Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007243.1 Corchorus olitorius cultivar O-4 contig07268, 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: 1690
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36


Found at i:791 original size:15 final size:15

Alignment explanation


    Indices: 758--800  Score: 52
    Period size: 15  Copynumber: 2.9  Consensus size: 15

        748 TACATACCAC

                      *    
        758 TAATAATAATTATTA
          1 TAATAATAATAATTA

                            
        773 TAATAATAATAAGTT-
          1 TAATAATAATAA-TTA

                   *     
        788 TAATAATTATAAT
          1 TAATAATAATAAT

        801 CTTAAGATGT


Statistics
Matches: 25,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  14    1  0.04
  15   22  0.88
  16    2  0.08

ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44


Consensus pattern (15 bp):   
TAATAATAATAATTA

Found at i:793 original size:18 final size:18

Alignment explanation


    Indices: 758--800  Score: 52
    Period size: 18  Copynumber: 2.4  Consensus size: 18

        748 TACATACCAC

                         *    
        758 TAATAATAATTATTATAA
          1 TAATAATAATTATAATAA

                               
        776 TAATAATAAGTT-TAATAA
          1 TAATAATAA-TTATAATAA

             *     
        794 TTATAAT
          1 TAATAAT

        801 CTTAAGATGT


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  18   20  0.91
  19    2  0.09

ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44


Consensus pattern (18 bp):   
TAATAATAATTATAATAA

Found at i:1494 original size:13 final size:13

Alignment explanation


    Indices: 1476--1506  Score: 55
    Period size: 13  Copynumber: 2.5  Consensus size: 13

       1466 CGATTCAATG

                         
       1476 ACAAGAAAAAAAA
          1 ACAAGAAAAAAAA

                         
       1489 ACAAGAAAAAAAA
          1 ACAAGAAAAAAAA

                  
       1502 A-AAGA
          1 ACAAGA

       1507 GAGATCTTCA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  12    4  0.22
  13   14  0.78

ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00


Consensus pattern (13 bp):   
ACAAGAAAAAAAA
Done.