Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012870.1 Corchorus olitorius cultivar O-4 contig12903, 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: 6060
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30


Found at i:709 original size:15 final size:16

Alignment explanation


    Indices: 679--718  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

        669 TTACTTTGCT

                            
        679 TTGTTTTCTAGTTTAA
          1 TTGTTTTCTAGTTTAA

                     *      
        695 TTGTTTTC-GGTTTAA
          1 TTGTTTTCTAGTTTAA

               *     
        710 TTGCTTTCT
          1 TTGTTTTCT

        719 GTCAATCTCT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  15   13  0.62
  16    8  0.38

ACGTcount: A:0.12, C:0.10, G:0.15, T:0.62


Consensus pattern (16 bp):   
TTGTTTTCTAGTTTAA

Found at i:3898 original size:26 final size:27

Alignment explanation


    Indices: 3857--3919  Score: 101
    Period size: 27  Copynumber: 2.3  Consensus size: 27

       3847 GAAAACACTT

                                         
       3857 CTTTTATGAAAACAA-TTTTTTAACTACC
          1 CTTTTAT--AAACAATTTTTTTAACTACC

                                       
       3885 CTTTTATAAACAATTTTTTTAACTACC
          1 CTTTTATAAACAATTTTTTTAACTACC

                    
       3912 CTTTTATA
          1 CTTTTATA

       3920 TATGTAGTCC


Statistics
Matches: 34,  Mismatches: 0, Indels: 3
        0.92            0.00        0.08

Matches are distributed among these distances:
  26    6  0.18
  27   21  0.62
  28    7  0.21

ACGTcount: A:0.33, C:0.17, G:0.02, T:0.48


Consensus pattern (27 bp):   
CTTTTATAAACAATTTTTTTAACTACC

Found at i:5476 original size:15 final size:16

Alignment explanation


    Indices: 5451--5489  Score: 53
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       5441 GAGGTTGAAA

                             
       5451 AAAAGCAATTAAAC-AG
          1 AAAA-CAATTAAACTAG

                      *     
       5467 AAAACAATTATACTAG
          1 AAAACAATTAAACTAG

                   
       5483 AAAACAA
          1 AAAACAA

       5490 AGCAAAGTAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  15    8  0.38
  16   13  0.62

ACGTcount: A:0.64, C:0.13, G:0.08, T:0.15


Consensus pattern (16 bp):   
AAAACAATTAAACTAG
Done.