Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016589.1 Corchorus olitorius cultivar O-4 contig16622, 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: 2957
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25


Found at i:1029 original size:120 final size:120

Alignment explanation


    Indices: 816--1057  Score: 378
    Period size: 120  Copynumber: 2.0  Consensus size: 120

        806 GTTAGGCCAT

                                                       *           *        *
        816 ACACAATCGAAAGAAAAGCATTGAGGTTTGCAAAATCGAAGACGATTCAAAAACTCACTAATGGT
          1 ACACAATCGAAAGAAAAGCATTGAGGTTTGCAAAATCGAAGACAATTCAAAAACTAACTAATGGG

                                                             *     
        881 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAGAGTGG
         66 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG

                   *                       *                                 
        936 ACACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTC-AAAACTGAACTAATGG
          1 ACACAATCGAAAGAAAAGCATTGAGGTTTGCAAAATCGAAGACAATTCAAAAACT-AACTAATGG

               *                          *  *          *           
       1000 GCCTCGATAGGCCCAAAATAACAAGTGTTCGAATTGAGCTAAAATCTTCACAGTGG
         65 GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG

              
       1056 AC
          1 AC

       1058 TAATCTCCCC


Statistics
Matches: 111,  Mismatches: 10, Indels: 2
        0.90            0.08        0.02

Matches are distributed among these distances:
 119    6  0.05
 120  105  0.95

ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20


Consensus pattern (120 bp):   
ACACAATCGAAAGAAAAGCATTGAGGTTTGCAAAATCGAAGACAATTCAAAAACTAACTAATGGG
CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG

Found at i:1224 original size:154 final size:154

Alignment explanation


    Indices: 938--2955  Score: 2972
    Period size: 154  Copynumber: 13.1  Consensus size: 154

        928 CAGAGTGGAC

                                                     *            *          
        938 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAAAAC-TGAACTAATGGGC
          1 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGT-CACTAATGGGC

             *                          *  *          *                    * 
       1002 CTCGATAGGCCCAAAATAACAAGTGTTCGAATTGAGCTAAAATCTTCACAGTGGACTAATCTCCC
         65 CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAC

                             *      *
       1067 CAAAATGATTATAGTTAAGCCATAC
        130 CAAAATGATTATAGTTAGGCCATAA

                                         *                                *  
       1092 ACAATGGAAAGAAAAGCATTGAGGTTTGCAAAATCGAAGACGATTCAAAACGTCACTAATGGTCC
          1 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC

                       *                                               *     
       1157 CCGATAGGCCCTAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATTTCACC
         66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC

                                    
       1222 AAAATGATTATAGTTAGGCCATAA
        131 AAAATGATTATAGTTAGGCCATAA

            * *                                                              
       1246 GCTATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC
          1 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC

            *                                        *                       
       1311 TCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAGCTTCACAGTGGACTAATCTCACC
         66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC

                                    
       1376 AAAATGATTATAGTTAGGCCATAA
        131 AAAATGATTATAGTTAGGCCATAA

            *      *        *                  *                     *      *
       1400 CCAATGGGAAGAAAAGAATTGAGGTTTGCCAAATCAAAGACGATTCAAAACGTCACTGATGGGCA
          1 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC

                   *          *                                    *         
       1465 CCGATAGCCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACAAATCTCACC
         66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC

                                    
       1530 AAAATGATTATAGTTAGGCCATAA
        131 AAAATGATTATAGTTAGGCCATAA

                               *  *                  *          **        *  
       1554 ACAATGGAAAGAAAAGCATCGAAGTTTGCCAAATCGAAGACCATTCAAAACGGAACTAATGGACC
          1 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC

                     *                                             *         
       1619 CCGATAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACAAATCTCA-C
         66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC

                                    
       1683 AAAATGATTATAGTTAGGCCATAA
        131 AAAATGATTATAGTTAGGCCATAA

                                             *       *            *        * 
       1707 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAACCGAAGACAATTCAAAACCG-AACTAATGGAC
          1 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA-CGTCACTAATGGGC

             *        *                *                *                    
       1771 CTCGATAGGCAC-AAATAACAAGTGCTACCAAATGAGACTAAAAGCTTCACAGTGGACTAATCTC
         65 CCCGATAGGCCCAAAATAACAAGTG-TTCCAAATGAG-CTAAAAACTTCACAGTGGACTAATCTC

                                       *
       1835 AACCAAAATGATTATAGTTAGGCCATAC
        128 -ACCAAAATGATTATAGTTAGGCCATAA

             *                 *                *                     *      
       1863 AGAATGGAAAAGAAAAGCAATGAGGTTTGCCAAATCAAAGACGATTCAAAACGTCACTGATGGGC
          1 ACAATGG-AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGC

                                                                           * 
       1928 CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT-AAAACTTCACAGTGGACTAATCTCTC
         65 CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAC

                   *                 
       1992 CAAAATGGTTATAGTTAGGCCAT-A
        130 CAAAATGATTATAGTTAGGCCATAA

                               *    *                           **  *     *  
       2016 ACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGAAACAAATGGACC
          1 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC

                *    *           *                                           
       2081 CCGAAAGGCACAAAATAACAACTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
         66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC

                                    
       2146 AAAATGATTATAGTTAGGCCATAA
        131 AAAATGATTATAGTTAGGCCATAA

                            *                                        *      *
       2170 ACAATGGAAAGAAAAGAATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTGATGGGCA
          1 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC

            **         *      *                            *       *         
       2235 TGGATAGGCCCGAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCATAGTGGACAAATCTCACC
         66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC

                                *   
       2300 AAAATGATTATAGTTAGGCCGTAA
        131 AAAATGATTATAGTTAGGCCATAA

                          *    *  *                  *                    *  
       2324 ACAATGGAAAGAAAGGCATCGAAGTTTGCCAAATCGAAGACTATTCAAAACGTCACTAATGGTCC
          1 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC

             *                                                     *        *
       2389 CTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACAAATCTCACA
         66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC

                     *              
       2454 AAAATGATTGTAGTTAGGCCATAA
        131 AAAATGATTATAGTTAGGCCATAA

                                                     *     *        *        
       2478 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTTTTAAAACAG-AACTAATGG
          1 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA--TTCAAAAC-GTCACTAATGG

            *                                       *                 *      
       2542 TCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTTAAAACTTCACAGTGGACAAATCTC
         63 GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC

                                        
       2607 A-CAAACATGATTATAGTTAGGCCATAA
        128 ACCAAA-ATGATTATAGTTAGGCCATAA

                          *                  *       *          **           
       2634 ACAATGGAAAGAAACGCATTGAGGTTTGCCAAACCGAAGACAATTCAAAACGGAACTAATGGGCC
          1 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC

                *    *                 *  *                               *  
       2699 CCGAAAGGCTCAAAATAACAAGTGTTCGAATTGAGCTAAAAACTTCACAGTGGACTAATCTCCCC
         66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC

                                   *
       2764 AAAATGATTATAGTTAGGCCATAC
        131 AAAATGATTATAGTTAGGCCATAA

                                       ***                             *  * *
       2788 ACAATGGAAAGAAAAGCATTGAGGTTTATAAAATCGAAGACGATTCAAAACGTCACTAAAGGTCT
          1 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC

                                   *      *                                  
       2853 CCGATAGGCCCAAAATAACAAGTTTTCCAACTGAGCTAAAAACTTCACAGTGGACTAATCTCACC
         66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC

                                    
       2918 AAAATGATTATAGTTAGGCCATAA
        131 AAAATGATTATAGTTAGGCCATAA

                          
       2942 ACAATGGAAAGAAA
          1 ACAATGGAAAGAAA

       2956 GG


Statistics
Matches: 1685,  Mismatches: 162, Indels: 34
        0.90            0.09        0.02

Matches are distributed among these distances:
 152   95  0.06
 153  157  0.09
 154  1147  0.68
 155   32  0.02
 156  174  0.10
 157   68  0.04
 158   12  0.01

ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21


Consensus pattern (154 bp):   
ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC
CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
AAAATGATTATAGTTAGGCCATAA

Done.