Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016111.1 Corchorus capsularis cultivar CVL-1 contig16132, 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: 21741
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33


Found at i:751 original size:16 final size:15

Alignment explanation


    Indices: 732--780  Score: 50
    Period size: 16  Copynumber: 3.3  Consensus size: 15

        722 CACAAACAAG

                            
        732 AAAACGCAACTTCCAT
          1 AAAAC-CAACTTCCAT

                            
        748 AAAACCAAAC--CC-T
          1 AAAACC-AACTTCCAT

               *           
        761 AAACCCAACTTCCAT
          1 AAAACCAACTTCCAT

                 
        776 AAAAC
          1 AAAAC

        781 AGTCGAATCT


Statistics
Matches: 27,  Mismatches: 2, Indels: 9
        0.71            0.05        0.24

Matches are distributed among these distances:
  12    3  0.11
  13    6  0.22
  14    4  0.15
  15    6  0.22
  16    8  0.30

ACGTcount: A:0.49, C:0.35, G:0.02, T:0.14


Consensus pattern (15 bp):   
AAAACCAACTTCCAT

Found at i:923 original size:30 final size:30

Alignment explanation


    Indices: 889--951  Score: 108
    Period size: 30  Copynumber: 2.1  Consensus size: 30

        879 TCGGTAAGAA

                              *           
        889 AAACGACAGAGGAAACGATGACAACGCTTC
          1 AAACGACAGAGGAAACGACGACAACGCTTC

                 *                        
        919 AAACGGCAGAGGAAACGACGACAACGCTTC
          1 AAACGACAGAGGAAACGACGACAACGCTTC

               
        949 AAA
          1 AAA

        952 TCTAGTCCAC


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  30   31  1.00

ACGTcount: A:0.44, C:0.24, G:0.24, T:0.08


Consensus pattern (30 bp):   
AAACGACAGAGGAAACGACGACAACGCTTC

Found at i:13985 original size:2 final size:2

Alignment explanation


    Indices: 13978--14009  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      13968 CATACTTTCG

                                                           
      13978 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      14010 AATTTTCATA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:21681 original size:2 final size:2

Alignment explanation


    Indices: 21674--21741  Score: 136
    Period size: 2  Copynumber: 34.0  Consensus size: 2

      21664 GACCAAGTTA

                                                                          
      21674 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

                                                  
      21716 AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG


Statistics
Matches: 66,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   66  1.00

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


Consensus pattern (2 bp):   
AG

Done.