Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008081.1 Corchorus capsularis cultivar CVL-1 contig08102, 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: 3629
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36


Found at i:319 original size:59 final size:59

Alignment explanation


    Indices: 250--588  Score: 499
    Period size: 59  Copynumber: 6.0  Consensus size: 59

        240 TTTTCTCCTG

                *               *                                      
        250 TACCCTCGTGTCTGGCCTCGTCTCACTTCACTGCGGAGGCCTCTCTCTTCTCGTGTACC
          1 TACCTTCGTGTCTGGCCTCGCCTCACTTCACTGCGGAGGCCTCTCTCTTCTCGTGTACC

                                                           *    *      
        309 TACCTTCGTGTCTGGCCTCGCCTCACTTCACTGCGGAGGCCTCTCTCCTCTCTTGTACC
          1 TACCTTCGTGTCTGGCCTCGCCTCACTTCACTGCGGAGGCCTCTCTCTTCTCGTGTACC

              *           *                   *                        
        368 TAACTTCGTGTCTGACCTCG---C-C-TCACTGCAGAGGCCTCTCTCTTCTCGTGTACC
          1 TACCTTCGTGTCTGGCCTCGCCTCACTTCACTGCGGAGGCCTCTCTCTTCTCGTGTACC

                                                                       
        422 TACCTTCGTGTCTGGCCTCGCCTCACTTCACTGCGGAGGCCTCTCTCTTCTCGTGTACC
          1 TACCTTCGTGTCTGGCCTCGCCTCACTTCACTGCGGAGGCCTCTCTCTTCTCGTGTACC

                                             *                         
        481 TACCTTCGTGTCTGGCCTCGCCT-ACTT-ACTGTGGAGG-C-CTCTCTTCTCGTGTACC
          1 TACCTTCGTGTCTGGCCTCGCCTCACTTCACTGCGGAGGCCTCTCTCTTCTCGTGTACC

                                             *                        
        536 TACCTTCGTGTCTGGCCTCG---C-C-TCACTGTGGAGGCCTCTCTCTTCTCGTGTAC
          1 TACCTTCGTGTCTGGCCTCGCCTCACTTCACTGCGGAGGCCTCTCTCTTCTCGTGTAC

        589 ATTCGTGTCT


Statistics
Matches: 258,  Mismatches: 13, Indels: 23
        0.88            0.04        0.08

Matches are distributed among these distances:
  51    1  0.00
  52   11  0.04
  53    1  0.00
  54   63  0.24
  55   38  0.15
  56    2  0.01
  57   10  0.04
  58    5  0.02
  59  127  0.49

ACGTcount: A:0.09, C:0.38, G:0.20, T:0.33


Consensus pattern (59 bp):   
TACCTTCGTGTCTGGCCTCGCCTCACTTCACTGCGGAGGCCTCTCTCTTCTCGTGTACC

Found at i:415 original size:113 final size:113

Alignment explanation


    Indices: 277--562  Score: 477
    Period size: 113  Copynumber: 2.5  Consensus size: 113

        267 TCGTCTCACT

                                                                             
        277 TCACTGCGGAGGCCTCTCTCTTCTCGTGTACCTACCTTCGTGTCTGGCCTCGCCTCACTTCACTG
          1 TCACTGCGGAGGCCTCTCTCTTCTCGTGTACCTACCTTCGTGTCTGGCCTCGCCTCACTTCACTG

                               *                            
        342 CGGAGGCCTCTCTCCTCTCTTGTACCTAACTTCGTGTCTGACCTCGCC
         66 CGGAGGCCTCTCTCCTCTCGTGTACCTAACTTCGTGTCTGACCTCGCC

                   *                                                         
        390 TCACTGCAGAGGCCTCTCTCTTCTCGTGTACCTACCTTCGTGTCTGGCCTCGCCTCACTTCACTG
          1 TCACTGCGGAGGCCTCTCTCTTCTCGTGTACCTACCTTCGTGTCTGGCCTCGCCTCACTTCACTG

                          *             *           *       
        455 CGGAGGCCTCTCTCTTCTCGTGTACCTACCTTCGTGTCTGGCCTCGCC
         66 CGGAGGCCTCTCTCCTCTCGTGTACCTAACTTCGTGTCTGACCTCGCC

                     *                                                    
        503 TACTTACTGTGGAGG-C-CTCTCTTCTCGTGTACCTACCTTCGTGTCTGGCCTCGCCTCACT
          1 T-C--ACTGCGGAGGCCTCTCTCTTCTCGTGTACCTACCTTCGTGTCTGGCCTCGCCTCACT

        563 GTGGAGGCCT


Statistics
Matches: 163,  Mismatches: 7, Indels: 5
        0.93            0.04        0.03

Matches are distributed among these distances:
 113  109  0.67
 114   45  0.28
 115    1  0.01
 116    8  0.05

ACGTcount: A:0.09, C:0.38, G:0.20, T:0.33


Consensus pattern (113 bp):   
TCACTGCGGAGGCCTCTCTCTTCTCGTGTACCTACCTTCGTGTCTGGCCTCGCCTCACTTCACTG
CGGAGGCCTCTCTCCTCTCGTGTACCTAACTTCGTGTCTGACCTCGCC

Done.