miR-Intess: classification

other hairpins

miRNAunknown_lenNOK_Multihit_loopOverlap_randfoldOK (1 loci)

miRNAunknown_lenNOK_Multihit_loopOverlap_randfoldOK_bulgeHIGH (1 loci)

block2205178 (miRNA) [miRNAunknown_lenNOK_Multihit_loopOverlap_randfoldOK_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	0.001	no	no	0.47/0.47	19/19/0.00	0.0	0.0	1	0	1	0	41	-4	5arm_loop_3arm	267	nd	0.21	4	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------GUGUGUG---------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	-----------------------------------------TGTGTGTGTGTGTGCTTGT----------------------------------------------------------	19	1
rat	gccttctggtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgTGTGTGTGTGTGTGCTTGTgcgcgcgcacgcgcacgcacacacgcgcacacgtgtgaaagcactgaaatctgaagca
	**********************************************************************************************************************
	..............>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>...............................	ENSRNOT00000063107 ENSRNOG00000041354
rat	((.(((.(((....((((.((..(((((((((((((((((((((((((((((((((....)))))))))))))))))))))))))))))))))..))...))))....))).))))).	1.000 -77.20

rat

chromosome:7:40202924:40203041:1

Same_strand|Exonic_non-coding|ENSRNOT00000063107|ENSRNOG00000041354 ## ENSRNOG00000041354|miRNA|| ## {Repeats: (CG)n 2 3 1 class=Simple_repeat,(TG)n 33 47 1 class=Simple_repeat,dust 40202969 40202988 0 class=dust,trf 1 15 0 class=trf,(CG)n 2 40 1 class=Simple_repeat,(TG)n 1 47 1 class=Simple_repeat}

miRNAunknown_lenNOK_Multihit_loopOverlap_randfoldOK_nonpairedHIGH (1 loci)

block582604 (miRNA) [miRNAunknown_lenNOK_Multihit_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
Ensembl miRNA	0.001	no	no	0.47/0.47	19/19/0.00	0.0	0.0	1	0	1	0	23	-3	3arm_loop	254	nd	0.32	2	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------UGUGUGU----------------------------------	1	novel
		len	cloning frequencies
			T4S1
	-------------------------------------------GTGTGTGTGTGTACACACA-----------------------	19	1
rat	tgtgtgtgtgtgtatgtgtgtgtgtgtgtgtgtgtgtgtgtgtGTGTGTGTGTGTACACACAcaagggcatgcgcacacacgcaa
	*************************************************************************************
	..<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<.....	ENSRNOT00000063263 ENSRNOG00000041510
rat	(((((((((((((((((...((((((((((..((..((........))..))..))))))))))...))))))))))))))))).	1.000 -46.60

rat

chromosome:16:64478013:64478097:1

Opposite_strand|Exonic_non-coding|ENSRNOT00000063263|ENSRNOG00000041510 ## ENSRNOG00000041510|miRNA|| ## {Repeats: (TG)n 44 56 1 class=Simple_repeat,dust 64478013 64478025 0 class=dust,trf 1 13 0 class=trf,(TG)n 2 56 1 class=Simple_repeat}

miRNAunknown_lenNOK_Multihit_loopOverlap_randfoldOK_nonpairedHIGH_bulgeHIGH (1 loci)

block2051571 (miRNA) [miRNAunknown_lenNOK_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	0.001	no	no	0.53/0.53	19/19/0.00	0.0	0.0	3	0	2	0	6	-3	5arm_loop	252	nd	0.32	4	3	2	na	na

		reads	miRBase family seed
seed	-------UGUGUGU-------------------------------------	3	novel
		len	cloning frequencies
			T1S2	T4S1
	------GTGTGTGTGTGTGTACGCA--------------------------	19	1	2
rat	gtgtgtGTGTGTGTGTGTGTACGCAcactagtgcacgcgcgcgtgcactca
	***************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000011599 ENSRNOG00000008754 Flvcr2
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.....	ENSRNOT00000063386 ENSRNOG00000041633
rat	.((.(((..(((((((((((((........)))))))))))))..))).))	1.000 -29.60

rat

chromosome:6:109871307:109871357:1

Same_strand|Intronic_coding|ENSRNOT00000011599|ENSRNOG00000008754 ## Same_strand|Exonic_non-coding|ENSRNOT00000063386|ENSRNOG00000041633 ## ENSRNOG00000008754|protein_coding|Flvcr2|major facilitator superfamily domain containing 7C Gene [Source:MGI Symbol;Acc:MGI:2384974] ## ENSRNOG00000041633|miRNA|| ## {Repeats: (TG)n 17 31 1 class=Simple_repeat,dust 109871297 109871311 0 class=dust,trf 1 15 0 class=trf,(TG)n 2 31 1 class=Simple_repeat}

miRNAunknown_lenNOK_Multihit_randfoldOK_bulgeHIGH (1 loci)

block113902 (miRNA) [miRNAunknown_lenNOK_Multihit_randfoldOK_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	0.001	no	no	0.39/0.39	18/18/0.00	0.0	0.0	1	0	1	0	6	10	3arm	21	nd	0.28	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------GUGUGUA----------------	1	novel
		len	cloning frequencies
			T2S2
	--------------------------------------------------TGTGTGTATGTTCTGTGT------	18	1
rat	tatgttattattgtttcatgcacacatatgtctgtgtatgcacatgcatgTGTGTGTATGTTCTGTGTacatac
	**************************************************************************
	.....................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063349 ENSRNOG00000041596
rat	(((((...(((.....(((((((((((((((.((((....)))).)))))))))))))))....))).))))).	1.000 -31.00

rat

chromosome:11:21533612:21533685:-1

Same_strand|Exonic_non-coding|ENSRNOT00000063349|ENSRNOG00000041596 ## ENSRNOG00000041596|miRNA|| ## {Repeats: trf 1 11 0 class=trf,(TG)n 2 49 -1 class=Simple_repeat}

miRNAunknown_lenNOK_Multihit_shortStem_loopOverlap (1 loci)

block1505252 (miRNA) [miRNAunknown_lenNOK_Multihit_shortStem_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
Ensembl miRNA	0.237	no	no	0.74/0.74	19/19/0.00	0.0	0.0	1	0	1	0	2	-1	5arm_loop	71	nd	0.21	2	1	1	na	na

		reads	miRBase family seed
seed	---CGGUCGG--------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	--TCGGTCGGTCGGTCGGTCG---------------------------	19	1
rat	ggTCGGTCGGTCGGTCGGTCGgtcggtctgtcggtctgtctgtctatc
	************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000021435 ENSRNOG00000015928 NP_001102071.1
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>........	ENSRNOT00000062196 ENSRNOG00000040443
rat	((.(((.(((((((.(((((....)).))))))).))).))).))...	0.990 -13.60

rat

chromosome:3:149586257:149586304:1

Same_strand|Exonic_non-coding|ENSRNOT00000062196|ENSRNOG00000040443 ## Same_strand|Intronic_coding|ENSRNOT00000021435|ENSRNOG00000015928 ## ENSRNOG00000040443|miRNA|| ## ENSRNOG00000015928|protein_coding|NP_001102071.1|DEAH (Asp-Glu-Ala-His) box polypeptide 35 [Source:RefSeq_peptide;Acc:NP_001102071] ## {Repeats: (CGGT)n 3 44 1 class=Simple_repeat,(CGGT)n 7 34 1 class=Simple_repeat,dust 149586263 149586290 0 class=dust,trf 20 47 0 class=trf}

miRNAunknown_lenNOK_Multihit_shortStem_nonpairedHIGH_bulgeHIGH (1 loci)

block974910 (miRNA) [miRNAunknown_lenNOK_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
Ensembl miRNA	0.168	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	3	4	3arm	18	nd	0.50	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------GCGAGUA-------------	1	novel
		len	cloning frequencies
			T2S1
	------------------------------GGCGAGTATCTCTTTGAG---	18	1
rat	gcgcagaccggcatggcccaggcatctctgGGCGAGTATCTCTTTGAGcgc
	***************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000047289 ENSRNOG00000001492 Slc8a2
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	ENSRNOT00000020402 ENSRNOG00000015128 Uble1a
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000054425 ENSRNOG00000032060
rat	(((((((...((...(((((((....)))))))..))...)))....))))	0.780 -17.80

rat

chromosome:1:76647415:76647465:1

Same_strand|Exonic_non-coding|ENSRNOT00000054425|ENSRNOG00000032060 ## Opposite_strand|Exonic_non-coding|ENSRNOT00000020402|ENSRNOG00000015128 ## Same_strand|Exonic_coding|ENSRNOT00000047289|ENSRNOG00000001492 ## Same_strand|Boundary_non-coding|ENSRNOT00000002042|ENSRNOG00000001492 ## ENSRNOG00000032060|miRNA|| ## ENSRNOG00000001492|protein_coding|Slc8a2|Sodium/calcium exchanger 2 precursor (Na(+)/Ca(2+)-exchange protein 2). [Source:UniProtKB/Swiss-Prot;Acc:P48768] ## ENSRNOG00000015128|protein_coding|Uble1a|SUMO-activating enzyme subunit 1 (Ubiquitin-like 1-activating enzyme E1A). [Source:UniProtKB/Swiss-Prot;Acc:Q6AXQ0]

miRNAunknown_lenNOK_Multihit_shortStem_randfoldOK_nonpairedHIGH (1 loci)

block2509424 (miRNA) [miRNAunknown_lenNOK_Multihit_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
Ensembl miRNA	0.004	no	no	0.37/0.37	19/19/0.00	0.0	0.0	1	0	1	0	0	1	5arm	264	nd	0.32	3	1	1	na	na

		reads	miRBase family seed
seed	-AUACAUA------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	CATACATACATGCATGCAT-------------------------------------------	19	1
rat	CATACATACATGCATGCATgcatacatacatacatacatacatgcatacacatatgaatatg
	**************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<........................	ENSRNOT00000063394 ENSRNOG00000041641
rat	....((((..((.(((((((....................))))))).))..))))......	0.980 -10.55

rat

chromosome:9:56063050:56063111:-1

Opposite_strand|Exonic_non-coding|ENSRNOT00000063394|ENSRNOG00000041641 ## ENSRNOG00000041641|miRNA|| ## {Repeats: (TATG)n 4 83 -1 class=Simple_repeat,trf 32 51 0 class=trf,dust 56063093 56063112 0 class=dust,(TATG)n 40 59 -1 class=Simple_repeat}

miRNAunknown_lenNOK_bulgeHIGH (1 loci)

block2309808 (miRNA) [miRNAunknown_lenNOK_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	0.137	no	no	0.56/0.60	18/20/0.25	0.5	1.0	4	0	2	0	9	4	5arm	6	nd	0.30	4	4	2	na	na

		reads	miRBase family seed
seed	----------UUCCGGC------------------------------------------------------------	3	novel
seed	------------CCGGCAA----------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T3S1
	---------ATTCCGGCAAGTCCACCA--------------------------------------------------	18	3	-
	-----------TCCGGCAAGTCCACCACAAC----------------------------------------------	20	-	1
rat	gacacatagATTCCGGCAAGTCCACCACAACtggactcctgatctacaaatgtggtgggatcggcaaaagaaccgtc
	*****************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000035438 ENSRNOG00000027199
	...........................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063281 ENSRNOG00000041528
rat	(((.........((((....(((((((((..((((.......))))....))))))))).))))..........)))	0.700 -18.61

rat

chromosome:8:55728692:55728768:-1

Same_strand|Boundary_non-coding|ENSRNOT00000063281|ENSRNOG00000041528 ## Same_strand|Exonic_coding|ENSRNOT00000035438|ENSRNOG00000027199 ## ENSRNOG00000041528|miRNA|| ## ENSRNOG00000027199|protein_coding||

miRNAunknown_lenNOK_cloningHIGH_multiarm_DicerNOK (1 loci)

sblock3172 (miRNA) [miRNAunknown_lenNOK_cloningHIGH_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	0.068	no	no	0.55/0.67	18/23/0.66	0.0 0.4	2.0 1.6	638 27	0 0	10 8	0 0	23 6	7 4	5arm 3arm	1 1	nd nd	0.33 0.18	6 3	815	10	0	5

		reads	miRBase family seed
seed	------------------------CACCUCC-----------------------------------------------------------	779	novel
seed	---------------------------------------------------------------ACGUUGG--------------------	16	novel
seed	----------------------------------------------------------------CGUUGGC-------------------	9	novel
seed	--------------------------CCUCCCC---------------------------------------------------------	5	novel
seed	-------------------------ACCUCCC----------------------------------------------------------	3	novel
seed	--------------------------------------------------------------GACGUUG---------------------	1	novel
seed	-----------------------CCACCUC------------------------------------------------------------	1	novel
seed	-------------------------------------------------------------GGACGUU----------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-----------------------CCACCTCCCCTGCAAACG-------------------------------------------------	18	27	45	5	7	43	32	23	24	17	17
	-----------------------CCACCTCCCCTGCAAACGTCC----------------------------------------------	21	17	36	4	6	37	18	28	32	11	14
	-----------------------CCACCTCCCCTGCAAACGTCCA---------------------------------------------	22	17	25	1	11	28	21	17	21	11	13
	-----------------------CCACCTCCCCTGCAAACGTC-----------------------------------------------	20	15	10	6	9	31	20	19	14	8	11
	-----------------------CCACCTCCCCTGCAAACGT------------------------------------------------	19	2	4	-	2	3	4	4	1	-	5
	---------------------------------------------------------------ACGTTGGCTCTGGTGGTGATG------	21	-	-	-	-	-	2	2	1	1	-
	--------------------------------------------------------------GACGTTGGCTCTGGTGGT----------	18	2	-	1	-	1	-	-	-	-	-
	--------------------------------------------------------------GACGTTGGCTCTGGTGGTG---------	19	3	-	-	-	-	1	-	-	-	-
	--------------------------------------------------------------GACGTTGGCTCTGGTGGTGA--------	20	-	-	-	-	1	2	-	-	-	-
	--------------------------------------------------------------GACGTTGGCTCTGGTGGTGATG------	22	1	-	-	-	1	1	-	-	-	-
	-----------------------CCACCTCCCCTGCAAACGTCCAG--------------------------------------------	23	-	2	-	-	-	-	-	-	1	-
	-------------------------ACCTCCCCTGCAAACGTCCA---------------------------------------------	20	2	1	-	-	-	-	-	-	-	-
	-------------------------ACCTCCCCTGCAAACGTCCAGT-------------------------------------------	22	-	-	-	-	-	-	1	1	-	-
	------------------------CACCTCCCCTGCAAACGTC-----------------------------------------------	19	-	-	-	-	-	-	1	1	-	-
	--------------------------------------------------------------GACGTTGGCTCTGGTGGTGAT-------	21	-	-	-	-	-	1	-	1	-	-
	------------------------------------------------------------TGGACGTTGGCTCTGGTGGTGA--------	22	-	-	-	-	-	-	1	-	-	-
	-------------------------------------------------------------GGACGTTGGCTCTGGTGGTG---------	20	-	1	-	-	-	-	-	-	-	-
	---------------------------------------------------------------ACGTTGGCTCTGGTGGTGA--------	19	-	-	-	-	-	1	-	-	-	-
	------------------------CACCTCCCCTGCAAACGT------------------------------------------------	18	1	-	-	-	-	-	-	-	-	-
	---------------------------------------------------------------ACGTTGGCTCTGGTGGTG---------	18	-	-	-	-	1	-	-	-	-	-
	----------------------ACCACCTCCCCTGCAAACGTCC----------------------------------------------	22	-	-	-	-	-	-	-	-	-	1
	---------------------------------------------------------------ACGTTGGCTCTGGTGGTGAT-------	20	-	-	-	-	-	-	-	1	-	-
rat	tgctgccccatgaacagtctccaCCACCTCCCCTGCAAACGTCCAgtgatgcagaggtaatggacgttggctctggtggtgatggacagt
	******************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000002581 ENSRNOG00000001886 NP_001099335.1
	............................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>..............	ENSRNOT00000063307 ENSRNOG00000041554
rat	.((((..((((..........(((((((......((.((((((((....(((....))).)))))))).))...))))))))))).))))	0.490 -32.00

rat

chromosome:11:84703702:84703791:1

Same_strand|Boundary_non-coding|ENSRNOT00000063307|ENSRNOG00000041554 ## Same_strand|Exonic_coding|ENSRNOT00000002581|ENSRNOG00000001886 ## ENSRNOG00000041554|miRNA|| ## ENSRNOG00000001886|protein_coding|NP_001099335.1|DiGeorge syndrome critical region gene 8 [Source:RefSeq_peptide;Acc:NP_001099335]

miRNAunknown_lenNOK_cloningHIGH_multiarm_DicerNOK_5varHIGH (1 loci)

sblock2992 (miRNA) [miRNAunknown_lenNOK_cloningHIGH_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	0.286	no	no	0.37/0.50	18/23/0.69	4.0 1.3 0.0	2.7 3.2 0.0	3 129 1	0 0 0	3 10 1	0 0 0	26 16 0	3 9 33	5arm 3arm 3arm	1 2 2	nd nd nd	0.32 0.21 0.50	4 2 7	227	10	9	12

		reads	miRBase family seed
seed	---------------------------------------------------------------------------UCCAGUG-------------------------------	65	novel
seed	--------------------------------------------------------------------------GUCCAGU--------------------------------	52	novel
seed	-------------------------------------------------------------------------UGUCCAG---------------------------------	46	novel
seed	------------------------------------------------------------------------AUGUCCA----------------------------------	20	novel
seed	-----------------------------------------------------------------------AAUGUCC-----------------------------------	18	novel
seed	------------------------------------------------------------------------------------------CAUAAGA----------------	8	novel
seed	----------------------------------------------------------------------------------------GUCAUAA------------------	3	novel
seed	---------------------------------UGCACUG-------------------------------------------------------------------------	2	novel
seed	----------------------------------------------------------------------UAAUGUC------------------------------------	2	novel
seed	------------------------------------------------------------------------------------CUUUGUC----------------------	2	novel
seed	-------------------------------------------------------------------------------GUGUCCU---------------------------	2	novel
seed	-----------------------------------------------------------------------------CAGUGUC-----------------------------	2	novel
seed	-----------------------------------------------------------------------------------------UCAUAAG-----------------	1	novel
seed	---------------------------AGUAACU-------------------------------------------------------------------------------	1	novel
seed	----------------------------------------------------------------------------------UCCUUUG------------------------	1	novel
seed	------------------------------------------------------------------------------AGUGUCC----------------------------	1	novel
seed	-----------------------------------------------------------------------------------------------GAUUCGG-----------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--------------------------------------------------------------------------GTCCAGTGTCCTTTGTCATAAGA----------------	23	4	8	-	4	14	6	2	4	18	2
	-------------------------------------------------------------------------TGTCCAGTGTCCTTTGTCA---------------------	19	4	11	2	3	3	6	6	2	14	1
	------------------------------------------------------------------------ATGTCCAGTGTCCTTTGTCA---------------------	20	4	1	6	1	12	5	-	3	7	3
	-----------------------------------------------------------------------AATGTCCAGTGTCCTTTGTCA---------------------	21	-	-	1	-	4	6	2	3	3	1
	----------------------------------------------------------------------TAATGTCCAGTGTCCTTTGTCA---------------------	22	-	-	1	1	7	8	-	-	-	-
	-----------------------------------------------------------------------------------------TCATAAGATTCGGTGCAAT-----	19	-	-	-	1	2	-	1	-	1	-
	------------------------------------------------------------------------ATGTCCAGTGTCCTTTGTC----------------------	19	1	-	1	-	1	1	-	-	-	-
	---------------------------------------------------------------------------------------TGTCATAAGATTCGGTGCAA------	20	-	-	-	-	1	-	-	-	-	2
	-----------------------------------------------------------------------------------------TCATAAGATTCGGTGCAA------	18	-	-	1	-	1	-	-	-	1	-
	------------------------------------------------------------------------------AGTGTCCTTTGTCATAAGA----------------	19	-	2	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------------GTCCAGTGTCCTTTGTCAT--------------------	19	-	-	-	1	-	1	-	-	-	-
	----------------------------------------------------------------------------CCAGTGTCCTTTGTCATAAGA----------------	21	-	-	-	-	2	-	-	-	-	-
	-----------------------------------------------------------------------------------CCTTTGTCATAAGATTCGGTG---------	21	-	-	-	-	-	-	-	-	-	1
	---------------------------------------------------------------------------------GTCCTTTGTCATAAGATTCGGTG---------	23	-	-	-	-	-	-	-	-	-	1
	--------------------------------CTGCACTGGATTCCAAAGAC-------------------------------------------------------------	20	-	-	-	-	-	-	-	-	1	-
	----------------------------------------------------------------------------------------GTCATAAGATTCGGTGCAA------	19	1	-	-	-	-	-	-	-	-	-
	--------------------------GAGTAACTGCACTGGATTCCAAA----------------------------------------------------------------	23	-	-	-	-	-	-	1	-	-	-
	-----------------------------------------------------------------------------------CCTTTGTCATAAGATTCGGTGCA-------	23	-	-	-	-	1	-	-	-	-	-
	---------------------------------------------------------------------TTAATGTCCAGTGTCCTTTG------------------------	20	-	-	-	-	1	-	-	-	-	-
	----------------------------------------------------------------------------------------------AGATTCGGTGCAATAAGTC	19	-	1	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------TAATGTCCAGTGTCCTTTGT-----------------------	20	-	-	-	-	1	-	-	-	-	-
	---------------------------------------------------------------------TTAATGTCCAGTGTCCTTTGTCA---------------------	23	-	-	-	-	-	1	-	-	-	-
	-----------------------------------------------------------------------------CAGTGTCCTTTGTCATAAGA----------------	20	-	-	-	-	1	-	-	-	-	-
	--------------------------------CTGCACTGGATTCCAAAGACTG-----------------------------------------------------------	22	-	-	-	-	-	1	-	-	-	-
	--------------------------------------------------------------------------GTCCAGTGTCCTTTGTCA---------------------	18	1	-	-	-	-	-	-	-	-	-
rat	tgctagcagagtacacacaagaagaagagtaactgcactggattccaaagactggggtggacctctttctTAATGTCCAGTGTCCTTTGTCATAAGAttcggtgcaataagtc
	*****************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000002484 ENSRNOG00000001815 Eif4a2
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.................................................................................	ENSRNOT00000063172 ENSRNOG00000041419
rat	(((..((.((((........((...((((.....(((((((((....((((..((((....))))..))))...))))))))).)))).)).....)))).))))).......	0.500 -27.32

rat

chromosome:11:79954044:79954156:-1

Same_strand|Boundary_non-coding|ENSRNOT00000063172|ENSRNOG00000041419 ## Same_strand|Intronic_coding|ENSRNOT00000002484|ENSRNOG00000001815 ## ENSRNOG00000001815|protein_coding|Eif4a2|Eukaryotic initiation factor 4A-II (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-2) (eIF4A-II) (eIF-4A-II). [Source:UniProtKB/Swiss-Prot;Acc:Q5RKI1] ## ENSRNOG00000041419|miRNA||

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