Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008507.1 Corchorus capsularis cultivar CVL-1 contig08528, 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: 20822
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:7689 original size:30 final size:30

Alignment explanation


    Indices: 7562--8255  Score: 807
    Period size: 30  Copynumber: 22.8  Consensus size: 30

       7552 ATTCAAAGTC

                 *      *                   *
       7562 TACAAATGACACAAGAAGTTGTCATGATAAATC
          1 TACAATTGACACCAGAAGTTGTCATGAT---TT

               *                       * **
       7595 T-CCATTGACACCAGAAGTTGTCAATGGTGC
          1 TACAATTGACACCAGAAGTTGTC-ATGATTT

                                      *  * 
       7625 TACAATTGACACCAGAAGTTGTCAATAATCT
          1 TACAATTGACACCAGAAGTTGTC-ATGATTT

                 *                       * 
       7656 TACAAATGACACCAGAAGTTGTCAT-AGTCT
          1 TACAATTGACACCAGAAGTTGTCATGA-TTT

                 *      *                 
       7686 TACAAATGACACTAGAAGTTGTCATGATTT
          1 TACAATTGACACCAGAAGTTGTCATGATTT

             *                            
       7716 TGCAATTGACACCAGAAGTTGTCATGATTT
          1 TACAATTGACACCAGAAGTTGTCATGATTT

             *                       *  * 
       7746 TCCAATTGACACCAGAAGTTGTCATAATCT
          1 TACAATTGACACCAGAAGTTGTCATGATTT

              *    *    * *           *  * 
       7776 TATAATTAACACTAAAAGTTGTCAATAATCT
          1 TACAATTGACACCAGAAGTTGTC-ATGATTT

                 *                        
       7807 TACAAATGACACCAGAAGTTGTCATGATTT
          1 TACAATTGACACCAGAAGTTGTCATGATTT

                                      *  * 
       7837 TACAATTGACACCAGAAGTTGTCAATAATCT
          1 TACAATTGACACCAGAAGTTGTC-ATGATTT

                 *                        
       7868 TACAAATGACACCAGAAGTTGTCATGATTT
          1 TACAATTGACACCAGAAGTTGTCATGATTT

                                      *  * 
       7898 TACAATTGACACCAGAAGTTGTCAATAATCT
          1 TACAATTGACACCAGAAGTTGTC-ATGATTT

                 *                    * * 
       7929 TACAAATGACACCAGAAGTTGTCATGGTCT
          1 TACAATTGACACCAGAAGTTGTCATGATTT

              *  *   *          *         
       7959 TATAAATGATACCAGAAGTTATCATGATTT
          1 TACAATTGACACCAGAAGTTGTCATGATTT

             *          *                 
       7989 TGCAATTGACACTAGAAGTTGTCATGATTT
          1 TACAATTGACACCAGAAGTTGTCATGATTT

             *            *               
       8019 TGCAATTGACACCATAAGTTGTCATGATTT
          1 TACAATTGACACCAGAAGTTGTCATGATTT

             *                            
       8049 TGCAATTGACACCAGAAGTTGTCATGATTT
          1 TACAATTGACACCAGAAGTTGTCATGATTT

             *                            
       8079 TGCAATTGACACCAGAAGTTGTCATGATTT
          1 TACAATTGACACCAGAAGTTGTCATGATTT

             * *                          
       8109 TGCGATTGACACCAGAAGTTGTCATGATTT
          1 TACAATTGACACCAGAAGTTGTCATGATTT

             *                            
       8139 TTCAATTGACACCAGAAGTTGTCATGATTT
          1 TACAATTGACACCAGAAGTTGTCATGATTT

             *            *               
       8169 TGCAATTGACACCAAAAGTTGTCATGATTT
          1 TACAATTGACACCAGAAGTTGTCATGATTT

             *          **    *           
       8199 TGCAATTGACACTTGAAGATGTCATGATTT
          1 TACAATTGACACCAGAAGTTGTCATGATTT

                          *            
       8229 TATTCAATTGACACTAGAAGTTGTCAT
          1 TA--CAATTGACACCAGAAGTTGTCAT

       8256 ATACACCATG


Statistics
Matches: 583,  Mismatches: 69, Indels: 19
        0.87            0.10        0.03

Matches are distributed among these distances:
  29    1  0.00
  30  412  0.71
  31  126  0.22
  32   39  0.07
  33    5  0.01

ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Consensus pattern (30 bp):   
TACAATTGACACCAGAAGTTGTCATGATTT

Found at i:8517 original size:118 final size:118

Alignment explanation


    Indices: 8309--8546  Score: 449
    Period size: 118  Copynumber: 2.0  Consensus size: 118

       8299 ATAACTAATT

                                                                             
       8309 CCCATTTGACACTAGAAGTTGCCATTGTGCTTTAATTACATGTCTAGGCAAATTCTGTCTAAGGA
          1 CCCATTTGACACTAGAAGTTGCCATTGTGCTTTAATTACATGTCTAGGCAAATTCTGTCTAAGGA

                                *                                
       8374 GTTGGATTTTAAGTGAGACCGTTTGTGACTCCTCCATCTTTCCTGGGAATTTA
         66 GTTGGATTTTAAGTGAGACCATTTGTGACTCCTCCATCTTTCCTGGGAATTTA

                     *           *                                           
       8427 CCCATTTGATACTAGAAGTTGTCATTGTGCTTTAATTACATGTCTAGGCAAATTCTGTCTAAGGA
          1 CCCATTTGACACTAGAAGTTGCCATTGTGCTTTAATTACATGTCTAGGCAAATTCTGTCTAAGGA

                                                                 
       8492 GTTGGATTTTAAGTGAGACCATTTGTGACTCCTCCATCTTTCCTGGGAATTTA
         66 GTTGGATTTTAAGTGAGACCATTTGTGACTCCTCCATCTTTCCTGGGAATTTA

              
       8545 CC
          1 CC

       8547 TGGTGTAATT


Statistics
Matches: 117,  Mismatches: 3, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
 118  117  1.00

ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37


Consensus pattern (118 bp):   
CCCATTTGACACTAGAAGTTGCCATTGTGCTTTAATTACATGTCTAGGCAAATTCTGTCTAAGGA
GTTGGATTTTAAGTGAGACCATTTGTGACTCCTCCATCTTTCCTGGGAATTTA

Found at i:9549 original size:65 final size:65

Alignment explanation


    Indices: 9440--9589  Score: 228
    Period size: 65  Copynumber: 2.3  Consensus size: 65

       9430 GGAAGCCATC

                                          *                  *               
       9440 ATTATGGGCCGTTATAGAGGCTAGTATCATGAGCCATAGCAAAGGCCATGAACATATTAGAAATT
          1 ATTATGGGCCGTTATAGAGGCTAGTATCATAAGCCATAGCAAAGGCCATCAACATATTAGAAATT

                                                   *               *  *      
       9505 ATTATGGGCCGTTATAGAGGCTAGTATCATAAGCCATAGTAAAGGCCATCAACATGTTTGAAATT
          1 ATTATGGGCCGTTATAGAGGCTAGTATCATAAGCCATAGCAAAGGCCATCAACATATTAGAAATT

              *  *    *         
       9570 ATGATAGGCCATTATAGAGG
          1 ATTATGGGCCGTTATAGAGG

       9590 TCATGACTAT


Statistics
Matches: 77,  Mismatches: 8, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  65   77  1.00

ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27


Consensus pattern (65 bp):   
ATTATGGGCCGTTATAGAGGCTAGTATCATAAGCCATAGCAAAGGCCATCAACATATTAGAAATT
Done.