Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004871.1 Corchorus capsularis cultivar CVL-1 contig04889, 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: 6980
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Found at i:3310 original size:15 final size:15

Alignment explanation


    Indices: 3290--3319  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       3280 TTTTTAAGAT

                           
       3290 AAAGTTTTGAAAAAA
          1 AAAGTTTTGAAAAAA

                    *      
       3305 AAAGTTTTTAAAAAA
          1 AAAGTTTTGAAAAAA

       3320 CATAAAAACA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30


Consensus pattern (15 bp):   
AAAGTTTTGAAAAAA

Found at i:3704 original size:69 final size:70

Alignment explanation


    Indices: 3583--3736  Score: 195
    Period size: 69  Copynumber: 2.2  Consensus size: 70

       3573 TTGTTTAGGT

                                      *           *                 *      * 
       3583 TTTTA-TAGTTTTACTCAACTAAAAATTATATTTTTATTTAATTAAATATAATATATTTATAATT
          1 TTTTACTA-TTTTACTCAACTAAAAACTATATTTTTATATAATTAAATATAATATACTTATAACT

               *  
       3647 ATTTTA
         65 ATTATA

                           *           *                   *      *          
       3653 TTTTACTATTTTACTTAACTAAAAACTCT-TTTTTATATAATTAAATCTAATATCCTTATAACTA
          1 TTTTACTATTTTACTCAACTAAAAACTATATTTTTATATAATTAAATATAATATACTTATAACTA

                 
       3717 TTATA
         66 TTATA

                  *        
       3722 TTTTACCATTTTACT
          1 TTTTACTATTTTACT

       3737 ATTTTAATTA


Statistics
Matches: 73,  Mismatches: 10, Indels: 3
        0.85            0.12        0.03

Matches are distributed among these distances:
  69   48  0.66
  70   23  0.32
  71    2  0.03

ACGTcount: A:0.37, C:0.10, G:0.01, T:0.53


Consensus pattern (70 bp):   
TTTTACTATTTTACTCAACTAAAAACTATATTTTTATATAATTAAATATAATATACTTATAACTA
TTATA
Done.