Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020768.1 Corchorus olitorius cultivar O-4 contig20801, 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: 44971
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:5006 original size:18 final size:18

Alignment explanation


    Indices: 4983--5020  Score: 76
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       4973 TTCCATGTTG

                              
       4983 CTGAAACCTTACTTGCAT
          1 CTGAAACCTTACTTGCAT

                              
       5001 CTGAAACCTTACTTGCAT
          1 CTGAAACCTTACTTGCAT

              
       5019 CT
          1 CT

       5021 TTTACGGAAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34


Consensus pattern (18 bp):   
CTGAAACCTTACTTGCAT

Found at i:22262 original size:10 final size:10

Alignment explanation


    Indices: 22247--22276  Score: 60
    Period size: 10  Copynumber: 3.0  Consensus size: 10

      22237 TTATTTGTTG

                      
      22247 TAAGAAAAAT
          1 TAAGAAAAAT

                      
      22257 TAAGAAAAAT
          1 TAAGAAAAAT

                      
      22267 TAAGAAAAAT
          1 TAAGAAAAAT

      22277 GAAAGCTTAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   20  1.00

ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20


Consensus pattern (10 bp):   
TAAGAAAAAT

Found at i:43700 original size:3 final size:3

Alignment explanation


    Indices: 43694--43723  Score: 51
    Period size: 3  Copynumber: 10.0  Consensus size: 3

      43684 AGCGTATTTT

                                            *      
      43694 ACA ACA ACA ACA ACA ACA ACA ACA GCA ACA
          1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA

      43724 GCAAACGCAG


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

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.63, C:0.33, G:0.03, T:0.00


Consensus pattern (3 bp):   
ACA

Done.