miR-Intess: classification

other hairpins

miRNAunknown_multiarm_5varHIGH_loopOverlap (1 loci)

miRNAunknown_multiarm_DicerNOK_shortStem_5varHIGH_loopOverlap_mirtron (1 loci)

sblock2584 (miRNA) [miRNAunknown_multiarm_DicerNOK_shortStem_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
Ensembl miRNA	0.110	no	no	0.70/0.80	20/24/1.00	0.0 1.2	0.0 1.2	1 4	0 0	1 2	0 0	6 1	5 -3	5arm 3arm	1 1	33 1	0.40 0.15	3 1	5	2	0	5

		reads	miRBase family seed
seed	------------------------------------CCGAGCC----------------	2	novel
seed	-------CUCGCGA---------------------------------------------	1	novel
seed	----------------------------------GACCGAG------------------	1	novel
seed	---------------------------------------AGCCCCU-------------	1	novel
		len	cloning frequencies
			T1S1	T1S2
	-----------------------------------ACCGAGCCCCTGTGCCGCCC----	20	-	2
	---------------------------------TGACCGAGCCCCTGTGCCGCCCCC--	24	-	1
	------TCTCGCGAGCCCAGGGTGCA---------------------------------	20	-	1
	--------------------------------------GAGCCCCTGTGCCGCCCCCA-	20	1	-
rat	cctgggTCTCGCGAGCCCAGGGTGCAgccggacTGACCGAGCCCCTGTGCCGCCCCCAg
	***********************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>	ENSRNOT00000015092 ENSRNOG00000010771 Q9ERV0_RAT
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.....	ENSRNOT00000063374 ENSRNOG00000041621
rat	.(((((....(((.((.(((((.((...(((.....))).))))))).))))).)))))	1.000 -28.20

rat

chromosome:10:13846752:13846810:1

Same_strand|Exonic_non-coding|ENSRNOT00000063374|ENSRNOG00000041621 ## Same_strand|Intronic_coding|ENSRNOT00000015092|ENSRNOG00000010771 ## ENSRNOG00000010771|protein_coding|Q9ERV0_RAT|Pkd1 (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q9ERV0] ## ENSRNOG00000041621|miRNA||

miRNAunknown_multiarm_Multihit_loopOverlap_randfoldOK (1 loci)

block3087626 (miRNA) [miRNAunknown_multiarm_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	0.40/0.47	19/21/0.75	0.0 0.5	0.5 1.0	2 2	0 0	1 2	0 0	27 35	2 -8	5arm 5arm_loop_3arm	318 349	nd nd	0.00 0.35	0 7	4	2	na	na

		reads	miRBase family seed
seed	----------------------------UGUGUGU------------------------------------------------------------------------	2	novel
seed	------------------------------------UGUGUGU----------------------------------------------------------------	1	novel
seed	-------------------------------------GUGUGUG---------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T3S1
	-----------------------------------TTGTGTGTGTGTATGTGTGT----------------------------------------------------	20	-	1
	---------------------------GTGTGTGTTTGTGTGTGTGT------------------------------------------------------------	20	1	-
	------------------------------------TGTGTGTGTGTATGTGTGTGT--------------------------------------------------	21	1	-
	---------------------------GTGTGTGTTTGTGTGTGTG-------------------------------------------------------------	19	1	-
rat	tcatggcctttgtgtgtgtgtgcatatGTGTGTGTTTGTGTGTGTGTATGTGTGTGTgtacacatacacaagcatacacaaaatacacacaaataaacaaaaatgaa
	***********************************************************************************************************
	.............<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<.......	ENSRNOT00000063002 ENSRNOG00000041249
rat	((((....(((((.((((((((....(((((((((((((((((((((((........)))))))))))))))))))))))...)))))))).....))))).)))).	1.000 -49.50

rat

chromosome:X:134100254:134100360:1

Opposite_strand|Exonic_non-coding|ENSRNOT00000063002|ENSRNOG00000041249 ## ENSRNOG00000041249|miRNA|| ## {Repeats: dust 134100266 134100296 0 class=dust,trf 3 33 0 class=trf,(TG)n 18 48 1 class=Simple_repeat,trf 4 34 0 class=trf,(TG)n 2 50 1 class=Simple_repeat}

miRNAunknown_nonpairedHIGH (1 loci)

block2174028 (miRNA) [miRNAunknown_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	0.68/0.68	22/22/1.00	0.0	0.0	1	0	1	0	28	3	5arm	1	nd	0.36	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------GAGGGAG--------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	----------------------------AGAGGGAGACCCAGGCTCGGAC------------------------------------------------------------------	22	1
rat	ccggaggggctgaggggggatggggggaAGAGGGAGACCCAGGCTCGGACcgaacaataagcaccctcgagatccgagcaccggggacccccctcccgcccctcccgagtcgctgg
	********************************************************************************************************************
	------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000022247 ENSRNOG00000016598 NP_001101586.1
	.....................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<.............	ENSRNOT00000054621 ENSRNOG00000036514
rat	((((...((((..((((((.(((((((....(((...(((..(((((((.(((.............)))...)))))))...)))..))).))))))).))))))..)))).))))	0.420 -55.92

rat

chromosome:7:141778222:141778337:-1

Opposite_strand|Exonic_non-coding|ENSRNOT00000054621|ENSRNOG00000036514 ## Opposite_strand|Intronic_coding|ENSRNOT00000022247|ENSRNOG00000016598 ## ENSRNOG00000016598|protein_coding|NP_001101586.1|homeo box C5 [Source:RefSeq_peptide;Acc:NP_001101586] ## ENSRNOG00000036514|miRNA|| ## {SimpF: oe = 0.80 -1 CpG}

miRNAunknown_nonpairedHIGH_bulgeHIGH (1 loci)

block284879 (miRNA) [miRNAunknown_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	0.095	no	no	0.38/0.38	21/21/1.00	0.0	0.0	1	0	1	0	5	39	3arm	2	nd	0.52	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------------ACACUGA------------------	1	novel
		len	cloning frequencies
			T1S1
	----------------------------------------------------------------------------------------------AACACTGATTTCAAATGGTGC-----	21	1
rat	gtcttcccttgatttcttgaaggagagagccagtcctgggtacagctgttcctctgcagtctaccctctgctgtgctgcaattcttactcctaaAACACTGATTTCAAATGGTGCtagat
	************************************************************************************************************************
	............................................................................................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	ENSRNOT00000053760 ENSRNOG00000035637 rno-mir-29b-2
rat	((((.((.((((..((.((.((((((((((((((...(((((..(((((......))))).)))))...)))).))......)))..)))))....))..))..))))..))....))))	0.940 -31.10

rat

chromosome:13:110967568:110967687:-1

miRNAunknown_rep_Multihit (1 loci)

block886370 (miRNA) [miRNAunknown_rep_Multihit]

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	0.250	no	LTR,LTR/ERVL	0.30/0.30	20/20/1.00	0.0	0.0	1	0	1	0	9	4	5arm	25	nd	0.30	3	1	1	na	na

		reads	miRBase family seed
seed	----------ACAUAAA----------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	---------TACATAAAGACATTGGAAGA----------------------------------------------	20	1
rat	gctgtagacTACATAAAGACATTGGAAGAaagaagactctctcttcttcacctgcttgccttgtgggactgagtg
	***************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063305 ENSRNOG00000041552
rat	(((.(((.(((((..(((.((...(((((((((......))).))))))...)))))....)))))..)))))).	0.990 -17.70

rat

chromosome:1:140962614:140962688:-1

Same_strand|Exonic_non-coding|ENSRNOT00000063305|ENSRNOG00000041552 ## ENSRNOG00000041552|miRNA|| ## {Repeats: MT2_Rat2 274 294 1 class=LTR/ERVL,MT2_Rat2 0 487 1 class=LTR}

miRNAunknown_rep_Multihit_loopOverlap_nonpairedHIGH_bulgeHIGH (1 loci)

block1224803 (miRNA) [miRNAunknown_rep_Multihit_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
Ensembl miRNA	0.072	no	SINE	0.71/0.71	24/24/1.00	0.0	0.0	1	0	1	0	10	-1	3arm	252	nd	0.38	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------GGCUGAG--------------------------	1	novel
		len	cloning frequencies
			T3S2
	-------------------------------------CGGCTGAGCCATCTCTCCAGCCCC----------	24	1
rat	tactaagtgcttttttggttgtgagcctagcctttaaCGGCTGAGCCATCTCTCCAGCCCCtactaagtgc
	***********************************************************************
	...............<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	ENSRNOT00000054533 ENSRNOG00000036421
rat	((((.((((.....((((..(((.((.(((((......))))).)))))....))))....)))).)))).	0.980 -18.70

rat

chromosome:2:234714003:234714073:-1

Opposite_strand|Exonic_non-coding|ENSRNOT00000054533|ENSRNOG00000036421 ## ENSRNOG00000036421|miRNA|| ## {Repeats: B4 1 47 -1 class=SINE}

miRNAunknown_rep_Multihit_loopOverlap_randfoldOK (1 loci)

block1707893 (miRNA) [miRNAunknown_rep_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	LTR/ERVK	0.30/0.30	20/20/1.00	0.0	0.0	1	0	1	0	37	-1	3arm	289	nd	0.10	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------GUGUGUA-------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	----------------------------------------------------------TGTGTGTATATATGTATGTG-------------------------------------	20	1
rat	atgtgtatatctgtgtgtatgtgtgtgtgcatgtgtatatatatgtatatatgtgcaaTGTGTGTATATATGTATGTGtacatgtgcatatgtgtatatgtatgcatgtatatat
	*******************************************************************************************************************
	.......................................................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063381 ENSRNOG00000041628
rat	((((((((((.((((..((((..((((((((((((((((((((((((((((..(((...)))..))))))))))))))))))))))))))))..))))..)))).))))))))))	1.000 -51.80

rat

chromosome:4:183611903:183612017:1

Same_strand|Boundary_non-coding|ENSRNOT00000063381|ENSRNOG00000041628 ## ENSRNOG00000041628|miRNA|| ## {Repeats: (TATG)n 3 8 1 class=Simple_repeat,RLTR21 1237 1254 1 class=LTR/ERVK,trf 184 204 0 class=trf,dust 183612053 183612073 0 class=dust,(TG)n 2 180 1 class=Simple_repeat}

miRNAunknown_rep_Multihit_loopOverlap_randfoldOK_nonpairedHIGH_bulgeHIGH (1 loci)

block181954 (miRNA) [miRNAunknown_rep_Multihit_loopOverlap_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
Ensembl miRNA	0.006	no	SINE,SINE/B4	0.71/0.71	24/24/1.00	0.0	0.0	1	0	1	0	15	-1	3arm	252	nd	0.42	5	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------GGCUGAG-------------------------------	1	novel
		len	cloning frequencies
			T3S2
	----------------------------------------------CGGCTGAGCCATCTCTCCAGCCCC---------------	24	1
rat	ctgggaaccgaactcttatatttttggttgtgagcctagcctttaaCGGCTGAGCCATCTCTCCAGCCCCggagagtggttctta
	*************************************************************************************
	.....................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<...	ENSRNOT00000054460 ENSRNOG00000036339
rat	.((((((((..((((((......((((..(((.((.(((((......))))).)))))....)))).....))))))))))))))	0.760 -29.50

rat

chromosome:12:10270919:10271003:-1

Opposite_strand|Exonic_non-coding|ENSRNOT00000054460|ENSRNOG00000036339 ## ENSRNOG00000036339|miRNA|| ## {Repeats: B4A 3 27 -1 class=SINE/B4,B4A 1 80 -1 class=SINE}

miRNAunknown_rep_Multihit_nonpairedHIGH (1 loci)

block2462794 (miRNA) [miRNAunknown_rep_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	0.464	no	SINE,SINE/Alu	0.67/0.67	21/21/1.00	0.0	0.0	1	0	1	0	8	6	5arm	271	nd	0.38	3	1	1	na	na

		reads	miRBase family seed
seed	---------CCAGCAC------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	--------CCCAGCACTCAGGAGGCAGAG-----------------------------------------------	21	1
rat	ccttgaatCCCAGCACTCAGGAGGCAGAGgcaggtggatctcaacaaactcaaggccagcctggctacatagcaag
	****************************************************************************
	--------------------------------------------------------------------------------------	ENSRNOT00000026073 ENSRNOG00000019271 RGD1565726_predicted
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<...........................................	ENSRNOT00000063230 ENSRNOG00000041477
rat	.((((......(((...((((.(((.(((....((........))...)))...)))..)))))))......))))	0.740 -17.90

rat

chromosome:8:126153356:126153431:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000055871|ENSRNOG00000019271 ## Opposite_strand|Exonic_non-coding|ENSRNOT00000063230|ENSRNOG00000041477 ## Opposite_strand|Intronic_coding|ENSRNOT00000026073|ENSRNOG00000019271 ## ENSRNOG00000019271|protein_coding|RGD1565726_predicted| ## ENSRNOG00000041477|miRNA|| ## {Repeats: B1_Mur1 3 147 1 class=SINE,B1_Mur1 29 50 1 class=SINE/Alu}

miRNAunknown_rep_Multihit_randfoldOK_nonpairedHIGH_bulgeHIGH (1 loci)

block2030670 (miRNA) [miRNAunknown_rep_Multihit_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
Ensembl miRNA	0.001	no	SINE,SINE/Alu	0.50/0.50	22/22/1.00	0.0	0.0	1	0	1	0	22	13	3arm	256	nd	0.32	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------CCUUGAA------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------------------------------------------------------------GCCTTGAACTCACAGAGATCTG----------------------	22	1
rat	tcattaggtttcttttgagacagggtttctctgtgtagctctggctgtcctggaactcactctgttgaccaggctgGCCTTGAACTCACAGAGATCTGcctgcctctgccttcttagtgt
	************************************************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<..................	ENSRNOT00000063213 ENSRNOG00000041460
rat	.(((((((........(((.((((...((((((((.((.((.((((..((((((((.......)))..)))))..))))..)).))))))))))....)))).)))......))))))).	0.990 -45.54

rat

chromosome:6:75747080:75747199:1

Opposite_strand|Exonic_non-coding|ENSRNOT00000063213|ENSRNOG00000041460 ## ENSRNOG00000041460|miRNA|| ## {Repeats: B1_Mur4 57 79 -1 class=SINE/Alu,B1_Mur4 -5 145 -1 class=SINE}

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miR-Intess™