Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018850.1 Corchorus olitorius cultivar O-4 contig18883, 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: 4809
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.35


Found at i:977 original size:5 final size:5

Alignment explanation


    Indices: 963--996  Score: 52
    Period size: 5  Copynumber: 6.8  Consensus size: 5

        953 AGTCTTCTTT

                                                     
        963 TTTTC TTTTTC TTTT- TTTTC TTTTC TTTTC TTTT
          1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTT

        997 AAGTTCTATA


Statistics
Matches: 27,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
   4    4  0.15
   5   18  0.67
   6    5  0.19

ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85


Consensus pattern (5 bp):   
TTTTC

Found at i:4277 original size:54 final size:54

Alignment explanation


    Indices: 4199--4306  Score: 216
    Period size: 54  Copynumber: 2.0  Consensus size: 54

       4189 GCAACATAGC

                                                                  
       4199 CTTCTCCCACTCTTTAATTGAACCCACACTTGCTGCTCTGTATAAAGCTTCCTT
          1 CTTCTCCCACTCTTTAATTGAACCCACACTTGCTGCTCTGTATAAAGCTTCCTT

                                                                  
       4253 CTTCTCCCACTCTTTAATTGAACCCACACTTGCTGCTCTGTATAAAGCTTCCTT
          1 CTTCTCCCACTCTTTAATTGAACCCACACTTGCTGCTCTGTATAAAGCTTCCTT

       4307 ATACTCCTCT


Statistics
Matches: 54,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  54   54  1.00

ACGTcount: A:0.20, C:0.33, G:0.09, T:0.37


Consensus pattern (54 bp):   
CTTCTCCCACTCTTTAATTGAACCCACACTTGCTGCTCTGTATAAAGCTTCCTT

Found at i:4695 original size:2 final size:2

Alignment explanation


    Indices: 4688--4717  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       4678 AAGCAAATAC

                                                        
       4688 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       4718 AAGAGAGAGA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.