Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004356.1 Corchorus capsularis cultivar CVL-1 contig04364, 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: 2049
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35


Found at i:276 original size:22 final size:22

Alignment explanation


    Indices: 174--294  Score: 113
    Period size: 22  Copynumber: 5.5  Consensus size: 22

        164 TATAGGCGGA

                 *        * *     
        174 TTATCAAAATTTCACACTGAGG
          1 TTATCGAAATTTCATAGTGAGG

                                   
        196 TTATCGAAATTTCATAGT-ATGG
          1 TTATCGAAATTTCATAGTGA-GG

               * *        *    *  
        218 TTACCAAAATTTCACAGTGTGG
          1 TTATCGAAATTTCATAGTGAGG

                              *    
        240 TTATC-AAATTTTCATAGGGAGG
          1 TTATCGAAA-TTTCATAGTGAGG

                            *   * 
        262 TTATCGAAATTTCATAATGATG
          1 TTATCGAAATTTCATAGTGAGG

                        
        284 TTA-CGAAATTT
          1 TTATCGAAATTT

        295 TCAAAATGTG


Statistics
Matches: 81,  Mismatches: 14, Indels: 9
        0.78            0.13        0.09

Matches are distributed among these distances:
  21   12  0.15
  22   66  0.81
  23    3  0.04

ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37


Consensus pattern (22 bp):   
TTATCGAAATTTCATAGTGAGG

Found at i:287 original size:66 final size:66

Alignment explanation


    Indices: 174--318  Score: 184
    Period size: 66  Copynumber: 2.2  Consensus size: 66

        164 TATAGGCGGA

                    *        *                    *                   * *    
        174 TTATCAAAATTTCACACTGAGGTTATCGAAATTTCATAGTATGGTTACCAAAATTTCACAGTGTG
          1 TTATCAAATTTTCACACGGAGGTTATCGAAATTTCATAATATGGTTACCAAAATTTCAAAATGTG

             
        239 G
         66 G

                          * *                                *   *           
        240 TTATCAAATTTTCATAGGGAGGTTATCGAAATTTCATAATGAT-GTTACGAAATTTTCAAAATGT
          1 TTATCAAATTTTCACACGGAGGTTATCGAAATTTCATAAT-ATGGTTACCAAAATTTCAAAATGT

              
        304 GG
         65 GG

                         
        306 TTATCAATATTTT
          1 TTATCAA-ATTTT

        319 TACATTGGAG


Statistics
Matches: 68,  Mismatches: 9, Indels: 3
        0.85            0.11        0.04

Matches are distributed among these distances:
  66   61  0.90
  67    7  0.10

ACGTcount: A:0.34, C:0.12, G:0.16, T:0.39


Consensus pattern (66 bp):   
TTATCAAATTTTCACACGGAGGTTATCGAAATTTCATAATATGGTTACCAAAATTTCAAAATGTG
G

Found at i:296 original size:22 final size:23

Alignment explanation


    Indices: 174--318  Score: 90
    Period size: 22  Copynumber: 6.6  Consensus size: 23

        164 TATAGGCGGA

                     *     * *     
        174 TTATC-AAAATTTCACACTGAGG
          1 TTATCGAAATTTTCATAATGAGG

                             *      
        196 TTATCGAAA-TTTCATAGT-ATGG
          1 TTATCGAAATTTTCATAATGA-GG

                 *   *     * *  *  
        218 TTA-CCAAAATTTCACAGTGTGG
          1 TTATCGAAATTTTCATAATGAGG

                             **    
        240 TTATC-AAATTTTCATAGGGAGG
          1 TTATCGAAATTTTCATAATGAGG

                                 * 
        262 TTATCGAAA-TTTCATAATGATG
          1 TTATCGAAATTTTCATAATGAGG

                           *    *  
        284 TTA-CGAAATTTTCAAAATGTGG
          1 TTATCGAAATTTTCATAATGAGG

                          
        306 TTATC-AATATTTT
          1 TTATCGAA-ATTTT

        319 TACATTGGAG


Statistics
Matches: 99,  Mismatches: 15, Indels: 17
        0.76            0.11        0.13

Matches are distributed among these distances:
  21   10  0.10
  22   76  0.77
  23   13  0.13

ACGTcount: A:0.34, C:0.12, G:0.16, T:0.39


Consensus pattern (23 bp):   
TTATCGAAATTTTCATAATGAGG
Done.