Pairwise Align Codons

Format Conversion

-Combine FASTA
-EMBL to FASTA
-EMBL Feature Extractor
-EMBL Trans Extractor
-Filter DNA
-Filter Protein
-GenBank to FASTA
-GenBank Feature Extractor
-GenBank Trans Extractor
-One to Three
-Range Extractor DNA
-Range Extractor Protein
-Reverse Complement

-Split FASTA
-Three to One

Sequence Analysis

Sequence Figures

-Color Align Conservation
-Color Align Properties
-Group DNA
-Group Protein
-Primer Map
-Restriction Map
-Translation Map

Random Sequences

-Mutate DNA
-Mutate Protein
-Random Coding DNA
-Random DNA Sequence
-Random DNA Regions
-Random Protein Sequence
-Random Protein Regions
-Sample DNA
-Sample Protein
-Shuffle DNA
-Shuffle Protein

Miscellaneous

-IUPAC codes
-Genetic codes
-Browser compatibility
-Mirror this site
-Use this site off-line
-About this site
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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 6000 characters.

Paste sequence two (in raw sequence or FASTA format) into the text area below. Input limit is 6000 characters.

Please check the browser compatibility page before using this program.

Use the following parameters to specify how alignments are scored.

Penalty for gaps preceding a sequence
Penalty for internal gaps
Penalty for gaps following a sequence

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