Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019510.1 Corchorus olitorius cultivar O-4 contig19543, 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: 23816
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32


Found at i:992 original size:111 final size:111

Alignment explanation


    Indices: 823--1043  Score: 406
    Period size: 111  Copynumber: 2.0  Consensus size: 111

        813 AAAAAAAAAG

                                                         *              *    
        823 AAGAAAAATCTTGGACAAGGTATTCCTTCTTTTATTAAATCCATGTTCAAAGCCAAAGAAGAACC
          1 AAGAAAAATCTTGGACAAGGTATTCCTTCTTTTATTAAATCCATGCTCAAAGCCAAAGAAAAACC

                                                  *       
        888 AAATTGAAAACAAGAATTAGATGAAAATATTGACGTCAGTGGCAAA
         66 AAATTGAAAACAAGAATTAGATGAAAATATTGACGTCAATGGCAAA

                                                                             
        934 AAGAAAAATCTTGGACAAGGTATTCCTTCTTTTATTAAATCCATGCTCAAAGCCAAAGAAAAACC
          1 AAGAAAAATCTTGGACAAGGTATTCCTTCTTTTATTAAATCCATGCTCAAAGCCAAAGAAAAACC

                  *                                      
        999 AAATTGTAAACAAGAATTAGATGAAAATATTGACGTCAATGGCAA
         66 AAATTGAAAACAAGAATTAGATGAAAATATTGACGTCAATGGCAA

       1044 TTTCTTCTTC


Statistics
Matches: 106,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
 111  106  1.00

ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25


Consensus pattern (111 bp):   
AAGAAAAATCTTGGACAAGGTATTCCTTCTTTTATTAAATCCATGCTCAAAGCCAAAGAAAAACC
AAATTGAAAACAAGAATTAGATGAAAATATTGACGTCAATGGCAAA

Found at i:6154 original size:2 final size:2

Alignment explanation


    Indices: 6149--6179  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       6139 TTTAGGTATC

                                                          
       6149 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       6180 TGTATAAGTG


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:16343 original size:21 final size:21

Alignment explanation


    Indices: 16292--16355  Score: 69
    Period size: 21  Copynumber: 3.1  Consensus size: 21

      16282 TTGACACTAT

                     *         * 
      16292 TTAGATACTATACAGATGAGA
          1 TTAGATACTGTACAGATGAAA

                 *           *   
      16313 TT--ACACTGTACAGATTAAA
          1 TTAGATACTGTACAGATGAAA

                               * 
      16332 TTAGATACTGTACAGATGAGA
          1 TTAGATACTGTACAGATGAAA

               
      16353 TTA
          1 TTA

      16356 TTAGAGTAGC


Statistics
Matches: 34,  Mismatches: 7, Indels: 4
        0.76            0.16        0.09

Matches are distributed among these distances:
  19   15  0.44
  21   19  0.56

ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31


Consensus pattern (21 bp):   
TTAGATACTGTACAGATGAAA

Found at i:21994 original size:22 final size:22

Alignment explanation


    Indices: 21969--22012  Score: 79
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      21959 ACAAGACATA

                                  
      21969 ATAATAAAATATAAATAATTAG
          1 ATAATAAAATATAAATAATTAG

                  *               
      21991 ATAATATAATATAAATAATTAG
          1 ATAATAAAATATAAATAATTAG

      22013 GAAGGGATAT


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34


Consensus pattern (22 bp):   
ATAATAAAATATAAATAATTAG
Done.