Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016429.1 Corchorus olitorius cultivar O-4 contig16462, 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: 25823
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35


Found at i:3819 original size:21 final size:19

Alignment explanation


    Indices: 3793--3850  Score: 62
    Period size: 19  Copynumber: 2.9  Consensus size: 19

       3783 GCTGCTCTAG

                                 
       3793 TAATCTCATCTGTACAGTACC
          1 TAATCTCATCTGTACAGT--C

                  *  *    *   *
       3814 TAATCTAATATGTATAGTG
          1 TAATCTCATCTGTACAGTC

                              
       3833 TAATCTCATCTGTACAGT
          1 TAATCTCATCTGTACAGT

       3851 TGTTAAACAG


Statistics
Matches: 30,  Mismatches: 7, Indels: 2
        0.77            0.18        0.05

Matches are distributed among these distances:
  19   15  0.50
  21   15  0.50

ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38


Consensus pattern (19 bp):   
TAATCTCATCTGTACAGTC

Found at i:4015 original size:5 final size:5

Alignment explanation


    Indices: 4005--4039  Score: 70
    Period size: 5  Copynumber: 7.0  Consensus size: 5

       3995 TGAAAAAAGG

                                                     
       4005 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
          1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT

       4040 TTCATCCGGA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   30  1.00

ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20


Consensus pattern (5 bp):   
AAAAT

Found at i:24136 original size:4 final size:4

Alignment explanation


    Indices: 24127--24152  Score: 52
    Period size: 4  Copynumber: 6.5  Consensus size: 4

      24117 GAACTTTCTC

                                            
      24127 CTTT CTTT CTTT CTTT CTTT CTTT CT
          1 CTTT CTTT CTTT CTTT CTTT CTTT CT

      24153 ATTGTCTTAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   22  1.00

ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73


Consensus pattern (4 bp):   
CTTT

Done.