Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011909.1 Corchorus olitorius cultivar O-4 contig11942, 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: 15174
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34


Found at i:3870 original size:89 final size:90

Alignment explanation


    Indices: 3734--3912  Score: 335
    Period size: 89  Copynumber: 2.0  Consensus size: 90

       3724 ACATAATGAA

                                                                             
       3734 GAGGTGCATAGGATGCAAATAATATAATTAAATTAGTCATTATAAGATTTTT-TTAAACATGTGT
          1 GAGGTGCATAGGATGCAAATAATATAATTAAATTAGTCATTATAAGATTTTTCTT-AACATGTGT

                                      
       3798 ATGGTTCTACTAATTTATTCGAACCT
         65 ATGGTTCTACTAATTTATTCGAACCT

                                                                             
       3824 GAGGTGCATAGGATGCAAA-AATATAATTAAATTAGTCATTATAAGATTTTTCTTAACATGTGTA
          1 GAGGTGCATAGGATGCAAATAATATAATTAAATTAGTCATTATAAGATTTTTCTTAACATGTGTA

                                     
       3888 TGGTTCTACTAATTTATTCGAACCT
         66 TGGTTCTACTAATTTATTCGAACCT

       3913 ATTAACATGA


Statistics
Matches: 88,  Mismatches: 0, Indels: 3
        0.97            0.00        0.03

Matches are distributed among these distances:
  89   67  0.76
  90   21  0.24

ACGTcount: A:0.35, C:0.11, G:0.16, T:0.39


Consensus pattern (90 bp):   
GAGGTGCATAGGATGCAAATAATATAATTAAATTAGTCATTATAAGATTTTTCTTAACATGTGTA
TGGTTCTACTAATTTATTCGAACCT

Found at i:13976 original size:16 final size:16

Alignment explanation


    Indices: 13955--13985  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      13945 TCTCATAATT

                            
      13955 ATTTTTAAATTATAAA
          1 ATTTTTAAATTATAAA

                    *      
      13971 ATTTTTAATTTATAA
          1 ATTTTTAAATTATAA

      13986 GTCAATATTT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55


Consensus pattern (16 bp):   
ATTTTTAAATTATAAA
Done.