Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018555.1 Corchorus olitorius cultivar O-4 contig18588, 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: 27583
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33


Found at i:26576 original size:5 final size:5

Alignment explanation


    Indices: 26562--26598  Score: 51
    Period size: 5  Copynumber: 7.8  Consensus size: 5

      26552 TTTTTGGTTG

                  *                                       
      26562 CTATA GTATA CTATA CTATA CTATA C--TA CTATA CTAT
          1 CTATA CTATA CTATA CTATA CTATA CTATA CTATA CTAT

      26599 TAAAGCTCGA


Statistics
Matches: 28,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
   3    3  0.11
   5   25  0.89

ACGTcount: A:0.38, C:0.19, G:0.03, T:0.41


Consensus pattern (5 bp):   
CTATA

Found at i:27218 original size:8 final size:9

Alignment explanation


    Indices: 27192--27220  Score: 51
    Period size: 9  Copynumber: 3.3  Consensus size: 9

      27182 CCTAAATTAC

                     
      27192 TTATGGAAA
          1 TTATGGAAA

                     
      27201 TTATGGAAA
          1 TTATGGAAA

                     
      27210 TTA-GGAAA
          1 TTATGGAAA

               
      27218 TTA
          1 TTA

      27221 AAGAAATTAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
   8    8  0.40
   9   12  0.60

ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34


Consensus pattern (9 bp):   
TTATGGAAA

Found at i:27226 original size:17 final size:17

Alignment explanation


    Indices: 27196--27229  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      27186 AATTACTTAT

                    **       
      27196 GGAAATTATGGAAATTA
          1 GGAAATTAAAGAAATTA

                             
      27213 GGAAATTAAAGAAATTA
          1 GGAAATTAAAGAAATTA

      27230 AATGTTTTTA


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26


Consensus pattern (17 bp):   
GGAAATTAAAGAAATTA
Done.