miR-Intess: classification

other hairpins

novel_cloningOK_shortStem_5varHIGH (5 loci)

block1600383 [novel_cloningOK_shortStem_5varHIGH]

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	0.123	no	no	0.42/0.58	19/24/0.80	1.8 0.0	1.6 0.0	9 1	0 0	3 1	0 0	4 0	29 40	3arm 3arm	1 1	nd nd	0.32 0.22	2 2	10	3	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------CCAUAAA----------------------	5	novel
seed	---------------------------------------------------------------------------------------------AAACAGU------------------	4	novel
seed	----------------------------------------------------------------------------------------------------GAACCAG-----------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T5S1
	----------------------------------------------------------------------------------------TCCATAAACAGTGAACCAGGGAAG------	24	-	-	2
	--------------------------------------------------------------------------------------------TAAACAGTGAACCAGGGAAG------	20	-	-	2
	--------------------------------------------------------------------------------------------TAAACAGTGAACCAGGGAAGTG----	22	1	-	1
	----------------------------------------------------------------------------------------TCCATAAACAGTGAACCAGGG---------	21	-	-	1
	----------------------------------------------------------------------------------------TCCATAAACAGTGAACCAGGGA--------	22	-	1	-
	----------------------------------------------------------------------------------------TCCATAAACAGTGAACCAG-----------	19	-	-	1
	---------------------------------------------------------------------------------------------------TGAACCAGGGAAGTGCCTG	19	-	-	1
rat	tagagtgcttgctggggcatggtgtctgaaccagctggtcctcagcagacgtctcctttgagaagtctgatttcttccgttcagcaggTCCATAAACAGTGAACCAGGGAAGTGCCTG
	**********************************************************************************************************************
rat	(((.((((((.((((..(((.((...((.(((.(((((.......(((((.((((....)))).)))))...........))))).))).))...)).)))..)))).)).)))))))	0.910 -39.37

rat

chromosome:4:164236359:164236476:-1

intergenic

novel_gcHIGH_shortStem (5 loci)

block365258 [novel_gcHIGH_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	0.034	no	no	1.00/1.00	20/20/1.00	0.0	0.0	1	0	1	0	1	36	5arm	1	nd	0.20	3	1	1	na	na

		reads	miRBase family seed
seed	--CCGCCCG---------------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	-CCCGCCCGCCGCGCCGGGCC---------------------------------------------------------------------------------------------------	20	1
rat	cCCCGCCCGCCGCGCCGGGCCcgccctcctggcgtagcccaaggccctcccggagctattttgaaagtgaccctgggctcgggcgcccaggacgcgtggagagggcgcagcgggcggcgg
	************************************************************************************************************************
rat	((((((((((.(((((...(((((..((((((.((.((((..(((((....((.(((........)))..))..))))).)))))))))))).))).))....))))).)))))))).))	0.940 -70.60

rat

chromosome:14:81340021:81340140:-1

intergenic ## {Repeats: GC_rich 1 29 -1 class=Low_complexity,GC_rich 6 26 -1 class=Low_complexity}

block599523 [novel_gcHIGH_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	0.058	no	no	0.91/0.91	23/23/1.00	0.0	0.0	1	0	1	0	2	16	3arm	1	nd	0.09	1	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------CCGCGGG-----------------	1	novel
		len	cloning frequencies
			T2S2
	--------------------------------------------------------------------CCCGCGGGCGCGGCGGCCATCCC--	23	1
rat	cacgggagccgtggccccgcgaaccccggctgctcgtcccgcggagggcgctctgtctgctgcgagtcCCCGCGGGCGCGGCGGCCATCCCgt
	*********************************************************************************************
rat	.((((((....((((((((((..((((((..((((((...(((((.((....)).))))).))))))..))).)))))))).)))))))))))	0.810 -54.50

rat

chromosome:17:14936335:14936427:-1

intergenic

block791221 [novel_gcHIGH_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	0.390	no	no	0.95/0.95	20/20/1.00	0.0	0.0	1	0	1	0	1	30	3arm	1	nd	0.10	1	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------------------CGGAGCG-------------	1	novel
		len	cloning frequencies
			T2S1
	-------------------------------------------------------------------------------------------------GCGGAGCGCCCGGGGCGGGG-	20	1
rat	cgctcactgcgaccgggagaaccgctcccccgaggacgctcgcgcgcgcccgacggcgaggggcgagtctggccaggaggcgcgccagtgggcgtggGCGGAGCGCCCGGGGCGGGGc
	**********************************************************************************************************************
rat	.(((..((((..(((((.....(((((((((....(((((((((((((((....(((.(((......))).)))....)))))))..))))))))))).))))))))))).)))))))	0.930 -67.40

rat

chromosome:19:55775203:55775320:-1

intergenic ## {Repeats: trf 148 168 0 class=trf} ## {SimpF: oe = 0.91 -1 CpG}

block1788480 [novel_gcHIGH_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	0.028	no	no	1.00/1.00	20/20/1.00	0.0	0.0	1	0	1	0	0	22	3arm	1	nd	0.16	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------GCCCCGC------------	1	novel
		len	cloning frequencies
			T2S1
	----------------------------------------------------------------------------CGCCCCGCCCGCGCGGGGGG	20	1
rat	tccccaccgcgctcggggaaactgaggccgggggcggtgtcgcgtgccgctgtcgccgcggccccgccctcctgctCGCCCCGCCCGCGCGGGGGG
	************************************************************************************************
rat	.((((.((((((.(((((....(((.((.((((((((.((((((.((.......)))))))).)))))).)).))))))))))...))))))))))	1.000 -63.10

rat

chromosome:5:149518973:149519068:-1

intergenic ## {Repeats: GC_rich 1 21 -1 class=Low_complexity,GC_rich 1 43 -1 class=Low_complexity}

block1791926 [novel_gcHIGH_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	0.398	no	no	0.91/0.91	23/23/1.00	0.0	0.0	1	0	1	0	1	27	3arm	1	nd	0.26	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------------GGCCCCC----------------	1	novel
		len	cloning frequencies
			T4S1
	----------------------------------------------------------------------------------------------TGGCCCCCCTCCCCCCCCCCCCC-	23	1
rat	ggcggggcgggcggctggctggtgcggggcgggcgggccccggaattgtcatttctttgtttccgaaggcggaggaggctcggcgcccccctccTGGCCCCCCTCCCCCCCCCCCCCc
	**********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000032623 ENSRNOG00000021448 LOC313618
rat	((.((((.(((.((..((..((.((.(((.(((.((((.((((....(((..(((((((((......)))))))))))))))).))))))).))).)))).))..)))))))))))..	0.860 -61.50

rat

chromosome:5:153626083:153626200:-1

Same_strand|Intronic_coding|ENSRNOT00000032623|ENSRNOG00000021448 ## ENSRNOG00000021448|protein_coding|LOC313618|Macoilin (Transmembrane protein 57). [Source:UniProtKB/Swiss-Prot;Acc:Q4V7D3] ## {Repeats: dust 153626084 153626107 0 class=dust,G-rich 1 33 -1 class=Low_complexity,G-rich 2 25 -1 class=Low_complexity} ## {SimpF: oe = 0.83 0 CpG}

novel_lenNOK_5varHIGH_randfoldOK_bulgeHIGH (5 loci)

block191116 [novel_lenNOK_5varHIGH_randfoldOK_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	0.002	no	no	0.48/0.53	19/21/0.50	1.5	0.5	2	0	1	0	29	5	3arm	1	nd	0.26	4	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------UGGGCUU-------------------------------------------	1	novel
seed	-----------------------------------------------------------------------GCUUUGG----------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	-------------------------------------------------------------------TTGGGCTTTGGTCACAGAAGA------------------------------	21	1
	----------------------------------------------------------------------GGCTTTGGTCACAGAAGAG-----------------------------	19	1
rat	aggcagaagtgcggctgaggaaggcctctttctcaaattgtgacaggaagcagccagtgtctttggcTTGGGCTTTGGTCACAGAAGAGggagagagatctctactcaggcagaggtc
	**********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000059227 ENSRNOG00000001457 Rfc2
	--------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000001996 ENSRNOG00000001470 Limk1
rat	.(((.....(((..(((((..((..(((((((((...(((((((..(((((((((((.....))))))...))))).)))))))....)))))))))..))...))))))))...)))	0.600 -46.60

rat

chromosome:12:23101971:23102088:-1

block555673 [novel_lenNOK_5varHIGH_randfoldOK_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	0.005	no	no	0.56/0.63	18/19/0.00	3.7	3.0	7	0	4	0	12	7	3arm	1	nd	0.22	4	7	4	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------GUGGUUC-----------------------	3	novel
seed	-------------------------------------------------------------------GGUGGUU------------------------	2	novel
seed	------------------------------------------------------------------GGGUGGU-------------------------	1	novel
seed	---------------------------------------------------------------GUAGGGU----------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S2	T3S2	T5S2
	-------------------------------------------------------------------GGTGGTTCAGTGGTAGGG-------------	18	-	1	-	1
	------------------------------------------------------------------GGGTGGTTCAGTGGTAGG--------------	18	-	-	1	1
	--------------------------------------------------------------GGTAGGGTGGTTCAGTGGT-----------------	19	1	-	-	-
	-------------------------------------------------------------------GGTGGTTCAGTGGTAGGGG------------	19	-	1	-	-
	-----------------------------------------------------------------AGGGTGGTTCAGTGGTAG---------------	18	1	-	-	-
rat	catcagcatgaggctctgcgttacaactcccacccaccctcagctgaaaagaaatggcagagGGTAGGGTGGTTCAGTGGTAGGGGttttgctcctga
	**************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000030102 ENSRNOG00000021966 RGD1565237_predicted
rat	((..((((.(((.((((((..(((.....((((((((((((.(((..........))).)))))).))))))....))))))))).)))))))..)).	0.980 -38.60

rat

chromosome:16:2300129:2300226:1

block1350833 [novel_lenNOK_5varHIGH_randfoldOK_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	0.003	no	no	0.61/0.63	18/19/0.00	2.4	1.6	5	0	5	0	17	0	3arm	1	nd	0.26	4	5	5	na	na

		reads	miRBase family seed
seed	--------------------------------------------------CAGGGAA---------------------------	4	novel
seed	-----------------------------------------------GCACAGG------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S2	T3S1	T5S1	T5S2
	-------------------------------------------------ACAGGGAAGAGCCCAGAC-----------------	18	1	-	1	1	1
	----------------------------------------------AGCACAGGGAAGAGCCCAG-------------------	19	-	1	-	-	-
rat	gggggagggtctgggtcccctctgctcccccagtttcttccagtaaAGCACAGGGAAGAGCCCAGACtttgtcctcctccccca
	************************************************************************************
rat	((((((((((((((((.((((.((((....................)))).))))....))))))))........)))))))).	0.960 -39.45

rat

chromosome:3:6717096:6717179:-1

intergenic

block1590429 [novel_lenNOK_5varHIGH_randfoldOK_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	0.002	no	no	0.44/0.50	18/22/0.25	1.5	2.5	4	0	3	0	16	4	3arm	2	14	0.27	4	4	3	na	na

		reads	miRBase family seed
seed	---------------------------------------------------GGUCAGA------------------------------	2	miR-540
seed	-----------------------------------------------------UCAGAGA----------------------------	1	novel
seed	-------------------------------------------------------AGAGAAA--------------------------	1	novel
		len	cloning frequencies
			T2S1	T2S2	T5S1
	----------------------------------------------------GTCAGAGAAACAATGGAG------------------	18	1	-	-
	--------------------------------------------------GGGTCAGAGAAACAATGG--------------------	18	1	-	-
	------------------------------------------------------CAGAGAAACAATGGAGTG----------------	18	-	1	-
	--------------------------------------------------GGGTCAGAGAAACAATGGAGTG----------------	22	-	-	1
rat	ggcctcttcagccctgacttcagcttctcggctcagtgtgaccagagcttGGGTCAGAGAAACAATGGAGTGagtgctgctgggggct
	****************************************************************************************
	...................................................>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++	ENSRNOT00000012136 ENSRNOG00000009153 LOC500292
rat	(((((((.((((.((.((((((..((((((((((((.((.......))))))))).)))))....)))))).)).))))..)))))))	1.000 -39.80