Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_cloningOK_shortStem_bulgeHIGH (27 loci)

block1767092 [novel_lenNOK_cloningOK_shortStem_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	0.066	no	no	0.37/0.47	18/22/0.28	0.0 0.0 0.0	0.4 0.0 0.0	11 1 2	0 0 0	4 1 2	0 0 0	2 9 18	20 11 5	5arm 5arm 5arm	1 1 1	nd nd nd	0.37 0.27 0.26	3 4 4	18	5	na	na

		reads	miRBase family seed
seed	---AAACCCU--------------------------------------------------------------------------------------	15	novel
seed	-------------------CCAAAUG----------------------------------------------------------------------	2	novel
seed	----------UGAAUGG-------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T4S2	T5S1	T5S2
	--TAAACCCTTGAATGGCTCC---------------------------------------------------------------------------	19	-	1	1	7	1
	--TAAACCCTTGAATGGCTCCA--------------------------------------------------------------------------	20	-	-	-	4	-
	------------------TCCAAATGTTGTGACAAAG-----------------------------------------------------------	19	1	-	-	1	-
	---------TTGAATGGCTCCAAATGTTGTG-----------------------------------------------------------------	22	-	-	-	1	-
	--TAAACCCTTGAATGGCTC----------------------------------------------------------------------------	18	-	1	-	-	-
rat	ccTAAACCCTTGAATGGCTCCAaatgttgtgacaaagcccattagcaatcggtattttgtctgttgacataacagtccaagttgaaggggcaagga
	************************************************************************************************
rat	(((...(((((.(((((((....((((((.(((((((((.((.....)).)))..))))))...))))))...))))...))).)))))...))).	0.990 -25.10

rat

chromosome:5:114557970:114558065:-1

intergenic

novel_Multihit_randfoldOK_bulgeHIGH (26 loci)

block836034 [novel_Multihit_randfoldOK_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	0.002	no	no	0.60/0.60	20/20/1.00	0.0	0.0	1	0	1	0	35	1	5arm	13	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------CCUUUGG---------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	-----------------------------------ACCTTTGGGAGGACACTGCC---------------------------------------------------------	20	1
rat	gctgactcccaagttctatccccaatcactggctaACCTTTGGGAGGACACTGCCaccctctgaaatgtcctccccagctgtttaccttccctggggcaaaccattccagca
	****************************************************************************************************************
rat	((((........(((....(((((......((..(((..(((((((((((....((.....))...))))))))).))..)))..)).....)))))..))).....)))).	0.530 -30.22

rat

chromosome:1:33531367:33531478:-1

intergenic

block844032 [novel_Multihit_randfoldOK_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	0.002	no	no	0.61/0.61	23/23/1.00	0.0	0.0	1	0	1	0	19	14	3arm	34	nd	0.26	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------GCUCCCU----------------------------------	1	novel
		len	cloning frequencies
			T3S2
	------------------------------------------------------------------------TGCTCCCTGTGCTTCCTCTCTGC-------------------	23	1
rat	ggtcggtgtggtcaaagatgagaaggaagcaagttcagggaatgagagtgcatctgtcgccctttcctctccTGCTCCCTGTGCTTCCTCTCTGCttccttgtccagacaggcc
	******************************************************************************************************************
rat	((((.((.(((.(((.((.(((.((((((((....((((((..(((((.((.......))......)))))....)))))))))))))))))....)).))).))).)).))))	1.000 -45.40

rat

chromosome:1:50055587:50055700:-1

intergenic

block846782 [novel_Multihit_randfoldOK_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	0.002	no	no	0.61/0.61	23/23/1.00	0.0	0.0	1	0	1	0	19	14	3arm	34	nd	0.26	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------GCUCCCU----------------------------------	1	novel
		len	cloning frequencies
			T3S2
	------------------------------------------------------------------------TGCTCCCTGTGCTTCCTCTCTGC-------------------	23	1
rat	ggtcggtgtggtcaaagatgagaaggaagcaagttcagggaatgagagtgcatctgtcgccctttcctctccTGCTCCCTGTGCTTCCTCTCTGCttccttgtccagacaggcc
	******************************************************************************************************************
rat	((((.((.(((.(((.((.(((.((((((((....((((((..(((((.((.......))......)))))....)))))))))))))))))....)).))).))).)).))))	1.000 -45.40

rat

chromosome:1:51443807:51443920:-1

intergenic

block846897 [novel_Multihit_randfoldOK_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	0.002	no	no	0.61/0.61	23/23/1.00	0.0	0.0	1	0	1	0	19	14	3arm	34	nd	0.26	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------GCUCCCU----------------------------------	1	novel
		len	cloning frequencies
			T3S2
	------------------------------------------------------------------------TGCTCCCTGTGCTTCCTCTCTGC-------------------	23	1
rat	ggtcggtgtggtcaaagatgagaaggaagcaagttcagggaatgagagtgcatctgtcgccctttcctctccTGCTCCCTGTGCTTCCTCTCTGCttccttgtccagacaggcc
	******************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000059938 ENSRNOG00000039174 RGD1563865_predicted
rat	((((.((.(((.(((.((.(((.((((((((....((((((..(((((.((.......))......)))))....)))))))))))))))))....)).))).))).)).))))	1.000 -45.40

rat

chromosome:1:51566236:51566349:-1

Same_strand|Boundary_non-coding|ENSRNOT00000048246|ENSRNOG00000039174 ## Same_strand|Intronic_non-coding|ENSRNOT00000059938|ENSRNOG00000039174 ## ENSRNOG00000039174|protein_coding|RGD1563865_predicted|

block846961 [novel_Multihit_randfoldOK_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	0.002	no	no	0.61/0.61	23/23/1.00	0.0	0.0	1	0	1	0	19	14	3arm	34	nd	0.26	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------GCUCCCU----------------------------------	1	novel
		len	cloning frequencies
			T3S2
	------------------------------------------------------------------------TGCTCCCTGTGCTTCCTCTCTGC-------------------	23	1
rat	ggtcggtgtggtcaaagatgagaaggaagcaagttcagggaatgagagtgcatctgtcgccctttcctctccTGCTCCCTGTGCTTCCTCTCTGCttccttgtccagacaggcc
	******************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000059938 ENSRNOG00000039174 RGD1563865_predicted
rat	((((.((.(((.(((.((.(((.((((((((....((((((..(((((.((.......))......)))))....)))))))))))))))))....)).))).))).)).))))	1.000 -45.40

rat

chromosome:1:51623530:51623643:-1

Same_strand|Boundary_non-coding|ENSRNOT00000048246|ENSRNOG00000039174 ## Same_strand|Intronic_non-coding|ENSRNOT00000059938|ENSRNOG00000039174 ## ENSRNOG00000039174|protein_coding|RGD1563865_predicted|

block847123 [novel_Multihit_randfoldOK_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	0.007	no	no	0.61/0.61	23/23/1.00	0.0	0.0	1	0	1	0	19	6	3arm	34	nd	0.26	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------GCUCCCU----------------------------------	1	novel
		len	cloning frequencies
			T3S2
	------------------------------------------------------------------------TGCTCCCTGTGCTTCCTCTCTGC-------------------	23	1
rat	ggtcggtgtggtcaaagatgagaaggaagcaggttcagggaatgagagtgcatctgtcacccattcctctccTGCTCCCTGTGCTTCCTCTCTGCttccttgtccaggcaggcc
	******************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000059938 ENSRNOG00000039174 RGD1563865_predicted
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000048246 ENSRNOG00000039174 RGD1563865_predicted
rat	((((.((.(((.(((.((.(((.((((((((....((((((..(((((..................)))))....)))))))))))))))))....)).))).))).)).))))	1.000 -45.27

rat

chromosome:1:51896960:51897073:-1

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

block847993 [novel_Multihit_randfoldOK_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	0.002	no	no	0.61/0.61	23/23/1.00	0.0	0.0	1	0	1	0	19	9	3arm	34	nd	0.26	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------GCUCCCU----------------------------------	1	novel
		len	cloning frequencies
			T3S2
	------------------------------------------------------------------------TGCTCCCTGTGCTTCCTCTCTGC-------------------	23	1
rat	ggtcggtgtggtcaaagatgagaaggaagcaagttcagggaatgagagtgaatctgtcgccctttcctctccTGCTCCCTGTGCTTCCTCTCTGCttccttgtccagacaggcc
	******************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000059909 ENSRNOG00000030267 RGD1561185_predicted
rat	((((.((.(((.(((.((.(((.((((((((....((((((..(((((.(((...........))))))))....)))))))))))))))))....)).))).))).)).))))	1.000 -48.40

rat

chromosome:1:52681061:52681174:-1

Same_strand|Boundary_non-coding|ENSRNOT00000059908|ENSRNOG00000030267 ## Same_strand|Intronic_non-coding|ENSRNOT00000059909|ENSRNOG00000030267 ## ENSRNOG00000030267|protein_coding|RGD1561185_predicted|

block848188 [novel_Multihit_randfoldOK_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	0.002	no	no	0.61/0.61	23/23/1.00	0.0	0.0	1	0	1	0	19	14	3arm	34	nd	0.26	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------GCUCCCU----------------------------------	1	novel
		len	cloning frequencies
			T3S2
	------------------------------------------------------------------------TGCTCCCTGTGCTTCCTCTCTGC-------------------	23	1
rat	ggtcggtgtggtcaaagatgagaaggaagcaagttcagggaatgagagtgcatctgtcgccctttcctctccTGCTCCCTGTGCTTCCTCTCTGCttccttgtccagacaggcc
	******************************************************************************************************************
rat	((((.((.(((.(((.((.(((.((((((((....((((((..(((((.((.......))......)))))....)))))))))))))))))....)).))).))).)).))))	1.000 -45.40

rat

chromosome:1:52883740:52883853:-1

intergenic

block951930 [novel_Multihit_randfoldOK_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	0.002	no	no	0.60/0.60	20/20/1.00	0.0	0.0	1	0	1	0	35	1	5arm	13	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------CCUUUGG---------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	-----------------------------------ACCTTTGGGAGGACACTGCC---------------------------------------------------------	20	1
rat	gctgactcccaagttctatccccaatcactggctaACCTTTGGGAGGACACTGCCaccctctgaaatgtcctccccagctgtttaccttccttggggcaaaccactccagca
	****************************************************************************************************************
rat	((((........(((....((((((.....((..(((..(((((((((((....((.....))...))))))))).))..)))..))....))))))..))).....)))).	0.590 -31.32

rat

chromosome:1:32151796:32151907:1

intergenic

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