Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000478.1 Corchorus olitorius cultivar O-4 contig00478, 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: 2533
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38


Found at i:181 original size:2 final size:2

Alignment explanation


    Indices: 174--210  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

        164 TTTAATTGAG

                                                                   
        174 TA TA TA 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

        211 GAAGAGCTAG


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:2267 original size:90 final size:89

Alignment explanation


    Indices: 2150--2327  Score: 302
    Period size: 90  Copynumber: 2.0  Consensus size: 89

       2140 ATATCTAAAA

                                              **                             
       2150 TGTCCTTTTTAATTTTAAATATTATCAATAACTTTTAAGATTTAATATGTAATTTTATTTATCAA
          1 TGTCCTTTTTAATTTTAAATATTATCAATAACTTGAAAGATTTAATATGTAATTTTATTTATCAA

                                    
       2215 TTAAATTAAGAATTATATATCATG
         66 TTAAATTAAGAATTATATATCATG

                                                    *                        
       2239 TGTCCTTTTTAATTTTTAAATATTATCAATAACTTGAAAGGTTTAATATGTAATTTTATTTATCA
          1 TGTCCTTTTTAA-TTTTAAATATTATCAATAACTTGAAAGATTTAATATGTAATTTTATTTATCA

                       *     *      
       2304 ATTAAATTAAGGATTATTTATCAT
         65 ATTAAATTAAGAATTATATATCAT

       2328 ATTCATGTGT


Statistics
Matches: 83,  Mismatches: 5, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
  89   12  0.14
  90   71  0.86

ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49


Consensus pattern (89 bp):   
TGTCCTTTTTAATTTTAAATATTATCAATAACTTGAAAGATTTAATATGTAATTTTATTTATCAA
TTAAATTAAGAATTATATATCATG
Done.