Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007147.1 Corchorus olitorius cultivar O-4 contig07172, 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, 660

Length: 1101
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28


Found at i:236 original size:13 final size:13

Alignment explanation


    Indices: 203--255  Score: 60
    Period size: 12  Copynumber: 4.4  Consensus size: 13

        193 GCACCCAAAA

                        *
        203 CATTTAT-TAAAA
          1 CATTTATATAAAG

                         
        215 CATTT-TATAAAG
          1 CATTTATATAAAG

                         
        227 CATTTATATAAAG
          1 CATTTATATAAAG

              *          
        240 CAGTTATA-AAA-
          1 CATTTATATAAAG

                 
        251 CATTT
          1 CATTT

        256 CCTCAACGGG


Statistics
Matches: 36,  Mismatches: 3, Indels: 5
        0.82            0.07        0.11

Matches are distributed among these distances:
  11    5  0.14
  12   17  0.47
  13   14  0.39

ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40


Consensus pattern (13 bp):   
CATTTATATAAAG

Found at i:661 original size:27 final size:27

Alignment explanation


    Indices: 631--704  Score: 80
    Period size: 28  Copynumber: 2.7  Consensus size: 27

        621 TCCGACGTTT

                                 *     
        631 AAGGGCAAAACTGTAATTTAGTCAACC
          1 AAGGGCAAAACTGTAATTTAGCCAACC

                 *                   *   
        658 AAGGGTAAAA-TGGTAATTTTAGCCGACC
          1 AAGGGCAAAACT-GTAA-TTTAGCCAACC

                                
        686 AAGGGCAAATAC-GTAATTT
          1 AAGGGCAAA-ACTGTAATTT

        705 CAACATCCTA


Statistics
Matches: 39,  Mismatches: 4, Indels: 8
        0.76            0.08        0.16

Matches are distributed among these distances:
  26    1  0.03
  27   16  0.41
  28   21  0.54
  29    1  0.03

ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24


Consensus pattern (27 bp):   
AAGGGCAAAACTGTAATTTAGCCAACC

Done.