Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016524.1 Corchorus olitorius cultivar O-4 contig16557, 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: 21707
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31


Found at i:5946 original size:101 final size:102

Alignment explanation


    Indices: 5812--6015  Score: 401
    Period size: 102  Copynumber: 2.0  Consensus size: 102

       5802 AATCAAAATC

                                                                             
       5812 GAATTTTGTCAGATTGACAGTAGGGTATGCTTTTC-GGCTACAGATGATAAAAATTTCGACCAAC
          1 GAATTTTGTCAGATTGACAGTAGGGTATGCTTTTCGGGCTACAGATGATAAAAATTTCGACCAAC

                                                 
       5876 TGGTTGGTTTAAGTGGTTCGGCACTTGTTCCTTTGAA
         66 TGGTTGGTTTAAGTGGTTCGGCACTTGTTCCTTTGAA

                                                                             
       5913 GAATTTTGTCAGATTGACAGTAGGGTATGCTTTTCGGGCTACAGATGATAAAAATTTCGACCAAC
          1 GAATTTTGTCAGATTGACAGTAGGGTATGCTTTTCGGGCTACAGATGATAAAAATTTCGACCAAC

                                                 
       5978 TGGTTGGTTTAAGTGGTTCGGCACTTGTTCCTTTGAA
         66 TGGTTGGTTTAAGTGGTTCGGCACTTGTTCCTTTGAA

             
       6015 G
          1 G

       6016 TAAGGTTTGA


Statistics
Matches: 102,  Mismatches: 0, Indels: 1
        0.99            0.00        0.01

Matches are distributed among these distances:
 101   35  0.34
 102   67  0.66

ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35


Consensus pattern (102 bp):   
GAATTTTGTCAGATTGACAGTAGGGTATGCTTTTCGGGCTACAGATGATAAAAATTTCGACCAAC
TGGTTGGTTTAAGTGGTTCGGCACTTGTTCCTTTGAA

Found at i:6392 original size:2 final size:2

Alignment explanation


    Indices: 6357--6383  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       6347 TATTATAGCA

                                                    
       6357 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 A

       6384 GGAATATATT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:18429 original size:28 final size:30

Alignment explanation


    Indices: 18388--18455  Score: 81
    Period size: 28  Copynumber: 2.4  Consensus size: 30

      18378 TGCAAATTTA

                                           
      18388 AAGG-GCAAAACGTCCAAAAT-TA-AAGTTT
          1 AAGGAGCAAAACGT-CAAAATCTACAAGTTT

                *            *            
      18416 -AGGTGCAAAACGTCAAGATCTACAAGTTT
          1 AAGGAGCAAAACGTCAAAATCTACAAGTTT

                       
      18445 AAGGAGCAAAA
          1 AAGGAGCAAAA

      18456 AGGGCATTAA


Statistics
Matches: 34,  Mismatches: 2, Indels: 6
        0.81            0.05        0.14

Matches are distributed among these distances:
  27    8  0.24
  28   11  0.32
  29    6  0.18
  30    9  0.26

ACGTcount: A:0.46, C:0.15, G:0.21, T:0.19


Consensus pattern (30 bp):   
AAGGAGCAAAACGTCAAAATCTACAAGTTT
Done.