Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023258.1 Corchorus olitorius cultivar O-4 contig23291, 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: 1874
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41


Found at i:342 original size:39 final size:40

Alignment explanation


    Indices: 299--414  Score: 155
    Period size: 39  Copynumber: 3.0  Consensus size: 40

        289 GTTTTCTAAG

                        *                           
        299 ATCCTTATACCATATTTCAATAATGTATTGTGTTTATC-C
          1 ATCCTTATACCACATTTCAATAATGTATTGTGTTTATCTC

                  *    *            *              *
        338 ATCCTTTTACCGCATTTCAATAATATATTGTGTTTA-CTG
          1 ATCCTTATACCACATTTCAATAATGTATTGTGTTTATCTC

                   *     *                        
        377 ATCCTTACACCACGTTTCAATAATGTATTGTGTTTATC
          1 ATCCTTATACCACATTTCAATAATGTATTGTGTTTATC

        415 GATTTTTATA


Statistics
Matches: 65,  Mismatches: 10, Indels: 3
        0.83            0.13        0.04

Matches are distributed among these distances:
  38    1  0.02
  39   63  0.97
  40    1  0.02

ACGTcount: A:0.27, C:0.19, G:0.09, T:0.45


Consensus pattern (40 bp):   
ATCCTTATACCACATTTCAATAATGTATTGTGTTTATCTC

Found at i:1703 original size:36 final size:36

Alignment explanation


    Indices: 1656--1725  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       1646 GAGATTTTGG

                         *      *               
       1656 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA

                                       *      
       1692 AGAAATATGATAACCAAAATCACAAAAGATGTAA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAA

       1726 GGTTATTGAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21


Consensus pattern (36 bp):   
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Done.