Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019353.1 Corchorus olitorius cultivar O-4 contig19386, 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: 20210
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:2070 original size:23 final size:23

Alignment explanation


    Indices: 2044--2104  Score: 67
    Period size: 20  Copynumber: 2.8  Consensus size: 23

       2034 ATAAATATAT

                                   
       2044 ATATTATGTTTATTAATAATGTG
          1 ATATTATGTTTATTAATAATGTG

                           *       
       2067 ATATT-TG--TATTATTAATGTG
          1 ATATTATGTTTATTAATAATGTG

                      *        
       2087 -TATTATGTTAATTTAATA
          1 ATATTATGTTTA-TTAATA

       2105 GTGTTGTATT


Statistics
Matches: 31,  Mismatches: 3, Indels: 8
        0.74            0.07        0.19

Matches are distributed among these distances:
  19    4  0.13
  20   14  0.45
  22    3  0.10
  23   10  0.32

ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54


Consensus pattern (23 bp):   
ATATTATGTTTATTAATAATGTG

Found at i:13559 original size:12 final size:12

Alignment explanation


    Indices: 13542--13567  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

      13532 CTTCGTACTA

                        
      13542 ATTATTATATCT
          1 ATTATTATATCT

                        
      13554 ATTATTATATCT
          1 ATTATTATATCT

              
      13566 AT
          1 AT

      13568 CTATAGTAGG


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

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58


Consensus pattern (12 bp):   
ATTATTATATCT

Found at i:14936 original size:10 final size:10

Alignment explanation


    Indices: 14921--14946  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

      14911 TCCCAACATA

                      
      14921 AAAGATCTCC
          1 AAAGATCTCC

                      
      14931 AAAGATCTCC
          1 AAAGATCTCC

                  
      14941 AAAGAT
          1 AAAGAT

      14947 TTTGGGTTCA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.46, C:0.23, G:0.12, T:0.19


Consensus pattern (10 bp):   
AAAGATCTCC

Found at i:19037 original size:21 final size:21

Alignment explanation


    Indices: 18998--19038  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      18988 TTACTTGAAA

                          *      
      18998 GTTATTAAAAATCTTTAATAT
          1 GTTATTAAAAATCTATAATAT

                                 
      19019 GTTATTAAATAA-CTATAATA
          1 GTTATTAAA-AATCTATAATA

      19039 ATACTATCAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  21   16  0.89
  22    2  0.11

ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44


Consensus pattern (21 bp):   
GTTATTAAAAATCTATAATAT

Found at i:19112 original size:17 final size:17

Alignment explanation


    Indices: 19090--19129  Score: 55
    Period size: 17  Copynumber: 2.4  Consensus size: 17

      19080 ATCACCCTCC

                   *          
      19090 AGATCACTAGTGAT-CTA
          1 AGATCACCAGTGATGC-A

                             
      19107 AGATCACCAGTGATGCA
          1 AGATCACCAGTGATGCA

                  
      19124 AGATCA
          1 AGATCA

      19130 ATGGTAATCT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  17   20  0.95
  18    1  0.05

ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23


Consensus pattern (17 bp):   
AGATCACCAGTGATGCA

Found at i:19449 original size:34 final size:33

Alignment explanation


    Indices: 19370--19434  Score: 94
    Period size: 34  Copynumber: 1.9  Consensus size: 33

      19360 TTTTTTTTTT

                *                             
      19370 ACTTCATATAATAGCTTAACACCGGAAAATAGGG
          1 ACTTAATATAATAGCTTAACACCGGAAAATA-GG

             *  *                          
      19404 AGTTCATATAATAGCTTAACACCGGAAAATA
          1 ACTTAATATAATAGCTTAACACCGGAAAATA

      19435 TTCTTAAATA


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  34   30  1.00

ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25


Consensus pattern (33 bp):   
ACTTAATATAATAGCTTAACACCGGAAAATAGG

Found at i:19554 original size:20 final size:19

Alignment explanation


    Indices: 19524--19574  Score: 75
    Period size: 19  Copynumber: 2.6  Consensus size: 19

      19514 GGGCACATGA

                                 
      19524 GAAAGAAAAAATGAGATGCAG
          1 GAAA-AAAAAATG-GATGCAG

                               
      19545 GAAAAAAAAATGGATGCAG
          1 GAAAAAAAAATGGATGCAG

                  *    
      19564 GAAAAAGAAAT
          1 GAAAAAAAAAT

      19575 TAATAAGCTA


Statistics
Matches: 29,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  19   17  0.59
  20    8  0.28
  21    4  0.14

ACGTcount: A:0.61, C:0.04, G:0.25, T:0.10


Consensus pattern (19 bp):   
GAAAAAAAAATGGATGCAG
Done.