Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024888.1 Corchorus olitorius cultivar O-4 contig24921, 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: 19341
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35


Found at i:54 original size:31 final size:29

Alignment explanation


    Indices: 19--84  Score: 105
    Period size: 31  Copynumber: 2.2  Consensus size: 29

          9 CCTAACGGAC

                                           
         19 TATATCCTTAATTGCTCGTTTTTCGTAACGT
          1 TATATCCTTAATTGCTCG-TTTT-GTAACGT

                            *            
         50 TATATCCTTAATTGCTTGTTTTGTAACGT
          1 TATATCCTTAATTGCTCGTTTTGTAACGT

                  
         79 TATATC
          1 TATATC

         85 TCAAATTGCA


Statistics
Matches: 34,  Mismatches: 1, Indels: 2
        0.92            0.03        0.05

Matches are distributed among these distances:
  29   13  0.38
  30    4  0.12
  31   17  0.50

ACGTcount: A:0.21, C:0.17, G:0.12, T:0.50


Consensus pattern (29 bp):   
TATATCCTTAATTGCTCGTTTTGTAACGT

Found at i:91 original size:29 final size:31

Alignment explanation


    Indices: 19--93  Score: 93
    Period size: 29  Copynumber: 2.5  Consensus size: 31

          9 CCTAACGGAC

                    *                      
         19 TATATCCTTAATTGCTCGTTTTTCGTAACGT
          1 TATATCCTAAATTGCTCGTTTTTCGTAACGT

                    *       *              
         50 TATATCCTTAATTGCTTG-TTTT-GTAACGT
          1 TATATCCTAAATTGCTCGTTTTTCGTAACGT

                            
         79 TATAT-CTCAAATTGC
          1 TATATCCT-AAATTGC

         94 ATTTTGCGGC


Statistics
Matches: 41,  Mismatches: 2, Indels: 4
        0.87            0.04        0.09

Matches are distributed among these distances:
  28    2  0.05
  29   18  0.44
  30    4  0.10
  31   17  0.41

ACGTcount: A:0.23, C:0.17, G:0.12, T:0.48


Consensus pattern (31 bp):   
TATATCCTAAATTGCTCGTTTTTCGTAACGT

Found at i:14879 original size:33 final size:33

Alignment explanation


    Indices: 14841--14908  Score: 136
    Period size: 33  Copynumber: 2.1  Consensus size: 33

      14831 TCTCCACTAT

                                             
      14841 TGGTTGTGTAATAGATTAAGATTACAATCCCAC
          1 TGGTTGTGTAATAGATTAAGATTACAATCCCAC

                                             
      14874 TGGTTGTGTAATAGATTAAGATTACAATCCCAC
          1 TGGTTGTGTAATAGATTAAGATTACAATCCCAC

              
      14907 TG
          1 TG

      14909 TGATAAGTCT


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  33   35  1.00

ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34


Consensus pattern (33 bp):   
TGGTTGTGTAATAGATTAAGATTACAATCCCAC
Done.