miR-Intess: classification

other hairpins

novel_lenNOK_shortStem_5varHIGH_loopOverlap_bulgeHIGH (2 loci)

block2644471 [novel_lenNOK_shortStem_5varHIGH_loopOverlap_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	0.078	no	no	0.48/0.50	24/25/0.50	1.5	2.0	2	0	1	0	2	-3	3arm	1	nd	0.29	4	2	1	na	na

		reads	miRBase family seed
seed	-------------------------------GAGAACU-------------------	1	miR-146a/146b
seed	----------------------------GGUGAGA----------------------	1	novel
		len	cloning frequencies
			T5S1
	------------------------------TGAGAACTCGTGATGCAAGAGCAGA--	25	1
	---------------------------TGGTGAGAACTCGTGATGCAAGAG------	24	1
rat	cgttctcgagtatgcatgtggactcacTGGTGAGAACTCGTGATGCAAGAGCAGAtg
	*********************************************************
rat	.(((((...((((.((((....((((....))))....)))))))).))))).....	0.990 -15.20

rat

chromosome:9:105082858:105082914:1

intergenic

novel_lenNOK_shortStem_5varHIGH_loopOverlap_randfoldOK (2 loci)

block1449643 [novel_lenNOK_shortStem_5varHIGH_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
no	0.002	no	no	0.50/0.56	18/22/0.50	1.2	2.8	4	0	3	0	0	-7	5arm_loop_3arm	1	nd	0.22	2	4	3	na	na

		reads	miRBase family seed
seed	---CUUCCAG-----------------------------	2	novel
seed	--CCUUCCA------------------------------	1	novel
seed	-ACCUUCC-------------------------------	1	novel
		len	cloning frequencies
			T3S1	T4S1	T5S2
	--CCTTCCAGTGAAGAGGGGTTTT---------------	22	1	-	-
	--CCTTCCAGTGAAGAGGGGTT-----------------	20	1	-	-
	-ACCTTCCAGTGAAGAGGG--------------------	18	-	1	-
	CACCTTCCAGTGAAGAGG---------------------	18	-	-	1
rat	CACCTTCCAGTGAAGAGGGGTTTTgttttttggagggtg
	***************************************
	-------------------------------------------------	ENSRNOT00000006549 ENSRNOG00000004864 NP_001099950.1
rat	((((((((((.(((.((.....)).))).))))))))))	1.000 -14.60

rat

chromosome:3:34694291:34694329:1

Opposite_strand|Intronic_coding|ENSRNOT00000006549|ENSRNOG00000004864 ## ENSRNOG00000004864|protein_coding|NP_001099950.1|pre-mRNA processing factor 40 homolog A [Source:RefSeq_peptide;Acc:NP_001099950] ## {Repeats: dust 34694344 34694349 0 class=dust}

block425169 [novel_lenNOK_shortStem_5varHIGH_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
no	0.003	no	no	0.48/0.58	19/25/0.00	4.0	1.0	2	0	2	0	4	-1	5arm_loop	10	nd	0.28	2	2	2	na	na

		reads	miRBase family seed
seed	-------------CAUCUUG----------------------------------------------	1	novel
seed	-----AAGUAAA------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T5S2
	----CAAGTAAACCATCTTGTGCACCCAC-------------------------------------	25	-	1
	------------CCATCTTGTGCACCCACGA-----------------------------------	19	1	-
rat	ggtcCAAGTAAACCATCTTGTGCACCCACGAagcctgtgggagcagaagtaagggatgctgaagcc
	******************************************************************
	>>>>>>>>>>>>>>>>............................................................	ENSRNOT00000010400 ENSRNOG00000022045 Rpl41
rat	(((...((((..((..(((.(((.((((((.....)))))).))).)))...))..))))...)))	1.000 -26.40

rat

chromosome:14:112193579:112193644:1

novel_lenNOK_shortStem_5varHIGH_mirtron (2 loci)

block7731 [novel_lenNOK_shortStem_5varHIGH_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	0.402	no	no	0.33/0.62	18/26/0.57	9.1	9.7	7	0	5	0	1	18	5arm	1	1	0.29	3	7	5	na	na

		reads	miRBase family seed
seed	------------GUCCCCU--------------------------------------------------------------------------------------------------	2	novel
seed	--CCCUUCU------------------------------------------------------------------------------------------------------------	1	novel
seed	----------------CCUGAAC----------------------------------------------------------------------------------------------	1	miR-345
seed	--------------CCCCUGA------------------------------------------------------------------------------------------------	1	novel
seed	---CCUUCUU-----------------------------------------------------------------------------------------------------------	1	novel
seed	-------------------GAACCAG-------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T3S1	T3S2	T4S1	T5S1
	-----------CGTCCCCTGAACCAGTCTTTGAA-----------------------------------------------------------------------------------	23	-	1	-	1	-
	------------------TGAACCAGTCTTTGAATA---------------------------------------------------------------------------------	18	-	1	-	-	-
	---------------CCCTGAACCAGTCTTTGAA-----------------------------------------------------------------------------------	19	1	-	-	-	-
	-------------TCCCCTGAACCAGTCTTTGAA-----------------------------------------------------------------------------------	21	-	-	1	-	-
	-GCCCTTCTTCCGTCCCCTGAA-----------------------------------------------------------------------------------------------	21	-	1	-	-	-
	--CCCTTCTTCCGTCCCCTGAACCAGTC-----------------------------------------------------------------------------------------	26	-	-	-	-	1
rat	gGCCCTTCTTCCGTCCCCTGAACCAGTCTTTGAATAaagcagaagtaggaaagaagactctgcctatttctctgcatgtgcaaagttttcgtgtgtggtatggggaagcttccagcc
	*********************************************************************************************************************
	>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000048977 ENSRNOG00000031686 LOC360504
rat	(((..........(((((...((((..(((((.(((.((.(((((((((..(((....))).)))))))))))...))).)))))..........))))..)))))........)))	0.830 -30.87

rat

chromosome:10:15570864:15570980:-1

block1371630 [novel_lenNOK_shortStem_5varHIGH_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	0.640	no	no	0.72/0.72	18/25/0.00	3.5	0.0	2	0	2	0	4	6	5arm	1	1	0.28	2	2	2	na	na

		reads	miRBase family seed
seed	------------GGCCGGG---------------------------------------------------------	1	novel
seed	-----GGUGAGA----------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S2	T3S1
	----CGGTGAGAGGCCGGGAGGACCAGCT-----------------------------------------------	25	1	-
	-----------AGGCCGGGAGGACCAGCT-----------------------------------------------	18	-	1
rat	gttgCGGTGAGAGGCCGGGAGGACCAGCTagcagcttcggtgtgctttcttggcgctcctaggttccacgggcggc
	****************************************************************************
	>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000011303 ENSRNOG00000008469 RGD1566062_predicted
rat	(((((.(((.((.((((((((..((((..((((((....)).))))...))))..))))).))))))))..)))))	1.000 -30.10

rat

chromosome:3:52022376:52022451:-1

novel_lenNOK_shortStem_5varHIGH_randfoldOK_nonpairedHIGH_bulgeHIGH (2 loci)

block1027598 [novel_lenNOK_shortStem_5varHIGH_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	0.006	no	no	0.26/0.26	19/23/0.33	3.0	0.3	3	0	3	0	4	22	5arm	1	15	0.48	5	3	3	na	na

		reads	miRBase family seed
seed	-----UAUAGUU------------------------------------------------------------------------------------	1	novel
seed	---------GUUACUA--------------------------------------------------------------------------------	1	novel
seed	----------UUACUAA-------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T4S1	T5S1
	---------GTTACTAAAAGCATAACAT--------------------------------------------------------------------	19	-	-	1
	--------AGTTACTAAAAGCATAACA---------------------------------------------------------------------	19	1	-	-
	----CTATAGTTACTAAAAGCATAACA---------------------------------------------------------------------	23	-	1	-
rat	gtttCTATAGTTACTAAAAGCATAACATttccatttacccaaggttctgaagattcagaagatggaatagaagtgccaacagcagcagtggagact
	************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000023376 ENSRNOG00000017299 LOC245925
rat	((((((((.(((.((....((((.....(((((((.........((((((....))))))))))))).....))))....)).))).)))))))).	0.410 -25.80

rat

chromosome:1:201431438:201431533:1

block1093654 [novel_lenNOK_shortStem_5varHIGH_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	0.001	no	no	0.47/0.52	19/25/0.33	1.7	4.0	3	0	1	0	1	23	5arm	1	nd	0.36	4	3	1	na	na

		reads	miRBase family seed
seed	--GAGACAG---------------------------------------------------------------------------------------------------	1	novel
seed	-----ACAGUAA------------------------------------------------------------------------------------------------	1	novel
seed	----GACAGUA-------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	---AGACAGTAAGAAGGCTGACTGGGGA--------------------------------------------------------------------------------	25	1
	-AGAGACAGTAAGAAGGCTG----------------------------------------------------------------------------------------	19	1
	----GACAGTAAGAAGGCTGACTG------------------------------------------------------------------------------------	20	1
rat	gAGAGACAGTAAGAAGGCTGACTGGGGAaggggagggcggaggggcaggccaagaggagacagagaagagcagggggccttcctgggaagaggcctgatggctgggct
	************************************************************************************************************
rat	.((...((((....(((((..((.(((((((.....((...........((....))............))......))))))).))....)))))....))))..))	0.500 -30.90

rat

chromosome:20:5543799:5543906:1

intergenic

novel_lenNOK_shortStem_loopOverlap_mirtron (2 loci)

block799278 [novel_lenNOK_shortStem_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	0.265	no	no	0.56/0.56	25/25/0.00	0.0	0.0	1	0	1	0	0	-2	5arm_loop	1	4	0.28	3	1	1	na	na

		reads	miRBase family seed
seed	-GUCCCCG----------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	TGTCCCCGTTTCACCCTGTCACCTT-----------------------------------------	25	1
rat	TGTCCCCGTTTCACCCTGTCACCTTgcagcaccggtgatgaacacagccgggggaactgggctcac
	******************************************************************
	++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000024622 ENSRNOG00000018292
rat	((..((((.(((.((((((((((..........)))))..........)))))))).))))..)).	0.590 -20.60

rat

chromosome:19:14988088:14988153:1

Same_strand|Intronic_coding|ENSRNOT00000024622|ENSRNOG00000018292 ## ENSRNOG00000018292|protein_coding||

block2271294 [novel_lenNOK_shortStem_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	0.028	no	no	0.72/0.72	18/18/0.00	0.0	0.0	1	0	1	0	0	-1	3arm	1	4	0.12	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------GACCUCC----------	1	novel
		len	cloning frequencies
			T1S1
	--------------------------------CGACCTCCCCTGCTCTCC	18	1
rat	ggaaggcaggaatgggaccggtccttaaccccCGACCTCCCCTGCTCTCC
	**************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>	ENSRNOT00000014310 ENSRNOG00000010588 NP_001101584.1
rat	(((..((((....((((..((((..........))))))))))))..)))	1.000 -18.50

rat

chromosome:7:140848188:140848237:1

novel_loopOverlap_mirtron_randfoldOK_nonpairedHIGH_bulgeHIGH (2 loci)

block183914 [novel_loopOverlap_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	0.004	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	45	-4	3arm_loop	1	4	0.45	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------GCCAUGU---------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	----------------------------------------------------AGCCATGTGTCCTCTCTGTG---------------------------------------------	20	1
rat	tcctctcaaggtgatcccagtctactgcgggcggtgtccctacaggactcatAGCCATGTGTCCTCTCTGTGcaggtaccgcctggctggcctgcctggagaacaccagcagaggaa
	*********************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000031149 ENSRNOG00000001103 RGD1560686_predicted
rat	((((((...((((.((((((......((((((((((.((.((((((((.(((....))).)))))....)))..)))))))))).))........)))).)).))))...)))))).	0.460 -47.64