miR-Intess: classification

other hairpins

miRNAunknown_lenNOK_nonpairedHIGH (2 loci)

block1403937 (miRNA) [miRNAunknown_lenNOK_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	0.094	no	no	0.68/0.68	19/19/0.00	0.0	0.0	1	0	1	0	5	5	3arm	6	nd	0.42	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------GGCAGAC----------------	1	novel
		len	cloning frequencies
			T2S1
	------------------------------------------GGGCAGACTGGGCAGGAGA-----	19	1
rat	tagggagctaaggttccagagagctgggcttcgagaggaagtGGGCAGACTGGGCAGGAGAgacct
	******************************************************************
	....................................................>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000062121 ENSRNOG00000040368
rat	.(((...((...((.((((...(((..(((((.....))))).)))...))))))...))...)))	0.970 -18.30

rat

chromosome:3:119122143:119122208:-1

Same_strand|Boundary_non-coding|ENSRNOT00000062121|ENSRNOG00000040368 ## ENSRNOG00000040368|miRNA||

miRNAunknown_lenNOK_shortStem_nonpairedHIGH (2 loci)

block344455 (miRNA) [miRNAunknown_lenNOK_shortStem_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	0.378	no	no	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	2	26	3arm	2	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------UGUGCUU------------	1	miR-218
		len	cloning frequencies
			T5S2
	--------------------------------------------------------------------------------TTGTGCTTGAGAGTGAGA--	18	1
rat	taggttcgtccaggtggaggtcctgaagctgactagtgagatgcagaggagggagtctcttggaaggcgcagaggcctagTTGTGCTTGAGAGTGAGAct
	****************************************************************************************************
	..................................................................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	ENSRNOT00000054495 ENSRNOG00000036377
rat	.((.(((((((((((..((((((((..(((..((((.(((((............)))))))))..))).))).)))))......))))).)).)))).))	0.830 -27.50

rat

chromosome:14:27986174:27986273:-1

Opposite_strand|Exonic_non-coding|ENSRNOT00000054495|ENSRNOG00000036377 ## ENSRNOG00000036377|miRNA||

block2286931 (miRNA) [miRNAunknown_lenNOK_shortStem_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	0.453	no	no	0.41/0.47	19/22/0.50	0.0	1.5	2	0	2	0	0	16	5arm	1	nd	0.32	3	2	2	na	na

		reads	miRBase family seed
seed	-CAGUAGU----------------------------------------------------------------------------	2	miR-199a
		len	cloning frequencies
			T4S2	T5S1
	ACAGTAGTCAGCACATTGG-----------------------------------------------------------------	19	1	-
	ACAGTAGTCAGCACATTGGTTA--------------------------------------------------------------	22	-	1
rat	ACAGTAGTCAGCACATTGGTTAggctgggcttgggtcagcagtgacagtgggaacagaccatctaaggtgagtgccatctctgt
	************************************************************************************
	----------------------------------------------------------------------------------------------	ENSRNOT00000010947 ENSRNOG00000007649 Dnm2
	----------------------------------------------------------------------------------------------	ENSRNOT00000010362 ENSRNOG00000007649 Dnm2
	----------------------------------------------------------------------------------------------	ENSRNOT00000052366 ENSRNOG00000007649 Dnm2
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>..................................................	ENSRNOT00000063014 ENSRNOG00000041261
rat	((((.((...((((.((((...(((((..(((..((((....))))...)))..))).))..)))).....))))...))))))	0.640 -22.80

rat

chromosome:8:20600449:20600532:-1

Opposite_strand|Intronic_coding|ENSRNOT00000052366|ENSRNOG00000007649 ## Same_strand|Exonic_non-coding|ENSRNOT00000063014|ENSRNOG00000041261 ## ENSRNOG00000041261|miRNA|| ## ENSRNOG00000007649|protein_coding|Dnm2|Dynamin-2 (EC 3.6.5.5). [Source:UniProtKB/Swiss-Prot;Acc:P39052]

miRNAunknown_loopOverlap_nonpairedHIGH_bulgeHIGH (2 loci)

block2835042 (miRNA) [miRNAunknown_loopOverlap_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
Ensembl miRNA	0.102	no	no	0.40/0.40	20/20/1.00	0.0	0.0	1	0	1	0	30	-2	3arm_loop	1	nd	0.40	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------UUGGGAA------------------------------------------	1	novel
		len	cloning frequencies
			T4S1
	----------------------------------------------------------------------ATTGGGAACATTTGGCATAC------------------------------	20	1
rat	tttgtttttgtaataggaatcagatacggaattctttttgcagtatgttcctgtataagaacataagcgtATTGGGAACATTTGGCATACataattttgtatcaatatatggggagggag
	************************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000046779 ENSRNOG00000037484
	...........................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>......................	ENSRNOT00000062142 ENSRNOG00000040389
rat	(((.(((..((.(((.......(((((((((((.....(((...(((((((((...................)))))))))...))).....)))))))))))..)))))..))).))).	0.810 -24.91

rat

chromosome:X:139994775:139994894:-1

Opposite_strand|Intronic_coding|ENSRNOT00000046779|ENSRNOG00000037484 ## Same_strand|Exonic_non-coding|ENSRNOT00000062142|ENSRNOG00000040389 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000056740|ENSRNOG00000037484 ## ENSRNOG00000040389|miRNA|| ## ENSRNOG00000037484|protein_coding||

block3181898 (miRNA) [miRNAunknown_loopOverlap_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
Ensembl miRNA	0.371	no	no	0.60/0.60	20/20/1.00	0.0	0.0	2	0	1	0	5	-3	5arm_loop	1	nd	0.45	4	2	1	na	na

		reads	miRBase family seed
seed	------GGAGAUG------------------------------------------------	2	novel
		len	cloning frequencies
			T2S1
	-----CGGAGATGGGAAAAGGCTCC------------------------------------	20	2
rat	ggctgCGGAGATGGGAAAAGGCTCCttaaagtatgcctgggtcctggacaaactgaaagct
	*************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000017180 ENSRNOG00000012863 LOC364172
	>>>>>>>>>>>>>>>>>>>>>..................................................	ENSRNOT00000063327 ENSRNOG00000041574
rat	((((.(((...(((((..((((............))))...)))))......)))..))))	0.980 -14.70

rat

chromosome:X:156023014:156023074:1

Same_strand|Boundary_non-coding|ENSRNOT00000063327|ENSRNOG00000041574 ## Same_strand|Exonic_coding|ENSRNOT00000017180|ENSRNOG00000012863 ## ENSRNOG00000041574|miRNA|| ## ENSRNOG00000012863|protein_coding|LOC364172|

miRNAunknown_multiarm_DicerNOK_Multihit_randfoldOK (2 loci)

sblock11473 (miRNA) [miRNAunknown_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	0.50/0.71	20/21/1.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	13 13	19 18	5arm 3arm	256 256	nd nd	0.29 0.20	2 2	2	2	-1	0

		reads	miRBase family seed
seed	----------------------------------------------------------------------------ACACACA-------------------------	1	novel
seed	--------------GUGCGUG---------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T2S2
	-------------CGTGCGTGCGTGCGTGCGTGT--------------------------------------------------------------------------	21	-	1
	---------------------------------------------------------------------------TACACACACACATGTGCGTG-------------	20	1	-
rat	gcgtgcgtgcgtgCGTGCGTGCGTGCGTGCGTGTgtgtgtgtgtgtgtgtgtatacatgcatgcgcatgtacatgTACACACACACATGTGCGTGcacacatgtacgc
	************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000055906 ENSRNOG00000015916 RGD1306041_predicted
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000021582 ENSRNOG00000015916 RGD1306041_predicted
	......<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<..........................	ENSRNOT00000063375 ENSRNOG00000041622
rat	(((((((((.((((..(((..((((.(((.(((((..((((..((((((((((....))))))))))..))))..))))).))).))))..))))))).)))))))))	0.820 -67.90

rat

chromosome:7:123853644:123853751:1

Same_strand|Intronic_coding|ENSRNOT00000021582|ENSRNOG00000015916 ## Opposite_strand|Exonic_non-coding|ENSRNOT00000063375|ENSRNOG00000041622 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000063375|ENSRNOG00000041622 ## Same_strand|Boundary_non-coding|ENSRNOT00000055905|ENSRNOG00000015916 ## ENSRNOG00000015916|protein_coding|RGD1306041_predicted| ## ENSRNOG00000041622|miRNA|| ## {Repeats: (CGTG)n 32 53 1 class=Simple_repeat,dust 123853640 123853661 0 class=dust,trf 16 37 0 class=trf,(CGTG)n 2 71 1 class=Simple_repeat}

sblock12613 (miRNA) [miRNAunknown_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	0.45/0.60	20/24/1.00	0.0 0.5	0.0 0.0	1 4	0 0	1 3	0 0	32 9	6 23	5arm 3arm	1 258	nd nd	0.30 0.12	2 3	5	3	15	19

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------------ACACACA------------------------	2	novel
seed	---------------------------------GUGCCUG------------------------------------------------------------------------------	1	novel
seed	--------------------------------------------------------------------------------------CACACAC-------------------------	1	novel
seed	----------------------------------------------------------------------------------------CACACAC-----------------------	1	novel
		len	cloning frequencies
			T1S1	T3S2	T5S1
	--------------------------------------------------------------------------------------CACACACACACACACACACATGT---------	23	2	-	-
	--------------------------------TGTGCCTGCTTGTGCGTGCT------------------------------------------------------------------	20	-	-	1
	-------------------------------------------------------------------------------------ACACACACACACACACACACATGT---------	24	-	1	-
	---------------------------------------------------------------------------------------ACACACACACACACACACATGT---------	22	-	-	1
rat	tgtgcatgcttgtgcatgtgtgtctctgtgtgTGTGCCTGCTTGTGCGTGCTtgtgcatatgtgtatgtctgcacacacacacaaACACACACACACACACACACATGTattgcacac
	**********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000022878 ENSRNOG00000016724 Epb4.1l3
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000022849 ENSRNOG00000016724 Epb4.1l3
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000045148 ENSRNOG00000016724 Epb4.1l3
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000046148 ENSRNOG00000016724 Epb4.1l3
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000049426 ENSRNOG00000016724 Epb4.1l3
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000047159 ENSRNOG00000016724 Epb4.1l3
	...................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.....	ENSRNOT00000063553 ENSRNOG00000041800
rat	((((((.....((((((((((((...((((((((((..((..((((.((((.((((((....))))))...)))).))))..))..))))))))))...)))))))))))))))))).	1.000 -56.80

rat

chromosome:9:108390476:108390593:1

Same_strand|Boundary_non-coding|ENSRNOT00000029010|ENSRNOG00000016724 ## Same_strand|Intronic_coding|ENSRNOT00000049426|ENSRNOG00000016724 ## Same_strand|Exonic_non-coding|ENSRNOT00000063553|ENSRNOG00000041800 ## ENSRNOG00000016724|protein_coding|Epb4.1l3|erythrocyte protein band 4.1-like 3 [Source:RefSeq_peptide;Acc:NP_446379] ## ENSRNOG00000041800|miRNA|| ## {Repeats: (CA)n 13 34 1 class=Simple_repeat,dust 108390379 108390399 0 class=dust,trf 1 22 0 class=trf,(TG)n 2 172 1 class=Simple_repeat,trf 14 34 0 class=trf,dust 108390548 108390569 0 class=dust,(CA)n 1 34 1 class=Simple_repeat,(TG)n 134 154 1 class=Simple_repeat}

miRNAunknown_rep_cloningHIGH_multiarm_DicerNOK_Multihit_randfoldOK (2 loci)

sblock5198 (miRNA) [miRNAunknown_rep_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	LTR/ERVK	0.24/0.41	19/24/0.93	0.4 0.0 0.0	0.6 0.5 0.0	20 122 1	0 0 0	6 8 1	0 0 0	36 17 6	-6 12 22	5arm_loop_3arm 3arm 3arm	7 307 307	nd nd nd	0.32 0.05 0.23	3 1 4	254	8	15	0

		reads	miRBase family seed
seed	----------------------------------------------------------------------UAUACAU------------------------------	195	novel
seed	---------------------------------------------------------------------AUAUACA-------------------------------	16	novel
seed	-----------------------------------------------------------------------AUACAUA-----------------------------	15	novel
seed	-------------------------------------GUGUAUA---------------------------------------------------------------	14	novel
seed	--------------------------------------UGUAUAU--------------------------------------------------------------	4	novel
seed	-------------------------------------------------------------------------ACAUACA---------------------------	3	novel
seed	---------------------------------------------------------------AUAUACA-------------------------------------	2	novel
seed	---------------------------------------GUAUAUG-------------------------------------------------------------	2	novel
seed	-------------------------------------------------------------GAAUAUA---------------------------------------	1	novel
seed	--------------------------------------------------------------------CAUAUAC--------------------------------	1	novel
seed	--------------------------------------------------------------------------------CACAUAC--------------------	1	miR-1*
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S2	T5S2
	---------------------------------------------------------------------ATATACATACACACATACACA-----------------	21	4	3	36	20	10	10	-	1
	---------------------------------------------------------------------ATATACATACACACATACAC------------------	20	5	1	29	37	6	3	-	1
	---------------------------------------------------------------------ATATACATACACACATACACATAC--------------	24	1	1	4	11	6	2	-	2
	----------------------------------------------------------------------TATACATACACACATACAC------------------	19	1	-	4	2	1	3	-	-
	------------------------------------TGTGTATATGTCCATGTGTGT--------------------------------------------------	21	-	1	3	2	-	1	-	3
	--------------------------------------------------------------------CATATACATACACACATACAC------------------	21	1	2	2	2	-	1	1	-
	--------------------------------------------------------------------CATATACATACACACATACACA-----------------	22	-	-	3	1	1	-	-	-
	----------------------------------------------------------------------TATACATACACACATACACA-----------------	20	-	-	2	1	1	-	-	-
	------------------------------------------------------------------------TACATACACACATACACAT----------------	19	1	-	1	1	-	-	-	-
	---------------------------------------------------------------------ATATACATACACACATACACAT----------------	22	1	1	-	-	-	-	-	-
	--------------------------------------TGTATATGTCCATGTGTGTAT------------------------------------------------	21	-	-	2	-	-	-	-	-
	--------------------------------------------------------------------CATATACATACACACATAC--------------------	19	-	-	-	1	-	1	-	-
	-------------------------------------GTGTATATGTCCATGTGTGT--------------------------------------------------	20	-	-	-	1	1	-	-	-
	--------------------------------------------------------------AATATACATATACATACACAC------------------------	21	-	-	-	2	-	-	-	-
	------------------------------------TGTGTATATGTCCATGTGTGTA-------------------------------------------------	22	-	-	1	-	1	-	-	-
	-------------------------------------GTGTATATGTCCATGTGTGTAT------------------------------------------------	22	-	-	1	-	-	-	-	-
	------------------------------------TGTGTATATGTCCATGTGTG---------------------------------------------------	20	-	-	-	1	-	-	-	-
	-------------------------------------------------------------------------------ACACATACACATACACACAAGC------	22	-	-	-	-	1	-	-	-
	------------------------------------TGTGTATATGTCCATGTGT----------------------------------------------------	19	-	-	-	1	-	-	-	-
	------------------------------------------------------------TGAATATACATATACATACAC--------------------------	21	-	-	-	1	-	-	-	-
	-------------------------------------GTGTATATGTCCATGTGTGTA-------------------------------------------------	21	-	-	-	1	-	-	-	-
	-------------------------------------------------------------------ACATATACATACACACATACAC------------------	22	-	-	-	-	1	-	-	-
rat	tgtgatgccccgtctatgtgcatatgtgtgtatgtctgtgtatatgtccatgtgtgtatatgaatatacATATACATACACACATACACAtacacacaagcacacac
	***********************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042430 ENSRNOG00000029235 Sfmbt2
	...........................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063055 ENSRNOG00000041302
rat	((((.(((...((.((((((..(((((((((((((.(((((((((...(((((....))))).))))))))).))))))))))))))))))).))....))))))).	0.980 -43.30

rat

chromosome:17:79251055:79251161:-1

Same_strand|Boundary_non-coding|ENSRNOT00000051529|ENSRNOG00000029235 ## Same_strand|Intronic_coding|ENSRNOT00000042430|ENSRNOG00000029235 ## Same_strand|Exonic_non-coding|ENSRNOT00000063055|ENSRNOG00000041302 ## ENSRNOG00000041302|miRNA|| ## ENSRNOG00000029235|protein_coding|Sfmbt2|Scm-like with four mbt domains 2 Gene [Source:MGI (curated);Acc:Sfmbt2-001] ## {Repeats: trf 10 37 0 class=trf,dust 79251103 79251126 0 class=dust,RMER12 836 850 -1 class=LTR/ERVK,trf 1 31 0 class=trf,trf 192 215 0 class=trf,dust 79251061 79251102 0 class=dust,(CA)n 1 46 -1 class=Simple_repeat,trf 12 49 0 class=trf,RMER12 785 808 1 class=LTR/ERVK,(TG)n 2 47 -1 class=Simple_repeat,RMER12 794 835 -1 class=LTR/ERVK,RMER12 809 850 1 class=LTR/ERVK,trf 150 191 0 class=trf}

sblock5199 (miRNA) [miRNAunknown_rep_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	LTR,LTR/ERVK	0.29/0.44	18/25/0.98	0.0 0.0 0.0	0.0 0.8 0.0	1 358 1	0 0 0	1 10 1	0 0 0	34 21 3	9 6 30	5arm 3arm 3arm	9 307 307	nd nd nd	0.11 0.12 0.11	1 1 1	738	10	-1	4

		reads	miRBase family seed
seed	-------------------------------------------------------------------------UAUACAU-------------------------------------	616	novel
seed	--------------------------------------------------------------------------AUACAUA------------------------------------	73	novel
seed	------------------------------------------------------------------------AUAUACA--------------------------------------	36	novel
seed	----------------------------------------------------------------------------ACAUACA----------------------------------	10	novel
seed	-----------------------------------UGUAUGU---------------------------------------------------------------------------	1	miR-297
seed	-----------------------------------------------------------------------CAUAUAC---------------------------------------	1	novel
seed	-------------------------------------------------------------------------------------------------CAAGCAC-------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	------------------------------------------------------------------------ATATACATACACACATACACAC-----------------------	22	14	9	104	87	31	16	1	2	6	7
	------------------------------------------------------------------------ATATACATACACACATACACACAC---------------------	24	3	3	51	43	27	12	-	3	4	1
	------------------------------------------------------------------------ATATACATACACACATACACA------------------------	21	4	3	36	20	10	10	-	-	-	1
	------------------------------------------------------------------------ATATACATACACACATACAC-------------------------	20	5	1	29	37	6	3	-	-	-	1
	-------------------------------------------------------------------------TATACATACACACATACACAC-----------------------	21	4	1	18	18	3	4	-	-	-	-
	------------------------------------------------------------------------ATATACATACACACATACACACA----------------------	23	1	-	8	10	4	-	-	-	1	-
	-----------------------------------------------------------------------CATATACATACACACATACACAC-----------------------	23	2	-	6	5	4	-	-	-	1	2
	-------------------------------------------------------------------------TATACATACACACATACAC-------------------------	19	1	-	4	2	1	3	-	-	-	-
	---------------------------------------------------------------------------TACATACACACATACACACACAC-------------------	23	-	-	4	3	3	-	-	-	-	-
	-------------------------------------------------------------------------TATACATACACACATACACACAC---------------------	23	-	-	6	2	1	-	-	-	-	-
	-----------------------------------------------------------------------CATATACATACACACATACAC-------------------------	21	1	2	2	2	-	1	-	1	-	-
	-----------------------------------------------------------------------CATATACATACACACATACACA------------------------	22	-	-	3	1	1	-	-	-	-	-
	-------------------------------------------------------------------------TATACATACACACATACACA------------------------	20	-	-	2	1	1	-	-	-	-	-
	------------------------------------------------------------------------ATATACATACACACATACACACACA--------------------	25	-	-	1	-	1	-	-	-	-	-
	-----------------------------------------------------------------------CATATACATACACACATAC---------------------------	19	-	-	-	1	-	1	-	-	-	-
	------------------------------------------------------------------------------------------------ACAAGCACACATACACAC---	18	-	-	-	-	-	1	-	-	-	-
	----------------------------------ATGTATGTCTGTATGTACA----------------------------------------------------------------	19	1	-	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------ACATATACATACACACATACAC-------------------------	22	-	-	-	-	1	-	-	-	-	-
	-------------------------------------------------------------------------TATACATACACACATACACACA----------------------	22	-	-	-	-	-	-	1	-	-	-
rat	ttcctgtgatgcacctatatatgtgcttgtgtgtatgtatgtctgtatgtacatgtaagtatatgaataaacATATACATACACACATACACACACacaagcacacatacacacgga
	*********************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042430 ENSRNOG00000029235 Sfmbt2
	......................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.....	ENSRNOT00000063115 ENSRNOG00000041362
rat	.((((((((((..........(((((((((((((.(((((((.((((((((.((((...(((....))).)))).)))))))).))))))).)))))))))))))))).)))).)))	0.980 -50.10

rat

chromosome:17:79251448:79251564:-1

Same_strand|Boundary_non-coding|ENSRNOT00000051529|ENSRNOG00000029235 ## Same_strand|Intronic_coding|ENSRNOT00000042430|ENSRNOG00000029235 ## Same_strand|Exonic_non-coding|ENSRNOT00000063115|ENSRNOG00000041362 ## ENSRNOG00000041362|miRNA|| ## ENSRNOG00000029235|protein_coding|Sfmbt2|Scm-like with four mbt domains 2 Gene [Source:MGI (curated);Acc:Sfmbt2-001] ## {Repeats: RMER12 827 851 1 class=LTR/ERVK,RMER12 791 810 1 class=LTR/ERVK,dust 79251467 79251494 0 class=dust,RMER12 -471 851 1 class=LTR,dust 79251451 79251469 0 class=dust,trf 540 558 0 class=trf,trf 601 620 0 class=trf,trf 556 584 0 class=trf}

miRNAunknown_rep_cloningOK_multiarm_DicerNOK_Multihit_5varHIGH_loopOverlap_randfoldOK (2 loci)

sblock12705 (miRNA) [miRNAunknown_rep_cloningOK_multiarm_DicerNOK_Multihit_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	0.001	no	SINE	0.50/0.67	19/24/0.82	0.0 4.1 1.2	0.0 0.6 1.8	1 8 13	0 0 0	1 5 7	0 0 0	14 33 16	14 -10 5	5arm 5arm_loop_3arm 3arm	349 358 358	nd nd nd	0.05 0.25 0.00	1 6 0	22	8	-7	-3

		reads	miRBase family seed
seed	----------------------------------------------------------------CGCACAC--------------------------------	4	novel
seed	------------------------------------------------------------------CACACAC------------------------------	3	novel
seed	---------------------------------------------------------------GCGCACA---------------------------------	3	novel
seed	-------------------------------------------------------------GCGCGCA-----------------------------------	2	novel
seed	----------------------------------------UGUGUGU--------------------------------------------------------	2	novel
seed	-----------------------------------------------------------------GCACACA-------------------------------	1	novel
seed	--------------------------------------UGUGUGU----------------------------------------------------------	1	novel
seed	-------------------------------------GUGUGUG-----------------------------------------------------------	1	novel
seed	-----------------------------------------GUGUGUG-------------------------------------------------------	1	novel
seed	------------------------------------UGUGUGU------------------------------------------------------------	1	novel
seed	---------------GUGUGUG---------------------------------------------------------------------------------	1	novel
seed	---------------------------------------GUGUGUG---------------------------------------------------------	1	novel
seed	----------------------------------UGUGUGU--------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T4S1	T4S2	T5S1
	---------------------------------------GTGTGTGTGTGTGTGTGCA---------------------------------------------	19	-	-	-	1	-	1	-	-
	------------------------------------------------------------CGCGCGCACACACACACACAC----------------------	21	-	-	1	-	1	-	-	-
	---------------------------------------------------------------GCGCACACACACACACACACAC------------------	22	2	-	-	-	-	-	-	-
	-----------------------------------------------------------------GCACACACACACACACACAC------------------	20	-	-	-	-	1	-	-	1
	-------------------------------------GTGTGTGTGTGTGTGTGTGC----------------------------------------------	20	-	-	-	-	1	-	-	-
	-----------------------------------------------------------------GCACACACACACACACACACAG----------------	22	-	-	-	-	-	-	1	-
	----------------------------------------TGTGTGTGTGTGTGTGCAC--------------------------------------------	19	1	-	-	-	-	-	-	-
	---------------------------------------------------------------GCGCACACACACACACACACA-------------------	21	1	-	-	-	-	-	-	-
	--------------------------------------------------------------CGCGCACACACACACACAC----------------------	19	-	-	-	1	-	-	-	-
	--------------------------------------------------------------CGCGCACACACACACACACA---------------------	20	1	-	-	-	-	-	-	-
	-----------------------------------GTGTGTGTGTGTGTGTGTGTGC----------------------------------------------	22	-	-	-	-	1	-	-	-
	----------------------------------------------------------------CGCACACACACACACACACA-------------------	20	-	-	-	-	1	-	-	-
	---------------------------------GTGTGTGTGTGTGTGTGTGTGTGC----------------------------------------------	24	-	-	-	-	-	-	-	1
	--------------GGTGTGTGTGTGTGTGTGTGT--------------------------------------------------------------------	21	-	-	-	-	-	-	-	1
	------------------------------------TGTGTGTGTGTGTGTGTGTGC----------------------------------------------	21	-	-	-	-	-	1	-	-
	--------------------------------------TGTGTGTGTGTGTGTGTGCA---------------------------------------------	20	-	-	-	-	1	-	-	-
	---------------------------------------------------------------GCGCACACACACACACACAC--------------------	20	-	1	-	-	-	-	-	-
	--------------------------------------------------------------CGCGCACACACACACACACAC--------------------	21	1	-	-	-	-	-	-	-
rat	tttctttatatttaGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCACgCGCGCGCACACACACACACACACACAGgctcaggtcaggaaac
	*******************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000034925 ENSRNOG00000012194 Morc4_predicted
	...................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>..............	ENSRNOT00000063027 ENSRNOG00000041274
rat	((((((...((((..((.(((((((((((((((((((((((((((((((......))))))))))))))))))))))))))))))).))..)))).)))))).	1.000 -67.40

rat

chromosome:X:127581819:127581921:-1

Same_strand|Exonic_non-coding|ENSRNOT00000063027|ENSRNOG00000041274 ## Same_strand|Intronic_coding|ENSRNOT00000034925|ENSRNOG00000012194 ## ENSRNOG00000041274|miRNA|| ## ENSRNOG00000012194|protein_coding|Morc4_predicted| ## {Repeats: (CA)n 1 24 -1 class=Simple_repeat,(CA)n 22 41 -1 class=Simple_repeat,(TG)n 28 30 -1 class=Simple_repeat,(CA)n 1 41 -1 class=Simple_repeat,dust 127581866 127581889 0 class=dust,trf 1 24 0 class=trf,trf 1 20 0 class=trf,dust 127581887 127581906 0 class=dust,AT_rich 1 32 -1 class=Low_complexity,dust 127581836 127581855 0 class=dust,RSINE1 1 50 -1 class=SINE,(TG)n 1 27 -1 class=Simple_repeat,trf 22 41 0 class=trf}

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