Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001306.1 Corchorus olitorius cultivar O-4 contig01306, 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: 1704
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39


Found at i:348 original size:49 final size:49

Alignment explanation


    Indices: 232--360  Score: 165
    Period size: 50  Copynumber: 2.6  Consensus size: 49

        222 CATTTCCTGT

                                *          *                  
        232 ACTTTTTCTCAATTTTTTACTACAAAATTGAACTTTTTATTTTTACTTGC
          1 ACTTTTTCTCAATTTTTTA-GACAAAATTGATCTTTTTATTTTTACTTGC

                              *                                
        282 ACCTTTTTCTCAATTTTTAAGACAAAATTGATC-TTTTACTTTTTA-TTGC
          1 A-CTTTTTCTCAATTTTTTAGACAAAATTGATCTTTTTA-TTTTTACTTGC

                   *            *          
        331 ACTTTTTATCAATTTTTT-GGCAAAATTGAT
          1 ACTTTTTCTCAATTTTTTAGACAAAATTGAT

        361 TGGCACGCCC


Statistics
Matches: 71,  Mismatches: 6, Indels: 7
        0.85            0.07        0.08

Matches are distributed among these distances:
  47   11  0.15
  48   15  0.21
  49   10  0.14
  50   18  0.25
  51   17  0.24

ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52


Consensus pattern (49 bp):   
ACTTTTTCTCAATTTTTTAGACAAAATTGATCTTTTTATTTTTACTTGC

Found at i:856 original size:19 final size:20

Alignment explanation


    Indices: 827--864  Score: 69
    Period size: 19  Copynumber: 1.9  Consensus size: 20

        817 CGCAATCAAA

                                
        827 TATTAAATTAAAAAGATATT
          1 TATTAAATTAAAAAGATATT

                               
        847 TATT-AATTAAAAAGATAT
          1 TATTAAATTAAAAAGATAT

        865 CATTCATCCC


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

Matches are distributed among these distances:
  19   14  0.78
  20    4  0.22

ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39


Consensus pattern (20 bp):   
TATTAAATTAAAAAGATATT
Done.