Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_5varHIGH_randfoldOK (31 loci)

block1723137 [novel_lenNOK_5varHIGH_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	0.42/0.45	19/22/0.50	2.0	0.5	2	0	1	0	14	8	5arm	2	nd	0.26	2	2	1	na	na

		reads	miRBase family seed
seed	-------------------AAGCUUA-----------------------------------------------------------------------	1	novel
seed	---------------GGAUAAG---------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	--------------TGGATAAGCTTAGTGGGACTGT-------------------------------------------------------------	22	1
	------------------TAAGCTTAGTGGGACTGTA------------------------------------------------------------	19	1
rat	ggagggatctgggcTGGATAAGCTTAGTGGGACTGTAggaagacaccagtgctctaagaagttcccagaagtctgtaccacagtcctaggcccacca
	*************************************************************************************************
rat	((.(((.(((((((((.(((..(((..(((((((.(((..((.((....)))))))...))).)))).)))..)))....))).))))))))).)).	0.980 -35.70

rat

chromosome:5:25426836:25426932:-1

intergenic

block1820968 [novel_lenNOK_5varHIGH_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	0.42/0.45	19/22/0.50	2.0	0.5	2	0	1	0	14	8	5arm	2	nd	0.26	2	2	1	na	na

		reads	miRBase family seed
seed	-------------------AAGCUUA-----------------------------------------------------------------------	1	novel
seed	---------------GGAUAAG---------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	--------------TGGATAAGCTTAGTGGGACTGT-------------------------------------------------------------	22	1
	------------------TAAGCTTAGTGGGACTGTA------------------------------------------------------------	19	1
rat	ggagggatctgggcTGGATAAGCTTAGTGGGACTGTAggaagacaccagtgctctaagaagttcccagaagtctgtaccacagtcctaggcccacca
	*************************************************************************************************
rat	((.(((.(((((((((.(((..(((..(((((((.(((..((.((....)))))))...))).)))).)))..)))....))).))))))))).)).	0.980 -35.70

rat

chromosome:5:25626654:25626750:1

intergenic

novel_lenNOK_Multihit_5varHIGH (31 loci)

block201475 [novel_lenNOK_Multihit_5varHIGH]

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	0.104	no	no	0.42/0.42	19/24/0.50	2.5	0.0	2	0	2	0	11	20	5arm	11	nd	0.26	3	2	2	na	na

		reads	miRBase family seed
seed	-----------------GGAGAUC--------------------------------------------------------------------------------------------	1	novel
seed	------------GAUCAGG-------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2	T5S2
	-----------AGATCAGGAGATCATTGAGGTAGA---------------------------------------------------------------------------------	24	1	-
	----------------AGGAGATCATTGAGGTAGA---------------------------------------------------------------------------------	19	-	1
rat	gtctcacccctAGATCAGGAGATCATTGAGGTAGAgcctgacaccaaggaaaagctgaagcttctggactttggcagtctctctaacctccaggtcactcagcttacggttgggat
	********************************************************************************************************************
rat	((((((.((..((...((..((((...(((((((((...(((.((((((..((((....)))).....))))))..))).))))).))))..)))).))...))...)).))))))	0.630 -35.40

rat

chromosome:12:41041164:41041279:-1

intergenic

block473211 [novel_lenNOK_Multihit_5varHIGH]

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	0.332	no	no	0.60/0.60	20/25/0.50	2.5	0.0	2	0	2	0	20	3	3arm	13	nd	0.20	2	2	2	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------AUGCCGA-------------------------------------	1	novel
seed	-------------------------------------------------------------------------GAGAGCC--------------------------------	1	novel
		len	cloning frequencies
			T1S1	T4S2
	-------------------------------------------------------------------CATGCCGAGAGCCATCATCCAGCCA--------------------	25	-	1
	------------------------------------------------------------------------CGAGAGCCATCATCCAGCCA--------------------	20	1	-
rat	ggggagctgatgacctgactggaggagattagagctctgcggttaggaaagtggtgcagtcagagccCATGCCGAGAGCCATCATCCAGCCAttccgacggtctgtgcccct
	****************************************************************************************************************
rat	((((.((....((((.((.(((.((((((....(((((.((((.......((((.((.......))))))))))))))).))).)))..))).))....)))).)).)))).	0.950 -39.21

rat

chromosome:15:5418584:5418695:1

intergenic

block643514 [novel_lenNOK_Multihit_5varHIGH]

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	0.178	no	no	0.50/0.60	18/20/0.67	1.3	0.7	3	0	3	0	9	18	5arm	22	nd	0.30	3	3	3	na	na

		reads	miRBase family seed
seed	------------CUCCCAA-------------------------------------------------------------------------------------------------	2	miR-150
seed	----------CUCUCCC---------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T4S2	T5S2
	-----------TCTCCCAAGTCTTGGACCAA-------------------------------------------------------------------------------------	20	-	1	-
	---------CCTCTCCCAAGTCTTGGACC---------------------------------------------------------------------------------------	20	-	-	1
	-----------TCTCCCAAGTCTTGGACC---------------------------------------------------------------------------------------	18	1	-	-
rat	gccctggagCCTCTCCCAAGTCTTGGACCAAgtaaaattaaagctttttgggaaaaaataaaaagaagtagcttaacaatcagattgatctcaaggtctggaaaggcagtctggct
	********************************************************************************************************************
rat	(((..(((((((...(((..(((((((.(((.........(((((((((...............)))).)))))..........))).)).)))))..)))..))))..)))))).	0.480 -25.87

rat

chromosome:17:11313432:11313547:1

intergenic

block704445 [novel_lenNOK_Multihit_5varHIGH]

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	0.721	no	no	0.43/0.53	19/23/0.67	1.3	0.0	3	0	2	0	5	11	3arm	20	nd	0.21	1	3	2	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------------AUUCCUA--------------------	2	novel
seed	--------------------------------------------------------------------CUACUGG----------------	1	novel
		len	cloning frequencies
			T4S1	T5S1
	---------------------------------------------------------------AATTCCTACTGGGTTGGTGAAGA-----	23	-	2
	-------------------------------------------------------------------CCTACTGGGTTGGTGAAGA-----	19	1	-
rat	ggaagccttcagtctgctgctgaggagagagctgggagccattgtgagactttgaaggtcctgAATTCCTACTGGGTTGGTGAAGAttcca
	*******************************************************************************************
rat	((((..(((((.((....(((.((.((.(((..((((.((.(((........))).))))))...))))).)).))).))))))).)))).	0.580 -22.70

rat

chromosome:18:44778587:44778677:-1

intergenic

block843912 [novel_lenNOK_Multihit_5varHIGH]

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	0.409	no	no	0.54/0.58	19/24/0.50	1.8	0.0	6	0	2	0	8	21	3arm	27	nd	0.25	3	6	2	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------------CUCACAG-------------------	3	novel
seed	--------------------------------------------------------------------------------CCAUUCU------------------------	2	novel
seed	------------------------------------------------------------------------------------UCUCACA--------------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	------------------------------------------------------------------------------------TCTCACAGGACCTCCAGTG--------	19	-	3
	-------------------------------------------------------------------------------TCCATTCTCACAGGACCTCCAGTG--------	24	1	1
	-----------------------------------------------------------------------------------TTCTCACAGGACCTCCAGTG--------	20	-	1
rat	acttcagtttgttggagctctcctatcagaggacatttacatttgctgtacttccagtgtcacagctgttataagaaccTCCATTCTCACAGGACCTCCAGTGcgtcagta
	***************************************************************************************************************
rat	(((...((...((((((...((((...((((((..(((......(((((((.......)).)))))........)))..)))..)))...)))).)))))).))...))).	0.700 -22.14

rat

chromosome:1:50002069:50002179:-1

intergenic

block846714 [novel_lenNOK_Multihit_5varHIGH]

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	0.529	no	no	0.35/0.37	19/20/0.67	2.0	1.7	3	0	3	0	7	8	5arm	39	nd	0.15	2	3	3	na	na

		reads	miRBase family seed
seed	-----------GUGUUCA-------------------------------------------------------------------------	2	miR-124*
seed	--------GUUGUGU----------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2	T5S1	T5S2
	----------TGTGTTCACTTCTATTCCT--------------------------------------------------------------	19	1	-	-
	-------TGTTGTGTTCACTTCTATTC----------------------------------------------------------------	20	-	-	1
	----------TGTGTTCACTTCTATTCCTA-------------------------------------------------------------	20	-	1	-
rat	gcgtctaTGTTGTGTTCACTTCTATTCCTAtttagtcctagagggaaatcagcaagggtagagaatgggaccgtaactggacaaagctgct
	*******************************************************************************************
rat	(((.((.((((..(((.((((((((((((((((..(((.....))).........)))))).))))))))..)))))..)))).)).))).	0.960 -20.50

rat

chromosome:1:51404758:51404848:-1

intergenic

block961867 [novel_lenNOK_Multihit_5varHIGH]

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	0.828	no	no	0.35/0.37	19/20/0.67	2.0	1.7	3	0	3	0	18	8	5arm	39	nd	0.20	2	3	3	na	na

		reads	miRBase family seed
seed	----------------------GUGUUCA-------------------------------------------------------------------------	2	miR-124*
seed	-------------------GUUGUGU----------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2	T5S1	T5S2
	---------------------TGTGTTCACTTCTATTCCTA-------------------------------------------------------------	20	-	1	-
	------------------TGTTGTGTTCACTTCTATTC----------------------------------------------------------------	20	-	-	1
	---------------------TGTGTTCACTTCTATTCCT--------------------------------------------------------------	19	1	-	-
rat	aggagaacaatgtgtctgTGTTGTGTTCACTTCTATTCCTAtttagtcctagagggaaatcagcaagggtagagaatgggaccgtaactggacaaagctgct
	******************************************************************************************************
rat	((.((.......((((((.(((((((((..((((..((((......(((.....)))........))))...))))..)))).)))))))))))...)).))	0.930 -20.34

rat

chromosome:1:51064348:51064449:1

intergenic

block963945 [novel_lenNOK_Multihit_5varHIGH]

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	0.306	no	no	0.36/0.40	22/25/0.67	2.0	0.0	3	0	2	0	13	3	5arm	15	nd	0.27	3	3	2	na	na

		reads	miRBase family seed
seed	-----------------CUAUCAC-----------------------------------------------------------------------	2	novel
seed	--------------ACUCUAU--------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	----------------TCTATCACCAACTAGACTTTTG---------------------------------------------------------	22	1	1
	-------------CACTCTATCACCAACTAGACTTTTG---------------------------------------------------------	25	-	1
rat	gtctcaggacatcCACTCTATCACCAACTAGACTTTTGcagaacttctactggaacagggtcttcattgtggctggtcttacattgtctaaggcc
	***********************************************************************************************
	---------------------------------------------------------------------------------------------------------	ENSRNOT00000048246 ENSRNOG00000039174 RGD1563865_predicted
rat	((((..(((((........(((((((...((((((((.(((........))).))..))))))......))).)))).......))))).)))).	0.830 -20.36

rat

chromosome:1:52002441:52002535:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000059936|ENSRNOG00000039174 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000048246|ENSRNOG00000039174 ## ENSRNOG00000039174|protein_coding|RGD1563865_predicted|

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