Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013636.1 Corchorus capsularis cultivar CVL-1 contig13657, 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: 6627
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30


Found at i:4615 original size:28 final size:28

Alignment explanation


    Indices: 4556--4625  Score: 88
    Period size: 28  Copynumber: 2.5  Consensus size: 28

       4546 TTACATCAAA

                                         
       4556 TGAAAAAGAAGAAAAGAAAAAATAAAAAT
          1 TGAAAAAGAA-AAAAGAAAAAATAAAAAT

                                    *  * 
       4585 TGAAAAAGAAAAAAGAAAAGAA-AGAAGT
          1 TGAAAAAGAAAAAAGAAAA-AATAAAAAT

                    *    
       4613 TGAAAAAGCAAAA
          1 TGAAAAAGAAAAA

       4626 GATGGAGGAA


Statistics
Matches: 37,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  28   25  0.68
  29   12  0.32

ACGTcount: A:0.73, C:0.01, G:0.17, T:0.09


Consensus pattern (28 bp):   
TGAAAAAGAAAAAAGAAAAAATAAAAAT

Found at i:5913 original size:33 final size:33

Alignment explanation


    Indices: 5801--5912  Score: 138
    Period size: 33  Copynumber: 3.4  Consensus size: 33

       5791 AGACAAAGGA

                                  *    *      
       5801 TCGCGTGGCCGGTTGTGGCCGGGCATGGCCGA-G
          1 TCGCGTGGCCGGTTGTGGCCGGACATGTCC-ATG

               **           *   *            
       5834 TCGTTTGGCCGGTTGTAGCCCGACATGTCCATG
          1 TCGCGTGGCCGGTTGTGGCCGGACATGTCCATG

                                              
       5867 TCGCGTGGCCGG-TGATGGCCGGACATGTCCATG
          1 TCGCGTGGCCGGTTG-TGGCCGGACATGTCCATG

                         
       5900 TCGCGTGGCCGGT
          1 TCGCGTGGCCGGT

       5913 GTTGCGCGGC


Statistics
Matches: 66,  Mismatches: 10, Indels: 5
        0.81            0.12        0.06

Matches are distributed among these distances:
  32    3  0.05
  33   63  0.95

ACGTcount: A:0.09, C:0.28, G:0.40, T:0.23


Consensus pattern (33 bp):   
TCGCGTGGCCGGTTGTGGCCGGACATGTCCATG
Done.