Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016128.1 Corchorus olitorius cultivar O-4 contig16161, 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: 3100
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31


Found at i:973 original size:17 final size:17

Alignment explanation


    Indices: 951--989  Score: 51
    Period size: 17  Copynumber: 2.3  Consensus size: 17

        941 AAATTAAATA

                    **       
        951 TTTTTATTTTAATATAT
          1 TTTTTATTGAAATATAT

                         *   
        968 TTTTTATTGAAATTTAT
          1 TTTTTATTGAAATATAT

                 
        985 TTTTT
          1 TTTTT

        990 TAATTAAAAA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  17   19  1.00

ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72


Consensus pattern (17 bp):   
TTTTTATTGAAATATAT

Found at i:2870 original size:23 final size:23

Alignment explanation


    Indices: 2842--2894  Score: 72
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       2832 CTAAAGTATA

                                    
       2842 AACTAAAATATAAGTCC-AAGCAT
          1 AACTAAAATATAAG-CCAAAGCAT

                     *          *  
       2865 AACTAAAATTTAAGCCAAAGTAT
          1 AACTAAAATATAAGCCAAAGCAT

                   
       2888 AACTAAA
          1 AACTAAA

       2895 GTCCAAAACC


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  22    2  0.07
  23   25  0.93

ACGTcount: A:0.55, C:0.15, G:0.08, T:0.23


Consensus pattern (23 bp):   
AACTAAAATATAAGCCAAAGCAT

Found at i:3074 original size:2 final size:2

Alignment explanation


    Indices: 3067--3096  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       3057 AAAACCCATG

                                                        
       3067 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

       3097 CTAC


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.