miR-Intess: classification

other hairpins

novel_lenNOK_cloningHIGH_loopOverlap_nonpairedHIGH_bulgeHIGH (83 loci)

block2599006 [novel_lenNOK_cloningHIGH_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	0.171	no	no	0.56/0.63	18/20/0.04	0.3	0.3	109	0	10	0	14	-6	5arm_loop_3arm	1	nd	0.44	5	181	10	na	na

		reads	miRBase family seed
seed	----------------CUGGACU-----------------------------------------	107	miR-378
seed	-----------------UGGACUU----------------------------------------	54	novel
seed	---------------GCUGGAC------------------------------------------	20	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	---------------GCTGGACTTGGAGTCAGG-------------------------------	18	3	1	7	4	5	2	16	26	8	25
	----------------CTGGACTTGGAGTCAGGC------------------------------	18	1	1	-	3	4	3	6	10	5	14
	--------------AGCTGGACTTGGAGTCAG--------------------------------	18	6	-	1	-	-	-	1	10	1	1
	---------------GCTGGACTTGGAGTCAGGC------------------------------	19	-	1	1	1	-	-	1	2	-	4
	----------------CTGGACTTGGAGTCAGGCTC----------------------------	20	-	-	-	-	-	-	-	4	-	3
rat	atgagcactcatgcAGCTGGACTTGGAGTCAGGCtcaacagaccaatgtgcagaggttttcatc
	****************************************************************
rat	(((((.(((..((((..(((.((..(((.....)))...)).)))...))))..))).))))).	0.730 -17.10

rat

chromosome:9:50613765:50613828:1

intergenic

block2599120 [novel_lenNOK_cloningHIGH_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	0.764	no	no	0.25/0.32	18/20/0.02	0.0	0.0	54	0	10	0	37	-5	3arm_loop	2	nd	0.50	4	123	10	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------AAAAAUU-----------------------------------------------	116	novel
seed	------------------------------------------------------------AAAAAAU------------------------------------------------	5	novel
seed	-----------------------------------------------------------GAAAAAA-------------------------------------------------	1	novel
seed	--------------------------------------------------------------AAAAUUC----------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	------------------------------------------------------------AAAAAATTCCACATACAC-------------------------------------	18	2	2	5	9	5	5	14	54	5	8
	-----------------------------------------------------------GAAAAAATTCCACATACAC-------------------------------------	19	-	-	1	1	-	-	1	2	-	-
	------------------------------------------------------------AAAAAATTCCACATACACA------------------------------------	19	-	-	1	-	-	-	-	1	-	2
	------------------------------------------------------------AAAAAATTCCACATACACAA-----------------------------------	20	-	-	-	-	1	-	-	2	-	-
	----------------------------------------------------------TGAAAAAATTCCACATAC---------------------------------------	18	-	-	-	-	-	-	-	1	-	-
	-------------------------------------------------------------AAAAATTCCACATACACAA-----------------------------------	19	-	-	-	-	-	-	-	1	-	-
rat	atagaactattgacgacataatgtttttttttaattaaaactgtaacacctggcatactgAAAAAATTCCACATACACaatttctctttctaagaacattacaagttactgctat
	*******************************************************************************************************************
rat	((((......((((....((((((((((.............((((.....(((.((.........)).)))..))))..............))))))))))...))))...))))	0.730 -9.23

rat

chromosome:9:50796058:50796172:1

intergenic

block2830290 [novel_lenNOK_cloningHIGH_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	0.295	no	no	0.50/0.53	18/20/0.01	0.0	0.0	103	0	10	0	16	-1	5arm_loop	1	nd	0.56	4	112	10	na	na

		reads	miRBase family seed
seed	-----------------AGGAGCU--------------------------------------------	112	miR-28/708
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	----------------AAGGAGCTCACAGTCTTG----------------------------------	18	5	10	2	15	16	5	9	14	15	14
	----------------AAGGAGCTCACAGTCTTGG---------------------------------	19	1	-	1	-	1	-	-	1	-	2
	----------------AAGGAGCTCACAGTCTTGGT--------------------------------	20	-	-	-	-	-	-	-	-	1	-
rat	acatccagcaaggaccAAGGAGCTCACAGTCTTGgtaaagaaaatggtgatatggtatttaagagatg
	********************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000040165 ENSRNOG00000030880 LOC683774
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000050835 ENSRNOG00000030880 LOC683774
rat	.((((........((((....((.((...((((....))))...))))....))))........))))	0.970 -11.49

rat

chromosome:X:138302805:138302872:-1

block2883631 [novel_lenNOK_cloningHIGH_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	0.167	no	no	0.47/0.53	18/19/0.00	0.0	0.0	41	0	10	0	21	-2	3arm_loop	1	nd	0.39	4	53	10	na	na

		reads	miRBase family seed
seed	--------------------------------------CAACUUC-------------------------------	48	novel
seed	-------------------------------------CCAACUU--------------------------------	5	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-------------------------------------CCAACTTCTTTCTCCCTG---------------------	18	6	5	4	6	3	-	2	9	4	4
	------------------------------------CCCAACTTCTTTCTCCCTG---------------------	19	1	2	-	1	-	1	-	-	-	-
	-------------------------------------CCAACTTCTTTCTCCCTGT--------------------	19	-	1	1	-	-	-	-	-	1	2
rat	actcaaccagtattggctcagttggcaagttttgttcCCAACTTCTTTCTCCCTGtcagatttttttctggtttag
	****************************************************************************
rat	.((.((((((..(((((..((..((.(((((........)))))))..))....)))))........)))))).))	0.790 -12.80

rat

chromosome:X:150815273:150815348:-1

intergenic

block2988433 [novel_lenNOK_cloningHIGH_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	0.475	no	no	0.44/0.47	18/19/0.00	0.0	0.0	87	0	10	0	28	-2	3arm_loop	1	nd	0.39	4	122	10	na	na

		reads	miRBase family seed
seed	------------------------------------------UGCUUAU--------------------------------------	113	novel
seed	-------------------------------------------GCUUAUC-------------------------------------	7	novel
seed	--------------------------------------------CUUAUCA------------------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-----------------------------------------CTGCTTATCAGACTGATG----------------------------	18	1	1	24	9	31	32	3	2	4	3
	------------------------------------------TGCTTATCAGACTGATGG---------------------------	18	-	-	2	2	1	1	-	-	1	-
	-----------------------------------------CTGCTTATCAGACTGATGG---------------------------	19	-	-	1	-	1	-	-	1	-	-
	-------------------------------------------GCTTATCAGACTGATGGA--------------------------	18	-	-	-	-	-	-	-	-	2	-
rat	gccttcatgttattttttatgctgacataggtattaagcagCTGCTTATCAGACTGATGgaaatagctatccttataaaacaaagct
	***************************************************************************************
rat	((.......((((.......((((.(((.(((..(((((....)))))....))).)))....)))).......))))......)).	0.480 -13.56

rat

chromosome:X:64244420:64244506:1

intergenic ## {Repeats: dust 64244540 64244541 0 class=dust}

block3057554 [novel_lenNOK_cloningHIGH_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	0.025	no	no	0.22/0.32	18/19/0.00	0.0	0.0	53	0	5	0	40	-3	5arm_loop	2	nd	0.44	4	61	5	na	na

		reads	miRBase family seed
seed	-----------------------------------------GGUUAAA--------------------------------------------------------------	56	novel
seed	----------------------------------------AGGUUAA---------------------------------------------------------------	3	novel
seed	------------------------------------------GUUAAAU-------------------------------------------------------------	2	novel
		len	cloning frequencies
			T1S2	T2S2	T3S2	T4S2	T5S2
	----------------------------------------AGGTTAAATTATTCTGAA----------------------------------------------------	18	22	12	2	19	1
	---------------------------------------GAGGTTAAATTATTCTGAA----------------------------------------------------	19	2	-	-	-	1
	-----------------------------------------GGTTAAATTATTCTGAAGC--------------------------------------------------	19	1	-	1	-	-
rat	agcagttgtacccactgtgagagtaagtcacttcctactgAGGTTAAATTATTCTGAAgcaagggtaagtaaagaagaggagtaactactttcaccaacaggacatgtta
	**************************************************************************************************************
rat	((((..(((.((....((((((((.(((.((.((((.((....(((..(((((((......))))))).)))...)))))))).))))))))))).....))))))))).	0.980 -27.70

rat

chromosome:X:116058143:116058252:1

intergenic

block2311677 [novel_lenNOK_cloningHIGH_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	0.062	no	no	0.45/0.54	19/26/0.38	0.0	0.0	37	0	5	0	12	-4	5arm_loop_3arm	1	nd	0.42	5	82	5	na	na

		reads	miRBase family seed
seed	-------------GCUUAAA--------------------------------------------------------	71	novel
seed	-----------------------------GGUUCGU----------------------------------------	6	novel
seed	-----------------AAAGCCA----------------------------------------------------	2	miR-742
seed	--------------------GCCACAG-------------------------------------------------	2	novel
seed	---------------------CCACAGA------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S2	T3S2	T4S2	T5S1
	------------TGCTTAAAGCCACAGATGGTTCGTGT--------------------------------------	26	2	-	-	1	37
	------------TGCTTAAAGCCACAGATGGTTCG-----------------------------------------	23	-	1	1	-	9
	------------TGCTTAAAGCCACAGATGGT--------------------------------------------	20	-	-	1	-	7
	------------TGCTTAAAGCCACAGATGG---------------------------------------------	19	-	-	1	1	4
	----------------------------TGGTTCGTGTAGGTGTAAGAG---------------------------	21	1	-	-	-	4
	------------TGCTTAAAGCCACAGATGGTTCGT----------------------------------------	24	-	-	-	-	3
	-------------------AGCCACAGATGGTTCGTGT--------------------------------------	19	-	-	-	-	2
	------------TGCTTAAAGCCACAGATGGTTCGTG---------------------------------------	25	-	-	-	-	2
	----------------TAAAGCCACAGATGGTTCGTGT--------------------------------------	22	-	-	-	-	2
	----------------------------TGGTTCGTGTAGGTGTAAGAGCCCT-----------------------	25	-	-	-	-	1
	--------------------GCCACAGATGGTTCGTGTAGGTGT--------------------------------	24	-	-	-	-	1
	------------TGCTTAAAGCCACAGATGGTTC------------------------------------------	22	-	-	-	-	1
rat	cttgggcggtctTGCTTAAAGCCACAGATGGTTCGTGTaggtgtaagagccctgtggtttttccttcagtctggga
	****************************************************************************
rat	((..(((..........((((((((((..(((((............))))))))))))))).......)))..)).	0.910 -25.43

rat

chromosome:8:57726284:57726359:-1

intergenic

block2324765 [novel_lenNOK_cloningHIGH_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	0.139	no	no	0.42/0.50	18/22/0.02	0.0	0.0	86	0	7	0	31	-6	5arm_loop_3arm	1	nd	0.47	4	98	7	na	na

		reads	miRBase family seed
seed	--------------------------------GUGACAU-----------------------------------------------	94	novel
seed	----------------------------------GACAUAG---------------------------------------------	2	novel
seed	---------------------------------------AGAUCAG----------------------------------------	1	novel
seed	------------------------------UUGUGAC-------------------------------------------------	1	miR-758
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T4S2	T5S1	T5S2
	-------------------------------TGTGACATAGATCAGGCGA------------------------------------	19	3	-	1	1	1	86	1
	-------------------------------TGTGACATAGATCAGGCG-------------------------------------	18	-	-	-	-	-	1	-
	---------------------------------TGACATAGATCAGGCGATCTCC-------------------------------	22	-	-	-	-	-	1	-
	-----------------------------TTTGTGACATAGATCAGGC--------------------------------------	19	-	-	-	-	-	1	-
	---------------------------------TGACATAGATCAGGCGATCTC--------------------------------	21	-	1	-	-	-	-	-
	--------------------------------------TAGATCAGGCGATCTCCA------------------------------	18	-	-	-	-	-	1	-
rat	ctgaagaaattcttcaagcctcaggtcgtttTGTGACATAGATCAGGCGAtctccaatgtggccaaggcagtgctgaagatcttag
	**************************************************************************************
rat	...((((..(((..((.((((..(((((..(((.((....((((....)))))))))..))))).))))..))..)))..))))..	0.840 -23.30

rat

chromosome:8:72057696:72057781:-1

intergenic

novel_shortStem_randfoldOK_nonpairedHIGH (82 loci)

block10380 [novel_shortStem_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	0.73/0.73	22/22/1.00	0.0	0.0	1	0	1	0	3	12	5arm	1	nd	0.36	3	1	1	na	na

		reads	miRBase family seed
seed	----CCAGUCA------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	---CCCAGTCAGGGGCCGCACTTGC----------------------------------------------------	22	1
rat	ggtCCCAGTCAGGGGCCGCACTTGCcgcattggacaacaaagaaattgccattaaagtgagcgctcctggaaggacc
	*****************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000011922 ENSRNOG00000027341 Odz2
rat	(((((...((((((((..(((((.......(((.(((........))))))...)))))...))))))))..)))))	0.980 -29.80

rat

chromosome:10:21370961:21371037:-1

block32517 [novel_shortStem_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	0.52/0.52	21/21/1.00	0.0	0.0	1	0	1	0	2	31	5arm	1	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	---CCUCUGA----------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S1
	--ACCTCTGATGGGCCACAGAAA---------------------------------------------------------------------------------------------	21	1
rat	agACCTCTGATGGGCCACAGAAAtaagactgccaagatctggctagtactcagttctctagctagtactcagttctctggctagtactcagttctctgcctagtactcagatctct
	********************************************************************************************************************
rat	(((..((((((((((...((((...((((((((((((.(((...((((((.(((......)))))))))))).))).)))).))).))...))))..)))))....)))))..)))	0.980 -36.50