Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024600.1 Corchorus olitorius cultivar O-4 contig24633, 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: 8850
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:717 original size:30 final size:29

Alignment explanation


    Indices: 683--749  Score: 82
    Period size: 30  Copynumber: 2.2  Consensus size: 29

        673 GGTTTGGTTG

                         **                
        683 TGGAAGGCCAGGGGGTCTT-GAGGAAGTGGA
          1 TGGAAGG-CAGGGAATCTTGGA-GAAGTGGA

                                          
        713 TGGAAGAGCAGGGAATCTTGGAGAAGTGGA
          1 TGGAAG-GCAGGGAATCTTGGAGAAGTGGA

                   
        743 TGGAAGG
          1 TGGAAGG

        750 GTAGGGTATC


Statistics
Matches: 33,  Mismatches: 2, Indels: 5
        0.82            0.05        0.12

Matches are distributed among these distances:
  29    1  0.03
  30   29  0.88
  31    3  0.09

ACGTcount: A:0.28, C:0.07, G:0.48, T:0.16


Consensus pattern (29 bp):   
TGGAAGGCAGGGAATCTTGGAGAAGTGGA

Found at i:7636 original size:21 final size:21

Alignment explanation


    Indices: 7610--7650  Score: 82
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       7600 TGTCTCTATA

                                 
       7610 TCGTTCACCGTAAGTTGCATT
          1 TCGTTCACCGTAAGTTGCATT

                                
       7631 TCGTTCACCGTAAGTTGCAT
          1 TCGTTCACCGTAAGTTGCAT

       7651 GGTATTTTTG


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.20, C:0.24, G:0.20, T:0.37


Consensus pattern (21 bp):   
TCGTTCACCGTAAGTTGCATT

Found at i:7742 original size:46 final size:46

Alignment explanation


    Indices: 7675--7767  Score: 186
    Period size: 46  Copynumber: 2.0  Consensus size: 46

       7665 TTTTTGATTA

                                                          
       7675 AGTCACATTCTCATGTCCTATTATCACATTAGCCTTTTACTTTAGC
          1 AGTCACATTCTCATGTCCTATTATCACATTAGCCTTTTACTTTAGC

                                                          
       7721 AGTCACATTCTCATGTCCTATTATCACATTAGCCTTTTACTTTAGC
          1 AGTCACATTCTCATGTCCTATTATCACATTAGCCTTTTACTTTAGC

             
       7767 A
          1 A

       7768 TATGAAGTCA


Statistics
Matches: 47,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  46   47  1.00

ACGTcount: A:0.25, C:0.26, G:0.09, T:0.41


Consensus pattern (46 bp):   
AGTCACATTCTCATGTCCTATTATCACATTAGCCTTTTACTTTAGC
Done.