Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020897.1 Corchorus olitorius cultivar O-4 contig20930, 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: 6665
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31


Found at i:517 original size:29 final size:29

Alignment explanation


    Indices: 477--544  Score: 136
    Period size: 29  Copynumber: 2.3  Consensus size: 29

        467 CATAAATAAT

                                         
        477 TTTTTCAATTTGGTCCTTACATTTTTCAA
          1 TTTTTCAATTTGGTCCTTACATTTTTCAA

                                         
        506 TTTTTCAATTTGGTCCTTACATTTTTCAA
          1 TTTTTCAATTTGGTCCTTACATTTTTCAA

                      
        535 TTTTTCAATT
          1 TTTTTCAATT

        545 CCATCCCCTA


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   39  1.00

ACGTcount: A:0.21, C:0.16, G:0.06, T:0.57


Consensus pattern (29 bp):   
TTTTTCAATTTGGTCCTTACATTTTTCAA

Found at i:1080 original size:25 final size:24

Alignment explanation


    Indices: 1013--1078  Score: 62
    Period size: 25  Copynumber: 2.7  Consensus size: 24

       1003 AATAATAATA

                   *                
       1013 AATTTGCAACGGTCTTTGCCACGG
          1 AATTTGCCACGGTCTTTGCCACGG

              *        **       *     
       1037 AAATT-CCACTACTCATTTGTCACGG
          1 AATTTGCCAC-GGTC-TTTGCCACGG

                             
       1062 AATTTGCCACGGTCTTT
          1 AATTTGCCACGGTCTTT

       1079 TGAAAAGCCC


Statistics
Matches: 31,  Mismatches: 8, Indels: 6
        0.69            0.18        0.13

Matches are distributed among these distances:
  23    3  0.10
  24    9  0.29
  25   15  0.48
  26    4  0.13

ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33


Consensus pattern (24 bp):   
AATTTGCCACGGTCTTTGCCACGG

Found at i:1864 original size:19 final size:17

Alignment explanation


    Indices: 1827--1866  Score: 53
    Period size: 17  Copynumber: 2.2  Consensus size: 17

       1817 CTTGAAAATT

                          *  
       1827 TGAAAAACTTTGATGGA
          1 TGAAAAACTTTGATAGA

                               
       1844 TGAAAAACTTGATGATAGA
          1 TGAAAAACTT--TGATAGA

                
       1863 TGAA
          1 TGAA

       1867 TAGAAGGATA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  17   10  0.50
  19   10  0.50

ACGTcount: A:0.45, C:0.05, G:0.23, T:0.28


Consensus pattern (17 bp):   
TGAAAAACTTTGATAGA
Done.