Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_Multihit_shortStem_loopOverlap (14 loci)

block1442390 [novel_lenNOK_Multihit_shortStem_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	0.046	no	no	0.44/0.44	25/25/0.00	0.0	0.0	1	0	1	0	2	-3	3arm_loop	17	nd	0.24	2	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------AGGCUGU-------------------	1	novel
		len	cloning frequencies
			T3S2
	-------------------------------TAGGCTGTTGAAGCACTTCATTCTC--	25	1
rat	ctgtaagaataacaaagtgtgtctctcagtaTAGGCTGTTGAAGCACTTCATTCTCag
	**********************************************************
rat	(((..(((((....((((((.((...((((....))))..)).)))))).))))))))	1.000 -14.00

rat

chromosome:3:17088435:17088492:1

intergenic

block1799592 [novel_lenNOK_Multihit_shortStem_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	0.022	no	no	0.61/0.62	18/21/0.50	1.0	2.5	2	0	2	0	0	-2	3arm	28	nd	0.25	2	2	2	na	na

		reads	miRBase family seed
seed	----------------------------AGGCCCC---------------	1	novel
seed	------------------------------GCCCCAC-------------	1	novel
		len	cloning frequencies
			T1S1	T5S2
	---------------------------CAGGCCCCACCATTGAAG-----	18	-	1
	-----------------------------GGCCCCACCATTGAAGAGGTC	21	1	-
rat	gagctcctccatctggtggtgcttcttCAGGCCCCACCATTGAAGAGGTC
	**************************************************
rat	((.(((.((....((((((.(((......))).))))))..)).))).))	1.000 -18.70

rat

chromosome:5:162476765:162476814:-1

intergenic

block1983602 [novel_lenNOK_Multihit_shortStem_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	0.022	no	no	0.61/0.62	18/21/0.50	1.0	2.5	2	0	2	0	0	-2	3arm	28	nd	0.25	2	2	2	na	na

		reads	miRBase family seed
seed	----------------------------AGGCCCC---------------	1	novel
seed	------------------------------GCCCCAC-------------	1	novel
		len	cloning frequencies
			T1S1	T5S2
	---------------------------CAGGCCCCACCATTGAAG-----	18	-	1
	-----------------------------GGCCCCACCATTGAAGAGGTC	21	1	-
rat	gagctcctccatctggtggtgcttcttCAGGCCCCACCATTGAAGAGGTC
	**************************************************
rat	((.(((.((....((((((.(((......))).))))))..)).))).))	1.000 -18.70

rat

chromosome:6:136880262:136880311:-1

intergenic

block2075539 [novel_lenNOK_Multihit_shortStem_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	0.040	no	no	0.56/0.56	18/18/0.00	0.0	0.0	1	0	1	0	2	-2	5arm_loop	12	nd	0.28	3	1	1	na	na

		reads	miRBase family seed
seed	---GGAGACU----------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	--TGGAGACTTCTGCAGAGG------------------------------	18	1
rat	acTGGAGACTTCTGCAGAGGcctgtcaatctgaaaaacagaagcttgggt
	**************************************************
rat	(((.(((.((((((((((..........)))).....))))))))).)))	0.940 -14.00

rat

chromosome:7:1044186:1044235:-1

intergenic

block2089736 [novel_lenNOK_Multihit_shortStem_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	0.014	no	no	0.58/0.58	19/19/0.00	0.0	0.0	1	0	1	0	1	-4	3arm_loop	11	nd	0.21	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------UCCCUUG------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------TTCCCTTGGACCCATGCTG-	19	1
rat	cagtgtgaggtctacagcataaTTCCCTTGGACCCATGCTGc
	******************************************
rat	(((((((.((((((.((.........))))))))))))))).	1.000 -14.30

rat

chromosome:7:17808096:17808137:-1

intergenic

block2706031 [novel_lenNOK_Multihit_shortStem_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	0.022	no	no	0.61/0.62	18/21/0.50	1.0	2.5	2	0	2	0	0	-2	3arm	28	nd	0.25	2	2	2	na	na

		reads	miRBase family seed
seed	----------------------------AGGCCCC---------------	1	novel
seed	------------------------------GCCCCAC-------------	1	novel
		len	cloning frequencies
			T1S1	T5S2
	---------------------------CAGGCCCCACCATTGAAG-----	18	-	1
	-----------------------------GGCCCCACCATTGAAGAGGTC	21	1	-
rat	gagctcctccatctggtggtgcttcttCAGGCCCCACCATTGAAGAGGTC
	**************************************************
rat	((.(((.((....((((((.(((......))).))))))..)).))).))	1.000 -18.70

rat

chromosome:X:53303779:53303828:-1

intergenic

block400737 [novel_lenNOK_Multihit_shortStem_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	0.183	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	3	-4	3arm_loop	19	nd	0.28	3	1	1	na	na

		reads	miRBase family seed
seed	------------------------AAGCAGU-------------	1	novel
		len	cloning frequencies
			T1S2
	-----------------------AAAGCAGTGGCAGAAGGA---	18	1
rat	gccccccttacccctgtcctgggAAAGCAGTGGCAGAAGGAggc
	********************************************
rat	(((..((((....((((((((......))).))))))))).)))	0.960 -15.10

rat

chromosome:14:49767379:49767422:1

intergenic

novel_lenNOK_Multihit_shortStem_loopOverlap_nonpairedHIGH (14 loci)

block174770 [novel_lenNOK_Multihit_shortStem_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	0.056	no	no	0.72/0.72	18/18/0.00	0.0	0.0	2	0	1	0	3	-2	5arm_loop	23	nd	0.44	3	2	1	na	na

		reads	miRBase family seed
seed	----GAGCACC---------------------------------------	2	novel
		len	cloning frequencies
			T4S1
	---GGAGCACCCCACCCAGTC-----------------------------	18	2
rat	gagGGAGCACCCCACCCAGTCcacctgtcctctctgagtgggagcacctc
	**************************************************
rat	((((..((..(((((.(((..............))).))))).)).))))	1.000 -17.64

rat

chromosome:11:84775554:84775603:1

intergenic ## {Repeats: trf 136 154 0 class=trf}

block946058 [novel_lenNOK_Multihit_shortStem_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	0.657	no	no	0.58/0.58	19/19/0.00	0.0	0.0	1	0	1	0	3	-2	3arm_loop	19	nd	0.37	3	1	1	na	na

		reads	miRBase family seed
seed	------------------------AGCUACU--------------	1	novel
		len	cloning frequencies
			T3S1
	-----------------------AAGCTACTGGCTGACCAGG---	19	1
rat	ctgaaggcagaccgggcccacagAAGCTACTGGCTGACCAGGcgg
	*********************************************
rat	(((..(((((.((((((........))..))))))).))...)))	0.660 -11.80

rat

chromosome:1:17295374:17295418:1

intergenic

block962050 [novel_lenNOK_Multihit_shortStem_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	0.231	no	no	0.56/0.60	18/25/0.00	1.0	2.5	2	0	1	0	2	-7	5arm_loop	51	nd	0.33	3	2	1	na	na

		reads	miRBase family seed
seed	-----UCCAGUG----------------------------------------------	1	novel
seed	---CCUCCAG------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----CTCCAGTGTCATAGGACC------------------------------------	18	1
	--CCCTCCAGTGTCATAGGACCTCCAC-------------------------------	25	1
rat	gcCCCTCCAGTGTCATAGGACCTCCACtatcccatgacgtccactgtctcaccaaggc
	**********************************************************
rat	(((....(((((((((.(((.........))).)))))....)))).........)))	0.800 -9.82

rat

chromosome:1:51122347:51122404:1

intergenic ## {Repeats: trf 22 47 0 class=trf}

Back to summary page

other hairpins:

Jump 10 pages back

Page 30908

Jump 10 pages forward

©2008 InteRNA Genomics B.V.