Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009232.1 Corchorus capsularis cultivar CVL-1 contig09253, 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: 2922
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27


Found at i:369 original size:6 final size:6

Alignment explanation


    Indices: 358--412  Score: 67
    Period size: 6  Copynumber: 9.2  Consensus size: 6

        348 CGTGTAAGGA

                                     *      *    *                  
        358 GGAGGT GGAGGT GGAGGT GGAGTT GGAGCT GGGGGT GG-GAGT GGAGGT
          1 GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAG-GT GGAGGT

                    
        406 GGAGGT G
          1 GGAGGT G

        413 ACACTGCAAG


Statistics
Matches: 43,  Mismatches: 4, Indels: 4
        0.84            0.08        0.08

Matches are distributed among these distances:
   5    1  0.02
   6   41  0.95
   7    1  0.02

ACGTcount: A:0.15, C:0.02, G:0.65, T:0.18


Consensus pattern (6 bp):   
GGAGGT

Found at i:468 original size:9 final size:9

Alignment explanation


    Indices: 454--485  Score: 55
    Period size: 9  Copynumber: 3.6  Consensus size: 9

        444 TCCAAAGATT

                     
        454 GGAGGGGGA
          1 GGAGGGGGA

                     
        463 GGAGGGGGA
          1 GGAGGGGGA

                 *   
        472 GGAGGAGGA
          1 GGAGGGGGA

                 
        481 GGAGG
          1 GGAGG

        486 TATTGGTCGT


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   9   22  1.00

ACGTcount: A:0.25, C:0.00, G:0.75, T:0.00


Consensus pattern (9 bp):   
GGAGGGGGA

Found at i:2891 original size:2 final size:2

Alignment explanation


    Indices: 2884--2922  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       2874 TAATAAGGGG

                                                                      
       2884 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

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


Consensus pattern (2 bp):   
GA

Done.