Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019822.1 Corchorus olitorius cultivar O-4 contig19855, 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: 18341
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36


Found at i:899 original size:30 final size:30

Alignment explanation


    Indices: 863--919  Score: 105
    Period size: 30  Copynumber: 1.9  Consensus size: 30

        853 AAATCCATCT

                                          
        863 AAAAAAAAAGCAAATCCATCTAAGCAATGA
          1 AAAAAAAAAGCAAATCCATCTAAGCAATGA

                      *                
        893 AAAAAAAAAGTAAATCCATCTAAGCAA
          1 AAAAAAAAAGCAAATCCATCTAAGCAA

        920 GGGCAGAAAG


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  30   26  1.00

ACGTcount: A:0.61, C:0.16, G:0.09, T:0.14


Consensus pattern (30 bp):   
AAAAAAAAAGCAAATCCATCTAAGCAATGA

Found at i:1415 original size:3 final size:3

Alignment explanation


    Indices: 1407--1436  Score: 51
    Period size: 3  Copynumber: 10.0  Consensus size: 3

       1397 TCAAGGTACC

                                             *     
       1407 CTT CTT CTT CTT CTT CTT CTT CTT CCT CTT
          1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT

       1437 TGATCATCAT


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63


Consensus pattern (3 bp):   
CTT

Found at i:5086 original size:14 final size:14

Alignment explanation


    Indices: 5047--5100  Score: 56
    Period size: 14  Copynumber: 3.9  Consensus size: 14

       5037 TGTGAGGGTT

                      *   
       5047 TATATACATACATA
          1 TATATACATATATA

            *      *      
       5061 CATATACGTATATA
          1 TATATACATATATA

                         *
       5075 TATATACATATATG
          1 TATATACATATATA

                 *       
       5089 TAT-TCCATATAT
          1 TATATACATATAT

       5101 GTAATACACA


Statistics
Matches: 33,  Mismatches: 7, Indels: 1
        0.80            0.17        0.02

Matches are distributed among these distances:
  13    8  0.24
  14   25  0.76

ACGTcount: A:0.43, C:0.13, G:0.04, T:0.41


Consensus pattern (14 bp):   
TATATACATATATA
Done.