Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013829.1 Corchorus olitorius cultivar O-4 contig13862, 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: 3394
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.24


Found at i:1414 original size:21 final size:21

Alignment explanation


    Indices: 1390--1502  Score: 158
    Period size: 21  Copynumber: 5.4  Consensus size: 21

       1380 CTTAGGCATT

                         *       
       1390 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
       1411 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *          * 
       1432 TCCAATGAACTTGGAACCTGC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       1453 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                                  
       1474 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
       1495 TCCAATGA
          1 TCCAATGA

       1503 ACTTCTAGCA


Statistics
Matches: 85,  Mismatches: 6, Indels: 2
        0.91            0.06        0.02

Matches are distributed among these distances:
  20    2  0.02
  21   83  0.98

ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:1894 original size:154 final size:154

Alignment explanation


    Indices: 1614--3394  Score: 2505
    Period size: 154  Copynumber: 11.6  Consensus size: 154

       1604 CATCACGTAC

                                    *                       *  *  *  *      *
       1614 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAATACAGATCTGATGGGCT
          1 ACAATGGAAAGAAAAGCATTGAGGATTGCCAAATCGAAGACAATTCAAAACGGAACTAATGGGCC

                *                         *               *                  
       1679 CCGAAAGGCCCAAAATAACAAGTGTTCCAATTGAGCTAAAAACTTCCCAGTGGACTAATCTCACC
         66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC

               *                    
       1744 AAAGTGATTATAGTTAGGCCATAA
        131 AAAATGATTATAGTTAGGCCATAA

                          *     **       *            *          **        * 
       1768 ACAATGGAAAGAAACGCATCAAAGG-TTGTCAAATCGAAGACGATTCAAAACGTCACTAATGGTC
          1 ACAATGGAAAGAAAAGCAT-TGAGGATTGCCAAATCGAAGACAATTCAAAACGGAACTAATGGGC

                                                             * *             
       1832 CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACCGAGGACTAATCTCAC
         65 CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAC

             *                  *    
       1897 CTAAATGATTATAGTTAGGCTATAA
        130 CAAAATGATTATAGTTAGGCCATAA

                                    *                         **      *      
       1922 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAAAATTGAACTATTGGGCC
          1 ACAATGGAAAGAAAAGCATTGAGGATTGCCAAATCGAAGACAATTCAAAACGGAACTAATGGGCC

            *        *                                                       
       1987 TCGATAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
         66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC

                               * *  *
       2052 AAAAAT-ATTATAGTTAGGTCGTAC
        131 -AAAATGATTATAGTTAGGCCATAA

                                    *              *                      *  
       2076 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGCCAATTCAAAACGGAACTAATGGTCC
          1 ACAATGGAAAGAAAAGCATTGAGGATTGCCAAATCGAAGACAATTCAAAACGGAACTAATGGGCC

            *       **                 *               *       *             
       2141 TCGATAGGTACAAAATAACAAGTGTTCAAAATGAGCTAAAAACGTCACAGTCGACTAATCTCACC
         66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC

                                    
       2206 AAAATGATTATAGTTAGGCCATAA
        131 AAAATGATTATAGTTAGGCCATAA

                                                      *             *    * * 
       2230 ACAATGGAAAGAAAAGCATTG-GGAATTGCCAAATCGAAGACGATTCAAAACGGAAATAATAGAC
          1 ACAATGGAAAGAAAAGCATTGAGG-ATTGCCAAATCGAAGACAATTCAAAACGGAACTAATGGGC

                 *                         *                                 
       2294 CCCGAAAGGCCCAAAATAACAAGTGTTCCAATTGAGCTAAAAACTTCACAGTGGACTAATCTCAC
         65 CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAC

                                     
       2359 CAAAATGATTATAGTTAGGCCATAA
        130 CAAAATGATTATAGTTAGGCCATAA

                                    *  *                                     
       2384 ACAATGGAAAGAAAAGCATTGAGGTTTACCAAATCGAAGACAATTCAAAACGGAACTAATGGGCC
          1 ACAATGGAAAGAAAAGCATTGAGGATTGCCAAATCGAAGACAATTCAAAACGGAACTAATGGGCC

            *        *      **     *                                         
       2449 TCGATAGGCACAAAATTGCAAGTCTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
         66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC

                             *      
       2514 AAAATGATTATAGTTAGCCCATAA
        131 AAAATGATTATAGTTAGGCCATAA

             *                                        *             *    * * 
       2538 AGAATGGAAAGAAAAGCATTG-GGAATTGCCAAATCGAAGACGATTCAAAACGGAAATAATCGAC
          1 ACAATGGAAAGAAAAGCATTGAGG-ATTGCCAAATCGAAGACAATTCAAAACGGAACTAATGGGC

                 *   *                   *                                   
       2602 CCCGAAAGGTCCAAAATAACAAGTGTTCCGAATGAGCTAAAAACTTCACAGTGGACTAATCTCAC
         65 CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAC

                *                    
       2667 CAAAGTGATTATAGTTAGGCCATAA
        130 CAAAATGATTATAGTTAGGCCATAA

                          *    *         *            *          **   *    * 
       2692 ACAATGGAAAGAAAGGCATCGAAGG-TTGTCAAATCGAAGACGATTCAAAACGTCACTGATGGTC
          1 ACAATGGAAAGAAAAGCATTG-AGGATTGCCAAATCGAAGACAATTCAAAACGGAACTAATGGGC

                                                               *             
       2756 CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGAGGACTAATCTCAC
         65 CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAC

             *                       
       2821 CTAAATGATTATAGTTAGGCCATAA
        130 CAAAATGATTATAGTTAGGCCATAA

                                    *                          *             
       2846 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAAAACTGAACTAATGGGCC
          1 ACAATGGAAAGAAAAGCATTGAGGATTGCCAAATCGAAGACAATTCAAAACGGAACTAATGGGCC

            **       *                      *              *                 
       2911 TTGATAGGCACAAAATAACAAGTGTTCCAAATTAGCTAAAAACTTCATAGTGGACTAATCTCACC
         66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC

                              * *  *
       2976 AAAATGATTATAGTTAGGTCGTAC
        131 AAAATGATTATAGTTAGGCCATAA

                                    *    *                      *            
       3000 ACAATGGAAAGAAAAGCATTGAGGTTTGCGAAATCGAAGACAATTCAAAACGAAACTAATGGGCC
          1 ACAATGGAAAGAAAAGCATTGAGGATTGCCAAATCGAAGACAATTCAAAACGGAACTAATGGGCC

            *      * *                 *               *     * *            *
       3065 TCGATAGTCACAAAATAACAAGTGTTCAAAATGAGCTAAAAACGTCACAATTGACTAATCTCACT
         66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC

                                    
       3130 AAAATGATTATAGTTAGGCCATAA
        131 AAAATGATTATAGTTAGGCCATAA

                                                      *               *      
       3154 ACAATGGAAAGAAAAGCATTG-GGAATTGCCAAATCGAAGACGATTCAAAACGGAACTTATGGGC
          1 ACAATGGAAAGAAAAGCATTGAGG-ATTGCCAAATCGAAGACAATTCAAAACGGAACTAATGGGC

                 *                                                           
       3218 CCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAC
         65 CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAC

                                     
       3283 CAAAATGATTATAGTTAGGCCATAA
        130 CAAAATGATTATAGTTAGGCCATAA

             *                 *               *      *             *      * 
       3308 AGAATGGAAAGAAAAGCATCG-GGAATTGCCAAATTGAAGACGATTCAAAACGGAAATAATGGAC
          1 ACAATGGAAAGAAAAGCATTGAGG-ATTGCCAAATCGAAGACAATTCAAAACGGAACTAATGGGC

                 *  *              
       3372 CCCGAAAGTCCCAAAATAACAAG
         65 CCCGATAGGCCCAAAATAACAAG


Statistics
Matches: 1447,  Mismatches: 169, Indels: 22
        0.88            0.10        0.01

Matches are distributed among these distances:
 153   17  0.01
 154  1419  0.98
 155    9  0.01
 156    2  0.00

ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21


Consensus pattern (154 bp):   
ACAATGGAAAGAAAAGCATTGAGGATTGCCAAATCGAAGACAATTCAAAACGGAACTAATGGGCC
CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
AAAATGATTATAGTTAGGCCATAA

Done.