miR-Intess: classification

other hairpins

novel_loopOverlap_randfoldOK_nonpairedHIGH (98 loci)

block949949 [novel_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	0.67/0.67	21/21/1.00	0.0	0.0	1	0	1	0	34	-2	5arm_loop	1	nd	0.38	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------CCAGAUC------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	----------------------------------GCCAGATCAGCGCTCCGGAAC-----------------------------------------------------	21	1
rat	cgaggcttcgagcatcccggcggcggctgctccgGCCAGATCAGCGCTCCGGAACccctcaggagcgctcctcgccgcctcttgctgcttcccttcgctcctcctcgg
	************************************************************************************************************
rat	(((((....((((.....((.((((((.....((((.((...((((((((.((.....)).)))))))).)).))))......)))))).))....))))..))))).	0.920 -48.40

rat

chromosome:1:27539516:27539623:1

intergenic

block378013 [novel_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	0.74/0.80	19/22/0.80	0.8	1.0	5	0	2	0	44	-21	3arm_loop	1	nd	0.32	2	5	2	na	na

		reads	miRBase family seed
seed	------------------------------------------------------ACACGCC--------------------------------------------------------	2	novel
seed	-----------------------------------------------------CACACGC---------------------------------------------------------	2	novel
seed	-------------------------------------------------------CACGCCU-------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2
	-----------------------------------------------------CACACGCCTCCCGCACCCCT--------------------------------------------	20	1	1
	------------------------------------------------------ACACGCCTCCCGCACCCCT--------------------------------------------	19	1	-
	----------------------------------------------------GCACACGCCTCCCGCACCCCTC-------------------------------------------	22	1	-
	----------------------------------------------------GCACACGCCTCCCGCACCCC---------------------------------------------	20	1	-
rat	ctcggggcggggaaaggggcgcgggcacggagaagctgggccgcgggagcgcGCACACGCCTCCCGCACCCCTCaagcttctgcggctcctcccagtcgcgcgccctccgccctggg
	*********************************************************************************************************************
rat	((((((((((((...((.((((((((.((.((((((((((..(((((((.(((....))))))))))..)))...))))))).))))).........))))).))))))))))))))	0.780 -75.00

rat

chromosome:14:111068743:111068859:-1

intergenic ## {Repeats: dust 111068807 111068808 0 class=dust} ## {SimpF: 1 Eponine,oe = 0.80 -1 CpG, -1 Eponine}

block1499775 [novel_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	0.009	no	no	0.42/0.42	24/24/1.00	0.0	0.0	1	0	1	0	34	-2	5arm_loop	2	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------ACUCUCA------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	----------------------------------TACTCTCATCTCCATTCTCAGTGT--------------------------------------------------------------	24	1
rat	catgttagggtgtgtggcatattgtacctcattcTACTCTCATCTCCATTCTCAGTGTtttcaggctgattggagatcatggaggagggaaggcttggcaggctagataccctcctcata
	************************************************************************************************************************
rat	.(((..(((((((.((((....(((......((((.((((.(((((((...(((((........))))).)))))))...))))...))))......))).)))).)))))))...))).	0.890 -41.90

rat

chromosome:3:141754279:141754398:1

intergenic

block1499826 [novel_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	0.009	no	no	0.42/0.42	24/24/1.00	0.0	0.0	1	0	1	0	34	-2	5arm_loop	2	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------ACUCUCA------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	----------------------------------TACTCTCATCTCCATTCTCAGTGT--------------------------------------------------------------	24	1
rat	catgttagggtgtgtggcatattgtacctcattcTACTCTCATCTCCATTCTCAGTGTtttcaggctgattggagatcatggaggagggaaggcttggcaggctagataccctcctcata
	************************************************************************************************************************
rat	.(((..(((((((.((((....(((......((((.((((.(((((((...(((((........))))).)))))))...))))...))))......))).)))).)))))))...))).	0.890 -41.90

rat

chromosome:3:141756087:141756206:1

intergenic

novel_lenNOK_shortStem_5varHIGH (97 loci)

block21223 [novel_lenNOK_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	0.641	no	no	0.61/0.67	18/23/0.40	4.4	1.2	5	0	3	0	0	1	5arm	1	nd	0.10	2	5	3	na	na

		reads	miRBase family seed
seed	-------GGCGGAU--------------------------------------------------------------	3	novel
seed	-CCAGUAG--------------------------------------------------------------------	1	novel
seed	-----UAGGCGG----------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S1	T3S1
	------AGGCGGATGGAAGCCAGC----------------------------------------------------	18	-	1	1
	GCCAGTAGGCGGATGGAAGCCAG-----------------------------------------------------	23	1	-	-
	------AGGCGGATGGAAGCCAGCTG--------------------------------------------------	20	1	-	-
	----GTAGGCGGATGGAAGCCA------------------------------------------------------	18	-	-	1
rat	GCCAGTAGGCGGATGGAAGCCAGCTGtcccgagaagcagtgaactgtggcgtcatcccgagcagtgccttaccggt
	****************************************************************************
	........>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000040910 ENSRNOG00000002342 Aldh3a2
	........>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000003200 ENSRNOG00000002342 Aldh3a2
rat	(((.((((((((((((..(((((((((........)))))......)))).))))))........)))).)).)))	0.580 -23.80

rat

chromosome:10:47420996:47421071:-1

Same_strand|Boundary_non-coding|ENSRNOT00000038081|ENSRNOG00000002342 ## ENSRNOG00000002342|protein_coding|Aldh3a2|Fatty aldehyde dehydrogenase (EC 1.2.1.3) (Aldehyde dehydrogenase, microsomal) (Aldehyde dehydrogenase family 3 member A2) (Aldehyde dehydrogenase 10). [Source:UniProtKB/Swiss-Prot;Acc:P30839]

block28452 [novel_lenNOK_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	0.046	no	no	0.50/0.53	18/19/0.00	1.3	0.7	3	0	3	0	1	35	5arm	1	nd	0.11	2	3	3	na	na

		reads	miRBase family seed
seed	----UGGUUUG-----------------------------------------------------------------------------------------------------------	2	novel
seed	--UCUGGUU-------------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T3S1	T5S1
	---CTGGTTTGGTAGTCAGGA-------------------------------------------------------------------------------------------------	18	1	1	-
	-GTCTGGTTTGGTAGTCAGG--------------------------------------------------------------------------------------------------	19	-	-	1
rat	gGTCTGGTTTGGTAGTCAGGAagtaaagagacatgtttggtgtaaatgctcttctgcatcaggagctgcagcgcctatatgcttggatttcgctggtgggtgtactgagaaccaagct
	**********************************************************************************************************************
rat	((..((((((..((((((((((((...(((.(((((..(((((...(((.((((((...))))))..)))))))).))))))))..))))).)))........)))).))))))..))	0.490 -37.80

rat

chromosome:10:62908229:62908346:-1

intergenic

block41706 [novel_lenNOK_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	0.425	no	no	0.61/0.68	19/23/0.25	2.8	3.8	4	0	4	0	0	29	3arm	1	nd	0.16	2	4	4	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------CUGCCUU-----------	2	novel
seed	------------------------------------------------------------------------------------AGUUGCU----------------	1	novel
seed	-------------------------------------------------------------------------------------GUUGCUG---------------	1	novel
		len	cloning frequencies
			T1S1	T3S1	T3S2	T5S2
	----------------------------------------------------------------------------------------GCTGCCTTGGCCAGAGTCC	19	1	-	-	1
	-----------------------------------------------------------------------------------GAGTTGCTGCCTTGGCCAG-----	19	-	-	1	-
	------------------------------------------------------------------------------------AGTTGCTGCCTTGGCCAGAGTCC	23	-	1	-	-
rat	ggagtctccctagggggcggagcttcaagggggcgagaggtgtggcttggctgtcaggtccctttgccttttgttcggttactGAGTTGCTGCCTTGGCCAGAGTCC
	***********************************************************************************************************
	.............................................................................................>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000021124 ENSRNOG00000015380 Jup
rat	(((.(((..(((..(((((((((((.((..((((((((((((.((((((.....))))))....))))))))))))..))...))))).)))))))))..))).)))	0.880 -38.90

rat

chromosome:10:89335538:89335644:-1

block46719 [novel_lenNOK_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	0.144	no	no	0.44/0.45	18/22/0.50	2.0	0.0	2	0	2	0	0	19	5arm	1	nd	0.27	3	2	2	na	na

		reads	miRBase family seed
seed	-----AUCUUCU-------------------------------------------------------------------------------	1	novel
seed	-CUUAAUC-----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T2S1
	----AATCTTCTGTGATCCCTG---------------------------------------------------------------------	18	-	1
	GCTTAATCTTCTGTGATCCCTG---------------------------------------------------------------------	22	1	-
rat	GCTTAATCTTCTGTGATCCCTGgactacacagcggacgctgcagtttcccggcttcttactcagtagtttgtgaacactttaaagattgag
	*******************************************************************************************
rat	.(((((((((..(((.((...(((((((..((.(((.((((........)))).)))..))..)))))))..)).)))....)))))))))	0.580 -22.80

rat

chromosome:10:97748690:97748780:-1

intergenic

block75396 [novel_lenNOK_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	0.690	no	no	0.50/0.52	18/21/0.50	2.5	1.0	2	0	2	0	1	28	5arm	1	nd	0.22	2	2	2	na	na

		reads	miRBase family seed
seed	-------GGGUUGG----------------------------------------------------------------------------------------------------------	1	novel
seed	--CCCUUGG---------------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T4S1
	------TGGGTTGGTCCCAAAAAC------------------------------------------------------------------------------------------------	18	-	1
	-TCCCTTGGGTTGGTCCCAAAA--------------------------------------------------------------------------------------------------	21	1	-
rat	tTCCCTTGGGTTGGTCCCAAAAACagccccaatgacaaagaaggaaggagagcttgttgactgtctctcagatttctgctaattttgattttttggtccccctaaccccatactcaggag
	************************************************************************************************************************
rat	.(((...(((((((..(((((((......(((......(((((....(((((............)))))...))))).......)))..)))))))..))...)))))........))).	0.500 -23.12

rat

chromosome:10:49104465:49104584:1

intergenic

block77738 [novel_lenNOK_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	0.113	no	no	0.63/0.68	19/19/0.00	3.4 0.0	3.4 0.0	5 1	0 0	5 1	0 0	2 12	0 -4	5arm 5arm_loop	3 3	17 13	0.26 0.42	2 5	6	6	na	na

		reads	miRBase family seed
seed	---------UCGCUGG----------------------------------------------	2	novel
seed	---CGGCCAU----------------------------------------------------	1	novel
seed	-------------UGGAUUG------------------------------------------	1	novel
seed	----GGCCAUC---------------------------------------------------	1	novel
seed	-------CAUCGCU------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T2S2	T3S2	T4S1	T5S1	T5S2
	--------ATCGCTGGATTGCAGCCGG-----------------------------------	19	-	-	1	-	-	1
	------CCATCGCTGGATTGCAGCC-------------------------------------	19	-	1	-	-	-	-
	--GCGGCCATCGCTGGATTGC-----------------------------------------	19	-	-	-	1	-	-
	---CGGCCATCGCTGGATTGCA----------------------------------------	19	-	-	-	-	1	-
	------------CTGGATTGCAGCCGGTGAG-------------------------------	19	1	-	-	-	-	-
rat	ttGCGGCCATCGCTGGATTGCAGCCGGTGAGttttcggcgggttgtcccgggtaatccgcag
	**************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000005588 ENSRNOG00000004214 RGD1565215_predicted
rat	.(((((...(((..((((.((.(((((.......)))))..)).))))))).....))))).	0.610 -23.20