Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000270.1 Corchorus capsularis cultivar CVL-1 contig00270, 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: 14764
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:800 original size:10 final size:10

Alignment explanation


    Indices: 785--820  Score: 63
    Period size: 10  Copynumber: 3.6  Consensus size: 10

        775 AAACAGTTTT

                      
        785 GATTAAACAA
          1 GATTAAACAA

                  *   
        795 GATTAATCAA
          1 GATTAAACAA

                      
        805 GATTAAACAA
          1 GATTAAACAA

                  
        815 GATTAA
          1 GATTAA

        821 TTGTTGATCG


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  10   24  1.00

ACGTcount: A:0.56, C:0.08, G:0.11, T:0.25


Consensus pattern (10 bp):   
GATTAAACAA

Found at i:9455 original size:24 final size:25

Alignment explanation


    Indices: 9407--9456  Score: 93
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       9397 AAAGGTTGGC

                                     
       9407 ATATTTACATTCAACTTTTTTTCAA
          1 ATATTTACATTCAACTTTTTTTCAA

                                     
       9432 ATATTTACATTCAAC-TTTTTTCAA
          1 ATATTTACATTCAACTTTTTTTCAA

             
       9456 A
          1 A

       9457 AGGATAAAAG


Statistics
Matches: 25,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24   10  0.40
  25   15  0.60

ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50


Consensus pattern (25 bp):   
ATATTTACATTCAACTTTTTTTCAA

Found at i:14521 original size:2 final size:2

Alignment explanation


    Indices: 14514--14552  Score: 69
    Period size: 2  Copynumber: 19.0  Consensus size: 2

      14504 CATGGAATCA

                                                                     
      14514 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT

      14553 GATGTTTGAT


Statistics
Matches: 36,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   2   34  0.94
   3    2  0.06

ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49


Consensus pattern (2 bp):   
AT

Done.