Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019555.1 Corchorus olitorius cultivar O-4 contig19588, 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: 19522
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29


Found at i:12062 original size:2 final size:2

Alignment explanation


    Indices: 12051--12079  Score: 51
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      12041 GAAAAACGCG

                                                        
      12051 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      12080 GATTCTCCCC


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   25  0.96

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
AT

Found at i:17704 original size:22 final size:22

Alignment explanation


    Indices: 17668--17710  Score: 59
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      17658 TTTTCCGCAA

                      *     *     
      17668 CAAGTCCTGGGCAGGAGTTGTC
          1 CAAGTCCTGGACAGGACTTGTC

                    *            
      17690 CAAGTCCTTGACAGGACTTGT
          1 CAAGTCCTGGACAGGACTTGT

      17711 TCTGAGTTTT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26


Consensus pattern (22 bp):   
CAAGTCCTGGACAGGACTTGTC

Found at i:17771 original size:50 final size:50

Alignment explanation


    Indices: 17689--17810  Score: 172
    Period size: 50  Copynumber: 2.4  Consensus size: 50

      17679 CAGGAGTTGT

                     * *                           *          
      17689 CCAAGTCCTTGACAGGACTTGTTCTGAGTTTTCTTCCGTTTTTCAACAGA
          1 CCAAGTCCTGGGCAGGACTTGTTCTGAGTTTTCTTCCGTCTTTCAACAGA

                             *     *   *                     *
      17739 CCAAGTCCTGGGCAGGAGTTGTTTTGATTTTTCTTCCGTCTTTCAACAGG
          1 CCAAGTCCTGGGCAGGACTTGTTCTGAGTTTTCTTCCGTCTTTCAACAGA

               *                  
      17789 CCAGGTCCTGGGCAGGACTTGT
          1 CCAAGTCCTGGGCAGGACTTGT

      17811 CCTGTTTTTA


Statistics
Matches: 63,  Mismatches: 9, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  50   63  1.00

ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35


Consensus pattern (50 bp):   
CCAAGTCCTGGGCAGGACTTGTTCTGAGTTTTCTTCCGTCTTTCAACAGA
Done.