Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014501.1 Corchorus olitorius cultivar O-4 contig14534, 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: 17214
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:9917 original size:3 final size:3

Alignment explanation


    Indices: 9909--9942  Score: 68
    Period size: 3  Copynumber: 11.3  Consensus size: 3

       9899 CATACTCTAA

                                                         
       9909 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
          1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C

       9943 CGTGTCTGCA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   31  1.00

ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65


Consensus pattern (3 bp):   
CTT

Found at i:16734 original size:15 final size:16

Alignment explanation


    Indices: 16716--16745  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

      16706 ATCGGGTTCG

                            
      16716 GGTCATTTT-GGGTTT
          1 GGTCATTTTCGGGTTT

                           
      16731 GGTCATTTTCGGGTT
          1 GGTCATTTTCGGGTT

      16746 CGGGTCGTTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    9  0.64
  16    5  0.36

ACGTcount: A:0.07, C:0.10, G:0.33, T:0.50


Consensus pattern (16 bp):   
GGTCATTTTCGGGTTT

Found at i:16780 original size:16 final size:16

Alignment explanation


    Indices: 16707--16782  Score: 66
    Period size: 16  Copynumber: 4.8  Consensus size: 16

      16697 GTCGGGTTAA

                        *   
      16707 TCGGGTTCGGGTCATT
          1 TCGGGTTCGGGTAATT

             *      *     *  
      16723 TTGGGTT-TGGTCATTT
          1 TCGGGTTCGGGT-AATT

                        **  
      16739 TCGGGTTCGGGTCGTT
          1 TCGGGTTCGGGTAATT

                *           
      16755 T-GGATTCGGGTAATT
          1 TCGGGTTCGGGTAATT

                         
      16770 TCGGGTTCGGGTA
          1 TCGGGTTCGGGTA

      16783 CCCAAAATTT


Statistics
Matches: 45,  Mismatches: 12, Indels: 6
        0.71            0.19        0.10

Matches are distributed among these distances:
  15   15  0.33
  16   27  0.60
  17    3  0.07

ACGTcount: A:0.08, C:0.13, G:0.38, T:0.41


Consensus pattern (16 bp):   
TCGGGTTCGGGTAATT
Done.