miR-Intess: classification

other hairpins

novel_Multihit_shortStem_nonpairedHIGH_bulgeHIGH (172 loci)

block74241 [novel_Multihit_shortStem_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	0.091	no	no	0.50/0.50	22/22/1.00	0.0	0.0	1	0	1	0	1	15	5arm	12	nd	0.36	4	1	1	na	na

		reads	miRBase family seed
seed	--UUGGUGG--------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	-CTTGGTGGCCAAAGCTGTTTCA------------------------------------------------------------------	22	1
rat	gCTTGGTGGCCAAAGCTGTTTCAtgcttgggcacactttaaaaaaaaatctgggtggtgatggcagcggctcaggcctttaatcctagc
	*****************************************************************************************
rat	(((.((.((((..((((((....((((...((.(((((.............)))))))...))))))))))..))))......)).)))	0.880 -27.52

rat

chromosome:10:46982217:46982305:1

intergenic

block1125500 [novel_Multihit_shortStem_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	0.667	no	no	0.38/0.38	21/21/1.00	0.0	0.0	2	0	1	0	1	15	5arm	110	nd	0.57	5	2	1	na	na

		reads	miRBase family seed
seed	--CAAGUAU------------------------------------------------------------	2	novel
		len	cloning frequencies
			T2S1
	-CCAAGTATGATGACATCAAGA-----------------------------------------------	21	2
rat	gCCAAGTATGATGACATCAAGAaggtggtgaagcaggcgtccgaggtcccactaaagagcatcctgggc
	*********************************************************************
rat	(((.((...((((...((.....(((((.((....((...))....)))))))...)).)))))).)))	0.900 -15.70

rat

chromosome:2:3773713:3773781:-1

intergenic

novel_lenNOK_cloningOK_loopOverlap (172 loci)

block18089 [novel_lenNOK_cloningOK_loopOverlap]

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	0.023	no	no	0.40/0.44	18/20/0.08	0.0	0.2	12	0	5	0	22	-3	3arm_loop	1	nd	0.25	3	12	5	na	na

		reads	miRBase family seed
seed	---------------------------------------------------GGGACUC----------------------------------	12	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1	T4S1	T4S2
	--------------------------------------------------AGGGACTCTGGGAAATTTT-----------------------	19	3	2	1	2	2
	--------------------------------------------------AGGGACTCTGGGAAATTT------------------------	18	-	-	-	1	-
	--------------------------------------------------AGGGACTCTGGGAAATTTTT----------------------	20	-	1	-	-	-
rat	ccagttatattgtaataacttatggaatttaggggttatgagcgaaagaaAGGGACTCTGGGAAATTTTTaggcagaaaataagtgtactgg
	********************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000016440 ENSRNOG00000011892 Slc36a2
rat	((((.((((((.......((((.(((((((.((((((................))))))...))))))))))).........))))))))))	0.830 -15.28

rat

chromosome:10:40575778:40575869:-1

block18891 [novel_lenNOK_cloningOK_loopOverlap]

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	0.50/0.56	18/19/0.00	0.4	0.3	12	0	7	0	27	-5	3arm_loop	1	nd	0.22	2	12	7	na	na

		reads	miRBase family seed
seed	------------------------------------------------AGGAGCU-------------------------------------	10	miR-28/708
seed	----------------------------------------------CUAGGAG---------------------------------------	1	novel
seed	---------------------------------------------UCUAGGA----------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S1	T4S1	T5S1	T5S2
	-----------------------------------------------TAGGAGCTCACAGTCCAT---------------------------	18	-	2	1	2	1	2	2
	--------------------------------------------CTCTAGGAGCTCACAGTC------------------------------	18	1	-	-	-	-	-	-
	---------------------------------------------TCTAGGAGCTCACAGTCCA----------------------------	19	-	1	-	-	-	-	-
rat	attgtatctacacacccttgtgaggacctgtgcttcactctgccCTCTAGGAGCTCACAGTCCATcactgagatgtaaactccaatgcagtg
	********************************************************************************************
rat	(((((((....(((..((((((((((.(((((.....((((........))))..)))))))).)))).))).)))........))))))).	0.450 -21.30

rat

chromosome:10:42596529:42596620:-1

intergenic

block23789 [novel_lenNOK_cloningOK_loopOverlap]

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	0.118	no	no	0.37/0.39	18/19/0.00	0.0	0.2	29	0	9	0	30	-2	3arm_loop	1	nd	0.21	2	38	9	na	na

		reads	miRBase family seed
seed	------------------------------------------------------GGGGCAA-----------------------------------------	38	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-----------------------------------------------------TGGGGCAAAAAAAAAAGG-------------------------------	18	6	1	4	1	4	-	7	3	1
	-----------------------------------------------------TGGGGCAAAAAAAAAAGGT------------------------------	19	5	-	2	-	-	2	2	-	-
rat	ctgtgaattcattaagacacttagtctgtcacttgttttgaaacttgcttattTGGGGCAAAAAAAAAAGGTgttcatctgaattctgttgaatttttcagc
	******************************************************************************************************
	<<<<<-----------------------------------------------------------------------------------------------------------	ENSRNOT00000043412 ENSRNOG00000031819 MYH8_RAT
	<<<<<-----------------------------------------------------------------------------------------------------------	ENSRNOT00000057260 ENSRNOG00000031819 MYH8_RAT
	<<<<<-----------------------------------------------------------------------------------------------------------	ENSRNOT00000004307 ENSRNOG00000031819 MYH8_RAT
	<<<<<-----------------------------------------------------------------------------------------------------------	ENSRNOT00000004630 ENSRNOG00000031819 MYH8_RAT
	<<<<<-----------------------------------------------------------------------------------------------------------	ENSRNOT00000004157 ENSRNOG00000031819 MYH8_RAT
rat	(((.(((((((...(((...((((.....(((((.((((.....((((((.....))))))..)))).))))).....))))..)))..)))))))..))).	0.580 -21.50

rat

chromosome:10:53990735:53990836:-1

Opposite_strand|Intronic_coding|ENSRNOT00000004157|ENSRNOG00000031819 ## ENSRNOG00000031819|protein_coding|MYH8_RAT|Myosin-8 (Myosin heavy chain 8) (Myosin heavy chain, skeletal muscle, perinatal) (MyHC-perinatal) (Fragment). [Source:UniProtKB/Swiss-Prot;Acc:P04462] ## {Repeats: dust 53990768 53990777 0 class=dust}

block48465 [novel_lenNOK_cloningOK_loopOverlap]

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	0.374	no	no	0.58/0.61	18/20/0.15	0.0	0.4	13	0	5	0	17	-2	5arm_loop	1	nd	0.11	1	13	5	na	na

		reads	miRBase family seed
seed	------------------GAGGGCU---------------------------------------------------	13	novel
		len	cloning frequencies
			T1S1	T2S2	T3S1	T4S2	T5S2
	-----------------TGAGGGCTGCTTGGTGTCT----------------------------------------	19	3	2	1	-	2
	-----------------TGAGGGCTGCTTGGTGTC-----------------------------------------	18	-	-	2	1	-
	-----------------TGAGGGCTGCTTGGTGTCTC---------------------------------------	20	1	-	-	-	1
rat	ggagtagaggcgagggaTGAGGGCTGCTTGGTGTCTCtggacagttctctgagcggcctcataagtagagggggtc
	****************************************************************************
rat	.........((.....((((.((((((((((((((....)))).....))))))))))))))..))..........	0.880 -22.00

rat

chromosome:10:101937107:101937182:-1

intergenic

block55369 [novel_lenNOK_cloningOK_loopOverlap]

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	0.520	no	no	0.21/0.21	19/19/0.00	0.0	0.0	26	0	3	0	15	-1	3arm_loop	2	nd	0.21	3	33	3	na	na

		reads	miRBase family seed
seed	---------------------------------------AGAUGUU--------------------------	31	novel
seed	----------------------------------------GAUGUUU-------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T5S1
	--------------------------------------TAGATGTTTTCGTTTTTTA---------------	19	4	1	26
	---------------------------------------AGATGTTTTCGTTTTTTAA--------------	19	-	-	2
rat	ttggacatgttcttaatgagtgaggttcttaataacagTAGATGTTTTCGTTTTTTAaaatattcatccaat
	************************************************************************
	----------------------------------------------------------------------------------	ENSRNOT00000003157 ENSRNOG00000002317 RGD1565890_predicted
rat	(((((.(((((.((((.((((((((.(((..........)))...)))))))).)))))))))...))))).	0.450 -9.20

rat

chromosome:10:4150053:4150124:1

block68601 [novel_lenNOK_cloningOK_loopOverlap]

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	0.424	no	no	0.44/0.52	18/25/0.12	0.0	0.2	9	0	7	0	25	-2	3arm	1	nd	0.21	1	17	7	na	na

		reads	miRBase family seed
seed	--------------------------------------------------AGUCAUG------------------------------------	13	novel
seed	---------------------------------------------------GUCAUGA-----------------------------------	2	novel
seed	----------------------------------------------------------UGAAGCA----------------------------	1	novel
seed	------------------------------------------------------------AAGCACU--------------------------	1	novel
		len	cloning frequencies
			T1S1	T2S1	T2S2	T3S1	T3S2	T4S2	T5S1
	-------------------------------------------------GAGTCATGATGAAGCACTG-------------------------	19	1	1	2	1	5	-	1
	-------------------------------------------------GAGTCATGATGAAGCACT--------------------------	18	-	-	-	2	-	-	-
	--------------------------------------------------AGTCATGATGAAGCACTGCCTTTCC------------------	25	-	-	-	-	1	-	-
	--------------------------------------------------AGTCATGATGAAGCACTGC------------------------	19	-	-	-	-	1	-	-
	---------------------------------------------------------ATGAAGCACTGCCTTTCCTG----------------	20	-	-	-	-	-	1	-
	-----------------------------------------------------------GAAGCACTGCCTTTCCTGAAC-------------	21	-	1	-	-	-	-	-
rat	agtgacactgcccaccctcaccaggcccagtgcctcaataacaggcctaGAGTCATGATGAAGCACTGcctttcctgaaccctggccattgct
	*********************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000043085 ENSRNOG00000003050 NP_001101744.1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000031097 ENSRNOG00000003050 NP_001101744.1
rat	(((((....(((.....(((..((((..(((((.(((....(((((.....))).)).))).)))))))))....))).....)))..)))))	0.560 -19.50

rat

chromosome:10:35701108:35701200:1

block70882 [novel_lenNOK_cloningOK_loopOverlap]

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	0.395	no	no	0.83/0.84	18/19/0.00	0.2	0.1	19	0	8	0	22	-3	5arm_loop_3arm	1	nd	0.26	3	24	8	na	na

		reads	miRBase family seed
seed	------------------------GCCCAUA-----------------------------------------------	17	novel
seed	-----------------------GGCCCAU------------------------------------------------	4	novel
seed	--------------------------CCAUACC---------------------------------------------	2	novel
seed	---------------------------CAUACCC--------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T4S1	T4S2	T5S1	T5S2
	-----------------------GGCCCATACCCCGGGGGC-------------------------------------	18	2	1	-	2	-	6	1	5
	----------------------GGGCCCATACCCCGGGGGC-------------------------------------	19	-	-	-	-	-	-	2	-
	----------------------GGGCCCATACCCCGGGGG--------------------------------------	18	-	-	-	-	-	-	-	2
	-------------------------CCCATACCCCGGGGGCCC-----------------------------------	18	-	-	1	-	-	-	-	-
	--------------------------CCATACCCCGGGGGCCCC----------------------------------	18	-	-	-	-	1	-	-	-
	-------------------------CCCATACCCCGGGGGCCCC----------------------------------	19	-	1	-	-	-	-	-	-
rat	aggtagcacagggcatctttgtGGGCCCATACCCCGGGGGCcccgggctggatgaaaggcttacgcctcagtggcacc
	******************************************************************************
rat	.(((..(((.((((......((((((((((..((((((...))))))....)))...)))))))))))..)))..)))	0.710 -29.50

rat

chromosome:10:39674330:39674407:1

intergenic

block72721 [novel_lenNOK_cloningOK_loopOverlap]

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	0.254	no	no	0.68/0.72	18/19/0.00	0.0	0.2	19	0	8	0	16	-1	5arm_loop	1	nd	0.17	2	19	8	na	na

		reads	miRBase family seed
seed	-----------------GGGUUGG--------------------------------------------------------	19	novel
		len	cloning frequencies
			T1S1	T1S2	T2S2	T3S1	T3S2	T4S2	T5S1	T5S2
	----------------TGGGTTGGGGGGGGGGAA----------------------------------------------	18	3	2	1	1	2	3	2	2
	----------------TGGGTTGGGGGGGGGGAAT---------------------------------------------	19	2	-	-	-	1	-	-	-
rat	gggctcctcccgggggTGGGTTGGGGGGGGGGAATgcatttccctattagttgactccctctcctgcagatgagagtctc
	********************************************************************************
rat	(((((.(((......(((((..((((((((((((.....)))))).........))))))..)))))....)))))))).	0.670 -29.80