Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015153.1 Corchorus olitorius cultivar O-4 contig15186, 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: 13622
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Found at i:185 original size:39 final size:40

Alignment explanation


    Indices: 126--206  Score: 119
    Period size: 39  Copynumber: 2.0  Consensus size: 40

        116 ATACCTAAGA

                           *                 *      
        126 ATTTAATTAATGCAAGTATTTCAGTTATTATA-GTATTAC
          1 ATTTAATTAATGCAAATATTTCAGTTATTATATATATTAC

                        *        *                  
        165 ATTTAATTAATGTAAATATTTTAGTTATTATATATATTAC
          1 ATTTAATTAATGCAAATATTTCAGTTATTATATATATTAC

              
        205 AT
          1 AT

        207 AGAAATTAAA


Statistics
Matches: 37,  Mismatches: 4, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  39   29  0.78
  40    8  0.22

ACGTcount: A:0.38, C:0.05, G:0.07, T:0.49


Consensus pattern (40 bp):   
ATTTAATTAATGCAAATATTTCAGTTATTATATATATTAC

Found at i:6241 original size:15 final size:15

Alignment explanation


    Indices: 6221--6257  Score: 56
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       6211 ACAATAACTC

                      *    
       6221 TTAATAAAAACAACA
          1 TTAATAAAAAAAACA

                           
       6236 TTAATAAAAAAAACA
          1 TTAATAAAAAAAACA

              *    
       6251 TTGATAA
          1 TTAATAA

       6258 CATTTTTTTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  15   20  1.00

ACGTcount: A:0.65, C:0.08, G:0.03, T:0.24


Consensus pattern (15 bp):   
TTAATAAAAAAAACA

Found at i:8237 original size:31 final size:31

Alignment explanation


    Indices: 8168--8361  Score: 248
    Period size: 31  Copynumber: 6.3  Consensus size: 31

       8158 AAAAATGACA

                *                  *    *  
       8168 CGTGGCACGTGTC-CTTTTT-GTGCACGAGG
          1 CGTGCCACGTGTCACTTTTTGGTACACGTGG

             *                  *          
       8197 CATGCCACGTGTCACTTTTTTGTACACGTGG
          1 CGTGCCACGTGTCACTTTTTGGTACACGTGG

                *                     *    
       8228 CGTGACACGTGTCACTTTTTGGTACATGTGG
          1 CGTGCCACGTGTCACTTTTTGGTACACGTGG

                                      *    
       8259 CGTGCCACGTGTCACTTTTTGGTACATGTGG
          1 CGTGCCACGTGTCACTTTTTGGTACACGTGG

                         *             *   
       8290 CGTGCCACGTGTCGCTTTTTGGTACACATGG
          1 CGTGCCACGTGTCACTTTTTGGTACACGTGG

                    *    *               * 
       8321 CGTGCCACATGTCGCTTTTTGGTACACGTTG
          1 CGTGCCACGTGTCACTTTTTGGTACACGTGG

             *        
       8352 CATGCCACGT
          1 CGTGCCACGT

       8362 CGGACACCGT


Statistics
Matches: 146,  Mismatches: 17, Indels: 2
        0.88            0.10        0.01

Matches are distributed among these distances:
  29   11  0.08
  30    6  0.04
  31  129  0.88

ACGTcount: A:0.14, C:0.25, G:0.28, T:0.34


Consensus pattern (31 bp):   
CGTGCCACGTGTCACTTTTTGGTACACGTGG

Done.