Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017385.1 Corchorus olitorius cultivar O-4 contig17418, 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: 10774
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34


Found at i:57 original size:11 final size:11

Alignment explanation


    Indices: 41--66  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

         31 CCTTTGCCTA

                       
         41 AAAACTAGAAG
          1 AAAACTAGAAG

                       
         52 AAAACTAGAAG
          1 AAAACTAGAAG

                
         63 AAAA
          1 AAAA

         67 GAAATTATCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08


Consensus pattern (11 bp):   
AAAACTAGAAG

Found at i:7105 original size:17 final size:17

Alignment explanation


    Indices: 7065--7108  Score: 52
    Period size: 17  Copynumber: 2.6  Consensus size: 17

       7055 CATGACTAAT

                        *    
       7065 ATAATGTTTTATTACCA
          1 ATAATGTTTTATGACCA

            * *            * 
       7082 TTCATGTTTTATGACTA
          1 ATAATGTTTTATGACCA

                      
       7099 ATAATGTTTT
          1 ATAATGTTTT

       7109 CCTTTTCATG


Statistics
Matches: 21,  Mismatches: 6, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
  17   21  1.00

ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52


Consensus pattern (17 bp):   
ATAATGTTTTATGACCA

Found at i:10208 original size:36 final size:36

Alignment explanation


    Indices: 10161--10230  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

      10151 TTTAATAACC

                         *      *               
      10161 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA

                  *                           
      10197 TTACATTTTTTGTAATTTTGATTATCATATTTCT
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCT

      10231 CCAAAATCTC


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


Consensus pattern (36 bp):   
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Done.