Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022662.1 Corchorus olitorius cultivar O-4 contig22695, 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, 859

Length: 1433
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.38


Found at i:349 original size:15 final size:16

Alignment explanation


    Indices: 318--358  Score: 66
    Period size: 15  Copynumber: 2.6  Consensus size: 16

        308 TTTACTTTGC

                            
        318 ATTGTTTTCTAGTTTA
          1 ATTGTTTTCTAGTTTA

                      *     
        334 ATTGTTTTC-CGTTTA
          1 ATTGTTTTCTAGTTTA

                      
        349 ATTGTTTTCT
          1 ATTGTTTTCT

        359 GTCAATCTCT


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  15   14  0.61
  16    9  0.39

ACGTcount: A:0.15, C:0.10, G:0.12, T:0.63


Consensus pattern (16 bp):   
ATTGTTTTCTAGTTTA

Found at i:740 original size:54 final size:52

Alignment explanation


    Indices: 682--796  Score: 131
    Period size: 54  Copynumber: 2.2  Consensus size: 52

        672 CGTTTTTTTC

                                                *   *             
        682 AAAAAAAAAATTATTTTGCGTTTTTAATTTTTTTTGTGTTTTTGCGTCGAAAAA
          1 AAAAAAAAAATTATTTTGCGTTTTTAATTTTTTTTGAG-TCTTGCGTC-AAAAA

                 *****  *                                     * 
        736 AAAAATCTTCTTGTTTTGCGTTTTTAATTTTTTTTGAGTCTTGCGTCAAAGA
          1 AAAAAAAAAATTATTTTGCGTTTTTAATTTTTTTTGAGTCTTGCGTCAAAAA

                     
        788 AAAAAAAAA
          1 AAAAAAAAA

        797 TTTGTGTTGC


Statistics
Matches: 48,  Mismatches: 13, Indels: 2
        0.76            0.21        0.03

Matches are distributed among these distances:
  52    9  0.19
  53    8  0.17
  54   31  0.65

ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45


Consensus pattern (52 bp):   
AAAAAAAAAATTATTTTGCGTTTTTAATTTTTTTTGAGTCTTGCGTCAAAAA

Found at i:807 original size:27 final size:26

Alignment explanation


    Indices: 776--846  Score: 90
    Period size: 27  Copynumber: 2.7  Consensus size: 26

        766 TTTTTGAGTC

                                        
        776 TTGCGTCAAAGAAAAAAAAAA-TTTGTG
          1 TTGCGTCAAA-AAAAAAAAAAGTTT-TG

                                       
        803 TTGCGTCGAAAAAAAAAAAAAGTTTTG
          1 TTGCGTC-AAAAAAAAAAAAAGTTTTG

            *       *        
        830 CTGCGTCATAAAAAAAA
          1 TTGCGTCAAAAAAAAAA

        847 TTTCTTGTTC


Statistics
Matches: 40,  Mismatches: 2, Indels: 5
        0.85            0.04        0.11

Matches are distributed among these distances:
  26    9  0.22
  27   25  0.62
  28    6  0.15

ACGTcount: A:0.49, C:0.10, G:0.17, T:0.24


Consensus pattern (26 bp):   
TTGCGTCAAAAAAAAAAAAAGTTTTG
Done.