Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008300.1 Corchorus capsularis cultivar CVL-1 contig08321, 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: 18826
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30


Found at i:15750 original size:2 final size:2

Alignment explanation


    Indices: 15745--15788  Score: 63
    Period size: 2  Copynumber: 22.0  Consensus size: 2

      15735 AAAATTAATA

                              *                                            
      15745 AT AT AT AT AT AT GT AT A- AT AT CAT 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 AT AT AT AT AT AT

              
      15787 AT
          1 AT

      15789 GTAGCACAAG


Statistics
Matches: 38,  Mismatches: 2, Indels: 4
        0.86            0.05        0.09

Matches are distributed among these distances:
   1    1  0.03
   2   35  0.92
   3    2  0.05

ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:15930 original size:12 final size:12

Alignment explanation


    Indices: 15913--15949  Score: 65
    Period size: 12  Copynumber: 3.1  Consensus size: 12

      15903 TTTCAACTTG

                        
      15913 ACTGGAAAATTA
          1 ACTGGAAAATTA

                       *
      15925 ACTGGAAAATTG
          1 ACTGGAAAATTA

                        
      15937 ACTGGAAAATTA
          1 ACTGGAAAATTA

             
      15949 A
          1 A

      15950 AGCAGTGGTA


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  12   23  1.00

ACGTcount: A:0.49, C:0.08, G:0.19, T:0.24


Consensus pattern (12 bp):   
ACTGGAAAATTA

Found at i:17835 original size:12 final size:12

Alignment explanation


    Indices: 17818--17842  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      17808 ACCAGACCAT

                        
      17818 TTGGATTCATAA
          1 TTGGATTCATAA

                        
      17830 TTGGATTCATAA
          1 TTGGATTCATAA

             
      17842 T
          1 T

      17843 AACATCAACA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44


Consensus pattern (12 bp):   
TTGGATTCATAA
Done.