miR-Intess: classification

other hairpins

novel_cloningOK_randfoldOK_nonpairedHIGH_bulgeHIGH (4 loci)

block1848466 [novel_cloningOK_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	0.60/0.69	18/26/0.88	0.0	0.0	9	0	5	0	31	8	5arm	1	nd	0.45	4	17	5	na	na

		reads	miRBase family seed
seed	--------------------------------GCCAAGC---------------------------------------------------------------------------------	16	novel
seed	-----------------------------------AAGCAGG------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T3S2	T4S1	T5S1
	-------------------------------TGCCAAGCAGGAGAAGCGTC---------------------------------------------------------------------	20	1	-	-	1	9
	-------------------------------TGCCAAGCAGGAGAAGCGTCCGG------------------------------------------------------------------	23	-	1	-	-	1
	-------------------------------TGCCAAGCAGGAGAAGCG-----------------------------------------------------------------------	18	-	-	1	-	-
	----------------------------------CAAGCAGGAGAAGCGTCCGGGGGT--------------------------------------------------------------	24	1	-	-	-	-
	-------------------------------TGCCAAGCAGGAGAAGCGTCCGGGGG---------------------------------------------------------------	26	-	-	-	-	1
	-------------------------------TGCCAAGCAGGAGAAGCGTCCG-------------------------------------------------------------------	22	-	-	-	-	1
rat	gctctgtccacagagagtgctgccatgcttcTGCCAAGCAGGAGAAGCGTCcgggggtctccggaacccttaaggaaagccgtctgcacagaagataagcattttctgtgagtcgtgagt
	************************************************************************************************************************
rat	((((((..(((((((((((((......((((((....(((((....((.(((.((((((....)).))))...)))..))..))))).))))))...)))))))))))))...)).))))	0.570 -47.40

rat

chromosome:5:79244959:79245078:1

intergenic

novel_lenNOK_5varHIGH_loopOverlap_mirtron (4 loci)

block1066846 [novel_lenNOK_5varHIGH_loopOverlap_mirtron]

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	0.50/0.53	19/20/0.43	1.3	0.9	7	0	1	0	31	-1	5arm	2	0	0.15	2	7	1	na	na

		reads	miRBase family seed
seed	-----------------------------------GUCCAUU---------------------------------------------------------------------	4	novel
seed	--------------------------------AAUGUCC------------------------------------------------------------------------	3	novel
		len	cloning frequencies
			T5S1
	----------------------------------TGTCCATTGCCTGACAGGA----------------------------------------------------------	19	4
	-------------------------------CAATGTCCATTGCCTGACAG------------------------------------------------------------	20	3
rat	accacaaaagcgcttggtggtttccctcagtCAATGTCCATTGCCTGACAGGAttcctgtggagcagggaggtcttgatgttgctgagcttggagcttgccgggtcagtgg
	***************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000038623 ENSRNOG00000028243 NP_001103047.1
rat	.((((......(((((((((.(((((((((.(((((((..((.(((((((((...)))))....)))).)).....))))))))))))...)))).)))))))))..))))	0.900 -38.90

rat

chromosome:20:13186506:13186616:-1

block1252477 [novel_lenNOK_5varHIGH_loopOverlap_mirtron]

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	0.814	no	no	0.56/0.67	18/19/0.00	2.3	2.7	3	0	2	0	35	-17	3arm_loop	1	4	0.22	3	3	2	na	na

		reads	miRBase family seed
seed	-------------------------------------------UGCCUUG--------------------------------------------------	1	novel
seed	---------------------------------------------CCUUGCG------------------------------------------------	1	novel
seed	------------------------------------------------UGCGGUG---------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	-----------------------------------------------TTGCGGTGAGTGGGAATG-----------------------------------	18	1	-
	--------------------------------------------GCCTTGCGGTGAGTGGGAA-------------------------------------	19	1	-
	------------------------------------------CTGCCTTGCGGTGAGTGG----------------------------------------	18	-	1
rat	gtgggcgggacctgaacggagcggcttccgctttccactttcCTGCCTTGCGGTGAGTGGGAATGagagcgggatcccctagggtgtgtggtggctagca
	****************************************************************************************************
	..........................................>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000047282 ENSRNOG00000031995 2810008M24Rik
rat	((.(((...(((...(((.((.((.(((((((((((((((..((((...)))).)))))))).....))))))).)).))....)))..))).))).)).	0.790 -34.20

rat

chromosome:2:39261960:39262059:1

block1826204 [novel_lenNOK_5varHIGH_loopOverlap_mirtron]

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	0.020	no	no	0.47/0.58	19/20/0.43	1.9	1.9	7	0	5	0	31	-1	5arm_loop	1	3	0.10	1	7	5	na	na

		reads	miRBase family seed
seed	-----------------------------------GUCUGGU---------------------------------------------------------------------------	3	novel
seed	--------------------------------------UGGUUGA------------------------------------------------------------------------	2	miR-380
seed	---------------------------------------GGUUGAG-----------------------------------------------------------------------	1	novel
seed	--------------------------------CCGGUCU------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S1	T5S1
	----------------------------------GGTCTGGTTGAGTAACACAG---------------------------------------------------------------	20	-	-	2	-	-
	-------------------------------------CTGGTTGAGTAACACAGTCC------------------------------------------------------------	20	-	-	-	1	-
	----------------------------------GGTCTGGTTGAGTAACACA----------------------------------------------------------------	19	1	-	-	-	-
	-------------------------------------CTGGTTGAGTAACACAGTC-------------------------------------------------------------	19	-	-	-	1	-
	-------------------------------GCCGGTCTGGTTGAGTAAC-------------------------------------------------------------------	19	-	-	-	-	1
	--------------------------------------TGGTTGAGTAACACAGTCC------------------------------------------------------------	19	-	1	-	-	-
rat	tctgactgcggttgctgttcagttcaatccaGCCGGTCTGGTTGAGTAACACAGTCCagggactgtgtctatggttgctccgcgggccgctttgccggctggtgcttttgtatcagg
	*********************************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000010655 ENSRNOG00000007719 Ccnc
	...........................................................................>>>>>>>>>>>>++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000043469 ENSRNOG00000007719 Ccnc
rat	.((((.(((((..((.............(((((((((((.((.(((((((((((((....)))))))).......))))).)).)).......))))))))).))..))))))))).	0.440 -46.36

rat

chromosome:5:36465470:36465586:1

block2123214 [novel_lenNOK_5varHIGH_loopOverlap_mirtron]

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	0.196	no	no	0.52/0.63	18/23/0.33	4.0	4.5	6	0	3	0	25	-1	3arm	1	3	0.19	2	6	3	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------UGCAGGU------------------------------------------	2	novel
seed	-------------------------------------------------------------CCGACCU------------------------------------------------	2	novel
seed	---------------------------------------------------------------------CAGGUAA----------------------------------------	1	novel
seed	-----------------------------------------------------------------CCUGCAG--------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T3S1	T5S1
	------------------------------------------------------------------CTGCAGGTAAGTGAGCTC--------------------------------	18	1	1	-
	------------------------------------------------------------GCCGACCTGCAGGTAAGTGAG-----------------------------------	21	-	-	1
	------------------------------------------------------------GCCGACCTGCAGGTAAGTG-------------------------------------	19	-	-	1
	----------------------------------------------------------------ACCTGCAGGTAAGTGAGC----------------------------------	18	-	1	-
	--------------------------------------------------------------------GCAGGTAAGTGAGCTCATCCTCT-------------------------	23	-	-	1
rat	cggcgcgtcctctaggacttacccagaaggcagctctctactcttaggtcaaaatggcggGCCGACCTGCAGGTAAGTGAGCTCATCCTCTtttgtgggtatcgtggggcggttgt
	********************************************************************************************************************
	...>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000037030 ENSRNOG00000024967 LOC690049
rat	((((.((.((.(((.((..((((((.((((.(((((.(((((..((((((.....((....))))))))..))).)).)))))...))....)).)))))))).))))))))))).	1.000 -40.60

rat

chromosome:7:67963645:67963760:-1

novel_lenNOK_5varHIGH_mirtron_nonpairedHIGH (4 loci)

block177242 [novel_lenNOK_5varHIGH_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	0.059	no	no	0.60/0.67	18/20/0.25	1.2	0.5	4	0	2	0	17	21	3arm	1	0	0.32	3	4	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------GCCUGUC---------------------------	2	novel
seed	--------------------------------------------------------------------------------AAUGCCU------------------------------	1	novel
seed	---------------------------------------------------------------------------------AUGCCUG-----------------------------	1	novel
		len	cloning frequencies
			T1S1	T2S2
	----------------------------------------------------------------------------------TGCCTGTCACCCTCCCAG-----------------	18	2	-
	-------------------------------------------------------------------------------CAATGCCTGTCACCCTCCC-------------------	19	1	-
	--------------------------------------------------------------------------------AATGCCTGTCACCCTCCCAG-----------------	20	-	1
rat	cctgggcatctcactggtaggttgggactgttgttgtaggactgggtgggaagccagggctctcttacctgctgttcagCAATGCCTGTCACCCTCCCAGgtggagctggcaacagg
	*********************************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000001384 ENSRNOG00000001047 Map2k7
	>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000061821 ENSRNOG00000001047 Map2k7
rat	((((.((..(((.((((.(((....(((...((((((.((((.(((((((((((....))).))))))))...)))).))))))...)))..))).))))...)))...))..))))	0.940 -45.80

rat

chromosome:12:1546357:1546473:-1

Same_strand|Intronic_coding|ENSRNOT00000001384|ENSRNOG00000001047 ## ENSRNOG00000001047|protein_coding|Map2k7|Dual specificity mitogen-activated protein kinase kinase 7 (EC 2.7.12.2) (MAP kinase kinase 7) (MAPKK 7) (MAPK/ERK kinase 7) (JNK-activating kinase 2) (c-Jun N-terminal kinase kinase 2) (JNK kinase 2) (JNKK 2). [Source:UniProtKB/Swiss-Prot;Acc:Q4KSH7]

block272834 [novel_lenNOK_5varHIGH_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	0.786	no	no	0.74/0.79	19/19/0.00	1.5	1.5	2	0	2	0	16	2	3arm	1	3	0.32	3	2	2	na	na

		reads	miRBase family seed
seed	-------------------------------------------CCGCCAC------------------------------	1	novel
seed	----------------------------------------------CCACGGG---------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S1
	---------------------------------------------GCCACGGGCACAGGAGAGC----------------	19	-	1
	------------------------------------------GCCGCCACGGGCACAGGAG-------------------	19	1	-
rat	gcctcatcacgctgacctctgcctgggatgtaaaccccacggGCCGCCACGGGCACAGGAGAGCtctcagcacctccggg
	********************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000005213 ENSRNOG00000003917 Uck2
rat	.(((......((((((((.((((((((.((....(((...))).)))).)))))).))).......)))))......)))	0.410 -23.61

rat

chromosome:13:82949294:82949373:-1

Same_strand|Boundary_non-coding|ENSRNOT00000005213|ENSRNOG00000003917 ## ENSRNOG00000003917|protein_coding|Uck2|uridine-cytidine kinase 2 [Source:RefSeq_peptide;Acc:NP_001095878] ## {SimpF: oe = 0.81 -1 CpG}

block1806304 [novel_lenNOK_5varHIGH_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	0.095	no	no	0.62/0.63	19/26/0.00	3.0	0.5	2	0	2	0	21	2	3arm	1	2	0.32	3	2	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------GCAUACC---------------------------------------	1	novel
seed	-----------------------------------------------------------------CAGUGAG---------------------------------	1	novel
		len	cloning frequencies
			T3S1	T5S2
	----------------------------------------------------------GGCATACCAGTGAGCAACGACCCACC---------------------	26	1	-
	----------------------------------------------------------------CCAGTGAGCAACGACCCAC----------------------	19	-	1
rat	ggagttgcgatagtgggagctggggtagttgtattcctcctccgcaagcaaagacagcGGCATACCAGTGAGCAACGACCCACCctcccagggctcaggactcca
	*********************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000018494 ENSRNOG00000013820 Tnfrsf14
rat	((((((..((...((((((...((((.(((((..((((...((((...........))))......)).))))))).))))...))))))....))..)))))).	0.790 -36.90

rat

chromosome:5:171729834:171729938:-1

block1355139 [novel_lenNOK_5varHIGH_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	0.828	no	no	0.58/0.63	19/22/0.33	2.3	0.3	3	0	3	0	10	30	5arm	1	1	0.32	3	3	3	na	na

		reads	miRBase family seed
seed	---------------CAGCCUG--------------------------------------------------------------------------------------------------	1	novel
seed	--------------GCAGCCU---------------------------------------------------------------------------------------------------	1	novel
seed	-----------CUGGCAG------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T3S2	T5S2
	-------------GGCAGCCTGTCAATCCCTC----------------------------------------------------------------------------------------	19	1	-	-
	----------ACTGGCAGCCTGTCAATCCCTC----------------------------------------------------------------------------------------	22	-	1	-
	--------------GCAGCCTGTCAATCCCTCA---------------------------------------------------------------------------------------	19	-	-	1
rat	agtgagtggcACTGGCAGCCTGTCAATCCCTCAgccgagcggccttcgagcccggtccacggcggctgctgactgggtgcgcggcaccggaggtggcggcggcgagttctcccgcctcat
	************************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000029600 ENSRNOG00000022162 NP_001101304.1
rat	.((((((((.(((.((.(((.((((...((((.((((.((.........((((((((...(((....))))))))))))).))))....))))))))))).)).)))....)))).))))	0.550 -50.60

rat

chromosome:3:13407218:13407337:-1

Same_strand|Boundary_non-coding|ENSRNOT00000029853|ENSRNOG00000022162 ## Same_strand|Intronic_non-coding|ENSRNOT00000029600|ENSRNOG00000022162 ## ENSRNOG00000022162|protein_coding|NP_001101304.1|pre B-cell leukemia transcription factor 3 [Source:RefSeq_peptide;Acc:NP_001101304] ## {SimpF: oe = 0.83 -1 CpG}

novel_lenNOK_5varHIGH_randfoldOK_nonpairedHIGH (4 loci)

block767887 [novel_lenNOK_5varHIGH_randfoldOK_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	0.009	no	no	0.60/0.67	24/25/0.67	1.3	1.7	3	0	1	0	10	0	5arm	2	nd	0.40	3	3	1	na	na

		reads	miRBase family seed
seed	-----------UGCUCCU--------------------------------------------------------------------	2	novel
seed	---------------CCUGCGC----------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	----------CTGCTCCTGCGCTGGCTCCTGCAA----------------------------------------------------	24	2
	--------------TCCTGCGCTGGCTCCTGCAAATGCA-----------------------------------------------	25	1
rat	tagatggatcCTGCTCCTGCGCTGGCTCCTGCAAATGCAaacaatgcaaatgcacctcctgcaagaaaagtgagttggatttattt
	**************************************************************************************
rat	.((((((((((.((((((...((.((...((((..((((.....))))..))))......)).))...)).)))).))))))))))	0.950 -26.90