Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004663.1 Corchorus capsularis cultivar CVL-1 contig04678, 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, 600

Length: 1000
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.24


Found at i:730 original size:48 final size:48

Alignment explanation


    Indices: 654--766  Score: 183
    Period size: 48  Copynumber: 2.4  Consensus size: 48

        644 TGGATTTCTA

                         *                                  
        654 ATTTTGGCCAATTATTGGGTCCGGAACTCATGATGGTTAACCTACGGC
          1 ATTTTGGCCAATTTTTGGGTCCGGAACTCATGATGGTTAACCTACGGC

                                          *              *   
        702 -TTTTCGGCCAATTTTTGGGTCCGGAACTCTTGATGGTTAACCTATGGC
          1 ATTTT-GGCCAATTTTTGGGTCCGGAACTCATGATGGTTAACCTACGGC

                             
        750 ATTTTGGCCAATTTTTG
          1 ATTTTGGCCAATTTTTG

        767 CCCCCGAAGC


Statistics
Matches: 60,  Mismatches: 3, Indels: 4
        0.90            0.04        0.06

Matches are distributed among these distances:
  47    4  0.07
  48   52  0.87
  49    4  0.07

ACGTcount: A:0.19, C:0.19, G:0.24, T:0.37


Consensus pattern (48 bp):   
ATTTTGGCCAATTTTTGGGTCCGGAACTCATGATGGTTAACCTACGGC

Found at i:830 original size:77 final size:77

Alignment explanation


    Indices: 703--856  Score: 211
    Period size: 77  Copynumber: 2.0  Consensus size: 77

        693 ACCTACGGCT

                                        *    ****                            
        703 TTTCGGCCAATTTTTGGGTCCGGAACTCTTGATGGTTAACCTATGGCATTTTGGCCAATTTTTGC
          1 TTTCGGCCAATTTTTGGGTCCGGAACTCATGATACAAAACCTATGGCATTTTGGCCAATTTTTGC

                   *    
        768 CCCCGAAGCTCA
         66 CCCCGAAACTCA

                     *          *                                     *      
        780 TTTCGGCCATTTTTTGGGTCTGGAACTCATGATACAAAACCTAAT-GCATTTTGGCCATTTTTTG
          1 TTTCGGCCAATTTTTGGGTCCGGAACTCATGATACAAAACCT-ATGGCATTTTGGCCAATTTTTG

                         
        844 CCCCCGAAACTCA
         65 CCCCCGAAACTCA

        857 GCGAACACCT


Statistics
Matches: 67,  Mismatches: 9, Indels: 2
        0.86            0.12        0.03

Matches are distributed among these distances:
  77   65  0.97
  78    2  0.03

ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35


Consensus pattern (77 bp):   
TTTCGGCCAATTTTTGGGTCCGGAACTCATGATACAAAACCTATGGCATTTTGGCCAATTTTTGC
CCCCGAAACTCA
Done.