Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019459.1 Corchorus olitorius cultivar O-4 contig19492, 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: 3012
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:2095 original size:20 final size:20

Alignment explanation


    Indices: 2070--2108  Score: 62
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       2060 AGCTTCCTAG

                                 
       2070 AAAAAACTCCAAAA-AAAAAA
          1 AAAAAACT-CAAAAGAAAAAA

                               
       2090 AAAAAACTCAAAAGAAAAA
          1 AAAAAACTCAAAAGAAAAA

       2109 TTGTTAGTAG


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  19    5  0.28
  20   13  0.72

ACGTcount: A:0.79, C:0.13, G:0.03, T:0.05


Consensus pattern (20 bp):   
AAAAAACTCAAAAGAAAAAA

Found at i:2245 original size:23 final size:23

Alignment explanation


    Indices: 2200--2244  Score: 72
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       2190 AATTTTCTTT

                                   
       2200 TCTTTTTTTTATGACGCAAAAAC
          1 TCTTTTTTTTATGACGCAAAAAC

                      *           
       2223 TCTTTTTTTTTTCGACGCAAAA
          1 TCTTTTTTTTAT-GACGCAAAA

       2245 CACAAAACAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  23   11  0.55
  24    9  0.45

ACGTcount: A:0.27, C:0.18, G:0.09, T:0.47


Consensus pattern (23 bp):   
TCTTTTTTTTATGACGCAAAAAC

Found at i:2673 original size:15 final size:15

Alignment explanation


    Indices: 2653--2684  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       2643 ACAGAGGTTG

                           
       2653 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                           
       2668 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

              
       2683 AC
          1 AC

       2685 TGGAAAAACA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.66, C:0.16, G:0.06, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.