Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013169.1 Corchorus capsularis cultivar CVL-1 contig13190, 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: 4260
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28


Found at i:72 original size:8 final size:8

Alignment explanation


    Indices: 44--77  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

         34 GAATTGGCTA

                    
         44 TGAATTTT
          1 TGAATTTT

                    *
         52 TGAAGTTTC
          1 TGAA-TTTT

                    
         61 TGAATTTT
          1 TGAATTTT

                    
         69 TGAATTTT
          1 TGAATTTT

             
         77 T
          1 T

         78 CAAGAAGGGT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   8   16  0.70
   9    7  0.30

ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59


Consensus pattern (8 bp):   
TGAATTTT

Found at i:3963 original size:50 final size:49

Alignment explanation


    Indices: 3853--4260  Score: 498
    Period size: 49  Copynumber: 8.3  Consensus size: 49

       3843 TTACCTACTT

                *               *  *     * *  *           *  *
       3853 TTTCTCAAAACGCCCTTCCCGGATGGAAGGCGTTTATTTTTA-TTAACTT
          1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTT-GCTA

                                *        *  *          *     *
       3902 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTCAATTTTTATTTGCTT
          1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTC-ATTTTTACTTGCTA

                  *            **        *                    
       3952 TTTCCCTAAACGCCCTTCCTGGACGGAAGACACTTCATTTTTACTTGCTA
          1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCA-TTCATTTTTACTTGCTA

                     *                           *           
       4002 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTCATCTTTACTTGCTA
          1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTA

                                                 *           
       4051 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTCATCTTTACTTGCTA
          1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTA

                                                 *     *     
       4100 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTCATCTTTACGTGCTA
          1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTA

             *         *                      *              
       4149 TCTCCCAAAACACCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTA
          1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTA

                     *         *   *                          
       4198 TTTCCCAAAGCGCCCTTCCTAGATGGAAGCCAGTT-A-TTTTACTTGCTA
          1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCA-TTCATTTTTACTTGCTA

                     *     
       4246 TTTCCCAAAGCGCCC
          1 TTTCCCAAAACGCCC


Statistics
Matches: 325,  Mismatches: 30, Indels: 9
        0.89            0.08        0.02

Matches are distributed among these distances:
  48   27  0.08
  49  214  0.66
  50   80  0.25
  51    4  0.01

ACGTcount: A:0.23, C:0.31, G:0.14, T:0.31


Consensus pattern (49 bp):   
TTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTA

Done.