Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013179.1 Corchorus olitorius cultivar O-4 contig13212, 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: 4184
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31


Found at i:1240 original size:2 final size:2

Alignment explanation


    Indices: 1235--1260  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       1225 AAAGATAAAG

                                                  
       1235 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       1261 TACTGTATAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:1921 original size:8 final size:8

Alignment explanation


    Indices: 1908--1941  Score: 54
    Period size: 7  Copynumber: 4.5  Consensus size: 8

       1898 TCAAATTCCA

                    
       1908 TCAAATCT
          1 TCAAATCT

                    
       1916 TCAAATCT
          1 TCAAATCT

                    
       1924 TC-AATCT
          1 TCAAATCT

                    
       1931 TC-AATCT
          1 TCAAATCT

                
       1938 TCAA
          1 TCAA

       1942 GAACATGCTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   7   14  0.56
   8   11  0.44

ACGTcount: A:0.35, C:0.26, G:0.00, T:0.38


Consensus pattern (8 bp):   
TCAAATCT

Found at i:2465 original size:25 final size:25

Alignment explanation


    Indices: 2437--2485  Score: 98
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       2427 CCAAACAATC

                                     
       2437 TTGAGCACTCTCGCTCGGTCTCTAT
          1 TTGAGCACTCTCGCTCGGTCTCTAT

                                    
       2462 TTGAGCACTCTCGCTCGGTCTCTA
          1 TTGAGCACTCTCGCTCGGTCTCTA

       2486 CAAATCAATC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   24  1.00

ACGTcount: A:0.12, C:0.33, G:0.20, T:0.35


Consensus pattern (25 bp):   
TTGAGCACTCTCGCTCGGTCTCTAT
Done.