Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016624.1 Corchorus olitorius cultivar O-4 contig16657, 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: 4675
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--41  Score: 57
    Period size: 2  Copynumber: 21.0  Consensus size: 2

                                                    *  *                  
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TC TT TA TA T- 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

         42 AGTCTAAACT


Statistics
Matches: 35,  Mismatches: 3, Indels: 2
        0.88            0.08        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   34  0.97

ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54


Consensus pattern (2 bp):   
TA

Found at i:871 original size:16 final size:16

Alignment explanation


    Indices: 824--865  Score: 66
    Period size: 16  Copynumber: 2.6  Consensus size: 16

        814 TTTATTTTTG

                            
        824 ATTATTATTAATTATA
          1 ATTATTATTAATTATA

                *  *        
        840 ATTAATAATAATTATA
          1 ATTATTATTAATTATA

                      
        856 ATTATTATTA
          1 ATTATTATTA

        866 TATATATTTT


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  16   22  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (16 bp):   
ATTATTATTAATTATA

Found at i:4637 original size:2 final size:2

Alignment explanation


    Indices: 4630--4673  Score: 88
    Period size: 2  Copynumber: 22.0  Consensus size: 2

       4620 TATTTACTAG

                                                                          
       4630 TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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

              
       4672 TA
          1 TA

       4674 AT


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   42  1.00

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


Consensus pattern (2 bp):   
TA

Done.