Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013647.1 Corchorus olitorius cultivar O-4 contig13680, 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: 13060
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:11 original size:2 final size:2

Alignment explanation


    Indices: 5--43  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

          1 ATAC

                                                                      
          5 AT AT 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 AT AT A

         44 ATTACAAAGC


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:1195 original size:2 final size:2

Alignment explanation


    Indices: 1188--1213  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       1178 TGATCAAAGA

                                                  
       1188 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

       1214 GAAAACATAG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
AG

Found at i:5741 original size:15 final size:16

Alignment explanation


    Indices: 5717--5756  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       5707 AGAGGTTGAA

                 *          
       5717 AGAAAGCAATTAAAC-
          1 AGAAAACAATTAAACT

                        *   
       5732 AGAAAACAATTATACT
          1 AGAAAACAATTAAACT

                     
       5748 AGAAAACAA
          1 AGAAAACAA

       5757 AACAAAGTAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15


Consensus pattern (16 bp):   
AGAAAACAATTAAACT

Found at i:12262 original size:2 final size:2

Alignment explanation


    Indices: 12255--12287  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      12245 ATAAAGGAAA

                                                             
      12255 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 A

      12288 AAAACGCAAG


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.