Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013099.1 Corchorus capsularis cultivar CVL-1 contig13120, 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: 6807
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32


Found at i:72 original size:21 final size:21

Alignment explanation


    Indices: 33--81  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

         23 TCAATGCTTT

                         **       
         33 AGGAATGCAAGAGGGATTTCAA
          1 AGGAA-GCAAGAGCCATTTCAA

                               * 
         55 AGGAAGCAAGAGCCATTTCCA
          1 AGGAAGCAAGAGCCATTTCAA

                   
         76 A-GAAGC
          1 AGGAAGC

         82 TACAATTCTT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  20    5  0.21
  21   14  0.58
  22    5  0.21

ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14


Consensus pattern (21 bp):   
AGGAAGCAAGAGCCATTTCAA

Found at i:2460 original size:13 final size:13

Alignment explanation


    Indices: 2440--2471  Score: 55
    Period size: 13  Copynumber: 2.5  Consensus size: 13

       2430 CTGCCAACAC

                         
       2440 CCATGCACCCATG
          1 CCATGCACCCATG

             *           
       2453 CTATGCACCCATG
          1 CCATGCACCCATG

                  
       2466 CCATGC
          1 CCATGC

       2472 CGTACTCACC


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.22, C:0.44, G:0.16, T:0.19


Consensus pattern (13 bp):   
CCATGCACCCATG

Found at i:5981 original size:21 final size:21

Alignment explanation


    Indices: 5955--6002  Score: 60
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       5945 GCACTGGAGG

                   *   * *       
       5955 ACATGGGTCGCGAGGCAAACC
          1 ACATGGGGCGCCAAGCAAACC

                             *   
       5976 ACATGGGGCGCCAAGCATACC
          1 ACATGGGGCGCCAAGCAAACC

                  
       5997 ACATGG
          1 ACATGG

       6003 ACCCCCAGCT


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.29, C:0.29, G:0.31, T:0.10


Consensus pattern (21 bp):   
ACATGGGGCGCCAAGCAAACC
Done.