Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019319.1 Corchorus olitorius cultivar O-4 contig19352, 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: 5038
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:1909 original size:58 final size:59

Alignment explanation


    Indices: 1847--2001  Score: 222
    Period size: 59  Copynumber: 2.6  Consensus size: 59

       1837 AGGTGACCGA

                    *       *                               *          
       1847 AATGCCCCCAGATATGTAAAAATTACCATAATGCCCCTAGATATGC-AGAAATTATCAT
          1 AATGCCCCTAGATATGCAAAAATTACCATAATGCCCCTAGATATGCAAAAAATTATCAT

                              *   *  *                                 
       1905 AATGCCCCTAGATATGCAGAAAGTATCATAATGCCCCTAGATATGCAAAAAATTATCAT
          1 AATGCCCCTAGATATGCAAAAATTACCATAATGCCCCTAGATATGCAAAAAATTATCAT

                     *             *         *    
       1964 AATGCCCCTGGATATGCAAAAATGACCATAATGTCCCT
          1 AATGCCCCTAGATATGCAAAAATTACCATAATGCCCCT

       2002 GGATCTGTAA


Statistics
Matches: 84,  Mismatches: 12, Indels: 1
        0.87            0.12        0.01

Matches are distributed among these distances:
  58   41  0.49
  59   43  0.51

ACGTcount: A:0.39, C:0.23, G:0.14, T:0.25


Consensus pattern (59 bp):   
AATGCCCCTAGATATGCAAAAATTACCATAATGCCCCTAGATATGCAAAAAATTATCAT

Found at i:2002 original size:29 final size:29

Alignment explanation


    Indices: 1801--2151  Score: 256
    Period size: 29  Copynumber: 12.0  Consensus size: 29

       1791 GAACCCAGAG

                                         
       1801 TATGCAAAAATGACCAAAATGCCCCTGGA
          1 TATGCAAAAATGACCAAAATGCCCCTGGA

            *  *    **     *         **  
       1830 CATACAAAGGTGACCGAAATGCCCCCAGA
          1 TATGCAAAAATGACCAAAATGCCCCTGGA

                *      *    *         *  
       1859 TATGTAAAAATTACCATAATGCCCCTAGA
          1 TATGCAAAAATGACCAAAATGCCCCTGGA

                  *    * *  *         *  
       1888 TATGCAGAAATTATCATAATGCCCCTAGA
          1 TATGCAAAAATGACCAAAATGCCCCTGGA

                  *       *  *         *  
       1917 TATGCAGAAA-GTATCATAATGCCCCTAGA
          1 TATGCAAAAATG-ACCAAAATGCCCCTGGA

                        * *  *            
       1946 TATGCAAAAAATTATCATAATGCCCCTGGA
          1 TATGC-AAAAATGACCAAAATGCCCCTGGA

                            *    *       
       1976 TATGCAAAAATGACCATAATGTCCCTGGA
          1 TATGCAAAAATGACCAAAATGCCCCTGGA

             *  *   * *             *     
       2005 TCTGTAAACACGACCAAAATG-CCTTCGGA
          1 TATGCAAAAATGACCAAAATGCCCCT-GGA

            **         * *             * 
       2034 CGTGCAAAAATAAACAAAATGCCCCTGAA
          1 TATGCAAAAATGACCAAAATGCCCCTGGA

              *      *     *         *    
       2063 TTGTGCAAACATGACAAAAATGCCCTTGGA
          1 -TATGCAAAAATGACCAAAATGCCCCTGGA

             *   *                  *    
       2093 TGTGCCAAAATGACCAAAATGCCCTTGGA
          1 TATGCAAAAATGACCAAAATGCCCCTGGA

                 *                  *    
       2122 TATGCGAAAATGACCAAAATGCCCTTGGA
          1 TATGCAAAAATGACCAAAATGCCCCTGGA

             
       2151 T
          1 T

       2152 TCACAAAAGG


Statistics
Matches: 263,  Mismatches: 53, Indels: 12
        0.80            0.16        0.04

Matches are distributed among these distances:
  28    3  0.01
  29  210  0.80
  30   50  0.19

ACGTcount: A:0.39, C:0.23, G:0.17, T:0.22


Consensus pattern (29 bp):   
TATGCAAAAATGACCAAAATGCCCCTGGA

Found at i:2026 original size:88 final size:85

Alignment explanation


    Indices: 1801--2116  Score: 222
    Period size: 88  Copynumber: 3.6  Consensus size: 85

       1791 GAACCCAGAG

                            *                *      *    *                 * 
       1801 TATGCAAAAATGACCAAAATGCCCCTGGA-CATACAAAGGTGACCGAAATGCCCCCAGATATGTA
          1 TATGCAAAAATGACCATAATGCCCCTGGATC-TGCAAA--AGACCAAAATGCCCCCAGATATGAA

                                   
       1865 AAAATTACCATAATGCCCCTAGA
         63 AAAATTACCATAATGCCCCTAGA

                  *    * *            *   *           *  *        *          
       1888 TATGCAGAAATTATCATAATGCCCCTAGATATGCAGAAAGTATCATAATGCCCCTAGATATGCAA
          1 TATGCAAAAATGACCATAATGCCCCTGGATCTGCA-AAAG-ACCAAAATGCCCCCAGATATG-AA

                   *            *  
       1953 AAAATTATCATAATGCCCCTGGA
         63 AAAATTACCATAATGCCCCTAGA

                                 *           *                  ** *  **  *  
       1976 TATGCAAAAATGACCATAATGTCCCTGGATCTGTAAACACGACCAAAATGCCTTCGGACGTGCAA
          1 TATGCAAAAATGACCATAATGCCCCTGGATCTGCAAA-A-GACCAAAATGCCCCCAGATATGAAA

                * *  *             
       2041 AAATAAACAAAATGCCCCT-GAA
         64 AAATTACCATAATGCCCCTAG-A

              *      *     * *       *     *                      
       2063 TTGTGCAAACATGACAAAAATGCCCTTGGATGTGCCAAAATGACCAAAATGCCC
          1 -TATGCAAAAATGACCATAATGCCCCTGGATCTG-CAAAA-GACCAAAATGCCC

       2117 TTGGATATGC


Statistics
Matches: 176,  Mismatches: 44, Indels: 17
        0.74            0.19        0.07

Matches are distributed among these distances:
  86    2  0.01
  87   65  0.37
  88  105  0.60
  89    4  0.02

ACGTcount: A:0.39, C:0.23, G:0.16, T:0.21


Consensus pattern (85 bp):   
TATGCAAAAATGACCATAATGCCCCTGGATCTGCAAAAGACCAAAATGCCCCCAGATATGAAAAA
ATTACCATAATGCCCCTAGA

Found at i:3881 original size:28 final size:28

Alignment explanation


    Indices: 3825--3899  Score: 100
    Period size: 28  Copynumber: 2.7  Consensus size: 28

       3815 AAGTCATATG

                                        
       3825 GGGGCATTTTGGTCA-TTTTTACATACA
          1 GGGGCATTTTGGTCATTTTTTACATACA

                                      *  
       3852 GGGGCATTTTGGTCATTTTTGTAC-TTCA
          1 GGGGCATTTTGGTCATTTTT-TACATACA

                  *   *         
       3880 GGGGCACTTTAGTCATTTTT
          1 GGGGCATTTTGGTCATTTTT

       3900 AAGTCATTAC


Statistics
Matches: 43,  Mismatches: 3, Indels: 3
        0.88            0.06        0.06

Matches are distributed among these distances:
  27   15  0.35
  28   25  0.58
  29    3  0.07

ACGTcount: A:0.17, C:0.15, G:0.24, T:0.44


Consensus pattern (28 bp):   
GGGGCATTTTGGTCATTTTTTACATACA
Done.