Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010708.1 Corchorus olitorius cultivar O-4 contig10740, 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: 5695
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36


Found at i:5132 original size:21 final size:21

Alignment explanation


    Indices: 5107--5174  Score: 77
    Period size: 21  Copynumber: 3.2  Consensus size: 21

       5097 TGAGTTAATG

                                 
       5107 TGTCTTAATTATTTTGTATAT
          1 TGTCTTAATTATTTTGTATAT

                   *     **       
       5128 TGTCTTACTT-TTGAGT-TAAT
          1 TGTCTTAATTATTTTGTAT-AT

                                  
       5148 GTGTCTTAATTATTTTGTATAT
          1 -TGTCTTAATTATTTTGTATAT

                 
       5170 TGTCT
          1 TGTCT

       5175 GCTCTTATGC


Statistics
Matches: 37,  Mismatches: 6, Indels: 8
        0.73            0.12        0.16

Matches are distributed among these distances:
  19    1  0.03
  20    6  0.16
  21   23  0.62
  22    6  0.16
  23    1  0.03

ACGTcount: A:0.21, C:0.07, G:0.13, T:0.59


Consensus pattern (21 bp):   
TGTCTTAATTATTTTGTATAT

Found at i:5141 original size:42 final size:42

Alignment explanation


    Indices: 5090--5174  Score: 170
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       5080 TGCACATATT

                                                      
       5090 TTACTTTTGAGTTAATGTGTCTTAATTATTTTGTATATTGTC
          1 TTACTTTTGAGTTAATGTGTCTTAATTATTTTGTATATTGTC

                                                      
       5132 TTACTTTTGAGTTAATGTGTCTTAATTATTTTGTATATTGTC
          1 TTACTTTTGAGTTAATGTGTCTTAATTATTTTGTATATTGTC

             
       5174 T
          1 T

       5175 GCTCTTATGC


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  42   43  1.00

ACGTcount: A:0.21, C:0.07, G:0.14, T:0.58


Consensus pattern (42 bp):   
TTACTTTTGAGTTAATGTGTCTTAATTATTTTGTATATTGTC
Done.