Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000907.1 Corchorus olitorius cultivar O-4 contig00907, 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: 2821
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--64  Score: 110
    Period size: 2  Copynumber: 31.5  Consensus size: 2

                                                                *          
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA GTA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA

                                           
         44 TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA T

         65 TTGAGAGAGA


Statistics
Matches: 59,  Mismatches: 2, Indels: 2
        0.94            0.03        0.03

Matches are distributed among these distances:
   2   57  0.97
   3    2  0.03

ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:178 original size:61 final size:61

Alignment explanation


    Indices: 104--225  Score: 244
    Period size: 61  Copynumber: 2.0  Consensus size: 61

         94 TTTTACATGT

                                                                         
        104 GCCATGCAGGTTCTAGTAGGAAATATTTATATACCAATTATCATCTAAAGTGGACTAATGA
          1 GCCATGCAGGTTCTAGTAGGAAATATTTATATACCAATTATCATCTAAAGTGGACTAATGA

                                                                         
        165 GCCATGCAGGTTCTAGTAGGAAATATTTATATACCAATTATCATCTAAAGTGGACTAATGA
          1 GCCATGCAGGTTCTAGTAGGAAATATTTATATACCAATTATCATCTAAAGTGGACTAATGA

        226 ACTAAAATTA


Statistics
Matches: 61,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  61   61  1.00

ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31


Consensus pattern (61 bp):   
GCCATGCAGGTTCTAGTAGGAAATATTTATATACCAATTATCATCTAAAGTGGACTAATGA

Found at i:2212 original size:2 final size:2

Alignment explanation


    Indices: 2207--2239  Score: 57
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       2197 TGTGTGCGTG

                                       *                     
       2207 TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       2240 GTTGATGCCT


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
TA

Done.