Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_multiarm_Multihit_nonpairedHIGH (6 loci)

sblock438 [novel_lenNOK_multiarm_Multihit_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	0.105	no	no	0.37/0.50	19/20/0.29	0.7 0.0 0.0	0.3 0.0 0.0	3 2 2	0 0 0	2 2 1	0 0 0	2 11 27	33 26 8	5arm 5arm 3arm	33 33 45	nd nd nd	0.45 0.42 0.42	5 3 5	7	3	na	na

		reads	miRBase family seed
seed	------------CCAGUAA---------------------------------------------------------------------------------------------------	2	novel
seed	---GUGCUAG------------------------------------------------------------------------------------------------------------	2	novel
seed	-------------------------------------------------------------------------GGUGUUU--------------------------------------	2	novel
seed	-----GCUAGGA----------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T2S2	T5S1
	------------------------------------------------------------------------TGGTGTTTTTAGAGTGTGA---------------------------	19	-	-	2
	-----------ACCAGTAACCTATGGAAGA----------------------------------------------------------------------------------------	19	1	-	1
	--TGTGCTAGGACCAGTAACCT------------------------------------------------------------------------------------------------	20	-	-	2
	----TGCTAGGACCAGTAACCTA-----------------------------------------------------------------------------------------------	19	-	1	-
rat	tgTGTGCTAGGACCAGTAACCTATGGAAGActtcatgagctcataccaatctccacctcactttgtggaagcTGGTGTTTTTAGAGTGTGAtgaacttcaggtgaatggatgcattca
	**********************************************************************************************************************
rat	((.((((.....(((...((((...((((..(((((..((((((((((...(((((........)))))...)))))).....))))...)))))))))))))...)))..)))).))	1.000 -32.80

rat

chromosome:1:51405506:51405623:-1

intergenic

sblock5636 [novel_lenNOK_multiarm_Multihit_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	0.531	no	no	0.45/0.58	19/20/0.50	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	8 27	32 2	5arm 3arm	24 24	nd nd	0.35 0.32	3 3	2	2	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------CCUGUUC--------------------------------------	1	novel
seed	---------GAAUUGA-------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2	T4S1
	--------GGAATTGACTTCTACACCTC-------------------------------------------------------------------------------------	20	-	1
	-------------------------------------------------------------------ACCTGTTCCGTGGCACACT---------------------------	19	1	-
rat	tctgtgagGGAATTGACTTCTACACCTCcgctacctgtgcttgatttgaggaattaattgaatgctaACCTGTTCCGTGGCACACTggacgctgtagagaaggcccttcaaga
	*****************************************************************************************************************
rat	(((..(((((..((...(((((((..((((.....((((((........(((((...(((.....)))...)))))..)))))).))))...)))))))))..)))))..)))	0.910 -27.10

rat

chromosome:18:23138366:23138478:1

intergenic

novel_multiarm_5varHIGH_loopOverlap_nonpairedHIGH (6 loci)

block842113 [novel_multiarm_5varHIGH_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	0.491	no	no	0.50/0.60	20/23/1.00	0.0 2.0	0.0 3.3	1 3	0 0	1 1	0 0	32 15	-16 -5	5arm_loop_3arm 3arm_loop	2 2	nd nd	0.55 0.38	6 3	4	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------AGCAGCA------------------------------	2	miR-15b/16/195/322/497
seed	--------------------------------------ACUAGCA---------------------------------	1	novel
seed	---------------------------------AGCAAAC--------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	--------------------------------TAGCAAACTAGCAGCAGGGA--------------------------	20	1	-
	-------------------------------------AACTAGCAGCAGGGACCAGG---------------------	20	-	1
	----------------------------------------TAGCAGCAGGGACCAGGACAAGA---------------	23	-	1
	----------------------------------------TAGCAGCAGGGACCAGGACAA-----------------	21	-	1
rat	aagcatttcagattaaaggtgtttggttagagTAGCAAACTAGCAGCAGGGACCAGGACAAGAtggctgcatagagct
	******************************************************************************
rat	.(((.((.(((.......((.(((((((...((.((......)).))...))))))))).......)))...)).)))	0.620 -14.64

rat

chromosome:1:48336423:48336500:-1

intergenic

block958744 [novel_multiarm_5varHIGH_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	0.491	no	no	0.50/0.60	20/23/1.00	0.0 2.0	0.0 3.3	1 3	0 0	1 1	0 0	32 15	-16 -5	5arm_loop_3arm 3arm_loop	2 2	nd nd	0.55 0.38	6 3	4	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------AGCAGCA------------------------------	2	miR-15b/16/195/322/497
seed	--------------------------------------ACUAGCA---------------------------------	1	novel
seed	---------------------------------AGCAAAC--------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	--------------------------------TAGCAAACTAGCAGCAGGGA--------------------------	20	1	-
	-------------------------------------AACTAGCAGCAGGGACCAGG---------------------	20	-	1
	----------------------------------------TAGCAGCAGGGACCAGGACAAGA---------------	23	-	1
	----------------------------------------TAGCAGCAGGGACCAGGACAA-----------------	21	-	1
rat	aagcatttcagattaaaggtgtttggttagagTAGCAAACTAGCAGCAGGGACCAGGACAAGAtggctgcatagagct
	******************************************************************************
rat	.(((.((.(((.......((.(((((((...((.((......)).))...))))))))).......)))...)).)))	0.620 -14.64

rat

chromosome:1:47747216:47747293:1

intergenic

block1109273 [novel_multiarm_5varHIGH_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	0.059	no	no	0.28/0.35	18/23/0.86	0.0 3.3	0.5 1.3	4 3	0 0	2 2	0 0	26 20	-14 -22	5arm_loop_3arm 3arm_loop	1 1	nd nd	0.44 0.35	8 3	7	2	na	na

		reads	miRBase family seed
seed	---------------------------GUGUUCU------------------------------------------	4	novel
seed	-------------------------------------AUUAGCA--------------------------------	2	novel
seed	--------------------------------CUUUUAU-------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	--------------------------TGTGTTCTTTTATTAGCACT------------------------------	20	1	2
	------------------------------------TATTAGCACTAAGGAAACAG--------------------	20	1	1
	-------------------------------TCTTTTATTAGCACTAAGGAAAC----------------------	23	-	1
	--------------------------TGTGTTCTTTTATTAGCA--------------------------------	18	-	1
rat	catgcaaatgaagaggctcaagtcctTGTGTTCTTTTATTAGCACTAAGGAAACAGcctatattagtggggctatg
	****************************************************************************
	--------------------------------------------------------------------------------------	ENSRNOT00000035355 ENSRNOG00000023712 Stox1_predicted
rat	(((((..((.((.(((((....((((((((((........))))).)))))...)))))...)).))...)).)))	0.930 -19.50

rat

chromosome:20:29935516:29935591:1

Opposite_strand|Intronic_non-coding|ENSRNOT00000035355|ENSRNOG00000023712 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000057578|ENSRNOG00000023712 ## ENSRNOG00000023712|protein_coding|Stox1_predicted|

block1379969 [novel_multiarm_5varHIGH_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	0.070	no	no	0.52/0.61	23/23/1.00	0.0 3.0	0.0 3.0	1 2	0 0	1 1	0 0	18 29	3 -14	5arm 5arm_loop_3arm	1 1	nd nd	0.39 0.43	3 5	3	2	na	na

		reads	miRBase family seed
seed	------------------------------------UGGUUGU-------------------------------------------------	1	novel
seed	------------------------------UCCCUCU-------------------------------------------------------	1	novel
seed	-------------------UUAGCGU------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T4S1
	------------------GTTAGCGTTCCATCCCTCTGGTT---------------------------------------------------	23	-	1
	-----------------------------ATCCCTCTGGTTGTCCGGGAGAC----------------------------------------	23	1	-
	-----------------------------------CTGGTTGTCCGGGAGACTTCTGA----------------------------------	23	1	-
rat	cagagcgccgacagccttGTTAGCGTTCCATCCCTCTGGTTGTCCGGGAGACTTCTGAgtgtttggagtgtggaaaaggcttggctccctga
	********************************************************************************************
rat	(((...((((..((((((....((((((((...(((.((..(((.....))).)).)))....))))))))....))))))))))...))).	0.580 -29.80

rat

chromosome:3:68036617:68036708:-1

intergenic

block1650326 [novel_multiarm_5varHIGH_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	0.275	no	no	0.58/0.71	21/24/1.00	0.0 1.5	0.0 1.0	1 2	0 0	1 2	0 0	38 15	-22 0	5arm_loop_3arm 3arm	2 2	nd nd	0.50 0.32	9 3	3	3	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------CCACUUG----------------------------	1	novel
seed	--------------------------------------------------UGGCCAC-------------------------------	1	novel
seed	---------------------------------------CUCACUA------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T4S2	T5S1
	----------------------------------------------------GCCACTTGCCGCCAGAACCGC---------------	21	1	-	-
	--------------------------------------ACTCACTAACCGTGGCCACTTGCC--------------------------	24	-	1	-
	-------------------------------------------------GTGGCCACTTGCCGCCAGAACC-----------------	22	-	-	1
rat	gcggacggcccgcgaactgaaactccgagcaccgggccACTCACTAACCGTGGCCACTTGCCGCCAGAACCGCgcccaggacgcccgc
	****************************************************************************************
rat	((((.((.((((((..(((......((.(((...((((((.........))))))...))))).)))...))))....)).)).))))	0.970 -30.90

rat

chromosome:4:75839169:75839256:1

intergenic ## {SimpF: 1 Eponine}

sblock12512 [novel_multiarm_5varHIGH_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	0.116	no	no	0.37/0.59	19/23/0.71	2.5 3.2	2.0 2.8	2 5	0 0	1 1	0 0	5 34	25 -4	5arm 3arm	2 2	nd nd	0.43 0.37	4 3	7	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------AGUGACU------------------------------------------------------	3	novel
seed	----------------------------------------------------------------CUGAAUG-----------------------------------------------	1	novel
seed	------CCCCUGG---------------------------------------------------------------------------------------------------------	1	miR-331
seed	------------------------------------------------------------------GAAUGUG---------------------------------------------	1	novel
seed	-----------GGUCUCC----------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	--------------------------------------------------------TAGTGACTCTGAATGTGATACAG---------------------------------------	23	2
	-----TCCCCTGGTCTCCAGCAGTTCT-------------------------------------------------------------------------------------------	22	1
	----------TGGTCTCCAGCAGTTCTATGA---------------------------------------------------------------------------------------	21	1
	--------------------------------------------------------TAGTGACTCTGAATGTGAT-------------------------------------------	19	1
	---------------------------------------------------------------TCTGAATGTGATACAGCACTG----------------------------------	21	1
	-----------------------------------------------------------------TGAATGTGATACAGCACTG----------------------------------	19	1
rat	ctgttTCCCCTGGTCTCCAGCAGTTCTATGAaagtagctttcaaaacttcaaagtcTAGTGACTCTGAATGTGATACAGCACTGgcactgactgtctgtttcccctggtctccagcag
	**********************************************************************************************************************
rat	(((((...((.((....((((((.((..((..(((.(((.(((....((((.((((....)))).))))..)))...))))))..))..))))).))).....)).)).....)))))	0.960 -29.60

rat

chromosome:9:90775875:90775992:1

intergenic ## {Repeats: trf 6 32 0 class=trf,trf 101 127 0 class=trf,trf 48 76 0 class=trf}

novel_multiarm_DicerNOK_Multihit_loopOverlap_nonpairedHIGH (6 loci)

sblock2049 [novel_multiarm_DicerNOK_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	0.042	no	no	0.38/0.65	20/21/1.00	0.0 0.0 0.0	0.0 0.0 0.0	1 1 1	0 0 0	1 1 1	0 0 0	16 28 8	-2 -14 13	5arm_loop 5arm_loop_3arm 3arm	15 15 15	nd nd nd	0.40 0.55 0.43	3 5 7	3	3	13	15

		reads	miRBase family seed
seed	-----------------CCUGAUC--------------------------------------------------------	1	novel
seed	-----------------------------AGCCCUC--------------------------------------------	1	novel
seed	----------------------------------------------------CAGGAAG---------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1
	----------------CCCTGATCATCAAAGCCCTC--------------------------------------------	20	-	1	-
	----------------------------AAGCCCTCAAGGAGCCACCC--------------------------------	20	-	-	1
	---------------------------------------------------ACAGGAAGAAGCAGAAAAACA--------	21	1	-	-
rat	gtgccctctgcctctgCCCTGATCATCAAAGCCCTCAAGGAGCCACCCgagACAGGAAGAAGCAGAAAAACAttggacac
	********************************************************************************
rat	(((.(((((((.(((..((((.((.((...((((....)).)).....)))))))).))).)))))........)).)))	1.000 -22.00

rat

chromosome:1:159304111:159304190:1

intergenic

sblock6159 [novel_multiarm_DicerNOK_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	0.624	no	no	0.39/0.55	20/23/1.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	5 0	-7 2	5arm_loop 3arm	1 12	nd nd	0.61 0.37	8 3	2	1	0	2

		reads	miRBase family seed
seed	---------------------------------------CUCCAUA------------	1	novel
seed	------GGCAAGA---------------------------------------------	1	miR-31
		len	cloning frequencies
			T5S1
	-----TGGCAAGATGAATGACTTTTTCC------------------------------	23	1
	--------------------------------------TCTCCATAGCCAGTGGACTG	20	1
rat	gtctgTGGCAAGATGAATGACTTTTTCCtgacccttgtTCTCCATAGCCAGTGGACTG
	**********************************************************
rat	(((((((((...(((...(((...............)))...))).)))).)))))..	0.940 -10.76

rat

chromosome:2:186401045:186401102:-1

intergenic ## {Repeats: trf 31 47 0 class=trf}

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