Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013317.1 Corchorus olitorius cultivar O-4 contig13350, 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: 17881
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:7957 original size:28 final size:28

Alignment explanation


    Indices: 7917--7975  Score: 118
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       7907 GTAATATATT

                                        
       7917 AATGAAAACATTTTTTGTTGTGGGTGGA
          1 AATGAAAACATTTTTTGTTGTGGGTGGA

                                        
       7945 AATGAAAACATTTTTTGTTGTGGGTGGA
          1 AATGAAAACATTTTTTGTTGTGGGTGGA

               
       7973 AAT
          1 AAT

       7976 TCAGTCTATT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   31  1.00

ACGTcount: A:0.31, C:0.03, G:0.27, T:0.39


Consensus pattern (28 bp):   
AATGAAAACATTTTTTGTTGTGGGTGGA

Found at i:11464 original size:79 final size:79

Alignment explanation


    Indices: 11333--11493  Score: 313
    Period size: 79  Copynumber: 2.0  Consensus size: 79

      11323 TTCTTTTCTT

                                                                             
      11333 TTAAACAATCAAATTTTTATTGGGAGGTCCTAGAATGGACATGGTGAATTTATATGGGAAAGGAG
          1 TTAAACAATCAAATTTTTATTGGGAGGTCCTAGAATGGACATGGTGAATTTATATGGGAAAGGAG

                          
      11398 AGGGTTAGTGTAAC
         66 AGGGTTAGTGTAAC

                        *                                                    
      11412 TTAAACAATCAATTTTTTATTGGGAGGTCCTAGAATGGACATGGTGAATTTATATGGGAAAGGAG
          1 TTAAACAATCAAATTTTTATTGGGAGGTCCTAGAATGGACATGGTGAATTTATATGGGAAAGGAG

                          
      11477 AGGGTTAGTGTAAC
         66 AGGGTTAGTGTAAC

               
      11491 TTA
          1 TTA

      11494 TTTCATTATC


Statistics
Matches: 81,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  79   81  1.00

ACGTcount: A:0.34, C:0.07, G:0.27, T:0.32


Consensus pattern (79 bp):   
TTAAACAATCAAATTTTTATTGGGAGGTCCTAGAATGGACATGGTGAATTTATATGGGAAAGGAG
AGGGTTAGTGTAAC

Found at i:12869 original size:19 final size:19

Alignment explanation


    Indices: 12829--12865  Score: 67
    Period size: 19  Copynumber: 2.0  Consensus size: 19

      12819 AATTTTTAAG

                               
      12829 TAAAAATATAATATATAAA
          1 TAAAAATATAATATATAAA

                               
      12848 TAAAAATATAATAT-TAAA
          1 TAAAAATATAATATATAAA

      12866 ATAATTAATT


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

Matches are distributed among these distances:
  18    4  0.22
  19   14  0.78

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (19 bp):   
TAAAAATATAATATATAAA
Done.