Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001658.1 Corchorus olitorius cultivar O-4 contig01658, 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, 611

Length: 1019
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30


Found at i:747 original size:50 final size:50

Alignment explanation


    Indices: 672--807  Score: 218
    Period size: 50  Copynumber: 2.7  Consensus size: 50

        662 TATTTTCCAA

                                                  *           
        672 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACAT
          1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT

                                                              
        722 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
          1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT

            *          *        **              
        772 GGGCTTTTCCATAAGCCACAGTTCGTTTCCATACGA
          1 AGGCTTTTCCACAAGCCA-AACTCGTTTCCATACGA

        808 TACATTACCA


Statistics
Matches: 80,  Mismatches: 5, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
  50   65  0.81
  51   15  0.19

ACGTcount: A:0.29, C:0.28, G:0.15, T:0.29


Consensus pattern (50 bp):   
AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT

Found at i:874 original size:35 final size:35

Alignment explanation


    Indices: 824--1019  Score: 333
    Period size: 35  Copynumber: 5.6  Consensus size: 35

        814 ACCATCTTCT

                *                              *
        824 CAGACGACTCGGTGTAGCATCTTCAAAGTT-ATATT
          1 CAGATGACTCGGTGTAGCATCTTCAAAGTTGA-ATC

                      *                        
        859 CAGATGACTCAGTGTAGCATCTTCAAAGTTGAATC
          1 CAGATGACTCGGTGTAGCATCTTCAAAGTTGAATC

                                               
        894 CAGATGACTCGGTGTAGCATCTTCAAAGTTGAA-C
          1 CAGATGACTCGGTGTAGCATCTTCAAAGTTGAATC

                                                
        928 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAATC
          1 -CAGATGACTCGGTGTAGCATCTTCAAAGTTGAATC

                                               
        964 CAGATGACTCGGTGTAGCATCTTCAAAGTTGAATC
          1 CAGATGACTCGGTGTAGCATCTTCAAAGTTGAATC

                                 
        999 CAGATGACTCGGTGTAGCATC
          1 CAGATGACTCGGTGTAGCATC


Statistics
Matches: 154,  Mismatches: 4, Indels: 6
        0.94            0.02        0.04

Matches are distributed among these distances:
  34    1  0.01
  35  151  0.98
  36    2  0.01

ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29


Consensus pattern (35 bp):   
CAGATGACTCGGTGTAGCATCTTCAAAGTTGAATC

Done.