miR-Intess: classification

other hairpins

novel_lenNOK_cloningHIGH_shortStem_randfoldOK (11 loci)

block757134 [novel_lenNOK_cloningHIGH_shortStem_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
no	0.010	no	no	0.44/0.44	18/18/0.00	0.0	0.0	55	0	4	0	3	33	3arm	1	nd	0.28	2	58	4	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------------UUCUGUC-------------	58	novel
		len	cloning frequencies
			T1S1	T2S1	T4S1	T5S1
	----------------------------------------------------------------------------------------------TTTCTGTCCCCAACCTAA---	18	3	14	16	25
rat	cagctaaggtgccaggcacaggaggtgtcctgtagactcaccagtaattattgttgtgaatgcagcaggagagctggtggtagggacatcggtgTTTCTGTCCCCAACCTAActg
	*******************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000024716 ENSRNOG00000018342 Gm672
rat	(((...((((....((.((((((((((((((....((.(((((((.....(((((((....)))))))....))))))))).)))))))).....)))))).))..))))..)))	1.000 -43.90

rat

chromosome:18:72478726:72478840:1

block1392609 [novel_lenNOK_cloningHIGH_shortStem_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
no	0.001	no	no	0.44/0.47	18/20/0.50	0.0	0.7	55	0	9	0	0	0	5arm	1	nd	0.16	2	66	9	na	na

		reads	miRBase family seed
seed	-AUUGCAC---------------------------------------------------	66	miR-25/32/363/92a/92b
		len	cloning frequencies
			T1S1	T1S2	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	CATTGCACTTGTCTCTCTCT---------------------------------------	20	-	1	1	11	9	1	1	4	5
	CATTGCACTTGTCTCTCT-----------------------------------------	18	1	-	2	6	7	1	1	-	-
	CATTGCACTTGTCTCTCTC----------------------------------------	19	1	-	-	9	-	-	4	-	1
rat	CATTGCACTTGTCTCTCTCTttcttatttccaaatcctcagcagaaggacaagcgcaat
	***********************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000006197 ENSRNOG00000004536 Bbox1
rat	.(((((.((((((..(((((...................)).)))..)))))).)))))	1.000 -16.31

rat

chromosome:3:95785869:95785927:-1

Same_strand|Intronic_coding|ENSRNOT00000006197|ENSRNOG00000004536 ## ENSRNOG00000004536|protein_coding|Bbox1|Gamma-butyrobetaine dioxygenase (EC 1.14.11.1) (Gamma-butyrobetaine,2- oxoglutarate dioxygenase) (Gamma-butyrobetaine hydroxylase) (Gamma- BBH). [Source:UniProtKB/Swiss-Prot;Acc:Q9QZU7]

block1475202 [novel_lenNOK_cloningHIGH_shortStem_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
no	0.009	no	no	0.39/0.39	18/18/0.00	0.0	0.0	108	0	6	0	3	10	5arm	1	nd	0.28	2	120	6	na	na

		reads	miRBase family seed
seed	----GGUAGAC----------------------------------------------------------------	120	miR-379
		len	cloning frequencies
			T1S1	T1S2	T3S1	T3S2	T4S2	T5S2
	---TGGTAGACTATGGAAACA------------------------------------------------------	18	63	45	6	4	1	1
rat	ccaTGGTAGACTATGGAAACAcggattagtttaacaaatgactctttatggtaattctttcactgtctccatgga
	***************************************************************************
	-------------------------------------------------------------------------------------	ENSRNOT00000010580 ENSRNOG00000007484 NP_001099963.1
rat	((((((.((((..(((((((...((..((((........))))..))...)).....)))))..)))))))))).	0.860 -20.60

rat

chromosome:3:88522299:88522373:1

block1666185 [novel_lenNOK_cloningHIGH_shortStem_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
no	0.002	no	no	0.47/0.50	18/19/0.00	0.0	0.0	92	0	10	0	2	26	3arm	1	nd	0.22	2	111	10	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------GACCACU------------	111	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--------------------------------------------------------------------------TGACCACTTGGAGTCAGA--	18	5	4	11	2	2	2	13	32	15	21
	--------------------------------------------------------------------------TGACCACTTGGAGTCAGAT-	19	-	-	-	-	-	-	-	1	2	1
rat	ctatctctttctatgtgcgtgtatatatatatatatatacacatatgtatgtctgtgtgtgtgtgtgttactgcTGACCACTTGGAGTCAGAta
	**********************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000046859 ENSRNOG00000038058
rat	.(((((..(((((.(((.(((((.(((((((((((((((.((((....)))).)))))))))))))))...)))..))))).)))))..)))))	0.980 -28.00

rat

chromosome:4:108285073:108285166:1

Same_strand|Intronic_coding|ENSRNOT00000046859|ENSRNOG00000038058 ## ENSRNOG00000038058|protein_coding||

block1805748 [novel_lenNOK_cloningHIGH_shortStem_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
no	0.003	no	no	0.63/0.67	18/20/0.01	0.0	0.0	269	0	10	0	1	28	5arm	1	nd	0.17	1	310	10	na	na

		reads	miRBase family seed
seed	--GCUGGCA----------------------------------------------------------------------------------------------	310	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-AGCTGGCACCACAGGCTG------------------------------------------------------------------------------------	18	160	109	2	1	11	6	1	1	1	1
	-AGCTGGCACCACAGGCTGT-----------------------------------------------------------------------------------	19	9	5	-	-	1	-	-	-	-	-
	-AGCTGGCACCACAGGCTGTG----------------------------------------------------------------------------------	20	2	-	-	-	-	-	-	-	-	-
rat	cAGCTGGCACCACAGGCTGtggagagagggttcacctgtctcagggctaccacatgcccagtcaggagcctcccttctctctgggtctggaggctgtgggctg
	*******************************************************************************************************
rat	(((((.(((((.((((((.(((((((((((....((((.((..((((........)))))).)))).....)))).)))))))))))))..)).))).)))))	1.000 -51.90

rat

chromosome:5:170614390:170614492:-1

intergenic

block2275453 [novel_lenNOK_cloningHIGH_shortStem_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
no	0.001	no	no	0.47/0.50	18/19/0.00	0.0	0.0	110	0	7	0	2	39	3arm	1	nd	0.22	3	148	7	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------------------------------------GGAGUGA------------	148	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T4S2	T5S1	T5S2
	-----------------------------------------------------------------------------------------------TGGAGTGACTGTTACCAC--	18	1	1	32	78	1	1	1
	-----------------------------------------------------------------------------------------------TGGAGTGACTGTTACCACT-	19	-	-	12	20	1	-	-
rat	agtggtaacactgcccaagagttaaaggactgaaagtaccagtgcattctaaggacttaagtgcattacaaaactcaattcaaagtcatgggtctTGGAGTGACTGTTACCACtg
	*******************************************************************************************************************
rat	((((((((((..((((((((.(((...((((((((((...((((((((.(((....))))))))))).....)))...))))..))).))).)))))).))...)))))))))).	0.970 -35.90

rat

chromosome:8:3417807:3417921:-1

intergenic

block2377928 [novel_lenNOK_cloningHIGH_shortStem_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
no	0.002	no	no	0.64/0.72	18/22/0.65	0.0	2.2	43	0	8	0	1	10	3arm	1	nd	0.11	1	63	8	na	na

		reads	miRBase family seed
seed	-----------------------------------------CCACAGG--------------	63	novel
		len	cloning frequencies
			T1S2	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	----------------------------------------CCCACAGGGACCCCCATCTGA-	21	6	-	4	2	8	7	6	-
	----------------------------------------CCCACAGGGACCCCCATC----	18	2	-	2	-	3	9	-	1
	----------------------------------------CCCACAGGGACCCCCATCT---	19	-	-	-	1	1	2	-	1
	----------------------------------------CCCACAGGGACCCCCATCTG--	20	-	1	-	-	2	2	-	-
	----------------------------------------CCCACAGGGACCCCCATCTGAA	22	-	-	2	-	-	-	1	-
rat	ttagcatgggcttgttcctgtgtgcgtccatgcatgttacCCCACAGGGACCCCCATCTGAa
	**************************************************************
rat	((((.(((((...(((((((((((((....))))........))))))))).))))))))).	1.000 -23.60

rat

chromosome:8:12537227:12537288:1

intergenic

block21811 [novel_lenNOK_cloningHIGH_shortStem_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
no	0.001	no	no	0.72/0.79	18/24/0.63	0.0	2.0	32	0	9	0	4	0	5arm_loop	1	nd	0.18	2	52	9	na	na

		reads	miRBase family seed
seed	-----CCCCCAA-------------------------------------------------	52	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S2	T4S1	T4S2	T5S1	T5S2
	----TCCCCCAAAAGGGGGGGGGGGGG----------------------------------	23	9	-	1	1	3	-	3	2	-
	----TCCCCCAAAAGGGGGGGG---------------------------------------	18	4	2	4	-	1	-	-	-	3
	----TCCCCCAAAAGGGGGGGGGGGG-----------------------------------	22	2	-	3	-	1	-	-	-	-
	----TCCCCCAAAAGGGGGGGGG--------------------------------------	19	2	-	1	1	-	1	-	-	-
	----TCCCCCAAAAGGGGGGGGGGG------------------------------------	21	3	-	1	-	-	-	-	-	-
	----TCCCCCAAAAGGGGGGGGGG-------------------------------------	20	1	-	1	-	-	-	-	-	-
	----TCCCCCAAAAGGGGGGGGGGGGGG---------------------------------	24	-	-	-	-	-	-	1	1	-
rat	ttttTCCCCCAAAAGGGGGGGGGGGGGgagaccccccctttttttatatttgggcaaaaaa
	*************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000057682 ENSRNOG00000002277 NCOR1_RAT
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000057681 ENSRNOG00000002277 NCOR1_RAT
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000003133 ENSRNOG00000002277 NCOR1_RAT
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000057680 ENSRNOG00000002277 NCOR1_RAT
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000057679 ENSRNOG00000002277 NCOR1_RAT
rat	.((((..((((((((..((((((((((....))))))))))..))...))))))..)))).	0.980 -32.90

rat

chromosome:10:48508424:48508484:-1

Same_strand|Boundary_non-coding|ENSRNOT00000003120|ENSRNOG00000002277 ## Same_strand|Intronic_coding|ENSRNOT00000057680|ENSRNOG00000002277 ## ENSRNOG00000002277|protein_coding|NCOR1_RAT|Nuclear receptor corepressor 1 (N-CoR1) (N-CoR) (Fragment). [Source:UniProtKB/Swiss-Prot;Acc:Q9WUB5] ## {Repeats: dust 48508457 48508470 0 class=dust}

novel_lenNOK_cloningOK_loopOverlap_randfoldOK_nonpairedHIGH (11 loci)

block140008 [novel_lenNOK_cloningOK_loopOverlap_randfoldOK_nonpairedHIGH]

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	0.006	no	no	0.50/0.53	18/20/0.04	0.0	0.2	23	0	8	0	26	-1	5arm_loop	1	nd	0.39	3	27	8	na	na

		reads	miRBase family seed
seed	---------------------------AAAGGUG--------------------------------------------------------	27	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S2	T4S2	T5S1	T5S2
	--------------------------TAAAGGTGCCCATGTCTG----------------------------------------------	18	5	3	2	3	1	3	1	3
	--------------------------TAAAGGTGCCCATGTCTGG---------------------------------------------	19	4	-	-	-	1	-	-	-
	--------------------------TAAAGGTGCCCATGTCTGGT--------------------------------------------	20	1	-	-	-	-	-	-	-
rat	tgttgcacaggactctgacaatatatTAAAGGTGCCCATGTCTGGtacagagaggagcaacccagaatccgctgtcaggctgtgctacaa
	******************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000044635 ENSRNOG00000001888 Arvcf
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000002585 ENSRNOG00000001888 Arvcf
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000040586 ENSRNOG00000001888 Arvcf
rat	(((.((((((...(((((((....(((...(((((((...((((...))))..)).))).))...)))....))))))))))))).))).	0.910 -28.70

rat

chromosome:11:84594854:84594943:-1

block210658 [novel_lenNOK_cloningOK_loopOverlap_randfoldOK_nonpairedHIGH]

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	0.006	no	no	0.56/0.58	18/19/0.00	0.0	0.3	14	0	2	0	21	-1	5arm	1	nd	0.33	3	16	2	na	na

		reads	miRBase family seed
seed	----------------------GCUGGUA----------------------------------------------------------------	16	novel
		len	cloning frequencies
			T4S1	T4S2
	---------------------AGCTGGTAGGGCAAGGATG-----------------------------------------------------	19	3	7
	---------------------AGCTGGTAGGGCAAGGAT------------------------------------------------------	18	4	2
rat	cttgctaggagacaaagtgggAGCTGGTAGGGCAAGGATGaaaatctgtgtgtagtggccagggaaggtctggctgggtcatcgaaggtgagg
	*********************************************************************************************
rat	((..((.((.(((..(((.(((.(((((...(((.((((....))))...)))....)))))......))).)))..))).))...))..)).	1.000 -29.90