Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011916.1 Corchorus capsularis cultivar CVL-1 contig11937, 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: 24936
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:13736 original size:24 final size:24

Alignment explanation


    Indices: 13723--13776  Score: 90
    Period size: 24  Copynumber: 2.2  Consensus size: 24

      13713 GCTGCTGAGC

                                    
      13723 CTGAGATTGAGGCTGCTGTAAAGA
          1 CTGAGATTGAGGCTGCTGTAAAGA

                     *             *
      13747 CTGAGATTGTGGCTGCTGTAAAGG
          1 CTGAGATTGAGGCTGCTGTAAAGA

                  
      13771 CTGAGA
          1 CTGAGA

      13777 AGCTGGCCTA


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  24   28  1.00

ACGTcount: A:0.26, C:0.13, G:0.35, T:0.26


Consensus pattern (24 bp):   
CTGAGATTGAGGCTGCTGTAAAGA

Found at i:17512 original size:3 final size:3

Alignment explanation


    Indices: 17504--17540  Score: 56
    Period size: 3  Copynumber: 12.3  Consensus size: 3

      17494 GTTCACCGAT

                                             *   *           
      17504 GGA GGA GGA GGA GGA GGA GGA GGA GCA GAA GGA GGA G
          1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA G

      17541 TCTTACTGAG


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   3   31  1.00

ACGTcount: A:0.35, C:0.03, G:0.62, T:0.00


Consensus pattern (3 bp):   
GGA

Found at i:24202 original size:15 final size:15

Alignment explanation


    Indices: 24181--24230  Score: 66
    Period size: 15  Copynumber: 3.4  Consensus size: 15

      24171 TGTTTGATAA

                           
      24181 ACTGAAAAATTAAGT
          1 ACTGAAAAATTAAGT

            *              
      24196 GCTGAAAAATTAAGT
          1 ACTGAAAAATTAAGT

                   **      
      24211 ACTGAAATTTTAA-T
          1 ACTGAAAAATTAAGT

                  
      24225 ACTGAA
          1 ACTGAA

      24231 TCTCATAAGT


Statistics
Matches: 31,  Mismatches: 4, Indels: 1
        0.86            0.11        0.03

Matches are distributed among these distances:
  14    7  0.23
  15   24  0.77

ACGTcount: A:0.48, C:0.08, G:0.14, T:0.30


Consensus pattern (15 bp):   
ACTGAAAAATTAAGT

Found at i:24514 original size:26 final size:29

Alignment explanation


    Indices: 24459--24515  Score: 82
    Period size: 31  Copynumber: 2.0  Consensus size: 29

      24449 ATTATCAAAT

                                           
      24459 ATAAATATCATATTAAATTTCCCTAAAAAAA
          1 ATAAATATCATATTAAATTT-CCT-AAAAAA

                                        
      24490 ATAAATATCATATTAAA-TT-CTAAAAA
          1 ATAAATATCATATTAAATTTCCTAAAAA

      24516 TAATTTATTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 4
        0.87            0.00        0.13

Matches are distributed among these distances:
  27    5  0.19
  28    2  0.08
  30    2  0.08
  31   17  0.65

ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33


Consensus pattern (29 bp):   
ATAAATATCATATTAAATTTCCTAAAAAA
Done.