miR-Intess: classification

other hairpins

novel_lenNOK_shortStem_loopOverlap_randfoldOK (211 loci)

block8277 [novel_lenNOK_shortStem_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	0.001	no	no	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	4	-1	5arm_loop	3	nd	0.28	3	1	1	na	na

		reads	miRBase family seed
seed	-----CUUCAUG-------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	----TCTTCATGTGTGTGCACT---------------------------	18	1
rat	gcacTCTTCATGTGTGTGCACTcttctgtgcacgtcctactaagggtgt
	*************************************************
rat	((((((((...((((((((((......)))))))...))).))))))))	1.000 -19.20

rat

chromosome:10:16477643:16477691:-1

intergenic ## {Repeats: trf 9 27 0 class=trf}

novel_lenNOK_gcHIGH (207 loci)

block7840 [novel_lenNOK_gcHIGH]

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	0.351	no	no	0.95/0.95	19/19/0.00	0.0	0.0	1	0	1	0	28	17	5arm	1	nd	0.21	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------CCCCGCC------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	----------------------------GCCCCGCCCGCCAGGCCGC-------------------------------------------------------------------------	19	1
rat	ggagacccggcgaggccaatgcccggctGCCCCGCCCGCCAGGCCGCgccgatccgaccacgggctatttctgtggggcgccgggctggaatccgggccgcgccgcctccgccggcgctc
	************************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000027965 ENSRNOG00000020594 Rhbdf1
rat	.(((..((((((((((........(((.((...(((((((((.(((((((.......(((((((.....)))))))))))).)).))))....))))).)))))))))).)))))..)))	0.420 -62.51

rat

chromosome:10:15654165:15654284:-1

Opposite_strand|Intronic_non-coding|ENSRNOT00000027965|ENSRNOG00000020594 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000060026|ENSRNOG00000020594 ## ENSRNOG00000020594|protein_coding|Rhbdf1|rhomboid family 1 [Source:RefSeq_peptide;Acc:NP_001025205] ## {SimpF: -1 Eponine}

block8418 [novel_lenNOK_gcHIGH]

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	0.261	no	no	1.00/1.00	18/19/0.00	0.0	0.5	4	0	3	0	27	8	3arm	1	nd	0.21	2	4	3	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------GCGCGGG--------------------------------------	4	novel
		len	cloning frequencies
			T1S2	T2S1	T3S1
	-----------------------------------------------------------------CGCGCGGGCGGGCGGCCCC---------------------------	19	1	-	1
	-----------------------------------------------------------------CGCGCGGGCGGGCGGCCC----------------------------	18	-	1	1
rat	cggggtcgccgatgcgagccggaccgggctgtccccgcggccgaccgttatataaaagacgggcaCGCGCGGGCGGGCGGCCCCgttagggccgtgccctttgcgctcccg
	***************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000028186 ENSRNOG00000020769 RGD1310862_predicted
rat	((((..(((.((((((.(((.(((.((((((((((((((.....(((((........))))).....))))))..)))))))).)))..)))))))...)).)))..))))	0.430 -55.80

rat

chromosome:10:16723573:16723683:-1

Same_strand|Intronic_non-coding|ENSRNOT00000028186|ENSRNOG00000020769 ## ENSRNOG00000020769|protein_coding|RGD1310862_predicted| ## {SimpF: 1 Eponine,oe = 0.89 0 CpG}

block20197 [novel_lenNOK_gcHIGH]

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	0.369	no	no	1.00/1.00	19/19/0.00	0.0	0.0	1	0	1	0	7	2	3arm	1	nd	0.11	1	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------CCGGCCC------------------	1	novel
		len	cloning frequencies
			T2S1
	-----------------------------------------CCCGGCCCGCCCGCGCCCC-------	19	1
rat	tccgcagccgcggccgcggggcggggcgccggccagctgggCCCGGCCCGCCCGCGCCCCggaggag
	*******************************************************************
	-----------------------------------------------------------------------------	ENSRNOT00000004165 ENSRNOG00000003066 NP_001099253.1
rat	(((....(((.((.(((.(((((((.((..((((.....)))))).)))))))))))).))).))).	0.520 -43.90

rat

chromosome:10:45613610:45613676:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000058327|ENSRNOG00000003066 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000004165|ENSRNOG00000003066 ## ENSRNOG00000003066|protein_coding|NP_001099253.1|wingless related MMTV integration site 9A [Source:RefSeq_peptide;Acc:NP_001099253] ## {Repeats: GC_rich 1 89 -1 class=Low_complexity,GC_rich 36 55 -1 class=Low_complexity} ## {SimpF: oe = 0.84 -1 CpG}

block26465 [novel_lenNOK_gcHIGH]

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	0.648	no	no	0.94/0.94	18/18/0.00	0.0	0.0	1	0	1	0	29	15	3arm	2	nd	0.28	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------CGGAGCG---------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	--------------------------------------------------------------------GCGGAGCGGGCGGGCGCC-----------------------------	18	1
rat	gcgcacccacgatcccaggcccacgtcgcccagttccccgaggctgcggacttccgcgctgagcagtgGCGGAGCGGGCGGGCGCCgagctgagccgcgggcgcggagtgcagcg
	*******************************************************************************************************************
rat	((((((((.((..(((.(((.((((((((((.((((((((..(((((((....))))....)))..))).))))))))))).))......)).)))..))))).)).)))).)).	0.660 -57.60

rat

chromosome:10:58607796:58607910:-1

intergenic

block26749 [novel_lenNOK_gcHIGH]

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	0.022	no	no	1.00/1.00	18/18/0.00	0.0	0.0	1	0	1	0	5	27	5arm	1	nd	0.28	3	1	1	na	na

		reads	miRBase family seed
seed	------CCCGCGC-------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	-----CCCCGCGCCCCCCGCGCC---------------------------------------------------------------------------------------	18	1
rat	gcgtcCCCCGCGCCCCCCGCGCCccccgccgccccggtcctggcgggcatgatgtgcctggaatgcgcctcggcggcggcgggcggcgcggaggaggaggaggcggacgc
	**************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000056525 ENSRNOG00000015801 Spns2
	.....................................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000021234 ENSRNOG00000015801 Spns2
rat	((((((.((...(((((((((((.(((((((((((((....(((((((((...))))).......)))))))).))))))))).))))))).)).))....)).))))))	0.990 -75.21

rat

chromosome:10:59374197:59374306:-1

Same_strand|Boundary_non-coding|ENSRNOT00000021234|ENSRNOG00000015801 ## Same_strand|Intronic_non-coding|ENSRNOT00000056525|ENSRNOG00000015801 ## ENSRNOG00000015801|protein_coding|Spns2|spinster homolog 2 (Drosophila) Gene [Source:MGI (curated);Acc:Spns2-001] ## {Repeats: trf 13 31 0 class=trf,dust 59374284 59374302 0 class=dust,GC_rich 15 33 -1 class=Low_complexity,GC_rich 1 33 -1 class=Low_complexity}

block30419 [novel_lenNOK_gcHIGH]

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	0.031	no	no	1.00/1.00	18/19/0.00	0.5	0.0	2	0	2	0	10	29	3arm	1	nd	0.26	2	2	2	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------------GGCGGCG---------------------	1	novel
seed	---------------------------------------------------------------------------------------------GCGGCGG--------------------	1	novel
		len	cloning frequencies
			T1S2	T5S2
	-------------------------------------------------------------------------------------------CGGCGGCGGGGCGGCGCGG----------	19	1	-
	--------------------------------------------------------------------------------------------GGCGGCGGGGCGGCGCGG----------	18	-	1
rat	ggtgcgggccgcccctcccccggtgggcagggctttcgctgcttcctgcaggagcggcctgggccgcgcagggggcggggagagcggagagCGGCGGCGGGGCGGCGCGGagaatcgctg
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000056128 ENSRNOG00000022536 RGD1309650_predicted
rat	((((((.((((((((.((.(((.........((((((.((((..(((((....(((((....))))))))))..)))).))))))......))).)).)))))))).))......)))).	0.940 -71.96

rat

chromosome:10:66624473:66624592:-1

Same_strand|Boundary_non-coding|ENSRNOT00000031618|ENSRNOG00000022536 ## Same_strand|Intronic_coding|ENSRNOT00000056128|ENSRNOG00000022536 ## ENSRNOG00000022536|protein_coding|RGD1309650_predicted| ## {Repeats: dust 66624483 66624502 0 class=dust}

block30798 [novel_lenNOK_gcHIGH]

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	0.163	no	no	1.00/1.00	19/19/0.00	0.0	0.0	1	0	1	0	19	9	3arm	1	nd	0.21	2	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------GCGGCGG------------------------------	1	novel
		len	cloning frequencies
			T4S1
	-----------------------------------------------------------GGCGGCGGCGGCCCGCCGG-------------------	19	1
rat	gctcgccatcttccagcaacgccgctaacaccgctccgctccagcggctccgcactccgGGCGGCGGCGGCCCGCCGGatcccctctgcgcctagca
	*************************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<................................................	ENSRNOT00000005262 ENSRNOG00000003873 Cpd
rat	((((((.....(((.((...((((((....((((.(((.....(((....)))....))))))).))))))..)).)))........)))...))).	0.910 -36.52

rat

chromosome:10:67327229:67327325:-1

intergenic ## {Repeats: GC_rich 1 20 -1 class=Low_complexity,GC_rich 1 22 -1 class=Low_complexity}

block31264 [novel_lenNOK_gcHIGH]

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	0.184	no	no	0.95/0.95	19/19/0.00	0.0	0.0	1	0	1	0	6	9	5arm	1	nd	0.26	2	1	1	na	na

		reads	miRBase family seed
seed	-------GCGGGGC------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	------CGCGGGGCCCCCGCCCCCA-------------------------------------------------	19	1
rat	gctgctCGCGGGGCCCCCGCCCCCAaggccgcccgcggggagggagggagggaaggagggggctggctgcagcg
	**************************************************************************
rat	(((((..((.((.(((((.(((((....((.(((.......))).))..)))..)).))))))).)).))))).	1.000 -40.80

rat

chromosome:10:68525011:68525084:-1

intergenic ## {Repeats: GC_rich 1 19 -1 class=Low_complexity,GC_rich 1 43 -1 class=Low_complexity} ## {SimpF: oe = 0.83 -1 CpG}

block32617 [novel_lenNOK_gcHIGH]

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	0.702	no	no	0.94/0.94	18/18/0.00	0.0	0.0	1	0	1	0	12	14	5arm	1	nd	0.17	1	1	1	na	na

		reads	miRBase family seed
seed	-------------GGGCUGG--------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	------------CGGGCTGGGGCGCGGGGG----------------------------------------------------------------	18	1
rat	gcccgggcgcggCGGGCTGGGGCGCGGGGGgccgcagcaccgagggtcgctcagctgctcgccctgcggagcgcgccgccccactcgcgccggc
	**********************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<-----------------------------------------------------------------------------------	ENSRNOT00000013687 ENSRNOG00000010302 Rasl10b_predicted
rat	(((..(((((((.((((.((.(((((.(((((.(((((...(((.....))).)))))..))))).))...))).))))))...))))))))))	0.490 -55.30

rat

chromosome:10:71493265:71493358:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000013687|ENSRNOG00000010302 ## ENSRNOG00000010302|protein_coding|Rasl10b_predicted| ## {Repeats: GC_rich 1 50 -1 class=Low_complexity,GC_rich 6 24 -1 class=Low_complexity,dust 71493332 71493347 0 class=dust}

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miR-Intess™