Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010683.1 Corchorus olitorius cultivar O-4 contig10715, 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: 14020
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:739 original size:14 final size:14

Alignment explanation


    Indices: 635--740  Score: 74
    Period size: 14  Copynumber: 7.4  Consensus size: 14

        625 ATTTTGCTAA

                        * 
        635 TTTCTAAATATTTT
          1 TTTCTAAATATTAT

                      *   
        649 TTTCTAAATAATAT
          1 TTTCTAAATATTAT

                    *       *
        663 TTAAT-TACATATATAA
          1 TT--TCTAAATAT-TAT

               *          
        679 TTTGTAAATATTAT
          1 TTTCTAAATATTAT

              *    *      
        693 TTCCTAATTA-TAT
          1 TTTCTAAATATTAT

                           
        706 TTTCTAAA-ATTTAT
          1 TTTCTAAATA-TTAT

             *             
        720 AATTCTAAATATTAT
          1 -TTTCTAAATATTAT

                  
        735 TTTCTA
          1 TTTCTA

        741 GTTATAATTT


Statistics
Matches: 70,  Mismatches: 14, Indels: 16
        0.70            0.14        0.16

Matches are distributed among these distances:
  12    1  0.01
  13    9  0.13
  14   32  0.46
  15   22  0.31
  16    6  0.09

ACGTcount: A:0.38, C:0.08, G:0.01, T:0.54


Consensus pattern (14 bp):   
TTTCTAAATATTAT

Found at i:778 original size:44 final size:43

Alignment explanation


    Indices: 632--793  Score: 175
    Period size: 44  Copynumber: 3.7  Consensus size: 43

        622 TTTATTTTGC

                           *   *    *          *      *  
        632 TAATTTCTAAATATTTTTTTCTAAATA-ATATTTAATTACATATA
          1 TAATTTCTAAATATTATTTCCTAATTATA-ATTT-CTTACATTTA

                  *                      *     * *     
        676 TAATTTGTAAATATTATTTCCTAATTATATTTTCTAAAATTTA
          1 TAATTTCTAAATATTATTTCCTAATTATAATTTCTTACATTTA

                               *   *                    
        719 TAA-TTCTAAATATTATTTTCTAGTTATAATTTCGTTACATTTA
          1 TAATTTCTAAATATTATTTCCTAATTATAATTTC-TTACATTTA

                  *                         
        762 TAATTTTTAAATATTATTTCCTAATTATAATT
          1 TAATTTCTAAATATTATTTCCTAATTATAATT

        794 ATATCATTTC


Statistics
Matches: 97,  Mismatches: 18, Indels: 6
        0.80            0.15        0.05

Matches are distributed among these distances:
  42   26  0.27
  43   19  0.20
  44   51  0.53
  45    1  0.01

ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54


Consensus pattern (43 bp):   
TAATTTCTAAATATTATTTCCTAATTATAATTTCTTACATTTA

Found at i:5553 original size:32 final size:32

Alignment explanation


    Indices: 5445--5556  Score: 134
    Period size: 32  Copynumber: 3.4  Consensus size: 32

       5435 AAAAAAACCA

                      *                     
       5445 AAATAGCGGCATTTATGTACGGAAACGCCATT
          1 AAATAGCGGCGTTTATGTACGGAAACGCCATT

                  *  *      * *         *     
       5477 AAATAGGGGTGTTTTTTTTTACGGAAACACCATT
          1 AAATAGCGGCG--TTTATGTACGGAAACGCCATT

                                *         * 
       5511 AAATAGCGGCGTTTATGTACTGAAACGCCAGT
          1 AAATAGCGGCGTTTATGTACGGAAACGCCATT

                          
       5543 AAATAGCGGCGTTT
          1 AAATAGCGGCGTTT

       5557 CTGGAAACGT


Statistics
Matches: 65,  Mismatches: 13, Indels: 4
        0.79            0.16        0.05

Matches are distributed among these distances:
  32   38  0.58
  34   27  0.42

ACGTcount: A:0.31, C:0.16, G:0.23, T:0.29


Consensus pattern (32 bp):   
AAATAGCGGCGTTTATGTACGGAAACGCCATT
Done.