Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004840.1 Corchorus capsularis cultivar CVL-1 contig04858, 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: 6415
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34


Found at i:232 original size:109 final size:109

Alignment explanation


    Indices: 104--378  Score: 428
    Period size: 109  Copynumber: 2.5  Consensus size: 109

         94 AAAAAAATTA

                                                                             
        104 TATAAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
          1 TATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG

                                 *                       
        167 AAAAAATTTTAATATATCCAATTTTTTTGGTAAAAATAAAGTAAT
         65 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT

                                                                             
        212 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
          1 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA

                      *                                 
        277 AAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGTAAT
         66 AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT

                     *                     *      *     *             
        321 TATAAAGATGTTAGATTTAATTTAATTGAATAAAAATATAGTTTCTAGTAGAATAAAA
          1 TATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTAGTAGAATAAAA

        379 CTATAATAGT


Statistics
Matches: 154,  Mismatches: 6, Indels: 8
        0.92            0.04        0.05

Matches are distributed among these distances:
 108    6  0.04
 109  117  0.76
 110    3  0.02
 111    1  0.01
 114   27  0.18

ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39


Consensus pattern (109 bp):   
TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT

Found at i:693 original size:3 final size:3

Alignment explanation


    Indices: 681--724  Score: 79
    Period size: 3  Copynumber: 14.7  Consensus size: 3

        671 CATCATCATC

                  *                                                   
        681 ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT

        725 ATATGTTCTC


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   3   39  1.00

ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64


Consensus pattern (3 bp):   
ATT

Found at i:5689 original size:2 final size:2

Alignment explanation


    Indices: 5682--5712  Score: 53
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       5672 GGTGTATCAA

                                                         
       5682 AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT

       5713 TATTTTTAAC


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   2   26  0.93
   3    2  0.07

ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.