Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006232.1 Corchorus capsularis cultivar CVL-1 contig06251, 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, 759

Length: 1265
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24


Found at i:493 original size:152 final size:153

Alignment explanation


    Indices: 1--1261  Score: 1917
    Period size: 154  Copynumber: 8.2  Consensus size: 153

                  *                      *                *               *  
          1 CCCGAATGGCCCGAAATAACAAGTGTTCTAAATGAG-TAAAGACTTGACAATGGACTAATCTTAT
          1 CCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAA-ACTTCACAATGGACTAATCTCAT

                        *               *             *                    * 
         65 CAAAATAATTATCGTTAGGCCATAAACATTGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAATA
         65 CAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGA

                      *             
        130 CGATTCAAAATAGCACTAATGGGC
        130 CGATTCAAAACAGCACTAATGGGC

                                                *                            
        154 CCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGTTAAAACTTCACAATGGACTAACTCTCAT
          1 CCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAACTTCACAATGGACTAA-TCTCAT

                *                                         *      *  *      * 
        219 CAAATTAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGCGGTTTGTCATATCGAATA
         65 CAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGA

                      *             
        284 CGATTC-AAATAGCACTAATGGGC
        130 CGATTCAAAACAGCACTAATGGGC

                  *                      *                                *  
        307 CCCGAATGGCCCGAAATAACAAGTGTTCTAAATGAGCTAAAGACTTCACAATGGACTAATCTTAT
          1 CCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAA-ACTTCACAATGGACTAATCTCAT

                        *               *             *                    * 
        372 CAAAATAATTATTGTTAGGCCATAAACATTGGAAAG-AAAGCATTGTGGTTTGCCAAATCGAATA
         65 CAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGA

                  *   *             
        436 CGATT-GAAATAGCACTAATGGGC
        130 CGATTCAAAACAGCACTAATGGGC

             *                                  *                            
        459 CTCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGTTAAAACTTCACAATGGACTAATCTCATC
          1 CCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAACTTCACAATGGACTAATCTCATC

                                                *                            
        524 AAAATAATTAGTAGTTAGGCCATAAACAATGGAAA-CAAAGCTTTGTGGTTTGCCAAATCGAAGA
         66 AAAATAATTA-TAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGA

                                    
        588 CGATTC-AAACAGCACTAATGGGC
        130 CGATTCAAAACAGCACTAATGGGC

                   *           *    *                                        
        611 CCC-AAACGCCCGAAATAAAAAGTTTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCAT
          1 CCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCT-AAAACTTCACAATGGACTAATCTCAT

                                               *                             
        675 CAAAATAATTATAGTTAGGCCATAAACAATGGAAACAAAAGCTTTGTGGTTTGCCAAATCGAAGA
         65 CAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGA

                                    
        740 CGATTCAAAACAGCACTAATGGGC
        130 CGATTCAAAACAGCACTAATGGGC

                    **         *                                *            
        764 CCCGAAAGTTCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATTGACTAATCTCAT
          1 CCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCT-AAAACTTCACAATGGACTAATCTCAT

                  *            * *      * *                                  
        829 CAAAATGATTATAGTTAGGTCGTAAACATTTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGA
         65 CAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGA

                                    
        894 CGATTCAAAACAGCACTAATGGGC
        130 CGATTCAAAACAGCACTAATGGGC

                               *                                             
        918 CCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCAT
          1 CCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCT-AAAACTTCACAATGGACTAATCTCAT

                                 *                                           
        983 CAAAATAATTATAGTTAGGCCGTAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGA
         65 CAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGA

                                    
       1048 CGATTCAAAACAGCACTAATGGGC
        130 CGATTCAAAACAGCACTAATGGGC

                                                                             
       1072 CCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAACGCTTCACAATGGACTAATCTCA
          1 CCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAA--CTTCACAATGGACTAATCTCA

                                * *        *                       *  *      
       1137 T-AAAATAATTATAGTTAGGTCGTAAACAATTGAAAGAAAAGCTTTGTGGTTTGCTAACTCGAAG
         64 TCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAG

                       *             
       1201 ACGATTCAAAATAGCACTAATGGGC
        129 ACGATTCAAAACAGCACTAATGGGC

                               *    *    *      
       1226 CCCGAAAGGCCCGAAATAATAAGTTTTCTTAATGAG
          1 CCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAG

       1262 ATAG


Statistics
Matches: 1030,  Mismatches: 65, Indels: 25
        0.92            0.06        0.02

Matches are distributed among these distances:
 151   87  0.08
 152  225  0.22
 153  167  0.16
 154  529  0.51
 155   22  0.02

ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24


Consensus pattern (153 bp):   
CCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAACTTCACAATGGACTAATCTCATC
AAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGAC
GATTCAAAACAGCACTAATGGGC

Done.