Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011558.1 Corchorus capsularis cultivar CVL-1 contig11579, 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: 34146
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32


Found at i:2457 original size:18 final size:19

Alignment explanation


    Indices: 2434--2471  Score: 60
    Period size: 18  Copynumber: 2.1  Consensus size: 19

       2424 GAAATAGGAT

                               
       2434 TTCAAATCCAACAGA-AGA
          1 TTCAAATCCAACAGATAGA

                   *           
       2452 TTCAAATTCAACAGATAGA
          1 TTCAAATCCAACAGATAGA

             
       2471 T
          1 T

       2472 AGAATAAATC


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18   14  0.78
  19    4  0.22

ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24


Consensus pattern (19 bp):   
TTCAAATCCAACAGATAGA

Found at i:29613 original size:11 final size:12

Alignment explanation


    Indices: 29589--29619  Score: 55
    Period size: 11  Copynumber: 2.7  Consensus size: 12

      29579 TTTTATAGAG

                        
      29589 AATGAAGATGAA
          1 AATGAAGATGAA

                        
      29601 AATGAAG-TGAA
          1 AATGAAGATGAA

                    
      29612 AATGAAGA
          1 AATGAAGA

      29620 ACACAATTAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  11   11  0.61
  12    7  0.39

ACGTcount: A:0.58, C:0.00, G:0.26, T:0.16


Consensus pattern (12 bp):   
AATGAAGATGAA

Found at i:30220 original size:5 final size:5

Alignment explanation


    Indices: 30210--30239  Score: 51
    Period size: 5  Copynumber: 5.8  Consensus size: 5

      30200 ACAATATTAC

                                               
      30210 ATAAA ATAAA ATAAA CATAAA ATAAA ATAA
          1 ATAAA ATAAA ATAAA -ATAAA ATAAA ATAA

      30240 TATCTAACAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
   5   19  0.79
   6    5  0.21

ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20


Consensus pattern (5 bp):   
ATAAA

Found at i:30229 original size:16 final size:16

Alignment explanation


    Indices: 30208--30239  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

      30198 CAACAATATT

                            
      30208 ACATAAAATAAAATAA
          1 ACATAAAATAAAATAA

                            
      30224 ACATAAAATAAAATAA
          1 ACATAAAATAAAATAA

      30240 TATCTAACAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19


Consensus pattern (16 bp):   
ACATAAAATAAAATAA
Done.