Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001043.1 Corchorus capsularis cultivar CVL-1 contig01043, 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: 2687
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39


Found at i:2571 original size:55 final size:54

Alignment explanation


    Indices: 2488--2619  Score: 160
    Period size: 55  Copynumber: 2.4  Consensus size: 54

       2478 TCTAGACGAA

                  *                 *        *      *          *  
       2488 AATTATATTATTTTTAT-ATTATATTACAAATTTATATGTGATTTATTATATTT
          1 AATTATTTTATTTTTATGATTATACTACAAATTAATATGTAATTTATTATACTT

                                                                    
       2541 AATT-TTTTATTTTTATGATTTATGACTACAAATTAATATGTAATTTATTATACTT
          1 AATTATTTTATTTTTATGA-TTAT-ACTACAAATTAATATGTAATTTATTATACTT

             *       *              
       2596 ATTTATTTTTTTTTTATGAATTAT
          1 AATTATTTTATTTTTATG-ATTAT

       2620 TAACACACGT


Statistics
Matches: 67,  Mismatches: 7, Indels: 7
        0.83            0.09        0.09

Matches are distributed among these distances:
  52   11  0.16
  53    5  0.07
  54    4  0.06
  55   30  0.45
  56   16  0.24
  57    1  0.01

ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59


Consensus pattern (54 bp):   
AATTATTTTATTTTTATGATTATACTACAAATTAATATGTAATTTATTATACTT

Found at i:2659 original size:2 final size:2

Alignment explanation


    Indices: 2652--2687  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       2642 CATTAGCTAG

                                                                 
       2652 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

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


Consensus pattern (2 bp):   
TA

Done.