Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018448.1 Corchorus olitorius cultivar O-4 contig18481, 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: 18670
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:8094 original size:2 final size:2

Alignment explanation


    Indices: 8087--8120  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       8077 ACCTAGTATG

                                                              
       8087 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       8121 ATGCCACTTT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:8303 original size:30 final size:30

Alignment explanation


    Indices: 8267--8340  Score: 103
    Period size: 30  Copynumber: 2.5  Consensus size: 30

       8257 ACGGCGTCCG

                                *     *   
       8267 ACGTGGCATGCCACGTGTACCAAAAATGAC
          1 ACGTGGCATGCCACGTGTACAAAAAAGGAC

                         *              * 
       8297 ACGTGGCATGCCATGTGTACAAAAAAGGTC
          1 ACGTGGCATGCCACGTGTACAAAAAAGGAC

              *           
       8327 ACATGGCATGCCAC
          1 ACGTGGCATGCCAC

       8341 ATGTTAAAAA


Statistics
Matches: 38,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  30   38  1.00

ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18


Consensus pattern (30 bp):   
ACGTGGCATGCCACGTGTACAAAAAAGGAC

Found at i:11145 original size:13 final size:13

Alignment explanation


    Indices: 11127--11155  Score: 58
    Period size: 13  Copynumber: 2.2  Consensus size: 13

      11117 TTAGTTAGGT

                         
      11127 TTTGTGGGGATTA
          1 TTTGTGGGGATTA

                         
      11140 TTTGTGGGGATTA
          1 TTTGTGGGGATTA

               
      11153 TTT
          1 TTT

      11156 TTATGATTGC


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

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.14, C:0.00, G:0.34, T:0.52


Consensus pattern (13 bp):   
TTTGTGGGGATTA

Found at i:17262 original size:12 final size:12

Alignment explanation


    Indices: 17247--17279  Score: 57
    Period size: 12  Copynumber: 2.8  Consensus size: 12

      17237 GGTGAAACTA

                        
      17247 GGGGCTAAACCT
          1 GGGGCTAAACCT

                        
      17259 GGGGCTAAACCT
          1 GGGGCTAAACCT

              *      
      17271 GGTGCTAAA
          1 GGGGCTAAA

      17280 TTTGTGCCTA


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

Matches are distributed among these distances:
  12   20  1.00

ACGTcount: A:0.27, C:0.21, G:0.33, T:0.18


Consensus pattern (12 bp):   
GGGGCTAAACCT
Done.