Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019101.1 Corchorus olitorius cultivar O-4 contig19134, 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: 12420
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Found at i:182 original size:22 final size:22

Alignment explanation


    Indices: 157--198  Score: 57
    Period size: 22  Copynumber: 1.9  Consensus size: 22

        147 AAAGCTTCAA

                 *         *      
        157 TGATTGTTCTAAAAAGTATAAG
          1 TGATTATTCTAAAAACTATAAG

                    *           
        179 TGATTATTTTAAAAACTATA
          1 TGATTATTCTAAAAACTATA

        199 TTATTATCTT


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   17  1.00

ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40


Consensus pattern (22 bp):   
TGATTATTCTAAAAACTATAAG

Found at i:2571 original size:7 final size:7

Alignment explanation


    Indices: 2559--2585  Score: 54
    Period size: 7  Copynumber: 3.9  Consensus size: 7

       2549 CGCATGTTTA

                   
       2559 TTTTTTG
          1 TTTTTTG

                   
       2566 TTTTTTG
          1 TTTTTTG

                   
       2573 TTTTTTG
          1 TTTTTTG

                  
       2580 TTTTTT
          1 TTTTTT

       2586 TTTAGAGGAT


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

Matches are distributed among these distances:
   7   20  1.00

ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89


Consensus pattern (7 bp):   
TTTTTTG

Found at i:7407 original size:59 final size:59

Alignment explanation


    Indices: 7315--7431  Score: 207
    Period size: 59  Copynumber: 2.0  Consensus size: 59

       7305 CAGAGACACT

                 *                                                     
       7315 TCTTCGAGATAACTGTTTGTCAACAGATATCTATTAAACTTGAAAAACTGTAAAACCAC
          1 TCTTCAAGATAACTGTTTGTCAACAGATATCTATTAAACTTGAAAAACTGTAAAACCAC

                        *           *                                 
       7374 TCTTCAAGATAATTGTTTGTCAACCGATATCTATTAAACTTGAAAAACTGTAAAACCA
          1 TCTTCAAGATAACTGTTTGTCAACAGATATCTATTAAACTTGAAAAACTGTAAAACCA

       7432 GTTTTTGACA


Statistics
Matches: 55,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  59   55  1.00

ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32


Consensus pattern (59 bp):   
TCTTCAAGATAACTGTTTGTCAACAGATATCTATTAAACTTGAAAAACTGTAAAACCAC
Done.