Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014679.1 Corchorus olitorius cultivar O-4 contig14712, 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: 3329
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37


Found at i:2001 original size:22 final size:22

Alignment explanation


    Indices: 1973--2187  Score: 127
    Period size: 22  Copynumber: 9.7  Consensus size: 22

       1963 TGTCTCTGTG

                                  
       1973 TGGTTATCAAAATTTCATAAGA
          1 TGGTTATCAAAATTTCATAAGA

                   * *          *  
       1995 TGGTTATTATAATTTCATGAGGA
          1 TGGTTATCAAAATTTCAT-AAGA

                          *       
       2018 -GGTTATCAAAATTCCAT-AG-
          1 TGGTTATCAAAATTTCATAAGA

                    *             *  
       2037 TGTGCTTACCAAAATTTCATATGGA
          1 TG-G-TTATCAAAATTTCATA-AGA

             * *              **  
       2062 -AGCTATCAAAATTTCATGGGA
          1 TGGTTATCAAAATTTCATAAGA

            *                     *
       2083 AGGTTATCAAAATTTCAT-AGTG
          1 TGGTTATCAAAATTTCATAAG-A

                  *            *  
       2105 TGGTTACCAAAATTTCATAGGA
          1 TGGTTATCAAAATTTCATAAGA

                     *           *  
       2127 TCAGGTTATTAAAATTTCATACGA
          1 T--GGTTATCAAAATTTCATAAGA

            *      **              
       2151 AGGTTATTGAAATTTCAT-AGTA
          1 TGGTTATCAAAATTTCATAAG-A

             *       *     
       2173 TAGTTATCACAATTT
          1 TGGTTATCAAAATTT

       2188 TCTAGAAAAG


Statistics
Matches: 147,  Mismatches: 33, Indels: 26
        0.71            0.16        0.13

Matches are distributed among these distances:
  20    2  0.01
  21    6  0.04
  22  115  0.78
  23    5  0.03
  24   19  0.13

ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37


Consensus pattern (22 bp):   
TGGTTATCAAAATTTCATAAGA

Found at i:2236 original size:22 final size:22

Alignment explanation


    Indices: 2211--2651  Score: 213
    Period size: 22  Copynumber: 19.9  Consensus size: 22

       2201 ATCAAAGAGA

                      *           
       2211 TTATCAAAATGTCATAGTGAGG
          1 TTATCAAAATTTCATAGTGAGG

                                *  
       2233 TTAT-AAGAATTTCATAGTGTGG
          1 TTATCAA-AATTTCATAGTGAGG

               *                   
       2255 TTAACAAAATTTCATAAG-GAGG
          1 TTATCAAAATTTCAT-AGTGAGG

                    *       * *    
       2277 TTA-CTAATATTTCATGGGGAGG
          1 TTATC-AAAATTTCATAGTGAGG

                               *  
       2299 TTATCAAAATTTCATAGTGTGG
          1 TTATCAAAATTTCATAGTGAGG

                        **     *  
       2321 TTATCAAAATTTTGTAGTGTGG
          1 TTATCAAAATTTCATAGTGAGG

                                   
       2343 TTATCAAAATTTCATA-TGAAGG
          1 TTATCAAAATTTCATAGTG-AGG

                       *           *   
       2365 TTAT-AAAAGTCTCAATTTCA-TAAGG
          1 TTATCAAAA-TTTC-A--T-AGTGAGG

             *  *     *  *     *   
       2390 AGTACCAAAAATTGATAG-AAGG
          1 -TTATCAAAATTTCATAGTGAGG

                      *      * * *
       2412 TTATC-AAATCTCATAGAGTGA
          1 TTATCAAAATTTCATAGTGAGG

                 *               * **
       2433 TTATCGAAATTTCATAAAGATTAAA
          1 TTATCAAAATTTCAT--AG-TGAGG

                                  *
       2458 TTATCAAAATTT-ATAG-GAAGA
          1 TTATCAAAATTTCATAGTG-AGG

                            *    * 
       2479 TTATCAAAATTTCATAAT-ATTG
          1 TTATCAAAATTTCATAGTGA-GG

                          *  *    
       2501 TTATCAAAATTTCAGAGCGAGG
          1 TTATCAAAATTTCATAGTGAGG

            *          *    *  * *
       2523 CTATCAAAATTACATAATGTGA
          1 TTATCAAAATTTCATAGTGAGG

                             * *  
       2545 TTATCAAAATTTCATAGAGGGG
          1 TTATCAAAATTTCATAGTGAGG

             * *        *    *    
       2567 TCAACAAAATTTTATAGAGAGG
          1 TTATCAAAATTTCATAGTGAGG

                        *   **    
       2589 TTATCAAAATTTTATAAAGAGG
          1 TTATCAAAATTTCATAGTGAGG

                           * *  * *
       2611 TTATC-AAATTTGCAAAATGTGA
          1 TTATCAAAATTT-CATAGTGAGG

               *               
       2633 TTACCAAAATTTCATAGTG
          1 TTATCAAAATTTCATAGTG

       2652 GTATTTCTGG


Statistics
Matches: 319,  Mismatches: 73, Indels: 54
        0.72            0.16        0.12

Matches are distributed among these distances:
  20    8  0.03
  21   40  0.13
  22  227  0.71
  23   14  0.04
  24    4  0.01
  25   17  0.05
  26    5  0.02
  27    4  0.01

ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34


Consensus pattern (22 bp):   
TTATCAAAATTTCATAGTGAGG

Done.