Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023737.1 Corchorus olitorius cultivar O-4 contig23770, 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: 9783
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29


Found at i:2501 original size:25 final size:27

Alignment explanation


    Indices: 2453--2510  Score: 84
    Period size: 25  Copynumber: 2.2  Consensus size: 27

       2443 AATGTAATGC

                    *                  
       2453 ATGCAAACTTAAGAAAAGAAAAAAAAA
          1 ATGCAAACATAAGAAAAGAAAAAAAAA

                               *       
       2480 ATGCAAACATAA-AAAAG-GAAAAAAA
          1 ATGCAAACATAAGAAAAGAAAAAAAAA

                  
       2505 ATGCAA
          1 ATGCAA

       2511 TTTCTTTAAC


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  25   13  0.45
  26    5  0.17
  27   11  0.38

ACGTcount: A:0.69, C:0.09, G:0.12, T:0.10


Consensus pattern (27 bp):   
ATGCAAACATAAGAAAAGAAAAAAAAA

Found at i:5065 original size:50 final size:50

Alignment explanation


    Indices: 4985--5210  Score: 307
    Period size: 50  Copynumber: 4.5  Consensus size: 50

       4975 AGATATCCAG

                *                                         *   
       4985 AAGAGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCATTT
          1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT

                                                              
       5035 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCC-TTT
          1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT

                              *     *    *            *       
       5084 AAGATTGAATTGGAAGACGGTTCAGAGGACAAGCGGAAGACGATCCTTTT
          1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT

                               *     *                          
       5134 AAGATTGAATTAGGAA-ACGGTTCAGAGGATAAGCGGAAGACGGTCCTTTTT
          1 AAGATTGAATT-GGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCC-TTTT

                   *     *              
       5185 AA-ATTGGATTGGGAGAC-GATTCAAAG
          1 AAGATTGAATTGGAAGACAG-TTCAAAG

       5211 AAGTTTATTC


Statistics
Matches: 161,  Mismatches: 10, Indels: 10
        0.89            0.06        0.06

Matches are distributed among these distances:
  49   49  0.30
  50  102  0.63
  51   10  0.06

ACGTcount: A:0.36, C:0.12, G:0.30, T:0.23


Consensus pattern (50 bp):   
AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT

Found at i:5163 original size:99 final size:99

Alignment explanation


    Indices: 4985--5182  Score: 308
    Period size: 99  Copynumber: 2.0  Consensus size: 99

       4975 AGATATCCAG

                                         *            *                      
       4985 AAGAGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCATTTAAGATTGAATTGGAA
          1 AAGAGTGAATTGGAAGACAGTTCAAAGGACAAGCGGAAGACGATCCATTTAAGATTGAATTGGAA

                                              
       5050 GACAGTTCAAAGGATAAGCGGAAGACGGTCCTTT
         66 GACAGTTCAAAGGATAAGCGGAAGACGGTCCTTT

                *             *     *                     *                  
       5084 AAGATTGAATTGGAAGACGGTTCAGAGGACAAGCGGAAGACGATCCTTTTAAGATTGAATTAGGA
          1 AAGAGTGAATTGGAAGACAGTTCAAAGGACAAGCGGAAGACGATCCATTTAAGATTGAATT-GGA

                *     *                        
       5149 A-ACGGTTCAGAGGATAAGCGGAAGACGGTCCTTT
         65 AGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTT

       5183 TTAAATTGGA


Statistics
Matches: 90,  Mismatches: 8, Indels: 2
        0.90            0.08        0.02

Matches are distributed among these distances:
  99   86  0.96
 100    4  0.04

ACGTcount: A:0.36, C:0.13, G:0.30, T:0.22


Consensus pattern (99 bp):   
AAGAGTGAATTGGAAGACAGTTCAAAGGACAAGCGGAAGACGATCCATTTAAGATTGAATTGGAA
GACAGTTCAAAGGATAAGCGGAAGACGGTCCTTT

Found at i:5551 original size:27 final size:27

Alignment explanation


    Indices: 5485--5576  Score: 112
    Period size: 27  Copynumber: 3.4  Consensus size: 27

       5475 TTTACTTCCT

                                     * *
       5485 ATTTTGGTCATTTGCATGTCCAAGGTGT
          1 ATTTTGGTCATTTGCATGTCC-AGGGGC

                          **           
       5513 ATTTTGGTCATTTGTTTGTCCAGGGGC
          1 ATTTTGGTCATTTGCATGTCCAGGGGC

                            **       * 
       5540 ATTTTGGTCATTTGCACATCCAGGGAC
          1 ATTTTGGTCATTTGCATGTCCAGGGGC

                      
       5567 ATTTTGGTCA
          1 ATTTTGGTCA

       5577 CTTCAAGTAC


Statistics
Matches: 55,  Mismatches: 9, Indels: 1
        0.85            0.14        0.02

Matches are distributed among these distances:
  27   36  0.65
  28   19  0.35

ACGTcount: A:0.17, C:0.16, G:0.25, T:0.41


Consensus pattern (27 bp):   
ATTTTGGTCATTTGCATGTCCAGGGGC
Done.