Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015020.1 Corchorus capsularis cultivar CVL-1 contig15041, 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: 14311
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33


Found at i:2735 original size:2 final size:2

Alignment explanation


    Indices: 2728--2758  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       2718 ATGATTTGAA

                                                          
       2728 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A

       2759 AATGGAGAGG


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

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


Consensus pattern (2 bp):   
AG

Found at i:4486 original size:3 final size:3

Alignment explanation


    Indices: 4478--4544  Score: 127
    Period size: 3  Copynumber: 22.7  Consensus size: 3

       4468 TTCCTAGTAG

                                                                           
       4478 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
          1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA

                                      
       4526 GAA GAA GAA GAA G-A GAA GA
          1 GAA GAA GAA GAA GAA GAA GA

       4545 TGAATAATAT


Statistics
Matches: 63,  Mismatches: 0, Indels: 2
        0.97            0.00        0.03

Matches are distributed among these distances:
   2    2  0.03
   3   61  0.97

ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00


Consensus pattern (3 bp):   
GAA

Found at i:12389 original size:17 final size:17

Alignment explanation


    Indices: 12343--12397  Score: 65
    Period size: 17  Copynumber: 3.2  Consensus size: 17

      12333 AACCCATGTA

                 *      *    
      12343 ATCTTTGATCACCAGTG
          1 ATCTTAGATCACTAGTG

                  *      *   
      12360 ATCTTACATCACTGGTG
          1 ATCTTAGATCACTAGTG

                          *  
      12377 ATCTTAGATCACTATTG
          1 ATCTTAGATCACTAGTG

                
      12394 ATCT
          1 ATCT

      12398 AGGGGGTGAT


Statistics
Matches: 31,  Mismatches: 7, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  17   31  1.00

ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38


Consensus pattern (17 bp):   
ATCTTAGATCACTAGTG
Done.