Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018791.1 Corchorus olitorius cultivar O-4 contig18824, 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: 14501
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:2112 original size:16 final size:16

Alignment explanation


    Indices: 2091--2122  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       2081 CAGTTTGTTA

                            
       2091 CTTTCCAAGAAGAGTG
          1 CTTTCCAAGAAGAGTG

                            
       2107 CTTTCCAAGAAGAGTG
          1 CTTTCCAAGAAGAGTG

       2123 ATTCTTAGAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25


Consensus pattern (16 bp):   
CTTTCCAAGAAGAGTG

Found at i:2181 original size:15 final size:15

Alignment explanation


    Indices: 2093--2182  Score: 54
    Period size: 15  Copynumber: 5.9  Consensus size: 15

       2083 GTTTGTTACT

                   *       *
       2093 TTCCAAGAAGAGTGCT
          1 TTCCAAGGAGAGTG-A

                   *       
       2109 TTCCAAGAAGAGTGA
          1 TTCCAAGGAGAGTGA

               **  * *    *
       2124 TTCTTAGAAAAGTGT
          1 TTCCAAGGAGAGTGA

                  *       * 
       2139 TCTCCATGGAGAGTTA
          1 T-TCCAAGGAGAGTGA

                   *       
       2155 TTCCAAGAAGAGTGA
          1 TTCCAAGGAGAGTGA

                *        
       2170 TTCCCAGGAGAGT
          1 TTCCAAGGAGAGT

       2183 ACTTTCCATG


Statistics
Matches: 56,  Mismatches: 17, Indels: 3
        0.74            0.22        0.04

Matches are distributed among these distances:
  15   34  0.61
  16   22  0.39

ACGTcount: A:0.32, C:0.16, G:0.26, T:0.27


Consensus pattern (15 bp):   
TTCCAAGGAGAGTGA

Found at i:2609 original size:23 final size:25

Alignment explanation


    Indices: 2583--2633  Score: 61
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       2573 ATATTTCATA

                          *          
       2583 TATTGAAAT-TAT-GAATAAAAAAT
          1 TATTGAAATATATCAAATAAAAAAT

                *      *             
       2606 TATTTAAATATCTCAAATAAAAAAT
          1 TATTGAAATATATCAAATAAAAAAT

               
       2631 TAT
          1 TAT

       2634 ACGAGAGAAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  23    8  0.35
  24    2  0.09
  25   13  0.57

ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37


Consensus pattern (25 bp):   
TATTGAAATATATCAAATAAAAAAT
Done.