Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017211.1 Corchorus olitorius cultivar O-4 contig17244, 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: 3894
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26


Found at i:46 original size:1 final size:1

Alignment explanation


    Indices: 1--31  Score: 62
    Period size: 1  Copynumber: 31.0  Consensus size: 1

                                           
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

         32 CTTAAGCCTA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   30  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:1191 original size:51 final size:51

Alignment explanation


    Indices: 1128--1293  Score: 262
    Period size: 51  Copynumber: 3.3  Consensus size: 51

       1118 TATCCAGAAA

                                                   *           
       1128 AGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTAAG
          1 AGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTTAAG

                                   *                           
       1179 AGTGAATTGGAAGACAGTTCAAATGATAAGCGGAAGACGATCCTTTTTAAG
          1 AGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTTAAG

                            *  *                            *  
       1230 AGTGAATTGGAAGACAATTTAAAGGATAAGCGGAAGACGATCC-TTTTGAG
          1 AGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTTAAG

             * *          
       1280 ATTAAATTGGAAGA
          1 AGTGAATTGGAAGA

       1294 TGGTTTTTTT


Statistics
Matches: 107,  Mismatches: 8, Indels: 1
        0.92            0.07        0.01

Matches are distributed among these distances:
  50   18  0.17
  51   89  0.83

ACGTcount: A:0.38, C:0.10, G:0.27, T:0.25


Consensus pattern (51 bp):   
AGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTTAAG

Found at i:1643 original size:28 final size:28

Alignment explanation


    Indices: 1603--1693  Score: 121
    Period size: 28  Copynumber: 3.2  Consensus size: 28

       1593 CTTACTCCTT

                   *                    
       1603 ATTTTGGCCATTTTGCATGTCCAAGGGC
          1 ATTTTGGTCATTTTGCATGTCCAAGGGC

                                         
       1631 ATTTTGGTCATTTTGCATGTCC-AGGAGC
          1 ATTTTGGTCATTTTGCATGTCCAAGG-GC

                  *          **    *    
       1659 ATTTTGATCATTTTGCACATCCAGGGGC
          1 ATTTTGGTCATTTTGCATGTCCAAGGGC

                   
       1687 ATTTTGG
          1 ATTTTGG

       1694 GTCACTTCAA


Statistics
Matches: 55,  Mismatches: 6, Indels: 4
        0.85            0.09        0.06

Matches are distributed among these distances:
  27    3  0.05
  28   50  0.91
  29    2  0.04

ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38


Consensus pattern (28 bp):   
ATTTTGGTCATTTTGCATGTCCAAGGGC
Done.