Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000300.1 Corchorus olitorius cultivar O-4 contig00300, 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, 717

Length: 1196
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:620 original size:22 final size:22

Alignment explanation


    Indices: 578--820  Score: 179
    Period size: 22  Copynumber: 11.1  Consensus size: 22

        568 TTACACATTC

                  * *       *     
        578 TCATAGGGAGGTTATCGAAATT
          1 TCATAGTGTGGTTATCAAAATT

               *      *            
        600 TCACAGTGTGCTTATCAAAATTT
          1 TCATAGTGTGGTTATCAAAA-TT

                    *        *    
        623 TCATAGTGCGGTTA-C-CAATT
          1 TCATAGTGTGGTTATCAAAATT

                       *           
        643 AT-ATAGTGTGATTATCAAAATT
          1 -TCATAGTGTGGTTATCAAAATT

                  * * *           
        665 TCATAGGGAGATTATCAAAATT
          1 TCATAGTGTGGTTATCAAAATT

             * * *  *             
        687 TTACACTGAGGTTATCAAAATT
          1 TCATAGTGTGGTTATCAAAATT

             *                    
        709 TTATAGTGTGGTTATCAAAATT
          1 TCATAGTGTGGTTATCAAAATT

               *               *  
        731 TCACAGTGTGGTTATCAAACTT
          1 TCATAGTGTGGTTATCAAAATT

                     *   *   *  *  
        753 TCATAG-GAAGGTAATCGAAGTT
          1 TCATAGTG-TGGTTATCAAAATT

                 *  **         *  
        775 TCATAATGAAGTTATCAAATTT
          1 TCATAGTGTGGTTATCAAAATT

                     *        *   
        797 TCATAGTGTTGTTATCAATATT
          1 TCATAGTGTGGTTATCAAAATT

              
        819 TC
          1 TC

        821 TACGTTTGAG


Statistics
Matches: 174,  Mismatches: 40, Indels: 14
        0.76            0.18        0.06

Matches are distributed among these distances:
  20   12  0.07
  21    6  0.03
  22  142  0.82
  23   14  0.08

ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38


Consensus pattern (22 bp):   
TCATAGTGTGGTTATCAAAATT

Found at i:731 original size:66 final size:65

Alignment explanation


    Indices: 587--736  Score: 176
    Period size: 65  Copynumber: 2.3  Consensus size: 65

        577 CTCATAGGGA

                   *           * * *               * *  *      *             
        587 GGTTATCGAAATTTCACAGTGTGCTTATCAAAATTTTCATAGTGCGGTTACCAATTATATAGTGT
          1 GGTTATCAAAATTTCACAGGGAGATTATCAAAATTTTCACACTGAGGTTACAAATTATATAGTGT

             *              *                                         *      
        652 GATTATCAAAATTTCATAGGGAGATTATCAAAATTTT-ACACTGAGGTTATCAAAATTTTATAGT
          1 GGTTATCAAAATTTCACAGGGAGATTATCAAAATTTTCACACTGAGGTTA-C-AAATTATATAGT

              
        716 GT
         64 GT

                               
        718 GGTTATCAAAATTTCACAG
          1 GGTTATCAAAATTTCACAG

        737 TGTGGTTATC


Statistics
Matches: 70,  Mismatches: 13, Indels: 3
        0.81            0.15        0.03

Matches are distributed among these distances:
  64    9  0.13
  65   32  0.46
  66   29  0.41

ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37


Consensus pattern (65 bp):   
GGTTATCAAAATTTCACAGGGAGATTATCAAAATTTTCACACTGAGGTTACAAATTATATAGTGT

Done.