Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_nonpairedHIGH (36989 loci)

block2189857 [novel_lenNOK_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	0.039	no	no	0.42/0.42	19/19/0.00	0.0	0.0	2	0	1	0	25	14	3arm	9	nd	0.37	3	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------AUGGCAU------------------------------------	2	novel
		len	cloning frequencies
			T5S1
	----------------------------------------------------------------------------TATGGCATGATCCAGTAGT-------------------------	19	2
rat	gagaataaattgtggggatagaaaatgtatggtcatggacaaagtctttgtgaaggccttcagcctaccccacattTATGGCATGATCCAGTAGTattaagtatgtctccattattttct
	************************************************************************************************************************
rat	(((((((....(((((((((......((((.....((((((..(((..((((.((((.....))))....)))).....))).)).))))...))))......)))))))))))))))).	0.670 -31.40

rat

chromosome:7:18365886:18366005:1

intergenic

block2216934 [novel_lenNOK_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	0.340	no	no	0.47/0.47	19/19/0.00	0.0	0.0	1	0	1	0	7	25	3arm	2	nd	0.32	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------------AAUGAAG------------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------------------------------------------------------------------------------AAATGAAGGGTTTGTGGGG-------	19	1
rat	gcccggagacattttcagtaactttttaagttggccttaaatactataattactaaatatcccaagtgctttggatatacagagtgttgttctaAAATGAAGGGTTTGTGGGGgtggggg
	************************************************************************************************************************
rat	.(((.....((((..((..(((((((((..((((.....((((((.......((..((((((.((....)).))))))..))))))))...))))..)))))))))..))..))))))).	0.830 -27.01

rat

chromosome:7:59678978:59679097:1

intergenic

block2188761 [novel_lenNOK_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	0.012	no	no	0.42/0.42	19/19/0.00	0.0	0.0	2	0	1	0	25	14	3arm	9	nd	0.37	3	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------AUGGCAU------------------------------------	2	novel
		len	cloning frequencies
			T5S1
	-------------------------------------------------------------------------TATGGCATGATCCAGTAGT-------------------------	19	2
rat	aagaaattgtggggatagaaaatgtatggtcatggaccaagtctttgtgaaggccttcagcctagcccacattTATGGCATGATCCAGTAGTattaagtatgtctccattattttct
	*********************************************************************************************************************
rat	.(((((..(((((((((......((((.....((((.((.(((..((((.((((.....))))....)))).....))).)).))))...))))......)))))))))...)))))	0.970 -33.60

rat

chromosome:7:17175957:17176073:1

intergenic

block2190444 [novel_lenNOK_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	0.012	no	no	0.42/0.42	19/19/0.00	0.0	0.0	2	0	1	0	25	14	3arm	9	nd	0.37	3	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------AUGGCAU------------------------------------	2	novel
		len	cloning frequencies
			T5S1
	-------------------------------------------------------------------------TATGGCATGATCCAGTAGT-------------------------	19	2
rat	aagaaattgtggggatagaaaatgtatggtcatggaccaagtctttgtgaaggccttcagcctagcccacattTATGGCATGATCCAGTAGTattaagtatgtctccattattttct
	*********************************************************************************************************************
rat	.(((((..(((((((((......((((.....((((.((.(((..((((.((((.....))))....)))).....))).)).))))...))))......)))))))))...)))))	0.970 -33.60

rat

chromosome:7:18837618:18837734:1

intergenic

novel_lenNOK_shortStem (20559 loci)

block97 [novel_lenNOK_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	0.252	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	0	39	3arm	1	nd	0.29	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------------------UCAACCC----------	1	novel
		len	cloning frequencies
			T4S1
	----------------------------------------------------------------------------------------------------TTCAACCCCGTTTGCCTT	18	1
rat	aaggaccatgcgatggtgaggggctctctattgctacactctgtacaggctgggcccacctgccacacccatgccccctgatagcagtcatgggcttgccTTCAACCCCGTTTGCCTT
	**********************************************************************************************************************
rat	((((.....(((..((((((((((((...(((((((((....(((..((.(((((......))).))))..)))....)).)))))))...))))...)))))).)).)))...))))	0.730 -35.90

rat

chromosome:10:186512:186629:-1

intergenic

block122 [novel_lenNOK_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	0.389	no	no	0.28/0.32	18/19/0.00	0.0	0.2	6	0	3	0	2	12	5arm	2	nd	0.22	2	6	3	na	na

		reads	miRBase family seed
seed	---CUUUGGU------------------------------------------------------------------	6	miR-9
		len	cloning frequencies
			T1S1	T1S2	T2S2
	--TCTTTGGTTAAAGCTATTG-------------------------------------------------------	19	3	1	1
	--TCTTTGGTTAAAGCTATT--------------------------------------------------------	18	-	1	-
rat	ttTCTTTGGTTAAAGCTATTGtaaaatgtttgaaacttgtttgacagcttcccacctagctgtagcctctctggga
	****************************************************************************
rat	.((((..(((((.(((((.((..((.((((.((......)).))))..))..))..))))).))))).....))))	0.940 -13.40

rat

chromosome:10:254782:254857:-1

intergenic

block304 [novel_lenNOK_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	0.517	no	no	0.28/0.32	18/19/0.00	0.0	0.2	6	0	3	0	2	14	5arm	2	11	0.26	2	6	3	na	na

		reads	miRBase family seed
seed	---CUUUGGU------------------------------------------------------------------	6	miR-9
		len	cloning frequencies
			T1S1	T1S2	T2S2
	--TCTTTGGTTAAAGCTATTG-------------------------------------------------------	19	3	1	1
	--TCTTTGGTTAAAGCTATT--------------------------------------------------------	18	-	1	-
rat	ttTCTTTGGTTAAAGCTATTGtaaaatgtttgaaacttgtttgaaagcttcccacctagctgtagcctctctggga
	****************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000061841 ENSRNOG00000032748 LOC688339
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000061840 ENSRNOG00000032748 LOC688339
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000061838 ENSRNOG00000032748 LOC688339
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000061835 ENSRNOG00000032748 LOC688339
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000061834 ENSRNOG00000032748 LOC688339
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000044108 ENSRNOG00000032748 LOC688339
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000046607 ENSRNOG00000032748 LOC688339
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000061831 ENSRNOG00000032748 LOC688339
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000041358 ENSRNOG00000032748 LOC688339
	++++++++++++++>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000061830 ENSRNOG00000032748 LOC688339
rat	.((((..(((((.(((((..((.....((((.(((....)))..)))).....)).))))).))))).....))))	0.940 -12.60

rat

chromosome:10:477163:477238:-1

Same_strand|Intronic_coding|ENSRNOT00000061841|ENSRNOG00000032748 ## Same_strand|Boundary_coding|ENSRNOT00000061830|ENSRNOG00000032748 ## ENSRNOG00000032748|protein_coding|LOC688339|Multidrug resistance-associated protein 1 (ATP-binding cassette sub- family C member 1) (Leukotriene C(4) transporter) (LTC4 transporter). [Source:UniProtKB/Swiss-Prot;Acc:Q8CG09]

block318 [novel_lenNOK_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	0.053	no	no	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	2	15	3arm	2	nd	0.22	2	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------GUUUUGU------------	1	novel
		len	cloning frequencies
			T2S1
	------------------------------------------------------------TGTTTTGTGGTTGTGGTG--	18	1
rat	tcattgtgattcaggtttatgaaacaagtctgcttgaaaacttgtggagtcatgctggttTGTTTTGTGGTTGTGGTGga
	********************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000061841 ENSRNOG00000032748 LOC688339
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000061840 ENSRNOG00000032748 LOC688339
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000061838 ENSRNOG00000032748 LOC688339
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000061834 ENSRNOG00000032748 LOC688339
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000044108 ENSRNOG00000032748 LOC688339
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000046607 ENSRNOG00000032748 LOC688339
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000061831 ENSRNOG00000032748 LOC688339
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000041358 ENSRNOG00000032748 LOC688339
rat	((((..((((.......((..(((((((((.((.(((...((...))..))).)).)))))))))..))))))..)))).	0.980 -16.31

rat

chromosome:10:511019:511098:-1

Same_strand|Boundary_non-coding|ENSRNOT00000061835|ENSRNOG00000032748 ## Same_strand|Intronic_coding|ENSRNOT00000061841|ENSRNOG00000032748 ## ENSRNOG00000032748|protein_coding|LOC688339|Multidrug resistance-associated protein 1 (ATP-binding cassette sub- family C member 1) (Leukotriene C(4) transporter) (LTC4 transporter). [Source:UniProtKB/Swiss-Prot;Acc:Q8CG09]

block519 [novel_lenNOK_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	0.082	no	no	0.21/0.21	19/19/0.00	0.0	0.0	1	0	1	0	3	2	5arm	1	nd	0.21	3	1	1	na	na

		reads	miRBase family seed
seed	----UUUUUGG--------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	---TTTTTTGGTTTGTTTACAA---------------------------------------------	19	1
rat	gatTTTTTTGGTTTGTTTACAAtgaaagagcatattataaccaaacatggaacaattaaggaagtca
	*******************************************************************
	-----------------------------------------------------------------------------	ENSRNOT00000003193 ENSRNOG00000002314 Lkap
rat	(((((((((((.((((((...(((.....................))).))))))))))))))))).	0.410 -11.90

rat

chromosome:10:829585:829651:-1

Opposite_strand|Intronic_non-coding|ENSRNOT00000003193|ENSRNOG00000002314 ## ENSRNOG00000002314|protein_coding|Lkap|Limkain-b1. [Source:UniProtKB/Swiss-Prot;Acc:Q8VIG2]

block590 [novel_lenNOK_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	0.079	no	no	0.61/0.61	18/18/0.00	0.0	0.0	1	0	1	0	4	34	5arm	2	nd	0.22	2	1	1	na	na

		reads	miRBase family seed
seed	-----GGGGUGG----------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	----TGGGGTGGGGTTGTTGGT------------------------------------------------------------------------------------------	18	1
rat	ttgtTGGGGTGGGGTTGTTGGTatgaatgatccaactgctgagatgattttacataatttcctgtgtgagattctggaaggacataatactcaaataaactggcaaacaaca
	****************************************************************************************************************
rat	.(((((..((.((.((((((((((..(((.(((..((....(((..((((((((((......)))))))))))))))..)))))).)))))..))))).)).))...)))))	0.840 -27.50

rat

chromosome:10:1025024:1025135:-1

intergenic

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