Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016627.1 Corchorus olitorius cultivar O-4 contig16660, 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: 10019
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36


Found at i:479 original size:17 final size:17

Alignment explanation


    Indices: 439--479  Score: 50
    Period size: 16  Copynumber: 2.5  Consensus size: 17

        429 GTACCCAAAA

                             
        439 TTTCGGGTCATTTCTGG
          1 TTTCGGGTCATTTCTGG

            *                 
        456 GTT-GGGTCAGTTTC-GG
          1 TTTCGGGTCA-TTTCTGG

                    
        472 TTTCGGGT
          1 TTTCGGGT

        480 TGGACGGATT


Statistics
Matches: 20,  Mismatches: 2, Indels: 4
        0.77            0.08        0.15

Matches are distributed among these distances:
  16   10  0.50
  17   10  0.50

ACGTcount: A:0.05, C:0.15, G:0.37, T:0.44


Consensus pattern (17 bp):   
TTTCGGGTCATTTCTGG

Found at i:3292 original size:21 final size:21

Alignment explanation


    Indices: 3266--3306  Score: 82
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       3256 AAGACGTAGG

                                 
       3266 TGGAGTGACTTTAGCATAATA
          1 TGGAGTGACTTTAGCATAATA

                                
       3287 TGGAGTGACTTTAGCATAAT
          1 TGGAGTGACTTTAGCATAAT

       3307 GTGGCATGAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34


Consensus pattern (21 bp):   
TGGAGTGACTTTAGCATAATA

Found at i:7991 original size:43 final size:41

Alignment explanation


    Indices: 7944--8061  Score: 139
    Period size: 43  Copynumber: 2.8  Consensus size: 41

       7934 TCATTCAACT

                            *         *           *    
       7944 TTTTTTATTAATTATGCAAAGATATTGTAAATCCAATATTTAA
          1 TTTTTTATTAATTATGGAAAGATATTTTAAATCC-AT-CTTAA

                    *                                
       7987 TTTTTTA-AAATTATGGAAAGATATTTTAAATCCATCTTAA
          1 TTTTTTATTAATTATGGAAAGATATTTTAAATCCATCTTAA

                   *              *            
       8027 TTTTATTTTTGAATTATGGAAATATATTTTAAATC
          1 TTTT-TTATT-AATTATGGAAAGATATTTTAAATC

       8062 TATATATTAA


Statistics
Matches: 65,  Mismatches: 7, Indels: 6
        0.83            0.09        0.08

Matches are distributed among these distances:
  40    8  0.12
  41    4  0.06
  42   23  0.35
  43   30  0.46

ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48


Consensus pattern (41 bp):   
TTTTTTATTAATTATGGAAAGATATTTTAAATCCATCTTAA

Found at i:8965 original size:23 final size:21

Alignment explanation


    Indices: 8948--8990  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       8938 ATTTGTTAAT

                         *       
       8948 ACCATTATAACTTTTTTGATA
          1 ACCATTATAACTTCTTTGATA

               *                 
       8969 ACCGTTATAACTTCTTTGATA
          1 ACCATTATAACTTCTTTGATA

             
       8990 A
          1 A

       8991 AATTATATTA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44


Consensus pattern (21 bp):   
ACCATTATAACTTCTTTGATA

Found at i:9759 original size:21 final size:22

Alignment explanation


    Indices: 9715--9764  Score: 66
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       9705 CTTTCTAAGG

                *                 
       9715 TTTTCATATAAAAAATGATGAA
          1 TTTTTATATAAAAAATGATGAA

                             * *  
       9737 TTTTTATATAAAAAA-GCTTAA
          1 TTTTTATATAAAAAATGATGAA

                   
       9758 TTTTTAT
          1 TTTTTAT

       9765 TCGTGAGAGT


Statistics
Matches: 25,  Mismatches: 3, Indels: 1
        0.86            0.10        0.03

Matches are distributed among these distances:
  21   11  0.44
  22   14  0.56

ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46


Consensus pattern (22 bp):   
TTTTTATATAAAAAATGATGAA

Found at i:10000 original size:29 final size:30

Alignment explanation


    Indices: 9958--10014  Score: 80
    Period size: 29  Copynumber: 1.9  Consensus size: 30

       9948 ATTTTTAGTA

                             *   *        
       9958 GGGTCAATACTATAAAATTTTGATTTTAAG
          1 GGGTCAATACTATAAAACTTTCATTTTAAG

                *                       
       9988 GGGTTAATA-TATAAAACTTTCATTTTA
          1 GGGTCAATACTATAAAACTTTCATTTTA

      10015 GAAGG


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  29   16  0.67
  30    8  0.33

ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42


Consensus pattern (30 bp):   
GGGTCAATACTATAAAACTTTCATTTTAAG
Done.