Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016227.1 Corchorus olitorius cultivar O-4 contig16260, 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: 22881
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30


Found at i:1564 original size:40 final size:40

Alignment explanation


    Indices: 1497--1899  Score: 644
    Period size: 40  Copynumber: 10.1  Consensus size: 40

       1487 AAGGAATAGG

                      *   *  * *         *    * *   
       1497 AACAACACCTCCCGATGAGAAAGGGCAAACTGGGAACTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTATTTA

                    *             *      *    *     
       1537 AACAACACTTTCCGGTGGGGAAAGGCAAACTGGGAATTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTATTTA

            *                            *          
       1577 GACAACACCTTCCGGTGGGGAAGGGCAAAATGGGTATTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTATTTA

                                               *    
       1617 AACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTTTTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTATTTA

                                         *          
       1657 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTATTTA

                                               *    
       1697 AACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTTTTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTATTTA

                                         *          
       1737 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTATTTA

                                                    
       1777 AACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTATTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTATTTA

                            *                       
       1817 AACAACACCTTCCGGTAGGGAAGGGCAAATTGGGTATTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTATTTA

                                                    
       1857 AACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTATTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTATTTA

               
       1897 AAC
          1 AAC

       1900 TAGACAAGAC


Statistics
Matches: 339,  Mismatches: 24, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  40  339  1.00

ACGTcount: A:0.32, C:0.19, G:0.29, T:0.21


Consensus pattern (40 bp):   
AACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTATTTA

Found at i:3011 original size:8 final size:8

Alignment explanation


    Indices: 2998--3022  Score: 50
    Period size: 8  Copynumber: 3.1  Consensus size: 8

       2988 TAGCTCAATT

                    
       2998 AGAAATCA
          1 AGAAATCA

                    
       3006 AGAAATCA
          1 AGAAATCA

                    
       3014 AGAAATCA
          1 AGAAATCA

             
       3022 A
          1 A

       3023 CATAAATCAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   17  1.00

ACGTcount: A:0.64, C:0.12, G:0.12, T:0.12


Consensus pattern (8 bp):   
AGAAATCA

Found at i:8124 original size:18 final size:18

Alignment explanation


    Indices: 8083--8142  Score: 66
    Period size: 18  Copynumber: 3.3  Consensus size: 18

       8073 TTGCGGTAGC

                        *   * 
       8083 GGAACATCCTGCGGCAAT
          1 GGAACATCCTGCAGCAGT

             *     *      *   
       8101 GCAACATTCTGCAGTAGT
          1 GGAACATCCTGCAGCAGT

                              
       8119 GGAACATCCTGCAGCAGT
          1 GGAACATCCTGCAGCAGT

             *    
       8137 GTAACA
          1 GGAACA

       8143 ATATTTTGTA


Statistics
Matches: 33,  Mismatches: 9, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  18   33  1.00

ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20


Consensus pattern (18 bp):   
GGAACATCCTGCAGCAGT

Found at i:18489 original size:1 final size:1

Alignment explanation


    Indices: 18483--18515  Score: 66
    Period size: 1  Copynumber: 33.0  Consensus size: 1

      18473 AATCTTCCGT

                                             
      18483 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      18516 GAGAGAGAAA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   32  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Done.