miR-Intess: classification

other hairpins

miRNAunknown_lenNOK_cloningHIGH_multiarm_DicerNOK_5varHIGH (1 loci)

miRNAunknown_lenNOK_cloningHIGH_multiarm_DicerNOK_loopOverlap_randfoldOK (1 loci)

sblock5201 (miRNA) [miRNAunknown_lenNOK_cloningHIGH_multiarm_DicerNOK_loopOverlap_randfoldOK]

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
Ensembl miRNA	0.001	no	no	0.30/0.56	18/24/0.60	0.0 0.0 0.7 0.0	0.0 2.3 0.9 0.0	2 65 13 1	0 0 0 0	1 10 6 1	0 0 0 0	22 37 19 12	13 -5 15 30	5arm 5arm_loop_3arm 3arm 3arm	10 10 278 278	nd nd nd nd	0.05 0.06 0.17 0.39	1 1 3 3	115	10	16	0

		reads	miRBase family seed
seed	--------------------------------------GUGAUGU---------------------------------------------------------------------------	93	miR-466c
seed	-------------------------------------------------------------------------------ACAUACA----------------------------------	10	novel
seed	----------------------------------------------------------------------------UUUACAU-------------------------------------	6	novel
seed	-----------------------UGUGCAU------------------------------------------------------------------------------------------	2	novel
seed	-----------------------------------------------------------------------------UUACAUA------------------------------------	1	novel
seed	---------------------------------------------------------------------------AUUUACA--------------------------------------	1	novel
seed	-------------------------------------UGUGAUG----------------------------------------------------------------------------	1	novel
seed	-------------------------------------------------------------------------------------------ACACACA----------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-------------------------------------TGTGATGTGTTTATGTACA----------------------------------------------------------------	19	1	2	5	6	8	2	-	6	-	1
	-------------------------------------TGTGATGTGTTTATGTACATGTGT-----------------------------------------------------------	24	1	2	5	7	1	4	-	3	-	-
	-------------------------------------TGTGATGTGTTTATGTACATGTG------------------------------------------------------------	23	-	-	5	2	2	1	3	-	-	-
	-------------------------------------TGTGATGTGTTTATGTAC-----------------------------------------------------------------	18	-	-	1	3	2	3	-	1	2	-
	------------------------------------------------------------------------------TACATACACACATACACACACAC-------------------	23	-	-	4	3	3	-	-	-	-	-
	-------------------------------------TGTGATGTGTTTATGTACATG--------------------------------------------------------------	21	-	-	1	-	2	4	-	-	-	-
	-------------------------------------TGTGATGTGTTTATGTACATGT-------------------------------------------------------------	22	-	3	-	-	2	1	-	-	-	-
	---------------------------------------------------------------------------ATTTACATACACACATACACAC-----------------------	22	-	-	-	3	-	-	1	-	-	1
	----------------------ATGTGCATGTGTGTATGTGAT-----------------------------------------------------------------------------	21	-	-	-	2	-	-	-	-	-	-
	------------------------------------------------------------------------------------------TACACACACACAGGCACG------------	18	-	-	-	1	-	-	-	-	-	-
	------------------------------------ATGTGATGTGTTTATGTACA----------------------------------------------------------------	20	-	-	-	-	-	-	1	-	-	-
	--------------------------------------------------------------------------CATTTACATACACACATAC---------------------------	19	-	-	-	1	-	-	-	-	-	-
	-------------------------------------TGTGATGTGTTTATGTACAT---------------------------------------------------------------	20	-	-	-	-	1	-	-	-	-	-
	---------------------------------------------------------------------------ATTTACATACACACATACAC-------------------------	20	-	-	-	-	1	-	-	-	-	-
	----------------------------------------------------------------------------TTTACATACACACATACAC-------------------------	19	-	1	-	-	-	-	-	-	-	-
rat	ggttcatgtgatgcccctgtatatgtgcatgtgtgtaTGTGATGTGTTTATGTACATGTGTgtatatgaagaaacATTTACATACACACATACACACACACaggcacgcacgcacacaca
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042430 ENSRNOG00000029235 Sfmbt2
	................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>...................	ENSRNOT00000062935 ENSRNOG00000041182
rat	.((...((((.(((.(((((...((((.(((((((((((((((((.((((((((((....))))))))))...))))).)))))))))))).))))...)))))...)))))))...)).	0.980 -48.20

rat

chromosome:17:79262987:79263106:-1

Same_strand|Exonic_non-coding|ENSRNOT00000062935|ENSRNOG00000041182 ## Same_strand|Boundary_non-coding|ENSRNOT00000051529|ENSRNOG00000029235 ## Same_strand|Intronic_coding|ENSRNOT00000042430|ENSRNOG00000029235 ## ENSRNOG00000041182|miRNA|| ## ENSRNOG00000029235|protein_coding|Sfmbt2|Scm-like with four mbt domains 2 Gene [Source:MGI (curated);Acc:Sfmbt2-001] ## {Repeats: trf 224 245 0 class=trf,trf 159 177 0 class=trf,trf 206 231 0 class=trf,(TG)n 37 58 -1 class=Simple_repeat,(CA)n 1 46 -1 class=Simple_repeat,dust 79262999 79263017 0 class=dust,(CATA)n 25 46 -1 class=Simple_repeat,dust 79263046 79263071 0 class=dust,(TG)n 2 58 -1 class=Simple_repeat,dust 79263064 79263085 0 class=dust,trf 29 47 0 class=trf,trf 166 193 0 class=trf,trf 5 30 0 class=trf,dust 79263006 79263023 0 class=dust,(CATA)n 7 32 -1 class=Simple_repeat,(TG)n 30 48 -1 class=Simple_repeat,trf 23 44 0 class=trf,trf 36 57 0 class=trf}

miRNAunknown_lenNOK_cloningHIGH_multiarm_DicerNOK_shortStem_mirtron (1 loci)

sblock3535 (miRNA) [miRNAunknown_lenNOK_cloningHIGH_multiarm_DicerNOK_shortStem_mirtron]

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
Ensembl miRNA	0.079	no	no	0.58/0.67	18/25/0.66	0.0 0.0	0.6 2.6	11 2968	0 0	6 10	0 0	13 3	27 26	5arm 3arm	1 1	1 0	0.32 0.10	3 2	4562	10	-3	1

		reads	miRBase family seed
seed	----------------------------------------------------------------------------------------------GCCCACC-------------------	4436	novel
seed	--------------------------------------------------------------------------------------------AUGCCCA---------------------	63	novel
seed	-----------------------------------------------------------------------------------------------CCCACCC------------------	30	novel
seed	---------------------------------------------------------------------------------------------UGCCCAC--------------------	20	novel
seed	--------------UGAGUGG---------------------------------------------------------------------------------------------------	11	novel
seed	-------------------------------------------------------------------------------------------------CACCCUU----------------	1	miR-336
seed	------------------------------------------------------------------------------------------------CCACCCU-----------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	---------------------------------------------------------------------------------------------TGCCCACCCTTTACCCCAC--------	19	526	353	25	7	24	28	23	35	30	43
	---------------------------------------------------------------------------------------------TGCCCACCCTTTACCCCACTCCA----	23	483	308	14	10	22	31	13	32	57	59
	---------------------------------------------------------------------------------------------TGCCCACCCTTTACCCCACTCCAG---	24	416	248	11	9	23	33	17	16	37	31
	---------------------------------------------------------------------------------------------TGCCCACCCTTTACCCCACTC------	21	233	138	9	8	21	8	11	16	24	23
	---------------------------------------------------------------------------------------------TGCCCACCCTTTACCCCACTCC-----	22	212	118	8	4	9	10	11	16	20	17
	---------------------------------------------------------------------------------------------TGCCCACCCTTTACCCCA---------	18	189	149	5	3	5	9	7	10	15	13
	---------------------------------------------------------------------------------------------TGCCCACCCTTTACCCCACT-------	20	68	43	-	2	4	6	6	5	5	8
	-------------------------------------------------------------------------------------------CATGCCCACCCTTTACCCCAC--------	21	10	7	-	-	-	-	-	1	1	-
	-------------------------------------------------------------------------------------------CATGCCCACCCTTTACCCCACTC------	23	4	10	-	-	-	-	-	-	-	-
	-------------------------------------------------------------------------------------------CATGCCCACCCTTTACCCCACTCC-----	24	5	4	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------------------------------GCCCACCCTTTACCCCACTCCAG---	23	5	3	-	-	-	-	-	-	-	1
	----------------------------------------------------------------------------------------------GCCCACCCTTTACCCCAC--------	18	3	3	-	-	-	1	-	-	1	1
	----------------------------------------------------------------------------------------------GCCCACCCTTTACCCCACTCCA----	22	4	1	-	1	-	-	-	-	-	1
	-------------------------------------------------------------------------------------------CATGCCCACCCTTTACCCC----------	19	4	3	-	-	-	-	-	-	-	-
	-------------GTGAGTGGGGTGGTTGGCATG--------------------------------------------------------------------------------------	21	3	2	-	-	1	1	-	-	-	-
	-------------------------------------------------------------------------------------------CATGCCCACCCTTTACCC-----------	18	4	1	-	-	-	-	-	-	-	1
	-------------------------------------------------------------------------------------------CATGCCCACCCTTTACCCCA---------	20	4	-	-	-	-	-	1	-	-	-
	--------------------------------------------------------------------------------------------ATGCCCACCCTTTACCCCACTC------	22	2	2	-	-	-	-	-	-	-	1
	--------------------------------------------------------------------------------------------ATGCCCACCCTTTACCCCACTCCA----	24	1	3	-	-	-	-	1	-	-	-
	----------------------------------------------------------------------------------------------GCCCACCCTTTACCCCACTC------	20	1	1	1	-	-	-	-	1	-	-
	---------------------------------------------------------------------------------------------TGCCCACCCTTTACCCCACTCCAGG--	25	2	-	-	-	1	1	-	-	-	-
	-------------GTGAGTGGGGTGGTTGGCA----------------------------------------------------------------------------------------	19	-	1	-	-	-	-	-	1	-	1
	--------------------------------------------------------------------------------------------ATGCCCACCCTTTACCCCA---------	19	2	1	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------------------------------ATGCCCACCCTTTACCCCACTCCAG---	25	2	1	-	-	-	-	-	-	-	-
	-------------------------------------------------------------------------------------------CATGCCCACCCTTTACCCCACT-------	22	2	1	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------------------------------ATGCCCACCCTTTACCCCACTCC-----	23	-	1	-	-	-	-	-	-	-	1
	--------------------------------------------------------------------------------------------ATGCCCACCCTTTACCCCAC--------	20	1	-	-	-	-	-	-	-	1	-
	----------------------------------------------------------------------------------------------GCCCACCCTTTACCCCACTCC-----	21	-	-	-	-	-	-	-	1	-	-
	------------------------------------------------------------------------------------------------CCACCCTTTACCCCACTCCA----	20	-	1	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------------------------------------CCCACCCTTTACCCCACTCCAG---	22	-	1	-	-	-	-	-	-	-	-
	-------------GTGAGTGGGGTGGTTGGCATGG-------------------------------------------------------------------------------------	22	-	1	-	-	-	-	-	-	-	-
rat	tgtccgggacaaggtgagtggggtggttggcatgggttgcccagtctggggactcgacgctgtgtcacagcctcctgatgtcctcctcacgcaTGCCCACCCTTTACCCCACTCCAGggc
	************************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000040015 ENSRNOG00000001418 Znhit1_predicted
	>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>	ENSRNOT00000001921 ENSRNOG00000001417 Plod3
	>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>	ENSRNOT00000035117 ENSRNOG00000001417 Plod3
	.........>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>..........	ENSRNOT00000054459 ENSRNOG00000036338
rat	.((((.(((........(((((((((..((..((((((((...((..((((((((((.((((.....)))).))..)).)))).))..))))).)))))))..)))))))))))).))))	0.530 -49.40

rat

chromosome:12:20861544:20861663:1

Same_strand|Boundary_coding|ENSRNOT00000035117|ENSRNOG00000001417 ## Opposite_strand|Intronic_coding|ENSRNOT00000040015|ENSRNOG00000001418 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000001922|ENSRNOG00000001418 ## Same_strand|Exonic_non-coding|ENSRNOT00000054459|ENSRNOG00000036338 ## Same_strand|Boundary_non-coding|ENSRNOT00000054459|ENSRNOG00000036338 ## ENSRNOG00000001417|protein_coding|Plod3|Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 precursor (EC 1.14.11.4) (Lysyl hydroxylase 3) (LH3). [Source:UniProtKB/Swiss-Prot;Acc:Q5U367] ## ENSRNOG00000036338|miRNA|| ## ENSRNOG00000001418|protein_coding|Znhit1_predicted|

miRNAunknown_lenNOK_cloningHIGH_nonpairedHIGH (1 loci)

block2304553 (miRNA) [miRNAunknown_lenNOK_cloningHIGH_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
Ensembl miRNA	0.152	no	no	0.62/0.72	18/21/0.01	0.0	0.0	749	0	10	0	18	6	3arm	6	nd	0.33	3	757	10	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------UCUCGCU----------------------------	752	novel
seed	------------------------------------------------------------------CUCGCUG---------------------------	5	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	----------------------------------------------------------------ATCTCGCTGGGGCCTCCA------------------	18	70	83	129	80	77	96	46	61	44	63
	-----------------------------------------------------------------TCTCGCTGGGGCCTCCAG-----------------	18	1	-	-	-	-	1	-	-	-	-
	-----------------------------------------------------------------TCTCGCTGGGGCCTCCAGAAA--------------	21	1	-	-	-	-	-	-	-	1	-
	----------------------------------------------------------------ATCTCGCTGGGGCCTCCAGAA---------------	21	1	-	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------TCTCGCTGGGGCCTCCAGA----------------	19	-	-	-	-	1	-	-	-	-	-
	----------------------------------------------------------------ATCTCGCTGGGGCCTCCAGA----------------	20	-	-	-	-	-	-	-	-	-	1
	----------------------------------------------------------------ATCTCGCTGGGGCCTCCAG-----------------	19	-	1	-	-	-	-	-	-	-	-
rat	aggtggcccttcagcccgagtcccagagtaagagtcaggccttagaatttggatgagtggtctgATCTCGCTGGGGCCTCCAgaaaatattagttccatc
	****************************************************************************************************
	......................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>......................	ENSRNOT00000054644 ENSRNOG00000036537
rat	.(((((..((.......(((((((((.....((((((((((.................))))))).))).))))))).))...........))..)))))	0.570 -30.90

rat

chromosome:8:47940272:47940371:-1

Same_strand|Boundary_non-coding|ENSRNOT00000054644|ENSRNOG00000036537 ## ENSRNOG00000036537|miRNA||

miRNAunknown_lenNOK_cloningOK_multiarm_DicerNOK (1 loci)

sblock6365 (miRNA) [miRNAunknown_lenNOK_cloningOK_multiarm_DicerNOK]

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
Ensembl miRNA	0.030	no	no	0.50/0.68	18/23/0.60	0.0 0.2	1.7 0.8	7 13	0 0	2 6	0 0	31 22	2 1	5arm 3arm	1 1	nd nd	0.26 0.10	5 1	20	6	-1	2

		reads	miRBase family seed
seed	-------------------------------------------------------------------------GCCACAG-----------------------------------	11	novel
seed	--------------------------------GGCAGUG----------------------------------------------------------------------------	7	miR-34a/34c/449a
seed	------------------------------------------------------------------------AGCCACA------------------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1	T3S2	T4S1	T5S1
	------------------------------------------------------------------------AGCCACAGCTACCCTGCCAC-----------------------	20	3	1	-	-	1	-
	-------------------------------AGGCAGTGTGTTGTTAGC------------------------------------------------------------------	18	-	-	1	2	-	-
	------------------------------------------------------------------------AGCCACAGCTACCCTGCCACT----------------------	21	1	-	-	1	-	1
	-------------------------------AGGCAGTGTGTTGTTAGCTG----------------------------------------------------------------	20	-	-	1	1	-	-
	------------------------------------------------------------------------AGCCACAGCTACCCTGCCA------------------------	19	1	-	1	-	-	-
	-----------------------------------------------------------------------CAGCCACAGCTACCCTGCC-------------------------	19	-	-	-	-	-	2
	------------------------------------------------------------------------AGCCACAGCTACCCTGCC-------------------------	18	-	-	-	-	-	1
	-------------------------------AGGCAGTGTGTTGTTAGCTGGCT-------------------------------------------------------------	23	-	-	1	-	-	-
	-------------------------------AGGCAGTGTGTTGTTAGCTGG---------------------------------------------------------------	21	-	-	-	1	-	-
rat	ccgggaaaatcagcgcttgccagactcaggtAGGCAGTGTGTTGTTAGCTGGCTgcgttgggttaagtaagCAGCCACAGCTACCCTGCCACTtgcttctggacgggtcttcttg
	*******************************************************************************************************************
	........................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.......	ENSRNOT00000054546 ENSRNOG00000036434
rat	.(((((.....((.((((((((((..(((((.(((((.(((((((.....((((((..............))))))))))).)).))))))))))..))))).))))))))))))	0.990 -44.64

rat

chromosome:2:44418143:44418257:1

Same_strand|Exonic_non-coding|ENSRNOT00000054546|ENSRNOG00000036434 ## ENSRNOG00000036434|miRNA||

miRNAunknown_lenNOK_cloningOK_multiarm_DicerNOK_5varHIGH (1 loci)

sblock9732 (miRNA) [miRNAunknown_lenNOK_cloningOK_multiarm_DicerNOK_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
Ensembl miRNA	0.258	no	no	0.48/0.58	19/26/0.56	0.0 0.0 4.2	0.0 1.5 2.9	1 2 13	0 0 0	1 1 3	0 0 0	8 38 8	14 -19 2	5arm 5arm_loop_3arm 3arm	1 1 1	nd nd nd	0.30 0.38 0.11	3 6 1	16	4	-9	-5

		reads	miRBase family seed
seed	---------------------------------------------------------GAGAGUC------------------------------	6	novel
seed	------------------------------------------------------GUUGAGA---------------------------------	3	novel
seed	---------------------------------------------------------------CCUUGCU------------------------	3	novel
seed	---------------------------------------ACCACGU------------------------------------------------	2	novel
seed	----------------------------------------------------------------CUUGCUC-----------------------	1	novel
seed	---------CCACAGC------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T3S1	T3S2	T5S1
	--------------------------------------------------------TGAGAGTCCTTGCTCACGG-------------------	19	-	1	-	3
	-----------------------------------------------------TGTTGAGAGTCCTTGCTCACGGCT-----------------	24	-	-	-	3
	--------------------------------------------------------TGAGAGTCCTTGCTCACGGCTAT---------------	23	-	-	-	2
	--------------------------------------------------------------TCCTTGCTCACGGCTATGA-------------	19	-	-	1	1
	--------------------------------------TACCACGTGTGACTGTGTTGAGAGTC------------------------------	26	-	-	-	1
	---------------------------------------------------------------CCTTGCTCACGGCTATGATGTCA--------	23	-	-	-	1
	--------------------------------------------------------------TCCTTGCTCACGGCTATGATGTCA--------	24	-	-	-	1
	--------TCCACAGCCGTGTCTAGAAGGGT---------------------------------------------------------------	23	1	-	-	-
	--------------------------------------TACCACGTGTGACTGTGTTGAGA---------------------------------	23	-	-	-	1
rat	agggagtcTCCACAGCCGTGTCTAGAAGGGTacctgcaTACCACGTGTGACTGTGTTGAGAGTCCTTGCTCACGGCTATGATGTCAttactcct
	**********************************************************************************************
	................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	ENSRNOT00000062199 ENSRNOG00000040446
rat	.((((((...((.(((((((...((.((((.((((.((...((((......)))).)))).)))))).))))))))).))........))))))	0.490 -26.30

rat

chromosome:5:79245623:79245716:1

Opposite_strand|Exonic_non-coding|ENSRNOT00000062199|ENSRNOG00000040446 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000062199|ENSRNOG00000040446 ## ENSRNOG00000040446|miRNA||

miRNAunknown_lenNOK_multiarm_5varHIGH_loopOverlap_randfoldOK (1 loci)

block2247822 (miRNA) [miRNAunknown_lenNOK_multiarm_5varHIGH_loopOverlap_randfoldOK]

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
Ensembl miRNA	0.002	no	no	0.37/0.55	19/21/0.60	0.0 1.3	0.0 1.0	2 3	0 0	1 1	0 0	24 28	2 -7	5arm 5arm_loop_3arm	1 1	nd nd	0.26 0.35	2 4	5	1	na	na

		reads	miRBase family seed
seed	---------------------------------ACCUUGU--------------------------------------------------	2	novel
seed	-------------------------GAGAACU----------------------------------------------------------	2	miR-146a/146b
seed	-----------------------------ACUUACC------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	------------------------TGAGAACTTACCTTGTTGT-----------------------------------------------	19	2
	--------------------------------TACCTTGTTGTGGGGGTCCA--------------------------------------	20	2
	----------------------------AACTTACCTTGTTGTGGGGGT-----------------------------------------	21	1
rat	aaactggagcagaaagttaggaccTGAGAACTTACCTTGTTGTGGGGGTCCAtggtgaggagtggttgtcaggggggacgaccaagttta
	******************************************************************************************
	......................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000054628 ENSRNOG00000036521
rat	(((((((........(((....(((((.((((..(((..((((((....))))))..)))...)))).)))))...)))..))).)))).	0.410 -29.50

rat

chromosome:7:112748651:112748740:1

Same_strand|Boundary_non-coding|ENSRNOT00000054628|ENSRNOG00000036521 ## ENSRNOG00000036521|miRNA||

miRNAunknown_lenNOK_multiarm_DicerNOK_Multihit (1 loci)

sblock10783 (miRNA) [miRNAunknown_lenNOK_multiarm_DicerNOK_Multihit]

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
Ensembl miRNA	0.082	no	no	0.32/0.40	19/20/0.25	0.7 0.0	0.7 0.0	3 1	0 0	2 1	0 0	4 24	29 14	5arm 3arm	12 12	nd nd	0.21 0.25	2 3	4	3	-19	-20

		reads	miRBase family seed
seed	-----UGGUUAA---------------------------------------------------------------------------------------------------------	2	novel
seed	-------GUUAAUG-------------------------------------------------------------------------------------------------------	1	novel
seed	--------------------------------------------------------------------------GUGUGUG------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T3S1	T3S2
	----CTGGTTAATGATAACAATG----------------------------------------------------------------------------------------------	19	-	-	2
	------GGTTAATGATAACAATGCA--------------------------------------------------------------------------------------------	19	-	1	-
	-------------------------------------------------------------------------TGTGTGTGGCAGTTTTAAGT------------------------	20	1	-	-
rat	aagaCTGGTTAATGATAACAATGCAttgtaaaaccttcagcaggaaagaaggttttgtggaccactttttttgTGTGTGTGGCAGTTTTAAGTtattcgttttcagaatcagtactt
	*********************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000010869 ENSRNOG00000008022 Apaf1
	......>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.........	ENSRNOT00000054633 ENSRNOG00000036526
rat	((((((((((..(((.(((((((.(((.((((((..((((((.(((((((((((.....))))..))))))).)))...)))..))))))))))))).))).))).))))))).)))	0.570 -25.50

rat

chromosome:7:27984327:27984443:-1

Same_strand|Intronic_coding|ENSRNOT00000010869|ENSRNOG00000008022 ## Same_strand|Exonic_non-coding|ENSRNOT00000054633|ENSRNOG00000036526 ## ENSRNOG00000036526|miRNA|| ## ENSRNOG00000008022|protein_coding|Apaf1|Apoptotic protease-activating factor 1 (Apaf-1). [Source:UniProtKB/Swiss-Prot;Acc:Q9EPV5]

miRNAunknown_lenNOK_multiarm_DicerNOK_Multihit_loopOverlap_randfoldOK_nonpairedHIGH_bulgeHIGH (1 loci)

sblock3506 (miRNA) [miRNAunknown_lenNOK_multiarm_DicerNOK_Multihit_loopOverlap_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
Ensembl miRNA	0.004	no	no	0.67/0.74	18/21/0.25	0.0 0.0 0.0	1.0 0.0 0.0	2 1 1	0 0 0	1 1 1	0 0 0	35 46 34	-4 -12 -2	5arm_loop_3arm 5arm_loop_3arm 3arm_loop	10 13 71	nd nd nd	0.47 0.33 0.42	3 4 2	4	2	0	0

		reads	miRBase family seed
seed	------------------------------------GGUCGGU----------------------------------------------------------------	2	novel
seed	-------------------------------------------------------CGGUCGG---------------------------------------------	1	novel
seed	-----------------------------------------------CGGUCAG-----------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2
	-----------------------------------CGGTCGGTCGGTCGGTCAG-----------------------------------------------------	19	-	1
	----------------------------------------------TCGGTCAGTCGGTCGGTC-------------------------------------------	18	1	-
	-----------------------------------CGGTCGGTCGGTCGGTCAGTC---------------------------------------------------	21	-	1
	------------------------------------------------------TCGGTCGGTCGGTCGGTCG----------------------------------	19	1	-
rat	gtttttgttttgttttgtttgttagtttggttggtCGGTCGGTCGGTCGGTCAGTCGGTCGGTCGGTCGGTCGgtcggtcggttggttggttttggtttgcagtagc
	***********************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000001709 ENSRNOG00000001265 LOC686419
	....................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>...................	ENSRNOT00000063089 ENSRNOG00000041336
rat	(((.((((..................(((..((..((..((..((..(((((....)))))..))..))..))..))..))).................)))).)))	0.840 -31.25

rat

chromosome:12:15047402:15047508:1

Same_strand|Exonic_non-coding|ENSRNOT00000063089|ENSRNOG00000041336 ## Same_strand|Intronic_coding|ENSRNOT00000001709|ENSRNOG00000001265 ## ENSRNOG00000041336|miRNA|| ## ENSRNOG00000001265|protein_coding|LOC686419| ## {Repeats: (CGGT)n 2 64 1 class=Simple_repeat,(CGGT)n 19 37 1 class=Simple_repeat,dust 15047421 15047439 0 class=dust,dust 15047429 15047450 0 class=dust,(CGGT)n 8 29 1 class=Simple_repeat,(CGGT)n 27 54 1 class=Simple_repeat,dust 15047404 15047431 0 class=dust,trf 11 38 0 class=trf,trf 28 46 0 class=trf,trf 36 57 0 class=trf}

miRNAunknown_lenNOK_multiarm_DicerNOK_Multihit_randfoldOK (1 loci)

sblock11982 (miRNA) [miRNAunknown_lenNOK_multiarm_DicerNOK_Multihit_randfoldOK]

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
Ensembl miRNA	0.001	no	no	0.58/0.60	19/20/0.50	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	16 9	21 29	5arm 3arm	53 351	nd nd	0.30 0.26	2 2	2	2	8	7

		reads	miRBase family seed
seed	-----------------GCGUGUG----------------------------------------------------------------------------------------------	1	novel
seed	-------------------------------------------------------------------------------------------GUGUGUG--------------------	1	novel
		len	cloning frequencies
			T1S2	T2S1
	------------------------------------------------------------------------------------------TGTGTGTGCGTGTGTGTGC---------	19	1	-
	----------------CGCGTGTGCATGTGTGTGTG----------------------------------------------------------------------------------	20	-	1
rat	ccacaatgtgtgtgcgCGCGTGTGCATGTGTGTGTGcacgtgtgtgtgcatgtgcatgagtgtgtgcatgtgcgtgcatgtgtgcatgcgTGTGTGTGCGTGTGTGTGCatgtgtgtg
	**********************************************************************************************************************
	.......................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063209 ENSRNOG00000041456
rat	.(((((((((..((((((((..((((..((((((..((((((..((..((((..(((....)))..))))..))..))))))..))))))..))))..))))))))..))))).))))	1.000 -74.00

rat

chromosome:8:46391197:46391314:1

Same_strand|Exonic_non-coding|ENSRNOT00000063209|ENSRNOG00000041456 ## Same_strand|Boundary_non-coding|ENSRNOT00000063209|ENSRNOG00000041456 ## ENSRNOG00000041456|miRNA|| ## {Repeats: (TG)n 84 103 1 class=Simple_repeat,(TG)n 10 30 1 class=Simple_repeat,(TG)n 1 262 1 class=Simple_repeat,dust 46391365 46391384 0 class=dust,dust 46391438 46391458 0 class=dust}

miRNAunknown_lenNOK_multiarm_DicerNOK_Multihit_randfoldOK_nonpairedHIGH (1 loci)

sblock7899 (miRNA) [miRNAunknown_lenNOK_multiarm_DicerNOK_Multihit_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
Ensembl miRNA	0.001	no	no	0.56/0.74	18/19/0.00	0.0 0.0	0.0 0.0	3 1	0 0	1 1	0 0	5 0	32 40	5arm 3arm	42 71	nd nd	0.50 0.56	2 4	4	1	-15	0

		reads	miRBase family seed
seed	------GUUGGUU---------------------------------------------------------------------------------------------------------	1	novel
seed	--------------------------------------------------------------------------GUUGGUU-------------------------------------	1	novel
seed	----------------------------------------------------------------------------------------------------CGGUCGG-----------	1	novel
seed	------------------------------------------------------GUUGGUU---------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	-----------------------------------------------------GGTTGGTTGGTCAGTTGG-----------------------------------------------	18	1
	---------------------------------------------------------------------------------------------------TCGGTCGGTCGGTCGGTCG	19	1
	-----GGTTGGTTGGTCAGTTGG-----------------------------------------------------------------------------------------------	18	1
	-------------------------------------------------------------------------GGTTGGTTGGTCAGTTGG---------------------------	18	1
rat	tggttGGTTGGTTGGTCAGTTGGttggttggttggctggttggtcagttggttGGTTGGTTGGTCAGTTGGttGGTTGGTTGGTCAGTTGGttggttggTCGGTCGGTCGGTCGGTCG
	**********************************************************************************************************************
	.......................................................................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063146 ENSRNOG00000041393
rat	((..((..((..((..(((..((..((((((..((((..((..(((..(((..((....))..)))..)))..))..))))..))))))..))..)))..))..))..))..))....	1.000 -38.30

rat

chromosome:3:57123260:57123377:1

Same_strand|Boundary_non-coding|ENSRNOT00000063146|ENSRNOG00000041393 ## Same_strand|Exonic_non-coding|ENSRNOT00000063146|ENSRNOG00000041393 ## ENSRNOG00000041393|miRNA|| ## {Repeats: dust 57123940 57123983 0 class=dust,(TTGG)n 1 975 1 class=Simple_repeat,(TTGG)n 153 171 1 class=Simple_repeat,(TTGG)n 179 222 1 class=Simple_repeat,dust 57123991 57124009 0 class=dust,trf 756 799 0 class=trf,trf 807 825 0 class=trf}

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