miR-Intess: classification

other hairpins

miRNAunknown_Multihit_loopOverlap_randfoldOK (3 loci)

block737475 (miRNA) [miRNAunknown_Multihit_loopOverlap_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	no	0.41/0.41	22/22/1.00	0.0	0.0	1	0	1	0	10	-4	3arm_loop	111	nd	0.14	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------UAUACAU------------------------	1	novel
		len	cloning frequencies
			T2S1
	----------------------------GTATACATACACACACACACAC----------	22	1
rat	gtgtgtgtgtgtgtgtgtgtgtgtatgtGTATACATACACACACACACACacacacacac
	************************************************************
	....>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063019 ENSRNOG00000041266
rat	((((((((((((((((((((((((((((....))))))))))))))))))))))))))))	1.000 -50.80

rat

chromosome:18:31776789:31776848:1

Same_strand|Exonic_non-coding|ENSRNOT00000063019|ENSRNOG00000041266 ## ENSRNOG00000041266|miRNA|| ## {Repeats: (CA)n 2 46 1 class=Simple_repeat,(CA)n 2 19 1 class=Simple_repeat,dust 31776789 31776791 0 class=dust,(TG)n 29 31 1 class=Simple_repeat,dust 31776852 31776865 0 class=dust,trf 28 45 0 class=trf,trf 1 3 0 class=trf,(TG)n 2 31 1 class=Simple_repeat}

block675541 (miRNA) [miRNAunknown_Multihit_loopOverlap_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	no	0.42/0.42	24/24/1.00	0.0	0.0	1	0	1	0	34	-1	5arm_loop	56	nd	0.21	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------GUGUGUG------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	----------------------------------TGTGTGTGTGTGTGTGTGTATATC--------------------------------------------------------------	24	1
rat	tgtgtctgtgtgtgtgtttgcatatgtgtgtatgTGTGTGTGTGTGTGTGTGTATATCttcatatacacacatgtacatactcacagacatatacacacatgcacatatataggggtacc
	************************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000042430 ENSRNOG00000029235 Sfmbt2
	...........<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<.......................	ENSRNOT00000063076 ENSRNOG00000041323
rat	.((..((.(((((((((..((((.(((((((((((.((((((((..(((((((((((....)))))))))))..))))....)))).))))))))))).))))))))))))).))..)).	1.000 -60.80

rat

chromosome:17:79285754:79285873:1

Opposite_strand|Intronic_coding|ENSRNOT00000042430|ENSRNOG00000029235 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000051529|ENSRNOG00000029235 ## Opposite_strand|Exonic_non-coding|ENSRNOT00000063076|ENSRNOG00000041323 ## ENSRNOG00000041323|miRNA|| ## ENSRNOG00000029235|protein_coding|Sfmbt2|Scm-like with four mbt domains 2 Gene [Source:MGI (curated);Acc:Sfmbt2-001] ## {Repeats: dust 79285754 79285773 0 class=dust,(TG)n 35 54 1 class=Simple_repeat,trf 1 20 0 class=trf,trf 184 208 0 class=trf,(TG)n 2 54 1 class=Simple_repeat}

miRNAunknown_lenNOK (3 loci)

block596083 (miRNA) [miRNAunknown_lenNOK]

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	0.299	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	7	17	3arm	8	nd	0.26	2	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------------GGCACAC------------------	1	novel
		len	cloning frequencies
			T1S1
	-----------------------------------------------------------------------AGGCACACAGCATAGCGTT-------	19	1
rat	gcctggaggccctgattggccagtgaatcttgagtgacatcaacccatcccgtaggattagagtgcgctgaAGGCACACAGCATAGCGTTtcctggc
	*************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.........	ENSRNOT00000043659 ENSRNOG00000036404
rat	(((.((((((.(((....((..(((..((((.((((.(((......((((....))))....))))))).))))..))).)).))).)))))).)))	0.670 -30.30

rat

chromosome:17:7856943:7857039:-1

Same_strand|Exonic_non-coding|ENSRNOT00000043659|ENSRNOG00000036404 ## ENSRNOG00000036404|miRNA||

block875797 (miRNA) [miRNAunknown_lenNOK]

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	0.157	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	11	10	3arm	6	nd	0.21	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------GAUCUGG----------------------	1	novel
		len	cloning frequencies
			T1S2
	--------------------------------------------------TGATCTGGCCAAAGCCTGA-----------	19	1
rat	gcttttatacttgttagactctggttagagtacactaatcggctggtaccTGATCTGGCCAAAGCCTGActttaaactgc
	********************************************************************************
	.>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.	ENSRNOT00000062154 ENSRNOG00000040401
rat	((.((((.....(((((.((.((((((((((((.((....))...))))....)))))))).)).)))))..))))..))	0.970 -18.70

rat

chromosome:1:115592418:115592497:-1

Same_strand|Exonic_non-coding|ENSRNOT00000062154|ENSRNOG00000040401 ## ENSRNOG00000040401|miRNA||

block875889 (miRNA) [miRNAunknown_lenNOK]

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	0.064	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	28	7	3arm	6	nd	0.16	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------GAUCUGG---------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	--------------------------------------------------------------------TGATCTGGCCAAAGCCTGA----------------------------	19	1
rat	cactctccggccttaggggtttttttcctgttagacttctggctagagtccactaatcttctggtaccTGATCTGGCCAAAGCCTGActataacctgctccagagaggaagactg
	*******************************************************************************************************************
	.........................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>......................	ENSRNOT00000062990 ENSRNOG00000041237
rat	((.(((((...(((.(((((.........(((((.(((.((((((((....((((......))))......))))))))))).)))))........))))).))).))).)).))	0.740 -33.33

rat

chromosome:1:115856368:115856482:-1

Same_strand|Exonic_non-coding|ENSRNOT00000062990|ENSRNOG00000041237 ## ENSRNOG00000041237|miRNA||

miRNAunknown_lenNOK_Multihit_nonpairedHIGH (3 loci)

block487552 (miRNA) [miRNAunknown_lenNOK_Multihit_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
Ensembl miRNA	0.123	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	14	0	5arm	18	nd	0.39	3	1	1	na	na

		reads	miRBase family seed
seed	---------------GCGAGUA------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	--------------GGCGAGTATCTCTTTGAG--------------------------------------------	18	1
rat	cccaggcatctctgGGCGAGTATCTCTTTGAGctccccactctcaaggatgactagacctctgagccttccaaggg
	****************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>..........	ENSRNOT00000054499 ENSRNOG00000036382
rat	(((((((.((...((...(((...((((((((.........))))))))..)))...))...)))))).....)))	0.840 -22.20

rat

chromosome:15:36824391:36824466:1

Same_strand|Exonic_non-coding|ENSRNOT00000054499|ENSRNOG00000036382 ## ENSRNOG00000036382|miRNA||

block609715 (miRNA) [miRNAunknown_lenNOK_Multihit_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
Ensembl miRNA	0.380	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	10	13	5arm	18	nd	0.44	3	1	1	na	na

		reads	miRBase family seed
seed	-----------GCGAGUA------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	----------GGCGAGTATCTCTTTGAG--------------------------------------------------	18	1
rat	ggcatctctgGGCGAGTATCTCTTTGAGcacctcactgtcaagcatgactaggaggcctctgagccttccaaggggct
	******************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.............	ENSRNOT00000054514 ENSRNOG00000036399
rat	(((..((((.((.(((...(((...(((..((((.((((((....)))).)))))).))).))).))))).)))))))	0.920 -23.10

rat

chromosome:17:33448444:33448521:-1

Same_strand|Exonic_non-coding|ENSRNOT00000054514|ENSRNOG00000036399 ## ENSRNOG00000036399|miRNA||

block1063479 (miRNA) [miRNAunknown_lenNOK_Multihit_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
Ensembl miRNA	0.025	no	no	0.79/0.79	19/19/0.00	0.5	0.5	2	0	1	0	12	26	3arm	623	nd	0.32	3	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------UGGGCUG------------------------	1	novel
seed	------------------------------------------------------------------------------------------GGGCUGG-----------------------	1	novel
		len	cloning frequencies
			T3S1
	-----------------------------------------------------------------------------------------TGGGCTGGGCTGGGCTGGG------------	19	1
	----------------------------------------------------------------------------------------CTGGGCTGGGCTGGGCTGG-------------	19	1
rat	gcagtgttctagaagtcggggccagcctgcgtgtgttgggcttctcggagggacagcaaggggctgggctgggcggggctgggcggggCTGGGCTGGGCTGGGCTGGGcggggcgaggcg
	************************************************************************************************************************
	............................................................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063534 ENSRNOG00000041781
rat	((..((..((...((((.((.(((((((((...((((.((((((((((.....((((.....))))..)))))..))))).))))..)).))))))).)).))))....))..))..)).	0.660 -54.50

rat

chromosome:20:8145549:8145668:-1

Same_strand|Exonic_non-coding|ENSRNOT00000063534|ENSRNOG00000041781 ## ENSRNOG00000041781|miRNA|| ## {Repeats: (CAGCC)n 4 71 -1 class=Simple_repeat,trf 21 41 0 class=trf,dust 8145561 8145581 0 class=dust,(CAGCC)n 24 44 -1 class=Simple_repeat}

miRNAunknown_lenNOK_randfoldOK (3 loci)

block118553 (miRNA) [miRNAunknown_lenNOK_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	0.005	no	no	0.32/0.32	19/19/0.00	0.0	0.0	1	0	1	0	34	2	3arm	1	nd	0.16	1	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------CAAGGAU---------------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	--------------------------------------------------------------ACAAGGATGAATCTTTGTT----------------------------------	19	1
rat	ttgcgaggtgaaggctattaattacactgagtgacaaagactctccgtgctgtatgatcgacACAAGGATGAATCTTTGTTactgactgcaaataataggactgtggccacgtaa
	*******************************************************************************************************************
	...........<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<..................	ENSRNOT00000062129 ENSRNOG00000040376
rat	.((((.(((..((.((((((.((.((...(((((((((((.(((((.((.(((.......))))).))).)).)))))))))))...)).)).))))))..))...))).)))).	1.000 -34.30

rat

chromosome:11:33538453:33538567:-1

Opposite_strand|Exonic_non-coding|ENSRNOT00000062129|ENSRNOG00000040376 ## ENSRNOG00000040376|miRNA||

block875849 (miRNA) [miRNAunknown_lenNOK_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	0.005	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	22	7	3arm	6	nd	0.16	2	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------GAUCUGG---------------------------------	1	novel
		len	cloning frequencies
			T1S2
	------------------------------------------------------------------TGATCTGGCCAAAGCCTGA----------------------	19	1
rat	ccctccggctgcagggctttttttcctgttagacttctggctagagtccactaatcctctggtaccTGATCTGGCCAAAGCCTGActataacctgctccagagagga
	***********************************************************************************************************
	.......................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>................	ENSRNOT00000063693 ENSRNOG00000041940
rat	(((((.((..(((((............(((((.(((.((((((((....((((......))))......))))))))))).))))).....))))).)).))).)).	0.990 -35.73