Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007512.1 Corchorus olitorius cultivar O-4 contig07537, 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: 2625
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33


Found at i:481 original size:21 final size:21

Alignment explanation


    Indices: 455--504  Score: 73
    Period size: 21  Copynumber: 2.4  Consensus size: 21

        445 CGGCCATTCA

                           **    
        455 CCGTGCCACCACCGGTTAAGC
          1 CCGTGCCACCACCGGGCAAGC

                              *  
        476 CCGTGCCACCACCGGGCATGC
          1 CCGTGCCACCACCGGGCAAGC

                    
        497 CCGTGCCA
          1 CCGTGCCA

        505 TCGCCATTCC


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   26  1.00

ACGTcount: A:0.16, C:0.46, G:0.26, T:0.12


Consensus pattern (21 bp):   
CCGTGCCACCACCGGGCAAGC

Found at i:885 original size:15 final size:14

Alignment explanation


    Indices: 865--894  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

        855 ATCTCTTTAA

                           
        865 TTTTCCTTGTATTAT
          1 TTTTCCTTG-ATTAT

                          
        880 TTTTCCTTGATTAT
          1 TTTTCCTTGATTAT

             
        894 T
          1 T

        895 GCTTTGATTG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67


Consensus pattern (14 bp):   
TTTTCCTTGATTAT

Found at i:2359 original size:11 final size:11

Alignment explanation


    Indices: 2343--2390  Score: 50
    Period size: 11  Copynumber: 4.7  Consensus size: 11

       2333 GAAGTTCGTG

                       
       2343 TTTGAAGACCA
          1 TTTGAAGACCA

                    ** 
       2354 TTTGAAGATAA
          1 TTTGAAGACCA

                       
       2365 TTTGAAGA-C-
          1 TTTGAAGACCA

                       
       2374 -TTGAAGACCA
          1 TTTGAAGACCA

                    
       2384 -TTGAAGA
          1 TTTGAAGA

       2391 TTTTGATGCC


Statistics
Matches: 32,  Mismatches: 3, Indels: 5
        0.80            0.08        0.12

Matches are distributed among these distances:
   8    7  0.22
   9    1  0.03
  10    7  0.22
  11   17  0.53

ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29


Consensus pattern (11 bp):   
TTTGAAGACCA
Done.