Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011363.1 Corchorus olitorius cultivar O-4 contig11396, 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: 4419
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:954 original size:33 final size:33

Alignment explanation


    Indices: 916--988  Score: 101
    Period size: 33  Copynumber: 2.2  Consensus size: 33

        906 AATTTTTTTT

                            *                
        916 TTAAAAACCTAAAACCGGCGGGAACTTTCCCAA
          1 TTAAAAACCTAAAACCAGCGGGAACTTTCCCAA

                    *      *  *              
        949 TTAAAAACTTAAAACTAGTGGGAACTTTCCCAA
          1 TTAAAAACCTAAAACCAGCGGGAACTTTCCCAA

                   
        982 TGTAAAA
          1 T-TAAAA

        989 CTTAATGAAA


Statistics
Matches: 35,  Mismatches: 4, Indels: 1
        0.88            0.10        0.03

Matches are distributed among these distances:
  33   30  0.86
  34    5  0.14

ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23


Consensus pattern (33 bp):   
TTAAAAACCTAAAACCAGCGGGAACTTTCCCAA

Found at i:4213 original size:39 final size:39

Alignment explanation


    Indices: 4118--4419  Score: 525
    Period size: 39  Copynumber: 7.8  Consensus size: 39

       4108 CAACATAAAA

                    *  *          **               
       4118 CTGAAAAGTTGACCTGTTTCCAGTCAACTTTGATAAATG
          1 CTGAAAAGATGGCCTGTTTCCAACCAACTTTGATAAATG

                       *          **               
       4157 CT-AAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
          1 CTGAAAAGATGGCCTGTTTCCAACCAACTTTGATAAATG

                                                   
       4195 CTGAAAAGATGGCCTGTTTCCAACCAACTTTGATAAATG
          1 CTGAAAAGATGGCCTGTTTCCAACCAACTTTGATAAATG

                                                   
       4234 CTGAAAAGATGGCCTGTTTCCAACCAACTTTGATAAATG
          1 CTGAAAAGATGGCCTGTTTCCAACCAACTTTGATAAATG

                                                   
       4273 CTGAAAAGATGGCCTGTTTCCAACCAACTTTGATAAATG
          1 CTGAAAAGATGGCCTGTTTCCAACCAACTTTGATAAATG

                                                   
       4312 CTGAAAAGATGGCCTGTTTCCAACCAACTTTGATAAATG
          1 CTGAAAAGATGGCCTGTTTCCAACCAACTTTGATAAATG

                               *                   
       4351 CTGAAAAGATGGCCTGTTTTCAACCAACTTTGATAAATG
          1 CTGAAAAGATGGCCTGTTTCCAACCAACTTTGATAAATG

                                          
       4390 CTGAAAAGATGGCCTGTTTCCAACCAACTT
          1 CTGAAAAGATGGCCTGTTTCCAACCAACTT


Statistics
Matches: 256,  Mismatches: 6, Indels: 2
        0.97            0.02        0.01

Matches are distributed among these distances:
  38   37  0.14
  39  219  0.86

ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29


Consensus pattern (39 bp):   
CTGAAAAGATGGCCTGTTTCCAACCAACTTTGATAAATG

Done.