Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_Multihit_shortStem_5varHIGH_nonpairedHIGH_bulgeHIGH (14 loci)

block964106 [novel_lenNOK_Multihit_shortStem_5varHIGH_nonpairedHIGH_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	0.216	no	no	0.33/0.37	19/21/0.50	1.5	0.5	2	0	1	0	4	4	5arm	26	nd	0.43	4	2	1	na	na

		reads	miRBase family seed
seed	--------AGAAUUG---------------------------------------------------	1	novel
seed	-----AUUAGAA------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----TATTAGAATTGTCTCAGACTC-----------------------------------------	21	1
	-------TAGAATTGTCTCAGACTCA----------------------------------------	19	1
rat	aagtTATTAGAATTGTCTCAGACTCAattggagaagcaagatgatgttggggtggatgaaaaactt
	******************************************************************
	----------------------------------------------------------------------------	ENSRNOT00000048246 ENSRNOG00000039174 RGD1563865_predicted
rat	(((((.((....((..(((((..(((.(((......)))..)))..)))))..))...)).)))))	0.980 -9.60

rat

chromosome:1:52045046:52045111:1

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

block845197 [novel_lenNOK_Multihit_shortStem_5varHIGH_nonpairedHIGH_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	0.216	no	no	0.33/0.37	19/21/0.50	1.5	0.5	2	0	1	0	4	4	5arm	26	nd	0.43	4	2	1	na	na

		reads	miRBase family seed
seed	--------AGAAUUG---------------------------------------------------	1	novel
seed	-----AUUAGAA------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----TATTAGAATTGTCTCAGACTC-----------------------------------------	21	1
	-------TAGAATTGTCTCAGACTCA----------------------------------------	19	1
rat	aagtTATTAGAATTGTCTCAGACTCAattggagaagcaagatgatgttggggtggatgaaaaactt
	******************************************************************
rat	(((((.((....((..(((((..(((.(((......)))..)))..)))))..))...)).)))))	0.980 -9.60

rat

chromosome:1:50585966:50586031:-1

intergenic

block1674429 [novel_lenNOK_Multihit_shortStem_5varHIGH_nonpairedHIGH_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	0.146	no	no	0.56/0.68	19/25/0.50	2.2	1.3	6	0	3	0	1	6	3arm	54	nd	0.32	5	6	3	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------UGACAUG-------------------	3	novel
seed	-----------------------------------------------------------------CCGCCUG------------	1	novel
seed	------------------------------------------------------GAUCUGA-----------------------	1	novel
seed	--------------------------------------------------------UCUGACA---------------------	1	novel
		len	cloning frequencies
			T2S2	T4S1	T5S1
	---------------------------------------------------------CTGACATGCCGCCTGGAGAAACC----	23	2	-	-
	-----------------------------------------------------GGATCTGACATGCCGCCTGGAGAA-------	24	1	-	-
	----------------------------------------------------------------GCCGCCTGGAGAAACCTGC-	19	-	-	1
	---------------------------------------------------------CTGACATGCCGCCTGGAGAAACCTG--	25	1	-	-
	-------------------------------------------------------ATCTGACATGCCGCCTGGAGAAACC----	25	-	1	-
rat	ggcaagctcactggcatggccctccatgttcctaaccccaatgtatccattgtGGATCTGACATGCCGCCTGGAGAAACCTGCc
	************************************************************************************
	----------------------------------------------------------------------------------------------	ENSRNOT00000023122 ENSRNOG00000017115 NP_001100078.1
rat	((((..(((...(((..(((.....(((((.....((.(((((....))))).))....)))))))))))..))).....))))	0.810 -23.10

rat

chromosome:4:123558292:123558375:1

Opposite_strand|Intronic_coding|ENSRNOT00000023122|ENSRNOG00000017115 ## ENSRNOG00000017115|protein_coding|NP_001100078.1|coiled-coil-helix-coiled-coil-helix domain containing 6 [Source:RefSeq_peptide;Acc:NP_001100078]

novel_lenNOK_Multihit_shortStem_loopOverlap (14 loci)

block135164 [novel_lenNOK_Multihit_shortStem_loopOverlap]

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	0.062	no	no	0.39/0.42	18/19/0.00	1.0	1.5	2	0	2	0	3	-2	3arm	15	nd	0.16	2	2	2	na	na

		reads	miRBase family seed
seed	-------------------------------AACAAAA--------------	1	novel
seed	-----------------------------UCAACAA----------------	1	novel
		len	cloning frequencies
			T2S2	T3S2
	------------------------------CAACAAAATGGATTCCACC---	19	-	1
	----------------------------GTCAACAAAATGGATTCC------	18	1	-
rat	cttgagtgtgaaatagctaattgttggtGTCAACAAAATGGATTCCACCaag
	****************************************************
rat	((((.(((.(((....(((.((((((....))))))..))).))))))))))	1.000 -11.80

rat

chromosome:11:75633250:75633301:-1

intergenic

block143682 [novel_lenNOK_Multihit_shortStem_loopOverlap]

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	0.022	no	no	0.61/0.62	18/21/0.50	1.0	2.5	2	0	2	0	0	-2	3arm	28	nd	0.25	2	2	2	na	na

		reads	miRBase family seed
seed	----------------------------AGGCCCC---------------	1	novel
seed	------------------------------GCCCCAC-------------	1	novel
		len	cloning frequencies
			T1S1	T5S2
	---------------------------CAGGCCCCACCATTGAAG-----	18	-	1
	-----------------------------GGCCCCACCATTGAAGAGGTC	21	1	-
rat	gagctcctccatctggtggtgcttcttCAGGCCCCACCATTGAAGAGGTC
	**************************************************
rat	((.(((.((....((((((.(((......))).))))))..)).))).))	1.000 -18.70

rat

chromosome:11:5436422:5436471:1

intergenic

block473078 [novel_lenNOK_Multihit_shortStem_loopOverlap]

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	0.56/0.56	18/18/0.00	0.0	0.0	1	0	1	0	4	-1	3arm	12	nd	0.17	2	1	1	na	na

		reads	miRBase family seed
seed	------------------------------GGAGACU--------------	1	novel
		len	cloning frequencies
			T4S2
	-----------------------------TGGAGACTTCTGCAGAGG----	18	1
rat	cagcctttccagactctctgctactcaacTGGAGACTTCTGCAGAGGcctg
	***************************************************
rat	..((((((.((((.(((((...........)))))..)))).))))))...	1.000 -16.60

rat

chromosome:15:5250158:5250208:1

intergenic ## {Repeats: trf 41 46 0 class=trf}

block516788 [novel_lenNOK_Multihit_shortStem_loopOverlap]

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	0.022	no	no	0.61/0.62	18/21/0.50	1.0	2.5	2	0	2	0	0	-2	3arm	28	nd	0.25	2	2	2	na	na

		reads	miRBase family seed
seed	----------------------------AGGCCCC---------------	1	novel
seed	------------------------------GCCCCAC-------------	1	novel
		len	cloning frequencies
			T1S1	T5S2
	---------------------------CAGGCCCCACCATTGAAG-----	18	-	1
	-----------------------------GGCCCCACCATTGAAGAGGTC	21	1	-
rat	gagctcctccatctggtggtgcttcttCAGGCCCCACCATTGAAGAGGTC
	**************************************************
	------------------------------------------------------------	ENSRNOT00000017887 ENSRNOG00000013346 Bm259
	------------------------------------------------------------	ENSRNOT00000033008 ENSRNOG00000013346 Bm259
rat	((.(((.((....((((((.(((......))).))))))..)).))).))	1.000 -18.70

rat

chromosome:16:2126356:2126405:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000061783|ENSRNOG00000013346 ## Opposite_strand|Intronic_coding|ENSRNOT00000017887|ENSRNOG00000013346 ## ENSRNOG00000013346|protein_coding|Bm259|BM259 (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q923J6]

block706413 [novel_lenNOK_Multihit_shortStem_loopOverlap]

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	0.022	no	no	0.61/0.62	18/21/0.50	1.0	2.5	2	0	2	0	0	-2	3arm	28	nd	0.25	2	2	2	na	na

		reads	miRBase family seed
seed	----------------------------AGGCCCC---------------	1	novel
seed	------------------------------GCCCCAC-------------	1	novel
		len	cloning frequencies
			T1S1	T5S2
	---------------------------CAGGCCCCACCATTGAAG-----	18	-	1
	-----------------------------GGCCCCACCATTGAAGAGGTC	21	1	-
rat	gagctcctccatctggtggtgcttcttCAGGCCCCACCATTGAAGAGGTC
	**************************************************
rat	((.(((.((....((((((.(((......))).))))))..)).))).))	1.000 -18.70

rat

chromosome:18:49532869:49532918:-1

intergenic

block920374 [novel_lenNOK_Multihit_shortStem_loopOverlap]

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	0.703	no	no	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	3	-1	3arm	130	nd	0.17	1	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------GACAAGA-------------	1	novel
		len	cloning frequencies
			T1S1
	------------------------------------AGACAAGATGGTGAAGGT---	18	1
rat	gccacatcttctcatgcagtgccagcctcgtctcatAGACAAGATGGTGAAGGTcgc
	*********************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000050860 ENSRNOG00000029732 RGD1561881_predicted
rat	((...((((((.........((((..((.(((.....))).)).)))))))))).))	0.820 -11.20

rat

chromosome:1:222797700:222797756:-1

Same_strand|Intronic_coding|ENSRNOT00000050860|ENSRNOG00000029732 ## ENSRNOG00000029732|protein_coding|RGD1561881_predicted|

block1305828 [novel_lenNOK_Multihit_shortStem_loopOverlap]

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	0.030	no	no	0.61/0.62	18/21/0.50	1.0	2.5	2	0	2	0	0	-2	3arm	28	nd	0.25	2	2	2	na	na

		reads	miRBase family seed
seed	-------------------------------GCCCCAC-------------	1	novel
seed	-----------------------------AGGCCCC---------------	1	novel
		len	cloning frequencies
			T1S1	T5S2
	----------------------------CAGGCCCCACCATTGAAG-----	18	-	1
	------------------------------GGCCCCACCATTGAAGAGGTC	21	1	-
rat	ggagctcctccatctggtggtgcttcttCAGGCCCCACCATTGAAGAGGTC
	***************************************************
rat	.((.(((.((....((((((.(((......))).))))))..)).))).))	0.930 -18.70

rat

chromosome:2:170310734:170310784:1

intergenic

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