Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007164.1 Corchorus olitorius cultivar O-4 contig07189, 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, 756

Length: 1261
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36


Found at i:857 original size:22 final size:22

Alignment explanation


    Indices: 787--891  Score: 92
    Period size: 22  Copynumber: 4.8  Consensus size: 22

        777 GCAAATCTCA

                                  *
        787 GATTATCAAAATTT-ATAA-GAA
          1 GATTATCAAAATTTCATAATG-C

                          *   *  *
        808 GATTATCAAAATTTTATAGTGT
          1 GATTATCAAAATTTCATAATGC

            *                     
        830 TATTATCAAAATTTCA-AA-GC
          1 GATTATCAAAATTTCATAATGC

                           *       *
        850 GAGGTTATCAAAATTACATAATGT
          1 GA--TTATCAAAATTTCATAATGC

                              
        874 GATTATCAAAATTTCATA
          1 GATTATCAAAATTTCATA

        892 GAAGGGTCAA


Statistics
Matches: 68,  Mismatches: 10, Indels: 11
        0.76            0.11        0.12

Matches are distributed among these distances:
  20    2  0.03
  21   15  0.22
  22   45  0.66
  23    3  0.04
  24    3  0.04

ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37


Consensus pattern (22 bp):   
GATTATCAAAATTTCATAATGC

Found at i:879 original size:44 final size:44

Alignment explanation


    Indices: 787--895  Score: 134
    Period size: 44  Copynumber: 2.5  Consensus size: 44

        777 GCAAATCTCA

                                               **   *   
        787 GATTATCAAAATTT-ATAAGAAGATTATCAAAATTTTATAGTGT
          1 GATTATCAAAATTTCATAAGAAGATTATCAAAATTACATAATGT

            *                    *  *                    
        830 TATTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGT
          1 GATTATCAAAATTTCATAAG-AAGATTATCAAAATTACATAATGT

                                   
        874 GATTATCAAAATTTCAT-AGAAG
          1 GATTATCAAAATTTCATAAGAAG

        896 GGTCAACAAA


Statistics
Matches: 55,  Mismatches: 8, Indels: 6
        0.80            0.12        0.09

Matches are distributed among these distances:
  43   18  0.33
  44   37  0.67

ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36


Consensus pattern (44 bp):   
GATTATCAAAATTTCATAAGAAGATTATCAAAATTACATAATGT

Found at i:906 original size:44 final size:44

Alignment explanation


    Indices: 787--908  Score: 124
    Period size: 44  Copynumber: 2.8  Consensus size: 44

        777 GCAAATCTCA

                                    *           **   *   
        787 GATTATCAAAATTT-ATAAGAA-GATTATCAAAATTTTATAGTGT
          1 GATTATCAAAATTTCAT-AGAAGGGTTATCAAAATTACATAATGT

            *               *   *                        
        830 TATTATCAAAATTTCAAAG-CGAGGTTATCAAAATTACATAATGT
          1 GATTATCAAAATTTCATAGAAG-GGTTATCAAAATTACATAATGT

                                     * *       
        874 GATTATCAAAATTTCATAGAAGGGTCAACAAAATT
          1 GATTATCAAAATTTCATAGAAGGGTTATCAAAATT

        909 TTATAGAGAG


Statistics
Matches: 63,  Mismatches: 12, Indels: 7
        0.77            0.15        0.09

Matches are distributed among these distances:
  43   15  0.24
  44   47  0.75
  45    1  0.02

ACGTcount: A:0.44, C:0.09, G:0.12, T:0.34


Consensus pattern (44 bp):   
GATTATCAAAATTTCATAGAAGGGTTATCAAAATTACATAATGT
Done.