Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_loopOverlap_randfoldOK (1244 loci)

block1504823 [novel_lenNOK_loopOverlap_randfoldOK]

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	0.003	no	no	0.50/0.50	18/20/0.60	0.0	1.2	5	0	4	0	36	-2	3arm_loop	3	nd	0.17	2	5	4	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------GGUCUGG------------------------------------------------	5	novel
		len	cloning frequencies
			T1S1	T1S2	T4S1	T4S2
	-------------------------------------------------------------TGGTCTGGTTCACACTTGTG------------------------------------	20	-	1	1	1
	-------------------------------------------------------------TGGTCTGGTTCACACTTG--------------------------------------	18	2	-	-	-
rat	acacttgtgctggaccctggacctgtggtctggttcacacctgtgctgggtcctggatctgTGGTCTGGTTCACACTTGTGctggaccctggacctgtggtctggttcacgcttgtg
	*********************************************************************************************************************
rat	.(((..(((.((((((..(((((...((((((((((((((..(((.((((.((.((((.....)))))))))))))..))).))))))..)))))...))))))))))))))..)))	1.000 -51.70

rat

chromosome:3:148873598:148873714:1

intergenic ## {Repeats: trf 299 319 0 class=trf}

block904048 [novel_lenNOK_loopOverlap_randfoldOK]

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	0.006	no	no	0.63/0.63	19/19/0.00	0.0	0.0	3	0	2	0	40	-1	5arm_loop	1	nd	0.26	2	3	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------GGCUGCA------------------------------------------------------------------------	3	novel
		len	cloning frequencies
			T2S2	T5S1
	----------------------------------------AGGCTGCAGGAGAGTGGAC-------------------------------------------------------------	19	1	2
rat	gagtcacagaacatgcttgagtccagagtgcagcaaggacAGGCTGCAGGAGAGTGGACagacttctacatcctcacagcctctcctccttgcagtagttttggggctggggtgtactcg
	************************************************************************************************************************
rat	((((........((((((.(((((.((.(((.(((((((.((((((.((((..(((((......))))).))))..))))))....))))))).))).))...))))).)))))))))).	0.980 -48.50

rat

chromosome:1:186374073:186374192:-1

intergenic

block1783821 [novel_lenNOK_loopOverlap_randfoldOK]

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	0.001	no	no	0.78/0.80	18/20/0.33	0.0	0.5	6	0	4	0	20	-1	3arm	1	nd	0.06	1	6	4	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------GCGUGCU--------------------------------	6	novel
		len	cloning frequencies
			T1S2	T3S2	T5S1	T5S2
	-------------------------------------------------------CGCGTGCTGGGCTGCTCCC---------------------	19	-	2	-	1
	-------------------------------------------------------CGCGTGCTGGGCTGCTCCCC--------------------	20	-	1	1	-
	-------------------------------------------------------CGCGTGCTGGGCTGCTCC----------------------	18	1	-	-	-
rat	tcggtctccgggctttcgccctgggggcagcccgcacgcacctctgccttccctgCGCGTGCTGGGCTGCTCCCCgcctccttccgggctccgag
	***********************************************************************************************
rat	((((..((((((.....((...(((((((((((((((((.................)))))).))))))))))).)).....))))))..)))).	0.490 -51.43

rat

chromosome:5:143208275:143208369:-1

intergenic

novel_lenNOK_Multihit (1224 loci)

block5897 [novel_lenNOK_Multihit]

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	0.40/0.50	19/20/0.50	0.0 0.0	0.0 0.3	1 3	0 0	1 1	0 0	13 21	8 0	5arm 5arm	18 18	nd nd	0.15 0.37	2 4	4	2	na	na

		reads	miRBase family seed
seed	----------------------GCAUUUU--------------------------------------------------------------------------	3	novel
seed	--------------AGAUGCA----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T5S2
	---------------------AGCATTTTGAACTGGGAGG---------------------------------------------------------------	19	-	2
	---------------------AGCATTTTGAACTGGGAGGC--------------------------------------------------------------	20	-	1
	-------------GAGATGCAAGCATTTTGAAC----------------------------------------------------------------------	20	1	-
rat	tgttggccattaaGAGATGCAAGCATTTTGAACTGGGAGGCgacaagaagagaaagggctaagtgatacagttccaaaacttgtgttttctgagaggaaaata
	*******************************************************************************************************
rat	((((..((.(((..(((((((((..(((.((((((....((.....................))....)))))).))).)))))))))..)))..))..))))	0.910 -20.70

rat

chromosome:10:12879120:12879222:-1

intergenic

block6499 [novel_lenNOK_Multihit]

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	0.342	no	no	0.58/0.58	19/19/0.00	0.0	0.0	1	0	1	0	19	12	3arm	46	nd	0.26	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------CCUUGGC------------------------------	1	novel
		len	cloning frequencies
			T3S1
	--------------------------------------------------------------------------------CCCTTGGCCATGTAGCTTC-------------------	19	1
rat	gagctgaatcctggaccttagctggagctttggcctctgccttgggttgagtcttggtctttggctggcagagcccacgaCCCTTGGCCATGTAGCTTCgaatcctcttcccaagctt
	**********************************************************************************************************************
rat	(((((.......(((.......(((((((.(((((........((((((.....(((.(((((.....))))).)))))))))..)))))...)))))))..)))........)))))	0.530 -36.46

rat

chromosome:10:13790944:13791061:-1

intergenic

block16459 [novel_lenNOK_Multihit]

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	0.097	no	no	0.44/0.52	18/23/0.67	0.0 0.0	0.0 0.0	2 1	0 0	1 1	0 0	15 24	8 4	5arm 5arm	24 34	nd nd	0.30 0.44	3 5	3	2	na	na

		reads	miRBase family seed
seed	----------------CCCCAUA----------------------------------------------------------------------	2	novel
seed	-------------------------UGUUACC-------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S1
	---------------GCCCCATAAGTGTTACCATGGCA-------------------------------------------------------	23	-	2
	------------------------GTGTTACCATGGCAAAAC---------------------------------------------------	18	1	-
rat	tgttcaaaaaggaatGCCCCATAAGTGTTACCATGGCAAAACcggaagagtctacaatgtcacctagcatgctgtgggcatcattgtaaacaa
	*********************************************************************************************
	-------------------------------------------------------------------------------------------------------	ENSRNOT00000007131 ENSRNOG00000005097 Cdkl3
	-------------------------------------------------------------------------------------------------------	ENSRNOT00000059040 ENSRNOG00000005097 Cdkl3
rat	((((.....((..((((((((...((((((...(((((.....(((....)))....)))))..))))))..)).))))))..))...)))).	0.970 -20.90

rat

chromosome:10:37536695:37536787:-1

Opposite_strand|Intronic_coding|ENSRNOT00000007131|ENSRNOG00000005097 ## ENSRNOG00000005097|protein_coding|Cdkl3|Cyclin-dependent kinase-like 3 (EC 2.7.11.22) (Serine/threonine protein kinase NKIATRE). [Source:UniProtKB/Swiss-Prot;Acc:Q9JM01]

block23084 [novel_lenNOK_Multihit]

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	0.087	no	no	0.56/0.58	18/19/0.00	0.5	1.0	2	0	2	0	19	1	5arm	17	nd	0.21	1	2	2	na	na

		reads	miRBase family seed
seed	---------------------CACUGGG----------------------------------------------------	1	novel
seed	--------------------ACACUGG-----------------------------------------------------	1	novel
		len	cloning frequencies
			T4S1	T5S1
	-------------------CACACTGGGAAGAGGAAC-------------------------------------------	18	1	-
	--------------------ACACTGGGAAGAGGAACCC-----------------------------------------	19	-	1
rat	ggagattgagccaatgtgaCACACTGGGAAGAGGAACCCcaaaaggggtctatgatctccaagtctgtctatctgtcttt
	********************************************************************************
rat	.(((((.((........((((.(((.((.(((((.(((((....)))))))....))))).))).))))..)).))))).	0.720 -22.80

rat

chromosome:10:51810781:51810860:-1

intergenic

block30600 [novel_lenNOK_Multihit]

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	0.237	no	no	0.78/0.78	18/18/0.00	0.0	0.0	1	0	1	0	7	20	5arm	11	nd	0.17	1	1	1	na	na

		reads	miRBase family seed
seed	--------GGGGGGG------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	-------GGGGGGGGGGGTGTTTGC--------------------------------------------------------------------------------	18	1
rat	agcttgtGGGGGGGGGGGTGTTTGCtatgggttgtgatgagtctttttctcttcttctagggctactacatagttatgggggaaacagtctgccaccgccacggc
	*********************************************************************************************************
rat	.((.(((((((((.(((.(((((.((...(((((((...((((((.............))))))....)))))))....)).))))).))).)).)).)))))))	0.520 -33.62

rat

chromosome:10:66907078:66907182:-1

intergenic ## {Repeats: dust 66907165 66907175 0 class=dust}

block35573 [novel_lenNOK_Multihit]

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	0.064	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	13	14	3arm	13	nd	0.26	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------CCUGACC------------------------	1	novel
		len	cloning frequencies
			T3S2
	----------------------------------------------------------------------ACCTGACCCCAGCTTTTCT-------------	19	1
rat	gcacgtaataaaaatgccgaggtcaggatcgttgctggaatcagtgcccctccatcagtgcacatgacccACCTGACCCCAGCTTTTCTgtacccatgtgcc
	******************************************************************************************************
rat	((((((.(((.(((.((...(((((((........(((..(((((((..((.....)).)))).))).))))))))))...)).))).)))....)))))).	0.820 -26.80

rat

chromosome:10:76769897:76769998:-1

intergenic

block54763 [novel_lenNOK_Multihit]

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	0.091	no	no	0.56/0.56	18/18/0.00	0.0	0.0	2	0	1	0	25	1	5arm	20	nd	0.28	2	2	1	na	na

		reads	miRBase family seed
seed	--------------------------GGAGCAC-------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T3S1
	-------------------------GGGAGCACATCATGGTCT---------------------------------------------------------	18	2
rat	gggatgggtagcgtgggttaagcctGGGAGCACATCATGGTCTgttatgatcttagaaatgcaagggtgtttgaggagtttaagttatggaaggcgtcct
	****************************************************************************************************
rat	((((((.....(((((.((((((((..((((((..(((..((((.........)))).))).....))))))..)).)))))).))))).....))))))	0.450 -26.60

rat

chromosome:10:2499037:2499136:1

intergenic

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