Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014543.1 Corchorus olitorius cultivar O-4 contig14576, 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: 10717
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35


Found at i:50 original size:36 final size:36

Alignment explanation


    Indices: 3--72  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

          1 GG

                         *      *               
          3 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA

                                       *      
         39 AGAAATATGATAACCAAAATCACAAAAGATGTAA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAA

         73 GGTTATTGAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21


Consensus pattern (36 bp):   
AGAAATATGATAACCAAAATCACAAAAAATGTAATA

Found at i:3854 original size:42 final size:40

Alignment explanation


    Indices: 3795--3878  Score: 141
    Period size: 42  Copynumber: 2.0  Consensus size: 40

       3785 TTTAATTCTT

                                                    
       3795 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

                                  *                   
       3835 ATGTAATAATACTATAATAACTGAAATACTTACATTAATTAA
          1 ATGTAAT-ATA-TATAATAACTAAAATACTTACATTAATTAA

              
       3877 AT
          1 AT

       3879 TCTTAGGTAT


Statistics
Matches: 41,  Mismatches: 1, Indels: 2
        0.93            0.02        0.05

Matches are distributed among these distances:
  40    7  0.17
  41    3  0.07
  42   31  0.76

ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37


Consensus pattern (40 bp):   
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

Found at i:9773 original size:37 final size:37

Alignment explanation


    Indices: 9729--9799  Score: 124
    Period size: 37  Copynumber: 1.9  Consensus size: 37

       9719 CTTGATCAAC

                        *  *                     
       9729 ATACATGTCTTTTCATATAGACATAACTTTATGATCA
          1 ATACATGTCTTTCCAAATAGACATAACTTTATGATCA

                                              
       9766 ATACATGTCTTTCCAAATAGACATAACTTTATGA
          1 ATACATGTCTTTCCAAATAGACATAACTTTATGA

       9800 ATAATTATGT


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  37   32  1.00

ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38


Consensus pattern (37 bp):   
ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
Done.