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Table 3 Parameters derived from the SUP sequence representation

From: Selection of antisense oligonucleotides based on multiple predicted target mRNA structures

Parameter

Definition

f NS

Number of bases in single-stranded region

f NP

Number of bases in double-stranded region

f PS

Percentage of bases in single-stranded region to the length of ODN

f PP

Percentage of bases in double-stranded region to the length of ODN

f CS

Maximum length of consecutive subsequence in single-stranded region

f CP

Maximum length of consecutive subsequence in base pairing

f 5S

Maximum length of consecutive subsequence in single-stranded region counting from 5' terminal

f 5P

Maximum length of consecutive subsequence in base pairing counting from 5' terminal

f 3S

Maximum length of consecutive subsequence in single-stranded region counting from 3' terminal

f 3P

Maximum length of consecutive subsequence in base pairing counting from 3' terminal

f SC

Structure consistency, f S C = 1 n 1 i = 1 n 1 E ( S i , S i 1 ) MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGMbGzdaWgaaWcbaGaem4uamLaem4qameabeaakiabg2da9maalaaabaGaeGymaedabaGaemOBa4MaeyOeI0IaeGymaedaamaaqahabaGaemyrauKaeiikaGIaem4uam1aaSbaaSqaaiabdMgaPbqabaGccqGGSaalcqWGtbWudaWgaaWcbaGaemyAaKMaeyOeI0IaeGymaedabeaakiabcMcaPaWcbaGaemyAaKMaeyypa0JaeGymaedabaGaemOBa4MaeyOeI0IaeGymaedaniabggHiLdaaaa@4994@ , where E ( x , y ) = { 1 , x = y ' U ' 0 , x = ' U ' , o r y = ' U ' -1 x y , x ' S ' , y ' P ' MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=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@6622@