Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009742.1 Corchorus olitorius cultivar O-4 contig09774, 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: 2166
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30


Found at i:1899 original size:21 final size:21

Alignment explanation


    Indices: 1875--1990  Score: 173
    Period size: 21  Copynumber: 5.6  Consensus size: 21

       1865 CTTAGGCAAT

                    *    *       
       1875 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAACTTGGAACCTTC

                    *            
       1896 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAACTTGGAACCTTC

                                 
       1917 TCCAATGAACTTGGAA-CTTC
          1 TCCAATGAACTTGGAACCTTC

                                 
       1937 TCCAATGAACTTGGAACCTTC
          1 TCCAATGAACTTGGAACCTTC

                    *             
       1958 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAACTTGGAACCTT-C

                        
       1979 TCCAATGAACTT
          1 TCCAATGAACTT

       1991 CTAGCATCTT


Statistics
Matches: 88,  Mismatches: 5, Indels: 4
        0.91            0.05        0.04

Matches are distributed among these distances:
  20   23  0.26
  21   65  0.74

ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30


Consensus pattern (21 bp):   
TCCAATGAACTTGGAACCTTC

Found at i:1940 original size:41 final size:41

Alignment explanation


    Indices: 1875--1990  Score: 187
    Period size: 41  Copynumber: 2.8  Consensus size: 41

       1865 CTTAGGCAAT

                         *               *            
       1875 TCCAATGAGCTTGAAACCTTCTCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAA-CTTCTCCAATGAACTTGGAACCTTC

                    *                                
       1917 TCCAATGAACTTGGAACTTCTCCAATGAACTTGGAACCTTC
          1 TCCAATGAGCTTGGAACTTCTCCAATGAACTTGGAACCTTC

                                             
       1958 TCCAATGAGCTTGGAACTTGCTCCAATGAACTT
          1 TCCAATGAGCTTGGAACTT-CTCCAATGAACTT

       1991 CTAGCATCTT


Statistics
Matches: 69,  Mismatches: 4, Indels: 2
        0.92            0.05        0.03

Matches are distributed among these distances:
  41   42  0.61
  42   27  0.39

ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30


Consensus pattern (41 bp):   
TCCAATGAGCTTGGAACTTCTCCAATGAACTTGGAACCTTC
Done.