TA TA TA TA CA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                          
       2327 TA TA TA TA TA
          1 TA TA TA TA TA

       2337 CACTAGTAAT


Statistics
Matches: 44,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   2   44  1.00

ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44


Consensus pattern (2 bp):   
TA

Done.