Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000465.1 Corchorus olitorius cultivar O-4 contig00465, 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, 823

Length: 1372
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38


Found at i:321 original size:91 final size:92

Alignment explanation


    Indices: 139--332  Score: 220
    Period size: 91  Copynumber: 2.2  Consensus size: 92

        129 AATCTCATTG

                                  *                        *     *           
        139 TGAAATTTCGATAACCTC----CCTATGAAAATTTGATAATCACACTGTGAAATTCTGATAACCA
          1 TGAAATTTCGATAACCTCATTGTCTATGAAAATTTGATAATCACACTATGAAAATCTGATAACCA

                *                      
        200 CACTGTGAAATTCTGATAACCACACAA
         66 CACTATGAAATTCTGATAACCACACAA

                *   *                      *             *            *   * *
        227 TGAAGTTTTGATAACCTCATTGTCTATGAAATTTTGATAATCACATTAT-AAAAT-TGGTAATCG
          1 TGAAATTTCGATAACCTCATTGTCTATGAAAATTTGATAATCACACTATGAAAATCTGATAACCA

                         *            * 
        290 CACTATGAAAATTTTGATAACCACACCA
         66 CACTATG-AAATTCTGATAACCACACAA

                           
        318 TGAAATTTCGATAAC
          1 TGAAATTTCGATAAC

        333 TTCCCTATAA


Statistics
Matches: 86,  Mismatches: 15, Indels: 7
        0.80            0.14        0.06

Matches are distributed among these distances:
  88   16  0.19
  90   12  0.14
  91   35  0.41
  92   23  0.27

ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32


Consensus pattern (92 bp):   
TGAAATTTCGATAACCTCATTGTCTATGAAAATTTGATAATCACACTATGAAAATCTGATAACCA
CACTATGAAATTCTGATAACCACACAA

Found at i:325 original size:22 final size:22

Alignment explanation


    Indices: 96--679  Score: 169
    Period size: 22  Copynumber: 26.4  Consensus size: 22

         86 CTCCAACGTA

                 *              **
         96 GAAATATTGATAACCACACTGC
          1 GAAATTTTGATAACCACACTAT

                *        * *  * * 
        118 GAAAATTTGATAATCTCATTGT
          1 GAAATTTTGATAACCACACTAT

                   *       * *    
        140 GAAATTTCGATAACCTCCCTAT
          1 GAAATTTTGATAACCACACTAT

                *        *      * 
        162 GAAAATTTGATAATCACACTGT
          1 GAAATTTTGATAACCACACTAT

                  *             * 
        184 GAAATTCTGATAACCACACTGT
          1 GAAATTTTGATAACCACACTAT

                  *            *  
        206 GAAATTCTGATAACCACACAAT
          1 GAAATTTTGATAACCACACTAT

               *           *          
        228 GAAGTTTTGATAACCTCATTGTCTAT
          1 GAAATTTTGATAACCACA----CTAT

                         *    *   
        254 GAAATTTTGATAATCACATTAT
          1 GAAATTTTGATAACCACACTAT

                 *   *   * *      
        276 -AAA-ATTGGTAATCGCACTAT
          1 GAAATTTTGATAACCACACTAT

                                *  
        296 GAAAATTTTGATAACCACACCAT
          1 G-AAATTTTGATAACCACACTAT

                   *         *           
        319 GAAATTTCGATAACTTCCCTA-TAAGAAT
          1 GAAATTTTGATAAC--CAC-ACT----AT

                  *     ** *       
        347 GAAATTGTGATATTCTCTA-TAT
          1 GAAATTTTGATAACCAC-ACTAT

             *             * * *  
        369 GTAATTTTGATAACCTCTCCAT
          1 GAAATTTTGATAACCACACTAT

                     *    * * *    
        391 -AATATTTTCATAAGCTCCCTAT
          1 GAA-ATTTTGATAACCACACTAT

                     * *          *
        413 GAAATTTTGTTCACCATC-CTAG
          1 GAAATTTTGATAACCA-CACTAT

                          *       
        435 GAAATTTTGATAA-GA-AC---
          1 GAAATTTTGATAACCACACTAT

                           ***     
        452 -AAATTTTGATAA-CGTTCTAAT
          1 GAAATTTTGATAACCACACT-AT

             *           *        
        473 -TAATTTTGATAATCACACTAT
          1 GAAATTTTGATAACCACACTAT

            *      **       **     
        494 AAAATTTCAATAA-CATTCGTAT
          1 GAAATTTTGATAACCACAC-TAT

                                   *
        516 GAAATTTTGATAATCTC-CA-TAA
          1 GAAATTTTGATAA-C-CACACTAT

              *             ****   
        538 GAGATTTTGATAACCTTTTTTAT
          1 GAAATTTTGATAACC-ACACTAT

                     *     * **   
        561 GAAATTTTGGTAACCTCTGTAT
          1 GAAATTTTGATAACCACACTAT

                         ** *    *
        583 GAAATTTTGATAATTAAACTAC
          1 GAAATTTTGATAACCACACTAT

               *            *      
        605 GAAGTTTTGATAACCTTCA-TAT
          1 GAAATTTTGATAACC-ACACTAT

                     *            
        627 GAAATTTTGGTAACCACACTAT
          1 GAAATTTTGATAACCACACTAT

                    *      **     
        649 GAAATTTTAATAACCTTACTAT
          1 GAAATTTTGATAACCACACTAT

             *       
        671 GTAATTTTG
          1 GAAATTTTG

        680 GTTTGATTGT


Statistics
Matches: 410,  Mismatches: 117, Indels: 70
        0.69            0.20        0.12

Matches are distributed among these distances:
  16   12  0.03
  17    1  0.00
  20   15  0.04
  21   24  0.06
  22  287  0.70
  23   32  0.08
  24    2  0.00
  25    2  0.00
  26   23  0.06
  28   12  0.03

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


Consensus pattern (22 bp):   
GAAATTTTGATAACCACACTAT

Done.