Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014639.1 Corchorus capsularis cultivar CVL-1 contig14660, 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: 33940
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33


Found at i:977 original size:22 final size:22

Alignment explanation


    Indices: 952--996  Score: 90
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        942 GATGAAGGAT

                                  
        952 GATCAAGGAAGAGCGACTGAAA
          1 GATCAAGGAAGAGCGACTGAAA

                                  
        974 GATCAAGGAAGAGCGACTGAAA
          1 GATCAAGGAAGAGCGACTGAAA

             
        996 G
          1 G

        997 TATGAGACAG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.44, C:0.13, G:0.33, T:0.09


Consensus pattern (22 bp):   
GATCAAGGAAGAGCGACTGAAA

Found at i:11729 original size:18 final size:18

Alignment explanation


    Indices: 11708--11743  Score: 63
    Period size: 18  Copynumber: 2.0  Consensus size: 18

      11698 ATCTCTATAT

                 *            
      11708 CCAAATATAAACTACCTA
          1 CCAAACATAAACTACCTA

                              
      11726 CCAAACATAAACTACCTA
          1 CCAAACATAAACTACCTA

      11744 ACTAACAAAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19


Consensus pattern (18 bp):   
CCAAACATAAACTACCTA

Found at i:11750 original size:18 final size:18

Alignment explanation


    Indices: 11709--11750  Score: 57
    Period size: 18  Copynumber: 2.3  Consensus size: 18

      11699 TCTCTATATC

                *            *
      11709 CAAATATAAACTACCTAC
          1 CAAACATAAACTACCTAA

                              
      11727 CAAACATAAACTACCTAA
          1 CAAACATAAACTACCTAA

             *    
      11745 CTAACA
          1 CAAACA

      11751 AATAAACAAA


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19


Consensus pattern (18 bp):   
CAAACATAAACTACCTAA

Found at i:18454 original size:11 final size:11

Alignment explanation


    Indices: 18411--18448  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

      18401 TTCCTATATA

                *      
      18411 AAATAAATTAT
          1 AAATTAATTAT

                        
      18422 CAAA-TAATTAT
          1 -AAATTAATTAT

                       
      18433 AAATTAATTAT
          1 AAATTAATTAT

                 
      18444 AAATT
          1 AAATT

      18449 TGTTATGAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  10    3  0.12
  11   18  0.75
  12    3  0.12

ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39


Consensus pattern (11 bp):   
AAATTAATTAT

Found at i:32591 original size:2 final size:2

Alignment explanation


    Indices: 32586--32615  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      32576 TAAAACAAAA

                                                        
      32586 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      32616 GTGTGTGTGT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Done.