Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011739.1 Corchorus olitorius cultivar O-4 contig11772, 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, 776

Length: 1294
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:24 original size:7 final size:7

Alignment explanation


    Indices: 12--82  Score: 51
    Period size: 7  Copynumber: 10.6  Consensus size: 7

          2 GTTTCATTTT

                   
         12 TTATATA
          1 TTATATA

                   
         19 TTATATA
          1 TTATATA

                  *
         26 -TATATT
          1 TTATATA

                   *
         32 TTCAT-TT
          1 TT-ATATA

              *   *
         39 TTTTATT
          1 TTATATA

                   
         46 TTATATA
          1 TTATATA

                   
         53 TTATATA
          1 TTATATA

                   
         60 -TA-ATA
          1 TTATATA

             *     
         65 TAATATA
          1 TTATATA

             *     
         72 TAATATA
          1 TTATATA

                
         79 TTAT
          1 TTAT

         83 TTTTTTATAT


Statistics
Matches: 53,  Mismatches: 6, Indels: 10
        0.77            0.09        0.14

Matches are distributed among these distances:
   5    3  0.06
   6    9  0.17
   7   39  0.74
   8    2  0.04

ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59


Consensus pattern (7 bp):   
TTATATA

Found at i:93 original size:20 final size:22

Alignment explanation


    Indices: 67--122  Score: 60
    Period size: 21  Copynumber: 2.5  Consensus size: 22

         57 ATATAATATA

                                   
         67 ATATATAATATATTATTTTTT-T
          1 ATATAT-ATATATTATTTTTTGT

                    * *           
         89 ATATATATTTTTTATTTTTTGT
          1 ATATATATATATTATTTTTTGT

               *        
        111 ATACATTATATA
          1 ATATA-TATATA

        123 CAATACAAAA


Statistics
Matches: 27,  Mismatches: 5, Indels: 3
        0.77            0.14        0.09

Matches are distributed among these distances:
  21   12  0.44
  22   11  0.41
  23    4  0.15

ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62


Consensus pattern (22 bp):   
ATATATATATATTATTTTTTGT

Found at i:1110 original size:19 final size:19

Alignment explanation


    Indices: 1086--1123  Score: 67
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       1076 CTAACTCTTT

                         *     
       1086 AGTATCTGTTCTTGTTTGA
          1 AGTATCTGTTCTTATTTGA

                               
       1105 AGTATCTGTTCTTATTTGA
          1 AGTATCTGTTCTTATTTGA

       1124 TACATTGTAG


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

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.18, C:0.11, G:0.18, T:0.53


Consensus pattern (19 bp):   
AGTATCTGTTCTTATTTGA
Done.