Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_shortStem_loopOverlap_nonpairedHIGH (633 loci)

block2988580 [novel_lenNOK_shortStem_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	0.125	no	no	0.63/0.63	19/19/0.00	0.0	0.0	1	0	1	0	1	-4	3arm_loop	1	nd	0.42	3	1	1	na	na

		reads	miRBase family seed
seed	------------------GGGGGUU------------	1	novel
		len	cloning frequencies
			T1S1
	-----------------TGGGGGTTGGACACACACC-	19	1
rat	tgggatggttaaaaatcTGGGGGTTGGACACACACCa
	*************************************
rat	.((..(((((...((((....)))).))).))..)).	0.990 -8.30

rat

chromosome:X:64360847:64360883:1

intergenic

block3064645 [novel_lenNOK_shortStem_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	0.015	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	0	-2	5arm_loop	1	nd	0.39	3	1	1	na	na

		reads	miRBase family seed
seed	-GCUCUCC---------------------------------	1	novel
		len	cloning frequencies
			T2S2
	TGCTCTCCAGGTATGGAA-----------------------	18	1
rat	TGCTCTCCAGGTATGGAAgaaatgctagaaacatgagagca
	*****************************************
rat	.((((((...((.(((........)))...))..)))))).	0.990 -10.90

rat

chromosome:X:120510023:120510063:1

intergenic

block3167719 [novel_lenNOK_shortStem_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	0.052	no	no	0.72/0.72	18/18/0.00	0.0	0.0	1	0	1	0	2	-3	3arm_loop	1	nd	0.39	3	1	1	na	na

		reads	miRBase family seed
seed	----------------------CCGCCUC------------	1	novel
		len	cloning frequencies
			T2S1
	---------------------GCCGCCTCTCACCCCTCA--	18	1
rat	ctgaaggttaggctaatcactGCCGCCTCTCACCCCTCAga
	*****************************************
rat	((((.(((.((((...........))))...)))..)))).	1.000 -10.20

rat

chromosome:X:152968475:152968515:1

intergenic

block924076 [novel_lenNOK_shortStem_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	0.376	no	no	0.56/0.56	18/18/0.00	0.0	0.0	1	0	1	0	2	-2	5arm_loop	1	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	---UGGGAAG---------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	--CTGGGAAGTGCAGGTGAA-----------------------------	18	1
rat	agCTGGGAAGTGCAGGTGAAggacacagtgatggcgtcatttcagagct
	*************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000020464 ENSRNOG00000015137 RGD1310039
rat	((((..((((((((.(((.....))).....))....))))))..))))	0.500 -9.90

rat

chromosome:1:232598434:232598482:-1

Same_strand|Intronic_coding|ENSRNOT00000020464|ENSRNOG00000015137 ## ENSRNOG00000015137|protein_coding|RGD1310039|Uncharacterized protein C9orf68 homolog. [Source:UniProtKB/Swiss-Prot;Acc:Q6AYJ3]

block2644716 [novel_lenNOK_shortStem_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	0.068	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	4	-2	5arm_loop	2	nd	0.37	3	1	1	na	na

		reads	miRBase family seed
seed	-----AGCCCAG--------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	----GAGCCCAGTGTGTACTTAG---------------------------	19	1
rat	agccGAGCCCAGTGTGTACTTAGttaagtttgaagatattgtgacttggc
	**************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000047326 ENSRNOG00000037286 LOC367336
rat	.((((((..((((((..((((....))))......))))))...))))))	1.000 -11.00

rat

chromosome:9:105243436:105243485:1

Same_strand|Intronic_coding|ENSRNOT00000047326|ENSRNOG00000037286 ## ENSRNOG00000037286|protein_coding|LOC367336|

block1093313 [novel_lenNOK_shortStem_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	0.057	no	no	0.50/0.58	19/24/0.17	0.0	0.8	6	0	3	0	4	-6	5arm_loop	1	nd	0.42	3	6	3	na	na

		reads	miRBase family seed
seed	-----GCACUUG---------------------------------------------------	6	novel
		len	cloning frequencies
			T1S1	T2S2	T5S1
	----TGCACTTGCAGCAGCACAC----------------------------------------	19	1	1	3
	----TGCACTTGCAGCAGCACACGAATA-----------------------------------	24	1	-	-
rat	tcagTGCACTTGCAGCAGCACACGAATAaacagaaggaacttggttgctgagagggggctggg
	***************************************************************
rat	(((((...((..(((((((.((...................)))))))))..))...))))).	0.990 -16.71

rat

chromosome:20:5525364:5525426:1

intergenic

block1370706 [novel_lenNOK_shortStem_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	0.139	no	no	0.28/0.28	18/18/0.00	0.0	0.0	1	0	1	0	3	-1	5arm_loop	2	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	----CAGUACA------------------------------------	1	novel
		len	cloning frequencies
			T4S1
	---TCAGTACATTTTAAAGCT--------------------------	18	1
rat	ctgTCAGTACATTTTAAAGCTctgttgcttttaagaaggcttttagt
	***********************************************
rat	(((..(((...(((((((((......))))).))))..)))..))).	1.000 -8.20

rat

chromosome:3:50137934:50137980:-1

intergenic

novel_Multihit_nonpairedHIGH_bulgeHIGH (626 loci)

block46864 [novel_Multihit_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	0.210	no	no	0.36/0.36	22/22/1.00	0.0	0.0	1	0	1	0	11	6	5arm	153	nd	0.36	4	1	1	na	na

		reads	miRBase family seed
seed	------------UGCUCUC----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	-----------TTGCTCTCAATGACAACTTTGT--------------------------------------------------------------------	22	1
rat	tggggctgccaTTGCTCTCAATGACAACTTTGTaaagctcatttcctggtatgacaatgaatatggttactgcaacagggtggtggcctacatggcctcca
	*****************************************************************************************************
	---------------------------------------------------------------------------------------------------------------	ENSRNOT00000037067 ENSRNOG00000024557 NP_001099319.1
rat	.(((((((((((..((((((.((((....((((...(((........)))...))))........)))).))....))))..)))))......)))).)).	0.490 -27.30

rat

chromosome:10:98020711:98020811:-1

Opposite_strand|Intronic_coding|ENSRNOT00000037067|ENSRNOG00000024557 ## ENSRNOG00000024557|protein_coding|NP_001099319.1|

block139531 [novel_Multihit_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	0.457	no	no	0.43/0.45	21/22/1.00	0.5	1.0	2	0	2	0	7	7	3arm	23	nd	0.33	4	2	2	na	na

		reads	miRBase family seed
seed	----------------------------------------------GGACAUC----------------------	1	novel
seed	-----------------------------------------------GACAUCA---------------------	1	novel
		len	cloning frequencies
			T2S2	T4S1
	----------------------------------------------GGACATCAGTGAGAACAAGAGA-------	22	-	1
	---------------------------------------------AGGACATCAGTGAGAACAAGA---------	21	1	-
rat	gaatgatcatcaatttcattgttgagtttaagtgaaagcacaagaAGGACATCAGTGAGAACAAGAGAgctgtct
	***************************************************************************
rat	((....((.((..((((((((.((..(((..(((....)))...)))..)).))))))))....))))....)).	0.760 -11.30

rat

chromosome:11:83514030:83514104:-1

intergenic

block139532 [novel_Multihit_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	0.050	no	no	0.43/0.43	23/23/1.00	0.0	0.0	1	0	1	0	6	1	5arm	22	nd	0.35	4	1	1	na	na

		reads	miRBase family seed
seed	-------CACUUUU-----------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	------GCACTTTTGATGTGTCAATCCTC--------------------------------	23	1
rat	gaggtgGCACTTTTGATGTGTCAATCCTCactattgaggatggaatttttgaagtcaaatc
	*************************************************************
rat	((..((((...(((((....((.(((((((....))))))).))....)))))))))..))	0.470 -15.10

rat

chromosome:11:83514149:83514209:-1

intergenic

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