Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019170.1 Corchorus olitorius cultivar O-4 contig19203, 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: 2397
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38


Found at i:90 original size:2 final size:2

Alignment explanation


    Indices: 79--114  Score: 65
    Period size: 2  Copynumber: 18.5  Consensus size: 2

         69 TAATTTGCTC

                                                                   
         79 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

        115 CTAGCTTAAA


Statistics
Matches: 33,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   32  0.97

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


Consensus pattern (2 bp):   
TA

Found at i:778 original size:21 final size:22

Alignment explanation


    Indices: 745--790  Score: 85
    Period size: 21  Copynumber: 2.1  Consensus size: 22

        735 CATATTATTT

                                  
        745 TTATTTTTGTAAGCAAGTGAAA
          1 TTATTTTTGTAAGCAAGTGAAA

                                  
        767 TTATTTTT-TAAGCAAGTGAAA
          1 TTATTTTTGTAAGCAAGTGAAA

               
        788 TTA
          1 TTA

        791 CTAAATGCTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  21   16  0.67
  22    8  0.33

ACGTcount: A:0.37, C:0.04, G:0.15, T:0.43


Consensus pattern (22 bp):   
TTATTTTTGTAAGCAAGTGAAA

Found at i:917 original size:13 final size:13

Alignment explanation


    Indices: 899--925  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

        889 CTCTATAACC

                         
        899 TCATAAATCATAT
          1 TCATAAATCATAT

                         
        912 TCATAAATCATAT
          1 TCATAAATCATAT

             
        925 T
          1 T

        926 TATTATATTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41


Consensus pattern (13 bp):   
TCATAAATCATAT
Done.