Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014626.1 Corchorus olitorius cultivar O-4 contig14659, 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: 12361
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29


Found at i:564 original size:24 final size:24

Alignment explanation


    Indices: 537--583  Score: 94
    Period size: 24  Copynumber: 2.0  Consensus size: 24

        527 CAATTTTATT

                                    
        537 TTCCTCTTAATTGTAATTAATAAA
          1 TTCCTCTTAATTGTAATTAATAAA

                                   
        561 TTCCTCTTAATTGTAATTAATAA
          1 TTCCTCTTAATTGTAATTAATAA

        584 TTTATGTAAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47


Consensus pattern (24 bp):   
TTCCTCTTAATTGTAATTAATAAA

Found at i:899 original size:42 final size:42

Alignment explanation


    Indices: 835--915  Score: 135
    Period size: 42  Copynumber: 1.9  Consensus size: 42

        825 ACCCACAAGT

                            *                         
        835 TACTTAGTTTGGTATCGCGGTTACAACTTGGAAAAGCTCCAA
          1 TACTTAGTTTGGTATCACGGTTACAACTTGGAAAAGCTCCAA

                           * *                     
        877 TACTTAGTTTGGTATTATGGTTACAACTTGGAAAAGCTC
          1 TACTTAGTTTGGTATCACGGTTACAACTTGGAAAAGCTC

        916 GGTTTGGTGA


Statistics
Matches: 36,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  42   36  1.00

ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35


Consensus pattern (42 bp):   
TACTTAGTTTGGTATCACGGTTACAACTTGGAAAAGCTCCAA

Found at i:4504 original size:27 final size:26

Alignment explanation


    Indices: 4434--4545  Score: 102
    Period size: 27  Copynumber: 4.2  Consensus size: 26

       4424 CTTTGAAGTA

                                        
       4434 TCATTCTCC-ACCTCAGGCTTTTGACCC
          1 TCATTC-CCTACCTCAGGC-TTTGACCC

               *                        
       4461 TCACTCCCTACAC-CAGGCTTCTGACCC
          1 TCATTCCCTAC-CTCAGGCTT-TGACCC

                     *             *   
       4488 TCATTCCCTGCCTCAGGCTTTGGCCCC
          1 TCATTCCCTACCTCAGGCTTT-GACCC

                  *   *            *   
       4515 TCATTCTCTATCTCAGGCTTTGGGCCC
          1 TCATTCCCTACCTCAGGCTTT-GACCC

                
       4542 TCAT
          1 TCAT

       4546 GCTCCACTGG


Statistics
Matches: 72,  Mismatches: 8, Indels: 10
        0.80            0.09        0.11

Matches are distributed among these distances:
  26    6  0.08
  27   65  0.90
  28    1  0.01

ACGTcount: A:0.13, C:0.41, G:0.14, T:0.31


Consensus pattern (26 bp):   
TCATTCCCTACCTCAGGCTTTGACCC

Found at i:8054 original size:28 final size:28

Alignment explanation


    Indices: 8014--8070  Score: 114
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       8004 TAAACAACAA

                                        
       8014 TTCTCAGTTCCACAAAACTTAGAGATGT
          1 TTCTCAGTTCCACAAAACTTAGAGATGT

                                        
       8042 TTCTCAGTTCCACAAAACTTAGAGATGT
          1 TTCTCAGTTCCACAAAACTTAGAGATGT

             
       8070 T
          1 T

       8071 CGTTAATTGG


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

Matches are distributed among these distances:
  28   29  1.00

ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33


Consensus pattern (28 bp):   
TTCTCAGTTCCACAAAACTTAGAGATGT
Done.