Table 1 Binary patterns for nucleotides, A, U, C, G, and a loop/bulge structure, denoted by L, in PHDCleav [14] and LBSizeCleav with k ones based on sequences and predicted secondary structures

PHDCleav

A

[1,0,0,0]

[1,0,0,0]

U

[0,1,0,0]

[0,1,0,0]

C

[0,0,1,0]

[0,0,1,0]

G

[0,0,0,1]

[0,0,0,1]

L

−

[0,0,0,0]

Extended PHDCleav

A

−

[1,0,0,0,0]

U

[0,1,0,0,0]

C

[0,0,1,0,0]

G

[0,0,0,1,0]

L

[0,0,0,0,1]

LBSizeCleav

A

−

[1,0,0,0,0, … 0]

U

[0,1,0,0,0, … 0]

C

[0,0,1,0,0, … 0]

G

[0,0,0,1,0, … 0]

L

\([0, 0, 0, 0, 0, \dots, 0, \overbrace {1, \dots, 1}^{k}, 0, \dots ]\)