Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_Multihit_shortStem_nonpairedHIGH_bulgeHIGH (342 loci)

novel_lenNOK_Multihit_loopOverlap_nonpairedHIGH (327 loci)

block90510 [novel_lenNOK_Multihit_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	0.618	no	no	0.67/0.67	18/18/0.00	0.0	0.0	2	0	1	0	29	-3	3arm_loop	55	nd	0.39	3	2	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------GCAGUGC---------------------------------------	2	novel
		len	cloning frequencies
			T4S2
	--------------------------------------------------TGCAGTGCCAGCCTCGTC-----------------------------	18	2
rat	atgtgtttgctctcgctccttcctgttccagagacagctgccttttctcaTGCAGTGCCAGCCTCGTCctgtagggaagatggtgaaggtcagtgtg
	*************************************************************************************************
rat	.((..((.((..(((((.((((((....(((.(((.(((((((..........)).)).)))...))))))..))))))..)))))..)).))..))	0.800 -25.40

rat

chromosome:10:80889960:80890056:1

intergenic

block123203 [novel_lenNOK_Multihit_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	0.789	no	no	0.56/0.56	18/18/0.00	0.0	0.0	2	0	1	0	18	-4	3arm_loop	13	nd	0.50	3	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------CCACGAC----------------------------	2	novel
		len	cloning frequencies
			T3S1
	----------------------------ACCACGACCTCCACCAAA------------------	18	2
rat	caccacgattcagacctgctggcgttgcACCACGACCTCCACCAAAgcccatgtaaagaggtga
	****************************************************************
rat	((((......((....((.(((.((((.....))))..))).)).......))......)))).	0.470 -9.00

rat

chromosome:11:45645217:45645280:-1

intergenic

block143648 [novel_lenNOK_Multihit_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	0.652	no	no	0.63/0.65	19/23/0.67	0.5 0.0	0.0 0.0	2 1	0 0	2 1	0 0	12 3	-2 4	3arm 3arm	9 18	nd nd	0.37 0.39	3 4	3	2	na	na

		reads	miRBase family seed
seed	-------------------------------------GCAGGCA------------------	1	novel
seed	-------------------------------AACGAUG------------------------	1	novel
seed	--------------------------------ACGAUGC-----------------------	1	novel
		len	cloning frequencies
			T2S1	T5S1
	-------------------------------AACGATGCAGGCAGGCCCA------------	19	1	-
	------------------------------GAACGATGCAGGCAGGCCCA------------	20	-	1
	------------------------------------TGCAGGCAGGCCCAAGGTCCAAG---	23	-	1
rat	tgacatgaagcactggcccttcatggtggtGAACGATGCAGGCAGGCCCAAGGTCCAAGtcg
	**************************************************************
rat	.(((.((..((...((((((((((.((.....)).))).)))..))))....)).)).))).	0.910 -15.80

rat

chromosome:11:5434791:5434852:1

intergenic

block156126 [novel_lenNOK_Multihit_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	0.789	no	no	0.58/0.58	19/19/0.00	0.0	0.0	1	0	1	0	6	-2	3arm_loop	19	nd	0.37	2	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------AGCUACU-----------------	1	novel
		len	cloning frequencies
			T3S1
	------------------------------AAGCTACTGGCTGACCAGG------	19	1
rat	ccacaaactgaacgcagacaaggcccgcagAAGCTACTGGCTGACCAGGttgagg
	*******************************************************
rat	((.(((.(((....(((.((.(((........)))..)).)))..))).))).))	0.590 -10.20

rat

chromosome:11:38432247:38432301:1

intergenic

block160580 [novel_lenNOK_Multihit_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	0.119	no	no	0.58/0.58	19/19/0.00	0.5	0.5	2	0	2	0	12	-1	3arm	105	nd	0.32	2	2	2	na	na

		reads	miRBase family seed
seed	-------------------------------------------GACCUCA------------------------	1	novel
seed	--------------------------------------------ACCUCAU-----------------------	1	novel
		len	cloning frequencies
			T2S1	T4S2
	-------------------------------------------GACCTCATGGCCTACATGG------------	19	-	1
	------------------------------------------GGACCTCATGGCCTACATG-------------	19	1	-
rat	ttcctggtaggacaatgaatatggctacaacaacagggtcttGGACCTCATGGCCTACATGGcctccaaggagt
	**************************************************************************
rat	(((((((.(((...(((.....(((((........(((((...)))))..)))))..)))..)))))).)))).	0.510 -20.70

rat

chromosome:11:50960077:50960150:1

intergenic

block174749 [novel_lenNOK_Multihit_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	0.134	no	no	0.72/0.72	18/18/0.00	0.0	0.0	2	0	1	0	24	-2	5arm_loop	23	nd	0.39	3	2	1	na	na

		reads	miRBase family seed
seed	-------------------------GAGCACC--------------------------------------------------------------	2	novel
		len	cloning frequencies
			T4S1
	------------------------GGAGCACCCCACCCAGTC----------------------------------------------------	18	2
rat	cagtccacctgtcctctctgagtgGGAGCACCCCACCCAGTCcacctgtcctctctgagtgggagcacctcacccagtccacctgtcctctctg
	**********************************************************************************************
rat	(((..............(((.(((((.((..(((((.(((..............))).))))).)).)).))).)))..............)))	0.830 -23.23

rat

chromosome:11:84773868:84773961:1

intergenic ## {Repeats: trf 1801 1819 0 class=trf}

block174751 [novel_lenNOK_Multihit_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	0.199	no	no	0.72/0.72	18/18/0.00	0.0	0.0	2	0	1	0	23	-2	5arm_loop	23	nd	0.44	3	2	1	na	na

		reads	miRBase family seed
seed	------------------------GAGCACC----------------------------------------------------------	2	novel
		len	cloning frequencies
			T4S1
	-----------------------GGAGCACCCCACCCAGTC------------------------------------------------	18	2
rat	agtccacctgtcctctctgagagGGAGCACCCCACCCAGTCcacctgtcctctctgagtgggagcacctcacccagtccacctgtcctc
	*****************************************************************************************
rat	((..((..((..((......((((..((..(((((.(((..............))).))))).)).))))....))..))..))..)).	0.660 -21.24

rat

chromosome:11:84774165:84774253:1

intergenic ## {Repeats: trf 1505 1523 0 class=trf}

block174755 [novel_lenNOK_Multihit_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	0.72/0.72	18/18/0.00	0.0	0.0	2	0	1	0	7	-2	5arm_loop	23	nd	0.39	3	2	1	na	na

		reads	miRBase family seed
seed	--------GAGCACC----------------------------------------------	2	novel
		len	cloning frequencies
			T4S1
	-------GGAGCACCCCACCCAGTC------------------------------------	18	2
rat	ctgagtgGGAGCACCCCACCCAGTCcaccggccctctctgagtgggagcacctcacccagt
	*************************************************************
rat	(((.(((((.((..(((((.(((..............))).))))).)).)).))).))).	0.950 -21.84

rat

chromosome:11:84774514:84774574:1

intergenic ## {Repeats: trf 1098 1116 0 class=trf}

block175826 [novel_lenNOK_Multihit_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	0.276	no	no	0.37/0.37	19/19/0.00	0.0	0.0	1	0	1	0	9	-2	5arm_loop	18	nd	0.32	3	1	1	na	na

		reads	miRBase family seed
seed	----------UGUUGAA---------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	---------TTGTTGAAGCAGTAAGTCA----------------------------------------------	19	1
rat	tcatctggaTTGTTGAAGCAGTAAGTCAgacatcacttgccacagtaatgcctgtcaaagtatctaatcatgaa
	**************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000002498 ENSRNOG00000001825 Pkp2
rat	((((.(((((..((((.(((((((((........))))))........)))...))))...)))))...)))).	0.540 -13.10

rat

chromosome:11:86511771:86511844:1

Same_strand|Intronic_non-coding|ENSRNOT00000002498|ENSRNOG00000001825 ## ENSRNOG00000001825|protein_coding|Pkp2|Pkp2 protein (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q562C0]

block245253 [novel_lenNOK_Multihit_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	0.273	no	no	0.45/0.47	19/20/0.33	0.3	0.7	3	0	2	0	35	-5	3arm_loop	20	nd	0.35	3	3	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------CAUCCAG------------------------------------------------	2	novel
seed	------------------------------------------AUCCAGU-----------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T3S1
	----------------------------------------GCATCCAGTTCATCTTGAG-------------------------------------	19	2	-
	-----------------------------------------CATCCAGTTCATCTTGAGGA-----------------------------------	20	-	1
rat	tgaaggaacaacacctaaatccaagagggcagctgttataGCATCCAGTTCATCTTGAGGAtttcaataggtctgaaaataaatgttctggtttca
	************************************************************************************************
rat	.(((((((((..((((((((((..((((..(((((..........)))))..))))..)))))....)))))...........))))))...))).	0.420 -18.52

rat

chromosome:13:19472297:19472392:-1

intergenic

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