Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020418.1 Corchorus olitorius cultivar O-4 contig20451, 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: 22247
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32


Found at i:3825 original size:87 final size:87

Alignment explanation


    Indices: 3691--3852  Score: 308
    Period size: 87  Copynumber: 1.9  Consensus size: 87

       3681 CCCCTAAATT

                                                                             
       3691 TTGAAATATTTCACTCTTATCAATTGAAAGAAAAGTGCAATTTTCCTCAACTTTTAATTCAAATT
          1 TTGAAATATTTCACTCTTATCAATTGAAAGAAAAGTGCAATTTTCCTCAACTTTTAATTCAAATT

                                  
       3756 AATTATTACACCCTAAATTTTA
         66 AATTATTACACCCTAAATTTTA

                                                                             
       3778 TTGAAATATTTCACTCTTAT-ACATTGAAAGAAAAGTGCAATTTTCCTCAACTTTTAATTCAAAT
          1 TTGAAATATTTCACTCTTATCA-ATTGAAAGAAAAGTGCAATTTTCCTCAACTTTTAATTCAAAT

                       
       3842 TAATTATTACA
         65 TAATTATTACA

       3853 AGCAGGGCGG


Statistics
Matches: 74,  Mismatches: 0, Indels: 2
        0.97            0.00        0.03

Matches are distributed among these distances:
  86    1  0.01
  87   73  0.99

ACGTcount: A:0.38, C:0.15, G:0.06, T:0.40


Consensus pattern (87 bp):   
TTGAAATATTTCACTCTTATCAATTGAAAGAAAAGTGCAATTTTCCTCAACTTTTAATTCAAATT
AATTATTACACCCTAAATTTTA

Found at i:10020 original size:12 final size:12

Alignment explanation


    Indices: 10003--10035  Score: 66
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       9993 CAAATGGCTG

                        
      10003 ATCACCACCACC
          1 ATCACCACCACC

                        
      10015 ATCACCACCACC
          1 ATCACCACCACC

                     
      10027 ATCACCACC
          1 ATCACCACC

      10036 GTCCCAACCG


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   21  1.00

ACGTcount: A:0.33, C:0.58, G:0.00, T:0.09


Consensus pattern (12 bp):   
ATCACCACCACC

Found at i:12027 original size:39 final size:39

Alignment explanation


    Indices: 11953--12028  Score: 100
    Period size: 39  Copynumber: 1.9  Consensus size: 39

      11943 GATCACCATA

                           *         *  * *        
      11953 ATCATGGACATCAACGTGATCATGCTCATAGTCATGAAG
          1 ATCATGGACATCAACATGATCATGCCCACAATCATGAAG

                                                  
      11992 ATCATGGACATCAACATGA-CAATGCCCACAATCATGA
          1 ATCATGGACATCAACATGATC-ATGCCCACAATCATGA

      12029 CCACCATGAT


Statistics
Matches: 32,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  38    1  0.03
  39   31  0.97

ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22


Consensus pattern (39 bp):   
ATCATGGACATCAACATGATCATGCCCACAATCATGAAG
Done.