Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013145.1 Corchorus capsularis cultivar CVL-1 contig13166, 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: 6441
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:893 original size:2 final size:2

Alignment explanation


    Indices: 886--913  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

        876 GGCCTTGAAA

                                                     
        886 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        914 TGGTAAATCG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:5266 original size:48 final size:47

Alignment explanation


    Indices: 4989--5465  Score: 497
    Period size: 49  Copynumber: 9.7  Consensus size: 47

       4979 TCTCAAATTT

                                                            
       4989 TGTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACC
          1 TGTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTT-ATTTTACC

                                     *                       
       5037 TGTTATTTCCCAAAATGCCCTTCCCAGACGGAAGGCATTTGATTTTACC
          1 TGTT-TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTT-ATTTTACC

                                        *   *                
       5086 TGTTATTTCCCAAAATGCCCTTCCCGGATGGAGGGCATTTGATTTTACC
          1 TGTT-TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTT-ATTTTACC

                *     *                 *               *    
       5135 TGCTATTTCCTAAAATGCCCTTCCCGGATGGAAGGCATTTACTTCTACC
          1 TG-TTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA-TTTTACC

                       *     *           *                    
       5184 TGCTATTTTCCAAAAATACCCTTCCCGGATGGAAGGCATTTACTTTTACC
          1 TG-T-TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA-TTTTACC

                     *    *          *          * *         
       5234 TGTTTTTCCTAAAACGCCCTTCCCGAACGGAAGGCACTAATCTTTACC
          1 TGTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTAT-TTTACC

                                             *  *             
       5282 TGTTTTTCCCAAAATGCCCTTCCCGGACGGAAGACACTTATTTTACTTGC
          1 TGTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTAC---C

               *       *                       * **            
       5332 TATTTTTTTCCAAAAATGCCCTTCCCGGACGGAAGACGCTTATTTTTACCC
          1 --TGTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA-TTTTA-CC

            **           *                      * *        *
       5383 ACTTTTTCCCAAAGTG-CCTTCCCGGACGGAAGGCACTAACTTTTACT
          1 TGTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA-TTTTACC

                      *    *                    
       5430 TGCTTTTTCCTAAAACGCCCTTCCCGGACGGAAGGC
          1 TG-TTTTTCCCAAAATGCCCTTCCCGGACGGAAGGC

       5466 GTTAGTTTTG


Statistics
Matches: 374,  Mismatches: 41, Indels: 27
        0.85            0.09        0.06

Matches are distributed among these distances:
  47    7  0.02
  48  113  0.30
  49  165  0.44
  50   45  0.12
  51    1  0.00
  52   37  0.10
  53    5  0.01
  54    1  0.00

ACGTcount: A:0.23, C:0.28, G:0.17, T:0.32


Consensus pattern (47 bp):   
TGTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTACC

Done.