miR-Intess: classification

other hairpins

novel_multiarm_DicerNOK_mirtron (8 loci)

novel_shortStem_mirtron_bulgeHIGH (8 loci)

block52161 [novel_shortStem_mirtron_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	0.051	no	no	0.52/0.52	21/21/1.00	0.0	0.0	1	0	1	0	0	13	3arm	1	4	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------CAGCUCA-------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------------------------------------TCAGCTCACCTTCTTCTTGCC	21	1
rat	aggaagacgagggtgtggagacaggccgggtgtagggggtgggcccagggtcTCAGCTCACCTTCTTCTTGCC
	*************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>	ENSRNOT00000047013 ENSRNOG00000003239 Cant1
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>	ENSRNOT00000040449 ENSRNOG00000003239 Cant1
rat	.((((((.(((((((..(((((...((((((.((.....)).)))).)))))))....))))))).)))).))	0.900 -30.80

rat

chromosome:10:108408942:108409014:-1

block85533 [novel_shortStem_mirtron_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	0.015	no	no	0.59/0.59	22/22/1.00	0.0	0.0	2	0	1	0	3	27	3arm	1	1	0.23	4	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------------CCCUGAC-----------------	2	novel
		len	cloning frequencies
			T1S1
	-------------------------------------------------------------------------------------------GCCCTGACTTCGGCATTCCCTA---	22	2
rat	tgcgtaggctggccaagaggtcagggcaagttcaagggaggagatgtgtgtgagccagggaaagccagggttgggtactattaaccccctaGCCCTGACTTCGGCATTCCCTAggt
	********************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>	ENSRNOT00000055999 ENSRNOG00000007455 RGD1565522_predicted
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>	ENSRNOT00000009822 ENSRNOG00000007455 RGD1565522_predicted
rat	.((.((((...(((..(((((((((((.......((((.((.((((.(((..((((..((....))..))))...)))))))..)))))).))))))))))))))....)))).))	0.940 -45.70

rat

chromosome:10:70636595:70636710:1

block759295 [novel_shortStem_mirtron_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	0.028	no	no	0.50/0.50	20/20/1.00	0.0	0.0	1	0	1	0	0	30	3arm	1	3	0.26	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------CCUCAGC------------	1	novel
		len	cloning frequencies
			T2S2
	----------------------------------------------------------------------------ACCTCAGCTCTTTACACCCA	20	1
rat	ggcagagagtctggggtggccctaggcagagaatctggggtgcaggccgggttcttggggtctggatggggtcgcgACCTCAGCTCTTTACACCCA
	************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>	ENSRNOT00000023737 ENSRNOG00000017596 AC131065.16
rat	((.((((((.(((((((((((((((((.((((((((((........))))))))))...))))....))))))...)))))))))))))....)).	1.000 -43.90

rat

chromosome:18:77105985:77106080:1

Same_strand|Intronic_non-coding|ENSRNOT00000023737|ENSRNOG00000017596 ## ENSRNOG00000017596|protein_coding|AC131065.16|Thioredoxin-like protein 4A (Thioredoxin-like U5 snRNP protein U5-15kD)(Spliceosomal U5 snRNP-specific 15 kDa protein)(DIM1 protein homolog) [Source:UniProtKB/Swiss-Prot;Acc:P83877]

block909487 [novel_shortStem_mirtron_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	0.166	no	no	0.57/0.58	23/24/1.00	0.0	0.3	3	0	1	0	0	28	3arm	1	3	0.30	4	3	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------------------CAGGCAC----------------	3	novel
		len	cloning frequencies
			T1S2
	--------------------------------------------------------------------------------------------TCAGGCACACATCTCTGTCCCCTC	24	2
	--------------------------------------------------------------------------------------------TCAGGCACACATCTCTGTCCCCT-	23	1
rat	gaggggtaccatttgggaaatgtaagagccttggatccaaaagcaggggacctggtgggcatgggttggggccttagcactgattcttgggcTCAGGCACACATCTCTGTCCCCTC
	********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>	ENSRNOT00000024369 ENSRNOG00000017897 RGD1566394_predicted
rat	((((((.((.....((((..(((..((((((.(((..((...((..(((.((..((........))..)).)))..))..))..))).))))))..)))....)))).))))))))	0.540 -40.00

rat

chromosome:1:199782517:199782632:-1

block1058740 [novel_shortStem_mirtron_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	0.304	no	no	0.60/0.60	20/20/1.00	0.0	0.0	1	0	1	0	0	29	5arm	1	3	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	-CACUGGC-------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	TCACTGGCTCCTGTCTCCCT-------------------------------------------------------------------------------------------	20	1
rat	TCACTGGCTCCTGTCTCCCTcaggaagaggatggctctacctgtctccatcatgcggccaaaattgggaacttggaaatggtcagcctgctgctgagcacagggcaggtgg
	***************************************************************************************************************
	++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000047370 ENSRNOG00000030630 Ehmt2
	++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000051433 ENSRNOG00000030630 Ehmt2
rat	.((((.((.(((((....(((((..(((((.(((((...((.((..(((...............)))..))..))....))))).))).)).))))).))))))).)))).	0.510 -37.16

rat

chromosome:20:4028304:4028414:-1

block2028614 [novel_shortStem_mirtron_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	0.021	no	no	0.70/0.70	20/20/1.00	0.0	0.0	1	0	1	0	4	17	5arm	1	1	0.25	4	1	1	na	na

		reads	miRBase family seed
seed	-----CAGCCUG--------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	----GCAGCCTGCAGTGCCCTACC--------------------------------------------------------------------------	20	1
rat	agggGCAGCCTGCAGTGCCCTACCtgaccttggcagagtcattgactggccctcaagccgaggccaaggccagctctgcagctctgagctgtagccct
	**************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000038074 ENSRNOG00000027444 Nubpl_predicted
	>>>>>>>>>>>+++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000038715 ENSRNOG00000027492
rat	(((((((((((((((.((....(((..(((((((((.((((.....)))).))...)))))))...)))...)).))))))......)))))..))))	0.460 -40.60

rat

chromosome:6:72306158:72306255:1

Same_strand|Boundary_coding|ENSRNOT00000038715|ENSRNOG00000027492 ## Same_strand|Intronic_coding|ENSRNOT00000038074|ENSRNOG00000027444 ## ENSRNOG00000027492|protein_coding|| ## ENSRNOG00000027444|protein_coding|Nubpl_predicted|

block2584444 [novel_shortStem_mirtron_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	0.251	no	no	0.35/0.35	20/20/1.00	0.0	0.0	1	0	1	0	2	11	3arm	1	0	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------UGUUUUG--------------	1	novel
		len	cloning frequencies
			T4S1
	----------------------------------------------------GTGTTTTGTATGTTCTCAAG--	20	1
rat	cccggagaacggaacagagggagagcgtccccccaccccctcgcttactcgtGTGTTTTGTATGTTCTCAAGga
	**************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>	ENSRNOT00000060007 ENSRNOG00000012207 NP_001101678.1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>	ENSRNOT00000046621 ENSRNOG00000012207 NP_001101678.1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>	ENSRNOT00000044452 ENSRNOG00000012207 NP_001101678.1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>	ENSRNOT00000050411 ENSRNOG00000012207 NP_001101678.1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>	ENSRNOT00000017235 ENSRNOG00000012207 NP_001101678.1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>	ENSRNOT00000039962 ENSRNOG00000012207 NP_001101678.1
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000048898 ENSRNOG00000012207 NP_001101678.1
rat	((..((((((((((((..(((.(((((..............))))).)))...)))))....)))))))..)).	0.930 -21.94

rat

chromosome:9:32996480:32996553:1

block2150980 [novel_shortStem_mirtron_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	0.140	no	no	0.50/0.50	20/20/1.00	0.0	0.0	2	0	1	0	4	16	3arm	1	4	0.30	4	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------UCACUAA----------------	2	novel
		len	cloning frequencies
			T5S2
	----------------------------------------------------------------CTCACTAATCTCCTGTGTCC----	20	2
rat	actgaggaggaggtgggcctgcactgaggtgggagtgggccccagccatgtctcctgatcccatCTCACTAATCTCCTGTGTCCccag
	****************************************************************************************
	>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>	ENSRNOT00000025134 ENSRNOG00000021773 Bop1
	>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>	ENSRNOT00000056365 ENSRNOG00000021773 Bop1
rat	.(((.(((((((((.((.......((((((((((..(((...((....))...)))..)))))))))))).))))))....))).)))	0.730 -31.81

rat

chromosome:7:114502331:114502418:-1

novel_5varHIGH_randfoldOK_nonpairedHIGH_bulgeHIGH (7 loci)

block8230 [novel_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	0.004	no	no	0.50/0.57	21/22/1.00	2.7	3.3	3	0	2	0	7	27	5arm	2	nd	0.52	5	3	2	na	na

		reads	miRBase family seed
seed	------------UUUUUGC-----------------------------------------------------------------------------------------------	2	miR-129
seed	--------UUUUUUU---------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2
	-----------TTTTTTGCCCCCCCCCCTTTTT---------------------------------------------------------------------------------	22	1	1
	-------CTTTTTTTTTGCCCCCCCCCC--------------------------------------------------------------------------------------	21	-	1
rat	tctttttCTTTTTTTTTGCCCCCCCCCCTTTTTtttaatagcatcgagaaccaaaccccagttctggggttggtgtgttttgttttcccactggggaacaattaaggaacaaga
	******************************************************************************************************************
rat	((((.((((((....(((..((((...............(((((.....(((.(((((((....))))))))))))))).............))))..)))..)))))).))))	0.570 -30.59

rat

chromosome:10:16356362:16356475:-1

intergenic ## {Repeats: dust 16356448 16356469 0 class=dust}

block1568499 [novel_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	0.004	no	no	0.62/0.65	20/21/1.00	1.5	2.0	2	0	2	0	25	0	5arm	1	65	0.35	4	2	2	na	na

		reads	miRBase family seed
seed	--------------------------GGGCGGA-------------------------------------------------------------------	1	novel
seed	-----------------------------CGGAAGC----------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T3S2
	----------------------------GCGGAAGCGCAGACTACAGGA---------------------------------------------------	21	-	1
	-------------------------AGGGCGGAAGCGCAGACTAC-------------------------------------------------------	20	1	-
rat	ccttgcgcccctctcacgtcagtagAGGGCGGAAGCGCAGACTACAGGAtgcagttcctggttgcgttgctcctgctgagtgtcgcggtggcgagtaagg
	****************************************************************************************************
	........................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++	ENSRNOT00000019713 ENSRNOG00000014617 Tgoln2
	.....................................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++	ENSRNOT00000051421 ENSRNOG00000014617 Tgoln2
rat	(((((((((((...(((.(((((((.(((((...((((((....(((((......))))).)))))))))))))))))))))....)).)))..))))))	1.000 -47.80