Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015735.1 Corchorus capsularis cultivar CVL-1 contig15756, 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: 11980
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:54 original size:33 final size:33

Alignment explanation


    Indices: 12--80  Score: 138
    Period size: 33  Copynumber: 2.1  Consensus size: 33

          2 GAGCAAGGAG

                                             
         12 GAGGTAAACCTAACACAAAGTCCATACTAATAT
          1 GAGGTAAACCTAACACAAAGTCCATACTAATAT

                                             
         45 GAGGTAAACCTAACACAAAGTCCATACTAATAT
          1 GAGGTAAACCTAACACAAAGTCCATACTAATAT

               
         78 GAG
          1 GAG

         81 TCCATGGTTC


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  33   36  1.00

ACGTcount: A:0.45, C:0.20, G:0.14, T:0.20


Consensus pattern (33 bp):   
GAGGTAAACCTAACACAAAGTCCATACTAATAT

Found at i:4551 original size:15 final size:16

Alignment explanation


    Indices: 4519--4552  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       4509 AAGAAGAATT

                 *          
       4519 TAAAATTAAATCTAAC
          1 TAAAAGTAAATCTAAC

                            
       4535 TAAAAGTAAAT-TAAC
          1 TAAAAGTAAATCTAAC

               
       4550 TAA
          1 TAA

       4553 GAAAGCAATC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    7  0.41
  16   10  0.59

ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29


Consensus pattern (16 bp):   
TAAAAGTAAATCTAAC

Found at i:8726 original size:11 final size:11

Alignment explanation


    Indices: 8710--8738  Score: 58
    Period size: 11  Copynumber: 2.6  Consensus size: 11

       8700 GGTCCAAAGG

                       
       8710 TGGCTGGGACA
          1 TGGCTGGGACA

                       
       8721 TGGCTGGGACA
          1 TGGCTGGGACA

                   
       8732 TGGCTGG
          1 TGGCTGG

       8739 ATGAGGTCCT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.14, C:0.17, G:0.48, T:0.21


Consensus pattern (11 bp):   
TGGCTGGGACA
Done.