Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005503.1 Corchorus capsularis cultivar CVL-1 contig05521, 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, 682

Length: 1138
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:290 original size:13 final size:14

Alignment explanation


    Indices: 272--304  Score: 50
    Period size: 14  Copynumber: 2.4  Consensus size: 14

        262 TGCTACAACA

                          
        272 CCCTCCA-ATTTGT
          1 CCCTCCATATTTGT

                    *     
        285 CCCTCCATTTTTGT
          1 CCCTCCATATTTGT

                  
        299 CCCTCC
          1 CCCTCC

        305 TGACGTGTCA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  13    7  0.39
  14   11  0.61

ACGTcount: A:0.09, C:0.45, G:0.06, T:0.39


Consensus pattern (14 bp):   
CCCTCCATATTTGT

Found at i:563 original size:13 final size:13

Alignment explanation


    Indices: 545--576  Score: 55
    Period size: 13  Copynumber: 2.5  Consensus size: 13

        535 TGCTACATGA

                         
        545 CCCTCCAATTTGT
          1 CCCTCCAATTTGT

                   *     
        558 CCCTCCATTTTGT
          1 CCCTCCAATTTGT

                  
        571 CCCTCC
          1 CCCTCC

        577 TGACGTGTCA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   18  1.00

ACGTcount: A:0.09, C:0.47, G:0.06, T:0.38


Consensus pattern (13 bp):   
CCCTCCAATTTGT

Found at i:755 original size:272 final size:272

Alignment explanation


    Indices: 226--833  Score: 925
    Period size: 272  Copynumber: 2.2  Consensus size: 272

        216 TTAATTATAA

                  *                                     *                    
        226 GGAGGGACAAATAGAATTATCCTAAGAAAAGAGTATTGCTACAACACCCTCCAATTTGTCCCTCC
          1 GGAGGGTCAAATAGAATTATCCTAAGAAAAGAGTATTGCTACAAGACCCTCCAATTTGTCCCTCC

                                                *                            
        291 ATTTTTGTCCCTCCTGACGTGTCATTAGAAAACTTATTATAATTTCTAAAACCATATTCAATAAA
         66 ATTTTTGTCCCTCCTGACGTGTCATTAGAAAACTTACTATAATTTCTAAAACCATATTCAAT-AA

                        *                   *     *                      *   
        356 ACAGCCTAAAATTAAGGCATTTACCCTGCAAACTCACCGTATTTATAACTAGGGGCTAAACCTGG
        130 ACAGCCTAAAATCAAGGCATTTACCCTGCAAAATCACCATATTTATAACTAGGGGCTAAACATGG

                                                  *          *             * 
        421 ATTTAATTTCTACATTAATTATCAGGGGGACTAAACATGGATTTAATTTTTTTCCTTAATTATTA
        195 ATTTAATTTCTACATTAATTATCAGGGGGACTAAACATAGATTTAATTTGTTTCCTTAATTATAA

              *  *       
        486 GGGGGGACAAATT
        260 GGAGGAACAAATT

                                                       *                     
        499 GGAGGGTCAAATAGAATTATCCTAAGAAAAGAGTATTGCTACATGACCCTCCAATTTGTCCCTCC
          1 GGAGGGTCAAATAGAATTATCCTAAGAAAAGAGTATTGCTACAAGACCCTCCAATTTGTCCCTCC

                                            *            *    *  *     *     
        564 A-TTTTGTCCCTCCTGACGTGTCATTAGAAAAGTTACTATAATTTTTAAATCCCTATTCGAT-AA
         66 ATTTTTGTCCCTCCTGACGTGTCATTAGAAAACTTACTATAATTTCTAAAACCATATTCAATAAA

            *               *                 *                              
        627 TAGCCTAAAATCAAGGGATTTACCCTGCAAAATCTCCATATTTATAACTAGGGGCTAAACATGGA
        131 CAGCCTAAAATCAAGGCATTTACCCTGCAAAATCACCATATTTATAACTAGGGGCTAAACATGGA

                         *      *         *      *                           
        692 TTTAATTTCTTACCTTAATTTTCAGAGGGGGCTAAACCTAGATTTAATTTGTTTCCTTAATTATA
        196 TTTAATTTC-TACATTAATTATCAG-GGGGACTAAACATAGATTTAATTTGTTTCCTTAATTATA

                          
        757 AGGAGGAACAAATT
        259 AGGAGGAACAAATT

                                                          *       *         
        771 GGAGGGTCAAATAGAATTATCCTAAG-AAAGAGTATTGCTACAAGAACCTCCAACTTGTCCCTC
          1 GGAGGGTCAAATAGAATTATCCTAAGAAAAGAGTATTGCTACAAGACCCTCCAATTTGTCCCTC

        834 TTGACGTGTC


Statistics
Matches: 305,  Mismatches: 28, Indels: 6
        0.90            0.08        0.02

Matches are distributed among these distances:
 270   69  0.23
 271   47  0.15
 272  126  0.41
 273   63  0.21

ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32


Consensus pattern (272 bp):   
GGAGGGTCAAATAGAATTATCCTAAGAAAAGAGTATTGCTACAAGACCCTCCAATTTGTCCCTCC
ATTTTTGTCCCTCCTGACGTGTCATTAGAAAACTTACTATAATTTCTAAAACCATATTCAATAAA
CAGCCTAAAATCAAGGCATTTACCCTGCAAAATCACCATATTTATAACTAGGGGCTAAACATGGA
TTTAATTTCTACATTAATTATCAGGGGGACTAAACATAGATTTAATTTGTTTCCTTAATTATAAG
GAGGAACAAATT

Found at i:948 original size:41 final size:41

Alignment explanation


    Indices: 895--979  Score: 134
    Period size: 41  Copynumber: 2.1  Consensus size: 41

        885 TCCAATTTGT

                   *       *                         
        895 CCCTCCTTATAATTAGGGAAACAAATTAAATCCAGGTTTAG
          1 CCCTCCTGATAATTAAGGAAACAAATTAAATCCAGGTTTAG

                              *  *                   
        936 CCCTCCTGATAATTAAGGTAAGAAATTAAATCCAGGTTTAG
          1 CCCTCCTGATAATTAAGGAAACAAATTAAATCCAGGTTTAG

               
        977 CCC
          1 CCC

        980 CTAGTTATAA


Statistics
Matches: 40,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  41   40  1.00

ACGTcount: A:0.35, C:0.21, G:0.15, T:0.28


Consensus pattern (41 bp):   
CCCTCCTGATAATTAAGGAAACAAATTAAATCCAGGTTTAG
Done.