Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018771.1 Corchorus olitorius cultivar O-4 contig18804, 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: 8200
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30


Found at i:1781 original size:31 final size:31

Alignment explanation


    Indices: 1745--1806  Score: 115
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       1735 CTAAGGAAAA

                                      *    
       1745 GAAGTATAAGAGTTTACCTACTCATGGATTG
          1 GAAGTATAAGAGTTTACCTACTCATGAATTG

                                           
       1776 GAAGTATAAGAGTTTACCTACTCATGAATTG
          1 GAAGTATAAGAGTTTACCTACTCATGAATTG

       1807 TTTCCAATCC


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  31   30  1.00

ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32


Consensus pattern (31 bp):   
GAAGTATAAGAGTTTACCTACTCATGAATTG

Found at i:2400 original size:21 final size:21

Alignment explanation


    Indices: 2371--2416  Score: 58
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       2361 CACCTGGGCG

                                * 
       2371 CCCACATGG-TTGCCTTGAGCA
          1 CCCACATGGTTTG-CTTGAGAA

                *                
       2392 CCCATATGGTTTGCTTGAGAA
          1 CCCACATGGTTTGCTTGAGAA

                
       2413 CCCA
          1 CCCA

       2417 GGTGGGCAGT


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  21   19  0.86
  22    3  0.14

ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26


Consensus pattern (21 bp):   
CCCACATGGTTTGCTTGAGAA

Found at i:2505 original size:76 final size:76

Alignment explanation


    Indices: 2355--2506  Score: 166
    Period size: 76  Copynumber: 2.0  Consensus size: 76

       2345 ACAAGGACCC

                                                               *           * 
       2355 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATATGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATATGGTTTGCCTGAGAACCCAGAT

             *         
       2420 GGGCAGTGTCA
         66 GAGCAGTGTCA

                    *     *              *              *             **     
       2431 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATATGGTTT-GCCTGAGAACCCA

                   *      
       2493 GATGAGCTGTGTCA
         63 GATGAGCAGTGTCA

       2507 TAGCTCATCA


Statistics
Matches: 63,  Mismatches: 10, Indels: 6
        0.80            0.13        0.08

Matches are distributed among these distances:
  75    4  0.06
  76   53  0.84
  77    6  0.10

ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATATGGTTTGCCTGAGAACCCAGAT
GAGCAGTGTCA
Done.