Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009867.1 Corchorus olitorius cultivar O-4 contig09899, 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: 6467
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31


Found at i:50 original size:2 final size:2

Alignment explanation


    Indices: 43--109  Score: 98
    Period size: 2  Copynumber: 33.0  Consensus size: 2

         33 TCGTAACTTT

                               *               *  *                        
         43 TA TA TA TA GTA TA GA TA TA TA TA TG TG TA TA TA TA TA TA TA TA
          1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                                               
         86 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

        110 GATGTGATTA


Statistics
Matches: 60,  Mismatches: 4, Indels: 2
        0.91            0.06        0.03

Matches are distributed among these distances:
   2   58  0.97
   3    2  0.03

ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48


Consensus pattern (2 bp):   
TA

Found at i:3267 original size:31 final size:30

Alignment explanation


    Indices: 3208--3281  Score: 105
    Period size: 31  Copynumber: 2.5  Consensus size: 30

       3198 GCCTACGGTG

                           *              
       3208 CAAAACGTCC-AAAATTAAAGTTCAGGGGA
          1 CAAAACGTCCAAAAAGTAAAGTTCAGGGGA

                                     *     
       3237 CAAAACGTCCAAAAAGTACAAGTTCGGGGGA
          1 CAAAACGTCCAAAAAGTA-AAGTTCAGGGGA

                *         
       3268 CAAACCGTCCAAAA
          1 CAAAACGTCCAAAA

       3282 CTCCGTCCGA


Statistics
Matches: 40,  Mismatches: 3, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  29   10  0.25
  30    6  0.15
  31   24  0.60

ACGTcount: A:0.45, C:0.22, G:0.20, T:0.14


Consensus pattern (30 bp):   
CAAAACGTCCAAAAAGTAAAGTTCAGGGGA
Done.