Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009639.1 Corchorus olitorius cultivar O-4 contig09671, 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: 4024
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.31


Found at i:1985 original size:11 final size:11

Alignment explanation


    Indices: 1958--2001  Score: 54
    Period size: 11  Copynumber: 4.0  Consensus size: 11

       1948 TAATATATAA

                       
       1958 TATAAACGAAC
          1 TATAAACGAAC

                     * 
       1969 -ATAAACGAGC
          1 TATAAACGAAC

                     * 
       1979 TATAAACGATC
          1 TATAAACGAAC

                        
       1990 TATTAAACGAAC
          1 TA-TAAACGAAC

       2002 ATTAATCGAG


Statistics
Matches: 28,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  10    9  0.32
  11   11  0.39
  12    8  0.29

ACGTcount: A:0.50, C:0.18, G:0.11, T:0.20


Consensus pattern (11 bp):   
TATAAACGAAC

Found at i:3719 original size:85 final size:86

Alignment explanation


    Indices: 3619--3794  Score: 237
    Period size: 86  Copynumber: 2.1  Consensus size: 86

       3609 GATGCACATA

                     *               **    *                                 
       3619 AAAACAAATTCTTAAATCCAATGTGGTTG-AGATTTGATTAGATGAATAAAGATATTTCAAAGAG
          1 AAAACAAATCCTTAAATCCAATGTGACTGAAAATTTGATTAGATGAATAAAGATATTTCAAAGAG

            *      *             
       3683 TCTCAGCGCCAAAAATCATGC
         66 GCTCAGCACCAAAAATCATGC

                              *                  *           *           *   
       3704 AAAACAAATCCTTAAATCTAATGTGACTGAAAATTTGGTTAGATGAATATAGATATTTCAAGGAG
          1 AAAACAAATCCTTAAATCCAATGTGACTGAAAATTTGATTAGATGAATAAAGATATTTCAAAGAG

               **                
       3769 GCTTGGCACCAAAAATCATGC
         66 GCTCAGCACCAAAAATCATGC

                 
       3790 AAAAC
          1 AAAAC

       3795 TGAGCCGGGC


Statistics
Matches: 78,  Mismatches: 12, Indels: 1
        0.86            0.13        0.01

Matches are distributed among these distances:
  85   25  0.32
  86   53  0.68

ACGTcount: A:0.42, C:0.14, G:0.16, T:0.27


Consensus pattern (86 bp):   
AAAACAAATCCTTAAATCCAATGTGACTGAAAATTTGATTAGATGAATAAAGATATTTCAAAGAG
GCTCAGCACCAAAAATCATGC

Done.