Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021661.1 Corchorus olitorius cultivar O-4 contig21694, 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: 6033
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33


Found at i:982 original size:19 final size:18

Alignment explanation


    Indices: 949--984  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

        939 TTGAAATAAA

                    *         
        949 TCTTCAATGGTCTTCAAG
          1 TCTTCAATAGTCTTCAAG

                              
        967 TCTTCAATTAGTCTTCAA
          1 TCTTCAA-TAGTCTTCAA

        985 ACACGAATTT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42


Consensus pattern (18 bp):   
TCTTCAATAGTCTTCAAG

Found at i:3897 original size:11 final size:12

Alignment explanation


    Indices: 3838--3898  Score: 61
    Period size: 12  Copynumber: 5.1  Consensus size: 12

       3828 GCGCGGCCCA

                     *  
       3838 AGCGCTTGGCCC
          1 AGCGCTTGGGCC

                  **     
       3850 AGGCGCGCGGGCC
          1 A-GCGCTTGGGCC

                     *  
       3863 AGCGCTTGGCCC
          1 AGCGCTTGGGCC

                 *      
       3875 AGCGCCTGGGCC
          1 AGCGCTTGGGCC

                        
       3887 AG-GCTTGGGCC
          1 AGCGCTTGGGCC

             
       3898 A
          1 A

       3899 CAAGCCCAAA


Statistics
Matches: 39,  Mismatches: 9, Indels: 3
        0.76            0.18        0.06

Matches are distributed among these distances:
  11    9  0.23
  12   21  0.54
  13    9  0.23

ACGTcount: A:0.10, C:0.38, G:0.41, T:0.11


Consensus pattern (12 bp):   
AGCGCTTGGGCC

Found at i:3897 original size:24 final size:25

Alignment explanation


    Indices: 3828--3894  Score: 86
    Period size: 25  Copynumber: 2.7  Consensus size: 25

       3818 GGCCAGCAAG

                  *                   
       3828 GCGCGGCCCAAGCGCTTGGCCCAGGC
          1 GCGCGGGCC-AGCGCTTGGCCCAGGC

                                     
       3854 GCGCGGGCCAGCGCTTGGCCCA-GC
          1 GCGCGGGCCAGCGCTTGGCCCAGGC

                               
       3878 GC-CTGGGCCAG-GCTTGG
          1 GCGC-GGGCCAGCGCTTGG

       3895 GCCACAAGCC


Statistics
Matches: 39,  Mismatches: 1, Indels: 5
        0.87            0.02        0.11

Matches are distributed among these distances:
  23    7  0.18
  24   11  0.28
  25   13  0.33
  26    8  0.21

ACGTcount: A:0.09, C:0.39, G:0.42, T:0.10


Consensus pattern (25 bp):   
GCGCGGGCCAGCGCTTGGCCCAGGC
Done.