Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007256.1 Corchorus olitorius cultivar O-4 contig07281, 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, 706

Length: 1177
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28


Found at i:819 original size:6 final size:6

Alignment explanation


    Indices: 810--856  Score: 62
    Period size: 6  Copynumber: 8.2  Consensus size: 6

        800 AACCCGAGGC

                           *                                  *    
        810 AGCCCG AGCCCG AACCCG A-CCCG AGCCCG A-CCCG AGCCCG AACCCG
          1 AGCCCG AGCCCG AGCCCG AGCCCG AGCCCG AGCCCG AGCCCG AGCCCG

             
        856 A
          1 A

        857 AATAATTTGA


Statistics
Matches: 37,  Mismatches: 2, Indels: 4
        0.86            0.05        0.09

Matches are distributed among these distances:
   5   10  0.27
   6   27  0.73

ACGTcount: A:0.23, C:0.51, G:0.26, T:0.00


Consensus pattern (6 bp):   
AGCCCG

Found at i:821 original size:22 final size:22

Alignment explanation


    Indices: 795--856  Score: 72
    Period size: 22  Copynumber: 2.8  Consensus size: 22

        785 ACCCGAAATT

                        **        
        795 ACCCGAACCCGAGGC-AGCCCG
          1 ACCCGAACCCGACCCGAGCCCG

                                   
        816 AGCCCGAACCCGACCCGAGCCCG
          1 A-CCCGAACCCGACCCGAGCCCG

                  *           
        839 ACCCGAGCCCGAACCCGA
          1 ACCCGAACCCG-ACCCGA

        857 AATAATTTGA


Statistics
Matches: 35,  Mismatches: 3, Indels: 4
        0.83            0.07        0.10

Matches are distributed among these distances:
  21    1  0.03
  22   21  0.60
  23   13  0.37

ACGTcount: A:0.24, C:0.50, G:0.26, T:0.00


Consensus pattern (22 bp):   
ACCCGAACCCGACCCGAGCCCG

Found at i:827 original size:28 final size:29

Alignment explanation


    Indices: 795--857  Score: 94
    Period size: 28  Copynumber: 2.2  Consensus size: 29

        785 ACCCGAAATT

                         *               
        795 ACCCGAACCCGAGGCAG-CCCGAGCCCGA
          1 ACCCGAACCCGAGCCAGACCCGAGCCCGA

                           *             
        823 ACCCG-ACCCGAGCCCGACCCGAGCCCGA
          1 ACCCGAACCCGAGCCAGACCCGAGCCCGA

                   
        851 ACCCGAA
          1 ACCCGAA

        858 ATAATTTGAA


Statistics
Matches: 31,  Mismatches: 2, Indels: 3
        0.86            0.06        0.08

Matches are distributed among these distances:
  27    9  0.29
  28   21  0.68
  29    1  0.03

ACGTcount: A:0.25, C:0.49, G:0.25, T:0.00


Consensus pattern (29 bp):   
ACCCGAACCCGAGCCAGACCCGAGCCCGA

Found at i:834 original size:17 final size:18

Alignment explanation


    Indices: 810--857  Score: 73
    Period size: 17  Copynumber: 2.8  Consensus size: 18

        800 AACCCGAGGC

                              
        810 AGCCCGAGCCCGAACCCG
          1 AGCCCGAGCCCGAACCCG

                              
        828 A-CCCGAGCCCG-ACCCG
          1 AGCCCGAGCCCGAACCCG

                   *      
        844 AGCCCGAACCCGAA
          1 AGCCCGAGCCCGAA

        858 ATAATTTGAA


Statistics
Matches: 27,  Mismatches: 1, Indels: 4
        0.84            0.03        0.12

Matches are distributed among these distances:
  16    6  0.22
  17   19  0.70
  18    2  0.07

ACGTcount: A:0.25, C:0.50, G:0.25, T:0.00


Consensus pattern (18 bp):   
AGCCCGAGCCCGAACCCG

Found at i:838 original size:11 final size:11

Alignment explanation


    Indices: 810--856  Score: 67
    Period size: 11  Copynumber: 4.1  Consensus size: 11

        800 AACCCGAGGC

                        
        810 AGCCCGAGCCCG
          1 AGCCCGA-CCCG

             *         
        822 AACCCGACCCG
          1 AGCCCGACCCG

                       
        833 AGCCCGACCCG
          1 AGCCCGACCCG

                        
        844 AGCCCGAACCCG
          1 AGCCCG-ACCCG

             
        856 A
          1 A

        857 AATAATTTGA


Statistics
Matches: 32,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  11   20  0.62
  12   12  0.38

ACGTcount: A:0.23, C:0.51, G:0.26, T:0.00


Consensus pattern (11 bp):   
AGCCCGACCCG

Done.