Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015792.1 Corchorus olitorius cultivar O-4 contig15825, 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: 12377
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35


Found at i:239 original size:22 final size:22

Alignment explanation


    Indices: 207--443  Score: 154
    Period size: 22  Copynumber: 10.6  Consensus size: 22

        197 TTATAGGGAA

                  *         *     
        207 GTTATCGAAATTTCATGGTGTG
          1 GTTATCAAAATTTCATAGTGTG

                                 * 
        229 GTTATCAAAATTTTCATAGTGCG
          1 GTTATCAAAA-TTTCATAGTGTG

            *      *     *   * *  
        252 ATTA-C-CAATTTTATAATATG
          1 GTTATCAAAATTTCATAGTGTG

            *                       * 
        272 ATTATCAAAATTTCATAGACAATGAG
          1 GTTATCAAAATTTCATAG----TGTG

                      *     *     
        298 GTTATCAAAACTTCATTGTGTG
          1 GTTATCAAAATTTCATAGTGTG

                   *       *      
        320 GTTATCAGAATTTCACAGTGTG
          1 GTTATCAAAATTTCATAGTGTG

                   *       * *    
        342 GTTATCAGAATTTCACATTGTG
          1 GTTATCAAAATTTCATAGTGTG

                     *        * * 
        364 GTTATCAAATTTTCATAGGGAG
          1 GTTATCAAAATTTCATAGTGTG

                  *        * *  * 
        386 GTTATCGAAATTTCACAATGAG
          1 GTTATCAAAATTTCATAGTGTG

            *        *    **      
        408 ATTATCAAATTTTCGCAGTGTG
          1 GTTATCAAAATTTCATAGTGTG

                    *     
        430 GTTATCAATATTTC
          1 GTTATCAAAATTTC

        444 TACGTTGGAG


Statistics
Matches: 165,  Mismatches: 43, Indels: 14
        0.74            0.19        0.06

Matches are distributed among these distances:
  20   12  0.07
  21    3  0.02
  22  120  0.73
  23   13  0.08
  26   17  0.10

ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39


Consensus pattern (22 bp):   
GTTATCAAAATTTCATAGTGTG

Found at i:3337 original size:31 final size:31

Alignment explanation


    Indices: 3299--3376  Score: 122
    Period size: 31  Copynumber: 2.5  Consensus size: 31

       3289 AATATCTTTA

                                           
       3299 ATAATAACTATATATTAAATTTCTATTATAT
          1 ATAATAACTATATATTAAATTTCTATTATAT

                              *            
       3330 ATAATAACTATATATTAACTTTCTATTATAT
          1 ATAATAACTATATATTAAATTTCTATTATAT

                             
       3361 ATATATATA-TATATAT
          1 ATA-ATA-ACTATATAT

       3377 GTTGATTATA


Statistics
Matches: 44,  Mismatches: 1, Indels: 3
        0.92            0.02        0.06

Matches are distributed among these distances:
  31   33  0.75
  32   10  0.23
  33    1  0.02

ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49


Consensus pattern (31 bp):   
ATAATAACTATATATTAAATTTCTATTATAT

Found at i:12221 original size:68 final size:68

Alignment explanation


    Indices: 12148--12279  Score: 255
    Period size: 68  Copynumber: 1.9  Consensus size: 68

      12138 AAAAGCTAAT

                                                                    *        
      12148 TATTGAAATTGATAATTAAAACCCAAGCCACATGTATCAATAACGTCAAAGGTATATAATTCAGA
          1 TATTGAAATTGATAATTAAAACCCAAGCCACATGTATCAATAACGTCAAAGGTATACAATTCAGA

               
      12213 AAC
         66 AAC

                                                                            
      12216 TATTGAAATTGATAATTAAAACCCAAGCCACATGTATCAATAACGTCAAAGGTATACAATTCAG
          1 TATTGAAATTGATAATTAAAACCCAAGCCACATGTATCAATAACGTCAAAGGTATACAATTCAG

      12280 GTATATAATT


Statistics
Matches: 63,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  68   63  1.00

ACGTcount: A:0.45, C:0.17, G:0.12, T:0.27


Consensus pattern (68 bp):   
TATTGAAATTGATAATTAAAACCCAAGCCACATGTATCAATAACGTCAAAGGTATACAATTCAGA
AAC
Done.