Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011597.1 Corchorus capsularis cultivar CVL-1 contig11618, 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: 9515
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33


Found at i:62 original size:22 final size:22

Alignment explanation


    Indices: 35--79  Score: 63
    Period size: 22  Copynumber: 2.0  Consensus size: 22

         25 AATGAAACTT

                     *             
         35 GAAAAATAAGGACATAAAATAAA
          1 GAAAAATAAAG-CATAAAATAAA

                             *    
         58 GAAAAATAAAGCATAAACTAAA
          1 GAAAAATAAAGCATAAAATAAA

         80 TAACTAAACT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  22   10  0.50
  23   10  0.50

ACGTcount: A:0.69, C:0.07, G:0.11, T:0.13


Consensus pattern (22 bp):   
GAAAAATAAAGCATAAAATAAA

Found at i:2810 original size:33 final size:33

Alignment explanation


    Indices: 2760--2883  Score: 135
    Period size: 33  Copynumber: 3.7  Consensus size: 33

       2750 CCGCGCAACA

                               *              *
       2760 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
          1 CCGGCCAC-A-ACCGGCCATGCGACATGGACATGC

                                             *
       2795 CCGGCCATC-ACCGGCCATGCGACATGGACATGG
          1 CCGGCCA-CAACCGGCCATGCGACATGGACATGC

                 *           **         *     
       2828 CCGGCTACAACCGGCCAAACGAC-TCGGCCATGC
          1 CCGGCCACAACCGGCCATGCGACAT-GGACATGC

                                   
       2861 CCGGCCACAACCGGCCATGCGAC
          1 CCGGCCACAACCGGCCATGCGAC

       2884 CCTTTGTCTA


Statistics
Matches: 76,  Mismatches: 10, Indels: 8
        0.81            0.11        0.09

Matches are distributed among these distances:
  32    2  0.03
  33   66  0.87
  35    7  0.09
  36    1  0.01

ACGTcount: A:0.23, C:0.40, G:0.27, T:0.09


Consensus pattern (33 bp):   
CCGGCCACAACCGGCCATGCGACATGGACATGC

Found at i:5079 original size:12 final size:13

Alignment explanation


    Indices: 5054--5087  Score: 52
    Period size: 12  Copynumber: 2.7  Consensus size: 13

       5044 ATAATTATTG

                         
       5054 TTTGCTTTATTAA
          1 TTTGCTTTATTAA

                         
       5067 TTTGCTTTA-TAA
          1 TTTGCTTTATTAA

             *       
       5079 TCTGCTTTA
          1 TTTGCTTTA

       5088 GATTTAGATC


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  12   11  0.55
  13    9  0.45

ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59


Consensus pattern (13 bp):   
TTTGCTTTATTAA
Done.