miR-Intess: classification

other hairpins

novel_lenNOK_Multihit_loopOverlap_randfoldOK_nonpairedHIGH (14 loci)

block1985571 [novel_lenNOK_Multihit_loopOverlap_randfoldOK_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
no	0.004	no	no	0.64/0.64	25/25/0.00	0.0	0.0	1	0	1	0	24	-2	5arm_loop	12	nd	0.40	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------------AAGGAGA--------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	------------------------GAAGGAGACAGGACCTGGCCTGGTG---------------------------------------------------	25	1
rat	agatgtcttgtcccatgtgcaactGAAGGAGACAGGACCTGGCCTGGTGcaaccaacatagaccctgtccctcacatgcactgtnnctgggttctcatta
	****************************************************************************************************
rat	.((((......((((.(((((..((.(((.((((((..(((...(((.....)))...)))..)))))))))))..)))))......))))....)))).	1.000 -32.90

rat

chromosome:6:139716221:139716320:-1

intergenic

block1985470 [novel_lenNOK_Multihit_loopOverlap_randfoldOK_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
no	0.003	no	no	0.64/0.64	25/25/0.00	0.0	0.0	1	0	1	0	23	-2	5arm_loop	12	nd	0.40	3	1	1	na	na

		reads	miRBase family seed
seed	------------------------AAGGAGA---------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	-----------------------GAAGGAGACAGGACCTGGCCTGGTG----------------------------------------------------------	25	1
rat	gctgtcttgtcccaggtgcagctGAAGGAGACAGGACCTGGCCTGGTGcaaccgacacagaccctgtccctcacctgcactgtctctgggttcacattaaccagta
	**********************************************************************************************************
rat	((((...((((((((((((((.((.(((.((((((..(((...(((.....)))...)))..))))))))))).)))))).....)))))...))).....)))).	1.000 -42.20

rat

chromosome:6:139444597:139444702:-1

intergenic

block1063657 [novel_lenNOK_Multihit_loopOverlap_randfoldOK_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
no	0.005	no	no	0.58/0.58	19/19/0.00	0.0	0.0	2	0	1	0	31	-2	5arm_loop	14	nd	0.32	3	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------GCAGGCC-------------------------------------------------------------	1	novel
seed	----------------------------------------------------------GCAGGCC-----------------------------------	1	novel
		len	cloning frequencies
			T1S1
	-------------------------------TGCAGGCCTTCAGAGTGCA--------------------------------------------------	19	1
	---------------------------------------------------------TGCAGGCCTTCAGAGTGCA------------------------	19	1
rat	cagagtgcagccactgtggaaaagcccacacTGCAGGCCTTCAGAGTGCAgccactgTGCAGGCCTTCAGAGTGCAgccactgtggaaaagcccacactg
	****************************************************************************************************
	--------------------------------------------------------------------------------------------------------------	ENSRNOT00000045636 ENSRNOG00000000539 Zfand3
rat	(((.(((...((((.((((.......(((.(((.((((((.((.((((....)))).)).)))))).))).)))...)))).)))).......))).)))	0.890 -40.20

rat

chromosome:20:8400256:8400355:-1

Opposite_strand|Intronic_coding|ENSRNOT00000045636|ENSRNOG00000000539 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000000648|ENSRNOG00000000539 ## ENSRNOG00000000539|protein_coding|Zfand3|AN1-type zinc finger protein 3 (Testis-expressed sequence 27). [Source:UniProtKB/Swiss-Prot;Acc:Q5U2M7] ## {Repeats: trf 10 29 0 class=trf,trf 51 70 0 class=trf,trf 63 82 0 class=trf}

block1063659 [novel_lenNOK_Multihit_loopOverlap_randfoldOK_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
no	0.001	no	no	0.58/0.58	19/19/0.00	0.0	0.0	2	0	1	0	38	-2	5arm_loop	14	nd	0.32	3	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------GCAGGCC-------------------------------------------	1	novel
seed	---------------------------------------GCAGGCC---------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	----------------------------------------------------------------TGCAGGCCTTCAGAGTGCA--------------------------------	19	1
	--------------------------------------TGCAGGCCTTCAGAGTGCA----------------------------------------------------------	19	1
rat	aggccttcagagtgcagccactgtggaaaagcccacacTGCAGGCCTTCAGAGTGCAgccactgTGCAGGCCTTCAGAGTGCAgccactgtggaaaagcccacactgcaggcctt
	*******************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000045636 ENSRNOG00000000539 Zfand3
rat	((((((.(((.(((...((((.((((.......(((.(((.((((((.((.((((....)))).)).)))))).))).)))...)))).)))).......))).))).)))))).	0.940 -52.90

rat

chromosome:20:8400248:8400362:-1

Opposite_strand|Intronic_coding|ENSRNOT00000045636|ENSRNOG00000000539 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000000648|ENSRNOG00000000539 ## ENSRNOG00000000539|protein_coding|Zfand3|AN1-type zinc finger protein 3 (Testis-expressed sequence 27). [Source:UniProtKB/Swiss-Prot;Acc:Q5U2M7] ## {Repeats: trf 28 47 0 class=trf,trf 77 96 0 class=trf,trf 118 137 0 class=trf,trf 36 54 0 class=trf}

block1063661 [novel_lenNOK_Multihit_loopOverlap_randfoldOK_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
no	0.001	no	no	0.58/0.58	19/19/0.00	0.0	0.0	2	0	1	0	38	-2	5arm_loop	14	nd	0.32	3	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------GCAGGCC-------------------------------------------	1	novel
seed	---------------------------------------GCAGGCC---------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	----------------------------------------------------------------TGCAGGCCTTCAGAGTGCA--------------------------------	19	1
	--------------------------------------TGCAGGCCTTCAGAGTGCA----------------------------------------------------------	19	1
rat	aggccttcagagtgcagccactgtggaaaagcccacacTGCAGGCCTTCAGAGTGCAgccactgTGCAGGCCTTCAGAGTGCAgccactgtggaaaagcccacactgcaggcctt
	*******************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000045636 ENSRNOG00000000539 Zfand3
rat	((((((.(((.(((...((((.((((.......(((.(((.((((((.((.((((....)))).)).)))))).))).)))...)))).)))).......))).))).)))))).	0.940 -52.90

rat

chromosome:20:8400315:8400429:-1

block1063662 [novel_lenNOK_Multihit_loopOverlap_randfoldOK_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
no	0.001	no	no	0.58/0.58	19/19/0.00	0.0	0.0	2	0	1	0	38	-2	5arm_loop	14	nd	0.32	3	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------GCAGGCC------------------------------------------	1	novel
seed	---------------------------------------GCAGGCC--------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	----------------------------------------------------------------TGCAGGCCTTCAGAGTGCA-------------------------------	19	1
	--------------------------------------TGCAGGCCTTCAGAGTGCA---------------------------------------------------------	19	1
rat	aggccttcagagtgcagccactgtggaaaagcccacacTGCAGGCCTTCAGAGTGCAgccactgTGCAGGCCTTCAGAGTGCAgccactgtggaaaagcccacactgcaggcct
	******************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000045636 ENSRNOG00000000539 Zfand3
rat	((((((.(((.(((...((((.((((.......(((.(((.((((((.((.((((....)))).)).)))))).))).)))...)))).)))).......))).))).))))))	0.940 -52.80

rat

chromosome:20:8400316:8400429:-1

Opposite_strand|Intronic_coding|ENSRNOT00000045636|ENSRNOG00000000539 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000000648|ENSRNOG00000000539 ## ENSRNOG00000000539|protein_coding|Zfand3|AN1-type zinc finger protein 3 (Testis-expressed sequence 27). [Source:UniProtKB/Swiss-Prot;Acc:Q5U2M7] ## {Repeats: trf 51 70 0 class=trf,trf 226 245 0 class=trf,trf 185 203 0 class=trf}

block1063663 [novel_lenNOK_Multihit_loopOverlap_randfoldOK_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
no	0.010	no	no	0.58/0.58	19/19/0.00	0.0	0.0	1	0	1	0	17	-4	3arm_loop	14	nd	0.32	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------GCAGGCC----------------------------	1	novel
		len	cloning frequencies
			T1S1
	--------------------------------------TGCAGGCCTTCAGAGTGCA-----------------	19	1
rat	aggccttcagagtgcagccactgtggaaaagcccacacTGCAGGCCTTCAGAGTGCAgccactgtgcaggcctt
	**************************************************************************
	------------------------------------------------------------------------------------	ENSRNOT00000045636 ENSRNOG00000000539 Zfand3
rat	((((((.((.(((((.((.(((.((((...(((.........))).)))).))))).)).))).)).)))))).	0.830 -29.30

rat

chromosome:20:8400356:8400429:-1

block1930494 [novel_lenNOK_Multihit_loopOverlap_randfoldOK_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
no	0.002	no	no	0.61/0.61	18/18/0.00	0.0	0.0	1	0	1	0	35	-3	3arm_loop	22	nd	0.33	2	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------------CAGGAUG---------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	-----------------------------------------------------CCAGGATGTGCAGAAGCC-----------------------------------	18	1
rat	ggcgcccagggtctcctcaaatttcagaatgatcgtaggggctgtgcactcttCCAGGATGTGCAGAAGCCatctcaagatgaatggggtaaaaccctggaggcca
	**********************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000010942 ENSRNOG00000008266 RGD1559651_predicted
rat	(((..(((((((..(((((...((((...(((.......((((.((((((((....))).)))))..))))...)))...)))))))))....)))))))..))).	0.820 -43.30

rat

chromosome:6:46393574:46393679:-1

block822942 [novel_lenNOK_Multihit_loopOverlap_randfoldOK_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
no	0.010	no	no	0.53/0.53	19/19/0.00	0.0	0.0	2	0	2	0	37	-2	3arm_loop	14	nd	0.32	3	2	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------GGCAAGC------------------------------------------------	2	novel
		len	cloning frequencies
			T3S2	T5S1
	----------------------------------------------------------------AGGCAAGCTCCAAAGTTGC-------------------------------------	19	1	1
rat	ccttcttaaatggtcctggcagctgtgctctgtgtcccacggttggattctgtgaggcatgctcAGGCAAGCTCCAAAGTTGCgacatggtgagcacattgtcagggcacacaaaggggt
	************************************************************************************************************************
rat	.((((((...((((((((((((.(((((((.(((((.((...(((((.........((.(((....))).)))))))...)).)))))...))))))))))))))))).))..)))))).	0.620 -48.10

rat

chromosome:1:825635:825754:-1

intergenic

novel_lenNOK_Multihit_shortStem_5varHIGH_nonpairedHIGH_bulgeHIGH (14 loci)

block366485 [novel_lenNOK_Multihit_shortStem_5varHIGH_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	0.193	no	no	0.54/0.56	18/24/0.50	2.0	1.0	2	0	2	0	2	5	3arm	61	nd	0.38	4	2	2	na	na

		reads	miRBase family seed
seed	---------------------------------AUGGCCA------------------	1	novel
seed	-------------------------------------CCAAGUC--------------	1	novel
		len	cloning frequencies
			T2S1	T4S2
	------------------------------------GCCAAGTCCAAGAACCAC----	18	-	1
	--------------------------------CATGGCCAAGTCCAAGAACCACAC--	24	1	-
rat	ggtgcttcaggagccgtgggttaccgtgcagaCATGGCCAAGTCCAAGAACCACACca
	**********************************************************
	--------------------------------------------------------------------	ENSRNOT00000040381 ENSRNOG00000031658 RGD1305469_predicted
rat	((((.(((.(((((((((.((......))...))))))....)))..)))...)))).	1.000 -17.40