Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006353.1 Corchorus capsularis cultivar CVL-1 contig06374, 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: 10743
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28


Found at i:97 original size:28 final size:28

Alignment explanation


    Indices: 66--159  Score: 64
    Period size: 28  Copynumber: 3.1  Consensus size: 28

         56 GAATAACATT

                                        
         66 ATTTATTTCAAGTTAAATAGGCCTCAGC
          1 ATTTATTTCAAGTTAAATAGGCCTCAGC

                                 *    ** *    *
         94 ATTT-TTATCAGAGCTTCAAGTTAGGAATAACGTT
          1 ATTTATT-TCA-AG-TT-AA-ATAGGCCTCA-G-C

                                *       
        128 ATTTATTTCAAGTTAAATAGACCTCAGC
          1 ATTTATTTCAAGTTAAATAGGCCTCAGC

                
        156 ATTT
          1 ATTT

        160 TTATCAGAGC


Statistics
Matches: 47,  Mismatches: 11, Indels: 16
        0.64            0.15        0.22

Matches are distributed among these distances:
  27    2  0.04
  28   11  0.23
  29    3  0.06
  30    7  0.15
  31    4  0.09
  32    8  0.17
  33    3  0.06
  34    7  0.15
  35    2  0.04

ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38


Consensus pattern (28 bp):   
ATTTATTTCAAGTTAAATAGGCCTCAGC

Found at i:101 original size:30 final size:31

Alignment explanation


    Indices: 62--163  Score: 79
    Period size: 31  Copynumber: 3.3  Consensus size: 31

         52 TTAGGAATAA

                                           
         62 CATTATTTATTTCAAGTTAAATAGGCCTCAG
          1 CATTATTTATTTCAAGTTAAATAGGCCTCAG

                                    *    **   *
         93 CATT-TTTA--TCAGAGCTTCAAGTTAGGAAT-AA
          1 CATTATTTATTTCA-AG-TT-AA-ATAGGCCTCAG

             *                      *      
        124 CGTTATTTATTTCAAGTTAAATAGACCTCAG
          1 CATTATTTATTTCAAGTTAAATAGGCCTCAG

                      
        155 CATT-TTTAT
          1 CATTATTTAT

        164 CAGAGCTTCA


Statistics
Matches: 52,  Mismatches: 11, Indels: 17
        0.65            0.14        0.21

Matches are distributed among these distances:
  28    3  0.06
  29    2  0.04
  30   15  0.29
  31   16  0.31
  32   11  0.21
  33    2  0.04
  34    3  0.06

ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40


Consensus pattern (31 bp):   
CATTATTTATTTCAAGTTAAATAGGCCTCAG

Found at i:153 original size:62 final size:62

Alignment explanation


    Indices: 51--176  Score: 234
    Period size: 62  Copynumber: 2.0  Consensus size: 62

         41 TCATTTGAGC

                                               *                          
         51 GTTAGGAATAACATTATTTATTTCAAGTTAAATAGGCCTCAGCATTTTTATCAGAGCTTCAA
          1 GTTAGGAATAACATTATTTATTTCAAGTTAAATAGACCTCAGCATTTTTATCAGAGCTTCAA

                        *                                                 
        113 GTTAGGAATAACGTTATTTATTTCAAGTTAAATAGACCTCAGCATTTTTATCAGAGCTTCAA
          1 GTTAGGAATAACATTATTTATTTCAAGTTAAATAGACCTCAGCATTTTTATCAGAGCTTCAA

              
        175 GT
          1 GT

        177 AAGTGATGAC


Statistics
Matches: 62,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  62   62  1.00

ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37


Consensus pattern (62 bp):   
GTTAGGAATAACATTATTTATTTCAAGTTAAATAGACCTCAGCATTTTTATCAGAGCTTCAA
Done.