Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014246.1 Corchorus olitorius cultivar O-4 contig14279, 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: 24082
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--42  Score: 59
    Period size: 2  Copynumber: 20.5  Consensus size: 2

                                                                           
          1 TA TA TA TA TA TA TA TA TA TA TA TA TGA -A CTA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA -TA TA TA TA TA TA T

         43 GAACTCATGT


Statistics
Matches: 37,  Mismatches: 0, Indels: 6
        0.86            0.00        0.14

Matches are distributed among these distances:
   1    1  0.03
   2   34  0.92
   3    2  0.05

ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48


Consensus pattern (2 bp):   
TA

Found at i:94 original size:17 final size:18

Alignment explanation


    Indices: 68--103  Score: 56
    Period size: 17  Copynumber: 2.1  Consensus size: 18

         58 TCTGGACGAC

                              
         68 AAAAAAAAAGAAA-AAAG
          1 AAAAAAAAAGAAAGAAAG

                 *            
         85 AAAAAGAAAGAAAGAAAG
          1 AAAAAAAAAGAAAGAAAG

             
        103 A
          1 A

        104 GAAGTACTCA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  17   12  0.71
  18    5  0.29

ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00


Consensus pattern (18 bp):   
AAAAAAAAAGAAAGAAAG

Found at i:98 original size:14 final size:13

Alignment explanation


    Indices: 68--106  Score: 53
    Period size: 14  Copynumber: 3.0  Consensus size: 13

         58 TCTGGACGAC

                         
         68 AAAA-AAAAAGAA
          1 AAAAGAAAAAGAA

                         
         80 AAAAGAAAAAGAA
          1 AAAAGAAAAAGAA

                     *    
         93 AGAAAGAAAGAGAA
          1 A-AAAGAAAAAGAA

        107 GTACTCATAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  12    4  0.17
  13    9  0.38
  14   11  0.46

ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00


Consensus pattern (13 bp):   
AAAAGAAAAAGAA
Done.