Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002294.1 Corchorus capsularis cultivar CVL-1 contig02300, 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, 676

Length: 1127
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31


Found at i:106 original size:27 final size:27

Alignment explanation


    Indices: 21--99  Score: 140
    Period size: 27  Copynumber: 2.9  Consensus size: 27

         11 GGAATCGAGC

                              *        
         21 AAAGATAGTGATAGAAATGCCAATAGA
          1 AAAGATAGTGATAGAAATACCAATAGA

                                       
         48 AAAGATAGTGATAGAAATACCAATAGA
          1 AAAGATAGTGATAGAAATACCAATAGA

                         *           
         75 AAAGATAGTGATAAAAATACCAATA
          1 AAAGATAGTGATAGAAATACCAATA

        100 ACGAAGAAAA


Statistics
Matches: 50,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27   50  1.00

ACGTcount: A:0.56, C:0.08, G:0.18, T:0.19


Consensus pattern (27 bp):   
AAAGATAGTGATAGAAATACCAATAGA

Found at i:404 original size:18 final size:18

Alignment explanation


    Indices: 381--472  Score: 70
    Period size: 18  Copynumber: 5.4  Consensus size: 18

        371 TTTCGACGAA

                              
        381 AATGATTTAGAAAGTTCT
          1 AATGATTTAGAAAGTTCT

                    *   *   **
        399 AATGATTTCG-ACG--AA
          1 AATGATTTAGAAAGTTCT

                              
        414 AATGATTTAGAAAGTTCT
          1 AATGATTTAGAAAGTTCT

                    *      ***
        432 AATGATTTCG--A-TGAA
          1 AATGATTTAGAAAGTTCT

                              
        447 AATGATTTAGAAAGTTCT
          1 AATGATTTAGAAAGTTCT

                    
        465 AATGATTT
          1 AATGATTT

        473 CGACGAAAAT


Statistics
Matches: 52,  Mismatches: 16, Indels: 12
        0.65            0.20        0.15

Matches are distributed among these distances:
  15   19  0.37
  16    3  0.06
  17    3  0.06
  18   27  0.52

ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37


Consensus pattern (18 bp):   
AATGATTTAGAAAGTTCT

Found at i:407 original size:33 final size:33

Alignment explanation


    Indices: 365--483  Score: 229
    Period size: 33  Copynumber: 3.6  Consensus size: 33

        355 GTTCTAATGA

                                             
        365 TAATGATTTCGACGAAAATGATTTAGAAAGTTC
          1 TAATGATTTCGACGAAAATGATTTAGAAAGTTC

                                             
        398 TAATGATTTCGACGAAAATGATTTAGAAAGTTC
          1 TAATGATTTCGACGAAAATGATTTAGAAAGTTC

                        *                    
        431 TAATGATTTCGATGAAAATGATTTAGAAAGTTC
          1 TAATGATTTCGACGAAAATGATTTAGAAAGTTC

                                
        464 TAATGATTTCGACGAAAATG
          1 TAATGATTTCGACGAAAATG

        484 GTAATGATTT


Statistics
Matches: 84,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  33   84  1.00

ACGTcount: A:0.39, C:0.08, G:0.18, T:0.34


Consensus pattern (33 bp):   
TAATGATTTCGACGAAAATGATTTAGAAAGTTC
Done.