Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012111.1 Corchorus capsularis cultivar CVL-1 contig12132, 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: 4172
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:3770 original size:109 final size:108

Alignment explanation


    Indices: 3646--3907  Score: 409
    Period size: 109  Copynumber: 2.4  Consensus size: 108

       3636 AAAATATTGA

                                                                             
       3646 ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATT-GTATATTAGAAAAAATTTTAATA
          1 ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTAGTATATTAGAAAAAATTTTAATA

                                                         
       3710 TATCCAAATTTTTTGGTAAAAATAAAGTAATTATAAAGACATTAG
         66 TATCC-AA-TTTTTGGTAAAAATAAAGTAATTATAAAGACATTAG

                                                                          *  
       3755 ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTAGTATATTAGAAAAAATTTTAGTA
          1 ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTAGTATATTAGAAAAAATTTTAATA

                                                 *     
       3820 TATCCAATTTTTGGTAAAAATAAAGTAATTATAAAGATATTAG
         66 TATCCAATTTTTGGTAAAAATAAAGTAATTATAAAGACATTAG

                             *             *             
       3863 ATTTAATTTAATTGAATAAAAATATGAGTTTCTAGTAGAATAAAA
          1 ATTTAA-TT-A---AATGAAAATA-GAGTTTTTAGTAGAATAAAA

       3908 CTATAATAGT


Statistics
Matches: 142,  Mismatches: 4, Indels: 9
        0.92            0.03        0.06

Matches are distributed among these distances:
 108   41  0.29
 109   45  0.32
 110   28  0.20
 113    9  0.06
 114   19  0.13

ACGTcount: A:0.48, C:0.02, G:0.11, T:0.38


Consensus pattern (108 bp):   
ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTAGTATATTAGAAAAAATTTTAATA
TATCCAATTTTTGGTAAAAATAAAGTAATTATAAAGACATTAG

Found at i:4143 original size:2 final size:2

Alignment explanation


    Indices: 4136--4170  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       4126 ATGTAATGTA

                                                                
       4136 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       4171 AT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.