Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008948.1 Corchorus olitorius cultivar O-4 contig08975, 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: 2283
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33


Found at i:765 original size:65 final size:65

Alignment explanation


    Indices: 695--888  Score: 180
    Period size: 65  Copynumber: 3.1  Consensus size: 65

        685 ATAATTATAA

                                                                             
        695 AAATATTGAATTTAATTCAATAAAAATAGAATTTTTAGTAGAATAAAACTATATATTAAAATTTT
          1 AAATATTGAATTTAATTCAATAAAAATAGAATTTTTAGTAGAATAAAACTATATATTAAAATTTT

                     *                     *      ** *             *        *
        760 AAATATATCCAAGTTT--TT-AATGAAAAATGGTAA--AATGGTA-AA-AATAA-AATA-ATTAT
          1 AAATAT-T-GAA-TTTAATTCAAT-AAAAATAG-AATTTTTAGTAGAATAA-AACTATATATTAA

                  
        816 AA----
         60 AATTTT

                                                                             
        818 AAATATTGAATTTAATTCAATAAAAATAGAATTTTTAGTAGAATAAAACTATATATTAAAATTTT
          1 AAATATTGAATTTAATTCAATAAAAATAGAATTTTTAGTAGAATAAAACTATATATTAAAATTTT

                  
        883 AAATAT
          1 AAATAT

        889 ATCCAAGTTT


Statistics
Matches: 96,  Mismatches: 14, Indels: 38
        0.65            0.09        0.26

Matches are distributed among these distances:
  55    3  0.03
  56    4  0.04
  57   10  0.10
  58   13  0.14
  59    4  0.04
  60    5  0.05
  61    6  0.06
  62    6  0.06
  63    5  0.05
  64    4  0.04
  65   19  0.20
  66   10  0.10
  67    4  0.04
  68    3  0.03

ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37


Consensus pattern (65 bp):   
AAATATTGAATTTAATTCAATAAAAATAGAATTTTTAGTAGAATAAAACTATATATTAAAATTTT

Found at i:802 original size:123 final size:123

Alignment explanation


    Indices: 667--954  Score: 576
    Period size: 123  Copynumber: 2.3  Consensus size: 123

        657 CCTTTTAAAT

                                                                             
        667 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTCAATAAAAATAGAATTTTTA
          1 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTCAATAAAAATAGAATTTTTA

                                                                      
        732 GTAGAATAAAACTATATATTAAAATTTTAAATATATCCAAGTTTTTAATGAAAAATGG
         66 GTAGAATAAAACTATATATTAAAATTTTAAATATATCCAAGTTTTTAATGAAAAATGG

                                                                             
        790 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTCAATAAAAATAGAATTTTTA
          1 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTCAATAAAAATAGAATTTTTA

                                                                      
        855 GTAGAATAAAACTATATATTAAAATTTTAAATATATCCAAGTTTTTAATGAAAAATGG
         66 GTAGAATAAAACTATATATTAAAATTTTAAATATATCCAAGTTTTTAATGAAAAATGG

                                                      
        913 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTA
          1 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTA

        955 TCCGACTTTA


Statistics
Matches: 165,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
 123  165  1.00

ACGTcount: A:0.54, C:0.03, G:0.08, T:0.35


Consensus pattern (123 bp):   
TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTCAATAAAAATAGAATTTTTA
GTAGAATAAAACTATATATTAAAATTTTAAATATATCCAAGTTTTTAATGAAAAATGG
Done.