Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008913.1 Corchorus olitorius cultivar O-4 contig08940, 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: 1788
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36


Found at i:233 original size:60 final size:61

Alignment explanation


    Indices: 166--293  Score: 170
    Period size: 67  Copynumber: 2.0  Consensus size: 61

        156 GCATTAAATT

                                                                          
        166 AAGGTTATAAACC-TATTAACAGACCTTTTTTTTAATTCCG-AAATTGCGGATTCGCGTTAA
          1 AAGGTTATAAACCTTATTAACAGACC-TTTTTTTAATTCCGTAAATTGCGGATTCGCGTTAA

                                                *                            
        226 AAGGTTATAAACCTATTTATTAACAGACCTTTTTTTCATTCCGTATTAAATTGCGGATTCGCGTT
          1 AAGGTTATAAACC---TTATTAACAGACCTTTTTTTAATTCCG---TAAATTGCGGATTCGCGTT

              
        291 AA
         60 AA

             
        293 A
          1 A

        294 TTGTTGCCAT


Statistics
Matches: 59,  Mismatches: 1, Indels: 9
        0.86            0.01        0.13

Matches are distributed among these distances:
  60   13  0.22
  63   13  0.22
  64   12  0.20
  67   21  0.36

ACGTcount: A:0.31, C:0.16, G:0.14, T:0.38


Consensus pattern (61 bp):   
AAGGTTATAAACCTTATTAACAGACCTTTTTTTAATTCCGTAAATTGCGGATTCGCGTTAA

Found at i:1671 original size:19 final size:19

Alignment explanation


    Indices: 1647--1703  Score: 114
    Period size: 19  Copynumber: 3.0  Consensus size: 19

       1637 CAAACTTTTC

                               
       1647 ATTGATCTATTTTTTTCAT
          1 ATTGATCTATTTTTTTCAT

                               
       1666 ATTGATCTATTTTTTTCAT
          1 ATTGATCTATTTTTTTCAT

                               
       1685 ATTGATCTATTTTTTTCAT
          1 ATTGATCTATTTTTTTCAT

       1704 TGGGATTCAA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   38  1.00

ACGTcount: A:0.21, C:0.11, G:0.05, T:0.63


Consensus pattern (19 bp):   
ATTGATCTATTTTTTTCAT

Done.