Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017001.1 Corchorus olitorius cultivar O-4 contig17034, 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: 4455
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31


Found at i:521 original size:45 final size:45

Alignment explanation


    Indices: 421--512  Score: 121
    Period size: 51  Copynumber: 1.9  Consensus size: 45

        411 GCCTGAACAG

                                             *               
        421 TAGAATATATATATACATAATGGAAAGCAAAAGGAATAACAAAAGATAA
          1 TAGAATATATATATACATAATGGAAAGCAAAAGAAATAAC---A-ATAA

                                                       
        470 TAGAATATATATATACATATGATGGAAAGCAAAAGAAATAACA
          1 TAGAATATATATATACATA--ATGGAAAGCAAAAGAAATAACA

        513 CATAGAATAA


Statistics
Matches: 40,  Mismatches: 1, Indels: 5
        0.87            0.02        0.11

Matches are distributed among these distances:
  48    1  0.03
  49   19  0.47
  51   20  0.50

ACGTcount: A:0.58, C:0.07, G:0.14, T:0.22


Consensus pattern (45 bp):   
TAGAATATATATATACATAATGGAAAGCAAAAGAAATAACAATAA

Found at i:3104 original size:22 final size:22

Alignment explanation


    Indices: 3062--3104  Score: 52
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       3052 AAATAAGAAA

                      *     *     
       3062 ACAAGGAAATGAGTTAGTAACC
          1 ACAAGGAAATAAGTTAATAACC

                                  
       3084 ACAAGGAAATTAAG-TAATAAC
          1 ACAAGGAAA-TAAGTTAATAAC

       3105 TGAAAATTAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  22   15  0.83
  23    3  0.17

ACGTcount: A:0.51, C:0.12, G:0.19, T:0.19


Consensus pattern (22 bp):   
ACAAGGAAATAAGTTAATAACC
Done.