Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020292.1 Corchorus olitorius cultivar O-4 contig20325, 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: 3388
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36


Found at i:371 original size:25 final size:24

Alignment explanation


    Indices: 337--383  Score: 85
    Period size: 25  Copynumber: 1.9  Consensus size: 24

        327 ACGTTTGCAC

                                     
        337 AAATACCTAAGAATTTGAATTAAAA
          1 AAATACCTAAGAATTT-AATTAAAA

                                  
        362 AAATACCTAAGAATTTAATTAA
          1 AAATACCTAAGAATTTAATTAA

        384 TGTAAGTATT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24    6  0.27
  25   16  0.73

ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30


Consensus pattern (24 bp):   
AAATACCTAAGAATTTAATTAAAA

Found at i:437 original size:44 final size:45

Alignment explanation


    Indices: 374--459  Score: 147
    Period size: 44  Copynumber: 1.9  Consensus size: 45

        364 ATACCTAAGA

                                             *           
        374 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTACATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTACATTAC

                                 *                    
        418 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTACAT
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTACAT

        460 AGGAATTAAA


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  44   31  0.79
  45    8  0.21

ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50


Consensus pattern (45 bp):   
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTACATTAC

Found at i:1664 original size:16 final size:16

Alignment explanation


    Indices: 1643--1674  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       1633 AAAAGGAGAT

                            
       1643 TAATATAATGAATTTA
          1 TAATATAATGAATTTA

                       *    
       1659 TAATATAATGACTTTA
          1 TAATATAATGAATTTA

       1675 ATACCAATCA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44


Consensus pattern (16 bp):   
TAATATAATGAATTTA
Done.