miR-Intess: classification

other hairpins

novel_mirtron_randfoldOK_nonpairedHIGH_bulgeHIGH (9 loci)

block1880013 [novel_mirtron_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	0.002	no	no	0.57/0.59	21/23/1.00	0.0	0.8	4	0	1	0	21	11	3arm	1	0	0.33	4	4	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------UAACCUG------------------------------------	4	novel
		len	cloning frequencies
			T1S2
	--------------------------------------------------------ATAACCTGCACCCCTGCCTCAGT---------------------	23	2
	--------------------------------------------------------ATAACCTGCACCCCTGCCTCA-----------------------	21	1
	--------------------------------------------------------ATAACCTGCACCCCTGCCTCAG----------------------	22	1
rat	ggcagagctctgtaggttggggcaggcagggagggtgaagttgttgctgcgccccaATAACCTGCACCCCTGCCTCAGTtctttccttacggagacgcct
	****************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000020486 ENSRNOG00000015193 Hpcal4
rat	(((....(((((((((((((((((((((((..(((((.(((....))).)))))......)))))....))))))))).......)))))))))..))).	0.760 -45.61

rat

chromosome:5:142495894:142495993:1

novel_multiarm (9 loci)

block1499842 [novel_multiarm]

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	0.361	no	no	0.37/0.54	19/24/0.84	0.0 0.0 0.0	0.0 0.0 1.5	26 5 2	0 0 0	1 1 1	0 0 0	25 33 41	2 -5 -18	5arm 5arm_loop_3arm 5arm_loop_3arm	1 2 2	nd nd nd	0.20 0.47 0.46	2 6 7	37	1	na	na

		reads	miRBase family seed
seed	--------------------------AGGAUGU-----------------------------------------------------------------	26	novel
seed	----------------------------------AACUGCU---------------------------------------------------------	6	novel
seed	------------------------------------------CCAUAGU-------------------------------------------------	2	novel
seed	-----------------------------------ACUGCUU--------------------------------------------------------	1	novel
seed	-------------------------UAGGAUG------------------------------------------------------------------	1	novel
seed	-------------------------------GUUAACU------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------TAGGATGTTAACTGCTTCCA-----------------------------------------------------	20	26
	---------------------------------TAACTGCTTCCATAGTCTG----------------------------------------------	19	5
	----------------------------------AACTGCTTCCATAGTCTGCA--------------------------------------------	20	1
	---------------------------------TAACTGCTTCCATAGTCTGC---------------------------------------------	20	1
	------------------------------TGTTAACTGCTTCCATAGTCTG----------------------------------------------	22	1
	------------------------TTAGGATGTTAACTGCTTC-------------------------------------------------------	19	1
	-----------------------------------------TCCATAGTCTGCATGAGGAGGTGG---------------------------------	24	1
	-----------------------------------------TCCATAGTCTGCATGAGGAGG------------------------------------	21	1
rat	ttgatgagtgtgttcttctttttgtTAGGATGTTAACTGCTTCCAtagtctgcatgaggaggtggttattcaattttccttcccagatgctccttgac
	**************************************************************************************************
rat	((((.((((((..........(((..((((((.((((..(((((.((.......)).)))))..))))..))....))))...))))))))).)))).	0.710 -19.40

rat

chromosome:3:141756597:141756694:1

intergenic

sblock11489 [novel_multiarm]

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	0.041	no	no	0.55/0.76	20/21/1.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	0 32	34 1	5arm 3arm	1 1	nd nd	0.43 0.20	5 2	2	2	na	na

		reads	miRBase family seed
seed	-GCCCCCA---------------------------------------------------------------------------------------------------------	1	novel
seed	--------------------------------------------------------------UUGCAGG--------------------------------------------	1	novel
		len	cloning frequencies
			T2S2	T3S2
	-------------------------------------------------------------CTTGCAGGTGGCTGTTCCTA--------------------------------	20	-	1
	CGCCCCCAAAAGCCCCGGACC--------------------------------------------------------------------------------------------	21	1	-
rat	CGCCCCCAAAAGCCCCGGACCggagtcacttttccggagcaagtctcttccagggtatttcCTTGCAGGTGGCTGTTCCTAgggaagtatcttgtccagattcttggcctttg
	*****************************************************************************************************************
rat	......((((.(((..((((.(((...(((((((.(((((.((((.(((.(((((.....))))).))).)))))))))..))))))).))).))))........))).))))	0.630 -37.70

rat

chromosome:7:127794234:127794346:1

intergenic

sblock12560 [novel_multiarm]

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	0.171	no	no	0.48/0.50	20/21/1.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	30 1	5 31	5arm 3arm	1 2	nd nd	0.40 0.29	4 3	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------------GAGAAUG--------------	1	novel
seed	-------------------------------GACAGCU------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------------------------------------------------------------------------------TGAGAATGTGACACCAGTGTC-	21	1
	------------------------------TGACAGCTGTGAGTGAGACT------------------------------------------------------------------	20	1
rat	ggcttgggtgtaccgttctgccacccagaaTGACAGCTGTGAGTGAGACTtttctagtgtccaagggtttacttgctgcacagctccatgcctcTGAGAATGTGACACCAGTGTCc
	********************************************************************************************************************
rat	(((...(((((..((((((......(((((((..(((((((((..((....((((........))))....))..)).))))))).)))...))))))))))..)))))...))).	0.600 -36.80

rat

chromosome:9:105069320:105069435:1

intergenic

sblock2136 [novel_multiarm]

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	0.105	no	no	0.73/0.89	19/22/0.80	0.0 0.0 0.0	0.0 0.5 1.0	1 2 2	0 0 0	1 2 1	0 0 0	3 34 11	32 2 25	5arm 3arm 3arm	1 1 1	98 38 15	0.26 0.27 0.20	3 4 1	5	3	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------------------------GCCCUGC-------------------------	2	novel
seed	-------------------------------------------------------------AGGGCUC------------------------------------------------	2	novel
seed	----CCCCCGC---------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T5S2
	------------------------------------------------------------CAGGGCTCGGTACCGCGCACC-----------------------------------	21	1	-	-
	-----------------------------------------------------------------------------------CGCCCTGCACTGACTGCCGCGC-----------	22	1	-	-
	-----------------------------------------------------------------------------------CGCCCTGCACTGACTGCCGC-------------	20	1	-	-
	---TCCCCCGCGGCGGGCCCAG----------------------------------------------------------------------------------------------	19	-	1	-
	------------------------------------------------------------CAGGGCTCGGTACCGCGCACCA----------------------------------	22	-	-	1
rat	gccTCCCCCGCGGCGGGCCCAGgcatggggttccgcggcccgagcccctctgcaggcgtgCAGGGCTCGGTACCGCGCACCAcCGCCCTGCACTGACTGCCGCGCggtaccctgcg
	********************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>	ENSRNOT00000025084 ENSRNOG00000018553 Pitpnm1
rat	((....((((((((((...((((((.(((((..(((((.((((((((...((((....))))))))))))..)))))....))).)).))).))).)))))))).))......)).	0.990 -61.60

rat

chromosome:1:206685066:206685181:1

Same_strand|Intronic_non-coding|ENSRNOT00000025084|ENSRNOG00000018553 ## ENSRNOG00000018553|protein_coding|Pitpnm1|Membrane-associated phosphatidylinositol transfer protein 1 (Phosphatidylinositol transfer protein, membrane-associated 1) (Pyk2 N-terminal domain-interacting receptor 2) (NIR-2). [Source:UniProtKB/Swiss-Prot;Acc:Q5U2N3] ## {SimpF: oe = 0.76 1 CpG}

sblock3398 [novel_multiarm]

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	0.093	no	no	0.42/0.50	21/24/1.00	0.0 1.0	0.0 0.0	1 6	0 0	1 1	0 0	16 10	-8 0	5arm_loop_3arm 3arm	1 1	nd nd	0.46 0.29	8 2	7	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------GGAAGUG--------------------------	4	novel
seed	--------------------------------------------AGUGAAA-----------------------	2	novel
seed	-----------------AUGCCUU--------------------------------------------------	1	miR-532
		len	cloning frequencies
			T1S1	T5S1
	----------------------------------------TGGAAGTGAAAGGTCACTGTGCAG----------	24	-	4
	-------------------------------------------AAGTGAAAGGTCACTGTGCAG----------	21	-	2
	----------------TATGCCTTAGACACCAGTCATCAA----------------------------------	24	1	-
rat	actggttcttgtgctatatgccttagacaccagtcatcaaTGGAAGTGAAAGGTCACTGTGCAGcgggacccag
	**************************************************************************
rat	.((((.((((((((.(((((((((..((.(((........)))..))..)))).)).)))))).))))).))))	0.880 -21.90

rat

chromosome:12:5607671:5607744:1

intergenic

sblock40 [novel_multiarm]

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	0.221	no	no	0.38/0.53	19/24/0.80	0.0 1.0 0.0	0.0 0.5 0.0	1 2 2	0 0 0	1 2 1	0 0 0	0 21 14	42 8 19	5arm 3arm 3arm	1 1 1	nd nd nd	0.68 0.22 0.38	6 3 3	5	2	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------------GAUCUCU---------------------------	2	novel
seed	--------------------------------------------------------------------------GACUGGG--------------------------------------	1	novel
seed	-UCAGGAU---------------------------------------------------------------------------------------------------------------	1	novel
seed	----------------------------------------------------------------------------CUGGGUC------------------------------------	1	novel
		len	cloning frequencies
			T3S2	T5S1
	------------------------------------------------------------------------------------TGATCTCTTTGTGTTAGGTGT--------------	21	-	2
	TTCAGGATGTGGCTGCAGA----------------------------------------------------------------------------------------------------	19	-	1
	-------------------------------------------------------------------------GGACTGGGTCTTGATCTCTTTGTG----------------------	24	1	-
	---------------------------------------------------------------------------ACTGGGTCTTGATCTCTTTGTGT---------------------	23	-	1
rat	TTCAGGATGTGGCTGCAGAttaagtgttgaaggctgagtcaggaacctggctgcttcctccagctggagcactGGACTGGGTCTTGATCTCTTTGTGTTAGGTGTttaggaaagctgca
	***********************************************************************************************************************
	---------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000044049 ENSRNOG00000040148
rat	.......((..(((.....(((((..((.((.((.((((((((.((((((((.....((((....))))....)).))))))))))).)))...)).)).))..)))))...)))..))	0.960 -36.30

rat

chromosome:1:13908121:13908239:-1

Opposite_strand|Intronic_coding|ENSRNOT00000044049|ENSRNOG00000040148 ## ENSRNOG00000040148|protein_coding||

sblock4753 [novel_multiarm]

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	0.727	no	no	0.45/0.71	20/21/1.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	20 1	1 39	5arm 3arm	6 6	nd nd	0.24 0.55	2 8	2	2	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------------GUCCUAU-------------	1	novel
seed	---------------------GGGGUGG-------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T5S1
	--------------------------------------------------------------------------------------AGTCCTATACATCTACCAGC-	20	-	1
	--------------------GGGGGTGGTCCTAGCCCAGGT------------------------------------------------------------------	21	1	-
rat	ggctctaagaacaactggagGGGGGTGGTCCTAGCCCAGGTgccgatcatgaagggcaggttttacatcacctacgagaaagatccAGTCCTATACATCTACCAGCt
	***********************************************************************************************************
rat	((((...(((...((((((.(((((((..(((.((((..(((.....)))...))))))).....)))).)))..........))))))........)))...))))	0.760 -26.10

rat

chromosome:16:27988013:27988119:-1

intergenic

sblock510 [novel_multiarm]

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	0.195	no	no	0.43/0.62	21/21/1.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	31 11	0 25	5arm 3arm	1 1	nd nd	0.48 0.19	3 1	2	2	na	na

		reads	miRBase family seed
seed	--------------------------------ACGCUAG---------------------------------------------------------------------------	1	novel
seed	-----------------------------------------------------------------------------------GCUUCGG------------------------	1	novel
		len	cloning frequencies
			T3S2	T5S1
	-------------------------------AACGCTAGTCTCCGAAAAGTT--------------------------------------------------------------	21	-	1
	----------------------------------------------------------------------------------CGCTTCGGGTGATTTCGAGGG-----------	21	1	-
rat	gcgaggacccacggaatcctccgaacgttgaAACGCTAGTCTCCGAAAAGTTaccgcaacttgggcagccggcaaaaatcctCGCTTCGGGTGATTTCGAGGGcgaccgtcgtc
	******************************************************************************************************************
rat	((((((.(((.(((((((.((((((((..((...((..((..((...(((((.....))))).))..))..)).....))..)).)))))).))))))).)))...)).)))).	0.990 -37.70

rat

chromosome:1:67517269:67517382:-1

intergenic ## {SimpF: oe = 1.00 -1 CpG}

sblock6767 [novel_multiarm]

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	0.485	no	no	0.48/0.68	19/21/0.78	0.0 0.0 0.0 0.2	0.0 0.0 0.0 0.0	2 1 1 5	0 0 0 0	1 1 1 2	0 0 0 0	4 50 31 26	40 -6 -2 2	5arm 5arm_loop_3arm 3arm_loop 3arm	1 1 1 1	nd nd nd nd	0.48 0.43 0.26 0.20	6 5 2 2	9	2	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------AGUGGAU--------------------------------------	4	novel
seed	-----UGAAGCC----------------------------------------------------------------------------------------------------------	2	novel
seed	---------------------------------------------------------------------UGCUAGU------------------------------------------	1	novel
seed	--------------------------------------------------------------------------GUGGAUC-------------------------------------	1	novel
seed	---------------------------------------------------GUUUCUC------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2	T5S1
	------------------------------------------------------------------------TAGTGGATCCAGACGGCCCC--------------------------	20	2	2
	----TTGAAGCCGTTAGTTCTCCCC---------------------------------------------------------------------------------------------	21	-	2
	-------------------------------------------------------------------------AGTGGATCCAGACGGCCCC--------------------------	19	-	1
	--------------------------------------------------TGTTTCTCTGCTGGTTGACTG-----------------------------------------------	21	-	1
	--------------------------------------------------------------------CTGCTAGTGGATCCAGACG-------------------------------	19	-	1
rat	ccctTTGAAGCCGTTAGTTCTCCCCtgggctccaagggctctgccaccacTGTTTCTCTGCTGGTTGACTGCTAGTGGATCCAGACGGCCCCtctgaccctggctatgtgcttggggg
	**********************************************************************************************************************
rat	((((...((((((.(((......((.(((.((..((((....(((....(((..(((..((((((.....)))))))))..)))..)))))))..))))).))))))).)))))))).	0.840 -37.70