miR-Intess: classification

other hairpins

novel_lenNOK_cloningOK_shortStem (308 loci)

block1520184 [novel_lenNOK_cloningOK_shortStem]

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	0.519	no	no	0.28/0.28	18/18/0.00	0.0	0.0	10	0	6	0	4	17	3arm	1	nd	0.22	3	10	6	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------AUUUUGU--------------	10	novel
		len	cloning frequencies
			T1S2	T2S1	T3S1	T3S2	T4S2	T5S2
	-------------------------------------------------------------------TATTTTGTAAACGTGTCT----	18	2	1	1	1	2	3
rat	ggaagaaaatcattttatgtctaattaataactacatagtcatcaacaaggttgaagaaatgtattcTATTTTGTAAACGTGTCTtttg
	*****************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000050686 ENSRNOG00000031855 Actr3b
rat	((((((.........(((((.((...((((..(((((..((.(((((...))))).)).)))))...))))...)).))))))))))).	0.850 -12.00

rat

chromosome:4:4727964:4728052:-1

Same_strand|Intronic_coding|ENSRNOT00000050686|ENSRNOG00000031855 ## Same_strand|Boundary_non-coding|ENSRNOT00000041876|ENSRNOG00000031855 ## ENSRNOG00000031855|protein_coding|Actr3b|ARP3 actin-related protein 3 homolog B (yeast) Gene [Source:MGI Symbol;Acc:MGI:2661120] ## {Repeats: trf 85 90 0 class=trf}

novel_loopOverlap_bulgeHIGH (305 loci)

block20728 [novel_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	0.537	no	no	0.62/0.62	21/21/1.00	0.0	0.0	1	0	1	0	21	-4	5arm_loop	1	nd	0.29	5	1	1	na	na

		reads	miRBase family seed
seed	----------------------UUCUGGC------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	---------------------CTTCTGGCCCATGCTGACGAC-----------------------------------------------------	21	1
rat	cagagaacagacatgaactcaCTTCTGGCCCATGCTGACGACagtactagctcggtagggctccaggatctagaggctccatctgctgtggtttg
	***********************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000058155 ENSRNOG00000003463 Srebf1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000058129 ENSRNOG00000003590 NP_001101747.1
rat	((((..((((..(((..(((..(((((((((.((((((.............))))))))))..)))))....)))....)))...))))..))))	0.420 -24.92

rat

chromosome:10:46589498:46589592:-1

block21558 [novel_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	0.383	no	no	0.83/0.83	24/24/1.00	0.0	0.0	1	0	1	0	5	-3	5arm_loop	1	nd	0.29	4	1	1	na	na

		reads	miRBase family seed
seed	------CGCCGAG--------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-----GCGCCGAGCCGGCCGCCGGTTCCT----------------------------------	24	1
rat	cgccgGCGCCGAGCCGGCCGCCGGTTCCTaagcagccgtcgcctccccggctcgccgactcgc
	***************************************************************
rat	.((.((((.((((((((.((.(((((.......))))).)).....)))))))).)).)).))	0.820 -26.60

rat

chromosome:10:48010112:48010174:-1

intergenic ## {SimpF: 1 Eponine,oe = 0.88 -1 CpG}

block40220 [novel_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	0.013	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	8	-1	3arm	1	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------CUCAGUA--------------------	1	novel
		len	cloning frequencies
			T5S2
	------------------------------------CCTCAGTAGCCATTCCTCTC--------	20	1
rat	tctgtaagaattcaggtgctgctcagcccacaacacCCTCAGTAGCCATTCCTCTCtcacagac
	****************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000055387 ENSRNOG00000036886
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000050829 ENSRNOG00000021536 NP_001100516.1
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000043561 ENSRNOG00000021536 NP_001100516.1
rat	(((((.(((....(((.((((((.((...........)).))))))....))).))).))))).	1.000 -15.30

rat

chromosome:10:86697645:86697708:-1

Same_strand|Intronic_coding|ENSRNOT00000043561|ENSRNOG00000021536 ## ENSRNOG00000036886|protein_coding|| ## ENSRNOG00000021536|protein_coding|NP_001100516.1|ADP-ribosylation factor-like 12 [Source:RefSeq_peptide;Acc:NP_001100516]

block57242 [novel_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	0.165	no	no	0.65/0.65	23/23/1.00	0.0	0.0	1	0	1	0	33	-1	3arm	6	nd	0.26	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------AGAGCUC------------------------------------------------	1	novel
		len	cloning frequencies
			T4S1
	----------------------------------------------------------CAGAGCTCCCTTGTCCGTCCTGC---------------------------------	23	1
rat	ggactagataggaaccagggaccagtgcacagggcagtggtgctgggagaactcttccCAGAGCTCCCTTGTCCGTCCTGCcccaggtctgagttttgaaccacgtagggtcca
	******************************************************************************************************************
rat	(((((..((.((.....((((((((.((...(((((((((....(((((..((((....)))))))))....)))..))))))...))))).)))))...))..))..))))).	0.500 -41.40

rat

chromosome:10:7922819:7922932:1

intergenic

block60181 [novel_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	0.351	no	no	0.70/0.70	23/23/1.00	0.0	0.0	2	0	1	0	16	-1	3arm	1	22	0.30	5	2	1	na	na

		reads	miRBase family seed
seed	----------------------------------------------GCGGGCU-------------------------------	2	novel
		len	cloning frequencies
			T1S2
	---------------------------------------------AGCGGGCTGCTCACCCTCTGCAC----------------	23	2
rat	ggaggtaaagctgaagacaaggaggtaggtgtgggccgctggcggAGCGGGCTGCTCACCCTCTGCACggagatgcagcccttt
	************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000019508 ENSRNOG00000014179 Rps2
rat	.((((....((((..........((.(((.((((((.(((.((...)).))).)))))))))))...........)))))))).	0.750 -29.10

rat

chromosome:10:13975651:13975734:1

block73390 [novel_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	0.380	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	17	-3	5arm_loop	1	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	------------------CCGUGCA--------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	-----------------TCCGTGCAAGTAACTAGCCC--------------------------------------	20	1
rat	acttgactggctggggaTCCGTGCAAGTAACTAGCCCaacctggatgcctttcatgggagatccgcctctaggtg
	***************************************************************************
	-------------------------------------------------------------------------------------	ENSRNOT00000036940 ENSRNOG00000022725 LOC364802
rat	(((((...(((.(((..((((((.(((((.((((......)))).))).)).))))))...))))))..))))).	0.670 -22.00

rat

chromosome:10:45467649:45467723:1

block79220 [novel_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	0.553	no	no	0.88/0.88	24/24/1.00	0.0	0.0	1	0	1	0	8	-4	5arm_loop	1	nd	0.29	5	1	1	na	na

		reads	miRBase family seed
seed	---------CUGCCGC--------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	--------GCTGCCGCCCCCGGGGCGCGATCC----------------------------------	24	1
rat	ccgcttctGCTGCCGCCCCCGGGGCGCGATCCgccgcccgccgcccggggacccggcgaggggcgg
	******************************************************************
rat	((((..((..(((((.((((((((((((......)))..)))..))))))...)))))))..))))	0.920 -37.90

rat

chromosome:10:57580590:57580655:1

intergenic ## {Repeats: dust 57580639 57580659 0 class=dust,GC_rich 1 96 1 class=Low_complexity,GC_rich 34 58 1 class=Low_complexity} ## {SimpF: oe = 0.86 1 CpG}

block81795 [novel_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	0.196	no	no	0.50/0.50	20/20/1.00	0.0	0.0	1	0	1	0	22	-3	3arm_loop	1	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------CCGUAGA----------------------------------	1	novel
		len	cloning frequencies
			T4S2
	------------------------------------------------------ACCGTAGAACTCCTGTGATG----------------------	20	1
rat	cctatctggccaccgtaaaagagatgttcgtatacatagcaatctctcccacacACCGTAGAACTCCTGTGATGcttatattctctggaaggatag
	************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000007100 ENSRNOG00000005290 Ywhae
rat	.((((((..((........((((((((..((((.(((((.....(((...((.....)))))....)))))))))..)))).))))))..))))))	0.570 -19.80

rat

chromosome:10:63108388:63108483:1

block107003 [novel_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	0.156	no	no	0.19/0.19	21/21/1.00	0.0	0.0	1	0	1	0	15	-4	5arm_loop	1	nd	0.29	5	1	1	na	na

		reads	miRBase family seed
seed	----------------UAAAUUU--------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	---------------TTAAATTTGAAAACCATTTCT-------------------------------------------	21	1
rat	tgtgttgagtggtagTTAAATTTGAAAACCATTTCTtttatggatttttgtgggattttattttcctctcttgtttaca
	*******************************************************************************
rat	.(((..(((.((.(((.(((((((((((((((.......)))).)))))...)))))).)))..)).))).....))).	0.950 -12.50