miR-Intess: classification

other hairpins

novel_cloningOK_shortStem_5varHIGH_loopOverlap (2 loci)

block1848597 [novel_cloningOK_shortStem_5varHIGH_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	0.099	no	no	0.35/0.43	21/24/1.00	1.5	1.0	11	0	2	0	2	-4	5arm_loop	2	nd	0.18	2	11	2	na	na

		reads	miRBase family seed
seed	--------GACUUUG-------------------------------------------------------------	6	novel
seed	------AUGACUU---------------------------------------------------------------	3	novel
seed	---CAUAUGA------------------------------------------------------------------	1	novel
seed	--------------GUGUUCU-------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T5S1
	-------TGACTTTGTGTTCTTGAGTGAG-----------------------------------------------	22	1	3
	-----TATGACTTTGTGTTCTTGAGTGAG-----------------------------------------------	24	1	2
	-------TGACTTTGTGTTCTTGAGTGA------------------------------------------------	21	-	2
	-------------TGTGTTCTTGAGTGAGCAAGA------------------------------------------	21	-	1
	--TCATATGACTTTGTGTTCTTGAG---------------------------------------------------	23	-	1
rat	ccTCATATGACTTTGTGTTCTTGAGTGAGCAAGAaaagcatgcgttcgtctccctggacgctcagtcacagctgag
	****************************************************************************
rat	.((((..(((((..((((((..((((((((.............))))).)))...))))))..)))))....))))	0.600 -22.22

rat

chromosome:5:79249650:79249725:1

intergenic

novel_cloningOK_shortStem_bulgeHIGH (2 loci)

block881687 [novel_cloningOK_shortStem_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	0.391	no	no	0.52/0.52	21/21/1.00	0.0	0.0	8	0	3	0	3	14	3arm	1	nd	0.24	4	10	3	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------CAGAACC----------------	10	novel
		len	cloning frequencies
			T1S2	T2S2	T5S1
	----------------------------------------------------------------------------TCAGAACCAACTGCAGGCACT---	21	1	1	8
rat	agggaggaaacagactgggcttgtgaggttaggaagggggagggagacactggaggcaagaatgcacaggaagggcTCAGAACCAACTGCAGGCACTtcc
	****************************************************************************************************
	--------------------------------------------------------------------------------------------------------------	ENSRNOT00000016427 ENSRNOG00000012031 St8sia2
rat	.(((((............((((((..((((.((....(((.........(((...(((....))).)))......)))....)))))))))))).)))))	0.450 -22.58

rat

chromosome:1:129026516:129026615:-1

block1562113 [novel_cloningOK_shortStem_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	0.283	no	no	0.55/0.57	20/21/1.00	0.0	0.0	19	0	8	0	2	17	3arm	1	nd	0.30	4	30	8	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------CACUGAG--------------	30	miR-674
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S2	T4S1	T5S1	T5S2
	-----------------------------------------------------------------GCACTGAGATGGGAGGATGT--	20	7	12	3	1	2	1	1	2
	-----------------------------------------------------------------GCACTGAGATGGGAGGATGTG-	21	-	1	-	-	-	-	-	-
rat	atgtttcttccagaatcaattttagcagcagatgtcattgtgggagacttcacaaaagcaagataGCACTGAGATGGGAGGATGTgt
	***************************************************************************************
	-------------------------------------------------------------------------------------------------	ENSRNOT00000008304 ENSRNOG00000006174 Grid2
rat	.....((((((.......(((((((..((...(((..(((((((....)))))))..))).....)).))))))).)))))).....	0.460 -18.50

rat

chromosome:4:92736354:92736440:-1

novel_cloningOK_shortStem_loopOverlap_nonpairedHIGH_bulgeHIGH (2 loci)

block842447 [novel_cloningOK_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	0.098	no	no	0.35/0.38	19/21/0.94	0.0	0.0	23	0	5	0	3	-6	5arm_loop	3	nd	0.38	7	31	5	na	na

		reads	miRBase family seed
seed	----GACAAAA------------------------------------------------------	31	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S2	T5S1
	---TGACAAAATGTAACCCTACTC-----------------------------------------	21	-	1	1	1	23
	---TGACAAAATGTAACCCTACT------------------------------------------	20	1	-	-	-	2
	---TGACAAAATGTAACCCTAC-------------------------------------------	19	-	-	-	-	2
rat	ggaTGACAAAATGTAACCCTACTCctnagtccatatgngnggtttattttgttnttggaacatcc
	*****************************************************************
rat	(((((((((((((.((((......................))))))))))))........)))))	0.960 -10.25

rat

chromosome:1:48366044:48366108:-1

intergenic

block1066924 [novel_cloningOK_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	0.211	no	no	0.41/0.44	18/23/0.98	0.0	0.0	34	0	4	0	0	-4	3arm_loop	1	nd	0.32	4	42	4	na	na

		reads	miRBase family seed
seed	-------------------------GCACAGG---------------	42	novel
		len	cloning frequencies
			T1S1	T3S1	T3S2	T5S1
	------------------------TGCACAGGGAACTTTATGATCTC	23	4	1	1	34
	------------------------TGCACAGGGAACTTTATGATCT-	22	-	-	-	1
	------------------------TGCACAGGGAACTTTATG-----	18	-	-	-	1
rat	gggaggaaagagttcaaacccttgTGCACAGGGAACTTTATGATCTC
	***********************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000038623 ENSRNOG00000028243 NP_001103047.1
rat	((((....((((((.....(((((....)))))))))))....))))	0.990 -10.40

rat

chromosome:20:13189535:13189581:-1

novel_cloningOK_shortStem_mirtron_nonpairedHIGH (2 loci)

block817256 [novel_cloningOK_shortStem_mirtron_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	0.166	no	no	0.42/0.52	19/23/0.73	0.8	1.1	11	0	3	0	3	31	3arm	1	0	0.39	3	11	3	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------------------CUGACAA------------------	6	novel
seed	----------------------------------------------------------------------------------------------UGACAAC-----------------	3	novel
seed	------------------------------------------------------------------------------------------GGCCUGA---------------------	1	novel
seed	------------------------------------------------------------------------------------------------ACAACAA---------------	1	novel
		len	cloning frequencies
			T2S1	T2S2	T5S2
	--------------------------------------------------------------------------------------------CCTGACAACAACTTTCTCTG------	20	1	2	-
	--------------------------------------------------------------------------------------------CCTGACAACAACTTTCTCTGCAG---	23	2	-	-
	---------------------------------------------------------------------------------------------CTGACAACAACTTTCTCTG------	19	1	1	-
	--------------------------------------------------------------------------------------------CCTGACAACAACTTTCTCT-------	19	-	-	1
	-----------------------------------------------------------------------------------------------GACAACAACTTTCTCTGCAG---	20	1	-	-
	---------------------------------------------------------------------------------------------CTGACAACAACTTTCTCTGCA----	21	1	-	-
	-----------------------------------------------------------------------------------------GGGCCTGACAACAACTTTCTCTG------	23	1	-	-
rat	ggggtgcctggcatgtgagtgtcggcttggagtagccttgttctccctccctcacacttggggaggggcggggtgctgctgtcctggccGGGCCTGACAACAACTTTCTCTGCAGtcc
	**********************************************************************************************************************
	>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>	ENSRNOT00000020225 ENSRNOG00000014948 Okl38
rat	(((.(((..((...((...((((((((((((((((((((((...(((((((.((....))))))))))))))..)))))).......))))))).))))...))...))..))).)))	0.960 -49.91

rat

chromosome:19:49687521:49687638:1

block1311164 [novel_cloningOK_shortStem_mirtron_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	0.352	no	no	0.38/0.50	18/22/0.73	0.5	2.0	11	0	6	0	3	32	3arm	1	0	0.38	3	11	6	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------------------------------------UCCUUAA-----------------	8	novel
seed	-----------------------------------------------------------------------------------------------CUCCUUA------------------	2	novel
seed	--------------------------------------------------------------------------------------------UUUCUCC---------------------	1	novel
		len	cloning frequencies
			T1S1	T2S1	T3S1	T3S2	T5S1	T5S2
	-----------------------------------------------------------------------------------------------CTCCTTAATTCCGTCAACCCAG---	22	1	2	1	-	1	-
	-----------------------------------------------------------------------------------------------CTCCTTAATTCCGTCAACCC-----	20	-	-	-	1	-	1
	----------------------------------------------------------------------------------------------TCTCCTTAATTCCGTCAA--------	18	-	1	1	-	-	-
	-----------------------------------------------------------------------------------------------CTCCTTAATTCCGTCAACC------	19	-	-	1	-	-	-
	-------------------------------------------------------------------------------------------GTTTCTCCTTAATTCCGTCAA--------	21	-	-	-	1	-	-
rat	ggtggtggtggtgtgtgaacagaagatgggtgggggtgggtggcaagggttttgcatttcctctgcttcccagccctgtcttgttgcataaGTTTCTCCTTAATTCCGTCAACCCAGgcc
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>	ENSRNOT00000027867 ENSRNOG00000020542 NP_001099914.1
rat	(((((((..((....(((..(((((..(((..(((.((((.((((..((..........))..)))).)))).)))..)))...........)))))..)))...))..)).))...)))	0.560 -38.92

rat

chromosome:2:181418173:181418292:1

novel_gcHIGH_loopOverlap_nonpairedHIGH_bulgeHIGH (2 loci)

block854168 [novel_gcHIGH_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	0.899	no	no	0.95/0.95	20/20/1.00	0.0	0.0	1	0	1	0	37	-1	5arm_loop	2	nd	0.45	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------GGCCCUG---------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	-------------------------------------CGGCCCTGGCGGCCCGGCGG---------------------------------------------------------	20	1
rat	gggaacaagggcttcttggccgtggcagcggcggcggCGGCCCTGGCGGCCCGGCGGgtccgcgttttcaccgccaccacctcctccgtctcctcctcctcctcagcaccgccc
	******************************************************************************************************************
rat	(((.....(((((....((....((..((((.((.((.((...((((((....(((....))).......)))))))).)).)).))))..))....)).....))).)).)))	0.490 -42.00

rat

chromosome:1:68210532:68210645:-1

intergenic ## {Repeats: GC_rich 2 22 -1 class=Low_complexity,GC_rich 1 31 -1 class=Low_complexity}

block971247 [novel_gcHIGH_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	0.899	no	no	0.95/0.95	20/20/1.00	0.0	0.0	1	0	1	0	37	-1	5arm_loop	2	nd	0.45	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------GGCCCUG---------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	-------------------------------------CGGCCCTGGCGGCCCGGCGG---------------------------------------------------------	20	1
rat	gggaacaagggcttcttggccgtggcagcggcggcggCGGCCCTGGCGGCCCGGCGGgtccgcgttttcaccgccaccacctcctccgtctcctcctcctcctcagcaccgccc
	******************************************************************************************************************
rat	(((.....(((((....((....((..((((.((.((.((...((((((....(((....))).......)))))))).)).)).))))..))....)).....))).)).)))	0.490 -42.00

rat

chromosome:1:67083240:67083353:1

intergenic ## {Repeats: GC_rich 10 30 1 class=Low_complexity,GC_rich 1 31 1 class=Low_complexity}

novel_gcHIGH_nonpairedHIGH (2 loci)

block1965445 [novel_gcHIGH_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	0.096	no	no	0.91/0.91	22/22/1.00	0.0	0.0	1	0	1	0	7	17	3arm	1	nd	0.36	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------GGUUGGG---------------------	1	novel
		len	cloning frequencies
			T4S2
	-------------------------------------------------------------------------GGGTTGGGGGGCGGGGGGGGGG-------	22	1
rat	tccccaaccctacactagtttttctaaccaggaactcaaggcaggaacctggggtggggtaggggccggggccGGGTTGGGGGGCGGGGGGGGGGcgggggg
	******************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000046940 ENSRNOG00000012094 Ltbp2
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000031331 ENSRNOG00000012094 Ltbp2
rat	.((((..((((...((...((..((((((.((..((...(((....((((......))))....)))))..)).))))))..))...))..))))..)))).	0.740 -43.70

rat

chromosome:6:108888381:108888482:-1

Same_strand|Intronic_coding|ENSRNOT00000031331|ENSRNOG00000012094 ## ENSRNOG00000012094|protein_coding|Ltbp2|Latent-transforming growth factor beta-binding protein 2 precursor (LTBP-2). [Source:UniProtKB/Swiss-Prot;Acc:O35806] ## {Repeats: trf 9 25 0 class=trf,C-rich 3 54 -1 class=Low_complexity,C-rich 10 32 -1 class=Low_complexity,dust 108888388 108888410 0 class=dust}

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miR-Intess™