Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021289.1 Corchorus olitorius cultivar O-4 contig21322, 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: 13609
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:1011 original size:21 final size:21

Alignment explanation


    Indices: 987--1120  Score: 200
    Period size: 21  Copynumber: 6.4  Consensus size: 21

        977 CTTAGGCAAT

                         *       
        987 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
       1008 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
       1029 TCCAATGAACTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
       1050 TCCAATGAACTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       1071 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                                  
       1092 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
       1113 TCCAATGA
          1 TCCAATGA

       1121 ACTTCTAGCA


Statistics
Matches: 108,  Mismatches: 4, Indels: 2
        0.95            0.04        0.02

Matches are distributed among these distances:
  20    3  0.03
  21  105  0.97

ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:3038 original size:21 final size:21

Alignment explanation


    Indices: 3012--3103  Score: 150
    Period size: 21  Copynumber: 4.4  Consensus size: 21

       3002 TGCTAGAAGT

                                  
       3012 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                 
       3033 TCATTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                                *
       3054 TCATTGGAGAAGGTTCCAAGA
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
       3075 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
       3096 TCATTGGA
          1 TCATTGGA

       3104 ATTGTCTAAG


Statistics
Matches: 67,  Mismatches: 3, Indels: 2
        0.93            0.04        0.03

Matches are distributed among these distances:
  20    2  0.03
  21   65  0.97

ACGTcount: A:0.29, C:0.17, G:0.27, T:0.26


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Done.