Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006386.1 Corchorus olitorius cultivar O-4 contig06411, 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: 4166
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32


Found at i:593 original size:5 final size:5

Alignment explanation


    Indices: 583--627  Score: 72
    Period size: 5  Copynumber: 9.0  Consensus size: 5

        573 TATATAGTAG

                           *    *                                
        583 TAAGA TAAGA TAAAA TATGA TAAGA TAAGA TAAGA TAAGA TAAGA
          1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA

        628 GATTGGTGGT


Statistics
Matches: 36,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
   5   36  1.00

ACGTcount: A:0.60, C:0.00, G:0.18, T:0.22


Consensus pattern (5 bp):   
TAAGA

Found at i:3157 original size:6 final size:6

Alignment explanation


    Indices: 3146--3178  Score: 66
    Period size: 6  Copynumber: 5.5  Consensus size: 6

       3136 GGTCGAGCCA

                                                  
       3146 GCAGGC GCAGGC GCAGGC GCAGGC GCAGGC GCA
          1 GCAGGC GCAGGC GCAGGC GCAGGC GCAGGC GCA

       3179 AATCAATGAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   27  1.00

ACGTcount: A:0.18, C:0.33, G:0.48, T:0.00


Consensus pattern (6 bp):   
GCAGGC

Found at i:3413 original size:9 final size:9

Alignment explanation


    Indices: 3399--3427  Score: 58
    Period size: 9  Copynumber: 3.2  Consensus size: 9

       3389 AATGGAGGCA

                     
       3399 GGCCAAAGT
          1 GGCCAAAGT

                     
       3408 GGCCAAAGT
          1 GGCCAAAGT

                     
       3417 GGCCAAAGT
          1 GGCCAAAGT

              
       3426 GG
          1 GG

       3428 GACAAGGGAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   20  1.00

ACGTcount: A:0.31, C:0.21, G:0.38, T:0.10


Consensus pattern (9 bp):   
GGCCAAAGT

Found at i:4128 original size:2 final size:2

Alignment explanation


    Indices: 4123--4162  Score: 80
    Period size: 2  Copynumber: 20.0  Consensus size: 2

       4113 CACACCATAT

                                                                       
       4123 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

       4163 TAGT


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   38  1.00

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


Consensus pattern (2 bp):   
AG

Done.