C.briggsae small RNAs

miR-Intess™

miR classification

miR expression

cbr-mir-235

cbr-mir-235

Cloning frequencies
absolute	AF16
cbr-mir-235 3arm	83
normalized	AF16
cbr-mir-235 3arm	0.216

cbr-mir-235 relative cloning frequencies

block171 (miRBase cbr-mir-235) [miRNAknown_cloningHIGH_randfoldOK]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
miRBase cbr-mir-235	0.002	no	no	0.50/0.53	19/22/0.86	0.0	0.0	70	0	1	0	6	10	3arm	1	nd	0.19	2	83	1	na	na

Clusters
Located in cluster 1: cbr-mir-235, cel-mir-235

Families
Member of family miR-235 (seed AUUGCAC): cel-mir-235, cbr-mir-235

block171 hairpin

		reads	miRBase family seed
seed	--------------------------------------------------------------AUUGCAC---------------------	83	miR-235
		len	cloning frequencies
			AF16
	-------------------------------------------------------------TATTGCACTTTCCCTGGCCAG--------	21	70
	-------------------------------------------------------------TATTGCACTTTCCCTGGCC----------	19	12
	-------------------------------------------------------------TATTGCACTTTCCCTGGCCA---------	20	1
cbr-miR-235	-------------------------------------------------------------TATTGCACTTTCCCTGGCCAGA-------	22	-
cbriggsae	--TCCGATCCGGCCATGGCCAATTGCATATATTGCTTTTACTTTT---TCAAAATGCG-AATATTGCACTTTCCCTGGCCAGATCTGA--
cremanei	TATCCTACCTTGGAATA-CTAGCCGCC-----GGCACTGGAGCTT---TCGGCGTGCGTAGTATTGCACTTGGC-------GGTCGGATG
cjaponica	--TCATGTATTGAGAAA---AGCAGTA-ATAGAACTATCAGGTTTGGGTTTGACTTTG-ATTATTGCACTTTCC-------GATGCGGTG
	** * * * * * * ** * * * * ********** * * * *
	+++++ +++++++++++++++++++++++++++++++++++++++++++ ++++++++++ +++++++++++++++++++++++++++++ +++++	NM_001032899
	----- ------------------------------------------- ---------- ----------------------------- -----	NM_199320
	+++++ +++++++++++++++++++++++++++++++++++++++++++ ++++++++++ +++++++++++++++++++++++++++++ +++++	NM_005073
cbriggsae	...((((.(((((.((..((.((((.(((((((((((...... ..)))).)). ))))))))).))..))))))).))))...	1.000 -24.50
cremanei	(((((.(((.((.(((( ((((((((( (((......)).. .))))).)).))))))).))...... ))).)))))	0.930 -27.30
cjaponica	...(((((((.(((( .(((((( ((.(((...(((((......))))).))). ))))))))..))))) ))))))...	0.839 -17.80

cbriggsae	chromosome:chrI:8823354:8823435:-1	Same_strand\|Intronic_non-coding\|NM_001032899\|SLC15A1 ## Opposite_strand\|Intronic_non-coding\|NM_199320\|PHF17 ## {Repeats: no} ## {MIR: cbr-mir-235}
cremanei	chromosome:chrUn:138336433:138336554:-1	Opposite_strand\|Intronic_coding\|NM_171077 ## Same_strand\|Intronic_coding\|NM_001093429
cjaponica	chromosome:chrUn:6633772:6633893:1	intergenic

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