miR-Intess: rno-mir-9

rno-mir-9

Cloning frequencies
absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-9 5arm	36798.500	16229	37.000	24	32.500	42	51	68.000	126	213
rno-mir-9 3arm	18250	9846.000	12	6	13	16	46	28	130	194
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-9 5arm	1.223	0.708	0.002	0.001	0.002	0.003	0.004	0.004	0.008	0.014
rno-mir-9 3arm	0.607	0.430	0.001	0.000	0.001	0.001	0.004	0.001	0.009	0.013

sblock2007 (miRBase rno-mir-9-3) [miRNAknown_lenNOK_cloningHIGH_multiarm_DicerNOK_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
miRBase rno-mir-9-3	0.001	no	no	0.30/0.43	18/25/0.46	0.0 0.0	0.6 0.6	38924 15064	0 0	10 10	0 0	15 14	7 7	5arm 3arm	3 3	nd nd	0.10 0.06	1 1	78843	10	0	2

Families
Member of family miR-9 (seed CUUUGGU): rno-mir-9, rno-mir-9, rno-mir-9, block753516_cand, block2303675_cand

		reads	miRBase family seed
seed	----------------------------------CUUUGGU---------------------------------------------------------------------------------------	49319	miR-9
seed	--------------------------------------------------------------------------AAAGCUA-----------------------------------------------	19983	novel
seed	-------------------------------------------------------------------------UAAAGCU------------------------------------------------	4525	miR-9*
seed	-----------------------------------UUUGGUU--------------------------------------------------------------------------------------	3982	novel
seed	---------------------------------------------------------------------------AAGCUAG----------------------------------------------	633	novel
seed	------------------------------------UUGGUUA-------------------------------------------------------------------------------------	272	novel
seed	----------------------------------------------------------------------------AGCUAGA---------------------------------------------	33	novel
seed	-------------------------------------UGGUUAU------------------------------------------------------------------------------------	28	novel
seed	--------------------------------------GGUUAUC-----------------------------------------------------------------------------------	16	novel
seed	---------------------------------------GUUAUCU----------------------------------------------------------------------------------	15	novel
seed	------------------------------------------------------------------------AUAAAGC-------------------------------------------------	12	novel
seed	---------------------------------------------------------------------GUCAUAA----------------------------------------------------	10	novel
seed	-----------------------------------------------------------------------------GCUAGAU--------------------------------------------	6	novel
seed	-----------------------------------------------------------------------CAUAAAG--------------------------------------------------	5	novel
seed	---------------------------------UCUUUGG----------------------------------------------------------------------------------------	2	novel
seed	------------------------------------------------------------------------------CUAGAUA-------------------------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	---------------------------------TCTTTGGTTATCTAGCTGT----------------------------------------------------------------------------	19	11611	5405	10	9	4	9	11	29	47	56
	---------------------------------TCTTTGGTTATCTAGCTG-----------------------------------------------------------------------------	18	10644	4871	4	4	10	10	23	14	22	67
	---------------------------------TCTTTGGTTATCTAGCTGTA---------------------------------------------------------------------------	20	6393	2672	3	1	4	7	7	11	26	45
	-------------------------------------------------------------------------TAAAGCTAGATAACCGAAAG-----------------------------------	20	4966	2755	1	1	8	3	8	10	50	64
	-------------------------------------------------------------------------TAAAGCTAGATAACCGAAAGT----------------------------------	21	3457	1672	5	1	1	3	9	2	21	33
	-------------------------------------------------------------------------TAAAGCTAGATAACCGAA-------------------------------------	18	2214	1045	1	2	3	4	11	4	15	37
	---------------------------------TCTTTGGTTATCTAGCTGTATG-------------------------------------------------------------------------	22	2189	789	4	2	4	3	2	7	15	16
	----------------------------------CTTTGGTTATCTAGCTGTA---------------------------------------------------------------------------	19	1561	762	-	1	-	-	-	2	4	6
rno-miR-9	---------------------------------TCTTTGGTTATCTAGCTGTATGA------------------------------------------------------------------------	23	1579	575	3	2	-	3	1	2	-	11
	-------------------------------------------------------------------------TAAAGCTAGATAACCGAAA------------------------------------	19	1241	753	2	-	-	1	4	6	10	20
	---------------------------------TCTTTGGTTATCTAGCTGTAT--------------------------------------------------------------------------	21	1402	573	8	-	2	5	3	3	7	6
rno-miR-9*	------------------------------------------------------------------------ATAAAGCTAGATAACCGAAAGT----------------------------------	22	1016	778	1	1	-	-	1	-	4	6
	-------------------------------------------------------------------------TAAAGCTAGATAACCGAAAGTA---------------------------------	22	987	407	-	1	-	-	3	1	5	13
	------------------------------------------------------------------------ATAAAGCTAGATAACCGAAAG-----------------------------------	21	641	334	-	-	-	1	-	-	6	1
	------------------------------------------------------------------------ATAAAGCTAGATAACCGAA-------------------------------------	19	596	365	-	-	-	-	1	1	4	3
	----------------------------------CTTTGGTTATCTAGCTGTATGA------------------------------------------------------------------------	22	677	247	1	-	-	1	1	-	-	1
	------------------------------------------------------------------------ATAAAGCTAGATAACCGAAA------------------------------------	20	222	144	2	-	-	1	-	-	2	1
	----------------------------------CTTTGGTTATCTAGCTGTAT--------------------------------------------------------------------------	20	227	122	-	1	-	-	-	-	3	2
	------------------------------------------------------------------------ATAAAGCTAGATAACCGA--------------------------------------	18	220	122	-	-	-	-	3	-	3	1
	--------------------------------------------------------------------------AAAGCTAGATAACCGAAAGT----------------------------------	20	205	82	-	-	-	-	1	1	2	1
	--------------------------------------------------------------------------AAAGCTAGATAACCGAAAG-----------------------------------	19	131	83	-	-	-	-	1	-	3	-
	----------------------------------CTTTGGTTATCTAGCTGT----------------------------------------------------------------------------	18	139	69	-	-	-	-	-	-	-	1
	----------------------------------CTTTGGTTATCTAGCTGTATG-------------------------------------------------------------------------	21	108	37	-	1	1	-	-	-	-	-
	-----------------------------------TTTGGTTATCTAGCTGTATGA------------------------------------------------------------------------	21	83	41	-	-	-	-	-	-	-	-
	-------------------------------------------------------------------------TAAAGCTAGATAACCGAAAGTAG--------------------------------	23	50	38	-	-	-	-	-	-	-	-
	---------------------------------TCTTTGGTTATCTAGCTGTATGAG-----------------------------------------------------------------------	24	64	10	-	-	-	-	-	-	-	-
	-----------------------------------TTTGGTTATCTAGCTGTA---------------------------------------------------------------------------	18	49	24	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------------AAAGCTAGATAACCGAAA------------------------------------	18	37	27	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------------AAAGCTAGATAACCGAAAGTA---------------------------------	21	37	17	-	-	-	-	-	-	-	-
	-----------------------------------TTTGGTTATCTAGCTGTAT--------------------------------------------------------------------------	19	29	19	-	-	-	-	-	-	-	-
	------------------------------------------------------------------------ATAAAGCTAGATAACCGAAAGTA---------------------------------	23	25	17	-	-	-	-	-	-	-	-
	-------------------------------------------------------------------------TAAAGCTAGATAACCGAAAGTAGA-------------------------------	24	21	12	-	-	-	-	1	-	-	-
	---------------------------------------------------------------------------AAGCTAGATAACCGAAAGT----------------------------------	19	18	4	-	-	-	-	-	-	-	-
	------------------------------------TTGGTTATCTAGCTGTATGA------------------------------------------------------------------------	20	12	6	-	-	1	-	-	-	-	-
	--------------------------------------GGTTATCTAGCTGTATGA------------------------------------------------------------------------	18	1	1	-	2	3	3	3	-	-	2
	-----------------------------------TTTGGTTATCTAGCTGTATG-------------------------------------------------------------------------	20	13	2	-	-	-	-	-	-	-	-
	-------------------------------------TGGTTATCTAGCTGTATGA------------------------------------------------------------------------	19	2	1	4	1	2	1	-	-	2	-
	-----------------------------------TTTGGTTATCTAGCTGTATGAG-----------------------------------------------------------------------	22	9	1	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------------CATAAAGCTAGATAACCGAAA------------------------------------	21	3	5	-	-	-	-	-	-	-	-
	---------------------------------------------------------------------------AAGCTAGATAACCGAAAGTA---------------------------------	20	4	2	-	-	-	-	-	-	-	1
	----------------------------------CTTTGGTTATCTAGCTGTATGAG-----------------------------------------------------------------------	23	6	1	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------CGTCATAAAGCTAGATAACCGA--------------------------------------	22	4	1	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------------AGCTAGATAACCGAAAGT----------------------------------	18	2	3	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------------AAAGCTAGATAACCGAAAGTAG--------------------------------	22	3	1	-	-	-	-	-	-	-	-
	------------------------------------TTGGTTATCTAGCTGTAT--------------------------------------------------------------------------	18	1	3	-	-	-	-	-	-	-	-
	------------------------------------TTGGTTATCTAGCTGTATG-------------------------------------------------------------------------	19	2	2	-	-	-	-	-	-	-	-
	---------------------------------------------------------------------------AAGCTAGATAACCGAAAG-----------------------------------	18	3	-	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------------CATAAAGCTAGATAACCGAA-------------------------------------	20	3	-	-	-	-	-	-	-	-	-
	-------------------------------------TGGTTATCTAGCTGTATG-------------------------------------------------------------------------	18	1	-	-	-	2	-	-	-	-	-
	----------------------------------------------------------------------TCATAAAGCTAGATAACCGA--------------------------------------	20	2	-	-	-	-	-	-	-	-	-
	------------------------------------------------------------------------ATAAAGCTAGATAACCGAAAGTAGA-------------------------------	25	2	-	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------CGTCATAAAGCTAGATAAC-----------------------------------------	19	2	-	-	-	-	-	-	-	-	-
	--------------------------------CTCTTTGGTTATCTAGCT------------------------------------------------------------------------------	18	2	-	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------TCATAAAGCTAGATAACCGAAA------------------------------------	22	2	-	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------CGTCATAAAGCTAGATAACCG---------------------------------------	21	2	-	-	-	-	-	-	-	-	-
	-----------------------------------TTTGGTTATCTAGCTGTATGAGT----------------------------------------------------------------------	23	2	-	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------------------GCTAGATAACCGAAAGTA---------------------------------	18	1	1	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------TCATAAAGCTAGATAACC----------------------------------------	18	1	-	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------CGTCATAAAGCTAGATAACCGAA-------------------------------------	23	1	-	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------------AGCTAGATAACCGAAAGTA---------------------------------	19	-	1	-	-	-	-	-	-	-	-
	------------------------------------TTGGTTATCTAGCTGTATGAG-----------------------------------------------------------------------	21	-	1	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------------CATAAAGCTAGATAACCGAAAG-----------------------------------	22	1	-	-	-	-	-	-	-	-	-
	-------------------------------------------------------------------------TAAAGCTAGATAACCGAAAGTAGAA------------------------------	25	1	-	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------------AAAGCTAGATAACCGAAAGTAGAA------------------------------	24	1	-	-	-	-	-	-	-	-	-
	---------------------------------------------------------------------------AAGCTAGATAACCGAAAGTAG--------------------------------	21	1	-	-	-	-	-	-	-	-	-
rat	------------------GGAGGCCCGTTTCTCTCTTTGGTTATCTAGCTGTATGAGTGCCACAGAGCCGTCATAAAGCTAGATAACCGAAAGTAGAAATGACTCTAA--------------------
human	GCAGCGGCACTGGCTAAGGGAGGCCCGTTTCTCTCTTTGGTTATCTAGCTGTATGAGTGCCACAGAGCCGTCATAAAGCTAGATAACCGAAAGTAGAAATGATTCTCACAACTTCTGCGTGCGAGCGC
mouse	--------------------------------CTCTTTGGTTATCTAGCTGTATGAGTGCCACAGAGCCGTCATAAAGCTAGATAACCGAAAG-----------------------------------
	*************************************************************
	..... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .....	ENSRNOT00000053703 ENSRNOG00000035580 rno-mir-9-3
rat	((((...(((((((((.(((((((((((((((.(((((..((......))..))))).))))))))))))))))).))))))).))))..	1.000 -40.10
human	((.((.((((..((.(((.((((..(((((((((.(((((((((((((((.(((((..((......))..))))).))))))))))))))))).)))))))..))))....)))..))))))..))))	0.985 -52.10
mouse	...(((((((((((((((.(((((..((......))..))))).)))))))))))))))..	1.000 -28.40

rat	chromosome:1:135254133:135254222:1	Same_strand\|Exonic_non-coding\|ENSRNOT00000053703\|ENSRNOG00000035580 ## ENSRNOG00000035580\|miRNA\|rno-mir-9-3\|rno-mir-9-3 [Source:miRBase;Acc:MI0000839] ## {MIR: rno-mir-9-3}
human	chromosome:15:87712234:87712361:1	Same_strand\|Boundary_non-coding\|ENST00000385084\|ENSG00000207819\|miRNA\|hsa-mir-9-3 [Source:miRBase;Acc:MI0000468] ## {SimpF: oe = 0.76 0 CpG,rank = 2 1 FirstEF} ## {MIR: hsa-mir-9-3}
mouse	chromosome:7:86650130:86650259:1	Same_strand\|Boundary_non-coding\|ENSMUST00000083611\|ENSMUSG00000065545\|miRNA\|mmu-mir-9-3 [Source:miRBase;Acc:MI0000721] ## {SimpF: oe = 0.93 -1 CpG} ## {MIR: mmu-mir-9-3}

sblock5961 (miRBase rno-mir-9-2) [miRNAknown_lenNOK_cloningHIGH_multiarm_DicerNOK_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
miRBase rno-mir-9-2	0.001	no	no	0.28/0.39	18/25/0.48	0.0 0.0	0.6 0.6	38924 15064	0 0	10 10	0 0	15 13	7 7	5arm 3arm	3 3	nd nd	0.10 0.11	1 1	82038	10	0	1

Families
Member of family miR-9 (seed CUUUGGU): rno-mir-9, rno-mir-9, rno-mir-9, block753516_cand, block2303675_cand

		reads	miRBase family seed
seed	-------------------------------CUUUGGU-----------------------------------------------------------------------------------	49319	miR-9
seed	---------------------------------------------------------------------AAAGCUA---------------------------------------------	23070	novel
seed	--------------------------------------------------------------------UAAAGCU----------------------------------------------	4554	miR-9*
seed	--------------------------------UUUGGUU----------------------------------------------------------------------------------	3982	novel
seed	----------------------------------------------------------------------AAGCUAG--------------------------------------------	714	novel
seed	---------------------------------UUGGUUA---------------------------------------------------------------------------------	272	novel
seed	-----------------------------------------------------------------------AGCUAGA-------------------------------------------	34	novel
seed	----------------------------------UGGUUAU--------------------------------------------------------------------------------	28	novel
seed	-----------------------------------GGUUAUC-------------------------------------------------------------------------------	17	novel
seed	------------------------------------GUUAUCU------------------------------------------------------------------------------	15	novel
seed	-------------------------------------------------------------------AUAAAGC-----------------------------------------------	12	novel
seed	------------------------------------------------------------------------GCUAGAU------------------------------------------	8	novel
seed	------------------------------------------------------------------CAUAAAG------------------------------------------------	5	novel
seed	------------------------------UCUUUGG------------------------------------------------------------------------------------	4	novel
seed	-------------------------------------------------------------------------CUAGAUA-----------------------------------------	2	novel
seed	----------------------------UAUCUUU--------------------------------------------------------------------------------------	1	novel
seed	--------------------------------------------------------------------------UAGAUAA----------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	------------------------------TCTTTGGTTATCTAGCTGT------------------------------------------------------------------------	19	11611	5405	10	9	4	9	11	29	47	56
	------------------------------TCTTTGGTTATCTAGCTG-------------------------------------------------------------------------	18	10644	4871	4	4	10	10	23	14	22	67
	------------------------------TCTTTGGTTATCTAGCTGTA-----------------------------------------------------------------------	20	6393	2672	3	1	4	7	7	11	26	45
	--------------------------------------------------------------------TAAAGCTAGATAACCGAAAG---------------------------------	20	4966	2755	1	1	8	3	8	10	50	64
	--------------------------------------------------------------------TAAAGCTAGATAACCGAAAGT--------------------------------	21	3457	1672	5	1	1	3	9	2	21	33
	--------------------------------------------------------------------TAAAGCTAGATAACCGAA-----------------------------------	18	2214	1045	1	2	3	4	11	4	15	37
	------------------------------TCTTTGGTTATCTAGCTGTATG---------------------------------------------------------------------	22	2189	789	4	2	4	3	2	7	15	16
	-------------------------------CTTTGGTTATCTAGCTGTA-----------------------------------------------------------------------	19	1561	762	-	1	-	-	-	2	4	6
rno-miR-9	------------------------------TCTTTGGTTATCTAGCTGTATGA--------------------------------------------------------------------	23	1579	575	3	2	-	3	1	2	-	11
	--------------------------------------------------------------------TAAAGCTAGATAACCGAAAGTAAA-----------------------------	24	1353	765	-	-	1	2	1	2	5	10
	--------------------------------------------------------------------TAAAGCTAGATAACCGAAA----------------------------------	19	1241	753	2	-	-	1	4	6	10	20
	------------------------------TCTTTGGTTATCTAGCTGTAT----------------------------------------------------------------------	21	1402	573	8	-	2	5	3	3	7	6
rno-miR-9*	-------------------------------------------------------------------ATAAAGCTAGATAACCGAAAGT--------------------------------	22	1016	778	1	1	-	-	1	-	4	6
	--------------------------------------------------------------------TAAAGCTAGATAACCGAAAGTA-------------------------------	22	987	407	-	1	-	-	3	1	5	13
	--------------------------------------------------------------------TAAAGCTAGATAACCGAAAGTAA------------------------------	23	688	352	-	-	-	1	2	1	-	3
	-------------------------------------------------------------------ATAAAGCTAGATAACCGAAAG---------------------------------	21	641	334	-	-	-	1	-	-	6	1
	-------------------------------------------------------------------ATAAAGCTAGATAACCGAA-----------------------------------	19	596	365	-	-	-	-	1	1	4	3
	-------------------------------CTTTGGTTATCTAGCTGTATGA--------------------------------------------------------------------	22	677	247	1	-	-	1	1	-	-	1
	-------------------------------------------------------------------ATAAAGCTAGATAACCGAAA----------------------------------	20	222	144	2	-	-	1	-	-	2	1
	-------------------------------CTTTGGTTATCTAGCTGTAT----------------------------------------------------------------------	20	227	122	-	1	-	-	-	-	3	2
	-------------------------------------------------------------------ATAAAGCTAGATAACCGA------------------------------------	18	220	122	-	-	-	-	3	-	3	1
	---------------------------------------------------------------------AAAGCTAGATAACCGAAAGT--------------------------------	20	205	82	-	-	-	-	1	1	2	1
	---------------------------------------------------------------------AAAGCTAGATAACCGAAAG---------------------------------	19	131	83	-	-	-	-	1	-	3	-
	-------------------------------CTTTGGTTATCTAGCTGT------------------------------------------------------------------------	18	139	69	-	-	-	-	-	-	-	1
	-------------------------------CTTTGGTTATCTAGCTGTATG---------------------------------------------------------------------	21	108	37	-	1	1	-	-	-	-	-
	--------------------------------TTTGGTTATCTAGCTGTATGA--------------------------------------------------------------------	21	83	41	-	-	-	-	-	-	-	-
	------------------------------TCTTTGGTTATCTAGCTGTATGAG-------------------------------------------------------------------	24	64	10	-	-	-	-	-	-	-	-
	--------------------------------TTTGGTTATCTAGCTGTA-----------------------------------------------------------------------	18	49	24	-	-	-	-	-	-	-	-
	---------------------------------------------------------------------AAAGCTAGATAACCGAAA----------------------------------	18	37	27	-	-	-	-	-	-	-	-
	---------------------------------------------------------------------AAAGCTAGATAACCGAAAGTA-------------------------------	21	37	17	-	-	-	-	-	-	-	-
	---------------------------------------------------------------------AAAGCTAGATAACCGAAAGTAAA-----------------------------	23	33	15	-	-	-	-	-	-	-	-
	--------------------------------TTTGGTTATCTAGCTGTAT----------------------------------------------------------------------	19	29	19	-	-	-	-	-	-	-	-
	-------------------------------------------------------------------ATAAAGCTAGATAACCGAAAGTA-------------------------------	23	25	17	-	-	-	-	-	-	-	-
	---------------------------------------------------------------------AAAGCTAGATAACCGAAAGTAA------------------------------	22	22	16	-	-	-	-	-	-	-	-
	-------------------------------------------------------------------ATAAAGCTAGATAACCGAAAGTAA------------------------------	24	18	13	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------TAAAGCTAGATAACCGAAAGTAAAA----------------------------	25	9	15	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------AAGCTAGATAACCGAAAGT--------------------------------	19	18	4	-	-	-	-	-	-	-	-
	---------------------------------TTGGTTATCTAGCTGTATGA--------------------------------------------------------------------	20	12	6	-	-	1	-	-	-	-	-
	--------------------------------TTTGGTTATCTAGCTGTATG---------------------------------------------------------------------	20	13	2	-	-	-	-	-	-	-	-
	-----------------------------------GGTTATCTAGCTGTATGA--------------------------------------------------------------------	18	1	1	-	2	3	3	3	-	-	2
	----------------------------------TGGTTATCTAGCTGTATGA--------------------------------------------------------------------	19	2	1	4	1	2	1	-	-	2	-
	--------------------------------TTTGGTTATCTAGCTGTATGAG-------------------------------------------------------------------	22	9	1	-	-	-	-	-	-	-	-
	------------------------------------------------------------------CATAAAGCTAGATAACCGAAA----------------------------------	21	3	5	-	-	-	-	-	-	-	-
	-------------------------------CTTTGGTTATCTAGCTGTATGAG-------------------------------------------------------------------	23	6	1	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------AAGCTAGATAACCGAAAGTA-------------------------------	20	4	2	-	-	-	-	-	-	-	1
	-----------------------------------------------------------------------AGCTAGATAACCGAAAGT--------------------------------	18	2	3	-	-	-	-	-	-	-	-
	---------------------------------TTGGTTATCTAGCTGTAT----------------------------------------------------------------------	18	1	3	-	-	-	-	-	-	-	-
	---------------------------------TTGGTTATCTAGCTGTATG---------------------------------------------------------------------	19	2	2	-	-	-	-	-	-	-	-
	----------------------------------TGGTTATCTAGCTGTATG---------------------------------------------------------------------	18	1	-	-	-	2	-	-	-	-	-
	------------------------------------------------------------------CATAAAGCTAGATAACCGAA-----------------------------------	20	3	-	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------AAGCTAGATAACCGAAAG---------------------------------	18	3	-	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------AAGCTAGATAACCGAAAGTAA------------------------------	21	1	1	-	-	-	-	-	-	-	-
	--------------------------------TTTGGTTATCTAGCTGTATGAGT------------------------------------------------------------------	23	2	-	-	-	-	-	-	-	-	-
	-----------------------------ATCTTTGGTTATCTAGCTGT------------------------------------------------------------------------	20	2	-	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------TCATAAAGCTAGATAACCGA------------------------------------	20	2	-	-	-	-	-	-	-	-	-
	------------------------------------------------------------------------GCTAGATAACCGAAAGTA-------------------------------	18	1	1	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------TCATAAAGCTAGATAACCGAAA----------------------------------	22	2	-	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------TCATAAAGCTAGATAACC--------------------------------------	18	1	-	-	-	-	-	-	-	-	-
	---------------------------------TTGGTTATCTAGCTGTATGAG-------------------------------------------------------------------	21	-	1	-	-	-	-	-	-	-	-
	----------------------------------TGGTTATCTAGCTGTATGAGTGT----------------------------------------------------------------	23	1	-	-	-	-	-	-	-	-	-
	-------------------------------------------------------------------------CTAGATAACCGAAAGTAA------------------------------	18	1	-	-	-	-	-	-	-	-	-
	-----------------------------ATCTTTGGTTATCTAGCT--------------------------------------------------------------------------	18	1	-	-	-	-	-	-	-	-	-
	---------------------------TTATCTTTGGTTATCTAGCTG-------------------------------------------------------------------------	21	1	-	-	-	-	-	-	-	-	-
	-----------------------------ATCTTTGGTTATCTAGCTG-------------------------------------------------------------------------	19	-	1	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------------AGCTAGATAACCGAAAGTA-------------------------------	19	-	1	-	-	-	-	-	-	-	-
	------------------------------------------------------------------CATAAAGCTAGATAACCGAAAG---------------------------------	22	1	-	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------------AGCTAGATAACCGAAAGTAAA-----------------------------	21	1	-	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------------AGCTAGATAACCGAAAGTAA------------------------------	20	1	-	-	-	-	-	-	-	-	-
rat	---------------GGAAGCGAGTTGTTATCTTTGGTTATCTAGCTGTATGAGTGTATTGGTCTTCATAAAGCTAGATAACCGAAAGTAAAAACTCCTTCA-------------------
human	ACAGAGGCCTGTGTGGGAAGCGAGTTGTTATCTTTGGTTATCTAGCTGTATGAGTGTATTGGTCTTCATAAAGCTAGATAACCGAAAGTAAAAACTCCTTCAAGATCGCCGGGGAGCGTGT
mouse	----------GTGAGGGAAGCGAGTTGTTATCTTTGGTTATCTAGCTGTATGAGTGTATTGGTCTTCATAAAGCTAGATAACCGAAAGTAAAAACTCCTTCAAGGTCAC------------
	***************************************************************************************
	..... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .....	ENSRNOT00000053751 ENSRNOG00000035628 rno-mir-9-2
rat	.((((.(((((.(((..(((((((((((((((.((((((..(....)..)))))).)))))))))))))))..))).))))))))).	1.000 -40.10
human	.......((((.((((((((.(((((.(((..(((((((((((((((.((((((..........)))))).)))))))))))))))..))).)))))))))....))))))))........	0.992 -47.30
mouse	((((..((((.(((((.(((..(((((((((((((((.((((((..........)))))).)))))))))))))))..))).)))))))))....))))	1.000 -42.30

rat	chromosome:2:12259506:12259592:-1	Same_strand\|Exonic_non-coding\|ENSRNOT00000053751\|ENSRNOG00000035628 ## ENSRNOG00000035628\|miRNA\|rno-mir-9-2\|rno-mir-9-2 [Source:miRBase;Acc:MI0000840] ## {MIR: rno-mir-9-2}
human	chromosome:5:87998408:87998528:-1	Same_strand\|Boundary_non-coding\|ENST00000384838\|ENSG00000207570\|miRNA\|hsa-mir-9-2 [Source:miRBase;Acc:MI0000467] ## {MIR: hsa-mir-9-2}
mouse	chromosome:13:83878406:83878504:1	Same_strand\|Boundary_non-coding\|ENSMUST00000083490\|ENSMUSG00000065424\|miRNA\|mmu-mir-9-2 [Source:miRBase;Acc:MI0000157] ## {MIR: mmu-mir-9-2}

sblock6529 (miRBase rno-mir-9-1) [miRNAknown_lenNOK_cloningHIGH_multiarm_DicerNOK_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
miRBase rno-mir-9-1	0.001	no	no	0.28/0.39	18/25/0.48	0.0 0.0	0.6 0.6	38924 15064	0 0	10 10	0 0	15 13	7 6	5arm 3arm	3 3	nd nd	0.10 0.11	1 1	82037	10	0	1

Families
Member of family miR-9 (seed CUUUGGU): rno-mir-9, rno-mir-9, rno-mir-9, block753516_cand, block2303675_cand

		reads	miRBase family seed
seed	----------------CUUUGGU----------------------------------------------------------------------------	49319	miR-9
seed	--------------------------------------------------------AAAGCUA------------------------------------	23070	novel
seed	-------------------------------------------------------UAAAGCU-------------------------------------	4554	miR-9*
seed	-----------------UUUGGUU---------------------------------------------------------------------------	3982	novel
seed	---------------------------------------------------------AAGCUAG-----------------------------------	714	novel
seed	------------------UUGGUUA--------------------------------------------------------------------------	272	novel
seed	----------------------------------------------------------AGCUAGA----------------------------------	34	novel
seed	-------------------UGGUUAU-------------------------------------------------------------------------	28	novel
seed	--------------------GGUUAUC------------------------------------------------------------------------	16	novel
seed	---------------------GUUAUCU-----------------------------------------------------------------------	15	novel
seed	------------------------------------------------------AUAAAGC--------------------------------------	12	novel
seed	-----------------------------------------------------------GCUAGAU---------------------------------	8	novel
seed	-----------------------------------------------------CAUAAAG---------------------------------------	5	novel
seed	---------------UCUUUGG-----------------------------------------------------------------------------	4	novel
seed	------------------------------------------------------------CUAGAUA--------------------------------	2	novel
seed	-------------UAUCUUU-------------------------------------------------------------------------------	1	novel
seed	-------------------------------------------------------------UAGAUAA-------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	---------------TCTTTGGTTATCTAGCTGT-----------------------------------------------------------------	19	11611	5405	10	9	4	9	11	29	47	56
	---------------TCTTTGGTTATCTAGCTG------------------------------------------------------------------	18	10644	4871	4	4	10	10	23	14	22	67
	---------------TCTTTGGTTATCTAGCTGTA----------------------------------------------------------------	20	6393	2672	3	1	4	7	7	11	26	45
	-------------------------------------------------------TAAAGCTAGATAACCGAAAG------------------------	20	4966	2755	1	1	8	3	8	10	50	64
	-------------------------------------------------------TAAAGCTAGATAACCGAAAGT-----------------------	21	3457	1672	5	1	1	3	9	2	21	33
	-------------------------------------------------------TAAAGCTAGATAACCGAA--------------------------	18	2214	1045	1	2	3	4	11	4	15	37
	---------------TCTTTGGTTATCTAGCTGTATG--------------------------------------------------------------	22	2189	789	4	2	4	3	2	7	15	16
	----------------CTTTGGTTATCTAGCTGTA----------------------------------------------------------------	19	1561	762	-	1	-	-	-	2	4	6
rno-miR-9	---------------TCTTTGGTTATCTAGCTGTATGA-------------------------------------------------------------	23	1579	575	3	2	-	3	1	2	-	11
	-------------------------------------------------------TAAAGCTAGATAACCGAAAGTAAA--------------------	24	1353	765	-	-	1	2	1	2	5	10
	-------------------------------------------------------TAAAGCTAGATAACCGAAA-------------------------	19	1241	753	2	-	-	1	4	6	10	20
	---------------TCTTTGGTTATCTAGCTGTAT---------------------------------------------------------------	21	1402	573	8	-	2	5	3	3	7	6
rno-miR-9*	------------------------------------------------------ATAAAGCTAGATAACCGAAAGT-----------------------	22	1016	778	1	1	-	-	1	-	4	6
	-------------------------------------------------------TAAAGCTAGATAACCGAAAGTA----------------------	22	987	407	-	1	-	-	3	1	5	13
	-------------------------------------------------------TAAAGCTAGATAACCGAAAGTAA---------------------	23	688	352	-	-	-	1	2	1	-	3
	------------------------------------------------------ATAAAGCTAGATAACCGAAAG------------------------	21	641	334	-	-	-	1	-	-	6	1
	------------------------------------------------------ATAAAGCTAGATAACCGAA--------------------------	19	596	365	-	-	-	-	1	1	4	3
	----------------CTTTGGTTATCTAGCTGTATGA-------------------------------------------------------------	22	677	247	1	-	-	1	1	-	-	1
	------------------------------------------------------ATAAAGCTAGATAACCGAAA-------------------------	20	222	144	2	-	-	1	-	-	2	1
	----------------CTTTGGTTATCTAGCTGTAT---------------------------------------------------------------	20	227	122	-	1	-	-	-	-	3	2
	------------------------------------------------------ATAAAGCTAGATAACCGA---------------------------	18	220	122	-	-	-	-	3	-	3	1
	--------------------------------------------------------AAAGCTAGATAACCGAAAGT-----------------------	20	205	82	-	-	-	-	1	1	2	1
	--------------------------------------------------------AAAGCTAGATAACCGAAAG------------------------	19	131	83	-	-	-	-	1	-	3	-
	----------------CTTTGGTTATCTAGCTGT-----------------------------------------------------------------	18	139	69	-	-	-	-	-	-	-	1
	----------------CTTTGGTTATCTAGCTGTATG--------------------------------------------------------------	21	108	37	-	1	1	-	-	-	-	-
	-----------------TTTGGTTATCTAGCTGTATGA-------------------------------------------------------------	21	83	41	-	-	-	-	-	-	-	-
	---------------TCTTTGGTTATCTAGCTGTATGAG------------------------------------------------------------	24	64	10	-	-	-	-	-	-	-	-
	-----------------TTTGGTTATCTAGCTGTA----------------------------------------------------------------	18	49	24	-	-	-	-	-	-	-	-
	--------------------------------------------------------AAAGCTAGATAACCGAAA-------------------------	18	37	27	-	-	-	-	-	-	-	-
	--------------------------------------------------------AAAGCTAGATAACCGAAAGTA----------------------	21	37	17	-	-	-	-	-	-	-	-
	--------------------------------------------------------AAAGCTAGATAACCGAAAGTAAA--------------------	23	33	15	-	-	-	-	-	-	-	-
	-----------------TTTGGTTATCTAGCTGTAT---------------------------------------------------------------	19	29	19	-	-	-	-	-	-	-	-
	------------------------------------------------------ATAAAGCTAGATAACCGAAAGTA----------------------	23	25	17	-	-	-	-	-	-	-	-
	--------------------------------------------------------AAAGCTAGATAACCGAAAGTAA---------------------	22	22	16	-	-	-	-	-	-	-	-
	------------------------------------------------------ATAAAGCTAGATAACCGAAAGTAA---------------------	24	18	13	-	-	-	-	-	-	-	-
	-------------------------------------------------------TAAAGCTAGATAACCGAAAGTAAAA-------------------	25	9	15	-	-	-	-	-	-	-	-
	---------------------------------------------------------AAGCTAGATAACCGAAAGT-----------------------	19	18	4	-	-	-	-	-	-	-	-
	------------------TTGGTTATCTAGCTGTATGA-------------------------------------------------------------	20	12	6	-	-	1	-	-	-	-	-
	--------------------GGTTATCTAGCTGTATGA-------------------------------------------------------------	18	1	1	-	2	3	3	3	-	-	2
	-----------------TTTGGTTATCTAGCTGTATG--------------------------------------------------------------	20	13	2	-	-	-	-	-	-	-	-
	-------------------TGGTTATCTAGCTGTATGA-------------------------------------------------------------	19	2	1	4	1	2	1	-	-	2	-
	-----------------TTTGGTTATCTAGCTGTATGAG------------------------------------------------------------	22	9	1	-	-	-	-	-	-	-	-
	-----------------------------------------------------CATAAAGCTAGATAACCGAAA-------------------------	21	3	5	-	-	-	-	-	-	-	-
	----------------CTTTGGTTATCTAGCTGTATGAG------------------------------------------------------------	23	6	1	-	-	-	-	-	-	-	-
	---------------------------------------------------------AAGCTAGATAACCGAAAGTA----------------------	20	4	2	-	-	-	-	-	-	-	1
	----------------------------------------------------------AGCTAGATAACCGAAAGT-----------------------	18	2	3	-	-	-	-	-	-	-	-
	------------------TTGGTTATCTAGCTGTAT---------------------------------------------------------------	18	1	3	-	-	-	-	-	-	-	-
	------------------TTGGTTATCTAGCTGTATG--------------------------------------------------------------	19	2	2	-	-	-	-	-	-	-	-
	-------------------TGGTTATCTAGCTGTATG--------------------------------------------------------------	18	1	-	-	-	2	-	-	-	-	-
	-----------------------------------------------------CATAAAGCTAGATAACCGAA--------------------------	20	3	-	-	-	-	-	-	-	-	-
	---------------------------------------------------------AAGCTAGATAACCGAAAG------------------------	18	3	-	-	-	-	-	-	-	-	-
	----------------------------------------------------TCATAAAGCTAGATAACCGAAA-------------------------	22	2	-	-	-	-	-	-	-	-	-
	----------------------------------------------------TCATAAAGCTAGATAACCGA---------------------------	20	2	-	-	-	-	-	-	-	-	-
	---------------------------------------------------------AAGCTAGATAACCGAAAGTAA---------------------	21	1	1	-	-	-	-	-	-	-	-
	--------------ATCTTTGGTTATCTAGCTGT-----------------------------------------------------------------	20	2	-	-	-	-	-	-	-	-	-
	-----------------TTTGGTTATCTAGCTGTATGAGT-----------------------------------------------------------	23	2	-	-	-	-	-	-	-	-	-
	-----------------------------------------------------------GCTAGATAACCGAAAGTA----------------------	18	1	1	-	-	-	-	-	-	-	-
	----------------------------------------------------TCATAAAGCTAGATAACC-----------------------------	18	1	-	-	-	-	-	-	-	-	-
	----------------------------------------------------------AGCTAGATAACCGAAAGTAAA--------------------	21	1	-	-	-	-	-	-	-	-	-
	----------------------------------------------------------AGCTAGATAACCGAAAGTA----------------------	19	-	1	-	-	-	-	-	-	-	-
	------------------TTGGTTATCTAGCTGTATGAG------------------------------------------------------------	21	-	1	-	-	-	-	-	-	-	-
	--------------ATCTTTGGTTATCTAGCT-------------------------------------------------------------------	18	1	-	-	-	-	-	-	-	-	-
	------------TTATCTTTGGTTATCTAGCTG------------------------------------------------------------------	21	1	-	-	-	-	-	-	-	-	-
	------------------------------------------------------------CTAGATAACCGAAAGTAA---------------------	18	1	-	-	-	-	-	-	-	-	-
	-----------------------------------------------------CATAAAGCTAGATAACCGAAAG------------------------	22	1	-	-	-	-	-	-	-	-	-
	--------------ATCTTTGGTTATCTAGCTG------------------------------------------------------------------	19	-	1	-	-	-	-	-	-	-	-
	----------------------------------------------------------AGCTAGATAACCGAAAGTAA---------------------	20	1	-	-	-	-	-	-	-	-	-
rat	CGGGGTTGGTTGTTATCTTTGGTTATCTAGCTGTATGAGTGGTGTGGAGTCTTCATAAAGCTAGATAACCGAAAGTAAAAATAACCCCA----------
human	---------------TCTTTGGTTATCTAGCTGTATGAGTGGTGTGGAGTCTTCATAAAGCTAGATAACCGAAAG------------------------
mouse	-GGGGTTGGTTGTTATCTTTGGTTATCTAGCTGTATGAGTGGTGTGGAGTCTTCATAAAGCTAGATAACCGAAAGTAAAAATAACCCCATACACTGCGC
	************************************************************
	.....>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .....	ENSRNOT00000053674 ENSRNOG00000035551 rno-mir-9-1
rat	.(((((((....(((..(((((((((((((((.((((((.((.......)))))))).)))))))))))))))..)))...))))))).	1.000 -42.00
human	..(((((((((((((((.((((((.((.......)))))))).)))))))))))))))..	1.000 -26.30
mouse	(((((((....(((..(((((((((((((((.((((((.((.......)))))))).)))))))))))))))..)))...)))))))...........	1.000 -41.70

rat	chromosome:2:180293009:180293097:1	Same_strand\|Boundary_non-coding\|ENSRNOT00000053674\|ENSRNOG00000035551 ## Same_strand\|Exonic_non-coding\|ENSRNOT00000053674\|ENSRNOG00000035551 ## ENSRNOG00000035551\|miRNA\|rno-mir-9-1\|rno-mir-9-1 [Source:miRBase;Acc:MI0000838] ## {SimpF: oe = 0.80 1 CpG} ## {MIR: rno-mir-9-1}
human	chromosome:1:154656737:154656865:-1	Same_strand\|Intronic_coding\|ENST00000368244\|ENSG00000125462\|protein_coding\|Protein CROC-4 (Contingent replication of cDNA 4) [Source:UniProtKB/Swiss-Prot;Acc:Q13536] ## Same_strand\|Boundary_non-coding\|ENST00000368242\|ENSG00000125462\|protein_coding\|Protein CROC-4 (Contingent replication of cDNA 4) [Source:UniProtKB/Swiss-Prot;Acc:Q13536] ## Same_strand\|Intronic_non-coding\|ENST00000368243\|ENSG00000125462\|protein_coding\|Protein CROC-4 (Contingent replication of cDNA 4) [Source:UniProtKB/Swiss-Prot;Acc:Q13536] ## {SimpF: rank = 1 1 FirstEF,oe = 0.88 0 CpG} ## {MIR: hsa-mir-9-1}
mouse	chromosome:3:88019521:88019618:1	Same_strand\|Boundary_non-coding\|ENSMUST00000083570\|ENSMUSG00000065504\|miRNA\|mmu-mir-9-1 [Source:miRBase;Acc:MI0000720] ## {SimpF: oe = 0.80 1 CpG} ## {MIR: mmu-mir-9-1}

miR-Intess™

rno-mir-9

sblock2007 (miRBase rno-mir-9-3) [miRNAknown_lenNOK_cloningHIGH_multiarm_DicerNOK_randfoldOK]

sblock5961 (miRBase rno-mir-9-2) [miRNAknown_lenNOK_cloningHIGH_multiarm_DicerNOK_randfoldOK]

sblock6529 (miRBase rno-mir-9-1) [miRNAknown_lenNOK_cloningHIGH_multiarm_DicerNOK_randfoldOK]