Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015856.1 Corchorus capsularis cultivar CVL-1 contig15877, 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: 6127
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33


Found at i:847 original size:25 final size:25

Alignment explanation


    Indices: 819--890  Score: 63
    Period size: 25  Copynumber: 3.2  Consensus size: 25

        809 CAAGCATAGC

                                     
        819 ACATGGGCGCCCAGCGCTAGTCGAG
          1 ACATGGGCGCCCAGCGCTAGTCGAG

                              *       
        844 ACAT--GC-CACCA--GCAAG-C---
          1 ACATGGGCGC-CCAGCGCTAGTCGAG

                                     
        861 ACATGGGCGCCCAGCGCTAGTCGAG
          1 ACATGGGCGCCCAGCGCTAGTCGAG

                 
        886 ACATG
          1 ACATG

        891 CCACCAGCAA


Statistics
Matches: 35,  Mismatches: 2, Indels: 20
        0.61            0.04        0.35

Matches are distributed among these distances:
  17    4  0.11
  19    5  0.14
  20    2  0.06
  21    8  0.23
  22    2  0.06
  23    5  0.14
  25    9  0.26

ACGTcount: A:0.25, C:0.33, G:0.31, T:0.11


Consensus pattern (25 bp):   
ACATGGGCGCCCAGCGCTAGTCGAG

Found at i:862 original size:42 final size:42

Alignment explanation


    Indices: 811--910  Score: 191
    Period size: 42  Copynumber: 2.4  Consensus size: 42

        801 TGGGGCGCCA

                                                       
        811 AGCATAGCACATGGGCGCCCAGCGCTAGTCGAGACATGCCACC
          1 AGCA-AGCACATGGGCGCCCAGCGCTAGTCGAGACATGCCACC

                                                      
        854 AGCAAGCACATGGGCGCCCAGCGCTAGTCGAGACATGCCACC
          1 AGCAAGCACATGGGCGCCCAGCGCTAGTCGAGACATGCCACC

                           
        896 AGCAAGCACATGGGC
          1 AGCAAGCACATGGGC

        911 ACTGGCGACA


Statistics
Matches: 57,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  42   53  0.93
  43    4  0.07

ACGTcount: A:0.27, C:0.34, G:0.29, T:0.10


Consensus pattern (42 bp):   
AGCAAGCACATGGGCGCCCAGCGCTAGTCGAGACATGCCACC
Done.