Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010674.1 Corchorus capsularis cultivar CVL-1 contig10695, 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: 9128
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30


Found at i:3804 original size:172 final size:169

Alignment explanation


    Indices: 3517--3840  Score: 479
    Period size: 172  Copynumber: 1.9  Consensus size: 169

       3507 AGGGAGAGGA

                                  *                                      ** *
       3517 GATGATGCGCCAAGGGCTTATCCTGGCTTAGAAGAACACATTGGAGCCAATGAAGATCATGGTGT
          1 GATGATGCGCCAAGGGCTTATCATGGCTTAGAAGAACACATTGGAGCCAATGAAGATCATGAAGA

                                                      **                     
       3582 TGTCATCGATGCTACCTTGAAGAAGCATGGAGATGGAAGCACTTGTGACCGGCCACGCGACTTGG
         66 TGTCATCGATGCTACCTTGAAGAAGCATGGAGATGGAAGCACAAGTGACCGGCCA-GCG-CTTGG

               *          *                            
       3647 AGATGCC-CGACCATCACCGGCCACACGACTCGGAGATGCCCG
        129 AGAAGCCGCG--CAACACCGGCCACACGACTCGGAGATGCCCG

                                                                *            
       3689 GATGATGCGCCAAGGGCTTATCATGGCTTAGAAGAACACATTGGAGCCAATGGAGATCATGAAGA
          1 GATGATGCGCCAAGGGCTTATCATGGCTTAGAAGAACACATTGGAGCCAATGAAGATCATGAAGA

                          *    *  *              *                 *         
       3754 TGTCATCGATGCTAGCTTGGAGGAGCATGGAGATGGAGGCACAAGTGACCGGCCATCGCTTGGAG
         66 TGTCATCGATGCTACCTTGAAGAAGCATGGAGATGGAAGCACAAGTGACCGGCCAGCGCTTGGAG

                                  
       3819 AAGCCGCGCAACACCGGCCACA
        131 AAGCCGCGCAACACCGGCCACA

       3841 AGACCGGCCA


Statistics
Matches: 137,  Mismatches: 14, Indels: 5
        0.88            0.09        0.03

Matches are distributed among these distances:
 169   13  0.09
 170   11  0.08
 171    4  0.03
 172  109  0.80

ACGTcount: A:0.27, C:0.24, G:0.30, T:0.18


Consensus pattern (169 bp):   
GATGATGCGCCAAGGGCTTATCATGGCTTAGAAGAACACATTGGAGCCAATGAAGATCATGAAGA
TGTCATCGATGCTACCTTGAAGAAGCATGGAGATGGAAGCACAAGTGACCGGCCAGCGCTTGGAG
AAGCCGCGCAACACCGGCCACACGACTCGGAGATGCCCG

Found at i:3913 original size:33 final size:33

Alignment explanation


    Indices: 3832--3950  Score: 134
    Period size: 33  Copynumber: 3.5  Consensus size: 33

       3822 CCGCGCAACA

                                              *
       3832 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
          1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGC

                                             *
       3867 CCGGCCATC-ACCGGCCACGCGACATGGACATGG
          1 CCGGCCA-CAACCGGCCACGCGACATGGACATGC

                 *           **         *     
       3900 CCGGCTACAACCGGCCAAACGAC-TCGGCCATGC
          1 CCGGCCACAACCGGCCACGCGACAT-GGACATGC

                              
       3933 CCGGCCACAACCGGCCAC
          1 CCGGCCACAACCGGCCAC

       3951 ACGATCCTTT


Statistics
Matches: 73,  Mismatches: 8, Indels: 8
        0.82            0.09        0.09

Matches are distributed among these distances:
  32    2  0.03
  33   63  0.86
  35    7  0.10
  36    1  0.01

ACGTcount: A:0.24, C:0.42, G:0.27, T:0.08


Consensus pattern (33 bp):   
CCGGCCACAACCGGCCACGCGACATGGACATGC
Done.