Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022205.1 Corchorus olitorius cultivar O-4 contig22238, 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: 3089
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32


Found at i:262 original size:21 final size:21

Alignment explanation


    Indices: 238--350  Score: 158
    Period size: 21  Copynumber: 5.4  Consensus size: 21

        228 CTTAGGCATT

                         *       
        238 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
        259 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *          * 
        280 TCCAATGAACTTGGAACCTGC
          1 TCCAATGAGCTTGGAACCTTC

                                  
        301 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                                  
        322 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
        343 TCCAATGA
          1 TCCAATGA

        351 ACTTCTAGCA


Statistics
Matches: 85,  Mismatches: 6, Indels: 2
        0.91            0.06        0.02

Matches are distributed among these distances:
  20    2  0.02
  21   83  0.98

ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:2841 original size:21 final size:21

Alignment explanation


    Indices: 2815--2857  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2805 CTTGCCCTTG

                   *  *          
       2815 TCAATGGGCCTAATGGCATCT
          1 TCAATGGACCAAATGGCATCT

                    *            
       2836 TCAATGGATCAAATGGCATCT
          1 TCAATGGACCAAATGGCATCT

             
       2857 T
          1 T

       2858 AGGCAACTCC


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30


Consensus pattern (21 bp):   
TCAATGGACCAAATGGCATCT
Done.