Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020506.1 Corchorus olitorius cultivar O-4 contig20539, 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: 3300
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30


Found at i:382 original size:21 final size:21

Alignment explanation


    Indices: 358--491  Score: 209
    Period size: 21  Copynumber: 6.4  Consensus size: 21

        348 CTTAGGCAAT

                         *       
        358 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
        379 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
        400 TCCAATGAACTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
        421 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
        442 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                                  
        463 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
        484 TCCAATGA
          1 TCCAATGA

        492 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:0.26, C:0.27, G:0.18, T:0.29


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:2247 original size:21 final size:21

Alignment explanation


    Indices: 2223--2377  Score: 226
    Period size: 21  Copynumber: 7.4  Consensus size: 21

       2213 TGCTAGAAGT

                                  
       2223 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                  
       2244 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                  
       2265 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                *
       2286 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
       2307 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
       2328 TCATTGGAGAAGGTTCCAAGA
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
       2349 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
       2370 TCATTGGA
          1 TCATTGGA

       2378 ATTGCCTAAG


Statistics
Matches: 129,  Mismatches: 4, Indels: 2
        0.96            0.03        0.01

Matches are distributed among these distances:
  20    2  0.02
  21  127  0.98

ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Done.