Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016625.1 Corchorus olitorius cultivar O-4 contig16658, 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: 2470
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.36


Found at i:264 original size:21 final size:21

Alignment explanation


    Indices: 238--303  Score: 68
    Period size: 17  Copynumber: 3.3  Consensus size: 21

        228 CGTAAGAATT

                                 
        238 TTATTAATGTAAGTATTTCAG
          1 TTATTAATGTAAGTATTTCAG

                             *  *
        259 TTATT-A--T-AGTATTACAT
          1 TTATTAATGTAAGTATTTCAG

                               *  
        276 TTAATTAATGTAAGTATTTTAG
          1 TT-ATTAATGTAAGTATTTCAG

                  
        298 TTATTA
          1 TTATTA

        304 TATATATTAC


Statistics
Matches: 35,  Mismatches: 5, Indels: 10
        0.70            0.10        0.20

Matches are distributed among these distances:
  17   10  0.29
  18    4  0.11
  19    1  0.03
  20    1  0.03
  21   10  0.29
  22    9  0.26

ACGTcount: A:0.35, C:0.03, G:0.11, T:0.52


Consensus pattern (21 bp):   
TTATTAATGTAAGTATTTCAG

Found at i:291 original size:39 final size:40

Alignment explanation


    Indices: 235--315  Score: 128
    Period size: 39  Copynumber: 2.0  Consensus size: 40

        225 CTACGTAAGA

                *                            *      
        235 ATTTTATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

                                 *                  
        274 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

              
        314 AT
          1 AT

        316 AGGAATTAAA


Statistics
Matches: 38,  Mismatches: 3, Indels: 1
        0.90            0.07        0.02

Matches are distributed among these distances:
  39   30  0.79
  40    8  0.21

ACGTcount: A:0.36, C:0.04, G:0.09, T:0.52


Consensus pattern (40 bp):   
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Done.