Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001607.1 Corchorus olitorius cultivar O-4 contig01607, 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, 660

Length: 1101
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42


Found at i:300 original size:2 final size:2

Alignment explanation


    Indices: 293--324  Score: 55
    Period size: 2  Copynumber: 16.0  Consensus size: 2

        283 TTTATTTTAT

                                  *                        
        293 TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

        325 CTTATTTCAT


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Found at i:776 original size:42 final size:41

Alignment explanation


    Indices: 700--784  Score: 136
    Period size: 43  Copynumber: 2.0  Consensus size: 41

        690 TTTAATTCCT

                                                     
        700 ATGTAATATATATAATAACTAAAATACTTAACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTAACATTAATTAA

                                  *                    
        741 ATGTAATAATACTATAATAACTGAAATACTT-ACATTAATTAA
          1 ATGTAAT-ATA-TATAATAACTAAAATACTTAACATTAATTAA

              
        783 AT
          1 AT

        785 TCTTAGGTAT


Statistics
Matches: 41,  Mismatches: 1, Indels: 3
        0.91            0.02        0.07

Matches are distributed among these distances:
  41    7  0.17
  42   16  0.39
  43   18  0.44

ACGTcount: A:0.52, C:0.08, G:0.04, T:0.36


Consensus pattern (41 bp):   
ATGTAATATATATAATAACTAAAATACTTAACATTAATTAA

Found at i:811 original size:25 final size:24

Alignment explanation


    Indices: 775--821  Score: 85
    Period size: 25  Copynumber: 1.9  Consensus size: 24

        765 AATACTTACA

                                    
        775 TTAATTAAATTCTTAGGTATTTTT
          1 TTAATTAAATTCTTAGGTATTTTT

                                   
        799 TTAATTCAAATTCTTAGGTATTT
          1 TTAATT-AAATTCTTAGGTATTT

        822 GTGCAAACGT


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


Consensus pattern (24 bp):   
TTAATTAAATTCTTAGGTATTTTT
Done.