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ExPASy logo SIM Alignment Tool for nucleic acid sequences

SIM (References) is a program which finds a user-defined number of best non-intersecting alignments between two nucleic acid sequences or within a sequence.

Notes:

  • You can also use the SIM Alignment Tool to align protein sequences.
  • You can use the ACNUC server to align nucleic acid sequences with a similar tool.
    Please enter two sequences. These sequences may either be specified by
    Please paste your sequences in the boxes below:
    Sequence 1:
    Name:

    Sequence 2:
    Name:

    Parameters:
    Number of alignments to be computed (k):
    Cost of a matching aligned pair:
    Cost of a transition:
    Cost of a transversion:
    Gap open penalty:
    Gap extension penalty:

    Last modified 4/Jun/1998 by ELG

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