Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020135.1 Corchorus olitorius cultivar O-4 contig20168, 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: 6386
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.35


Found at i:276 original size:21 final size:21

Alignment explanation


    Indices: 250--289  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        240 TAGTGCCATA

                                 
        250 TTTAATCTGGGTAACTACGTG
          1 TTTAATCTGGGTAACTACGTG

                  *            
        271 TTTAATTTGGGTAACTACG
          1 TTTAATCTGGGTAACTACG

        290 AACCCAACTA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40


Consensus pattern (21 bp):   
TTTAATCTGGGTAACTACGTG

Found at i:336 original size:14 final size:14

Alignment explanation


    Indices: 319--346  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

        309 ATCCAAAATT

                          
        319 CTAAATTACTAATA
          1 CTAAATTACTAATA

                          
        333 CTAAATTACTAATA
          1 CTAAATTACTAATA

        347 TATGAAAAAG


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36


Consensus pattern (14 bp):   
CTAAATTACTAATA

Found at i:4304 original size:3 final size:3

Alignment explanation


    Indices: 4298--4386  Score: 169
    Period size: 3  Copynumber: 29.7  Consensus size: 3

       4288 ATGGTTCTTA

                                                                           
       4298 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

                          *                                       
       4346 AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA

       4387 AATTGGAGAA


Statistics
Matches: 84,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
   3   84  1.00

ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31


Consensus pattern (3 bp):   
AAT

Done.