Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019922.1 Corchorus olitorius cultivar O-4 contig19955, 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: 4836
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32


Found at i:2688 original size:11 final size:11

Alignment explanation


    Indices: 2672--2745  Score: 69
    Period size: 11  Copynumber: 6.3  Consensus size: 11

       2662 GCCCAAGCCT

                       
       2672 GCGCTGGCCCA
          1 GCGCTGGCCCA

                    *  
       2683 GCGCTGGCAC-
          1 GCGCTGGCCCA

                        
       2693 GCGTCTGGCCCA
          1 GCG-CTGGCCCA

                          
       2705 GGCGCTGGCCCGCA
          1 -GCGCTGG-CC-CA

                        
       2719 GCGTCTGGCCCA
          1 GCG-CTGGCCCA

                      * 
       2731 GGCGCTGGCCTA
          1 -GCGCTGGCCCA

               
       2743 GCG
          1 GCG

       2746 TCTAGGCCGC


Statistics
Matches: 53,  Mismatches: 3, Indels: 14
        0.76            0.04        0.20

Matches are distributed among these distances:
  10    3  0.06
  11   18  0.34
  12   13  0.25
  13   13  0.25
  14    6  0.11

ACGTcount: A:0.08, C:0.41, G:0.39, T:0.12


Consensus pattern (11 bp):   
GCGCTGGCCCA

Found at i:2728 original size:14 final size:14

Alignment explanation


    Indices: 2693--2740  Score: 52
    Period size: 13  Copynumber: 3.7  Consensus size: 14

       2683 GCGCTGGCAC

                          
       2693 GCGTCTGG-CCCAG
          1 GCGTCTGGCCCCAG

                           
       2706 GCG-CTGGCCCGCA-
          1 GCGTCTGGCCC-CAG

                          
       2719 GCGTCTGG-CCCAG
          1 GCGTCTGGCCCCAG

                      
       2732 GCG-CTGGCC
          1 GCGTCTGGCC

       2741 TAGCGTCTAG


Statistics
Matches: 30,  Mismatches: 0, Indels: 10
        0.75            0.00        0.25

Matches are distributed among these distances:
  12   10  0.33
  13   14  0.47
  14    6  0.20

ACGTcount: A:0.06, C:0.42, G:0.40, T:0.12


Consensus pattern (14 bp):   
GCGTCTGGCCCCAG
Done.