miR-Intess: classification

other hairpins

miRNAunknown_Multihit_shortStem_nonpairedHIGH (1 loci)

block1981451 (miRNA) [miRNAunknown_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	0.152	no	no	0.67/0.67	24/24/1.00	0.0	0.0	1	0	1	0	8	5	5arm	1	nd	0.25	4	1	1	na	na

		reads	miRBase family seed
seed	---------GUAGUGG----------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	--------GGTAGTGGGCCGAGCCGAGTGACA------------------------------------------------	24	1
rat	ccgcgttgGGTAGTGGGCCGAGCCGAGTGACAtacacctacgttaagtgcatgctcacccgaggcacacttacctgaagg
	********************************************************************************
	.............<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<...........	ENSRNOT00000062113 ENSRNOG00000040360
rat	((...((((((((((.(((....((.(((((((.(((.........))).))).)))).)).))).)))).)))))).))	1.000 -26.90

rat

chromosome:6:134416220:134416299:-1

Opposite_strand|Exonic_non-coding|ENSRNOT00000062113|ENSRNOG00000040360 ## ENSRNOG00000040360|miRNA||

miRNAunknown_cloningHIGH_Multihit_shortStem_randfoldOK (1 loci)

block2398358 (miRNA) [miRNAunknown_cloningHIGH_Multihit_shortStem_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	0.32/0.38	18/23/0.88	0.3	0.4	37	0	6	0	2	6	3arm	257	nd	0.23	3	59	6	na	na

		reads	miRBase family seed
seed	----------------------------------------UAUACAU----------------	44	novel
seed	-----------------------------------------AUACAUA---------------	15	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T5S1
	---------------------------------------ATATACATACACACACACACAC--	22	2	2	12	6	-	1
	----------------------------------------TATACATACACACACACACAC--	21	1	-	4	6	-	-
	---------------------------------------ATATACATACACACACACAC----	20	-	1	5	2	1	1
	---------------------------------------ATATACATACACACACACACA---	21	-	-	2	4	-	-
	---------------------------------------ATATACATACACACACACA-----	19	-	-	2	1	-	-
	----------------------------------------TATACATACACACACACAC----	19	-	-	1	-	1	-
	----------------------------------------TATACATACACACACACA-----	18	-	-	-	1	-	-
	---------------------------------------ATATACATACACACACACACACA-	23	-	-	-	1	-	-
	----------------------------------------TATACATACACACACACACA---	20	-	-	-	-	1	-
	---------------------------------------ATATACATACACACACAC------	18	-	-	1	-	-	-
rat	tggatgtctatgtgtatgtatatgatgtatgtgtatcttATATACATACACACACACACACac
	***************************************************************
	.....>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063083 ENSRNOG00000041330
rat	((..(((...(((((((((((((((.(((....))).)))))))))))))))...)))..)).	1.000 -21.50

rat

chromosome:8:44515566:44515628:1

Same_strand|Exonic_non-coding|ENSRNOT00000063083|ENSRNOG00000041330 ## ENSRNOG00000041330|miRNA|| ## {Repeats: dust 44515639 44515653 0 class=dust,(CA)n 2 62 1 class=Simple_repeat,trf 27 45 0 class=trf,(CA)n 2 20 1 class=Simple_repeat}

miRNAunknown_cloningHIGH_multiarm_DicerNOK_Multihit_randfoldOK (1 loci)

sblock5200 (miRNA) [miRNAunknown_cloningHIGH_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	0.24/0.37	18/24/0.92	0.0 0.7	0.0 0.7	2 33	0 0	2 10	0 0	28 30	9 1	5arm 3arm	23 38	nd nd	0.18 0.12	3 2	64	10	-8	-6

		reads	miRBase family seed
seed	-------------------------------------------------------------------UAUACAU----------------------------------------------	39	novel
seed	----------------------------------------------------------------------ACAUACA-------------------------------------------	11	novel
seed	--------------------------------------------------------------------AUACAUA---------------------------------------------	6	novel
seed	---------------------------------------------------------------------------CACACAU--------------------------------------	2	novel
seed	-----------------------------UGUAUGU------------------------------------------------------------------------------------	2	miR-297
seed	-------------------------------------------------------------------------UACACAC----------------------------------------	1	novel
seed	------------------------------------------------------------------AUAUACA-----------------------------------------------	1	novel
seed	-----------------------------------------------------------------------CAUACAC------------------------------------------	1	novel
seed	---------------------------------------------------------------------UACAUAC--------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	------------------------------------------------------------------ATATACATACACACATAAACACAC------------------------------	24	1	-	10	3	1	1	-	1	2	-
	------------------------------------------------------------------ATATACATACACACATAAACAC--------------------------------	22	1	1	3	3	2	6	-	-	-	-
	---------------------------------------------------------------------TACATACACACATAAACACAC------------------------------	21	-	-	3	-	5	-	-	1	-	-
	-------------------------------------------------------------------TATACATACACACATAAACAC--------------------------------	21	-	-	2	2	-	-	-	-	-	-
	------------------------------------------------------------------ATATACATACACACATAAAC----------------------------------	20	-	-	-	2	-	-	-	-	-	-
	---------------------------------------------------------------------TACATACACACATAAACAC--------------------------------	19	-	-	1	-	-	-	-	-	-	1
	----------------------------ATGTATGTGTGTATGTACATGT----------------------------------------------------------------------	22	-	-	1	1	-	-	-	-	-	-
	------------------------------------------------------------------ATATACATACACACATAAACA---------------------------------	21	1	-	-	-	-	1	-	-	-	-
	-------------------------------------------------------------------TATACATACACACATAAACACAC------------------------------	23	-	-	-	1	-	1	-	-	-	-
	--------------------------------------------------------------------------ACACACATAAACACACATG---------------------------	19	-	-	-	-	-	-	-	-	-	1
	--------------------------------------------------------------------ATACATACACACATAAACACAC------------------------------	22	-	-	-	1	-	-	-	-	-	-
	----------------------------------------------------------------------ACATACACACATAAACACAC------------------------------	20	-	-	-	1	-	-	-	-	-	-
	-----------------------------------------------------------------CATATACATACACACATAAACAC--------------------------------	23	-	-	-	-	1	-	-	-	-	-
	------------------------------------------------------------------------ATACACACATAAACACAC------------------------------	18	-	-	1	-	-	-	-	-	-	-
	--------------------------------------------------------------------------ACACACATAAACACACAT----------------------------	18	-	-	-	-	-	-	1	-	-	-
rat	atgcccctattcatgtgcatgcgtgtatatgtatgtgtgtatgtacatgtgtgtatatgcataaacATATACATACACACATAAACACACatgctgcacacacacacgaatggtaagcat
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042430 ENSRNOG00000029235 Sfmbt2
	........................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>..................	ENSRNOT00000062215 ENSRNOG00000040462
rat	((((..((((((.((((..((.(((((...((((((((((((((...((((((((((((......)))))))))))).))))..))))))))))))))).)))))).))))))...))))	1.000 -48.50

rat

chromosome:17:79259043:79259162:-1

Same_strand|Boundary_non-coding|ENSRNOT00000051529|ENSRNOG00000029235 ## Same_strand|Intronic_coding|ENSRNOT00000042430|ENSRNOG00000029235 ## Same_strand|Exonic_non-coding|ENSRNOT00000062215|ENSRNOG00000040462 ## ENSRNOG00000040462|miRNA|| ## ENSRNOG00000029235|protein_coding|Sfmbt2|Scm-like with four mbt domains 2 Gene [Source:MGI (curated);Acc:Sfmbt2-001] ## {Repeats: dust 79259070 79259098 0 class=dust,trf 13 35 0 class=trf,trf 313 341 0 class=trf,(CATATA)n 18 40 -1 class=Simple_repeat,dust 79259113 79259135 0 class=dust,trf 356 378 0 class=trf,(TG)n 2 79 -1 class=Simple_repeat,(CATATA)n 3 44 -1 class=Simple_repeat,(TG)n 51 79 -1 class=Simple_repeat}

miRNAunknown_cloningHIGH_multiarm_DicerNOK_randfoldOK_nonpairedHIGH_bulgeHIGH (1 loci)

sblock2993 (miRNA) [miRNAunknown_cloningHIGH_multiarm_DicerNOK_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	0.37/0.44	18/23/0.72	0.0 0.5	0.0 2.0	15 2	0 0	9 2	0 0	9 12	24 25	5arm 3arm	3 3	nd nd	0.35 0.33	6 4	54	9	-2	0

		reads	miRBase family seed
seed	----------CCUUCUU--------------------------------------------------------------------------------------------------	47	novel
seed	---------ACCUUCU---------------------------------------------------------------------------------------------------	5	novel
seed	-----------------------------------------------------------------------------------GAGUACA-------------------------	1	novel
seed	----------------------------------------------------------------------------------AGAGUAC--------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	---------ACCTTCTTGTATAAGCACTG--------------------------------------------------------------------------------------	20	-	-	-	15	2	-	-	3	1
	---------ACCTTCTTGTATAAGCAC----------------------------------------------------------------------------------------	18	-	-	1	4	1	-	1	1	-
	---------ACCTTCTTGTATAAGCACTGTG------------------------------------------------------------------------------------	22	1	1	-	2	-	1	-	1	1
	---------ACCTTCTTGTATAAGCACT---------------------------------------------------------------------------------------	19	-	1	-	1	-	2	-	-	2
	---------ACCTTCTTGTATAAGCACTGTGC-----------------------------------------------------------------------------------	23	1	1	-	2	1	-	-	-	-
	--------TACCTTCTTGTATAAGCACTGTG------------------------------------------------------------------------------------	23	-	-	2	2	-	-	-	-	-
	--------TACCTTCTTGTATAAGCACTG--------------------------------------------------------------------------------------	21	-	-	-	-	-	-	1	-	-
	---------------------------------------------------------------------------------CAGAGTACACACAAGAAG----------------	18	-	-	-	1	-	-	-	-	-
	----------------------------------------------------------------------------------AGAGTACACACAAGAAGAAGA------------	21	-	-	-	-	-	-	-	-	1
rat	agggtttttACCTTCTTGTATAAGCACTGtgctaaaattacaggaactaggattatatcttggtttttgtaataatgctagcagagtacacacaagaagaagagtaactgcactg
	*******************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000002484 ENSRNOG00000001815 Eif4a2
	...........>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>........	ENSRNOT00000063172 ENSRNOG00000041419
rat	.((((..((((((((((((......(((.(((((..(((((((((((((((((...))))))))))))))))).....))))).)))....))))))))....))))..)).)).	0.980 -36.30

rat

chromosome:11:79954117:79954231:-1

Same_strand|Intronic_coding|ENSRNOT00000002484|ENSRNOG00000001815 ## Same_strand|Exonic_non-coding|ENSRNOT00000063172|ENSRNOG00000041419 ## 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||

miRNAunknown_cloningHIGH_multiarm_DicerNOK_shortStem_bulgeHIGH (1 loci)

sblock2014 (miRNA) [miRNAunknown_cloningHIGH_multiarm_DicerNOK_shortStem_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	0.043	no	no	0.35/0.44	18/25/0.72	0.0 0.1	0.5 1.0	2 2456	0 0	1 10	0 0	16 3	6 33	5arm 3arm	1 1	nd nd	0.24 0.44	4 5	5124	10	0	-19

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------AGGUAGA-----------------	3892	novel
seed	----------------------------------------------------------------------------------GGUAGAU----------------	1211	novel
seed	--------------------------------------------------------------------------------AAGGUAG------------------	17	novel
seed	-----------------UGGAGAC---------------------------------------------------------------------------------	2	novel
seed	-----------------------------------------------------------------------------------GUAGAUA---------------	1	novel
seed	------------------------------------------------------------------------------------UAGAUAG--------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--------------------------------------------------------------------------------AAGGTAGATAGAACAGGTCTT----	21	258	161	21	35	106	72	34	76	99	81
	--------------------------------------------------------------------------------AAGGTAGATAGAACAGGTCTTG---	22	249	235	29	23	55	46	39	14	60	98
	--------------------------------------------------------------------------------AAGGTAGATAGAACAGGTCT-----	20	215	162	16	25	57	40	30	38	66	72
	--------------------------------------------------------------------------------AAGGTAGATAGAACAGGTC------	19	216	151	18	24	58	40	39	27	60	54
	---------------------------------------------------------------------------------AGGTAGATAGAACAGGTCTTG---	21	139	81	7	11	36	24	12	10	63	60
	--------------------------------------------------------------------------------AAGGTAGATAGAACAGGT-------	18	120	85	8	11	39	21	13	36	27	26
	--------------------------------------------------------------------------------AAGGTAGATAGAACAGGTCTTGT--	23	77	43	20	10	22	15	20	16	24	47
	---------------------------------------------------------------------------------AGGTAGATAGAACAGGTC------	18	50	51	4	13	24	22	9	6	26	34
	---------------------------------------------------------------------------------AGGTAGATAGAACAGGTCTT----	20	49	40	5	7	19	14	9	13	23	27
	---------------------------------------------------------------------------------AGGTAGATAGAACAGGTCTTGT--	22	38	30	5	5	18	12	6	7	25	11
	---------------------------------------------------------------------------------AGGTAGATAGAACAGGTCT-----	19	35	28	4	8	14	11	5	6	12	18
	---------------------------------------------------------------------------------AGGTAGATAGAACAGGTCTTGTT-	23	5	1	2	-	4	1	-	1	2	8
	--------------------------------------------------------------------------------AAGGTAGATAGAACAGGTCTTGTT-	24	5	1	-	-	-	2	1	1	1	1
	-------------------------------------------------------------------------------AAAGGTAGATAGAACAGGTCT-----	21	-	1	-	-	-	-	-	1	2	-
	-------------------------------------------------------------------------------AAAGGTAGATAGAACAGGTC------	20	1	-	-	-	-	1	-	-	-	1
	-------------------------------------------------------------------------------AAAGGTAGATAGAACAGGTCTTG---	23	1	-	-	1	-	-	-	-	1	-
	-------------------------------------------------------------------------------AAAGGTAGATAGAACAGGTCTT----	22	-	1	-	-	1	-	-	-	-	-
	-------------------------------------------------------------------------------AAAGGTAGATAGAACAGGTCTTGT--	24	-	1	-	1	-	-	-	-	-	-
	-------------------------------------------------------------------------------AAAGGTAGATAGAACAGG--------	18	1	1	-	-	-	-	-	-	-	-
	----------------TTGGAGACTAAGACAATAGAG--------------------------------------------------------------------	21	-	-	1	-	-	-	-	-	-	-
	-------------------------------------------------------------------------------AAAGGTAGATAGAACAGGT-------	19	-	-	-	-	-	-	-	-	-	1
	--------------------------------------------------------------------------------AAGGTAGATAGAACAGGTCTTGTTT	25	-	-	-	-	-	-	-	-	1	-
	----------------TTGGAGACTAAGACAATAGA---------------------------------------------------------------------	20	-	-	1	-	-	-	-	-	-	-
	-----------------------------------------------------------------------------------GTAGATAGAACAGGTCTTG---	19	-	-	-	-	1	-	-	-	-	-
	---------------------------------------------------------------------------------AGGTAGATAGAACAGGTCTTGTTT	24	-	1	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------------------GGTAGATAGAACAGGTCTT----	19	-	-	-	1	-	-	-	-	-	-
rat	gtttagtcatattcttttggagactaagacaatagagtccttgaagtcaagctgactctgcctttagcctcctacatgaaAAGGTAGATAGAACAGGTCTTGttt
	*********************************************************************************************************
	.....................................................................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063179 ENSRNOG00000041426
rat	((((.(((.(((..((((((((.(((((....(((((((((((....))))..)))))))..))))).)))).....))))..)))))).))))...........	0.980 -26.90

rat

chromosome:1:137743970:137744074:1

Same_strand|Boundary_non-coding|ENSRNOT00000063179|ENSRNOG00000041426 ## intergenic ## ENSRNOG00000041426|miRNA||

miRNAunknown_cloningHIGH_multiarm_Multihit_loopOverlap_randfoldOK (1 loci)

block2815640 (miRNA) [miRNAunknown_cloningHIGH_multiarm_Multihit_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	0.37/0.48	18/24/0.78	0.0 0.0 1.0	0.0 0.0 0.7	1 59 7	0 0 0	1 10 4	0 0 0	43 49 29	-11 -18 0	5arm_loop_3arm 3arm_loop 3arm	31 346 346	nd nd nd	0.58 0.55 0.15	10 10 1	193	10	na	na

		reads	miRBase family seed
seed	--------------------------------------------------ACACACA-------------------------------------------------------	164	novel
seed	---------------------------------------------------CACACAC------------------------------------------------------	11	novel
seed	----------------------------------------------------ACACACA-----------------------------------------------------	5	novel
seed	-----------------------------------------------------------------CACACAC----------------------------------------	4	novel
seed	---------------------------------------------------------------CACACAC------------------------------------------	2	novel
seed	-------------------------------------------------UACACAC--------------------------------------------------------	1	novel
seed	-----------------------------------------------------------CAUACAC----------------------------------------------	1	novel
seed	-----------------------------------------------------CACACAC----------------------------------------------------	1	novel
seed	------------------------------------------------------ACACACA---------------------------------------------------	1	novel
seed	--------------------------------------------AUGUGUA-------------------------------------------------------------	1	novel
seed	--------------------------------------------------------------ACACACA-------------------------------------------	1	novel
seed	--------------------------------------------------------ACACAUA-------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-------------------------------------------------TACACACACACATACACACA-------------------------------------------	20	4	3	20	39	5	10	-	4	1	4
	-------------------------------------------------TACACACACACATACACACAC------------------------------------------	21	3	3	10	11	2	1	1	1	2	-
	-------------------------------------------------TACACACACACATACACAC--------------------------------------------	19	-	1	5	11	2	4	-	-	-	-
	-------------------------------------------------TACACACACACATACACACACAC----------------------------------------	23	2	1	3	3	2	-	-	-	-	1
	-------------------------------------------------TACACACACACATACACACACA-----------------------------------------	22	-	-	-	4	-	-	-	-	-	-
	--------------------------------------------------ACACACACACATACACACACAC----------------------------------------	22	-	-	-	1	3	-	-	-	-	-
	--------------------------------------------------ACACACACACATACACAC--------------------------------------------	18	-	-	1	1	-	1	-	-	-	-
	--------------------------------------------------ACACACACACATACACACA-------------------------------------------	19	-	-	2	1	-	-	-	-	-	-
	---------------------------------------------------CACACACACATACACACACAC----------------------------------------	21	-	-	-	1	-	2	-	-	-	-
	---------------------------------------------------CACACACACATACACACAC------------------------------------------	19	-	-	-	-	2	-	-	-	-	-
	----------------------------------------------------------------ACACACACAAACACACACA-----------------------------	19	-	-	1	-	1	-	-	-	-	-
	----------------------------------------------------------------ACACACACAAACACACAC------------------------------	18	-	-	2	-	-	-	-	-	-	-
	----------------------------------------------------ACACACACATACACACACA-----------------------------------------	19	-	-	-	1	-	-	-	-	-	-
	-----------------------------------------------------CACACACATACACACACAC----------------------------------------	19	-	-	-	-	1	-	-	-	-	-
	-------------------------------------------------------------TACACACACACAAACACAC--------------------------------	19	-	1	-	-	-	-	-	-	-	-
	-------------------------------------------------TACACACACACATACACACACACA---------------------------------------	24	-	-	1	-	-	-	-	-	-	-
	--------------------------------------------------ACACACACACATACACACAC------------------------------------------	20	-	-	1	-	-	-	-	-	-	-
	-------------------------------------------TATGTGTACACACACACAT--------------------------------------------------	19	-	-	1	-	-	-	-	-	-	-
	----------------------------------------------------------ACATACACACACACAAAC------------------------------------	18	-	-	1	-	-	-	-	-	-	-
	--------------------------------------------------------------ACACACACACAAACACACA-------------------------------	19	-	-	-	-	1	-	-	-	-	-
	------------------------------------------------GTACACACACACATACACACA-------------------------------------------	21	-	-	-	-	-	1	-	-	-	-
	--------------------------------------------------------------ACACACACACAAACACACAC------------------------------	20	-	-	-	1	-	-	-	-	-	-
	-------------------------------------------------------CACACATACACACACACAA--------------------------------------	19	-	-	-	-	-	-	-	-	1	-
rat	tattcatttttgtttatttgtgtgtattttgtgtatgcttgtgtatgtgTACACACACACATACACACAcacaaacacacacatatgcacacacacacaaaggccatgagtg
	****************************************************************************************************************
	.........>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>................	ENSRNOT00000063002 ENSRNOG00000041249
rat	(((((((((((((.....(((((((((..(((((.((.((((((.((((((..........)))))).)))))).)).))))).)))))))))...))))))...)))))))	1.000 -37.70

rat

chromosome:X:134100251:134100362:-1

Same_strand|Exonic_non-coding|ENSRNOT00000063002|ENSRNOG00000041249 ## ENSRNOG00000041249|miRNA|| ## {Repeats: dust 134100280 134100312 0 class=dust,(TG)n 18 50 -1 class=Simple_repeat,trf 15 48 0 class=trf,dust 134100318 134100320 0 class=dust,trf 17 49 0 class=trf,(TG)n 2 50 -1 class=Simple_repeat}

miRNAunknown_cloningOK_multiarm_DicerNOK_Multihit_randfoldOK_bulgeHIGH (1 loci)

sblock5211 (miRNA) [miRNAunknown_cloningOK_multiarm_DicerNOK_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	0.33/0.47	18/22/0.86	0.0 0.0	0.4 0.3	5 30	0 0	3 7	0 0	25 24	12 2	5arm 3arm	17 66	nd nd	0.28 0.18	4 4	42	7	-8	-5

		reads	miRBase family seed
seed	---------------------------------------------------------------UAUACAU--------------------------------------	34	novel
seed	--------------------------GUCUGUG---------------------------------------------------------------------------	5	novel
seed	----------------------------------------------------------------AUACAUA-------------------------------------	3	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T5S1
	--------------------------------------------------------------ATATACATACACACATGCACAC------------------------	22	-	1	5	6	3	5	2
	--------------------------------------------------------------ATATACATACACACATGCACA-------------------------	21	-	-	2	4	3	1	1
	-------------------------TGTCTGTGTGTATGTCCAG----------------------------------------------------------------	19	-	-	2	-	1	-	-
	-------------------------TGTCTGTGTGTATGTCCA-----------------------------------------------------------------	18	-	-	-	1	1	-	-
	---------------------------------------------------------------TATACATACACACATGCACA-------------------------	20	-	-	-	-	1	-	-
	--------------------------------------------------------------ATATACATACACACATGCAC--------------------------	20	1	-	-	-	-	-	-
	---------------------------------------------------------------TATACATACACACATGCAC--------------------------	19	-	-	-	1	-	-	-
	---------------------------------------------------------------TATACATACACACATGCACAC------------------------	21	-	-	-	1	-	-	-
rat	ccggatgtatatgcatgtgtttataTGTCTGTGTGTATGTCCAGgagtgtatatgaatattcATATACATACACACATGCACACacacaagaatggcaaacatttggg
	************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042430 ENSRNOG00000029235 Sfmbt2
	..................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.........................	ENSRNOT00000063008 ENSRNOG00000041255
rat	((((((((...(((....((((...(((.(((((((((((......((((((((((....))))))))))....))))))))))).))).)))).))).)))))))).	0.910 -38.20

rat

chromosome:17:79294390:79294497:-1

Same_strand|Boundary_non-coding|ENSRNOT00000051529|ENSRNOG00000029235 ## Same_strand|Intronic_coding|ENSRNOT00000042430|ENSRNOG00000029235 ## Same_strand|Exonic_non-coding|ENSRNOT00000063008|ENSRNOG00000041255 ## ENSRNOG00000041255|miRNA|| ## ENSRNOG00000029235|protein_coding|Sfmbt2|Scm-like with four mbt domains 2 Gene [Source:MGI (curated);Acc:Sfmbt2-001] ## {Repeats: (CATATA)n 36 55 -1 class=Simple_repeat,trf 231 250 0 class=trf,trf 191 213 0 class=trf,(CATATA)n 3 18 -1 class=Simple_repeat,(CATATA)n 3 75 -1 class=Simple_repeat}

miRNAunknown_lenNOK_5varHIGH (1 loci)

block581373 (miRNA) [miRNAunknown_lenNOK_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	0.016	no	no	0.44/0.52	18/21/0.50	1.2	1.0	6	0	1	0	21	5	5arm	10	nd	0.28	3	6	1	na	na

		reads	miRBase family seed
seed	-----------------------UCUUCCU-----------------------------------------------------------------------------------	2	novel
seed	----------------------GUCUUCC------------------------------------------------------------------------------------	2	novel
seed	-------------------------UUCCUGU---------------------------------------------------------------------------------	1	novel
seed	------------------------CUUCCUG----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	---------------------TGTCTTCCTGTGGTTTGTTG------------------------------------------------------------------------	20	2
	----------------------GTCTTCCTGTGGTTTGTT-------------------------------------------------------------------------	18	2
	-----------------------TCTTCCTGTGGTTTGTTG------------------------------------------------------------------------	18	1
	------------------------CTTCCTGTGGTTTGTTGGCTC--------------------------------------------------------------------	21	1
rat	tcaagcagacgcctaaagagcTGTCTTCCTGTGGTTTGTTGGCTCttctggacttcaatagagagtgacttttccatctggaagaaacaaccccttgttgtgtctggtttgac
	*****************************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.......................................................................................	ENSRNOT00000063272 ENSRNOG00000041519
rat	((((((((((((...(((.....((((((.((((...(((.((((.((((........)))))))))))....))))..))))))........)))...))))))).))))).	0.780 -34.92

rat

chromosome:16:61728574:61728686:1

Same_strand|Boundary_non-coding|ENSRNOT00000063272|ENSRNOG00000041519 ## ENSRNOG00000041519|miRNA||

miRNAunknown_lenNOK_5varHIGH_randfoldOK (1 loci)

block2029350 (miRNA) [miRNAunknown_lenNOK_5varHIGH_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	0.009	no	no	0.44/0.52	18/21/0.50	1.2	1.0	6	0	1	0	21	5	5arm	10	nd	0.28	3	6	1	na	na

		reads	miRBase family seed
seed	-----------------------UCUUCCU-----------------------------------------------------------------------------------	2	novel
seed	----------------------GUCUUCC------------------------------------------------------------------------------------	2	novel
seed	-------------------------UUCCUGU---------------------------------------------------------------------------------	1	novel
seed	------------------------CUUCCUG----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	---------------------TGTCTTCCTGTGGTTTGTTG------------------------------------------------------------------------	20	2
	----------------------GTCTTCCTGTGGTTTGTT-------------------------------------------------------------------------	18	2
	-----------------------TCTTCCTGTGGTTTGTTG------------------------------------------------------------------------	18	1
	------------------------CTTCCTGTGGTTTGTTGGCTC--------------------------------------------------------------------	21	1
rat	tcaagcagacgcctagagaacTGTCTTCCTGTGGTTTGTTGGCTCttctggacttcaatagagagtgactattccatttggaagaaacaaccccttgttgtgtctggtttgac
	*****************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000049945 ENSRNOG00000032407 Npas3
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.......................................................................................	ENSRNOT00000063231 ENSRNOG00000041478
rat	((((((((((((...(((.....((((((.((((...(((.((((.((((........)))))))))))....))))..))))))........)))...))))))).))))).	0.850 -35.42

rat

chromosome:6:73866686:73866798:1

Same_strand|Intronic_coding|ENSRNOT00000049945|ENSRNOG00000032407 ## Same_strand|Boundary_non-coding|ENSRNOT00000063231|ENSRNOG00000041478 ## ENSRNOG00000041478|miRNA|| ## ENSRNOG00000032407|protein_coding|Npas3|neuronal PAS domain protein 3 Gene [Source:MGI Symbol;Acc:MGI:1351610]

miRNAunknown_lenNOK_Multihit_loopOverlap_randfoldOK (1 loci)

block1880983 (miRNA) [miRNAunknown_lenNOK_Multihit_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	0.63/0.65	19/20/0.67	0.0	0.7	3	0	3	0	39	-1	3arm	286	nd	0.30	2	3	3	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------GUGCGUG---------------------------------------------------	3	novel
		len	cloning frequencies
			T2S1	T3S1	T3S2
	-------------------------------------------------------------CGTGCGTGTGTGCGTGTGTG---------------------------------------	20	1	1	-
	-------------------------------------------------------------CGTGCGTGTGTGCGTGTGT----------------------------------------	19	-	-	1
rat	gaagagcagcctgtgcgcgcgcgcgcgcgcgtgcgtgcgtgcgtgcgcgcgtgcgtgcgtgCGTGCGTGTGTGCGTGTGTGcgtgcgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtcc
	************************************************************************************************************************
	............................................................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063225 ENSRNOG00000041472
rat	((...(((((.((..((((((((((((((((..((..((..((..((((((..(((((....)))))..))))))..))..))..))..))))))))))))))))..)).)).))).)).	1.000 -77.10

rat

chromosome:5:143898597:143898716:1

Same_strand|Boundary_non-coding|ENSRNOT00000063225|ENSRNOG00000041472 ## ENSRNOG00000041472|miRNA|| ## {Repeats: dust 143898646 143898666 0 class=dust,(CGTG)n 1 106 1 class=Simple_repeat,(CGTG)n 50 70 1 class=Simple_repeat,trf 37 57 0 class=trf}

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