Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013222.1 Corchorus olitorius cultivar O-4 contig13255, 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: 4662
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35


Found at i:4027 original size:42 final size:42

Alignment explanation


    Indices: 3980--4064  Score: 152
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       3970 GCATAGAGAT

                                             *        
       3980 TTATTTGAAATGTAATGAGATTTCAGTATATTTGAAATGTAA
          1 TTATTTGAAATGTAATGAGATTTCAGTATATTTAAAATGTAA

                                       *              
       4022 TTATTTGAAATGTAATGAGATTTCAGTCTATTTAAAATGTAA
          1 TTATTTGAAATGTAATGAGATTTCAGTATATTTAAAATGTAA

             
       4064 T
          1 T

       4065 GAGATTTCAG


Statistics
Matches: 41,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  42   41  1.00

ACGTcount: A:0.38, C:0.04, G:0.15, T:0.44


Consensus pattern (42 bp):   
TTATTTGAAATGTAATGAGATTTCAGTATATTTAAAATGTAA

Found at i:4028 original size:15 final size:15

Alignment explanation


    Indices: 4008--4037  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       3998 GATTTCAGTA

                           
       4008 TATTTGAAATGTAAT
          1 TATTTGAAATGTAAT

                           
       4023 TATTTGAAATGTAAT
          1 TATTTGAAATGTAAT

       4038 GAGATTTCAG


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47


Consensus pattern (15 bp):   
TATTTGAAATGTAAT

Found at i:4061 original size:27 final size:27

Alignment explanation


    Indices: 4023--4075  Score: 97
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       4013 GAAATGTAAT

                 *                     
       4023 TATTTGAAATGTAATGAGATTTCAGTC
          1 TATTTAAAATGTAATGAGATTTCAGTC

                                      
       4050 TATTTAAAATGTAATGAGATTTCAGT
          1 TATTTAAAATGTAATGAGATTTCAGT

       4076 AATGAGATTT


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27   25  1.00

ACGTcount: A:0.36, C:0.06, G:0.17, T:0.42


Consensus pattern (27 bp):   
TATTTAAAATGTAATGAGATTTCAGTC

Found at i:4079 original size:14 final size:14

Alignment explanation


    Indices: 4060--4087  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       4050 TATTTAAAAT

                          
       4060 GTAATGAGATTTCA
          1 GTAATGAGATTTCA

                          
       4074 GTAATGAGATTTCA
          1 GTAATGAGATTTCA

       4088 CTGGGTTTGT


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:0.36, C:0.07, G:0.21, T:0.36


Consensus pattern (14 bp):   
GTAATGAGATTTCA
Done.