Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_Multihit_shortStem_5varHIGH_loopOverlap_nonpairedHIGH (17 loci)

block1641523 [novel_Multihit_shortStem_5varHIGH_loopOverlap_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	0.188	no	no	0.52/0.55	20/23/1.00	2.0	0.5	2	0	2	0	2	-2	3arm	29	nd	0.35	3	2	2	na	na

		reads	miRBase family seed
seed	----------------------------------------AGGAUGU--------------	1	novel
seed	------------------------------------CUUGAGG------------------	1	miR-327
		len	cloning frequencies
			T3S1	T4S1
	-----------------------------------CCTTGAGGATGTTCCCCAACTCT---	23	1	-
	---------------------------------------GAGGATGTTCCCCAACTCTG--	20	-	1
rat	ggcctagtcttagaaggcacatctcaaacctacctCCTTGAGGATGTTCCCCAACTCTGcc
	*************************************************************
	-----------------------------------------------------------------------	ENSRNOT00000051405 ENSRNOG00000032252 LOC681850
	-----------------------------------------------------------------------	ENSRNOT00000047545 ENSRNOG00000032252 LOC681850
	-----------------------------------------------------------------------	ENSRNOT00000040942 ENSRNOG00000032252 LOC681850
	-----------------------------------------------------------------------	ENSRNOT00000038063 ENSRNOG00000032252 LOC681850
rat	(((..(((.......((.(((((((((..........))))).)))).))...)))..)))	0.860 -11.70

rat

chromosome:4:57770568:57770628:1

Opposite_strand|Intronic_coding|ENSRNOT00000040942|ENSRNOG00000032252 ## ENSRNOG00000032252|protein_coding|LOC681850|LOC501224 protein. [Source:UniProtKB/TrEMBL;Acc:Q0P5Q7]

novel_lenNOK_Multihit_5varHIGH_bulgeHIGH (17 loci)

block844260 [novel_lenNOK_Multihit_5varHIGH_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	0.099	no	no	0.50/0.53	18/19/0.00	1.5	1.0	2	0	1	0	9	12	3arm	22	nd	0.21	4	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------CUCUGGU----------------------	1	novel
seed	-----------------------------------------------------------------------------------UGGUUUG-------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------------------------------------------------------------GCTCTGGTTTGTCTTGGGT-----------	19	1
	----------------------------------------------------------------------------------CTGGTTTGTCTTGGGTAC---------	18	1
rat	tttggaccatcataagtataacccaggaagagttcaggggcatcaaaagtgttagcaccgtagtataggttcagcatttGCTCTGGTTTGTCTTGGGTACtaaggccaa
	*************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------	ENSRNOT00000041575 ENSRNOG00000031160 LOC685793
rat	.((((.((......(((...((((((((.....(((.(((((.....((((((...(((........)))..))))))))))))))....)))))))))))..))))))	0.880 -29.10

rat

chromosome:1:50174526:50174634:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000049496|ENSRNOG00000031160 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000041575|ENSRNOG00000031160 ## ENSRNOG00000031160|protein_coding|LOC685793|

block844788 [novel_lenNOK_Multihit_5varHIGH_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	0.078	no	no	0.50/0.53	18/19/0.00	1.5	1.0	2	0	1	0	9	14	3arm	22	nd	0.21	4	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------CUCUGGU----------------------	1	novel
seed	-----------------------------------------------------------------------------------UGGUUUG-------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------------------------------------------------------------GCTCTGGTTTGTCTTGGGT-----------	19	1
	----------------------------------------------------------------------------------CTGGTTTGTCTTGGGTAC---------	18	1
rat	tttggaccatcgtaagtataacccaggaagagttcaggggcatcaaaagtgttagcactgtagtacaggttcagcatttGCTCTGGTTTGTCTTGGGTACtaaggccaa
	*************************************************************************************************************
rat	.((((.((......(((...((((((((.....(((.(((((.....(((((((((.(((.....)))))).))))))))))))))....)))))))))))..))))))	0.900 -31.30

rat

chromosome:1:50350403:50350511:-1

intergenic

block845505 [novel_lenNOK_Multihit_5varHIGH_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	0.058	no	no	0.50/0.53	18/19/0.00	1.5	1.0	2	0	1	0	9	14	3arm	22	nd	0.21	4	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------CUCUGGU----------------------	1	novel
seed	-----------------------------------------------------------------------------------UGGUUUG-------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------------------------------------------------------------GCTCTGGTTTGTCTTGGGT-----------	19	1
	----------------------------------------------------------------------------------CTGGTTTGTCTTGGGTAC---------	18	1
rat	tttggaccatcataagtataacccaggaagagttcaggggcatcaaaagtgttagcactgtagtacaggttcagcatttGCTCTGGTTTGTCTTGGGTACtaaggccaa
	*************************************************************************************************************
rat	.((((.((......(((...((((((((.....(((.(((((.....(((((((((.(((.....)))))).))))))))))))))....)))))))))))..))))))	0.880 -31.30

rat

chromosome:1:50779406:50779514:-1

intergenic

block847557 [novel_lenNOK_Multihit_5varHIGH_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	0.058	no	no	0.50/0.53	18/19/0.00	1.5	1.0	2	0	1	0	9	14	3arm	22	nd	0.21	4	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------CUCUGGU----------------------	1	novel
seed	-----------------------------------------------------------------------------------UGGUUUG-------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------------------------------------------------------------GCTCTGGTTTGTCTTGGGT-----------	19	1
	----------------------------------------------------------------------------------CTGGTTTGTCTTGGGTAC---------	18	1
rat	tttggaccatcataagtataacccaggaagagttcaggggcatcaaaagtgttagcactgtagtacaggttcagcatttGCTCTGGTTTGTCTTGGGTACtaaggccaa
	*************************************************************************************************************
rat	.((((.((......(((...((((((((.....(((.(((((.....(((((((((.(((.....)))))).))))))))))))))....)))))))))))..))))))	0.880 -31.30

rat

chromosome:1:52389611:52389719:-1

intergenic

block961717 [novel_lenNOK_Multihit_5varHIGH_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	0.038	no	no	0.50/0.53	18/19/0.00	1.5	1.0	2	0	1	0	12	14	3arm	22	nd	0.26	4	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------CUCUGGU-------------------------	1	novel
seed	-----------------------------------------------------------------------------UGGUUUG----------------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------------------------------------------------------------CTGGTTTGTCTTGGGTAC------------	18	1
	-------------------------------------------------------------------------GCTCTGGTTTGTCTTGGGT--------------	19	1
rat	aacattataagtataacccaggaagagttcaggggcatcaaaatgttagcaccgtagtacgggttcagcatttGCTCTGGTTTGTCTTGGGTACtaaggccaatgt
	**********************************************************************************************************
rat	.(((((.........((((((((.....(((.(((((....(((((((((.(((.....)))))).))))))))))))))....)))))))).........)))))	0.990 -30.77

rat

chromosome:1:51029214:51029319:1

intergenic

block962852 [novel_lenNOK_Multihit_5varHIGH_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	0.106	no	no	0.50/0.53	18/19/0.00	1.5	1.0	2	0	1	0	9	12	3arm	22	nd	0.21	4	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------CUCUGGU----------------------	1	novel
seed	-----------------------------------------------------------------------------------UGGUUUG-------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------------------------------------------------------------GCTCTGGTTTGTCTTGGGT-----------	19	1
	----------------------------------------------------------------------------------CTGGTTTGTCTTGGGTAC---------	18	1
rat	tttggaccatcataagtataacccaggaagagttcaggggcatcaaaagtgttagcaccatagtacaggttcagcatttGCTCTGGTTTGTCTTGGGTACtaaggccaa
	*************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------	ENSRNOT00000059938 ENSRNOG00000039174 RGD1563865_predicted
rat	.((((.((......(((...((((((((.....(((.(((((.....((((((...(((........)))..))))))))))))))....)))))))))))..))))))	0.870 -28.40

rat

chromosome:1:51544378:51544486:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000059936|ENSRNOG00000039174 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000059938|ENSRNOG00000039174 ## ENSRNOG00000039174|protein_coding|RGD1563865_predicted|

block963345 [novel_lenNOK_Multihit_5varHIGH_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	0.058	no	no	0.50/0.53	18/19/0.00	1.5	1.0	2	0	1	0	9	14	3arm	22	nd	0.21	4	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------CUCUGGU----------------------	1	novel
seed	-----------------------------------------------------------------------------------UGGUUUG-------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------------------------------------------------------------GCTCTGGTTTGTCTTGGGT-----------	19	1
	----------------------------------------------------------------------------------CTGGTTTGTCTTGGGTAC---------	18	1
rat	tttggaccatcataagtataacccaggaagagttcaggggcatcaaaagtgttagcactgtagtacaggttcagcatttGCTCTGGTTTGTCTTGGGTACtaaggccaa
	*************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------	ENSRNOT00000059938 ENSRNOG00000039174 RGD1563865_predicted
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000040973 ENSRNOG00000033340 RGD1561446_predicted
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000046337 ENSRNOG00000033340 RGD1561446_predicted
rat	.((((.((......(((...((((((((.....(((.(((((.....(((((((((.(((.....)))))).))))))))))))))....)))))))))))..))))))	0.880 -31.30

rat

chromosome:1:51657272:51657380:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000059936|ENSRNOG00000039174 ## Same_strand|Boundary_non-coding|ENSRNOT00000048434|ENSRNOG00000033340 ## Same_strand|Intronic_non-coding|ENSRNOT00000046337|ENSRNOG00000033340 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000059938|ENSRNOG00000039174 ## ENSRNOG00000039174|protein_coding|RGD1563865_predicted| ## ENSRNOG00000033340|protein_coding|RGD1561446_predicted|

block963997 [novel_lenNOK_Multihit_5varHIGH_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	0.399	no	no	0.50/0.53	18/19/0.00	1.5	1.0	2	0	1	0	17	14	3arm	22	nd	0.26	4	2	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------CUCUGGU------------------------------	1	novel
seed	----------------------------------------------------------------------------UGGUUUG---------------------------	1	novel
		len	cloning frequencies
			T5S1
	------------------------------------------------------------------------GCTCTGGTTTGTCTTGGGT-------------------	19	1
	---------------------------------------------------------------------------CTGGTTTGTCTTGGGTAC-----------------	18	1
rat	catcataagtataacccaggaagagttcaggggcatcaaaagggttagcactgtagtacaggttcagcatttGCTCTGGTTTGTCTTGGGTACtaagccaatgtcgatga
	**************************************************************************************************************
	------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000048246 ENSRNOG00000039174 RGD1563865_predicted
rat	(((((((.((.((((((((((.....((((((....((((...((((((.(((.....)))))).))).))))))))))....))))))))..)).))...))).)))).	0.840 -26.80

rat

chromosome:1:52005678:52005787:1

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

block964450 [novel_lenNOK_Multihit_5varHIGH_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	0.393	no	no	0.50/0.53	18/19/0.00	1.5	1.0	2	0	1	0	9	14	3arm	22	nd	0.26	4	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------CUCUGGU----------------------	1	novel
seed	-----------------------------------------------------------------------------------UGGUUUG-------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------------------------------------------------------------GCTCTGGTTTGTCTTGGGT-----------	19	1
	----------------------------------------------------------------------------------CTGGTTTGTCTTGGGTAC---------	18	1
rat	tttggaccatcatatgtataacacaggaagagttcaggggcatcaaaagtgttagtactgtaatacaggttcagcatttGCTCTGGTTTGTCTTGGGTACtaaggccaa
	*************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------	ENSRNOT00000048246 ENSRNOG00000039174 RGD1563865_predicted
rat	.((((.((.......((((....(((((.....(((.(((((.....((((((....(((.....)))....))))))))))))))....))))).))))...))))))	0.950 -24.70

rat

chromosome:1:52238578:52238686:1

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

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