Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01004204.1 Corchorus olitorius cultivar O-4 contig04217, 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, 750

Length: 1251
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30


Found at i:757 original size:18 final size:18

Alignment explanation


    Indices: 734--786  Score: 106
    Period size: 18  Copynumber: 2.9  Consensus size: 18

        724 CCTGGGTCGC

                              
        734 TATCGGTACCAAGAGGAA
          1 TATCGGTACCAAGAGGAA

                              
        752 TATCGGTACCAAGAGGAA
          1 TATCGGTACCAAGAGGAA

                             
        770 TATCGGTACCAAGAGGA
          1 TATCGGTACCAAGAGGA

        787 GTAAAAGTAT


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   35  1.00

ACGTcount: A:0.38, C:0.17, G:0.28, T:0.17


Consensus pattern (18 bp):   
TATCGGTACCAAGAGGAA

Found at i:1055 original size:24 final size:24

Alignment explanation


    Indices: 1027--1122  Score: 183
    Period size: 24  Copynumber: 4.0  Consensus size: 24

       1017 AAATTACTTC

                           *        
       1027 TTTTCAATTTTAATGAAAATGAAA
          1 TTTTCAATTTTAATGGAAATGAAA

                                    
       1051 TTTTCAATTTTAATGGAAATGAAA
          1 TTTTCAATTTTAATGGAAATGAAA

                                    
       1075 TTTTCAATTTTAATGGAAATGAAA
          1 TTTTCAATTTTAATGGAAATGAAA

                                    
       1099 TTTTCAATTTTAATGGAAATGAAA
          1 TTTTCAATTTTAATGGAAATGAAA

       1123 AAATTAATAA


Statistics
Matches: 71,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  24   71  1.00

ACGTcount: A:0.43, C:0.04, G:0.11, T:0.42


Consensus pattern (24 bp):   
TTTTCAATTTTAATGGAAATGAAA

Found at i:1140 original size:12 final size:12

Alignment explanation


    Indices: 1120--1163  Score: 54
    Period size: 12  Copynumber: 3.8  Consensus size: 12

       1110 AATGGAAATG

                      * 
       1120 AAAAA-ATTAAT
          1 AAAAATATTATT

                        
       1131 AAAAATATTATT
          1 AAAAATATTATT

            *           
       1143 GAAAATATTATT
          1 AAAAATATTATT

            *        
       1155 GAAAATATT
          1 AAAAATATT

       1164 GAAAATAAAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  11    5  0.17
  12   25  0.83

ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36


Consensus pattern (12 bp):   
AAAAATATTATT

Found at i:1145 original size:24 final size:24

Alignment explanation


    Indices: 1118--1163  Score: 65
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       1108 TTAATGGAAA

                                    
       1118 TGAAAAAATTAATAAAAATATTAT
          1 TGAAAAAATTAATAAAAATATTAT

                  *    * *        
       1142 TGAAAATATTATTGAAAATATT
          1 TGAAAAAATTAATAAAAATATT

       1164 GAAAATAAAA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  24   19  1.00

ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37


Consensus pattern (24 bp):   
TGAAAAAATTAATAAAAATATTAT
Done.