Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016522.1 Corchorus olitorius cultivar O-4 contig16555, 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: 17808
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33


Found at i:1363 original size:16 final size:16

Alignment explanation


    Indices: 1342--1384  Score: 70
    Period size: 16  Copynumber: 2.7  Consensus size: 16

       1332 GTGAGTTTTC

                            
       1342 TTTGTAATTTATTTGT
          1 TTTGTAATTTATTTGT

                            
       1358 TTTGTAATTTATTTGT
          1 TTTGTAATTTATTTGT

                        
       1374 TTGTGT-ATTTA
          1 TT-TGTAATTTA

       1385 ATATATTAGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  16   23  0.88
  17    3  0.12

ACGTcount: A:0.19, C:0.00, G:0.14, T:0.67


Consensus pattern (16 bp):   
TTTGTAATTTATTTGT

Found at i:7715 original size:28 final size:28

Alignment explanation


    Indices: 7675--7733  Score: 118
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       7665 ATTGTTTTGT

                                        
       7675 CTTTATCTTATGGCCCTCGTACTAGTAA
          1 CTTTATCTTATGGCCCTCGTACTAGTAA

                                        
       7703 CTTTATCTTATGGCCCTCGTACTAGTAA
          1 CTTTATCTTATGGCCCTCGTACTAGTAA

               
       7731 CTT
          1 CTT

       7734 GTAAGACATA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   31  1.00

ACGTcount: A:0.20, C:0.25, G:0.14, T:0.41


Consensus pattern (28 bp):   
CTTTATCTTATGGCCCTCGTACTAGTAA

Found at i:15990 original size:28 final size:28

Alignment explanation


    Indices: 15950--16014  Score: 112
    Period size: 28  Copynumber: 2.3  Consensus size: 28

      15940 TACATCAAGC

                          *      *      
      15950 GAAGTTCTTTTCATCATTAAAGTTCATG
          1 GAAGTTCTTTTCATAATTAAAATTCATG

                                        
      15978 GAAGTTCTTTTCATAATTAAAATTCATG
          1 GAAGTTCTTTTCATAATTAAAATTCATG

                     
      16006 GAAGTTCTT
          1 GAAGTTCTT

      16015 AATGGAAGGC


Statistics
Matches: 35,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  28   35  1.00

ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43


Consensus pattern (28 bp):   
GAAGTTCTTTTCATAATTAAAATTCATG

Found at i:17786 original size:2 final size:2

Alignment explanation


    Indices: 17781--17806  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      17771 AGGGAGATTG

                                                  
      17781 GA GA GA GA GA GA GA GA GA GA GA GA GA
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA

      17807 AG


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:0.50, T:0.00


Consensus pattern (2 bp):   
GA

Done.