miR-Intess: classification

other hairpins

novel_Multihit_shortStem_randfoldOK (69 loci)

block914700 [novel_Multihit_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	0.59/0.59	22/22/1.00	0.0	0.0	1	0	1	0	2	32	3arm	12	nd	0.18	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------------CCAUGGA----------------	1	novel
		len	cloning frequencies
			T5S2
	----------------------------------------------------------------------------------------------CCCATGGATGCTGGAGTACCCT--	22	1
rat	ccggagtaccctagcccccgtggatgctagagtaccctagcccctgtggatgctggagtaccctagcccccgtggatgctggagtaccctagccCCCATGGATGCTGGAGTACCCTgg
	**********************************************************************************************************************
rat	((((.((((.(((((..((((((..(((((.((((.(((((..((..((..(((((......)))))..))..))..))))).)))).)))))..))))))..))))).)))).))))	1.000 -61.00

rat

chromosome:1:209383180:209383297:-1

intergenic ## {Repeats: trf 52 74 0 class=trf}

block914703 [novel_Multihit_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	0.59/0.59	22/22/1.00	0.0	0.0	3	0	1	0	4	31	5arm	12	nd	0.18	2	3	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------CCAUGGA--------------------------------------------------------	1	novel
seed	-----CCAUGGA------------------------------------------------------------------------------------------------------------	1	novel
seed	-----------------------------------------------------------------------------------CCAUGGA------------------------------	1	novel
		len	cloning frequencies
			T5S2
	----CCCATGGATGCTGGAGTACCCT----------------------------------------------------------------------------------------------	22	1
	--------------------------------------------------------CCCATGGATGCTGGAGTACCCT------------------------------------------	22	1
	----------------------------------------------------------------------------------CCCATGGATGCTGGAGTACCCT----------------	22	1
rat	agccCCCATGGATGCTGGAGTACCCTagcacctgtggatgccagagtaccctagccCCCATGGATGCTGGAGTACCCTagccCCCATGGATGCTGGAGTACCCTagcccccgtggatgct
	************************************************************************************************************************
rat	(((..((((((..(((((.((((.((((((.((((((..((.((.((((.(((((((....))..))))).)))).)).))..)))))).)))))).)))).)))))..))))))..)))	1.000 -58.90

rat

chromosome:1:209383452:209383571:-1

intergenic ## {Repeats: trf 416 438 0 class=trf}

block914706 [novel_Multihit_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	0.59/0.59	22/22/1.00	0.0	0.0	3	0	1	0	4	31	5arm	12	nd	0.18	2	3	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------CCAUGGA--------------------------------------------------------	1	novel
seed	-----CCAUGGA------------------------------------------------------------------------------------------------------------	1	novel
seed	-----------------------------------------------------------------------------------CCAUGGA------------------------------	1	novel
		len	cloning frequencies
			T5S2
	----CCCATGGATGCTGGAGTACCCT----------------------------------------------------------------------------------------------	22	1
	--------------------------------------------------------CCCATGGATGCTGGAGTACCCT------------------------------------------	22	1
	----------------------------------------------------------------------------------CCCATGGATGCTGGAGTACCCT----------------	22	1
rat	agccCCCATGGATGCTGGAGTACCCTagcacctgtggatgccagagtaccctagccCCCATGGATGCTGGAGTACCCTagccCCCATGGATGCTGGAGTACCCTagcccccgtggatgct
	************************************************************************************************************************
rat	(((..((((((..(((((.((((.((((((.((((((..((.((.((((.(((((((....))..))))).)))).)).))..)))))).)))))).)))).)))))..))))))..)))	1.000 -58.90

rat

chromosome:1:209384145:209384264:-1

intergenic ## {Repeats: trf 340 362 0 class=trf}

block914709 [novel_Multihit_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	0.59/0.59	22/22/1.00	0.0	0.0	3	0	1	0	3	31	5arm	12	nd	0.18	2	3	1	na	na

		reads	miRBase family seed
seed	----CCAUGGA-----------------------------------------------------------------------------------------------------------	1	novel
seed	----------------------------------------------------------------------------------CCAUGGA-----------------------------	1	novel
seed	--------------------------------------------------------CCAUGGA-------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	-------------------------------------------------------CCCATGGATGCTGGAGTACCCT-----------------------------------------	22	1
	---CCCATGGATGCTGGAGTACCCT---------------------------------------------------------------------------------------------	22	1
	---------------------------------------------------------------------------------CCCATGGATGCTGGAGTACCCT---------------	22	1
rat	gccCCCATGGATGCTGGAGTACCCTagcctccatggatgctggagtactctagccCCCATGGATGCTGGAGTACCCTagccCCCATGGATGCTGGAGTACCCTagcccccatggaagc
	**********************************************************************************************************************
rat	((..((((((..(((((.((((.(((((.(((((((..(((((.((((((((((((....))..)))))))))).)))))..))))))).))))).)))).)))))..))))))..))	1.000 -70.40

rat

chromosome:1:209384562:209384679:-1

intergenic ## {Repeats: trf 704 726 0 class=trf}

block914710 [novel_Multihit_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	0.59/0.59	22/22/1.00	0.0	0.0	3	0	1	0	4	31	5arm	12	nd	0.18	2	3	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------CCAUGGA--------------------------------------------------------	1	novel
seed	-----CCAUGGA------------------------------------------------------------------------------------------------------------	1	novel
seed	-----------------------------------------------------------------------------------CCAUGGA------------------------------	1	novel
		len	cloning frequencies
			T5S2
	----CCCATGGATGCTGGAGTACCCT----------------------------------------------------------------------------------------------	22	1
	--------------------------------------------------------CCCATGGATGCTGGAGTACCCT------------------------------------------	22	1
	----------------------------------------------------------------------------------CCCATGGATGCTGGAGTACCCT----------------	22	1
rat	agccCCCATGGATGCTGGAGTACCCTagcctccatggatgctggagtactctagccCCCATGGATGCTGGAGTACCCTagccCCCATGGATGCTGGAGTACCCTagcccccatggaagct
	************************************************************************************************************************
rat	(((..((((((..(((((.((((.(((((.(((((((..(((((.((((((((((((....))..)))))))))).)))))..))))))).))))).)))).)))))..))))))..)))	1.000 -72.00

rat

chromosome:1:209384561:209384680:-1

intergenic ## {Repeats: trf 756 778 0 class=trf}

novel_lenNOK_cloningHIGH_shortStem (67 loci)

block31929 [novel_lenNOK_cloningHIGH_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	0.122	no	no	0.52/0.56	18/21/0.05	0.0	0.0	61	0	10	0	4	10	3arm	1	nd	0.22	1	105	10	na	na

		reads	miRBase family seed
seed	---------------------------------------------------GGCUCAG--------------	103	miR-24
seed	----------------------------------------------------GCUCAGC-------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--------------------------------------------------TGGCTCAGCCTGCACTTT----	18	10	6	4	5	7	3	16	34	11	3
	--------------------------------------------------TGGCTCAGCCTGCACTTTACA-	21	-	1	-	1	-	-	1	-	-	-
	---------------------------------------------------GGCTCAGCCTGCACTTTACA-	20	2	-	-	-	-	-	-	-	-	-
	--------------------------------------------------TGGCTCAGCCTGCACTTTA---	19	-	-	-	-	-	-	1	-	-	-
rat	tgttaggactggaggtagaatccataaccatttgtctccagacaactcagTGGCTCAGCCTGCACTTTacat
	************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000049846 ENSRNOG00000007019 Accn1
rat	(((.(((..((.((((.((..((((......(((((....)))))....)))).)).)))).))))).))).	0.450 -16.90

rat

chromosome:10:69874267:69874338:-1

Same_strand|Boundary_non-coding|ENSRNOT00000009348|ENSRNOG00000007019 ## Same_strand|Intronic_coding|ENSRNOT00000049846|ENSRNOG00000007019 ## ENSRNOG00000007019|protein_coding|Accn1|Amiloride-sensitive cation channel 1, neuronal (Amiloride-sensitive brain sodium channel) (Amiloride-sensitive brain sodium channel 2) (Amiloride-sensitive cation channel neuronal 1) (Acid-sensing ion channel 2) (Brain sodium channel 1) (BNaC1) (BNC1) (Ma [Source:UniProtKB/Swiss-Prot;Acc:Q62962]

block84978 [novel_lenNOK_cloningHIGH_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	0.029	no	no	0.79/0.84	18/19/0.00	0.0	0.0	28	0	10	0	3	29	3arm	1	nd	0.22	2	54	10	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------------------------------------CAGGGAG-------------	44	novel
seed	---------------------------------------------------------------------------------------CCAGGGA--------------	9	novel
seed	--------------------------------------------------------------------------------------CCCAGGG---------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	---------------------------------------------------------------------------------------CCAGGGAGGCCTGGCCCC---	18	1	15	1	1	3	3	4	8	5	2
	--------------------------------------------------------------------------------------CCCAGGGAGGCCTGGCCCC---	19	-	4	1	-	-	-	1	1	2	-
	-------------------------------------------------------------------------------------TCCCAGGGAGGCCTGGCCC----	19	-	1	-	-	-	-	-	-	-	-
	---------------------------------------------------------------------------------------CCAGGGAGGCCTGGCCCCT--	19	-	-	-	-	-	-	-	-	1	-
rat	gagatggcttgttttttcttctgcttgctgctactgtcctctggcactttcaaaattgttgatccattgccactttcaggacagttcCCAGGGAGGCCTGGCCCCtcc
	************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------	ENSRNOT00000009348 ENSRNOG00000007019 Accn1
	----------------------------------------------------------------------------------------------------------------------	ENSRNOT00000049846 ENSRNOG00000007019 Accn1
rat	(((..((((.((...........(((.(((..((((((((.(((((...((((.....)))).....))))).....))))))))...))).)))))..)))).))).	0.590 -31.10

rat

chromosome:10:69114220:69114327:1

Opposite_strand|Intronic_coding|ENSRNOT00000049846|ENSRNOG00000007019 ## ENSRNOG00000007019|protein_coding|Accn1|Amiloride-sensitive cation channel 1, neuronal (Amiloride-sensitive brain sodium channel) (Amiloride-sensitive brain sodium channel 2) (Amiloride-sensitive cation channel neuronal 1) (Acid-sensing ion channel 2) (Brain sodium channel 1) (BNaC1) (BNC1) (Ma [Source:UniProtKB/Swiss-Prot;Acc:Q62962]

block95883 [novel_lenNOK_cloningHIGH_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	0.198	no	no	0.61/0.67	18/21/0.01	0.0	0.0	89	0	4	0	3	23	5arm	3	nd	0.28	2	97	4	na	na

		reads	miRBase family seed
seed	----UGCUGUG------------------------------------------------------------------------------------	96	novel
seed	-----GCUGUGG-----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S2	T3S1	T3S2	T4S2
	---GTGCTGTGGGAAGCAGGC--------------------------------------------------------------------------	18	3	45	44	2
	---GTGCTGTGGGAAGCAGGCAGA-----------------------------------------------------------------------	21	-	1	-	-
	----TGCTGTGGGAAGCAGGCA-------------------------------------------------------------------------	18	-	-	-	1
	---GTGCTGTGGGAAGCAGGCA-------------------------------------------------------------------------	19	-	1	-	-
rat	gtgGTGCTGTGGGAAGCAGGCagactggttggttttgcatcagaaataatctccaaaaagaacacagaattcctgtgactcacatgaggcttatg
	***********************************************************************************************
	---------------------------------------------------------------------------------------------------------	ENSRNOT00000028084 ENSRNOG00000020684 Vat1
rat	((((.((((((((..(((((....((((((..(((((....(((.....))).)))))..))).)))....)))))..))))))....)))))).	0.980 -23.20

rat

chromosome:10:90487198:90487292:1

block161713 [novel_lenNOK_cloningHIGH_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	0.085	no	no	0.50/0.58	18/19/0.00	0.0	0.0	27	0	10	0	3	14	3arm	1	nd	0.28	3	58	10	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------UGCCCAC-------------	51	novel
seed	---------------------------------------------------------------GCCCACG------------	5	novel
seed	-----------------------------------------------------------GUGUGCC----------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-------------------------------------------------------------GTGCCCACGAAGCACAAA---	18	7	4	2	4	2	5	1	3	3	15
	-------------------------------------------------------------GTGCCCACGAAGCACAAAA--	19	-	-	-	-	1	-	1	1	-	2
	--------------------------------------------------------------TGCCCACGAAGCACAAAA--	18	-	-	-	-	-	2	-	1	-	2
	----------------------------------------------------------TGTGTGCCCACGAAGCACA-----	19	-	-	-	-	-	-	2	-	-	-
rat	tccttgatgctgctttcaaggactagttccttagtggcctttcatcttcctggggaattgtGTGCCCACGAAGCACAAAagg
	**********************************************************************************
rat	.((((..((.((((((...(((((((((((((((.((..........))))))))))))).)).))...)))))))).))))	0.460 -23.90

rat

chromosome:11:53998766:53998847:1

intergenic

block196061 [novel_lenNOK_cloningHIGH_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	0.300	no	no	0.33/0.39	18/21/0.00	0.0	0.0	134	0	10	0	1	18	5arm	1	nd	0.22	3	206	10	na	na

		reads	miRBase family seed
seed	--UAUCAGG----------------------------------------------------------------------------------------	206	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-TTATCAGGGCTCTTGAAA------------------------------------------------------------------------------	18	51	55	7	11	14	11	8	28	10	6
	-TTATCAGGGCTCTTGAAAT-----------------------------------------------------------------------------	19	-	2	1	-	-	1	-	-	-	-
	-TTATCAGGGCTCTTGAAATAT---------------------------------------------------------------------------	21	-	1	-	-	-	-	-	-	-	-
rat	tTTATCAGGGCTCTTGAAAtatattgctgagattttctccgaaattatttttaccagtctatgtttctcttcattttccccaaagtccatgttaaaa
	*************************************************************************************************
rat	((((.(((((((...(((((((((((.(((((.((((...))))....))))).))))..)))))))................))))).)).)))).	0.520 -12.31