Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007270.1 Corchorus olitorius cultivar O-4 contig07295, 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, 610

Length: 1018
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42


Found at i:53 original size:22 final size:22

Alignment explanation


    Indices: 4--313  Score: 93
    Period size: 22  Copynumber: 14.0  Consensus size: 22

          1 ATT

                         *    *   
          4 TGTA-GTTATCAAGATTTAATA
          1 TGTAGGTTATCAAAATTTCATA

            * *               *   
         25 AGAAGGTTATCAAAATTTTATA
          1 TGTAGGTTATCAAAATTTCATA

                      *         *   
         47 TGTAGGTT-TAAATTAATTTTATA
          1 TGTAGGTTATCAA--AATTTCATA

            * *         *          
         70 GGAAGGTTTATCCAAATTTCATA
          1 TGTAGG-TTATCAAAATTTCATA

               *  *      *         
         93 -GCGAGATTATCACAATTTCATA
          1 TG-TAGGTTATCAAAATTTCATA

                  *              * 
        115 GTGT-GATTATCAAAATTTCAGA
          1 -TGTAGGTTATCAAAATTTCATA

                  *                  
        137 GTGT-GATTA-CTAACAA-TTCATA
          1 -TGTAGGTTATC-AA-AATTTCATA

              *     * *   *        
        159 TGGAGGTTTTTAAATTTTCATAA
          1 TGTAGGTTATCAAAATTTCAT-A

            *            *  *     
        182 CGT-GGTTATCAATATATCATA
          1 TGTAGGTTATCAAAATTTCATA

              *  *       *  *     
        203 TGGAGATTATCAACATCTCATA
          1 TGTAGGTTATCAAAATTTCATA

                *      *       *   
        225 GTGTTGGTTATGAAAATTTTAT-
          1 -TGTAGGTTATCAAAATTTCATA

               * *                 
        247 TCGGAAGTTATCAAAATTTCATA
          1 T-GTAGGTTATCAAAATTTCATA

                               * *  
        270 T-TGAGGTCT-TCAAAATTCCTTA
          1 TGT-AGGT-TATCAAAATTTCATA

            * *      *            
        292 CGGAGGTTAACAAAATTTCATA
          1 TGTAGGTTATCAAAATTTCATA

        314 AGAAGATTAA


Statistics
Matches: 209,  Mismatches: 58, Indels: 43
        0.67            0.19        0.14

Matches are distributed among these distances:
  21   13  0.06
  22  148  0.71
  23   43  0.21
  24    3  0.01
  25    2  0.01

ACGTcount: A:0.35, C:0.10, G:0.15, T:0.39


Consensus pattern (22 bp):   
TGTAGGTTATCAAAATTTCATA

Found at i:87 original size:23 final size:23

Alignment explanation


    Indices: 9--93  Score: 57
    Period size: 23  Copynumber: 3.7  Consensus size: 23

          1 ATTTGTAG

                         *   *      
          9 TTAT-CAAGATTTAATAAGAAGG-
          1 TTATCCAA-ATTTTATAGGAAGGT

                 *          * *    
         31 TTATCAAAATTTTATATGTAGGT
          1 TTATCCAAATTTTATAGGAAGGT

               ****                
         54 TTAAATTAATTTTATAGGAAGGT
          1 TTATCCAAATTTTATAGGAAGGT

                        *    
         77 TTATCCAAATTTCATAG
          1 TTATCCAAATTTTATAG

         94 CGAGATTATC


Statistics
Matches: 46,  Mismatches: 15, Indels: 3
        0.72            0.23        0.05

Matches are distributed among these distances:
  22   15  0.33
  23   31  0.67

ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41


Consensus pattern (23 bp):   
TTATCCAAATTTTATAGGAAGGT
Done.