Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024554.1 Corchorus olitorius cultivar O-4 contig24587, 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: 27069
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31


Found at i:86 original size:26 final size:25

Alignment explanation


    Indices: 44--92  Score: 71
    Period size: 26  Copynumber: 1.9  Consensus size: 25

         34 TGTCCCTTTG

                        *            
         44 AAAAAAAAAGAGCGTTAGTAACCTC
          1 AAAAAAAAAGAGAGTTAGTAACCTC

                       *            
         69 AAAAGAAAAAGGGAGTTAGTAACC
          1 AAAA-AAAAAGAGAGTTAGTAACC

         93 CCTAAATCAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  25    4  0.19
  26   17  0.81

ACGTcount: A:0.53, C:0.12, G:0.20, T:0.14


Consensus pattern (25 bp):   
AAAAAAAAAGAGAGTTAGTAACCTC

Found at i:12276 original size:2 final size:2

Alignment explanation


    Indices: 12269--12301  Score: 57
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      12259 CAAATTAAAC

                                     *                       
      12269 TA TA TA TA TA TA TA TA TG 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 T

      12302 GTGCGTGTGT


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:15077 original size:32 final size:32

Alignment explanation


    Indices: 15036--15099  Score: 110
    Period size: 32  Copynumber: 2.0  Consensus size: 32

      15026 AGGCTTCAGA

                              *      *      
      15036 GAGATATCACTCATCTCACAAACCATCTCTTG
          1 GAGATATCACTCATCTCAAAAACCAGCTCTTG

                                            
      15068 GAGATATCACTCATCTCAAAAACCAGCTCTTG
          1 GAGATATCACTCATCTCAAAAACCAGCTCTTG

      15100 AAGTTACAAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  32   30  1.00

ACGTcount: A:0.33, C:0.30, G:0.11, T:0.27


Consensus pattern (32 bp):   
GAGATATCACTCATCTCAAAAACCAGCTCTTG
Done.