Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017503.1 Corchorus olitorius cultivar O-4 contig17536, 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: 17973
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32


Found at i:3798 original size:15 final size:15

Alignment explanation


    Indices: 3778--3811  Score: 68
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       3768 AATAGTCCAA

                           
       3778 AATGCAAACATGACT
          1 AATGCAAACATGACT

                           
       3793 AATGCAAACATGACT
          1 AATGCAAACATGACT

                
       3808 AATG
          1 AATG

       3812 TAAATAGTAC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   19  1.00

ACGTcount: A:0.47, C:0.18, G:0.15, T:0.21


Consensus pattern (15 bp):   
AATGCAAACATGACT

Found at i:4033 original size:27 final size:27

Alignment explanation


    Indices: 3974--4067  Score: 116
    Period size: 27  Copynumber: 3.4  Consensus size: 27

       3964 AAAAACAACC

                      *    *            *
       3974 AAAATGCCCCAGAACCTGCAAAAATGACC
          1 AAAATGCCCCTGAACGTGC--AAATGACT

                        * *            
       4003 AAAATGCCCCTGGATGTGCAAATGACT
          1 AAAATGCCCCTGAACGTGCAAATGACT

                                       
       4030 AAAATGCCCCTGAACGTGCAAATGACT
          1 AAAATGCCCCTGAACGTGCAAATGACT

              *        
       4057 AACATGCCCCT
          1 AAAATGCCCCT

       4068 TATGTGACCC


Statistics
Matches: 57,  Mismatches: 8, Indels: 2
        0.85            0.12        0.03

Matches are distributed among these distances:
  27   42  0.74
  29   15  0.26

ACGTcount: A:0.37, C:0.29, G:0.17, T:0.17


Consensus pattern (27 bp):   
AAAATGCCCCTGAACGTGCAAATGACT

Found at i:14739 original size:81 final size:81

Alignment explanation


    Indices: 14601--14797  Score: 234
    Period size: 81  Copynumber: 2.4  Consensus size: 81

      14591 GATGCTCCTG

                        *   **  *    *                                 *     
      14601 CAGTTGGGACTCGTGCAAAAACTCCTGCAGTTGGGACTCATACCAAAGCCTCCGCAGTTGGGACT
          1 CAGTTGGGACTCATGCTGAAGCTCCCGCAGTTGGGACTCATACCAAAGCCTCCGCAGTTCGGACT

                       *     
      14666 CATGCCT-AAGTTCCCA
         66 CATG-CTGAAGCTCCCA

             *                                  *    **         *            
      14682 CGGTTGGGACTCATGCTGAAGCTCCCGCAGTTGGGATTCATGGCAAAGCCTCTGCAGTTCGGACT
          1 CAGTTGGGACTCATGCTGAAGCTCCCGCAGTTGGGACTCATACCAAAGCCTCCGCAGTTCGGACT

                           *
      14747 CATGCTGAAGCTCCCG
         66 CATGCTGAAGCTCCCA

                           *      *      *     
      14763 CAGTTGGGACTCATGTTGAAGCACCCGCATTTGGG
          1 CAGTTGGGACTCATGCTGAAGCTCCCGCAGTTGGG

      14798 TTTTGTGTTG


Statistics
Matches: 98,  Mismatches: 17, Indels: 2
        0.84            0.15        0.02

Matches are distributed among these distances:
  80    2  0.02
  81   96  0.98

ACGTcount: A:0.21, C:0.28, G:0.27, T:0.23


Consensus pattern (81 bp):   
CAGTTGGGACTCATGCTGAAGCTCCCGCAGTTGGGACTCATACCAAAGCCTCCGCAGTTCGGACT
CATGCTGAAGCTCCCA

Found at i:14789 original size:27 final size:27

Alignment explanation


    Indices: 14594--14797  Score: 173
    Period size: 27  Copynumber: 7.6  Consensus size: 27

      14584 AAAGAAAGAT

                 *             *   **  
      14594 GCTCCTGCAGTTGGGACTCGTGCAAAA
          1 GCTCCCGCAGTTGGGACTCATGCTGAA

            *    *               * **  
      14621 ACTCCTGCAGTTGGGACTCATACCAAA
          1 GCTCCCGCAGTTGGGACTCATGCTGAA

                                         
      14648 GC-CTCCGCAGTTGGGACTCATGCCT-AA
          1 GCTC-CCGCAGTTGGGACTCATG-CTGAA

             *    * *                  
      14675 GTTCCCACGGTTGGGACTCATGCTGAA
          1 GCTCCCGCAGTTGGGACTCATGCTGAA

                            *        *  
      14702 GCTCCCGCAGTTGGGATTCATGGC-AAA
          1 GCTCCCGCAGTTGGGACTCAT-GCTGAA

                  *      *              
      14729 GC-CTCTGCAGTTCGGACTCATGCTGAA
          1 GCTC-CCGCAGTTGGGACTCATGCTGAA

                                  *    
      14756 GCTCCCGCAGTTGGGACTCATGTTGAA
          1 GCTCCCGCAGTTGGGACTCATGCTGAA

              *      *     
      14783 GCACCCGCATTTGGG
          1 GCTCCCGCAGTTGGG

      14798 TTTTGTGTTG


Statistics
Matches: 144,  Mismatches: 25, Indels: 16
        0.78            0.14        0.09

Matches are distributed among these distances:
  26    6  0.04
  27  133  0.92
  28    5  0.03

ACGTcount: A:0.21, C:0.28, G:0.27, T:0.24


Consensus pattern (27 bp):   
GCTCCCGCAGTTGGGACTCATGCTGAA
Done.