Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004952.1 Corchorus capsularis cultivar CVL-1 contig04970, 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: 7293
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35


Found at i:5749 original size:2 final size:2

Alignment explanation


    Indices: 5742--5771  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       5732 ACATACATAC

                                                        
       5742 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       5772 GCTAGTTAAT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:6973 original size:6 final size:6

Alignment explanation


    Indices: 6962--7019  Score: 71
    Period size: 6  Copynumber: 9.5  Consensus size: 6

       6952 TTCTTGGTGC

                                            *      *      *      * 
       6962 AAAATA AAAATA AAAATA AAAATA AAAACA AAAACA AAAACA AAAACA
          1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA

                       
       7010 AAAACTA AAA
          1 AAAA-TA AAA

       7020 GCTTACATCC


Statistics
Matches: 49,  Mismatches: 2, Indels: 1
        0.94            0.04        0.02

Matches are distributed among these distances:
   6   45  0.92
   7    4  0.08

ACGTcount: A:0.83, C:0.09, G:0.00, T:0.09


Consensus pattern (6 bp):   
AAAATA

Found at i:6985 original size:18 final size:18

Alignment explanation


    Indices: 6962--7019  Score: 80
    Period size: 18  Copynumber: 3.2  Consensus size: 18

       6952 TTCTTGGTGC

                      *       
       6962 AAAATAAAAATAAAAATA
          1 AAAATAAAAACAAAAATA

                            * 
       6980 AAAATAAAAACAAAAACA
          1 AAAATAAAAACAAAAATA

                *              
       6998 AAAACAAAAACAAAAACTA
          1 AAAATAAAAACAAAAA-TA

               
       7017 AAA
          1 AAA

       7020 GCTTACATCC


Statistics
Matches: 35,  Mismatches: 4, Indels: 1
        0.88            0.10        0.03

Matches are distributed among these distances:
  18   31  0.89
  19    4  0.11

ACGTcount: A:0.83, C:0.09, G:0.00, T:0.09


Consensus pattern (18 bp):   
AAAATAAAAACAAAAATA
Done.