First Sequence Name (optional)
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Paste Your FIRST "Secondary Structure" (see allowed alphabet)
Second Sequence Name (optional)
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Paste Your SECOND "Secondary Structure" (see allowed alphabet)
Select Score Matrix: Blosum62 Pam250 Identity Score the ending gap penalties Y N
Open gap penalty
Open extension penalty
Weight score (secondary structure only = 0.0 / sequence only = 1.0) 1.0<= w <=0.0)
Amplification factor for gap opening in the secondary structure segments (>=1.0)
Upload secondary structure score matrix a file (leave ti blank if you want to use the internal) :
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