Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012463.1 Corchorus olitorius cultivar O-4 contig12496, 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: 2220
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.34


Found at i:785 original size:25 final size:24

Alignment explanation


    Indices: 749--795  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

        739 TCCTTCTATT

                                    
        749 CATCTATCATC-AAGTTTTTCATC
          1 CATCTATCATCAAAGTTTTTCATC

                                    
        772 CATCTCATCCATCAAAGTTTTTCA
          1 CATCT-AT-CATCAAAGTTTTTCA

        796 AATTTTCTAG


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

Matches are distributed among these distances:
  23    5  0.24
  24    2  0.10
  25    4  0.19
  26   10  0.48

ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40


Consensus pattern (24 bp):   
CATCTATCATCAAAGTTTTTCATC

Found at i:924 original size:12 final size:11

Alignment explanation


    Indices: 907--945  Score: 53
    Period size: 11  Copynumber: 3.5  Consensus size: 11

        897 TAGTTAATCG

                        
        907 AAAAATATCAAA
          1 AAAAATAT-AAA

                       
        919 AAAAATATAAA
          1 AAAAATATAAA

              *        
        930 AATAATA-AAA
          1 AAAAATATAAA

                  
        940 AAAAAT
          1 AAAAAT

        946 TCGACCAGAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  10    8  0.32
  11    9  0.36
  12    8  0.32

ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18


Consensus pattern (11 bp):   
AAAAATATAAA

Found at i:932 original size:20 final size:21

Alignment explanation


    Indices: 907--945  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        897 TAGTTAATCG

                     *           
        907 AAAAAT-ATCAAAAAAAATAT
          1 AAAAATAATAAAAAAAAATAT

                               
        927 AAAAATAATAAAAAAAAAT
          1 AAAAATAATAAAAAAAAAT

        946 TCGACCAGAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20    6  0.35
  21   11  0.65

ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18


Consensus pattern (21 bp):   
AAAAATAATAAAAAAAAATAT

Done.