Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005546.1 Corchorus olitorius cultivar O-4 contig05570, 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, 731

Length: 1219
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26


Found at i:198 original size:6 final size:6

Alignment explanation


    Indices: 187--217  Score: 62
    Period size: 6  Copynumber: 5.2  Consensus size: 6

        177 TTAAGCATTC

                                                
        187 GTGTTG GTGTTG GTGTTG GTGTTG GTGTTG G
          1 GTGTTG GTGTTG GTGTTG GTGTTG GTGTTG G

        218 CGAGGCGGCG


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   25  1.00

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


Consensus pattern (6 bp):   
GTGTTG

Found at i:701 original size:9 final size:8

Alignment explanation


    Indices: 678--707  Score: 51
    Period size: 8  Copynumber: 3.6  Consensus size: 8

        668 TCGCCTAACA

                    
        678 CTTCCAGG
          1 CTTCCAGG

                    
        686 CTTCCAGG
          1 CTTCCAGG

                     
        694 CATTCCAGG
          1 C-TTCCAGG

                 
        703 CTTCC
          1 CTTCC

        708 GGGCAGAAAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
   8   13  0.62
   9    8  0.38

ACGTcount: A:0.13, C:0.40, G:0.20, T:0.27


Consensus pattern (8 bp):   
CTTCCAGG

Found at i:701 original size:17 final size:17

Alignment explanation


    Indices: 679--712  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

        669 CGCCTAACAC

                             
        679 TTCCAGGCTTCCAGGCA
          1 TTCCAGGCTTCCAGGCA

                        *    
        696 TTCCAGGCTTCCGGGCA
          1 TTCCAGGCTTCCAGGCA

        713 GAAAGTTTTG


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.15, C:0.35, G:0.26, T:0.24


Consensus pattern (17 bp):   
TTCCAGGCTTCCAGGCA
Done.