miR-Intess: classification

other hairpins

novel_lenNOK_shortStem_randfoldOK_bulgeHIGH (350 loci)

block3194357 [novel_lenNOK_shortStem_randfoldOK_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	0.50/0.53	19/24/0.67	0.3	1.3	3	0	2	0	4	9	3arm	1	42	0.29	4	3	2	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------UGGCUUC--------------------	2	novel
seed	-----------------------------------------------------------GGCUUCC-------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2
	---------------------------------------------------------TTGGCTTCCATGACTTCACCC-------	21	-	1
	---------------------------------------------------------TTGGCTTCCATGACTTCACCCCTT----	24	1	-
	----------------------------------------------------------TGGCTTCCATGACTTCACC--------	19	1	-
rat	ggagaggaaagtgaaggtaaggggtaaaggttctgggctgggaacaggtcctagctcTTGGCTTCCATGACTTCACCCCTTcttc
	*************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000023934 ENSRNOG00000017798 Atp2b3
	>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000044650 ENSRNOG00000017798 Atp2b3
	>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000024025 ENSRNOG00000017798 Atp2b3
	>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000029079 ENSRNOG00000017798 Atp2b3
	>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042813 ENSRNOG00000017798 Atp2b3
	>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000049237 ENSRNOG00000017798 Atp2b3
	>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000029091 ENSRNOG00000017798 Atp2b3
rat	(((((((...((((((.....(((....((((..(((((((((.....)))))))))..)))))))....))))))..)))))))	1.000 -33.70

rat

chromosome:X:159428045:159428129:1

Same_strand|Intronic_coding|ENSRNOT00000044650|ENSRNOG00000017798 ## ENSRNOG00000017798|protein_coding|Atp2b3|Plasma membrane calcium-transporting ATPase 3 (EC 3.6.3.8) (PMCA3) (Plasma membrane calcium pump isoform 3) (Plasma membrane calcium ATPase isoform 3). [Source:UniProtKB/Swiss-Prot;Acc:Q64568]

block2632521 [novel_lenNOK_shortStem_randfoldOK_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	0.52/0.54	25/26/0.00	0.0	0.5	2	0	1	0	0	22	3arm	1	nd	0.16	4	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------GGGUGAC------------------	2	novel
		len	cloning frequencies
			T5S1
	----------------------------------------------------------------------------------TGGGTGACTGTTTCTCCCACTTCTGG	26	1
	----------------------------------------------------------------------------------TGGGTGACTGTTTCTCCCACTTCTG-	25	1
rat	ctggaagtgggaaatgtctcggtcacccggctggttccagagtatagcttcttggtgtccaccagataggccatctgggtgtTGGGTGACTGTTTCTCCCACTTCTGG
	************************************************************************************************************
rat	((((((((((((.......((((((((((((....((((((.....((((.(((((....)))))..))))..)))))).))))))))))))....))))))))))))	0.960 -53.60

rat

chromosome:9:90775101:90775208:1

intergenic

block51552 [novel_lenNOK_shortStem_randfoldOK_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	0.007	no	no	0.61/0.63	18/19/0.00	0.0	0.3	3	0	3	0	0	15	5arm	2	nd	0.26	4	3	3	na	na

		reads	miRBase family seed
seed	-GAGAACU-------------------------------------------------------------------	3	miR-146a/146b
		len	cloning frequencies
			T1S2	T2S1	T4S2
	TGAGAACTGGGCCTTGGG---------------------------------------------------------	18	1	-	1
	TGAGAACTGGGCCTTGGGC--------------------------------------------------------	19	-	1	-
rat	TGAGAACTGGGCCTTGGGCccgcgtccttactctgggaaagagtgggcgtggttagcgggcaaggccttggcctt
	***************************************************************************
	-------------------------------------------------------------------------------------	ENSRNOT00000003891 ENSRNOG00000002807 Sept9
	-------------------------------------------------------------------------------------	ENSRNOT00000010365 ENSRNOG00000002807 Sept9
rat	.(((....((((((((.((((((((((..(((((.....)))))))))))))...))...))))))))....)))	0.930 -33.70

rat

chromosome:10:107396064:107396138:-1

block215909 [novel_lenNOK_shortStem_randfoldOK_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	0.61/0.62	18/23/0.50	0.0	2.0	4	0	3	0	0	5	5arm	1	42	0.26	4	4	3	na	na

		reads	miRBase family seed
seed	-AGGCCAA-------------------------------------------------------	4	novel
		len	cloning frequencies
			T1S2	T4S2	T5S1
	AAGGCCAAAGGGAGGGCA---------------------------------------------	18	2	-	-
	AAGGCCAAAGGGAGGGCACTG------------------------------------------	21	-	-	1
	AAGGCCAAAGGGAGGGCACTGGA----------------------------------------	23	-	1	-
rat	AAGGCCAAAGGGAGGGCACTGGAgctggcatccttcctggcctccttttcccccctctggcct
	***************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>	ENSRNOT00000001727 ENSRNOG00000022599 Ints1
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>	ENSRNOT00000001725 ENSRNOG00000022599 Ints1
rat	.((((((.((((.(((....((((((((........))))).)))....))))))).))))))	1.000 -31.90

rat

chromosome:12:15342852:15342914:1

block257746 [novel_lenNOK_shortStem_randfoldOK_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	0.78/0.80	18/20/0.50	0.0	1.0	2	0	2	0	4	25	5arm	1	nd	0.30	4	2	2	na	na

		reads	miRBase family seed
seed	-----CCCCCAC----------------------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T2S1	T5S2
	----TCCCCCACCCCTGGGGACCC----------------------------------------------------------------------------------	20	-	1
	----TCCCCCACCCCTGGGGAC------------------------------------------------------------------------------------	18	1	-
rat	ctccTCCCCCACCCCTGGGGACCCcttcggaagagcgcggctctggatctaatctgatctaatcagtcatcttctcgctggcagatccctggctccggggagagga
	**********************************************************************************************************
rat	.(((((((((....(((((((..((..(((((((....((((.((((((......))))))...)))).))))).))..))....)))))))....)))).)))))	0.970 -43.50

rat

chromosome:13:46095409:46095514:-1

intergenic

block1105285 [novel_lenNOK_shortStem_randfoldOK_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	0.53/0.53	19/19/0.00	0.0	0.0	2	0	1	0	1	34	5arm	2	nd	0.26	4	2	1	na	na

		reads	miRBase family seed
seed	----------------------------------------------CUUCCAU---------------------------------------------------	1	novel
seed	--CUUCCAU-----------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	-CCTTCCATGGGAACATGGT------------------------------------------------------------------------------------	19	1
	---------------------------------------------CCTTCCATGGGAACATGGT----------------------------------------	19	1
rat	gCCTTCCATGGGAACATGGTtgtccacctggggttgggcgtgtggCCTTCCATGGGAACATGGTtgtccacctggggttgggtgtgtggccttccatgggagca
	********************************************************************************************************
rat	((.((((((((((....((((((((((((.(((.((((((.........(((((....))))).))))))))).)))).)))....))))))))))))))))).	0.850 -46.00

rat

chromosome:20:23335778:23335881:1

intergenic ## {Repeats: trf 50 69 0 class=trf}

block1427505 [novel_lenNOK_shortStem_randfoldOK_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	0.83/0.83	18/18/0.00	0.0	0.0	3	0	1	0	2	19	5arm	6	nd	0.28	4	3	1	na	na

		reads	miRBase family seed
seed	---CCGCGGA--------------------------------------------------------------------------	3	novel
		len	cloning frequencies
			T1S2
	--TCCGCGGAGGGGCGGGGT----------------------------------------------------------------	18	3
rat	tcTCCGCGGAGGGGCGGGGTcaggtctctgcggaggggcggggtcaggtctctgcggaggggcggggtcaggtctccgcggagg
	************************************************************************************
rat	.(((((((((((....((.((..((((((.((.((((((........)))))).)).)))))).)).))...))))))))))).	1.000 -46.80

rat

chromosome:3:163184658:163184741:-1

intergenic ## {Repeats: trf 9 27 0 class=trf}

block1572836 [novel_lenNOK_shortStem_randfoldOK_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	0.55/0.60	19/25/0.38	0.5	1.9	8	0	3	0	1	19	5arm	1	nd	0.16	4	8	3	na	na

		reads	miRBase family seed
seed	--CCAGAGA------------------------------------------------------------------------------------------------------	6	novel
seed	----AGAGACA----------------------------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T2S2	T4S1	T5S1
	-CCCAGAGACAGTGAAGACCCACACC-------------------------------------------------------------------------------------	25	1	-	3
	---CAGAGACAGTGAAGACCCAC----------------------------------------------------------------------------------------	20	-	-	2
	-CCCAGAGACAGTGAAGACC-------------------------------------------------------------------------------------------	19	-	1	-
	-CCCAGAGACAGTGAAGACCCAC----------------------------------------------------------------------------------------	22	-	-	1
rat	cCCCAGAGACAGTGAAGACCCACACCgaggatgttctttcttgtcccagtgccgacagatatgtgatacttggtgtgggtttttttttttttttttttttttttttggggg
	***************************************************************************************************************
rat	(((((((((....((((((((((((((((.........((.((((........)))))).........)))))))))))))))).................))))))))).	0.990 -40.37

rat

chromosome:4:116142499:116142609:-1

intergenic

novel_lenNOK_Multihit_shortStem_nonpairedHIGH_bulgeHIGH (342 loci)

block14738 [novel_lenNOK_Multihit_shortStem_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	0.161	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	2	16	5arm	20	nd	0.47	4	1	1	na	na

		reads	miRBase family seed
seed	---UCCGCAA---------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	--ATCCGCAAAGCCACCAAGT----------------------------------------------------------------------	19	1
rat	atATCCGCAAAGCCACCAAGTatctgaaggatgtcactttaaagaagcagtgtgtgctattccggcagtaaaatggtggagtcggtaggtg
	*******************************************************************************************
rat	.((((.((....((((((.....(((..(((.(((((..............))).))...)))..))).....)))))).....)).))))	0.830 -22.94

rat

chromosome:10:34020663:34020753:-1

intergenic

block40300 [novel_lenNOK_Multihit_shortStem_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	0.120	no	no	0.58/0.58	19/19/0.00	0.0	0.0	1	0	1	0	3	22	5arm	20	nd	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	----CUAUGCC--------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	---CCTATGCCCATATGCCTGC---------------------------------------------------------------------	19	1
rat	tcaCCTATGCCCATATGCCTGCccttccgtcgggccaaggtgttcttccggcatcgagcccgggaatggacagtcacaggcttccggatga
	*******************************************************************************************
	---------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	ENSRNOT00000006359 ENSRNOG00000004741 Rpl19
rat	(((((...(((....((.(((((.((((..(((((...((((((.....))))))..))))))))).)).))).))..)))....)).)))	1.000 -31.90