Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001319.1 Corchorus capsularis cultivar CVL-1 contig01319, 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: 8774
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:142 original size:2 final size:2

Alignment explanation


    Indices: 135--163  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

        125 CAAAAGGAAT

                                                       
        135 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

        164 GAGTTGTGAC


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:3598 original size:6 final size:6

Alignment explanation


    Indices: 3587--3614  Score: 56
    Period size: 6  Copynumber: 4.7  Consensus size: 6

       3577 CTGCTATTTT

                                            
       3587 TTAATA TTAATA TTAATA TTAATA TTAA
          1 TTAATA TTAATA TTAATA TTAATA TTAA

       3615 CCTGACATGA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   22  1.00

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


Consensus pattern (6 bp):   
TTAATA

Found at i:8713 original size:2 final size:2

Alignment explanation


    Indices: 8700--8774  Score: 141
    Period size: 2  Copynumber: 37.5  Consensus size: 2

       8690 GGTCGAGTGT

                   *                                                      
       8700 GA GA GC GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA

                                                             
       8742 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 G


Statistics
Matches: 71,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
   2   71  1.00

ACGTcount: A:0.48, C:0.01, G:0.51, T:0.00


Consensus pattern (2 bp):   
GA

Done.