Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021765.1 Corchorus olitorius cultivar O-4 contig21798, 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: 8224
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31


Found at i:2011 original size:6 final size:6

Alignment explanation


    Indices: 2000--2054  Score: 83
    Period size: 6  Copynumber: 9.2  Consensus size: 6

       1990 TCCCTACTCT

                                   *    * *                        
       2000 CGAGTC CGAGTC CGAGTC CGGGTC GGGGTC CGAGTC CGAGTC CGAGTC
          1 CGAGTC CGAGTC CGAGTC CGAGTC CGAGTC CGAGTC CGAGTC CGAGTC

                    
       2048 CGAGTC C
          1 CGAGTC C

       2055 CAGTACGAGA


Statistics
Matches: 45,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   6   45  1.00

ACGTcount: A:0.13, C:0.33, G:0.38, T:0.16


Consensus pattern (6 bp):   
CGAGTC

Found at i:2063 original size:18 final size:18

Alignment explanation


    Indices: 2027--2063  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       2017 CCGGGTCGGG

                      *   *   
       2027 GTCCGAGTCCGAGTCCGA
          1 GTCCGAGTCCCAGTACGA

                              
       2045 GTCCGAGTCCCAGTACGA
          1 GTCCGAGTCCCAGTACGA

             
       2063 G
          1 G

       2064 AAGAAATTTA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.19, C:0.32, G:0.32, T:0.16


Consensus pattern (18 bp):   
GTCCGAGTCCCAGTACGA

Found at i:3453 original size:15 final size:15

Alignment explanation


    Indices: 3433--3464  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       3423 ATTCCAAATC

                           
       3433 AGGGAATGGAAGGAA
          1 AGGGAATGGAAGGAA

                           
       3448 AGGGAATGGAAGGAA
          1 AGGGAATGGAAGGAA

              
       3463 AG
          1 AG

       3465 TGATTACAGA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.47, C:0.00, G:0.47, T:0.06


Consensus pattern (15 bp):   
AGGGAATGGAAGGAA
Done.