Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002662.1 Corchorus capsularis cultivar CVL-1 contig02670, 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: 2024
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.29


Found at i:1251 original size:13 final size:13

Alignment explanation


    Indices: 1222--1268  Score: 78
    Period size: 13  Copynumber: 3.7  Consensus size: 13

       1212 AATCTAAATC

                   *     
       1222 TAAAGCAGATT-A
          1 TAAAGCAAATTAA

                         
       1234 TAAAGCAAATTAA
          1 TAAAGCAAATTAA

                         
       1247 TAAAGCAAATTAA
          1 TAAAGCAAATTAA

                     
       1260 TAAAGCAAA
          1 TAAAGCAAA

       1269 CAATAACTAA


Statistics
Matches: 33,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  12   10  0.30
  13   23  0.70

ACGTcount: A:0.60, C:0.09, G:0.11, T:0.21


Consensus pattern (13 bp):   
TAAAGCAAATTAA

Found at i:1273 original size:25 final size:25

Alignment explanation


    Indices: 1222--1274  Score: 72
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       1212 AATCTAAATC

                   *              *  
       1222 TAAAGCAGATTATAAAGCAAATTAA
          1 TAAAGCAAATTATAAAGCAAATCAA

                                      
       1247 TAAAGCAAATTAATAAAGCAAA-CAA
          1 TAAAGCAAATT-ATAAAGCAAATCAA

               
       1272 TAA
          1 TAA

       1275 CTAAAAAGCA


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

Matches are distributed among these distances:
  25   15  0.60
  26   10  0.40

ACGTcount: A:0.60, C:0.09, G:0.09, T:0.21


Consensus pattern (25 bp):   
TAAAGCAAATTATAAAGCAAATCAA
Done.