Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004609.1 Corchorus capsularis cultivar CVL-1 contig04621, 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, 663

Length: 1106
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.23


Found at i:281 original size:154 final size:155

Alignment explanation


    Indices: 1--1106  Score: 1458
    Period size: 154  Copynumber: 7.1  Consensus size: 155

                                                                             
          1 GCCCGAAATAACAAGTGTTCTGAATGAAGCTAAAAAACTTCACAATGGACTAATCTCATC-AAAT
          1 GCCCGAAATAACAAGTGTTCTGAATG-AGCT-AAAAACTTCACAATGGACTAATCTCATCAAAAT

                    * **                     *               *               
         65 AATTATAGTTCTGCCA-T-AACAA-AGGAAAGATAAGCTTTGTGGTTTGCCAAATCGAAGACGAT
         64 AATTATAGCTAGGCCAGTAAACAATAGG-AAGAAAAGCTTTGTGGTTTGGCAAATCGAAGACGAT

                                        
        127 TCAAAACAGCACTAATGGGCCCCGAAAG
        128 TCAAAACAGCACTAATGGGCCCCGAAAG

                                      *                                      
        155 GCCCGAAATAACAAGTGTTCTGAATGTGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAA
          1 GCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAA

                  *                                                        * 
        220 TTATAGATAGGCCAG-AAACAATAGGAAGAAAAGCTTTGTGGTTTGGCAAATCGAAGACGATTAA
         66 TTATAGCTAGGCCAGTAAACAATAGGAAGAAAAGCTTTGTGGTTTGGCAAATCGAAGACGATTCA

                                     
        284 AAACAGCACTAATGGGCCCCGAAAG
        131 AAACAGCACTAATGGGCCCCGAAAG

                *                                                   *      * 
        309 GCCCAAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGA
          1 GCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAA

                       *           * *                           *    *     *
        374 TTATAGCTAGGTC-GTAAACAATTGAAAGAAAAGCTTTGTTGG-TT-GCAAATTGAAGCCGATTT
         66 TTATAGCTAGGCCAGTAAACAATAGGAAGAAAAGCTTTG-TGGTTTGGCAAATCGAAGACGATTC

              *                *      
        436 AACACAGCACTAATGGGCCTCGAAAG
        130 AAAACAGCACTAATGGGCCCCGAAAG

                                       *       *                             
        462 GCCCGAAATAACAAGTGTTCATGAATGTGCTAAAATCTTCACAATGGACTAATCTCATCAAAATA
          1 GCCCGAAATAACAAGTGTTC-TGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATA

                    *        *          *                                    
        527 ATTTATAGTTAGGCCAGAAAACAATAGGTAGAAAAGCTTTTGTGGTTTGGCAAATCGAAGACGAT
         65 A-TTATAGCTAGGCCAGTAAACAATAGGAAGAAAAGC-TTTGTGGTTTGGCAAATCGAAGACGAT

                                        
        592 TCAAAACAGCACTAATGGGCCCCGAAAG
        128 TCAAAACAGCACTAATGGGCCCCGAAAG

                *                                                    *      *
        620 GCCCAAAATAACAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATG
          1 GCCCGAAATAAC-AAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATA

                                         *                             *    *
        685 ATTATAGCTAGG-CACGTAAACAAATTAGAAAGAAAAGCTTTAGTTGG-TT-GCAAAATTGAAGC
         65 ATTATAGCTAGGCCA-GTAAAC-AA-TAGGAAGAAAAGCTTT-G-TGGTTTGGC-AAATCGAAGA

                 *  *           *    *      
        747 CGATTTAACACAGCACTAATAGGCCTCGAAAG
        124 CGATTCAAAACAGCACTAATGGGCCCCGAAAG

               *                       *                                     
        779 GCTACGAAATAACAAGTGTTCTGAATGTGCTAAAAACTTCACAAGTGGACTAATCTACAATC-AA
          1 GC-CCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAA-TGGACTAATCT-C-ATCAAA

                      *                                                      
        843 AT-ATTATAGTTAGGCCAG-AAACAATAGGATAG-AAAGCTTTGTGGTTTGGCAAATCGAAGACG
         62 ATAATTATAGCTAGGCCAGTAAACAATAGGA-AGAAAAGCTTTGTGGTTTGGCAAATCGAAGACG

                                          
        905 ATTC-AAACAGCACTAATGGGCCCCGAAAG
        126 ATTCAAAACAGCACTAATGGGCCCCGAAAG

                                                                     *      *
        934 GCCCGAAATAACAAGGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATG
          1 GCCCGAAATAACAA-GTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATA

                        *           * *                           *    *     
        999 ATTATAGCTAGGTC-GTAAACAATTGAAAGAAAAGCTTTGTTGG-TT-GCAAATTGAAGCCGATT
         65 ATTATAGCTAGGCCAGTAAACAATAGGAAGAAAAGCTTTG-TGGTTTGGCAAATCGAAGACGATT

            *  *           *    *      
       1061 TAACACAGCACTAATAGGCCTCGAAAG
        129 CAAAACAGCACTAATGGGCCCCGAAAG

                               
       1088 GCCCGAAATAACAAGTGTT
          1 GCCCGAAATAACAAGTGTT


Statistics
Matches: 842,  Mismatches: 76, Indels: 69
        0.85            0.08        0.07

Matches are distributed among these distances:
 152   30  0.04
 153  107  0.13
 154  318  0.38
 155   75  0.09
 156   38  0.05
 157   35  0.04
 158  102  0.12
 159   94  0.11
 160   34  0.04
 161    7  0.01
 162    2  0.00

ACGTcount: A:0.39, C:0.18, G:0.19, T:0.23


Consensus pattern (155 bp):   
GCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAA
TTATAGCTAGGCCAGTAAACAATAGGAAGAAAAGCTTTGTGGTTTGGCAAATCGAAGACGATTCA
AAACAGCACTAATGGGCCCCGAAAG
Done.