Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024014.1 Corchorus olitorius cultivar O-4 contig24047, 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: 6024
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32


Found at i:1138 original size:17 final size:17

Alignment explanation


    Indices: 1116--1150  Score: 70
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       1106 GTTGCTCCAC

                             
       1116 TATATGTCGGGCGAAGG
          1 TATATGTCGGGCGAAGG

                             
       1133 TATATGTCGGGCGAAGG
          1 TATATGTCGGGCGAAGG

             
       1150 T
          1 T

       1151 TCACCTAGAG


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.23, C:0.11, G:0.40, T:0.26


Consensus pattern (17 bp):   
TATATGTCGGGCGAAGG

Found at i:5525 original size:25 final size:25

Alignment explanation


    Indices: 5495--5542  Score: 87
    Period size: 25  Copynumber: 1.9  Consensus size: 25

       5485 ATGCAATGTC

                                     
       5495 AAATTAGATTTGAGCTACATGAATG
          1 AAATTAGATTTGAGCTACATGAATG

                   *               
       5520 AAATTAGCTTTGAGCTACATGAA
          1 AAATTAGATTTGAGCTACATGAA

       5543 CGCAAAATAC


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  25   22  1.00

ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31


Consensus pattern (25 bp):   
AAATTAGATTTGAGCTACATGAATG

Found at i:5718 original size:27 final size:27

Alignment explanation


    Indices: 5685--5743  Score: 100
    Period size: 27  Copynumber: 2.2  Consensus size: 27

       5675 AGTGGACTCA

                      **               
       5685 AAATGACCAACTTGCCCCTGAATATGC
          1 AAATGACCAAAATGCCCCTGAATATGC

                                       
       5712 AAATGACCAAAATGCCCCTGAATATGC
          1 AAATGACCAAAATGCCCCTGAATATGC

                 
       5739 AAATG
          1 AAATG

       5744 GGTGTCTACA


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  27   30  1.00

ACGTcount: A:0.39, C:0.25, G:0.15, T:0.20


Consensus pattern (27 bp):   
AAATGACCAAAATGCCCCTGAATATGC

Found at i:6020 original size:49 final size:50

Alignment explanation


    Indices: 5922--6020  Score: 148
    Period size: 49  Copynumber: 2.0  Consensus size: 50

       5912 CGATCAACTT

                   *     *                                    
       5922 CTTTGAATTGTCTTCCAATCTAATATTAAAAGGACCGTCTTCCGCTTATC
          1 CTTTGAACTGTCTACCAATCTAATATTAAAAGGACCGTCTTCCGCTTATC

                                     *                         
       5972 CTTTGAACTGTCTACCAAT-TCAATCTT-AAAGGACCGTCTTCCGCTTATC
          1 CTTTGAACTGTCTACCAATCT-AATATTAAAAGGACCGTCTTCCGCTTATC

       6021 TTTT


Statistics
Matches: 45,  Mismatches: 3, Indels: 3
        0.88            0.06        0.06

Matches are distributed among these distances:
  49   23  0.51
  50   22  0.49

ACGTcount: A:0.25, C:0.26, G:0.12, T:0.36


Consensus pattern (50 bp):   
CTTTGAACTGTCTACCAATCTAATATTAAAAGGACCGTCTTCCGCTTATC
Done.