Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006629.1 Corchorus capsularis cultivar CVL-1 contig06650, 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, 894

Length: 1491
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23


Found at i:838 original size:153 final size:154

Alignment explanation


    Indices: 1--1490  Score: 2260
    Period size: 154  Copynumber: 9.7  Consensus size: 154

                                                             *               
          1 CCGAAAGGACCCGAAATAACAAGTTGTTTCTGAATGAGACTAAAAACTTAACAATGGACTAATCT
          1 CCGAAAGG-CCCGAAATAACAAG-TG-TTCTGAATGAG-CTAAAAACTTCACAATGGACTAATCT

                                                         *   *               
         66 CATCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGCGGTTTGCCAAATCGA
         62 CATCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGA

                   *                *   
        131 AGACGATACAAAACAGCACTAATGCGCC
        127 AGACGATTCAAAACAGCACTAATGGGCC

                    * *                                      *             * 
        159 CCGAAAGGGCTGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
          1 CCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATC

                 *          *                      *     *      *  *         
        224 AAAATGATTATAGTTATGCCATAAACAATGGAAAGAAAACCTTTGCGGTTTGTCATATCGAAGAC
         66 AAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGAC

               *                *   
        289 GATACAAAACAGCACTAATGCGCC
        131 GATTCAAAACAGCACTAATGGGCC

                      *                                       *             *
        313 CCGAAAGGCCTGAAATAACAAGTGTTCTGAATGAGCTAAAGAACTTCACAGTGGACTAATCTCAC
          1 CCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAA-AACTTCACAATGGACTAATCTCAT

                              *                                              
        378 CAAAA-AGATTATAGTTATGCCATAAACAATGGAAAGAAAAG-TATTGTGGTTTGCCAAATCGAA
         65 CAAAATA-ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCT-TTGTGGTTTGCCAAATCGAA

            *           *              
        441 TACGATTCAAAATAGCACTAATGGGCC
        128 GACGATTCAAAACAGCACTAATGGGCC

                      *                                      *             * 
        468 CCGAAAGGCCTGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
          1 CCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATC

                                *     *  *                               * * 
        533 AAAATAATTATAGTTAGGCCGTAAACTATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGATGCC
         66 AAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGAC

                       * *          
        598 GATTCAAAACAACTCTAATGGGCC
        131 GATTCAAAACAGCACTAATGGGCC

                                        *                                    
        622 CCGAAAGGCCCGAAATAACAAGTGTTCTTAATGAGCTAAAAACTTCACAATGGACTAATCTCATC
          1 CCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATC

                                                     *                    *  
        687 AAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAATAC
         66 AAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGAC

                      *             
        752 GATTCAAAA-TGCACTAATGGGCC
        131 GATTCAAAACAGCACTAATGGGCC

                                                                             
        775 CCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATC
          1 CCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATC

                                        *       *                            
        840 AAAATAATTATAGTTAGGCCATAAACAAAGG-AAGATAAGCTTAT-TGGTTTGCCAAATCGAAGA
         66 AAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTT-TGTGGTTTGCCAAATCGAAGA

                                     
        903 CGATTCAAAACAGCACTAATGGGCC
        130 CGATTCAAAACAGCACTAATGGGCC

                                                                             
        928 CCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATC
          1 CCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATC

                                        *                        *           
        993 AAAATAATTATAGTTAGGCCATAAACAAAGGAAAG-AAAGCTTTGTGGTTTGCTAAATCGAAAGA
         66 AAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCG-AAGA

                               *      
       1057 CGATTCGAAAACAGCACTAGTGGGCC
        130 CGATTC-AAAACAGCACTAATGGGCC

            *      *                         *                             * 
       1083 ACGAAAGACCCGAAATAACAAGTGTTCTGAATGTGCTAAAAACTTCACAATGGACTAATCTCACC
          1 CCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATC

              *  *       *    * *        *                             *    *
       1148 AAGATGATTATAGCTAGGTCGTAAACAATTGAAAGAAAAGCTTTGTTGG-TTG-CAAATTGAAGC
         66 AAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTG-TGGTTTGCCAAATCGAAGA

                 *  *                
       1211 CGATTTAACACAGCACTAATGGGCC
        130 CGATTCAAAACAGCACTAATGGGCC

            *                                                                
       1236 TCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATC
          1 CCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATC

                                 *                               *           
       1301 AAAATAATTATAGTTAGGCCAGAAACAATCGG-AAGAAAAGCTTTGTGGTTTGGCAAATCGAAGA
         66 AAAATAATTATAGTTAGGCCATAAACAAT-GGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGA

                                     
       1365 CGATTCAAAACAGCACTAATGGGCC
        130 CGATTCAAAACAGCACTAATGGGCC

                                              *                              
       1390 CCGAAAGGCCCGAAATAACAAGTGTTCTGAATGACCTAAAAACTTCACAATGGACTAATCTCATC
          1 CCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATC

                                        *       
       1455 AAAATAATTATAGTTAGGCCATAAACAAAGGAAAGA
         66 AAAATAATTATAGTTAGGCCATAAACAATGGAAAGA

       1491 T


Statistics
Matches: 1225,  Mismatches: 90, Indels: 38
        0.91            0.07        0.03

Matches are distributed among these distances:
 152   41  0.03
 153  354  0.29
 154  526  0.43
 155  267  0.22
 156   14  0.01
 157   15  0.01
 158    8  0.01

ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23


Consensus pattern (154 bp):   
CCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATC
AAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGAC
GATTCAAAACAGCACTAATGGGCC

Done.