Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024161.1 Corchorus olitorius cultivar O-4 contig24194, 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: 22823
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31


Found at i:3445 original size:24 final size:24

Alignment explanation


    Indices: 3417--3471  Score: 92
    Period size: 24  Copynumber: 2.3  Consensus size: 24

       3407 GATGAACCCA

                                    
       3417 GAAAAGATGGCGCAACCACCATAG
          1 GAAAAGATGGCGCAACCACCATAG

                                  * 
       3441 GAAAAGATGGCGCAACCACCATGG
          1 GAAAAGATGGCGCAACCACCATAG

             *     
       3465 GGAAAGA
          1 GAAAAGA

       3472 CAAGAATATA


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  24   29  1.00

ACGTcount: A:0.42, C:0.22, G:0.29, T:0.07


Consensus pattern (24 bp):   
GAAAAGATGGCGCAACCACCATAG

Found at i:6001 original size:18 final size:18

Alignment explanation


    Indices: 5978--6014  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       5968 AAAGGGTAGT

                     *        
       5978 TAAAAAAAATTGTTTTCA
          1 TAAAAAAAAGTGTTTTCA

                  *           
       5996 TAAAAAGAAGTGTTTTCA
          1 TAAAAAAAAGTGTTTTCA

             
       6014 T
          1 T

       6015 GCAAGAGGAG


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

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38


Consensus pattern (18 bp):   
TAAAAAAAAGTGTTTTCA

Found at i:6915 original size:11 final size:10

Alignment explanation


    Indices: 6899--6950  Score: 54
    Period size: 11  Copynumber: 5.1  Consensus size: 10

       6889 AAGTTCGTGT

                       
       6899 TTGAAGACTTA
          1 TTGAAGA-TTA

                    * 
       6910 TTGAAGATAA
          1 TTGAAGATTA

                       
       6920 TTTGAAGA-T-
          1 -TTGAAGATTA

                      
       6929 TTGAAGATTA
          1 TTGAAGATTA

                       
       6939 TTGAAGAATTA
          1 TTGAAG-ATTA

             
       6950 T
          1 T

       6951 CTCAAGAGGC


Statistics
Matches: 35,  Mismatches: 2, Indels: 8
        0.78            0.04        0.18

Matches are distributed among these distances:
   8    7  0.20
   9    1  0.03
  10    8  0.23
  11   19  0.54

ACGTcount: A:0.40, C:0.02, G:0.19, T:0.38


Consensus pattern (10 bp):   
TTGAAGATTA

Found at i:6934 original size:19 final size:18

Alignment explanation


    Indices: 6910--6945  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       6900 TGAAGACTTA

                               
       6910 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
       6929 TTGAAGATTATTGAAGA
          1 TTGAAGATAATTGAAGA

       6946 ATTATCTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT

Found at i:15534 original size:11 final size:11

Alignment explanation


    Indices: 15515--15546  Score: 55
    Period size: 11  Copynumber: 2.9  Consensus size: 11

      15505 AAACTTAGAA

                *      
      15515 ACCAACCGACC
          1 ACCACCCGACC

                       
      15526 ACCACCCGACC
          1 ACCACCCGACC

                      
      15537 ACCACCCGAC
          1 ACCACCCGAC

      15547 TATCGCCAAC


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  11   20  1.00

ACGTcount: A:0.31, C:0.59, G:0.09, T:0.00


Consensus pattern (11 bp):   
ACCACCCGACC
Done.