Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016287.1 Corchorus olitorius cultivar O-4 contig16320, 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: 18779
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34


Found at i:1813 original size:21 final size:19

Alignment explanation


    Indices: 1788--1844  Score: 69
    Period size: 19  Copynumber: 2.9  Consensus size: 19

       1778 GCTGCTCTAA

                                 
       1788 TAATCTCATCTGTACAGCACC
          1 TAATCTCATCTGTACAG--CC

                  *          **
       1809 TAATCTAATCTGTACAGTG
          1 TAATCTCATCTGTACAGCC

                             
       1828 TAATCTCATCTGTACAG
          1 TAATCTCATCTGTACAG

       1845 TTACTAAACA


Statistics
Matches: 32,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  19   16  0.50
  21   16  0.50

ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33


Consensus pattern (19 bp):   
TAATCTCATCTGTACAGCC

Found at i:9825 original size:20 final size:20

Alignment explanation


    Indices: 9800--9839  Score: 80
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       9790 TTAGGTTCAA

                                
       9800 CTCTCACGGAATGTGAGTTT
          1 CTCTCACGGAATGTGAGTTT

                                
       9820 CTCTCACGGAATGTGAGTTT
          1 CTCTCACGGAATGTGAGTTT

       9840 GTTTGTAATT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35


Consensus pattern (20 bp):   
CTCTCACGGAATGTGAGTTT

Found at i:11703 original size:2 final size:2

Alignment explanation


    Indices: 11696--11726  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

      11686 TTTTCTAGCA

                                                          
      11696 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      11727 AATGCTGAAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:15961 original size:25 final size:24

Alignment explanation


    Indices: 15933--15994  Score: 81
    Period size: 25  Copynumber: 2.6  Consensus size: 24

      15923 GTGGATTGTA

                        *            
      15933 AAATAAATTGAATAATTAAGACATT
          1 AAATAAATTGAAGAATTAA-ACATT

                     *              
      15958 AAATAAATTTAAGAATTAAACATT
          1 AAATAAATTGAAGAATTAAACATT

                     *    
      15982 AAA-AAATTCAAGA
          1 AAATAAATTGAAGA

      15995 CTGACCCAAT


Statistics
Matches: 34,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  23    9  0.26
  24    8  0.24
  25   17  0.50

ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29


Consensus pattern (24 bp):   
AAATAAATTGAAGAATTAAACATT

Found at i:17121 original size:25 final size:26

Alignment explanation


    Indices: 17084--17135  Score: 97
    Period size: 25  Copynumber: 2.0  Consensus size: 26

      17074 GAAATATCTA

                                      
      17084 AAATACCCTTTTAATTTTAAAATTTT
          1 AAATACCCTTTTAATTTTAAAATTTT

                                      
      17110 AAATA-CCTTTTAATTTTAAAATTTT
          1 AAATACCCTTTTAATTTTAAAATTTT

             
      17135 A
          1 A

      17136 GTTTAAGCAA


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

Matches are distributed among these distances:
  25   21  0.81
  26    5  0.19

ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50


Consensus pattern (26 bp):   
AAATACCCTTTTAATTTTAAAATTTT
Done.