Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016336.1 Corchorus olitorius cultivar O-4 contig16369, 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: 36738
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32


Found at i:24969 original size:13 final size:13

Alignment explanation


    Indices: 24951--24976  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      24941 ATACAACAAC

                         
      24951 ATTAATACAAGGG
          1 ATTAATACAAGGG

                         
      24964 ATTAATACAAGGG
          1 ATTAATACAAGGG

      24977 GTAGAAGGTA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.46, C:0.08, G:0.23, T:0.23


Consensus pattern (13 bp):   
ATTAATACAAGGG

Found at i:26808 original size:20 final size:20

Alignment explanation


    Indices: 26783--26824  Score: 57
    Period size: 20  Copynumber: 2.1  Consensus size: 20

      26773 TTTTCTTTCA

                           *    
      26783 CTTCTTCCTCTCCTATTTTT
          1 CTTCTTCCTCTCCTAGTTTT

                   *    *       
      26803 CTTCTTCTTCTCTTAGTTTT
          1 CTTCTTCCTCTCCTAGTTTT

              
      26823 CT
          1 CT

      26825 ATGGAATGTG


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.05, C:0.31, G:0.02, T:0.62


Consensus pattern (20 bp):   
CTTCTTCCTCTCCTAGTTTT

Found at i:30461 original size:7 final size:7

Alignment explanation


    Indices: 30449--30482  Score: 68
    Period size: 7  Copynumber: 4.9  Consensus size: 7

      30439 TTGAGGTTGC

                   
      30449 AAATTGA
          1 AAATTGA

                   
      30456 AAATTGA
          1 AAATTGA

                   
      30463 AAATTGA
          1 AAATTGA

                   
      30470 AAATTGA
          1 AAATTGA

                  
      30477 AAATTG
          1 AAATTG

      30483 CAAGGCCACG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   27  1.00

ACGTcount: A:0.56, C:0.00, G:0.15, T:0.29


Consensus pattern (7 bp):   
AAATTGA

Found at i:32439 original size:78 final size:78

Alignment explanation


    Indices: 32310--32521  Score: 343
    Period size: 78  Copynumber: 2.7  Consensus size: 78

      32300 TAACTGAAGA

                                               *                        *    
      32310 AGTTGCCATCCAATTAGATGAGAAACTGGGCAGTCTCTCTTTAAGATCCGAGGAGACGGATAATC
          1 AGTTGCCATCCAATTAGATGAGAAACTGGGCAGTCCCTCTTTAAGATCCGAGGAGACGGAGAATC

                        *
      32375 CGATAAGTGACGT
         66 CGATAAGTGACGG

                                                       *            *        
      32388 AGTTGCCATCCAATTAGATGAGAAACTGGGCAGTCCCTCTTTAGGATCCGAGGAGATGGAGAATC
          1 AGTTGCCATCCAATTAGATGAGAAACTGGGCAGTCCCTCTTTAAGATCCGAGGAGACGGAGAATC

                         
      32453 CGATAAGTGACGG
         66 CGATAAGTGACGG

                                              *** *                 
      32466 AGTTGCCATCCAATTAGATGAGAAACTGGGCAGTTTTTGTTTAAGATCCGAGGAGA
          1 AGTTGCCATCCAATTAGATGAGAAACTGGGCAGTCCCTCTTTAAGATCCGAGGAGA

      32522 GTTTCATCTT


Statistics
Matches: 124,  Mismatches: 10, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  78  124  1.00

ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25


Consensus pattern (78 bp):   
AGTTGCCATCCAATTAGATGAGAAACTGGGCAGTCCCTCTTTAAGATCCGAGGAGACGGAGAATC
CGATAAGTGACGG

Found at i:34612 original size:40 final size:40

Alignment explanation


    Indices: 34568--34647  Score: 160
    Period size: 40  Copynumber: 2.0  Consensus size: 40

      34558 AAGAAACGGT

                                                    
      34568 TTTTGCCCTAGCCGATTGACAAAGTTTACTCAATTCCAAA
          1 TTTTGCCCTAGCCGATTGACAAAGTTTACTCAATTCCAAA

                                                    
      34608 TTTTGCCCTAGCCGATTGACAAAGTTTACTCAATTCCAAA
          1 TTTTGCCCTAGCCGATTGACAAAGTTTACTCAATTCCAAA

      34648 GACTTTCTTC


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  40   40  1.00

ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33


Consensus pattern (40 bp):   
TTTTGCCCTAGCCGATTGACAAAGTTTACTCAATTCCAAA
Done.