Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_shortStem_mirtron_nonpairedHIGH_bulgeHIGH (25 loci)

novel_lenNOK_cloningOK_loopOverlap_randfoldOK_nonpairedHIGH_bulgeHIGH (24 loci)

block121934 [novel_lenNOK_cloningOK_loopOverlap_randfoldOK_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	0.002	no	no	0.56/0.56	18/18/0.00	0.0	0.0	12	0	7	0	24	-3	5arm_loop	1	nd	0.33	4	12	7	na	na

		reads	miRBase family seed
seed	-------------------------AGCAGUU----------------------------------------------------	12	novel
		len	cloning frequencies
			T1S1	T2S1	T3S1	T3S2	T4S1	T4S2	T5S1
	------------------------GAGCAGTTTTCCCAGGAG------------------------------------------	18	1	1	1	2	1	3	3
rat	aaggctggacttggttgctgaagaGAGCAGTTTTCCCAGGAGcactgggtaggctgtaaggggaagtgagcgagacagagcttc
	************************************************************************************
rat	(((.(((..((((.(((((.......(((((((.(((((.....))))).))))))).......))))).)))).)))..))).	1.000 -30.04

rat

chromosome:11:42721581:42721664:-1

intergenic

block385247 [novel_lenNOK_cloningOK_loopOverlap_randfoldOK_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	0.001	no	no	0.33/0.33	18/18/0.00	0.0	0.0	20	0	8	0	32	-3	5arm_loop	2	nd	0.39	4	28	8	na	na

		reads	miRBase family seed
seed	---------------------------------CCAAUUU----------------------------------------------------------	28	novel
		len	cloning frequencies
			T1S1	T2S1	T2S2	T3S1	T3S2	T4S2	T5S1	T5S2
	--------------------------------CCCAATTTCATCTTTCTT------------------------------------------------	18	1	1	2	11	9	2	1	1
rat	tggacggttacctccggtaccttccatttaccCCCAATTTCATCTTTCTTaaaaagatggcattccattgtgcgattgtaccattacttaattgtcca
	**************************************************************************************************
rat	.(((((((((.....(((((..(((((........(((.((((((((.....)))))))).))).....))).))..)))))......))))))))).	0.850 -25.62

rat

chromosome:14:14207100:14207197:1

intergenic

block494295 [novel_lenNOK_cloningOK_loopOverlap_randfoldOK_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	0.001	no	no	0.50/0.56	18/19/0.00	0.0	0.0	8	0	7	0	36	-5	5arm_loop_3arm	1	nd	0.37	4	17	7	na	na

		reads	miRBase family seed
seed	-------------------------------------CAGGACU------------------------------------------------------------------------	16	novel
seed	--------------------------------------AGGACUU-----------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S1	T2S2	T4S1	T4S2	T5S1	T5S2
	------------------------------------ACAGGACTTGGAGTCAGAG-------------------------------------------------------------	19	1	1	-	1	6	1	2
	------------------------------------ACAGGACTTGGAGTCAGA--------------------------------------------------------------	18	-	-	1	-	1	1	1
	-------------------------------------CAGGACTTGGAGTCAGAG-------------------------------------------------------------	18	-	-	-	-	-	-	1
rat	cactgctgtgctccagcccctctggaccaggagtaaACAGGACTTGGAGTCAGAGctctactaccctgtttcctcttccagaggagctctcaggagtcatttaatcctagctgtgt
	********************************************************************************************************************
rat	(((.(((((((((((((.((((((((...((((.(((((((...((((((....))))))....))))))).)))))))))))).)))....)))).)))........))).))).	0.990 -48.10

rat

chromosome:15:52715938:52716053:1

intergenic

block611599 [novel_lenNOK_cloningOK_loopOverlap_randfoldOK_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	0.001	no	no	0.37/0.39	18/19/0.00	0.0	0.0	8	0	3	0	37	-2	5arm_loop	1	nd	0.44	4	10	3	na	na

		reads	miRBase family seed
seed	--------------------------------------AAGGCAA------------------------------------------------------------------------	10	novel
		len	cloning frequencies
			T2S2	T4S1	T4S2
	-------------------------------------AAAGGCAATGGTAATGCA--------------------------------------------------------------	18	1	2	6
	-------------------------------------AAAGGCAATGGTAATGCAA-------------------------------------------------------------	19	-	-	1
rat	cctgtgtgctaacttcagaccactgcaatccaagctgAAAGGCAATGGTAATGCAaaggacattgccagtgataaaatcagcacacgatcagtgtggtctgactacagcagtaacag
	*********************************************************************************************************************
	-------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000048557 ENSRNOG00000021789 RGD1565323_predicted
rat	.((((.((((....(((((((((....(((...(((((....((.((((((((.......)))))))).))......)))))....)))....)))))))))....))))...))))	0.860 -40.40

rat

chromosome:17:38059512:38059628:-1

Opposite_strand|Intronic_non-coding|ENSRNOT00000048557|ENSRNOG00000021789 ## ENSRNOG00000021789|protein_coding|RGD1565323_predicted|

block641820 [novel_lenNOK_cloningOK_loopOverlap_randfoldOK_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	0.010	no	no	0.44/0.47	18/19/0.00	0.0	0.1	38	0	9	0	34	-5	5arm_loop_3arm	1	nd	0.32	4	49	9	na	na

		reads	miRBase family seed
seed	-----------------------------------UAUCAGA------------------------------------------------------------	49	miR-361
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S2	T5S1	T5S2
	----------------------------------CTATCAGAGTCTAGTCTGC-------------------------------------------------	19	6	1	4	4	1	7	1	5	9
	----------------------------------CTATCAGAGTCTAGTCTG--------------------------------------------------	18	2	-	2	-	-	2	-	2	3
rat	caaaccccagacctggaagagcacactggtggatCTATCAGAGTCTAGTCTGCtagactaggatgtgctgtttgccacactgttcttttggttcatgtgttg
	******************************************************************************************************
rat	.........((.((..(((((((...(((..(((.((((..(((((((....)))))))..))))....)))..)))...)))))))..)).))........	1.000 -34.70

rat

chromosome:17:7903114:7903215:1

intergenic

block748133 [novel_lenNOK_cloningOK_loopOverlap_randfoldOK_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	0.008	no	no	0.42/0.45	18/20/0.24	0.0	0.4	38	0	10	0	7	-6	5arm_loop_3arm	1	nd	0.35	4	45	10	na	na

		reads	miRBase family seed
seed	--------UCACAUU---------------------------	43	miR-23a/23b
seed	-------AUCACAU----------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-------ATCACATTGCCAGAGATG-----------------	18	2	2	4	2	2	5	2	1	5	6
	-------ATCACATTGCCAGAGATGTC---------------	20	-	2	1	-	-	-	1	6	1	-
	------CATCACATTGCCAGAGAT------------------	18	-	-	-	-	-	-	-	1	1	-
	-------ATCACATTGCCAGAGATGT----------------	19	1	-	-	-	-	-	-	-	-	-
rat	tgactgcATCACATTGCCAGAGATGTCggcagtgtcaagtca
	******************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000037498 ENSRNOG00000016402 LOC688914
	++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000021974 ENSRNOG00000016402 LOC688914
rat	.((((.....((((((((.((....))))))))))..)))).	1.000 -15.10

rat

chromosome:18:53516409:53516450:1

Same_strand|Intronic_coding|ENSRNOT00000021974|ENSRNOG00000016402 ## ENSRNOG00000016402|protein_coding|LOC688914|

block1027727 [novel_lenNOK_cloningOK_loopOverlap_randfoldOK_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	0.008	no	no	0.61/0.67	18/21/0.07	0.0	0.3	15	0	7	0	37	-7	5arm_loop_3arm	1	nd	0.32	4	15	7	na	na

		reads	miRBase family seed
seed	--------------------------------------AGCAGCA-------------------------------------------------------------------	15	miR-15b/16/195/322/497
		len	cloning frequencies
			T1S1	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2
	-------------------------------------TAGCAGCACAGAGGAGCC---------------------------------------------------------	18	3	-	3	2	2	1	1
	-------------------------------------TAGCAGCACAGAGGAGCCC--------------------------------------------------------	19	-	1	-	1	-	-	-
	-------------------------------------TAGCAGCACAGAGGAGCCCCG------------------------------------------------------	21	-	1	-	-	-	-	-
rat	gcctgggctgcctcacaaccaagtttatgaagaccggTAGCAGCACAGAGGAGCCCCGcctgagctgccatacatgttttccacacttcacctatccccagctcagcccagg
	****************************************************************************************************************
rat	.(((((((((.((.......((((....((((((..((((((((.(((.((....))..))).)))))..)))..))))))...))))...........))..)))))))))	0.460 -36.77

rat

chromosome:1:201534189:201534300:1

intergenic

block1051675 [novel_lenNOK_cloningOK_loopOverlap_randfoldOK_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	0.003	no	no	0.44/0.52	18/21/0.05	0.0	0.0	13	0	5	0	38	-5	3arm_loop	1	nd	0.39	4	22	5	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------ACCCUGU------------------------------------------------	21	miR-10a
seed	------------------------------------------------------------CCCUGUU-----------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T3S1	T3S2	T5S1	T5S2
	----------------------------------------------------------TACCCTGTTCTTGGCTTT--------------------------------------	18	1	2	1	6	7
	----------------------------------------------------------TACCCTGTTCTTGGCTTTG-------------------------------------	19	-	-	-	1	2
	----------------------------------------------------------TACCCTGTTCTTGGCTTTGGG-----------------------------------	21	-	-	-	1	-
	-----------------------------------------------------------ACCCTGTTCTTGGCTTTG-------------------------------------	18	-	-	-	-	1
rat	cagccattcaagagccaggatcatactgatcattgggatataccaaggcccttgacaaTACCCTGTTCTTGGCTTTgggacatagccaagggatggtaggttctggaagtggtt
	******************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000016017 ENSRNOG00000011313 Sorcs1_predicted
rat	.(((((((......((((((((.((((.(((.((((..(((.((((((((...((((......))))...))))))))...))).))))..))))))))))))))).)))))))	0.840 -41.10

rat

chromosome:1:255765802:255765915:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000040487|ENSRNOG00000011313 ## Opposite_strand|Intronic_coding|ENSRNOT00000016017|ENSRNOG00000011313 ## ENSRNOG00000011313|protein_coding|Sorcs1_predicted|

block1070200 [novel_lenNOK_cloningOK_loopOverlap_randfoldOK_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	0.005	no	no	0.33/0.39	18/21/0.03	0.1	0.1	22	0	10	0	15	-1	3arm	1	nd	0.39	4	31	10	na	na

		reads	miRBase family seed
seed	------------------------------------CACUUAC-------------------------	24	novel
seed	-----------------------------------GCACUUA--------------------------	7	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-----------------------------------GCACTTACTGTGATAACA---------------	18	2	-	3	2	1	3	2	4	2	2
	----------------------------------AGCACTTACTGTGATAAC----------------	18	1	1	-	-	-	1	-	-	1	2
	-----------------------------------GCACTTACTGTGATAACAA--------------	19	-	-	-	1	-	1	-	-	-	-
	-----------------------------------GCACTTACTGTGATAACAAAA------------	21	1	-	-	-	-	-	-	-	-	-
	----------------------------------AGCACTTACTGTGATAACA---------------	19	-	-	-	-	-	-	1	-	-	-
rat	tggatttaaatcccaagtatcacagcatgctttgAGCACTTACTGTGATAACAaaatcatgtttccat
	********************************************************************
rat	((((..((.........((((((((..(((.....)))....)))))))).........))..)))).	0.940 -16.07

rat

chromosome:20:18480790:18480857:-1

intergenic

block1189799 [novel_lenNOK_cloningOK_loopOverlap_randfoldOK_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	0.001	no	no	0.39/0.42	18/19/0.00	0.0	0.0	28	0	2	0	6	-2	3arm_loop	1	nd	0.33	4	29	2	na	na

		reads	miRBase family seed
seed	--------------------------AAGGCAC----------------	29	miR-124
		len	cloning frequencies
			T1S1	T1S2
	-------------------------TAAGGCACATAACAGGTA------	18	16	12
	-------------------------TAAGGCACATAACAGGTAG-----	19	-	1
rat	gaacaccctacctgccaagtcctctTAAGGCACATAACAGGTAggttca
	*************************************************
rat	(((...((((((((....(((((....))).))....))))))))))).	1.000 -16.20

rat

chromosome:2:160778405:160778453:-1

intergenic

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