Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005864.1 Corchorus olitorius cultivar O-4 contig05889, 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, 684

Length: 1140
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27


Found at i:863 original size:11 final size:11

Alignment explanation


    Indices: 842--880  Score: 62
    Period size: 11  Copynumber: 3.5  Consensus size: 11

        832 AGCCGGGATC

                       
        842 ACTAA-CTAAT
          1 ACTAATCTAAT

                       
        852 ACTAATCTAAT
          1 ACTAATCTAAT

                        
        863 ACTAATCTTAAT
          1 ACTAATC-TAAT

                  
        875 ACTAAT
          1 ACTAAT

        881 AGAATAGAAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  10    5  0.19
  11   12  0.44
  12   10  0.37

ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36


Consensus pattern (11 bp):   
ACTAATCTAAT

Found at i:901 original size:5 final size:6

Alignment explanation


    Indices: 846--908  Score: 64
    Period size: 6  Copynumber: 11.2  Consensus size: 6

        836 GGGATCACTA

                                                         *      *   
        846 ACTAAT ACTAAT -CTAAT ACTAAT -CTTAAT ACTAAT A-GAAT A-GAAT
          1 ACTAAT ACTAAT ACTAAT ACTAAT AC-TAAT ACTAAT ACTAAT ACTAAT

                                  
        891 ACTAAT -CTAAT ACTAAT A
          1 ACTAAT ACTAAT ACTAAT A

        909 GAATAGAAAA


Statistics
Matches: 50,  Mismatches: 2, Indels: 10
        0.81            0.03        0.16

Matches are distributed among these distances:
   5   20  0.40
   6   29  0.58
   7    1  0.02

ACGTcount: A:0.49, C:0.14, G:0.03, T:0.33


Consensus pattern (6 bp):   
ACTAAT

Found at i:908 original size:27 final size:28

Alignment explanation


    Indices: 860--916  Score: 107
    Period size: 27  Copynumber: 2.1  Consensus size: 28

        850 ATACTAATCT

                                        
        860 AATACTAATCTTAATACTAATAGAATAG
          1 AATACTAATCTTAATACTAATAGAATAG

                                        
        888 AATACTAATC-TAATACTAATAGAATAG
          1 AATACTAATCTTAATACTAATAGAATAG

              
        915 AA
          1 AA

        917 AAAATAGAAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  27   19  0.66
  28   10  0.34

ACGTcount: A:0.53, C:0.11, G:0.07, T:0.30


Consensus pattern (28 bp):   
AATACTAATCTTAATACTAATAGAATAG

Found at i:924 original size:14 final size:14

Alignment explanation


    Indices: 905--932  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

        895 ATCTAATACT

                          
        905 AATAGAATAGAAAA
          1 AATAGAATAGAAAA

                          
        919 AATAGAATAGAAAA
          1 AATAGAATAGAAAA

        933 TACTAATATA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14


Consensus pattern (14 bp):   
AATAGAATAGAAAA
Done.