Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001886.1 Corchorus olitorius cultivar O-4 contig01886, 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, 776

Length: 1294
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34


Found at i:116 original size:22 final size:22

Alignment explanation


    Indices: 91--341  Score: 90
    Period size: 22  Copynumber: 11.3  Consensus size: 22

         81 TGTGGTTACT

                                  
         91 AAAATTTCATATGGAGGTTATC
          1 AAAATTTCATATGGAGGTTATC

                **  *     *        
        113 AAAACGTCCTAGTGTA-GTTATC
          1 AAAATTTCATA-TGGAGGTTATC

                   *    *   *    * 
        135 AAAATTTTATACAGG-CGTTACC
          1 AAAATTTCATA-TGGAGGTTATC

                       ***        
        157 AAAATTTCATAAAAAGGTTATC
          1 AAAATTTCATATGGAGGTTATC

               *    *      *       * 
        179 AAATTTTCTTA-GAGTGTCGTTAAC
          1 AAAATTTCATATG-GAG--GTTATC

                   *   * *        
        203 AAAATTTTATAAGAAGGTTATC
          1 AAAATTTCATATGGAGGTTATC

                           *       
        225 AAAATTT-ATA-GTGTGGTTATC
          1 AAAATTTCATATG-GAGGTTATC

                       *  *          
        246 AAAATTTCAT-GGGGGGAAATTATC
          1 AAAATTTCATATGGAGG---TTATC

               *    *  *        * 
        270 AAAGTTTCTTAGGGAGGTTAAC
          1 AAAATTTCATATGGAGGTTATC

                                   
        292 AAAATTTCAT-TGGAAGGTTA-C
          1 AAAATTTCATATGG-AGGTTATC

                                     
        313 AAAAATTT--TATGGAGATGTTATC
          1 -AAAATTTCATATGGAG--GTTATC

                  
        336 AAAATT
          1 AAAATT

        342 AGATAAAGAG


Statistics
Matches: 170,  Mismatches: 39, Indels: 40
        0.68            0.16        0.16

Matches are distributed among these distances:
  20    4  0.02
  21   27  0.16
  22  102  0.60
  23    4  0.02
  24   27  0.16
  25    6  0.04

ACGTcount: A:0.38, C:0.10, G:0.18, T:0.35


Consensus pattern (22 bp):   
AAAATTTCATATGGAGGTTATC

Found at i:462 original size:22 final size:21

Alignment explanation


    Indices: 431--508  Score: 75
    Period size: 22  Copynumber: 3.6  Consensus size: 21

        421 TGCGCTTACC

                 *                
        431 AATTTTATAGTGTGATTATCAA
          1 AATTTCATAG-GTGATTATCAA

                        *         
        453 AATTTCATAGGAAGATTATCAA
          1 AATTTCATAGG-TGATTATCAA

                   *   *  *       
        475 AATTTCACAGACTGGTTATCAA
          1 AATTTCATAG-GTGATTATCAA

             *          
        497 ATTTTCATAGGT
          1 AATTTCATAGGT

        509 TATCAATTTC


Statistics
Matches: 45,  Mismatches: 9, Indels: 5
        0.76            0.15        0.08

Matches are distributed among these distances:
  21    2  0.04
  22   43  0.96

ACGTcount: A:0.37, C:0.10, G:0.14, T:0.38


Consensus pattern (21 bp):   
AATTTCATAGGTGATTATCAA
Done.