Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_Multihit_shortStem_5varHIGH_loopOverlap (12 loci)

block962740 [novel_lenNOK_Multihit_shortStem_5varHIGH_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	0.408	no	no	0.54/0.58	19/24/0.50	1.8	0.0	6	0	2	0	1	-4	3arm	27	nd	0.15	2	6	2	na	na

		reads	miRBase family seed
seed	--------------------------------------CUCACAG------------	3	novel
seed	---------------------------------CCAUUCU-----------------	2	novel
seed	-------------------------------------UCUCACA-------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	-------------------------------------TCTCACAGGACCTCCAGTG-	19	-	3
	--------------------------------TCCATTCTCACAGGACCTCCAGTG-	24	1	1
	------------------------------------TTCTCACAGGACCTCCAGTG-	20	-	1
rat	gtacttccagtgtcacagctgttataagaaccTCCATTCTCACAGGACCTCCAGTGc
	*********************************************************
	-------------------------------------------------------------------	ENSRNOT00000059938 ENSRNOG00000039174 RGD1563865_predicted
rat	(((((...((.(((....((((....((((......)))).)))))))))..)))))	0.640 -8.50

rat

chromosome:1:51538017:51538073:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000059936|ENSRNOG00000039174 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000059938|ENSRNOG00000039174 ## ENSRNOG00000039174|protein_coding|RGD1563865_predicted|

block962787 [novel_lenNOK_Multihit_shortStem_5varHIGH_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	0.408	no	no	0.54/0.58	19/24/0.50	1.8	0.0	6	0	2	0	1	-4	3arm	27	nd	0.15	2	6	2	na	na

		reads	miRBase family seed
seed	--------------------------------------CUCACAG------------	3	novel
seed	---------------------------------CCAUUCU-----------------	2	novel
seed	-------------------------------------UCUCACA-------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	-------------------------------------TCTCACAGGACCTCCAGTG-	19	-	3
	--------------------------------TCCATTCTCACAGGACCTCCAGTG-	24	1	1
	------------------------------------TTCTCACAGGACCTCCAGTG-	20	-	1
rat	gtacttccagtgtcacagctgttataagaaccTCCATTCTCACAGGACCTCCAGTGc
	*********************************************************
	-------------------------------------------------------------------	ENSRNOT00000059938 ENSRNOG00000039174 RGD1563865_predicted
rat	(((((...((.(((....((((....((((......)))).)))))))))..)))))	0.640 -8.50

rat

chromosome:1:51539903:51539959:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000059936|ENSRNOG00000039174 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000059938|ENSRNOG00000039174 ## ENSRNOG00000039174|protein_coding|RGD1563865_predicted|

block963023 [novel_lenNOK_Multihit_shortStem_5varHIGH_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	0.408	no	no	0.54/0.58	19/24/0.50	1.8	0.0	6	0	2	0	1	-4	3arm	27	nd	0.15	2	6	2	na	na

		reads	miRBase family seed
seed	--------------------------------------CUCACAG------------	3	novel
seed	---------------------------------CCAUUCU-----------------	2	novel
seed	-------------------------------------UCUCACA-------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	-------------------------------------TCTCACAGGACCTCCAGTG-	19	-	3
	--------------------------------TCCATTCTCACAGGACCTCCAGTG-	24	1	1
	------------------------------------TTCTCACAGGACCTCCAGTG-	20	-	1
rat	gtacttccagtgtcacagctgttataagaaccTCCATTCTCACAGGACCTCCAGTGc
	*********************************************************
	-------------------------------------------------------------------	ENSRNOT00000059938 ENSRNOG00000039174 RGD1563865_predicted
rat	(((((...((.(((....((((....((((......)))).)))))))))..)))))	0.640 -8.50

rat

chromosome:1:51598408:51598464:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000059936|ENSRNOG00000039174 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000059938|ENSRNOG00000039174 ## ENSRNOG00000039174|protein_coding|RGD1563865_predicted|

block964122 [novel_lenNOK_Multihit_shortStem_5varHIGH_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	0.403	no	no	0.54/0.58	19/24/0.50	1.8	0.0	6	0	2	0	1	-4	3arm	27	nd	0.15	2	6	2	na	na

		reads	miRBase family seed
seed	--------------------------------------CUCACAG------------	3	novel
seed	---------------------------------CCAUUCU-----------------	2	novel
seed	-------------------------------------UCUCACA-------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	-------------------------------------TCTCACAGGACCTCCAGTG-	19	-	3
	--------------------------------TCCATTCTCACAGGACCTCCAGTG-	24	1	1
	------------------------------------TTCTCACAGGACCTCCAGTG-	20	-	1
rat	gtacttccagtgtcacagctgttataagaactTCCATTCTCACAGGACCTCCAGTGc
	*********************************************************
	-------------------------------------------------------------------	ENSRNOT00000048246 ENSRNOG00000039174 RGD1563865_predicted
rat	(((((...((.(((....((((....((((......)))).)))))))))..)))))	0.670 -8.50

rat

chromosome:1:52045576:52045632:1

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

block1799521 [novel_lenNOK_Multihit_shortStem_5varHIGH_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	0.034	no	no	0.42/0.47	19/23/0.33	2.3	3.7	3	0	3	0	1	-18	3arm	136	nd	0.26	3	3	3	na	na

		reads	miRBase family seed
seed	----------------CAUCCAU-------------------	2	novel
seed	-----------------------GACAACU------------	1	novel
		len	cloning frequencies
			T1S2	T3S1	T3S2
	---------------TCATCCATGACAACTTTGGCATC----	23	1	-	-
	---------------TCATCCATGACAACTTTGG--------	19	-	-	1
	----------------------TGACAACTTTGGCATCGTG-	19	-	1	-
rat	ccgccctggccaaggTCATCCATGACAACTTTGGCATCGTGg
	******************************************
rat	((((....((((((((..((...))..))))))))...))))	1.000 -14.80

rat

chromosome:5:162350401:162350442:-1

intergenic

novel_lenNOK_Multihit_shortStem_5varHIGH_nonpairedHIGH (12 loci)

block266107 [novel_lenNOK_Multihit_shortStem_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	0.081	no	no	0.58/0.68	19/19/0.00	1.5	1.5	2	0	2	0	4	18	5arm	13	nd	0.37	3	2	2	na	na

		reads	miRBase family seed
seed	--------ACAGGGA------------------------------------------------------------------------------	1	novel
seed	-----AGCACAG---------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T4S1
	-------CACAGGGAGATGCGTGGGC-------------------------------------------------------------------	19	1	-
	----AAGCACAGGGAGATGCGTG----------------------------------------------------------------------	19	-	1
rat	ccacAAGCACAGGGAGATGCGTGGGCtgacatctgctggccaccagagcggtggccttggaaagggccacaagttccaccacactgttggtgg
	*********************************************************************************************
rat	((((.((((..((..((...((((.((....(((...(((((((.....)))))))..)))..)).))))....))..))....)))).))))	0.660 -35.90

rat

chromosome:13:67802408:67802500:-1

intergenic

block961700 [novel_lenNOK_Multihit_shortStem_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	0.447	no	no	0.35/0.37	19/23/0.67	1.7	1.0	3	0	3	0	2	21	5arm	22	nd	0.41	3	3	3	na	na

		reads	miRBase family seed
seed	---AAGACAG------------------------------------------------------------------------------------------	2	novel
seed	--------AGAAACG-------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T4S2	T5S1
	-------CAGAAACGATTTTGCAGAA--------------------------------------------------------------------------	19	1	-	-
	--TAAGACAGAAACGATTTTGCAG----------------------------------------------------------------------------	22	-	-	1
	--TAAGACAGAAACGATTTTGCAGA---------------------------------------------------------------------------	23	-	1	-
rat	gtTAAGACAGAAACGATTTTGCAGAAaaggataccagagacagagctaatcaacacaaagcaaactgggtagaacaaagcacaaaggtacctgtctatgc
	****************************************************************************************************
rat	....((((((..((..((.(((.........((((.....(((.(((...........)))...))))))).......))).))..))..))))))....	0.720 -14.79

rat

chromosome:1:51028172:51028271:1

intergenic

block1125504 [novel_lenNOK_Multihit_shortStem_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	0.489	no	no	0.42/0.47	19/23/0.33	2.3	3.7	3	0	3	0	2	5	5arm	136	nd	0.37	3	3	3	na	na

		reads	miRBase family seed
seed	---CAUCCAU------------------------------------------------------------------	2	novel
seed	----------GACAACU-----------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T3S1	T3S2
	---------TGACAACTTTGGCATCGTG------------------------------------------------	19	-	1	-
	--TCATCCATGACAACTTTGGCATC---------------------------------------------------	23	1	-	-
	--TCATCCATGACAACTTTGG-------------------------------------------------------	19	-	-	1
rat	ggTCATCCATGACAACTTTGGCATCGTGgaagggctcatgaccacaatccatgccatcacagctactcagaagact
	****************************************************************************
rat	((((.((..(((...((.(((((...((((.((........))....)))))))))....))....))))).))))	0.430 -14.00

rat

chromosome:2:3773977:3774052:-1

intergenic

block1125510 [novel_lenNOK_Multihit_shortStem_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	0.238	no	no	0.55/0.58	19/22/0.50	1.5	0.0	2	0	2	0	2	2	3arm	129	nd	0.32	3	2	2	na	na

		reads	miRBase family seed
seed	--------------------------------ACGGCAC----------------	1	novel
seed	-----------------------------------GCACAGU-------------	1	novel
		len	cloning frequencies
			T3S1	T4S2
	----------------------------------GGCACAGTCAAGGCTGAGA--	19	1	-
	-------------------------------AACGGCACAGTCAAGGCTGAGA--	22	-	1
rat	gttccagtatgactctacccatggcaagttcAACGGCACAGTCAAGGCTGAGAat
	*******************************************************
rat	((((((((.(((((...((..(((.....)))..))...)))))..)))).))))	0.970 -12.10

rat

chromosome:2:3774340:3774394:-1

intergenic

block1225732 [novel_lenNOK_Multihit_shortStem_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	0.049	no	no	0.45/0.53	19/22/0.67	2.7	1.0	3	0	2	0	3	22	5arm	14	nd	0.32	3	3	2	na	na

		reads	miRBase family seed
seed	-------GACUGUU-------------------------------------------------------------------------------------------------	1	novel
seed	----AAAGACU----------------------------------------------------------------------------------------------------	1	novel
seed	---------CUGUUAC-----------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2
	---GAAAGACTGTTACCAATGCCGT--------------------------------------------------------------------------------------	22	1	-
	--------ACTGTTACCAATGCCGTGG------------------------------------------------------------------------------------	19	-	1
	------AGACTGTTACCAATGCCGTG-------------------------------------------------------------------------------------	20	-	1
rat	ttgGAAAGACTGTTACCAATGCCGTGGtcacggtgcctgcttacttcagtgactctcagtggcaggcaacaaacgatgctggaactattgctggcctcagtgtacttccaa
	***************************************************************************************************************
rat	.(((((..((((...(((..((.(((((..((((((((((.((((..((.....)).))))))))))..........))))..))))).)))))...))))....))))).	0.430 -34.40

rat

chromosome:2:236511750:236511860:-1

intergenic

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