Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012382.1 Corchorus olitorius cultivar O-4 contig12415, 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: 18884
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32


Found at i:67 original size:5 final size:6

Alignment explanation


    Indices: 38--78  Score: 50
    Period size: 6  Copynumber: 7.0  Consensus size: 6

         28 TTCAAATTAT

                          *                                  
         38 TTCGGG TTCGGG CTC-GG TCTCGGG -TCGGG TTCGGG TTCGGG
          1 TTCGGG TTCGGG TTCGGG T-TCGGG TTCGGG TTCGGG TTCGGG

         79 CTGCCTCAGG


Statistics
Matches: 30,  Mismatches: 2, Indels: 6
        0.79            0.05        0.16

Matches are distributed among these distances:
   5    7  0.23
   6   21  0.70
   7    2  0.07

ACGTcount: A:0.00, C:0.22, G:0.49, T:0.29


Consensus pattern (6 bp):   
TTCGGG

Found at i:109 original size:16 final size:16

Alignment explanation


    Indices: 90--127  Score: 67
    Period size: 16  Copynumber: 2.4  Consensus size: 16

         80 TGCCTCAGGT

                            
         90 TCGGGTAATTTCGGGC
          1 TCGGGTAATTTCGGGC

                           *
        106 TCGGGTAATTTCGGGT
          1 TCGGGTAATTTCGGGC

                  
        122 TCGGGT
          1 TCGGGT

        128 TCGGGCGGGT


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  16   21  1.00

ACGTcount: A:0.11, C:0.16, G:0.39, T:0.34


Consensus pattern (16 bp):   
TCGGGTAATTTCGGGC

Found at i:13513 original size:16 final size:16

Alignment explanation


    Indices: 13492--13526  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

      13482 TTACTTTGCT

                            
      13492 TTGTTTTCTAGTTTAA
          1 TTGTTTTCTAGTTTAA

                     **     
      13508 TTGTTTTCTTTTTTAA
          1 TTGTTTTCTAGTTTAA

               
      13524 TTG
          1 TTG

      13527 CGATTTTTAA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.14, C:0.06, G:0.11, T:0.69


Consensus pattern (16 bp):   
TTGTTTTCTAGTTTAA

Found at i:17845 original size:23 final size:25

Alignment explanation


    Indices: 17796--17845  Score: 59
    Period size: 27  Copynumber: 2.0  Consensus size: 25

      17786 TGAATGTTTG

                               *       
      17796 TCTTAATCTCTCCATTCATTTGCATCA
          1 TCTTAATCTCTCCATT-ATCT-CATCA

                                     
      17823 TCTTAATCTCTCCATT-TCT-ATCA
          1 TCTTAATCTCTCCATTATCTCATCA

      17846 AGGATAAAAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 4
        0.81            0.04        0.15

Matches are distributed among these distances:
  23    4  0.18
  25    2  0.09
  27   16  0.73

ACGTcount: A:0.22, C:0.30, G:0.02, T:0.46


Consensus pattern (25 bp):   
TCTTAATCTCTCCATTATCTCATCA
Done.