Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020510.1 Corchorus olitorius cultivar O-4 contig20543, 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: 8312
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:907 original size:25 final size:24

Alignment explanation


    Indices: 868--914  Score: 60
    Period size: 26  Copynumber: 1.9  Consensus size: 24

        858 CTTGAAAATT

                  *                   
        868 TGAAAATCTTTGATGGATGAGATGGA
          1 TGAAAAACTTTGAT-GAT-AGATGGA

                                  
        894 TGAAAAAC-TTGATGATAGATG
          1 TGAAAAACTTTGATGATAGATG

        915 AATAGAAGGA


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  23    5  0.25
  24    3  0.15
  25    5  0.25
  26    7  0.35

ACGTcount: A:0.38, C:0.04, G:0.28, T:0.30


Consensus pattern (24 bp):   
TGAAAAACTTTGATGATAGATGGA

Found at i:1795 original size:21 final size:21

Alignment explanation


    Indices: 1771--1904  Score: 216
    Period size: 21  Copynumber: 6.4  Consensus size: 21

       1761 CTTAGGCAAT

                         *       
       1771 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
       1792 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
       1813 TCCAATGAACTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
       1834 TCCAATGAACTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
       1855 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       1876 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
       1897 TCCAATGA
          1 TCCAATGA

       1905 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:0.28, G:0.16, T:0.29


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Done.