Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016621.1 Corchorus olitorius cultivar O-4 contig16654, 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: 3082
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30


Found at i:1924 original size:15 final size:15

Alignment explanation


    Indices: 1904--1940  Score: 65
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       1894 ATTATTGTCA

                           
       1904 CACCATTGTTGTTCG
          1 CACCATTGTTGTTCG

                         * 
       1919 CACCATTGTTGTTTG
          1 CACCATTGTTGTTCG

                   
       1934 CACCATT
          1 CACCATT

       1941 CAACCTAGCA


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  15   21  1.00

ACGTcount: A:0.16, C:0.27, G:0.16, T:0.41


Consensus pattern (15 bp):   
CACCATTGTTGTTCG

Found at i:2867 original size:50 final size:47

Alignment explanation


    Indices: 2765--2907  Score: 162
    Period size: 49  Copynumber: 3.0  Consensus size: 47

       2755 GAGCGTGCCA

                        *                   *       *      
       2765 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCGATGAAAATTAAAAG
          1 ATCAATTTTGTCTAAAAATTGATAAAAAGTGCAATGAAAAATAAAAG

                                    *                          
       2812 ATCAATTTTGTCTTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAAG
          1 ATCAATTTTGTC--TAAAAATTGATAAAAAG-TGCAATG-AAAAATAAAAG

            *           *                     *      *    
       2862 TTCAATTTTGTAGTAAAAATTGATAAAAAGTGCAGTGAAAAGTAAA
          1 ATCAATTTTGT-CTAAAAATTGATAAAAAGTGCAATGAAAAATAAA

       2908 GGATTGCTTG


Statistics
Matches: 81,  Mismatches: 9, Indels: 11
        0.80            0.09        0.11

Matches are distributed among these distances:
  47   12  0.15
  48   12  0.15
  49   33  0.41
  50   24  0.30

ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29


Consensus pattern (47 bp):   
ATCAATTTTGTCTAAAAATTGATAAAAAGTGCAATGAAAAATAAAAG
Done.