Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_Multihit_5varHIGH_nonpairedHIGH (32 loci)

block730606 [novel_lenNOK_Multihit_5varHIGH_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	0.659	no	no	0.53/0.55	19/22/0.50	2.0	0.5	2	0	2	0	14	19	5arm	13	nd	0.36	3	2	2	na	na

		reads	miRBase family seed
seed	---------------GCUGGCC---------------------------------------------------------------------------------------------	1	novel
seed	-------------------GCCUCAA-----------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S1
	--------------TGCTGGCCTCAACGTACTTCGA-------------------------------------------------------------------------------	22	-	1
	------------------GGCCTCAACGTACTTCGAA------------------------------------------------------------------------------	19	1	-
rat	gatgctggaactatTGCTGGCCTCAACGTACTTCGAAttatcaatgagccacctgctgctgctattgcctatggcttagataagaaggtcggggctgaaaggaatgtgctcattt
	*******************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000041961 ENSRNOG00000027230 Q5D003_RAT
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000036240 ENSRNOG00000027230 Q5D003_RAT
rat	((((..((.((.(((.((((((((.((...((((...(((((..(((((((...((..........))...)))))))))))))))))).))))))...)).))))).)))))).	0.670 -27.00

rat

chromosome:18:16733628:16733742:1

Same_strand|Intronic_coding|ENSRNOT00000036240|ENSRNOG00000027230 ## ENSRNOG00000027230|protein_coding|Q5D003_RAT|Putative uncharacterized protein (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q5D003]

block1280542 [novel_lenNOK_Multihit_5varHIGH_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	0.050	no	no	0.53/0.55	19/22/0.50	2.0	0.5	2	0	2	0	8	19	5arm	13	nd	0.36	3	2	2	na	na

		reads	miRBase family seed
seed	---------GCUGGCC----------------------------------------------------------------------------------------	1	novel
seed	-------------GCCUCAA------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S1
	------------GGCCTCAACGTACTTCGAA-------------------------------------------------------------------------	19	1	-
	--------TGCTGGCCTCAACGTACTTCGA--------------------------------------------------------------------------	22	-	1
rat	ggcactatTGCTGGCCTCAACGTACTTCGAAttatcaatgagccaactgctgctgctattgcctatggcttagataagaaggtcggggctgaaaggaatgtgct
	********************************************************************************************************
rat	(((((.(((.((((((((.((...((((...(((((..(((((((...((..........))...)))))))))))))))))).))))))...)).))))))))	0.970 -32.30

rat

chromosome:2:108278895:108278998:1

intergenic

block1305800 [novel_lenNOK_Multihit_5varHIGH_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	0.606	no	no	0.53/0.55	19/22/0.50	2.0	0.5	2	0	2	0	9	19	5arm	13	nd	0.41	3	2	2	na	na

		reads	miRBase family seed
seed	--------------GCCUCAA--------------------------------------------------------------------------------------	1	novel
seed	----------GCUGGCC------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S1
	-------------GGCCTCAACGTACTTCGAA---------------------------------------------------------------------------	19	1	-
	---------TGCTGGCCTCAACGTACTTCGA----------------------------------------------------------------------------	22	-	1
rat	tggaactatTGCTGGCCTCAACGTACTTCGAAttatcaatgagccaactgctgctgctattgcctatggcttagataagaaggtcagggctgaaaggaatgtgctca
	***********************************************************************************************************
rat	.((.((.(((.(((((((..((...((((...(((((..(((((((...((..........))...))))))))))))))))))..)))))...)).)))))..)).	0.730 -24.00

rat

chromosome:2:170309332:170309438:1

intergenic

block1799621 [novel_lenNOK_Multihit_5varHIGH_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	0.516	no	no	0.53/0.55	19/22/0.50	2.0	0.5	2	0	2	0	16	19	5arm	13	8	0.36	3	2	2	na	na

		reads	miRBase family seed
seed	-----------------GCUGGCC----------------------------------------------------------------------------------------------	1	novel
seed	---------------------GCCUCAA------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S1
	----------------TGCTGGCCTCAACGTACTTCGA--------------------------------------------------------------------------------	22	-	1
	--------------------GGCCTCAACGTACTTCGAA-------------------------------------------------------------------------------	19	1	-
rat	aagatgctggaactatTGCTGGCCTCAACGTACTTCGAAttatcaatgagccaactgctgctgctattgcctatggcttagataagaaggtcggggctgaaaggaatgtgctcatttt
	**********************************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>++++++++++++++++	ENSRNOT00000041306 ENSRNOG00000032585 Q7M081_RAT
rat	((((((..((.((.(((.((((((((.((...((((...(((((..(((((((...((..........))...)))))))))))))))))).))))))...)).))))).))))))))	0.920 -28.40

rat

chromosome:5:162478107:162478224:-1

Same_strand|Boundary_coding|ENSRNOT00000041306|ENSRNOG00000032585 ## ENSRNOG00000032585|protein_coding|Q7M081_RAT|DnaK-type molecular chaperone P72 (Fragments). [Source:UniProtKB/TrEMBL;Acc:Q7M081]

block461172 [novel_lenNOK_Multihit_5varHIGH_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	0.463	no	no	0.56/0.68	19/25/0.50	2.2	1.3	6	0	3	0	8	15	5arm	54	nd	0.32	3	6	3	na	na

		reads	miRBase family seed
seed	-------------UGACAUG---------------------------------------------------------------------------	3	novel
seed	-----------UCUGACA-----------------------------------------------------------------------------	1	novel
seed	--------------------CCGCCUG--------------------------------------------------------------------	1	novel
seed	---------GAUCUGA-------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S2	T4S1	T5S1
	------------CTGACATGCCGCCTGGAGAAACC------------------------------------------------------------	23	2	-	-
	-------------------GCCGCCTGGAGAAACCTGC---------------------------------------------------------	19	-	-	1
	------------CTGACATGCCGCCTGGAGAAACCTG----------------------------------------------------------	25	1	-	-
	----------ATCTGACATGCCGCCTGGAGAAACC------------------------------------------------------------	25	-	1	-
	--------GGATCTGACATGCCGCCTGGAGAA---------------------------------------------------------------	24	1	-	-
rat	tccattgtGGATCTGACATGCCGCCTGGAGAAACCTGCcaagtatgatgacatcaagatggtaatgaagcaggtgtccgagggcccactaaaggg
	***********************************************************************************************
rat	.((.((((((............(((((((...((((((....(((.....(((....)))...)))..)))))).)))..)))))))).)).)).	0.720 -23.10

rat

chromosome:15:84510835:84510929:-1

intergenic

novel_lenNOK_cloningHIGH_bulgeHIGH (32 loci)

block4769 [novel_lenNOK_cloningHIGH_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	0.014	no	no	0.47/0.50	18/19/0.00	0.0	0.0	101	0	10	0	13	20	5arm	2	nd	0.22	4	170	10	na	na

		reads	miRBase family seed
seed	--------------GAGAUGA---------------------------------------------------------------------------------------------------	170	miR-143
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-------------TGAGATGAAGCACTGCTC-----------------------------------------------------------------------------------------	18	6	10	9	9	26	12	20	55	7	14
	-------------TGAGATGAAGCACTGCTCA----------------------------------------------------------------------------------------	19	-	-	-	-	2	-	-	-	-	-
rat	ctgaggaagtattTGAGATGAAGCACTGCTCaggatggcttacaaggtttgttctagaacttcactcctttgctttacccaacaacttctgagcacatcgtttatctttgtgcttctcag
	************************************************************************************************************************
rat	((((.(((((((..((((((((....(((((((((.(((....((((..((...........))..)))).)))............))))))))).....)))))))).)))))))))))	0.890 -33.52

rat

chromosome:10:10820063:10820182:-1

intergenic

block304240 [novel_lenNOK_cloningHIGH_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	0.043	no	no	0.58/0.61	18/19/0.00	0.0	0.1	70	0	10	0	8	19	5arm	1	nd	0.26	4	79	10	na	na

		reads	miRBase family seed
seed	---------AGGUGGG----------------------------------------------------------------------------------------------	79	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--------TAGGTGGGGAGGGTTTCC------------------------------------------------------------------------------------	18	18	14	1	1	5	1	9	12	11	1
	--------TAGGTGGGGAGGGTTTCCA-----------------------------------------------------------------------------------	19	6	-	-	-	-	-	-	-	-	-
rat	aggtagtcTAGGTGGGGAGGGTTTCCAgccttttcttgtcatctggtctccttcatatggtcctctcaatgctgctgcctcctcttcttcctcctcctcctcctcttcct
	**************************************************************************************************************
rat	(((.((...(((.((((((((....((((.........((((.(((......))).))))..........))))..............)))))).)).)))...)).)))	0.680 -24.38

rat

chromosome:13:43311904:43312013:1

intergenic

block393712 [novel_lenNOK_cloningHIGH_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	0.384	no	no	0.32/0.33	18/19/0.00	0.0	0.0	199	0	3	0	10	4	3arm	1	nd	0.28	4	220	3	na	na

		reads	miRBase family seed
seed	----------------------------------------------CCUUACA--------------------	220	novel
		len	cloning frequencies
			T4S1	T4S2	T5S2
	---------------------------------------------ACCTTACATTTCTTCATC----------	18	88	111	1
	---------------------------------------------ACCTTACATTTCTTCATCT---------	19	4	16	-
rat	ctgtggtgagtggtcaagaactagaaggaggggaggaactaccagACCTTACATTTCTTCATCttcccccagg
	*************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000003088 ENSRNOG00000002272 NP_001101828.1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000032822 ENSRNOG00000002272 NP_001101828.1
rat	(((.((.(((.(((.(((((....((((..((.........))...))))....))))).)))))))).))).	0.940 -18.40

rat

chromosome:14:35976612:35976684:1

Same_strand|Boundary_non-coding|ENSRNOT00000059702|ENSRNOG00000002272 ## Same_strand|Intronic_coding|ENSRNOT00000003088|ENSRNOG00000002272 ## ENSRNOG00000002272|protein_coding|NP_001101828.1|ligand of numb-protein X 1 [Source:RefSeq_peptide;Acc:NP_001101828]

block599207 [novel_lenNOK_cloningHIGH_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	0.013	no	no	0.63/0.67	18/20/0.02	0.0	0.0	57	0	10	0	10	13	5arm	1	nd	0.28	4	84	10	na	na

		reads	miRBase family seed
seed	-----------AGCACCC--------------------------------------------------------------------------	84	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	----------TAGCACCCTCTGGGGCTG----------------------------------------------------------------	18	35	11	6	1	1	1	4	5	11	3
	----------TAGCACCCTCTGGGGCTGA---------------------------------------------------------------	19	2	-	-	-	1	-	1	-	-	-
	----------TAGCACCCTCTGGGGCTGAG--------------------------------------------------------------	20	-	-	-	-	-	-	1	-	1	-
rat	acttcgctttTAGCACCCTCTGGGGCTGaggtgggaggcctttgctaggatctccatttctgggttcacagggactctctgaaggcaaggtc
	********************************************************************************************
rat	((((.((((((((....((((((((((.(((..((((((((.....))).)))))...))).))))).))))).....)))))))).)))).	0.990 -37.20

rat

chromosome:17:14230292:14230383:-1

intergenic

block667518 [novel_lenNOK_cloningHIGH_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	0.022	no	no	0.72/0.78	18/19/0.00	0.0	0.0	37	0	10	0	23	16	5arm	1	nd	0.28	4	59	10	na	na

		reads	miRBase family seed
seed	------------------------CCCACCC---------------------------------------------------------------------------------------	57	novel
seed	-------------------------CCACCCA--------------------------------------------------------------------------------------	1	novel
seed	-----------------------GCCCACC----------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-----------------------GCCCACCCAGGGACCCCA-----------------------------------------------------------------------------	18	3	5	6	14	4	7	3	5	3	3
	-----------------------GCCCACCCAGGGACCCCAA----------------------------------------------------------------------------	19	-	-	-	-	1	-	-	1	-	2
	------------------------CCCACCCAGGGACCCCAA----------------------------------------------------------------------------	18	-	-	-	-	1	-	-	-	-	-
	----------------------AGCCCACCCAGGGACCCCA-----------------------------------------------------------------------------	19	-	-	-	-	-	1	-	-	-	-
rat	gtcccttctgctgtcactccagaGCCCACCCAGGGACCCCAaactgttgctcttgagtagcatcctcaagttagcatttcttcctgagggatgggcctgaccttagttttaacaggac
	**********************************************************************************************************************
rat	((((.....((((......(((.((((((((.((((....(((.(((((..((((((.......)))))).))))))))..))))..))).))))))))....)))).......))))	0.780 -36.60

rat

chromosome:17:60147371:60147488:1

intergenic

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