Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019159.1 Corchorus olitorius cultivar O-4 contig19192, 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: 10684
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34


Found at i:1218 original size:20 final size:21

Alignment explanation


    Indices: 1163--1218  Score: 62
    Period size: 20  Copynumber: 2.8  Consensus size: 21

       1153 AAAAAAAGGT

                                 
       1163 TTATAAGGTTACTAAAAAAAA
          1 TTATAAGGTTACTAAAAAAAA

              *    *   *    *    
       1184 TTCTAA-ATTAGTAAATAAAA
          1 TTATAAGGTTACTAAAAAAAA

                            
       1204 -TATAAGGTTACTAAA
          1 TTATAAGGTTACTAAA

       1219 CAAACAGTAA


Statistics
Matches: 27,  Mismatches: 7, Indels: 3
        0.73            0.19        0.08

Matches are distributed among these distances:
  19    4  0.15
  20   18  0.67
  21    5  0.19

ACGTcount: A:0.54, C:0.05, G:0.09, T:0.32


Consensus pattern (21 bp):   
TTATAAGGTTACTAAAAAAAA

Found at i:2788 original size:3 final size:3

Alignment explanation


    Indices: 2780--2809  Score: 51
    Period size: 3  Copynumber: 10.0  Consensus size: 3

       2770 AGGAGAATGA

                          *                        
       2780 GAG GAG GAG GAA GAG GAG GAG GAG GAG GAG
          1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG

       2810 TCAGGGTGGT


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00


Consensus pattern (3 bp):   
GAG

Found at i:9810 original size:20 final size:17

Alignment explanation


    Indices: 9768--9801  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       9758 TTACTTTTCT

                             
       9768 TAATTATTTTTAGATTA
          1 TAATTATTTTTAGATTA

                       *     
       9785 TAATTATTTTTTGATTA
          1 TAATTATTTTTAGATTA

       9802 AAATAATTAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62


Consensus pattern (17 bp):   
TAATTATTTTTAGATTA
Done.