Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006544.1 Corchorus capsularis cultivar CVL-1 contig06565, 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: 4015
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33


Found at i:124 original size:42 final size:42

Alignment explanation


    Indices: 73--161  Score: 142
    Period size: 42  Copynumber: 2.1  Consensus size: 42

         63 CGTGTCTCAT

                *                             *       
         73 GTCTTTTTGCCATAGACTTGATGCCAAAATGTTTGACGCCGC
          1 GTCTCTTTGCCATAGACTTGATGCCAAAATGTTTAACGCCGC

                            *         *               
        115 GTCTCTTTGCCATAGATTTGATGCCATAATGTTTAACGCCGC
          1 GTCTCTTTGCCATAGACTTGATGCCAAAATGTTTAACGCCGC

                 
        157 GTCTC
          1 GTCTC

        162 ATGTCATTAC


Statistics
Matches: 43,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  42   43  1.00

ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35


Consensus pattern (42 bp):   
GTCTCTTTGCCATAGACTTGATGCCAAAATGTTTAACGCCGC

Found at i:1667 original size:24 final size:25

Alignment explanation


    Indices: 1627--1902  Score: 366
    Period size: 26  Copynumber: 11.0  Consensus size: 25

       1617 AGTTCCATAT

                                     *
       1627 GCCATGTGGGGACTTGGTTGCCATGG
          1 GCCA-GTGGGGACTTGGTTGCCATGA

                       *             
       1653 GCCA-TGGGGATTTGGTTGCCATGA
          1 GCCAGTGGGGACTTGGTTGCCATGA

                                      
       1677 GCCATGTGGGGACTTGGTTGCCATGA
          1 GCCA-GTGGGGACTTGGTTGCCATGA

                                *    
       1703 GCCA-TGGGGACTTGGTTGCGATGA
          1 GCCAGTGGGGACTTGGTTGCCATGA

             *                        
       1727 GTCATGTGGGGACTTGGTTGCCATGA
          1 GCCA-GTGGGGACTTGGTTGCCATGA

                                     
       1753 GCCA-TGGGGACTTGGTTGCCATGA
          1 GCCAGTGGGGACTTGGTTGCCATGA

             *                        
       1777 GTCATGTGGGGACTTGGTTGCCATGA
          1 GCCA-GTGGGGACTTGGTTGCCATGA

             *        *              
       1803 GTCA-TGGGGGCTTGGTTGCCATGA
          1 GCCAGTGGGGACTTGGTTGCCATGA

                                      
       1827 GCCATGTGGGGACTTGGTTGCCATGA
          1 GCCA-GTGGGGACTTGGTTGCCATGA

             *                        
       1853 GTCA-TGGAGG-CTTGGTTGCCATGA
          1 GCCAGTGG-GGACTTGGTTGCCATGA

                                 *    
       1877 GCCATGTGGGGACTTGGTTGCTATGA
          1 GCCA-GTGGGGACTTGGTTGCCATGA

       1903 TACGGCACAT


Statistics
Matches: 224,  Mismatches: 14, Indels: 24
        0.85            0.05        0.09

Matches are distributed among these distances:
  24  109  0.49
  25    4  0.02
  26  111  0.50

ACGTcount: A:0.15, C:0.17, G:0.39, T:0.28


Consensus pattern (25 bp):   
GCCAGTGGGGACTTGGTTGCCATGA

Found at i:1684 original size:50 final size:50

Alignment explanation


    Indices: 1627--1902  Score: 455
    Period size: 50  Copynumber: 5.5  Consensus size: 50

       1617 AGTTCCATAT

                                     *          *             
       1627 GCCATGTGGGGACTTGGTTGCCATGGGCCATGGGGATTTGGTTGCCATGA
          1 GCCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA

                                                         *    
       1677 GCCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCGATGA
          1 GCCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA

             *                                                
       1727 GTCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA
          1 GCCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA

             *                         *       *              
       1777 GTCATGTGGGGACTTGGTTGCCATGAGTCATGGGGGCTTGGTTGCCATGA
          1 GCCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA

                                       *                       
       1827 GCCATGTGGGGACTTGGTTGCCATGAGTCATGGAGG-CTTGGTTGCCATGA
          1 GCCATGTGGGGACTTGGTTGCCATGAGCCATGG-GGACTTGGTTGCCATGA

                                 *    
       1877 GCCATGTGGGGACTTGGTTGCTATGA
          1 GCCATGTGGGGACTTGGTTGCCATGA

       1903 TACGGCACAT


Statistics
Matches: 216,  Mismatches: 9, Indels: 2
        0.95            0.04        0.01

Matches are distributed among these distances:
  50  214  0.99
  51    2  0.01

ACGTcount: A:0.15, C:0.17, G:0.39, T:0.28


Consensus pattern (50 bp):   
GCCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA

Done.