Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016274.1 Corchorus capsularis cultivar CVL-1 contig16295, 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: 3689
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33


Found at i:587 original size:18 final size:18

Alignment explanation


    Indices: 552--588  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

        542 AAGAATGCCG

                         *    
        552 AAGGTAAGTTCAATGAAA
          1 AAGGTAAGTTCAACGAAA

                      *       
        570 AAGGTAAGTTTAACGAAA
          1 AAGGTAAGTTCAACGAAA

             
        588 A
          1 A

        589 TTAAATAATA


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:0.51, C:0.05, G:0.22, T:0.22


Consensus pattern (18 bp):   
AAGGTAAGTTCAACGAAA

Found at i:1018 original size:30 final size:30

Alignment explanation


    Indices: 984--1044  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 30

        974 CTTAACTGGT

                  *         **            
        984 AGTTGTTTATATTTAAGGTTTAAGGAAATG
          1 AGTTGTATATATTTAACATTTAAGGAAATG

                      *    *              
       1014 AGTTGTATATGTTTATCATTTAAGGAAATG
          1 AGTTGTATATATTTAACATTTAAGGAAATG

             
       1044 A
          1 A

       1045 CTAAGGAAAT


Statistics
Matches: 26,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  30   26  1.00

ACGTcount: A:0.34, C:0.02, G:0.21, T:0.43


Consensus pattern (30 bp):   
AGTTGTATATATTTAACATTTAAGGAAATG

Found at i:1450 original size:25 final size:25

Alignment explanation


    Indices: 1416--1467  Score: 77
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       1406 AAAATCTGTA

                        *            
       1416 GAAACATGAAAATGTGTATTTCCAT
          1 GAAACATGAAAAGGTGTATTTCCAT

                             *    *  
       1441 GAAACATGAAAAGGTGTCTTTCTAT
          1 GAAACATGAAAAGGTGTATTTCCAT

              
       1466 GA
          1 GA

       1468 GAGATTGCAT


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  25   24  1.00

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


Consensus pattern (25 bp):   
GAAACATGAAAAGGTGTATTTCCAT
Done.