Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017039.1 Corchorus olitorius cultivar O-4 contig17072, 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: 6860
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36


Found at i:3459 original size:124 final size:124

Alignment explanation


    Indices: 3319--3553  Score: 400
    Period size: 124  Copynumber: 1.9  Consensus size: 124

       3309 CCTTTTAAAT

                                                       * *   *               
       3319 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTCAATTAAAATAGAGTTTTTA
          1 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAAGTAAATGAAAATAGAGTTTTTA

                       * *                                              
       3384 GTAGAATAAAACTGTATATTAAAAAATTTTAATATATCCAA-ATTTTTAATGAAAAATAG
         66 GTAGAATAAAAATCTATATT-AAAAATTTTAATATATCCAAGATTTTTAATGAAAAATAG

                                                                             
       3443 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAAGTAAATGAAAATAGAGTTTTTA
          1 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAAGTAAATGAAAATAGAGTTTTTA

                                                *         
       3508 GTAGAATAAAAATCTATATTAAAAATTTTAATATATGCAAGATTTT
         66 GTAGAATAAAAATCTATATTAAAAATTTTAATATATCCAAGATTTT

       3554 AATAGAGTTT


Statistics
Matches: 104,  Mismatches: 6, Indels: 2
        0.93            0.05        0.02

Matches are distributed among these distances:
 123   19  0.18
 124   85  0.82

ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36


Consensus pattern (124 bp):   
TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAAGTAAATGAAAATAGAGTTTTTA
GTAGAATAAAAATCTATATTAAAAATTTTAATATATCCAAGATTTTTAATGAAAAATAG

Found at i:6620 original size:2 final size:2

Alignment explanation


    Indices: 6613--6652  Score: 71
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       6603 ATTGCATGTA

                                                                       
       6613 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A

       6653 AGTCTAAACT


Statistics
Matches: 37,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   2   35  0.95
   3    2  0.05

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Done.