Pairwise Align Codons

Format Conversion

-Combine FASTA
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Sequence Analysis

-Codon Plot
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-DNA Molecular Weight
-DNA Pattern Find
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-Fuzzy Search DNA
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-Ident and Sim
-Multi Rev Trans
-Mutate for Digest
-ORF Finder
-Pairwise Align Codons
-Pairwise Align DNA
-Pairwise Align Protein
-PCR Primer Stats
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-Protein GRAVY
-Protein Isoelectric Point
-Protein Molecular Weight
-Protein Pattern Find
-Protein Stats
-Restriction Digest
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Sequence Figures

-Color Align Conservation
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-Group DNA
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-Primer Map
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-Translation Map

Random Sequences

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Sequence Manipulation Suite:

Pairwise Align Codons

Pairwise Align Codons accepts two coding sequences and determines the optimal global alignment. The scoring matrix used to calculate the alignment is described in Schneider et al. (2005). Use Pairwise Align Codons to look for conserved coding sequence regions. Only the bases A,C,G,T and U are used in the alignment.

Paste sequence one (in raw sequence or FASTA format) into the text area below. Input limit is 6,000,000 characters.

Paste sequence two (in raw sequence or FASTA format) into the text area below. Input limit is 6,000,000 characters.

Use the following parameters to specify how alignments are scored.

Value for gaps preceding a sequence
Value for internal gaps
Value for gaps following a sequence

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