Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_Multihit_loopOverlap_bulgeHIGH (13 loci)

block1346544 [novel_Multihit_loopOverlap_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	0.036	no	no	0.43/0.43	21/21/1.00	0.0	0.0	1	0	1	0	17	-1	3arm	13	nd	0.24	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------CCUCUUG------------------------------	1	novel
		len	cloning frequencies
			T2S1
	------------------------------------------ACCTCTTGGCATAGAACATCA-----------------	21	1
rat	tgggttgcaatgggagctcaaagttctggttaagttaaggaaACCTCTTGGCATAGAACATCAttccagcttataatcct
	********************************************************************************
rat	.((((((...(((((.......((((((((((((...(((...))))))))).))))))....))))).....)))))).	0.950 -20.10

rat

chromosome:3:89730:89809:-1

intergenic

block1686745 [novel_Multihit_loopOverlap_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	0.352	no	no	0.65/0.65	20/20/1.00	0.0	0.0	1	0	1	0	7	-4	5arm_loop	30	nd	0.30	5	1	1	na	na

		reads	miRBase family seed
seed	--------UGGGCCA----------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	-------GTGGGCCAGGAATCACCCCA----------------------------------------	20	1
rat	gtgcactGTGGGCCAGGAATCACCCCAtagtaggttctgagaatggatttccacagggttcagcatg
	*******************************************************************
rat	((((.((((((.(((((((((((......)).)))))).....)))....))))))......)))).	0.600 -17.90

rat

chromosome:4:150442373:150442439:1

intergenic

block1686753 [novel_Multihit_loopOverlap_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	0.352	no	no	0.65/0.65	20/20/1.00	0.0	0.0	1	0	1	0	7	-4	5arm_loop	30	nd	0.30	5	1	1	na	na

		reads	miRBase family seed
seed	--------UGGGCCA----------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	-------GTGGGCCAGGAATCACCCCA----------------------------------------	20	1
rat	gtgcactGTGGGCCAGGAATCACCCCAtagtaggttctgagaatggatttccacagggttcagcatg
	*******************************************************************
rat	((((.((((((.(((((((((((......)).)))))).....)))....))))))......)))).	0.600 -17.90

rat

chromosome:4:150444542:150444608:1

intergenic

block1686770 [novel_Multihit_loopOverlap_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	0.222	no	no	0.65/0.65	20/20/1.00	0.0	0.0	1	0	1	0	6	-4	5arm_loop	30	nd	0.25	5	1	1	na	na

		reads	miRBase family seed
seed	-------UGGGCCA------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	------GTGGGCCAGGAATCACCCCA------------------------------------	20	1
rat	tgaactGTGGGCCAGGAATCACCCCAtagtaggttctcagaatggactttccacagggttca
	**************************************************************
rat	....((((((((((((((((((......)).)))))).....)))....)))))))......	0.610 -15.80

rat

chromosome:4:150448892:150448953:1

intergenic

block1686802 [novel_Multihit_loopOverlap_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	0.133	no	no	0.65/0.65	20/20/1.00	0.0	0.0	1	0	1	0	8	-4	5arm_loop	30	nd	0.25	5	1	1	na	na

		reads	miRBase family seed
seed	---------UGGGCCA--------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	--------GTGGGCCAGGAATCACCCCA--------------------------------------	20	1
rat	ggtgaactGTGGGCCAGGAATCACCCCAtagtaggttctcagaatggactttccacagggttcatc
	******************************************************************
rat	(((((.((((((((((((((((((......)).)))))).....)))....)))))))...)))))	0.630 -19.10

rat

chromosome:4:150455400:150455465:1

intergenic

block1686864 [novel_Multihit_loopOverlap_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	0.352	no	no	0.65/0.65	20/20/1.00	0.0	0.0	1	0	1	0	7	-4	5arm_loop	30	nd	0.30	5	1	1	na	na

		reads	miRBase family seed
seed	--------UGGGCCA----------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	-------GTGGGCCAGGAATCACCCCA----------------------------------------	20	1
rat	gtgcactGTGGGCCAGGAATCACCCCAtagtaggttctgagaatggatttccacagggttcagcatg
	*******************************************************************
rat	((((.((((((.(((((((((((......)).)))))).....)))....))))))......)))).	0.600 -17.90

rat

chromosome:4:150581451:150581517:1

intergenic

novel_Multihit_shortStem_randfoldOK_nonpairedHIGH_bulgeHIGH (13 loci)

block577074 [novel_Multihit_shortStem_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	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	3	18	5arm	12	nd	0.40	4	1	1	na	na

		reads	miRBase family seed
seed	----CCAUUGC------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	---GCCATTGCCACCATCAAGAC------------------------------------------------------------------	20	1
rat	gctGCCATTGCCACCATCAAGACcaagtgaagcatccagtttatggactggtgtcccactggcttcaaggttggcattaattaccagtc
	*****************************************************************************************
rat	((((....(((((((...(((.((.((((..(((.((((((....)))))))))..)))))))))...))).))))........)))).	1.000 -29.70

rat

chromosome:16:50244033:50244121:1

intergenic

block869144 [novel_Multihit_shortStem_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	0.59/0.59	22/22/1.00	0.0	0.0	2	0	1	0	1	18	5arm	100	nd	0.41	4	2	1	na	na

		reads	miRBase family seed
seed	--CACCAGC---------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T2S1
	-CCACCAGCTCAATGGGGTCTAC-------------------------------------------------------------	22	2
rat	aCCACCAGCTCAATGGGGTCTACattatgggcagtcaccaccaaggtagtgactgtatcgacccctgctctgaggacaggcggt
	************************************************************************************
rat	(((.((..((((..((((((..........((((((((.((....)).))))))))...)))))).....))))....)).)))	0.410 -31.72

rat

chromosome:1:97577578:97577661:-1

intergenic

block961575 [novel_Multihit_shortStem_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	0.004	no	no	0.48/0.48	21/21/1.00	0.0	0.0	1	0	1	0	1	31	5arm	19	nd	0.38	4	1	1	na	na

		reads	miRBase family seed
seed	--UGGAGAC-----------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-GTGGAGACATTGTAGGGAACT----------------------------------------------------------------------------------------------	21	1
rat	tGTGGAGACATTGTAGGGAACTataccaatttccttggatgccaggctgtgcagaagtgcagagtttggtcacaatccatagggaatggacaggacaattacaggctacgctctgc
	********************************************************************************************************************
rat	.((((((...((((((....((...((.((((((((((((((((((((.((((....)))).))))))))....))))).)))))))))..)).....))))))......))))))	0.590 -40.30

rat

chromosome:1:51000273:51000388:1

intergenic

block965819 [novel_Multihit_shortStem_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	0.35/0.35	20/20/1.00	0.0	0.0	1	0	1	0	3	7	5arm	41	nd	0.40	4	1	1	na	na

		reads	miRBase family seed
seed	----GAUAAAC----------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	---TGATAAACTTCAGGTGAATG----------------------------------------	20	1
rat	gtgTGATAAACTTCAGGTGAATGgatgcagtcagctgcaccacgctctagagtgggctacaca
	***************************************************************
rat	(((((....(((..(((((..(((.(((((....))))))))))).))..)))....))))).	0.990 -23.20

rat

chromosome:1:52916609:52916671:1

intergenic

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