Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018427.1 Corchorus olitorius cultivar O-4 contig18460, 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: 2032
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.29


Found at i:740 original size:67 final size:66

Alignment explanation


    Indices: 632--764  Score: 239
    Period size: 67  Copynumber: 2.0  Consensus size: 66

        622 TTTAAGTTTC

                          *                                                  
        632 AACTAATACCTAAACTAAGCAAATTCAAGAAATTCAGCTTTTCCAAGAGCAAAATGAGCCAAAAA
          1 AACTAATACCTAAAATAAGCAAATTCAAGAAATTCAGCTTTTCCAAGAGCAAAATGAG-CAAAAA

              
        697 AA
         65 AA

                                                          *                  
        699 AACTAATACCTAAAATAAGCAAATTCAAGAAATTCAGCTTTTCCAATAGCAAAATGAGCAAAAAA
          1 AACTAATACCTAAAATAAGCAAATTCAAGAAATTCAGCTTTTCCAAGAGCAAAATGAGCAAAAAA

             
        764 A
         66 A

        765 GCAAGGTTTT


Statistics
Matches: 64,  Mismatches: 2, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
  66    8  0.12
  67   56  0.88

ACGTcount: A:0.52, C:0.18, G:0.10, T:0.20


Consensus pattern (66 bp):   
AACTAATACCTAAAATAAGCAAATTCAAGAAATTCAGCTTTTCCAAGAGCAAAATGAGCAAAAAA
A

Found at i:2024 original size:19 final size:18

Alignment explanation


    Indices: 1986--2029  Score: 61
    Period size: 19  Copynumber: 2.4  Consensus size: 18

       1976 AAAATAAAAG

                              
       1986 TAGATAATAGTAAATAAA
          1 TAGATAATAGTAAATAAA

                            *  
       2004 TAGATAATAGCTAAATTAA
          1 TAGATAATAG-TAAATAAA

              *    
       2023 TAAATAA
          1 TAGATAA

       2030 AGG


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  18   10  0.43
  19   13  0.57

ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30


Consensus pattern (18 bp):   
TAGATAATAGTAAATAAA
Done.