Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002635.1 Corchorus olitorius cultivar O-4 contig02637, 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: 2175
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34


Found at i:149 original size:64 final size:62

Alignment explanation


    Indices: 16--162  Score: 172
    Period size: 64  Copynumber: 2.3  Consensus size: 62

          6 TCGAAATAGT

                         *        * *                                     
         16 GGCGTTTAAACGCTGCTATATATACTTTAAAAAACTTAGTATTTTCGAAAAAACTATATTGC
          1 GGCGTTTAAACGCCGCTATATACAATTTAAAAAACTTAGTATTTTCGAAAAAACTATATTGC

                                                    *        *               
         78 GGCGTTTAAACGCCGCTATATACAATTTAAAAAAAACTTATTATTTTCGGAAAAA-TAGTA-TGA
          1 GGCGTTTAAACGCCGCTATATACAATTT--AAAAAACTTAGTATTTTCGAAAAAACTA-TATTG-

             
        141 C
         62 C

              *      *    *      
        142 GGTGTTTAACCGCCTCTATAT
          1 GGCGTTTAAACGCCGCTATAT

        163 GACGGCGTTT


Statistics
Matches: 73,  Mismatches: 8, Indels: 6
        0.84            0.09        0.07

Matches are distributed among these distances:
  62   25  0.34
  63    4  0.05
  64   44  0.60

ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34


Consensus pattern (62 bp):   
GGCGTTTAAACGCCGCTATATACAATTTAAAAAACTTAGTATTTTCGAAAAAACTATATTGC

Found at i:2004 original size:32 final size:32

Alignment explanation


    Indices: 1968--2057  Score: 144
    Period size: 32  Copynumber: 2.8  Consensus size: 32

       1958 GATTTAGGGT

                             * *            
       1968 GTCTATTGAAGAAAACGACGCTATTTACCGGC
          1 GTCTATTGAAGAAAACGCCCCTATTTACCGGC

                                       *   *
       2000 GTCTATTGAAGAAAACGCCCCTATTTAGCGGT
          1 GTCTATTGAAGAAAACGCCCCTATTTACCGGC

                                      
       2032 GTCTATTGAAGAAAACGCCCCTATTT
          1 GTCTATTGAAGAAAACGCCCCTATTT

       2058 TGCGGCTTCT


Statistics
Matches: 54,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  32   54  1.00

ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28


Consensus pattern (32 bp):   
GTCTATTGAAGAAAACGCCCCTATTTACCGGC

Found at i:2074 original size:32 final size:32

Alignment explanation


    Indices: 1969--2079  Score: 143
    Period size: 32  Copynumber: 3.5  Consensus size: 32

       1959 ATTTAGGGTG

                            * *       *    *
       1969 TCTATTGAAGAAAACGACGCTATTTACCGGCG
          1 TCTATTGAAGAAAACGCCCCTATTTAGCGGCT

                                            
       2001 TCTATTGAAGAAAACGCCCCTATTTAGCGG-T
          1 TCTATTGAAGAAAACGCCCCTATTTAGCGGCT

                                      *      
       2032 GTCTATTGAAGAAAACGCCCCTATTTTGCGGCT
          1 -TCTATTGAAGAAAACGCCCCTATTTAGCGGCT

                *     *    
       2065 TCTAGTGAAGCAAAC
          1 TCTATTGAAGAAAAC

       2080 ACTGTAAAAT


Statistics
Matches: 70,  Mismatches: 7, Indels: 4
        0.86            0.09        0.05

Matches are distributed among these distances:
  32   69  0.99
  33    1  0.01

ACGTcount: A:0.30, C:0.23, G:0.21, T:0.27


Consensus pattern (32 bp):   
TCTATTGAAGAAAACGCCCCTATTTAGCGGCT

Found at i:2074 original size:64 final size:63

Alignment explanation


    Indices: 1959--2079  Score: 170
    Period size: 64  Copynumber: 1.9  Consensus size: 63

       1949 AAAGCCCCAG

                                        *                 *                
       1959 ATTTAGGGTGTCTATTGAAGAAAACGACGCTATTTACCGGCGTCTATTGAAGAAAACGCCCCT
          1 ATTTAGGGTGTCTATTGAAGAAAACGACCCTATTTACCGGCGTCTAGTGAAGAAAACGCCCCT

                                       *        **    *          *    
       2022 ATTTAGCGGTGTCTATTGAAGAAAACGCCCCTATTTTGCGGCTTCTAGTGAAGCAAAC
          1 ATTTAG-GGTGTCTATTGAAGAAAACGACCCTATTTACCGGCGTCTAGTGAAGAAAAC

       2080 ACTGTAAAAT


Statistics
Matches: 50,  Mismatches: 7, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  63    6  0.12
  64   44  0.88

ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28


Consensus pattern (63 bp):   
ATTTAGGGTGTCTATTGAAGAAAACGACCCTATTTACCGGCGTCTAGTGAAGAAAACGCCCCT
Done.