Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001889.1 Corchorus capsularis cultivar CVL-1 contig01891, 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: 1971
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31


Found at i:62 original size:32 final size:32

Alignment explanation


    Indices: 3--140  Score: 190
    Period size: 32  Copynumber: 4.3  Consensus size: 32

          1 CG

                              *    *         
          3 AGCCGCCCCACCGGCG-CAGCCTACCGTGGCGA
          1 AGCCGCCCCACC-GCGACGGCCTGCCGTGGCGA

                *                            
         35 AGCCACCCCACCGACG-CGGCCTGCCGTGGCGA
          1 AGCCGCCCCACCG-CGACGGCCTGCCGTGGCGA

                         *                  
         67 AGCCGCCCCACCGGGACGGCCTGCCGTGGCGA
          1 AGCCGCCCCACCGCGACGGCCTGCCGTGGCGA

                         *           *      
         99 AGCCGCCCCACCGGGACGGCCTGCCCTGGCGA
          1 AGCCGCCCCACCGCGACGGCCTGCCGTGGCGA

                      
        131 AGCCGCCCCA
          1 AGCCGCCCCA

        141 GTGGGGCGGC


Statistics
Matches: 98,  Mismatches: 6, Indels: 4
        0.91            0.06        0.04

Matches are distributed among these distances:
  31    2  0.02
  32   96  0.98

ACGTcount: A:0.14, C:0.47, G:0.33, T:0.06


Consensus pattern (32 bp):   
AGCCGCCCCACCGCGACGGCCTGCCGTGGCGA

Found at i:151 original size:32 final size:32

Alignment explanation


    Indices: 50--222  Score: 159
    Period size: 32  Copynumber: 5.3  Consensus size: 32

         40 CCCCACCGAC

                      *                **   
         50 GCGGCCTGCCGTGGCGAAGCCGCCCCACCGGG
          1 GCGGCCTGCCCTGGCGAAGCCGCCCCAGTGGG

            *         *                **   
         82 ACGGCCTGCCGTGGCGAAGCCGCCCCACCGGG
          1 GCGGCCTGCCCTGGCGAAGCCGCCCCAGTGGG

            *                               
        114 ACGGCCTGCCCTGGCGAAGCCGCCCCAGTGGG
          1 GCGGCCTGCCCTGGCGAAGCCGCCCCAGTGGG

                    ** * * *          *      
        146 GCGGCCTATTCATAGTGAAGCCGCCCTAGT-GG
          1 GCGGCCT-GCCCTGGCGAAGCCGCCCCAGTGGG

                   *        *          *      
        178 GCGGCCTACCCAATGGTGAAGCCGCCCTAGTGGG
          1 GCGGCCTGCCC--TGGCGAAGCCGCCCCAGTGGG

                       
        212 GCGGCCTGCCC
          1 GCGGCCTGCCC

        223 ATGGTAAGCC


Statistics
Matches: 121,  Mismatches: 16, Indels: 6
        0.85            0.11        0.04

Matches are distributed among these distances:
  31    1  0.01
  32   75  0.62
  33   33  0.27
  34   12  0.10

ACGTcount: A:0.13, C:0.39, G:0.36, T:0.12


Consensus pattern (32 bp):   
GCGGCCTGCCCTGGCGAAGCCGCCCCAGTGGG

Found at i:171 original size:33 final size:34

Alignment explanation


    Indices: 129--248  Score: 131
    Period size: 33  Copynumber: 3.6  Consensus size: 34

        119 CTGCCCTGGC

                      *              **       
        129 GAAGCCGCCCCAGTGGGGCGGCCTATTC-ATAGT
          1 GAAGCCGCCCTAGTGGGGCGGCCTACCCAATAGT

                                           *  
        162 GAAGCCGCCCTAGT-GGGCGGCCTACCCAATGGT
          1 GAAGCCGCCCTAGTGGGGCGGCCTACCCAATAGT

                                    *      *  
        195 GAAGCCGCCCTAGTGGGGCGGCCTGCCC-ATGGT
          1 GAAGCCGCCCTAGTGGGGCGGCCTACCCAATAGT

                    *  **         
        228 -AAGCCGCACTCCTGGGGCGGC
          1 GAAGCCGCCCTAGTGGGGCGGC

        249 ACGGGTCATC


Statistics
Matches: 77,  Mismatches: 8, Indels: 5
        0.86            0.09        0.06

Matches are distributed among these distances:
  32   29  0.38
  33   36  0.47
  34   12  0.16

ACGTcount: A:0.16, C:0.33, G:0.36, T:0.15


Consensus pattern (34 bp):   
GAAGCCGCCCTAGTGGGGCGGCCTACCCAATAGT

Found at i:183 original size:64 final size:63

Alignment explanation


    Indices: 31--221  Score: 184
    Period size: 64  Copynumber: 3.0  Consensus size: 63

         21 GCCTACCGTG

                    *         *          *                **   *         * *
         31 GCGAAGCCACCCCACCGACGCGGCCTGCCGTGGCGAAGCCGCCCCACCGGGACGGCCTGCCGTG
          1 GCGAAGCCGCCCCACCG-GGCGGCCTGCCCTGGCGAAGCCGCCCCAGTGGGGCGGCCTGCCATA

                                                                       **    
         95 GCGAAGCCGCCCCACCGGGACGGCCTGCCCTGGCGAAGCCGCCCCAGTGGGGCGGCCTATTCATA
          1 GCGAAGCCGCCCCACCGGG-CGGCCTGCCCTGGCGAAGCCGCCCCAGTGGGGCGGCCT-GCCATA

             *          * **         *        *          *                
        160 GTGAAGCCGCCCTAGTGGGCGGCCTACCCAATGGTGAAGCCGCCCTAGTGGGGCGGCCTGCC
          1 GCGAAGCCGCCCCACCGGGCGGCCTGCCC--TGGCGAAGCCGCCCCAGTGGGGCGGCCTGCC

        222 CATGGTAAGC


Statistics
Matches: 104,  Mismatches: 19, Indels: 7
        0.80            0.15        0.05

Matches are distributed among these distances:
  63    1  0.01
  64   59  0.57
  65   18  0.17
  66   26  0.25

ACGTcount: A:0.15, C:0.40, G:0.35, T:0.10


Consensus pattern (63 bp):   
GCGAAGCCGCCCCACCGGGCGGCCTGCCCTGGCGAAGCCGCCCCAGTGGGGCGGCCTGCCATA

Found at i:244 original size:32 final size:34

Alignment explanation


    Indices: 142--248  Score: 105
    Period size: 32  Copynumber: 3.3  Consensus size: 34

        132 GCCGCCCCAG

                        **    *          *   *
        142 TGGGGCGGCCTATTC-ATAGTGAAGCCGCCCTAG
          1 TGGGGCGGCCTACCCAATGGTGAAGCCGCACTAC

                                         *   *
        175 T-GGGCGGCCTACCCAATGGTGAAGCCGCCCTAG
          1 TGGGGCGGCCTACCCAATGGTGAAGCCGCACTAC

                       *                    * 
        208 TGGGGCGGCCTGCCC-ATGGT-AAGCCGCACTCC
          1 TGGGGCGGCCTACCCAATGGTGAAGCCGCACTAC

                     
        240 TGGGGCGGC
          1 TGGGGCGGC

        249 ACGGGTCATC


Statistics
Matches: 65,  Mismatches: 7, Indels: 5
        0.84            0.09        0.06

Matches are distributed among these distances:
  32   29  0.45
  33   24  0.37
  34   12  0.18

ACGTcount: A:0.15, C:0.32, G:0.36, T:0.17


Consensus pattern (34 bp):   
TGGGGCGGCCTACCCAATGGTGAAGCCGCACTAC
Done.