Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006804.1 Corchorus capsularis cultivar CVL-1 contig06825, 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, 766

Length: 1278
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23


Found at i:380 original size:154 final size:153

Alignment explanation


    Indices: 1--1278  Score: 1794
    Period size: 154  Copynumber: 8.3  Consensus size: 153

                                  *    *  *                  *               
          1 TAATGGGCCCCGAAAGGCCCGAGATAAAAACTGTTCTGAATGAGCTAAAGACTTCACAATGGACT
          1 TAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACT

                                      *                  *                   
         66 AATCTCATCAAAATAATTATAGTTAGCCCATAAACAAAGGAAAGATAAGCTTTGTGGTTTGCCAA
         66 AATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGAAAAGCTTTGTGGTTTG-CAA

               *                     
        131 ATCAAAGACGAATTCAAAACAGCAC
        130 ATCGAAGACG-ATTCAAAACAGCAC

                            *       *                 *                 *    
        156 TAATGGGCCCCGAAAGACCCGAAAAAACAAGTGTTCTGAATGTGCTAAAAACTTCACAATAGACT
          1 TAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACT

                                    *         *          *                   
        221 AATCTCATCAAAATAATTATAGTTTGGCCATAAATAAAGGAAAGATAAGCTTAT-TGGTTTGCCA
         66 AATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGAAAAGCTT-TGTGGTTTG-CA

                          *        * 
        285 AATCGAAGACGATTGAAAACAGCTC
        129 AATCGAAGACGATTCAAAACAGCAC

                                       *                                     
        310 TAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACT
          1 TAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACT

                                                                             
        375 AATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGATAAA-CTTTGTGGTTTGCCA
         66 AATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGA-AAAGCTTTGTGGTTTG-CA

                *                    
        439 AATCAAAGACGATTCAAAACAGCAC
        129 AATCGAAGACGATTCAAAACAGCAC

              *      *      *                         *                      
        464 TACTGGGCCACGAAAGACCCGAAATAACAAGTGTTCTGAATGTGCTAAAAACTTCACAATGGACT
          1 TAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACT

                   *      *       *    * *       **                          
        529 AATCTCACCAAAATGATTATAGCTAGGTCGTAAACAATTGAAAGAAAAGCTTTGTTCGG-TTGCA
         66 AATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGAAAAGCTTTG-T-GGTTTGCA

                     *     *  *       
        593 AATTCGAAGCCGATTTAACACAGCAC
        129 AA-TCGAAGACGATTCAAAACAGCAC

                     *    *                                                  
        619 TAATGGGCCTCGAAGGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACT
          1 TAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACT

                   *      *       *    * *       **                          
        684 AATCTCACCAAAATGATTATAGCTAGGTCGTAAACAATTGAAAGAAAAGCTTTGTTGG-TTGCAA
         66 AATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGAAAAGCTTTG-TGGTTTGCAA

              *    *     *  *       
        748 ATTGAAGCCGATTTAACACAGCAC
        130 ATCGAAGACGATTCAAAACAGCAC

                     *                                                       
        772 TAATGGGCCTCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACT
          1 TAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACT

                                    **                   *                   
        837 AATCTCATCAAAATAATTATAGTTCTGCCATAAACAAAGGAAAGATAAGCTTTGTGGTTTGGCAA
         66 AATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGAAAAGCTTTGTGGTTT-GCAA

                                    
        902 ATCGAAGACGATTCAAAACAGCAC
        130 ATCGAAGACGATTCAAAACAGCAC

                                                                             
        926 TAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACT
          1 TAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACT

                   *      *       *    * *   *   **                          
        991 AATCTCACCAAAATGATTATAGCTAGGTCGTAAGCAATTGAAAGAAAAGCTTTGTTGG-TTGCAA
         66 AATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGAAAAGCTTTG-TGGTTTGCAA

              *    *     *  *       
       1055 ATTGAAGCCGATTTAACACAGCAC
        130 ATCGAAGACGATTCAAAACAGCAC

                     *                           *    *                      
       1079 TAATGGGCCTCGAAAGGCCCGAAATAACAAGTGTTCTAAATGTGCTAAAAACTTCACAATGGACT
          1 TAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACT

                                          *                                  
       1144 AATCTCATCAAAATAATTATAGTTAGGCCAGAAACAATAGG-AAGAAAAGCTTTGTGGTTTGGCA
         66 AATCTCATCAAAATAATTATAGTTAGGCCATAAACAA-AGGAAAGAAAAGCTTTGTGGTTT-GCA

                                     
       1208 AATCGAAGACGATTCAAAACAGCAC
        129 AATCGAAGACGATTCAAAACAGCAC

                             *                            
       1233 TAATGGGCCCCGAAAGGTCCGAAATAACAAGTGTTCTGAATGAGCT
          1 TAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCT


Statistics
Matches: 1012,  Mismatches: 98, Indels: 27
        0.89            0.09        0.02

Matches are distributed among these distances:
 152    6  0.01
 153  267  0.26
 154  466  0.46
 155  270  0.27
 156    3  0.00

ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23


Consensus pattern (153 bp):   
TAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACT
AATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGAAAAGCTTTGTGGTTTGCAAA
TCGAAGACGATTCAAAACAGCAC

Found at i:1012 original size:307 final size:308

Alignment explanation


    Indices: 1--1278  Score: 1836
    Period size: 307  Copynumber: 4.1  Consensus size: 308

                                  *    *  *                  *               
          1 TAATGGGCCCCGAAAGGCCCGAGATAAAAACTGTTCTGAATGAGCTAAAGACTTCACAATGGACT
          1 TAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACT

                   *              *   *                  *                   
         66 AATCTCATCAAAATAATTATAGTTAGCCCATAAACAAAGGAAAGATAAGCTTTGTGGTTTGCCAA
         66 AATCTCACCAAAATAATTATAGCTAGGCCATAAACAAAGGAAAGAAAAGCTTTGTGGTTTGCCAA

                                              *              *               
        131 ATCAAAGACGAATTCAAAACAGCACTAATGGGCCCCGAAAGACCCGAAAAAACAAGTGTTCTGAA
        131 ATCAAAGACG-ATTCAAAACAGCACTAATGGGCCTCGAAAGACCCGAAATAACAAGTGTTCTGAA

                                *                            *         *     
        196 TGTGCTAAAAACTTCACAATAGACTAATCTCATCAAAATAATTATAGTTTGGCCATAAATAAAGG
        195 TGTGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGG

                 *                *                *        * 
        261 AAAGATAAGCTTAT-TGGTTTGCCAAATCGAAGACGATTGAAAACAGCTC
        260 AAAGAAAAGCTT-TGTGGTTTGGCAAATCGAAGACGATTCAAAACAGCAC

                                       *                                     
        310 TAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACT
          1 TAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACT

                   *              *                                          
        375 AATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGATAAA-CTTTGTGGTTTGCCA
         66 AATCTCACCAAAATAATTATAGCTAGGCCATAAACAAAGGAAAGA-AAAGCTTTGTGGTTTGCCA

                                       *      *                              
        439 AATCAAAGACGATTCAAAACAGCACTACTGGGCCACGAAAGACCCGAAATAACAAGTGTTCTGAA
        130 AATCAAAGACGATTCAAAACAGCACTAATGGGCCTCGAAAGACCCGAAATAACAAGTGTTCTGAA

                                            *      *       *    * *       ** 
        504 TGTGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGCTAGGTCGTAAACAATTG
        195 TGTGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGG

                                               *     *  *       
        569 AAAGAAAAGCTTTGTTCGG-TT-GCAAATTCGAAGCCGATTTAACACAGCAC
        260 AAAGAAAAGCTTTG-T-GGTTTGGCAAA-TCGAAGACGATTCAAAACAGCAC

                     *    *                                                  
        619 TAATGGGCCTCGAAGGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACT
          1 TAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACT

                          *            * *       **                          
        684 AATCTCACCAAAATGATTATAGCTAGGTCGTAAACAATTGAAAGAAAAGCTTTGTTGG-TTG-CA
         66 AATCTCACCAAAATAATTATAGCTAGGCCATAAACAAAGGAAAGAAAAGCTTTG-TGGTTTGCCA

               **   *     *  *                       *                       
        747 AATTGAAGCCGATTTAACACAGCACTAATGGGCCTCGAAAGGCCCGAAATAACAAGTGTTCTGAA
        130 AATCAAAGACGATTCAAAACAGCACTAATGGGCCTCGAAAGACCCGAAATAACAAGTGTTCTGAA

              *                                              **              
        812 TGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTCTGCCATAAACAAAGG
        195 TGTGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGG

                 *                                           
        877 AAAGATAAGCTTTGTGGTTTGGCAAATCGAAGACGATTCAAAACAGCAC
        260 AAAGAAAAGCTTTGTGGTTTGGCAAATCGAAGACGATTCAAAACAGCAC

                                                                             
        926 TAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACT
          1 TAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACT

                          *            * *   *   **                          
        991 AATCTCACCAAAATGATTATAGCTAGGTCGTAAGCAATTGAAAGAAAAGCTTTGTTGG-TTG-CA
         66 AATCTCACCAAAATAATTATAGCTAGGCCATAAACAAAGGAAAGAAAAGCTTTG-TGGTTTGCCA

               **   *     *  *                       *                    *  
       1054 AATTGAAGCCGATTTAACACAGCACTAATGGGCCTCGAAAGGCCCGAAATAACAAGTGTTCTAAA
        130 AATCAAAGACGATTCAAAACAGCACTAATGGGCCTCGAAAGACCCGAAATAACAAGTGTTCTGAA

                                                                   *         
       1119 TGTGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCAGAAACAATAG
        195 TGTGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAA-AG

                                                              
       1184 G-AAGAAAAGCTTTGTGGTTTGGCAAATCGAAGACGATTCAAAACAGCAC
        259 GAAAGAAAAGCTTTGTGGTTTGGCAAATCGAAGACGATTCAAAACAGCAC

                             *                            
       1233 TAATGGGCCCCGAAAGGTCCGAAATAACAAGTGTTCTGAATGAGCT
          1 TAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCT


Statistics
Matches: 893,  Mismatches: 66, Indels: 22
        0.91            0.07        0.02

Matches are distributed among these distances:
 306    2  0.00
 307  363  0.41
 308  259  0.29
 309  262  0.29
 310    7  0.01

ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23


Consensus pattern (308 bp):   
TAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACT
AATCTCACCAAAATAATTATAGCTAGGCCATAAACAAAGGAAAGAAAAGCTTTGTGGTTTGCCAA
ATCAAAGACGATTCAAAACAGCACTAATGGGCCTCGAAAGACCCGAAATAACAAGTGTTCTGAAT
GTGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGA
AAGAAAAGCTTTGTGGTTTGGCAAATCGAAGACGATTCAAAACAGCAC
Done.