Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016754.1 Corchorus olitorius cultivar O-4 contig16787, 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: 6208
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.31


Found at i:1754 original size:2 final size:2

Alignment explanation


    Indices: 1747--1781  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       1737 ACCATGATCA

                                                                
       1747 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       1782 GACTTTGCCC


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:5059 original size:13 final size:13

Alignment explanation


    Indices: 5041--5070  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

       5031 AACCGTTAAT

                         
       5041 ATCAAAATCATAA
          1 ATCAAAATCATAA

                  *      
       5054 ATCAAAGTCATAA
          1 ATCAAAATCATAA

                
       5067 ATCA
          1 ATCA

       5071 GAGTAAAACT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.57, C:0.17, G:0.03, T:0.23


Consensus pattern (13 bp):   
ATCAAAATCATAA

Found at i:6161 original size:2 final size:2

Alignment explanation


    Indices: 6154--6201  Score: 64
    Period size: 2  Copynumber: 24.5  Consensus size: 2

       6144 CTTCATTTAT

                                                             *             
       6154 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TCA -A AA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA

                      
       6195 TA TA TA T
          1 TA TA TA T

       6202 TTTACGG


Statistics
Matches: 42,  Mismatches: 1, Indels: 6
        0.86            0.02        0.12

Matches are distributed among these distances:
   1    2  0.05
   2   39  0.93
   3    1  0.02

ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48


Consensus pattern (2 bp):   
TA

Done.