Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008409.1 Corchorus capsularis cultivar CVL-1 contig08430, 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: 4400
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30


Found at i:120 original size:6 final size:6

Alignment explanation


    Indices: 111--137  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

        101 AAAGCAAAGC

                                           
        111 AAATCT AAATCT AAATCT AAATCT AAA
          1 AAATCT AAATCT AAATCT AAATCT AAA

        138 GCAGATTATA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30


Consensus pattern (6 bp):   
AAATCT

Found at i:149 original size:12 final size:13

Alignment explanation


    Indices: 134--178  Score: 74
    Period size: 13  Copynumber: 3.5  Consensus size: 13

        124 AATCTAAATC

                         
        134 TAAAGCAGATT-A
          1 TAAAGCAGATTAA

                   *     
        146 TAAAGCAAATTAA
          1 TAAAGCAGATTAA

                         
        159 TAAAGCAGATTAA
          1 TAAAGCAGATTAA

                   
        172 TAAAGCA
          1 TAAAGCA

        179 AACAATAATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  12   10  0.33
  13   20  0.67

ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22


Consensus pattern (13 bp):   
TAAAGCAGATTAA

Found at i:185 original size:25 final size:25

Alignment explanation


    Indices: 134--186  Score: 81
    Period size: 25  Copynumber: 2.1  Consensus size: 25

        124 AATCTAAATC

                                  *  
        134 TAAAGCAGATTATAAAGCAAATTAA
          1 TAAAGCAGATTATAAAGCAAATCAA

                                      
        159 TAAAGCAGATTAATAAAGCAAA-CAA
          1 TAAAGCAGATT-ATAAAGCAAATCAA

               
        184 TAA
          1 TAA

        187 TTATAAAGCA


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  25   16  0.62
  26   10  0.38

ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21


Consensus pattern (25 bp):   
TAAAGCAGATTATAAAGCAAATCAA
Done.