Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_Multihit_shortStem_loopOverlap_nonpairedHIGH_bulgeHIGH (12 loci)

block846448 [novel_Multihit_shortStem_loopOverlap_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	0.030	no	no	0.45/0.45	20/20/1.00	0.0	0.0	1	0	1	0	3	-4	5arm_loop	31	nd	0.50	5	1	1	na	na

		reads	miRBase family seed
seed	----CCCCAUU----------------------------------	1	novel
		len	cloning frequencies
			T5S1
	---TCCCCATTGGAATTGGTTCA----------------------	20	1
rat	attTCCCCATTGGAATTGGTTCAtcctttaatgcctctgggaaat
	*********************************************
rat	(((((((....((.(((((........))))).))...)))))))	1.000 -10.60

rat

chromosome:1:51293390:51293434:-1

intergenic

block962598 [novel_Multihit_shortStem_loopOverlap_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	0.030	no	no	0.45/0.45	20/20/1.00	0.0	0.0	1	0	1	0	3	-4	5arm_loop	31	nd	0.50	5	1	1	na	na

		reads	miRBase family seed
seed	----CCCCAUU----------------------------------	1	novel
		len	cloning frequencies
			T5S1
	---TCCCCATTGGAATTGGTTCA----------------------	20	1
rat	attTCCCCATTGGAATTGGTTCAtcctttaatgcctctgggaaat
	*********************************************
rat	(((((((....((.(((((........))))).))...)))))))	1.000 -10.60

rat

chromosome:1:51487401:51487445:1

intergenic

block1112858 [novel_Multihit_shortStem_loopOverlap_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	0.186	no	no	0.60/0.60	20/20/1.00	0.0	0.0	1	0	1	0	4	-1	3arm	17	nd	0.55	5	1	1	na	na

		reads	miRBase family seed
seed	----------------------------------GCUCCAU----------------	1	novel
		len	cloning frequencies
			T2S1
	---------------------------------TGCTCCATGCTCGTGCTCTG----	20	1
rat	gctccatgctcgtgcactgtgctccacactcaaTGCTCCATGCTCGTGCTCTGtgct
	*********************************************************
rat	((.....((.((.(((....((............))....))).)).)).....)).	0.900 -11.80

rat

chromosome:20:37106395:37106451:1

intergenic ## {Repeats: trf 740 760 0 class=trf}

block1574088 [novel_Multihit_shortStem_loopOverlap_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	0.531	no	no	0.58/0.58	24/24/1.00	0.0	0.0	1	0	1	0	4	-3	5arm_loop	24	nd	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	-----CUGUGAC------------------------------------------------	1	novel
		len	cloning frequencies
			T4S1
	----GCTGTGACACACCCACCTACACAC--------------------------------	24	1
rat	gactGCTGTGACACACCCACCTACACACtatttgcagatgaccagtgtcctatgctgttt
	************************************************************
rat	(((.((((.(((((...((.((.((.......)).)).))....))))).)).)).))).	0.730 -8.90

rat

chromosome:4:117807274:117807333:-1

intergenic

block2091600 [novel_Multihit_shortStem_loopOverlap_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	0.115	no	no	0.45/0.45	20/20/1.00	0.0	0.0	1	0	1	0	1	-3	5arm_loop	11	nd	0.35	4	1	1	na	na

		reads	miRBase family seed
seed	--UGCUCUU--------------------------------	1	novel
		len	cloning frequencies
			T1S2
	-TTGCTCTTCTGGTATGCTGA--------------------	20	1
rat	tTTGCTCTTCTGGTATGCTGAtgtgggctcagtgggtagac
	*****************************************
rat	(((((((..(((((.(((....))).)).))).))))))).	1.000 -10.90

rat

chromosome:7:19366780:19366820:-1

intergenic

block2322174 [novel_Multihit_shortStem_loopOverlap_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	0.147	no	no	0.57/0.57	21/21/1.00	0.0	0.0	1	0	1	0	1	-3	5arm_loop	18	nd	0.38	4	1	1	na	na

		reads	miRBase family seed
seed	--GGCUGGU---------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	-AGGCTGGTCCCAAGATGGAGT--------------------------	21	1
rat	gAGGCTGGTCCCAAGATGGAGTaggtttggccttttaggttcagtctt
	************************************************
rat	(((((((..((.((((.((...........)))))).))..)))))))	0.810 -12.90

rat

chromosome:8:69589872:69589919:-1

intergenic

block844560 [novel_Multihit_shortStem_loopOverlap_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	0.113	no	no	0.54/0.54	24/24/1.00	0.0	0.0	1	0	1	0	2	-4	5arm_loop	17	nd	0.38	5	1	1	na	na

		reads	miRBase family seed
seed	---AGCAGCC------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	--TAGCAGCCAGACTTTTGCAGGACC--------------------------------	24	1
rat	ttTAGCAGCCAGACTTTTGCAGGACCtctactggcacaataattcctctgttgctgga
	**********************************************************
	--------------------------------------------------------------------	ENSRNOT00000041575 ENSRNOG00000031160 LOC685793
rat	((((((((.((((...((((((........)))...))).......))))))))))))	0.970 -11.40

rat

chromosome:1:50289956:50290013:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000049496|ENSRNOG00000031160 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000041575|ENSRNOG00000031160 ## ENSRNOG00000031160|protein_coding|LOC685793|

novel_cloningOK_bulgeHIGH (12 loci)

block537218 [novel_cloningOK_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	0.059	no	no	0.55/0.58	18/21/0.71	0.0	0.3	9	0	2	0	25	9	3arm	1	nd	0.29	4	14	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------UGUCAGA--------------------------------------	10	novel
seed	----------------------------------------------------------------------UUGUCAG---------------------------------------	4	novel
		len	cloning frequencies
			T1S1	T1S2
	----------------------------------------------------------------------TTGTCAGATGTCGGTGCCAG--------------------------	20	2	4
	----------------------------------------------------------------------TTGTCAGATGTCGGTGCCAGG-------------------------	21	3	-
	---------------------------------------------------------------------CTTGTCAGATGTCGGTGC-----------------------------	18	1	1
	---------------------------------------------------------------------CTTGTCAGATGTCGGTGCCAG--------------------------	21	1	-
	---------------------------------------------------------------------CTTGTCAGATGTCGGTGCC----------------------------	19	1	-
	----------------------------------------------------------------------TTGTCAGATGTCGGTGCC----------------------------	18	-	1
rat	ttttgctaaaactgttagcctttgttgtaaatgaccctggtcctctgtgggtgtgcatgcggcaagacacTTGTCAGATGTCGGTGCCAGGgttgtataaacttcaggagcgaaac
	********************************************************************************************************************
rat	(((((((....(((..((......(((((...((((((((((((((((((((((((.....))...))))))).))))....)).))))))))).))))).)).))).))))))).	0.750 -36.40

rat

chromosome:16:47710994:47711109:-1

intergenic

block1061187 [novel_cloningOK_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	0.037	no	no	0.45/0.55	20/24/1.00	0.2	1.0	12	0	4	0	6	5	5arm	1	nd	0.27	4	14	4	na	na

		reads	miRBase family seed
seed	--------AUUCGGG------------------------------------------------------------	10	novel
seed	-------UAUUCGG-------------------------------------------------------------	2	novel
seed	----------UCGGGCA----------------------------------------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T4S2	T5S1
	-------TATTCGGGCATTCAGAACGGTCCT--------------------------------------------	24	2	-	-	6
	------TTATTCGGGCATTCAGAACGGT-----------------------------------------------	22	-	-	-	2
	-------TATTCGGGCATTCAGAACGGT-----------------------------------------------	21	-	-	-	2
	---------TTCGGGCATTCAGAACGGTC----------------------------------------------	20	-	1	1	-
rat	gtccccTTATTCGGGCATTCAGAACGGTCCTacagtagtaggcagaggggcctgggtggctgctgtaaaggggcg
	***************************************************************************
rat	(((((.((((.(((.((((((....((((((...((.....))...)))))))))))).)))..)))).))))).	0.930 -29.30

rat

chromosome:20:5530823:5530897:-1

intergenic

block1092644 [novel_cloningOK_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	0.027	no	no	0.75/0.83	18/22/0.79	0.0 0.5	0.0 1.2	1 13	0 0	1 5	0 0	30 21	10 15	3arm 3arm	1 1	nd nd	0.33 0.23	4 4	14	5	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------UCGGCUC----------------------------------	7	novel
seed	------------------------------------------------------------------------CUCGGCU-----------------------------------	6	novel
seed	-------------------------------------------------------------------GCCUCCU----------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T3S2	T4S1	T5S2
	-----------------------------------------------------------------------CCTCGGCTCGCCCTCCTCCCTG---------------------	22	-	2	2	-	-
	------------------------------------------------------------------------CTCGGCTCGCCCTCCTCCCTG---------------------	21	-	-	1	1	1
	------------------------------------------------------------------------CTCGGCTCGCCCTCCTCCC-----------------------	19	2	-	-	-	-
	------------------------------------------------------------------------CTCGGCTCGCCCTCCTCCCT----------------------	20	2	-	-	-	-
	-----------------------------------------------------------------------CCTCGGCTCGCCCTCCTCCC-----------------------	20	2	-	-	-	-
	------------------------------------------------------------------CGCCTCCTCGGCTCGCCC------------------------------	18	-	-	-	-	1
rat	gcccctcctcggaggcgtccggctacgggggggaggggagggaggagggctgcagagcagcgccgcCGCCTCCTCGGCTCGCCCTCCTCCCTGgcgctgaccgatggaagaggc
	******************************************************************************************************************
rat	(((.((((((((.((((((.......(((((((((((((((((((.(((((((...))))).))....)))))....))).)))))))))))))))))..)))).)).)).)))	0.920 -67.01

rat

chromosome:20:4863413:4863526:1

intergenic ## {SimpF: oe = 0.79 1 CpG}

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