miR-Intess: classification

other hairpins

block4844 [novel_shortStem]

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
no	0.088	no	no	0.48/0.48	21/21/1.00	0.0	0.0	1	0	1	0	1	15	3arm	1	nd	0.29	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------UACGUGA--------------	1	novel
		len	cloning frequencies
			CE1
	-------------------------------------------------------TTACGTGAGAGTGGTTGTAGC-	21	1
celegans	gcttgcagcgcccccacgagaaatttccacggtggtacacactagtgtcggatatTTACGTGAGAGTGGTTGTAGCt
	*****************************************************************************
celegans	((.((((((((...((((..((((.((((((.((((....)))).))).))).)))).))))...))).))))))).	1.000 -23.40

celegans

chromosome:IV:14781667:14781743:-1

intergenic

block4851 [novel_shortStem]

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
no	0.734	no	no	0.30/0.30	20/20/1.00	0.0	0.0	1	0	1	0	3	26	3arm	1	nd	0.30	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------------------UGGUUGU---------------	1	novel
		len	cloning frequencies
			CE1
	--------------------------------------------------------------------------------------------TTGGTTGTTGTTTTTTTTCG---	20	1
celegans	agtcgaaaatggcttcgattttttcgcatttcttttaatatttcttctgtttcacgtactccattttagattttgaataccattatagttgtTTGGTTGTTGTTTTTTTTCGtct
	*******************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------------	Y57G11C.22a Y57G11C.22 Y57G11C.22
celegans	((.((((((.(((..(((((.....(((...((..((((..(((.((((.................))))....)))....)))).)).)))..)))))..)))..)))))).))	0.490 -11.53

celegans

chromosome:IV:14847763:14847877:-1

Opposite_strand|Intronic_coding|Y57G11C.22a|Y57G11C.22 ## Y57G11C.22|protein_coding|Y57G11C.22|Y57G11C.22a [Source:RefSeq_peptide;Acc:NP_001041046] ## {Repeats: dust 45288 45295 0 class=dust} ## {SimpF: CEOP4661 -1 Operon,WRM062cD10 -1 fosmid,WRM0618dC06 -1 fosmid,WRM0629dF03 -1 fosmid,WRM0626cH10 -1 fosmid}

block5298 [novel_shortStem]

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
no	0.243	no	no	0.45/0.45	20/20/1.00	0.0	0.0	2	0	1	0	0	3	3arm	1	nd	0.05	1	2	1	na	na

		reads	miRBase family seed
seed	---------------------------------------AUGGCAG------------	2	novel
		len	cloning frequencies
			CE1
	--------------------------------------GATGGCAGCTTGAAGAAATC	20	2
celegans	cgattatctgatcaatgttgtcctgctcgattccggttGATGGCAGCTTGAAGAAATC
	**********************************************************
celegans	.((((.(((..((((.((((.((...(((((....))))).)))))))))))))))))	0.990 -13.10

celegans

chromosome:IV:3052119:3052176:1

intergenic ## {SimpF: WRM0636bG07 1 fosmid}

block5428 [novel_shortStem]

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
no	0.686	no	no	0.40/0.40	20/20/1.00	0.0	0.0	1	0	1	0	3	13	5arm	2	nd	0.30	3	1	1	na	na

		reads	miRBase family seed
seed	----UAUUUGU------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	---CTATTTGTGCATACGATCCT------------------------------------------------------	20	1
celegans	tttCTATTTGTGCATACGATCCTaaaaaaatcttttcgaggaaatattttcagggttttcagggtgacactggaggc
	*****************************************************************************
celegans	.(((((...((((((..((((((...(((((.((((....)))).))))).))))))......))).))))))))..	0.930 -12.50

celegans

chromosome:IV:5262022:5262098:1

intergenic ## {SimpF: WRM0613dD04 1 fosmid}

block5966 [novel_shortStem]

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
no	0.367	no	no	0.09/0.09	22/22/1.00	0.0	0.0	1	0	1	0	1	20	3arm	1	nd	0.09	1	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------AAAGAAA---------------	1	novel
		len	cloning frequencies
			CE1
	------------------------------------------------------------------------TAAAGAAATATTTAATTTTGTT-	22	1
celegans	caaactgaattttgaaaaattttaatttgtttcaagatgtgtgtgaaacaatttctaaatgagtcttggaagTAAAGAAATATTTAATTTTGTTt
	***********************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	Y57G11C.31 Y57G11C.31 Y57G11C.31
	.......................................................<<<<<<<<<<<<<<<<<<<<<.............................	Y57G11C.269 Y57G11C.269 21ur-1553
celegans	.((((.(((((...(((.(((((..(((((((((((((.(((..(((.....)))...))).))))))))).))))))))).)))))))).))))	0.580 -12.40

celegans

chromosome:IV:14686260:14686354:1

Same_strand|Intronic_coding|Y57G11C.31|Y57G11C.31 ## Y57G11C.31|protein_coding|Y57G11C.31|Y57G11C.31 [Source:RefSeq_peptide;Acc:NP_502775] ## {SimpF: Y57G11C.31 1 Expression_profile,WRM0617bD03 1 fosmid,yk372g2 1 RNAi}

block6053 [novel_shortStem]

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
no	0.243	no	no	0.43/0.43	21/21/1.00	0.0	0.0	3	0	1	0	4	7	5arm	1	nd	0.29	2	3	1	na	na

		reads	miRBase family seed
seed	-----UCGAGUA----------------------------------------------------------------	3	novel
		len	cloning frequencies
			CE1
	----TTCGAGTAACCATTGGATACG---------------------------------------------------	21	3
celegans	atgaTTCGAGTAACCATTGGATACGtattcaattttaatgttttttgaactgtaaaacaatgtatgagttgattca
	****************************************************************************
celegans	.(((.((((.((..(((((..((((..(((((............))))).))))...)))))..))..)))).)))	0.880 -11.30

celegans

chromosome:IV:15319627:15319702:1

intergenic

block6059 [novel_shortStem]

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
no	0.202	no	no	0.55/0.55	20/20/1.00	0.0	0.0	2	0	1	0	0	2	5arm	1	nd	0.20	3	2	1	na	na

		reads	miRBase family seed
seed	-ACGAAAG---------------------------------------------------	2	novel
		len	cloning frequencies
			CE1
	TACGAAAGAGGACGCTAGCC---------------------------------------	20	2
celegans	TACGAAAGAGGACGCTAGCCagccagaaactgaaaaagagtgtcaaaaatccattttgt
	***********************************************************
celegans	.((((((((.((((((...(((.......)))......)))))).....))..))))))	0.880 -9.50

celegans

chromosome:IV:15377910:15377968:1

intergenic ## {SimpF: WRM062aG10 1 fosmid,WRM0615cD07 1 fosmid}

block7877 [novel_shortStem]

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
no	0.061	no	no	0.45/0.45	22/22/1.00	0.0	0.0	1	0	1	0	2	0	3arm	1	nd	0.23	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------AUGUCAU----------------	1	novel
		len	cloning frequencies
			CE1
	-------------------------------AATGTCATCAACCACGAGGAGT--	22	1
celegans	tattgcttgtcgtttccgacattcttttgtcAATGTCATCAACCACGAGGAGTgg
	*******************************************************
celegans	((((.(((((.(((...((((((........))))))...))).))))).)))).	0.900 -13.80

celegans

chromosome:X:11692522:11692576:-1

intergenic ## {SimpF: WRM0625aC06 -1 fosmid,WRM0623bE03 -1 fosmid,WRM0633dG01 -1 fosmid,WRM0629bD12 -1 fosmid,WRM0632dE01 -1 fosmid,WRM0630bC04 -1 fosmid,WRM064bH08 -1 fosmid,WRM0628cH06 -1 fosmid}

novel_lenNOK_nonpairedHIGH_bulgeHIGH (22 loci)

block481 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

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
no	0.354	no	no	0.21/0.21	19/19/0.00	0.0	0.0	1	0	1	0	19	0	5arm	2	nd	0.32	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------AUUUUUA------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	-------------------GATTTTTAGACCAAAAATT-------------------------------------------------	19	1
celegans	ggaatgtgtttttttttttGATTTTTAGACCAAAAATTccaaaaaaaatttaaattttttaaaatcaaataaagtaaaagcttttca
	***************************************************************************************
	-------------------------------------------------------------------------------------------------	T22A3.8 T22A3.8 lam-3
celegans	.(((...((((((...(((((((((.(((....(((((........))))).....))).)))))))))......))))))..))).	0.900 -9.60

celegans

chromosome:I:10620522:10620608:-1

Opposite_strand|Intronic_coding|T22A3.8|T22A3.8 ## T22A3.8|protein_coding|lam-3|lam-3 is orthologous to human LAMININ ALPHA-2 (LAMA2. OMIM:156225), which when mutated leads to merosin-deficient congenital muscular dystrophy. [Source: WormBase] ## {Repeats: dust 47275 47282 0 class=dust,dust 47263 47269 0 class=dust} ## {SimpF: WRM0638bF09 -1 fosmid,WRM0634cH02 -1 fosmid,C43H8.3 -1 Expression_profile,WRM0640dB10 -1 fosmid,WRM0618aD12 -1 fosmid,WRM0619aD09 -1 fosmid,WRM068bC05 -1 fosmid}

block2030 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

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
no	0.155	no	no	0.58/0.58	26/26/0.00	0.0	0.0	1	0	1	0	22	3	3arm	1	nd	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------GCGAGUA----------------------------------------	1	novel
		len	cloning frequencies
			CE1
	----------------------------------------------------GGCGAGTAACGGCTTGATGTAGTCCG----------------------	26	1
celegans	aggttcgtgtaaacacttttttaaaggaccatccggatgcttcatgtttcatGGCGAGTAACGGCTTGATGTAGTCCGcaaagaagcctcctttgaacca
	****************************************************************************************************
celegans	.((((((........(((((((...((((((((.((.(((((((((...))))..)))))....)).))))..))))..))))))).......)))))).	0.540 -25.46