Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015280.1 Corchorus olitorius cultivar O-4 contig15313, 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: 11263
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34


Found at i:2941 original size:94 final size:94

Alignment explanation


    Indices: 2843--3027  Score: 307
    Period size: 94  Copynumber: 2.0  Consensus size: 94

       2833 TTTTTTTATT

                  *   *                                                      
       2843 AAATTAGTAATATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGA
          1 AAATTAATAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGA

                   *    *                
       2908 GTTTTTAGTTGAGTAAAACTATAAAAGTA
         66 GTTTTTAATTGACTAAAACTATAAAAGTA

                         *               *   *                               
       2937 AAATTAATAAAATGGTAAAAATAAAATAGTTATGAGGATATTAGATTTAATTAAATAAAAATAGA
          1 AAATTAATAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGA

                                      
       3002 GTTTTTAATTGACTAAAACTATAAAA
         66 GTTTTTAATTGACTAAAACTATAAAA

       3028 ATTTAAACAA


Statistics
Matches: 84,  Mismatches: 7, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  94   84  1.00

ACGTcount: A:0.52, C:0.02, G:0.12, T:0.33


Consensus pattern (94 bp):   
AAATTAATAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGA
GTTTTTAATTGACTAAAACTATAAAAGTA

Found at i:3167 original size:24 final size:24

Alignment explanation


    Indices: 3135--3182  Score: 87
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       3125 AAAGTCGTAC

                                    
       3135 TTTTATATATAGTATAAATTAAAA
          1 TTTTATATATAGTATAAATTAAAA

                            *       
       3159 TTTTATATATAGTATAGATTAAAA
          1 TTTTATATATAGTATAAATTAAAA

       3183 ATTAACAAAT


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46


Consensus pattern (24 bp):   
TTTTATATATAGTATAAATTAAAA

Found at i:5507 original size:20 final size:20

Alignment explanation


    Indices: 5482--5521  Score: 80
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       5472 TTAGGTTCAA

                                
       5482 CTCTCACGGAATGTGAGTTT
          1 CTCTCACGGAATGTGAGTTT

                                
       5502 CTCTCACGGAATGTGAGTTT
          1 CTCTCACGGAATGTGAGTTT

       5522 GTTTGTAATT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35


Consensus pattern (20 bp):   
CTCTCACGGAATGTGAGTTT

Found at i:7497 original size:2 final size:2

Alignment explanation


    Indices: 7490--7515  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       7480 CAATTCTACT

                                                  
       7490 TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA

       7516 AACATAGGAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
TA

Done.