Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006509.1 Corchorus capsularis cultivar CVL-1 contig06530, 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: 9939
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:1777 original size:19 final size:18

Alignment explanation


    Indices: 1744--1779  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       1734 TTGAAATAAT

                              
       1744 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       1762 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       1780 GAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:7640 original size:1 final size:1

Alignment explanation


    Indices: 7634--7671  Score: 76
    Period size: 1  Copynumber: 38.0  Consensus size: 1

       7624 TTTGATTTGC

                                                  
       7634 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

       7672 TCTTTTCAAG


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   37  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:9112 original size:23 final size:23

Alignment explanation


    Indices: 9086--9130  Score: 90
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       9076 TCACATAGTC

                                   
       9086 CAGAACAAGAAGAAGGAAAAGAG
          1 CAGAACAAGAAGAAGGAAAAGAG

                                  
       9109 CAGAACAAGAAGAAGGAAAAGA
          1 CAGAACAAGAAGAAGGAAAAGA

       9131 AAAGTTGAGA


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

Matches are distributed among these distances:
  23   22  1.00

ACGTcount: A:0.62, C:0.09, G:0.29, T:0.00


Consensus pattern (23 bp):   
CAGAACAAGAAGAAGGAAAAGAG
Done.