miR-Intess: classification

other hairpins

miRNAunknown_rep_Multihit_randfoldOK (4 loci)

block1945336 (miRNA) [miRNAunknown_rep_Multihit_randfoldOK]

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
Ensembl miRNA	0.001	no	SINE,SINE/Alu	0.60/0.60	20/20/1.00	0.0	0.0	2	0	1	0	18	5	3arm	255	nd	0.25	3	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------CCAGGAC------------------------------	2	novel
		len	cloning frequencies
			T2S1
	----------------------------------------------------TCCAGGACAGCCAGAGCTAC------------------	20	2
rat	gaggcaggcagatctctgtgagttcaaggccagcctggtcaacagagtgagtTCCAGGACAGCCAGAGCTACacagagaaaccctgtctc
	******************************************************************************************
	....>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063213 ENSRNOG00000041460
rat	((((((((....(((((((((((((..(((...((((((((......)))...)))))...))).))))).))))))))...))))))))	1.000 -44.10

rat

chromosome:6:75747096:75747185:-1

Same_strand|Exonic_non-coding|ENSRNOT00000063213|ENSRNOG00000041460 ## ENSRNOG00000041460|miRNA|| ## {Repeats: B1_Mur4 83 103 1 class=SINE/Alu,B1_Mur4 -5 145 1 class=SINE}

block2051938 (miRNA) [miRNAunknown_rep_Multihit_randfoldOK]

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
Ensembl miRNA	0.001	no	SINE,SINE/B4	0.52/0.52	21/21/1.00	0.0	0.0	1	0	1	0	26	0	3arm	253	nd	0.29	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------GUGUGUG---------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	--------------------------------------------------TGTGTGTGTGTGTGCATGCAC--------------------------	21	1
rat	tgcatgtgcgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgTGTGTGTGTGTGTGCATGCACatgcacacatgtacatgcacatgcac
	*************************************************************************************************
	.....................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	ENSRNOT00000063109 ENSRNOG00000041356
rat	((((((((((((((..((((((((((((((((((..((..((..((....))..))..))..))))))))))))))))))..)))))))))))))).	0.700 -57.50

rat

chromosome:6:110509526:110509622:1

Opposite_strand|Exonic_non-coding|ENSRNOT00000063109|ENSRNOG00000041356 ## ENSRNOG00000041356|miRNA|| ## {Repeats: (TG)n 1 60 1 class=Simple_repeat,trf 30 40 0 class=trf,trf 28 34 0 class=trf,dust 110509530 110509544 0 class=dust,(TG)n 46 60 1 class=Simple_repeat,trf 1 15 0 class=trf,B4 275 281 1 class=SINE/B4,B4 277 292 1 class=SINE}

block1082417 (miRNA) [miRNAunknown_rep_Multihit_randfoldOK]

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
Ensembl miRNA	0.001	no	LTR/ERVK	0.29/0.29	21/21/1.00	0.0	0.0	1	0	1	0	31	6	5arm	172	nd	0.00	0	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------AUGUAUG---------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	-------------------------------TATGTATGTGTGTGTGTATAT--------------------------------------------------------------------	21	1
rat	tatatatctctctctaatatatatatgtataTATGTATGTGTGTGTGTATATatatgtatatacatatatatatatatacacatacatatatacatatacatacacatacatatatatat
	************************************************************************************************************************
	.............................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063255 ENSRNOG00000041502
rat	(((((((..........(((.(((((((((((((((((((((((((((((((((((((....))))))))))))))))))))))))))))))))))))).))).........))))))).	0.990 -50.51

rat

chromosome:20:40980423:40980542:-1

Same_strand|Exonic_non-coding|ENSRNOT00000063255|ENSRNOG00000041502 ## ENSRNOG00000041502|miRNA|| ## {Repeats: RMER12 772 793 1 class=LTR/ERVK,trf 98 119 0 class=trf,RMER12 1240 1253 -1 class=LTR/ERVK,dust 40980491 40980512 0 class=dust,(TA)n 2 153 -1 class=Simple_repeat}

miRNAunknown_rep_lenNOK_Multihit_nonpairedHIGH_bulgeHIGH (4 loci)

block318012 (miRNA) [miRNAunknown_rep_lenNOK_Multihit_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
Ensembl miRNA	0.747	no	LTR,LTR/ERVL	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	13	0	3arm	11	nd	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	----------------------------------GCUGUGA------------------------	1	novel
		len	cloning frequencies
			T3S1
	---------------------------------GGCTGTGAATGGAAGTCCA-------------	19	1
rat	ctgtagtcaaactccccaacaatggtcagcagcGGCTGTGAATGGAAGTCCAaggatctagcagt
	*****************************************************************
	.....................................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	ENSRNOT00000063325 ENSRNOG00000041572
rat	((((((((..(((..(((...((((((......))))))...))).))).....)).))).))).	0.420 -12.30

rat

chromosome:13:77185084:77185148:1

Opposite_strand|Exonic_non-coding|ENSRNOT00000063325|ENSRNOG00000041572 ## ENSRNOG00000041572|miRNA|| ## {Repeats: MT2_Rat2 -78 409 -1 class=LTR,MT2_Rat2 355 374 -1 class=LTR/ERVL}

block895565 (miRNA) [miRNAunknown_rep_lenNOK_Multihit_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
Ensembl miRNA	0.140	no	LTR,LTR/ERVL	0.32/0.32	19/19/0.00	0.0	0.0	1	0	1	0	19	7	3arm	43	nd	0.42	5	1	1	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------CUUCCAA------------------------------	1	novel
		len	cloning frequencies
			T5S1
	---------------------------------------------------------TCTTCCAATGTCCTTATAT-------------------	19	1
rat	gcagttgctcagtcccacaaggcaggcaggcaaagaagagagagagagaatctttctTCTTCCAATGTCCTTATATaggtctccagcagaaggtg
	***********************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<....	ENSRNOT00000063224 ENSRNOG00000041471
rat	((..(((((.((.((...((((((....((..(((((((((((.......)))))))))))))..)).)))).....)).))..)))))...)).	0.870 -26.00

rat

chromosome:1:165836281:165836375:-1

Opposite_strand|Exonic_non-coding|ENSRNOT00000063224|ENSRNOG00000041471 ## ENSRNOG00000041471|miRNA|| ## {Repeats: MT2_Rat2 1 487 -1 class=LTR,MT2_Rat2 272 291 -1 class=LTR/ERVL}

block1015555 (miRNA) [miRNAunknown_rep_lenNOK_Multihit_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
Ensembl miRNA	0.838	no	SINE,SINE/Alu	0.67/0.68	18/19/0.00	0.3	0.0	3	0	2	0	13	23	5arm	220	nd	0.37	4	3	2	na	na

		reads	miRBase family seed
seed	---------------GGCAGAG---------------------------------------------------------------------------------------------	2	novel
seed	--------------AGGCAGA----------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T3S1
	--------------AGGCAGAGGCAGGAGGAC-----------------------------------------------------------------------------------	18	-	2
	-------------GAGGCAGAGGCAGGAGGAC-----------------------------------------------------------------------------------	19	1	-
rat	ccccagcacttggGAGGCAGAGGCAGGAGGACgtaaggtgagaggccaacctatgatgcatagcaagttccaggccaccagtgacactttttctcaatctccggggattcttggg
	*******************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042088 ENSRNOG00000034303 Spon1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000049946 ENSRNOG00000034303 Spon1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000044994 ENSRNOG00000034303 Spon1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000055130 ENSRNOG00000034303 Spon1
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.........................................................................................	ENSRNOT00000054414 ENSRNOG00000036292
rat	.(((((..(((.(((((..((((.(((((.......(((....((((((((((((...)))))...)))...))))))).......)))))))))..))))).)))....)))))	0.950 -31.74

rat

chromosome:1:171870061:171870175:1

Same_strand|Intronic_coding|ENSRNOT00000044994|ENSRNOG00000034303 ## Same_strand|Exonic_non-coding|ENSRNOT00000054414|ENSRNOG00000036292 ## ENSRNOG00000036292|miRNA|| ## ENSRNOG00000034303|protein_coding|Spon1|Spondin-1 precursor (F-spondin). [Source:UniProtKB/Swiss-Prot;Acc:P35446] ## {Repeats: B1F2 41 60 1 class=SINE/Alu,B1F2 2 139 1 class=SINE}

block2138776 (miRNA) [miRNAunknown_rep_lenNOK_Multihit_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
Ensembl miRNA	0.015	no	LINE,LINE/L1,SINE	0.63/0.65	19/20/0.50	0.5	0.0	2	0	1	0	18	4	3arm	262	nd	0.37	4	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------AGCCAUC------------------------------	1	novel
seed	---------------------------------------------------------GCCAUCU-----------------------------	1	novel
		len	cloning frequencies
			T1S1
	--------------------------------------------------------AGCCATCTCTCCAGCCCGA------------------	19	1
	-------------------------------------------------------GAGCCATCTCTCCAGCCCGA------------------	20	1
rat	ttgagttaattttatattcttatatttttggttgtgagcctagcctttaacggctGAGCCATCTCTCCAGCCCGAgttaattttatactcaat
	*********************************************************************************************
	.........................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	ENSRNOT00000054629 ENSRNOG00000036522
rat	(((((((((..(((.((((........((((..(((.((.(((((......))))).)))))....))))...)))))))..))).)))))).	0.490 -20.50

rat

chromosome:7:94029460:94029552:-1

Opposite_strand|Exonic_non-coding|ENSRNOT00000054629|ENSRNOG00000036522 ## ENSRNOG00000036522|miRNA|| ## {Repeats: B4 2 47 -1 class=SINE,L1_Rat3 4231 4251 -1 class=LINE/L1,L1_Rat3 3940 4281 -1 class=LINE}

miRNAunknown_rep_lenNOK_Multihit_randfoldOK (4 loci)

block157865 (miRNA) [miRNAunknown_rep_lenNOK_Multihit_randfoldOK]

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
Ensembl miRNA	0.001	no	LINE,LINE/L1	0.39/0.39	18/18/0.00	0.0	0.0	1	0	1	0	23	11	3arm	269	nd	0.11	2	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------UGCAUAC---------------------------------	1	novel
		len	cloning frequencies
			T2S2
	-------------------------------------------------------------------ATGCATACACACACATAC-----------------------	18	1
rat	gtttgtatgtatgtatttagtgatatgtgtgtgtgatatgtgatatatatcatttagtgatgcatatATGCATACACACACATACacacacacacacacacacacaca
	************************************************************************************************************
	...........................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.....	ENSRNOT00000063181 ENSRNOG00000041428
rat	((.(((.(((.(((.....(((...((((((((((.((((((((((.((((((...)))))).)))).))))))))))))))))..)))....))).))).))).)).	0.500 -33.00

rat

chromosome:11:43420669:43420776:1

Same_strand|Exonic_non-coding|ENSRNOT00000063181|ENSRNOG00000041428 ## ENSRNOG00000041428|miRNA|| ## {Repeats: trf 32 43 0 class=trf,dust 43420773 43420784 0 class=dust,(CA)n 1 15 1 class=Simple_repeat,Lx9 7509 7513 1 class=LINE/L1,(CA)n 1 46 1 class=Simple_repeat,Lx9 7230 7515 1 class=LINE}

block675547 (miRNA) [miRNAunknown_rep_lenNOK_Multihit_randfoldOK]

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
Ensembl miRNA	0.001	no	LTR	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	19	18	5arm	15	nd	0.17	2	1	1	na	na

		reads	miRBase family seed
seed	--------------------GCAUGUG------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	-------------------TGCATGTGCTTGCATGTG--------------------------------------------------------------------------------	18	1
rat	agtgtttgccattcatgtgTGCATGTGCTTGCATGTGtgtatgaatatgtatgttcataaacagacatgtacatacatacatacatattcacacatgcacatacagaggtgcatcac
	*********************************************************************************************************************
	-------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000042430 ENSRNOG00000029235 Sfmbt2
	......<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<...........................	ENSRNOT00000063160 ENSRNOG00000041407
rat	.(((..(((..(((.((((((((((((..((.(((((((((((.((((((.((((....)))).)))))).))))))))))).))......))))))))))))..)))..))).)))	1.000 -46.20

rat

chromosome:17:79292594:79292710:1

Opposite_strand|Intronic_coding|ENSRNOT00000042430|ENSRNOG00000029235 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000051529|ENSRNOG00000029235 ## Opposite_strand|Exonic_non-coding|ENSRNOT00000063160|ENSRNOG00000041407 ## ENSRNOG00000041407|miRNA|| ## ENSRNOG00000029235|protein_coding|Sfmbt2|Scm-like with four mbt domains 2 Gene [Source:MGI (curated);Acc:Sfmbt2-001] ## {Repeats: trf 691 709 0 class=trf,(CATA)n 3 78 1 class=Simple_repeat,(CATA)n 3 10 1 class=Simple_repeat,RMER12 728 850 1 class=LTR}

block1974990 (miRNA) [miRNAunknown_rep_lenNOK_Multihit_randfoldOK]

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
Ensembl miRNA	0.001	no	SINE,SINE/Alu	0.58/0.58	19/19/0.00	0.0	0.0	1	0	1	0	25	10	5arm	257	nd	0.21	2	1	1	na	na

		reads	miRBase family seed
seed	--------------------------CUCUGUG------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	-------------------------TCTCTGTGAGTTCGAGGCC-------------------------------------------------------------------	19	1
rat	cacttgggaggcagaggaaggtggaTCTCTGTGAGTTCGAGGCCagcctggtctacagagagagttcaaggacagccaggactacacagagaaaccctgtctcaaaaaagt
	***************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000057540 ENSRNOG00000027300 NP_001102189.1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000057539 ENSRNOG00000027300 NP_001102189.1
	.................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063298 ENSRNOG00000041545
rat	.((((..(((((((.....(((...(((((((((((((..(((...((((..((........))..)).))...))).))))).)))))))).))))))))))....))))	0.890 -41.90

rat

chromosome:6:124745143:124745253:-1

Same_strand|Boundary_non-coding|ENSRNOT00000037892|ENSRNOG00000027300 ## Same_strand|Intronic_coding|ENSRNOT00000057539|ENSRNOG00000027300 ## Same_strand|Exonic_non-coding|ENSRNOT00000063298|ENSRNOG00000041545 ## ENSRNOG00000041545|miRNA|| ## ENSRNOG00000027300|protein_coding|NP_001102189.1|tetratricopeptide repeat domain 7B [Source:RefSeq_peptide;Acc:NP_001102189] ## {Repeats: B1_Mur4 0 150 1 class=SINE,trf 49 60 0 class=trf,B1_Mur4 60 79 1 class=SINE/Alu}

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miR-Intess™