Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019847.1 Corchorus olitorius cultivar O-4 contig19880, 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: 8806
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32


Found at i:75 original size:11 final size:11

Alignment explanation


    Indices: 59--84  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

         49 CCTTTGCCTA

                       
         59 AAAACTAGAAG
          1 AAAACTAGAAG

                       
         70 AAAACTAGAAG
          1 AAAACTAGAAG

                
         81 AAAA
          1 AAAA

         85 TAAATTATCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08


Consensus pattern (11 bp):   
AAAACTAGAAG

Found at i:2134 original size:10 final size:10

Alignment explanation


    Indices: 2119--2176  Score: 50
    Period size: 10  Copynumber: 6.0  Consensus size: 10

       2109 AAGAAAAAAA

                      
       2119 CTAATTAAAT
          1 CTAATTAAAT

                    * 
       2129 CTAATTAAGT
          1 CTAATTAAAT

                     *
       2139 CTAATTAAAC
          1 CTAATTAAAT

                 *     
       2149 CTTAAAT-AAT
          1 C-TAATTAAAT

                *     
       2159 CTAAATAAA-
          1 CTAATTAAAT

                      
       2168 -TAATTAAAT
          1 CTAATTAAAT

       2177 ACTAGCCCTA


Statistics
Matches: 39,  Mismatches: 6, Indels: 7
        0.75            0.12        0.13

Matches are distributed among these distances:
   8    7  0.18
   9    5  0.13
  10   23  0.59
  11    4  0.10

ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36


Consensus pattern (10 bp):   
CTAATTAAAT

Found at i:3851 original size:39 final size:39

Alignment explanation


    Indices: 3808--4388  Score: 553
    Period size: 39  Copynumber: 14.9  Consensus size: 39

       3798 TCTTAACCGA

                     **     *       **             
       3808 AAACTCTAAGTAGAGATCTAAGCAAATTTACTTAAATGG
          1 AAACTCTAAACAGAGACCTAAGCAGGTTTACTTAAATGG

                 *    *                             
       3847 AAACTATAAATAGAGACCTAAGCAGGTTTACTTAAAATGG
          1 AAACTCTAAACAGAGACCTAAGCAGGTTTACTT-AAATGG

                      *     *   *                  
       3887 -AACTCTAAATAGAGATCTAGGCAGGTTTACTTAAATGG
          1 AAACTCTAAACAGAGACCTAAGCAGGTTTACTTAAATGG

                 *  *   *                          
       3925 AAACTTTAGACACAGACCTAAGCAGGTTTACTTAAATGG
          1 AAACTCTAAACAGAGACCTAAGCAGGTTTACTTAAATGG

                 *  *   *           *              
       3964 AAACTTTAGACATAGACCTAAGCATGTTTACTTAAATGG
          1 AAACTCTAAACAGAGACCTAAGCAGGTTTACTTAAATGG

                 *       *                 *       
       4003 AAACTTTAAACAGGGACCTAAGCAGGTTTACCTAAATGG
          1 AAACTCTAAACAGAGACCTAAGCAGGTTTACTTAAATGG

             *    *    *                   *         
       4042 TTAA-TTTAAATAGAGACCTAAGCAGGTTTTTCTTAAAT-G
          1 -AAACTCTAAACAGAGACCTAAGCAGG-TTTACTTAAATGG

                   * *     *                       
       4081 AAACTCTGAGCAGAGGCCTAAGCAGGTTTACTTAAAT-G
          1 AAACTCTAAACAGAGACCTAAGCAGGTTTACTTAAATGG

                       *  *   *                  * *
       4119 ACAACTCTAAATAGGGACTTAAGCAGGTTTACTTAAACGA
          1 A-AACTCTAAACAGAGACCTAAGCAGGTTTACTTAAATGG

               *                                   
       4159 AAATTCTAAACAGAGACCTAAGCAGGTTTACTTAAAT-G
          1 AAACTCTAAACAGAGACCTAAGCAGGTTTACTTAAATGG

                     *     *     *  *             **
       4197 AAACTCTAAGCAGAGGCCTAAACAAGTTTACTTAAATAAA
          1 AAACTCTAAACAGAGACCTAAGCAGGTTTACTTAAAT-GG

               **  *  *   *              *       * 
       4237 AAAAACTTAATAGAAACCTAAGCAGGTTTCCTTAAA-AG
          1 AAACTCTAAACAGAGACCTAAGCAGGTTTACTTAAATGG

                     *                      *     *
       4275 AAACTCTAAGCAGAGACCTAAGCAGGTTTACTCAAATGA
          1 AAACTCTAAACAGAGACCTAAGCAGGTTTACTTAAATGG

               *       *        * *     * *       *
       4314 AAATTCTAAACGGAGACCTAGGTAGGTTCAATTAAATGA
          1 AAACTCTAAACAGAGACCTAAGCAGGTTTACTTAAATGG

               *                          *     
       4353 AAATTCTAAACAGAGACCTAAGCAGGTTTAATTAAA
          1 AAACTCTAAACAGAGACCTAAGCAGGTTTACTTAAA

       4389 CAAAACTCTA


Statistics
Matches: 446,  Mismatches: 86, Indels: 20
        0.81            0.16        0.04

Matches are distributed among these distances:
  38   81  0.18
  39  321  0.72
  40   44  0.10

ACGTcount: A:0.41, C:0.15, G:0.17, T:0.26


Consensus pattern (39 bp):   
AAACTCTAAACAGAGACCTAAGCAGGTTTACTTAAATGG

Done.