Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011400.1 Corchorus olitorius cultivar O-4 contig11433, 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: 1698
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.22


Found at i:290 original size:154 final size:154

Alignment explanation


    Indices: 9--1696  Score: 2564
    Period size: 154  Copynumber: 11.0  Consensus size: 154

          1 ATAGGCCA

                                                                     *       
          9 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATATCACCAA
          1 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA

                                         *      *                    **      
         74 AATGATTATAGTTAGGCCATAAACAACT-TAAAGAATAGCTTTGAGGTTTGCCAAATTTAAGACG
         66 AATGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACG

                      **            *
        138 ATTCAAAACGGAACTAATGGGCCCA
        130 ATTCAAAACGTCACTAATGGGCCCC

                                                     *                       
        163 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTAATCTCACCAA
          1 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA

                           *                       *                         
        228 AATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCCTTGAGGTTTGCCAAATCGAAGACGA
         66 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGA

                                    
        293 TTCAAAACGTCACTAATGGGCCCC
        131 TTCAAAACGTCACTAATGGGCCCC

                                                 *                           
        317 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAA
          1 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA

             *                       *                                       
        382 ATTGATTATAGTTAGGCCATAAACATTGGAAAGATAAA-CTTTGAGGTTTGCCAAATCGAAGACG
         66 AATGATTATAGTTAGGCCATAAACAATGGAAAGA-AAAGCTTTGAGGTTTGCCAAATCGAAGACG

                                     
        446 ATTCAAAACGTCACTAATGGGCCCC
        130 ATTCAAAACGTCACTAATGGGCCCC

                                                 *    *       *          *   
        471 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTGCACAGTGTACTAATCTCATCAA
          1 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA

                                         *                               *   
        536 AATGATTATAGTTAGGCCATAAACAACT-TAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAAACG
         66 AATGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACG

                                    *
        600 ATTCAAAACGTCACTAATGGGCCCA
        130 ATTCAAAACGTCACTAATGGGCCCC

                                                                             
        625 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
          1 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA

                   *       *       *                  *          *           
        690 AATGATTGTAGTTAGTCCATAAATAATGGAAAGAAAAGCTTTAAGGTTTGCCACATCGAAGACGA
         66 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGA

              *      **     *       
        755 TTTAAAACGGAACTAAAGGGCCCC
        131 TTCAAAACGTCACTAATGGGCCCC

                                 * *             *   *   *                   
        779 GATAGGCCCAAAATAACAAGTCTACCAAATGAGCTAAGAACATCATAGTGGACTAATCTCACCAA
          1 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA

                                         *        *          *       *    ** 
        844 AATGATTATAGTTAGGCCATAAACAACT-TAAA-AAAAACTTTGAGGTTAGCCAAATTGAAGGTG
         66 AATGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACG

                      **      *      
        907 ATTCAAAACGGAACTAATAGG-CCC
        130 ATTCAAAACGTCACTAATGGGCCCC

                               *      *      *                               
        931 GATAGGCCCAAAATAACAACTGTTCCGAATGAGTTAAAAACTTCACAGTGGACTAATCTCACCAA
          1 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA

                                         *         * *                       
        996 AATGATTATAGTTAGGCCATAAACAATGGTAAGAAAAGCCTAGAGGTTTGCCAAATCGAAGACGA
         66 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGA

                   *    *           
       1061 TTCAAAATGTCAGTAATGGGCCCC
        131 TTCAAAACGTCACTAATGGGCCCC

                            *     *                        *                 
       1085 GATAGGCCCAAAAT-AGAAGTGATCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAA
          1 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA

             * *                     *             *                         
       1149 ATTAATTATAGTTAGGCCATAAACATTGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
         66 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGA

                                  * 
       1214 TTCAAAACGTCACTAATGGGCCGC
        131 TTCAAAACGTCACTAATGGGCCCC

                                                *                    *       
       1238 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAGAAACTTCACAGTGGACTAATATCACCAA
          1 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA

                                *       *          *         *              *
       1303 AATGATTATAGTTAGGCCATCAACAATGTAAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGG
         66 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGA

                     *              
       1368 TTCAAAACGACACTAATGGGCCCC
        131 TTCAAAACGTCACTAATGGGCCCC

                                          *                                  
       1392 GATAGGCCCAAAATAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
          1 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA

                           *                *      *                         
       1457 AATGATTATAGTTAGTCCATAAACAATGGAAATAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
         66 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGA

                       *             
       1522 TTCAAAACAG-AACTAATGGGCCCC
        131 TTCAAAAC-GTCACTAATGGGCCCC

                 *                        *             *                    
       1546 GATAGTCCCAAAATAACAAGTGTTCCAAATAAGCTAAAAACTTCCCAGTGGACTAATCTCACCAA
          1 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA

                                                   *      *        *         
       1611 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAAACGAAGACGA
         66 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGA

                                 
       1676 TTCAAAACGTCACTAATGGGC
        131 TTCAAAACGTCACTAATGGGC

       1697 GT


Statistics
Matches: 1394,  Mismatches: 128, Indels: 24
        0.90            0.08        0.02

Matches are distributed among these distances:
 151    1  0.00
 152   88  0.06
 153  226  0.16
 154  1073  0.77
 155    6  0.00

ACGTcount: A:0.40, C:0.19, G:0.18, T:0.22


Consensus pattern (154 bp):   
GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGA
TTCAAAACGTCACTAATGGGCCCC

Done.