Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019960.1 Corchorus olitorius cultivar O-4 contig19993, 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: 23377
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:2532 original size:23 final size:22

Alignment explanation


    Indices: 2501--2551  Score: 84
    Period size: 23  Copynumber: 2.3  Consensus size: 22

       2491 CGGGAGAGGG

                                  
       2501 TTTTTTGGTGTGAACAAACTTA
          1 TTTTTTGGTGTGAACAAACTTA

                                  *
       2523 TTTTTCTGGTGTGAACAAACTTT
          1 TTTTT-TGGTGTGAACAAACTTA

                  
       2546 TTTTTT
          1 TTTTTT

       2552 TCTGGTATTG


Statistics
Matches: 27,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  22    6  0.22
  23   21  0.78

ACGTcount: A:0.22, C:0.10, G:0.16, T:0.53


Consensus pattern (22 bp):   
TTTTTTGGTGTGAACAAACTTA

Found at i:6845 original size:32 final size:32

Alignment explanation


    Indices: 6808--6887  Score: 115
    Period size: 32  Copynumber: 2.5  Consensus size: 32

       6798 AAAAACCGAG

                           *   *  *         
       6808 CTCGAGCTCGGCTCGGATCGAGTATCGAGCTA
          1 CTCGAGCTCGGCTCGAATCAAGCATCGAGCTA

                                     *      
       6840 CTCGAGCTCGGCTCGAATCAAGCATTGAGCTA
          1 CTCGAGCTCGGCTCGAATCAAGCATCGAGCTA

                      *     
       6872 CTCGAGCTCGACTCGA
          1 CTCGAGCTCGGCTCGA

       6888 CAAGTTCGAT


Statistics
Matches: 43,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  32   43  1.00

ACGTcount: A:0.21, C:0.30, G:0.28, T:0.21


Consensus pattern (32 bp):   
CTCGAGCTCGGCTCGAATCAAGCATCGAGCTA

Found at i:7045 original size:14 final size:16

Alignment explanation


    Indices: 7015--7046  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       7005 TTTTAATAAA

                            
       7015 ATATATAATATTATGT
          1 ATATATAATATTATGT

                            
       7031 ATATATAA-ATT-TGT
          1 ATATATAATATTATGT

              
       7045 AT
          1 AT

       7047 CGAGTAGTTC


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  14    5  0.31
  15    3  0.19
  16    8  0.50

ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50


Consensus pattern (16 bp):   
ATATATAATATTATGT

Found at i:20700 original size:20 final size:20

Alignment explanation


    Indices: 20672--20710  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      20662 GTAGAGTAAG

                                
      20672 GAAAAATATCTTCATAAAAT
          1 GAAAAATATCTTCATAAAAT

                *       *      
      20692 GAAATATATCTTGATAAAA
          1 GAAAAATATCTTCATAAAA

      20711 AGGTTTTATG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31


Consensus pattern (20 bp):   
GAAAAATATCTTCATAAAAT
Done.