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Pairwise Align Codons
Pairwise Align Codons accepts two coding sequences and determines the optimal global alignment. 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.
>sequence one atgtttcagaaagaggatcttgctacatggatgcaaatttcaatgagtggtcaatttgatgatacagcattagaggaatggagtacaaatggtaaagaacctgagatctgtgagaaatctccaaaagctgatggagttactacgattatggagagagctctatgtccatgggatagcagagtcaactaccaagagagccgagaacctaaattgattgctgaatcagtttgtctatgccgtaagagccgtggttctacaggagctttctgtatgccaattgttcgaaaagttccaattctccgacgtgtctcttgtgatcgttcaacaggtttatggaattatgtaagatcaactgagctaataactgttggatgtcattctgtattgccaagaactcaaagagcagcacgtcttgcccatttatcatcttctcgtattattgtttaa
Paste sequence two (in raw sequence or FASTA format) into the text area below. Input limit is 6000 characters.
>sequence two caggttacaattggagccatttcatcttctgactgaggaaatcaggtccgacagcgtagatgtatacacgctctattcacaaaattggtaacgattctg
Use the following parameters to specify how alignments are scored.
Penalty for gaps preceding a sequence
5
4
3
2
1
0
-1
-2
-3
-4
-5
Penalty for internal gaps
5
4
3
2
1
0
-1
-2
-3
-4
-5
Penalty for gaps following a sequence
5
4
3
2
1
0
-1
-2
-3
-4
-5
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