Table 1. Open in new tab List of...

Features evaluated by MirCure	Condition	Score range or penalty value
Structure
Hairpin-like	Lack of loop	−5	−5
Arms complementarity	<16 nt complementary	−5	−5
Endonuclease cleavage	2 nt overhang on the 3′ end.	[0, 1] _x2	[0, 1] _x2
Arm length	Arm length <20 or >26 nt	−2 _x2	0
Expression
miRNA arms	Zero reads in both arms	−5	−5
	Reds in both miRNA arms	[0, 2.5]	[0, 2.5]
Loop	Reads mapping in the loop	[−2, −0.75]	[−2, −0.75]
Flanking regions	Reads mapping in the two flanking nucleotides	[−2, −0.25]	[−2, −0.25]
Read homogeneity at 5′ end	No homogeneity	−0.5	−0.5
Conservation
Mature arm conservation	No putative orthologs found	−0.25	−0.5
	Putative orthologs found	[0, 1]	[0, 2]

Features evaluated by MirCure	Condition	Score range or penalty value
Structure
Hairpin-like	Lack of loop	−5	−5
Arms complementarity	<16 nt complementary	−5	−5
Endonuclease cleavage	2 nt overhang on the 3′ end.	[0, 1] _x2	[0, 1] _x2
Arm length	Arm length <20 or >26 nt	−2 _x2	0
Expression
miRNA arms	Zero reads in both arms	−5	−5
	Reds in both miRNA arms	[0, 2.5]	[0, 2.5]
Loop	Reads mapping in the loop	[−2, −0.75]	[−2, −0.75]
Flanking regions	Reads mapping in the two flanking nucleotides	[−2, −0.25]	[−2, −0.25]
Read homogeneity at 5′ end	No homogeneity	−0.5	−0.5
Conservation
Mature arm conservation	No putative orthologs found	−0.25	−0.5
	Putative orthologs found	[0, 1]	[0, 2]

Table 1.

List of features evaluated by MirCure,range of score and penalty values

Features evaluated by MirCure	Condition	Score range or penalty value
Features evaluated by MirCure	Condition	Animals	Plants
Structure
Hairpin-like	Lack of loop	−5	−5
Arms complementarity	<16 nt complementary	−5	−5
Endonuclease cleavage	2 nt overhang on the 3′ end.	[0, 1] _x2	[0, 1] _x2
Arm length	Arm length <20 or >26 nt	−2 _x2	0
Expression
miRNA arms	Zero reads in both arms	−5	−5
	Reds in both miRNA arms	[0, 2.5]	[0, 2.5]
Loop	Reads mapping in the loop	[−2, −0.75]	[−2, −0.75]
Flanking regions	Reads mapping in the two flanking nucleotides	[−2, −0.25]	[−2, −0.25]
Read homogeneity at 5′ end	No homogeneity	−0.5	−0.5
Conservation
Mature arm conservation	No putative orthologs found	−0.25	−0.5
	Putative orthologs found	[0, 1]	[0, 2]

Features evaluated by MirCure	Condition	Score range or penalty value
Features evaluated by MirCure	Condition	Animals	Plants
Structure
Hairpin-like	Lack of loop	−5	−5
Arms complementarity	<16 nt complementary	−5	−5
Endonuclease cleavage	2 nt overhang on the 3′ end.	[0, 1] _x2	[0, 1] _x2
Arm length	Arm length <20 or >26 nt	−2 _x2	0
Expression
miRNA arms	Zero reads in both arms	−5	−5
	Reds in both miRNA arms	[0, 2.5]	[0, 2.5]
Loop	Reads mapping in the loop	[−2, −0.75]	[−2, −0.75]
Flanking regions	Reads mapping in the two flanking nucleotides	[−2, −0.25]	[−2, −0.25]
Read homogeneity at 5′ end	No homogeneity	−0.5	−0.5
Conservation
Mature arm conservation	No putative orthologs found	−0.25	−0.5
	Putative orthologs found	[0, 1]	[0, 2]

Note: Ranges are provided within breaks and penalties are indicated in red. ‘x2’: the score or penalty applies to each of the two miRNA arms. More details are provided as Supplementary Table S1.

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