miR-Intess: classification

other hairpins

block2979946 [novel_lenNOK_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	0.583	no	no	1.00/1.00	18/18/0.00	0.0	0.0	1	0	1	0	0	22	5arm	1	nd	0.28	3	1	1	na	na

		reads	miRBase family seed
seed	-GCGGGCC-----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	GGCGGGCCGGGGCCCCCC-------------------------------------------------------------------------	18	1
rat	GGCGGGCCGGGGCCCCCCtctggagcgcagagctaggtgctggaggcgagctaaggagctcaggagggctttccccgcggtacgcgtcgcc
	*******************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000038352 ENSRNOG00000025383 Pdha1
rat	.(((..((((((...((((((.((((....((((...(((.....))))))).....)))).)))))).....))).)))..)))......	0.890 -40.90

rat

chromosome:X:55899652:55899742:1

block2069312 [novel_lenNOK_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	0.110	no	no	1.00/1.00	18/18/0.00	0.0	0.0	1	0	1	0	2	36	5arm	2	nd	0.11	1	1	1	na	na

		reads	miRBase family seed
seed	---GCCGCCG------------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	--CGCCGCCGCCCGCGCCCG--------------------------------------------------------------------------------------------------	18	1
rat	gcCGCCGCCGCCCGCGCCCGctatagccgccgcgccggcctccagcgcccgcccgccctccgagcccggcggcgcacaggcggcggcggccgcacaggcggcgcgggcggggtcgagc
	**********************************************************************************************************************
rat	((((((.(((((((((.(((((...((.((((((((.((((...(((.(((((.((.......))..))))))))..)))))))).)))).))...)))))))))))))))).)).))	1.000 -78.70

rat

chromosome:6:137931148:137931265:1

intergenic ## {Repeats: dust 137931169 137931187 0 class=dust,C-rich 1 116 1 class=Low_complexity,C-rich 52 70 1 class=Low_complexity} ## {SimpF: 1 Eponine, -1 Eponine,oe = 0.86 0 CpG}

novel_5varHIGH_loopOverlap_nonpairedHIGH_bulgeHIGH (45 loci)

block195112 [novel_5varHIGH_loopOverlap_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	0.068	no	no	0.55/0.57	20/23/1.00	1.5	3.0	2	0	2	0	14	-9	5arm_loop_3arm	4	nd	0.50	4	2	2	na	na

		reads	miRBase family seed
seed	------------------CCUCCCU---------------------------------------------------	1	novel
seed	---------------CGACCUC------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T3S2
	--------------ACGACCTCCCTACGAGAACA------------------------------------------	20	1	-
	-----------------ACCTCCCTACGAGAACATGCCTC------------------------------------	23	-	1
rat	cctttctggcggtgACGACCTCCCTACGAGAACATGCCTCtcgcaaaggatctccttcatccctctccagaagagg
	****************************************************************************
rat	(((((((((.(((((.((..(((...(((((.......)))))....)))..))..))))).....))))).))))	0.710 -20.90

rat

chromosome:12:29143800:29143875:-1

intergenic

block209372 [novel_5varHIGH_loopOverlap_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	0.044	no	no	0.55/0.67	20/25/0.80	3.4	4.8	5	0	2	0	5	-16	5arm_loop_3arm	1	nd	0.48	5	5	2	na	na

		reads	miRBase family seed
seed	--------CCUCCUC--------------------------------------------	3	novel
seed	------CUCCUCC----------------------------------------------	1	novel
seed	-----------------CGUCUCC-----------------------------------	1	novel
		len	cloning frequencies
			T1S2	T5S1
	----------------TCGTCTCCACCTACCAAGACAG---------------------	22	-	1
	-------TCCTCCTCGTCGTCTCCACC--------------------------------	20	-	1
	-------TCCTCCTCGTCGTCTCCACCTACC----------------------------	24	-	1
	-------TCCTCCTCGTCGTCTCCACCTACCA---------------------------	25	-	1
	-----CCTCCTCCTCGTCGTCTCCAC---------------------------------	21	1	-
rat	gaaccCCTCCTCCTCGTCGTCTCCACCTACCAAGACAGcttaactggggatttgggttc
	***********************************************************
rat	((((((.(((((...((.((((..........)))).))......)))))...))))))	0.990 -15.90

rat

chromosome:12:5630682:5630740:1

intergenic

block258584 [novel_5varHIGH_loopOverlap_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	0.181	no	no	0.50/0.55	20/22/1.00	2.5	1.5	2	0	2	0	19	-4	3arm	5	nd	0.45	4	2	2	na	na

		reads	miRBase family seed
seed	-------------------------------UAAGGAC------------------------------------	1	novel
seed	------------------------------------ACGAAGC-------------------------------	1	novel
		len	cloning frequencies
			T3S2	T5S2
	------------------------------GTAAGGACGAAGCCATGTTCAG----------------------	22	1	-
	-----------------------------------GACGAAGCCATGTTCAGCTC-------------------	20	-	1
rat	ctttatgtgctctttctaagctggcactccGTAAGGACGAAGCCATGTTCAGCTCgagcgccaagattgtgaag
	**************************************************************************
rat	((((((((((((...((.(((((((..(((....)))....)))).))).))...)))))).......))))))	0.990 -22.61

rat

chromosome:13:47451225:47451298:-1

intergenic

block305293 [novel_5varHIGH_loopOverlap_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	0.123	no	no	0.52/0.59	21/22/1.00	2.5	2.0	2	0	2	0	36	-3	3arm	1	nd	0.43	4	2	2	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------------GCAGUCU-------------------------------------------------	1	novel
seed	-----------------------------------------------------------AGCCAGC------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T3S1
	----------------------------------------------------------CAGCCAGCAGTCTCTCCTCAAC----------------------------------------	22	1	-
	---------------------------------------------------------------AGCAGTCTCTCCTCAACAAGC------------------------------------	21	-	1
rat	ccacaccccttctcactccagccagtctcctgctagggaattcggttatacttttggtCAGCCAGCAGTCTCTCCTCAACAAGCagccaaagaatgggagagtgagatcaaatgaatgga
	************************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000000036 ENSRNOG00000000033 RGD1311960_predicted
rat	(((((.....((((((((...(((.(((.(((((...((....((....(((.((((....)))).)))....))))....)))))....))).)))..)))))))).....))..))).	0.820 -31.60

rat

chromosome:13:45280808:45280927:1

block307401 [novel_5varHIGH_loopOverlap_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	0.059	no	no	0.61/0.64	19/23/0.75	4.0	3.5	4	0	2	0	41	-19	3arm	1	nd	0.32	4	4	2	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------CGUACCC--------------------------------------------------------	2	novel
seed	-------------------------------------------------------------CCCGGGU----------------------------------------------------	1	novel
seed	-----------------------------------------------------GGCACGU------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T3S2
	----------------------------------------------------AGGCACGTACCCGGGTTCACCT----------------------------------------------	22	1	-
	--------------------------------------------------------ACGTACCCGGGTTCACCTAGCC------------------------------------------	22	-	1
	------------------------------------------------------------ACCCGGGTTCACCTAGCCA-----------------------------------------	19	-	1
	--------------------------------------------------------ACGTACCCGGGTTCACCTAGCCA-----------------------------------------	23	-	1
rat	gaggccccaaggtgagactcctcctaaactttggcggtggcttttgggtctcAGGCACGTACCCGGGTTCACCTAGCCAttacgctctgcagaaagcgagttttgcccttggcagtctct
	************************************************************************************************************************
rat	(((((.((((((..((((((((..........((((((((((...((..(((.((......)).)))....)).))))))..))))........)).))))))..)).))))..))))).	0.700 -43.17

rat

chromosome:13:49157617:49157736:1

intergenic

block724019 [novel_5varHIGH_loopOverlap_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	0.443	no	no	0.50/0.57	21/24/1.00	4.3	2.7	3	0	3	0	28	-22	3arm	9	nd	0.41	4	3	3	na	na

		reads	miRBase family seed
seed	--------------------------------------------------GAACCAA-----------------------------------------	1	novel
seed	-------------------------------------------------GGAACCA------------------------------------------	1	novel
seed	-------------------------------------------CUGUUUG------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T4S1	T4S2
	------------------------------------------CCTGTTTGGAACCAACAACAGCAG--------------------------------	24	-	1	-
	-------------------------------------------------GGAACCAACAACAGCAGCTCC----------------------------	21	1	-	-
	------------------------------------------------TGGAACCAACAACAGCAGCTCC----------------------------	22	-	-	1
rat	gcgattggacaaactgagaaagaatgcctttgctagtgttatCCTGTTTGGAACCAACAACAGCAGCTCCatttctggggtttgggtcttccgaggcc
	**************************************************************************************************
rat	((..(((((((((((.(((((....((...((((..((((.(((.....)))...))))..))))))....))))).)).)))).....))))).)).	0.690 -25.40

rat

chromosome:18:950328:950425:1

intergenic

block812116 [novel_5varHIGH_loopOverlap_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	0.388	no	no	0.42/0.50	23/24/1.00	2.7	2.3	3	0	1	0	10	-10	5arm_loop_3arm	1	nd	0.50	4	3	1	na	na

		reads	miRBase family seed
seed	------------------UCAUGUG-------------------------------------------	1	novel
seed	------------CAUGUUU-------------------------------------------------	1	novel
seed	-----------UCAUGUU--------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-----------------TTCATGTGTGAGCCAGATGGAGAG---------------------------	24	1
	----------TTCATGTTTCATGTGTGAGCCAGA----------------------------------	24	1
	-----------TCATGTTTCATGTGTGAGCCAGA----------------------------------	23	1
rat	agtctcagcgTTCATGTTTCATGTGTGAGCCAGATGGAGAGcggaagggaacccggggcgcctggatt
	********************************************************************
rat	(((((..((((((..(((((...(((...((....))...)))....)))))...))))))..)))))	0.640 -20.00

rat

chromosome:19:40004736:40004803:1

intergenic

block959156 [novel_5varHIGH_loopOverlap_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	0.289	no	no	0.33/0.41	18/22/0.71	1.3	1.6	7	0	1	0	12	-8	5arm_loop_3arm	6	nd	0.36	5	7	1	na	na

		reads	miRBase family seed
seed	-------------CAUAGAG--------------------------------------------	4	novel
seed	----------------AGAGUAA-----------------------------------------	3	novel
		len	cloning frequencies
			T5S1
	------------TCATAGAGTAAATTGGGTAG--------------------------------	20	3
	---------------TAGAGTAAATTGGGTAGGAC-----------------------------	20	1
	---------------TAGAGTAAATTGGGTAGGACCT---------------------------	22	1
	---------------TAGAGTAAATTGGGTAGG-------------------------------	18	1
	------------TCATAGAGTAAATTGGGT----------------------------------	18	1
rat	caggaggaaccaTCATAGAGTAAATTGGGTAGGACCTagcacaaaggtacttgggttgggcctg
	****************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000043702 ENSRNOG00000034080 RGD1563490_predicted
rat	((((...((((......(((((..(((((.....)))))........))))).))))...))))	0.530 -13.50