Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010450.1 Corchorus olitorius cultivar O-4 contig10482, 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: 1711
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32


Found at i:541 original size:13 final size:13

Alignment explanation


    Indices: 519--549  Score: 53
    Period size: 13  Copynumber: 2.4  Consensus size: 13

        509 TCTTTTAATT

                 *       
        519 ATTTTTGTAAATG
          1 ATTTTAGTAAATG

                         
        532 ATTTTAGTAAATG
          1 ATTTTAGTAAATG

                 
        545 ATTTT
          1 ATTTT

        550 GCTTGTTATT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55


Consensus pattern (13 bp):   
ATTTTAGTAAATG

Found at i:1467 original size:19 final size:19

Alignment explanation


    Indices: 1447--1483  Score: 67
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       1437 AATTAATTAT

                               
       1447 TTTA-ATATTATATTTTTA
          1 TTTATATATTATATTTTTA

                               
       1465 TTTATATATTATATTTTTA
          1 TTTATATATTATATTTTTA

       1484 CTTAAAAATT


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

Matches are distributed among these distances:
  18    4  0.22
  19   14  0.78

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (19 bp):   
TTTATATATTATATTTTTA

Found at i:1494 original size:19 final size:19

Alignment explanation


    Indices: 1453--1494  Score: 57
    Period size: 19  Copynumber: 2.2  Consensus size: 19

       1443 TTATTTTAAT

                        *   * *
       1453 ATTATATTTTTATTTATAT
          1 ATTATATTTTTACTTAAAA

                               
       1472 ATTATATTTTTACTTAAAA
          1 ATTATATTTTTACTTAAAA

                
       1491 ATTA
          1 ATTA

       1495 CTCCTAATTA


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60


Consensus pattern (19 bp):   
ATTATATTTTTACTTAAAA
Done.