miR-Intess™

confident miRBase miRNAs

miRNAknown_cloningHIGH_multiarm_DicerOK_randfoldOK (58 loci)

rno-mir-345

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-345 5arm	2126	1652	967	737	1282	857	1289	1035	1475	1588
rno-mir-345 3arm	77	48	23	15	26	25	37	26	67	76
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-345 5arm	0.071	0.072	0.052	0.044	0.062	0.065	0.100	0.054	0.097	0.106
rno-mir-345 3arm	0.003	0.002	0.001	0.001	0.001	0.002	0.003	0.001	0.004	0.005

sblock10433 (miRBase rno-mir-345) [miRNAknown_cloningHIGH_multiarm_DicerOK_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-345

0.002

no

no

0.52/0.65

18/24/0.71

0.5 0.0 0.1 0.0

0.7 0.0 0.5 0.0

6425 1 223 1

0 0 0 0

10 1 10 1

0 0 0 0

15 30 21 1

5 -9 8 29

5arm 5arm_loop_3arm 3arm 3arm

1 1 1 1

nd nd nd nd

0.14 0.24 0.16 0.62

1 3 1 11

13428

10

2

2

Families

Member of family miR-345 (seed GCUGACC): rno-mir-345, block1421300_cand

		reads	miRBase family seed
seed	----------------GCUGACC-------------------------------------------------------------------------	7581	miR-345
seed	-----------------CUGACCC------------------------------------------------------------------------	5353	novel
seed	-------------------------------------------------------CUGAACU----------------------------------	314	novel
seed	------------------------------------------------------CCUGAAC-----------------------------------	103	miR-345
seed	-------------------GACCCCU----------------------------------------------------------------------	67	novel
seed	--------------------ACCCCUA---------------------------------------------------------------------	4	novel
seed	-------------------------------AGUGCUU----------------------------------------------------------	1	novel
seed	--------------------------------------------------------UGAACUA---------------------------------	1	novel
seed	---------------UGCUGAC--------------------------------------------------------------------------	1	novel
seed	------------------UGACCCC-----------------------------------------------------------------------	1	novel
seed	---------------------------------------------------------GAACUAG--------------------------------	1	novel
seed	---------------------------------------------------------------------------CCUGGGU--------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	----------------GCTGACCCCTAGTCCAGTGCT-----------------------------------------------------------	21	559	517	120	84	228	156	254	287	455	360
rno-miR-345-5p	---------------TGCTGACCCCTAGTCCAGTGC------------------------------------------------------------	21	346	200	252	191	269	165	294	165	244	244
	---------------TGCTGACCCCTAGTCCAGTGCT-----------------------------------------------------------	22	134	209	120	97	196	139	164	43	168	176
	---------------TGCTGACCCCTAGTCCAG---------------------------------------------------------------	18	208	125	139	103	152	101	156	114	99	154
	---------------TGCTGACCCCTAGTCCAGTG-------------------------------------------------------------	20	174	129	118	90	111	77	135	132	120	159
	---------------TGCTGACCCCTAGTCCAGT--------------------------------------------------------------	19	216	102	98	78	123	86	107	59	105	122
	----------------GCTGACCCCTAGTCCAGTGC------------------------------------------------------------	20	209	128	39	24	64	55	82	86	122	152
	----------------GCTGACCCCTAGTCCAGT--------------------------------------------------------------	18	169	120	41	22	63	44	56	77	86	113
	----------------GCTGACCCCTAGTCCAGTG-------------------------------------------------------------	19	84	104	23	20	50	24	26	54	48	76
	------------------------------------------------------CCTGAACTAGGGGTCTGGAG----------------------	20	24	14	6	3	6	10	13	3	24	10
	------------------------------------------------------CCTGAACTAGGGGTCTGGAGA---------------------	21	17	12	4	7	4	5	8	12	13	19
	---------------TGCTGACCCCTAGTCCAGTGCTT----------------------------------------------------------	23	5	7	13	15	8	4	7	-	7	7
	----------------GCTGACCCCTAGTCCAGTGCTT----------------------------------------------------------	22	9	6	2	8	10	4	7	5	5	15
	-----------------------------------------------------CCCTGAACTAGGGGTCTGGAG----------------------	21	12	5	4	-	4	4	2	1	3	15
	------------------------------------------------------CCTGAACTAGGGGTCTGGA-----------------------	19	10	7	2	2	3	3	4	1	7	10
	------------------------------------------------------CCTGAACTAGGGGTCTGGAGAC--------------------	22	3	3	3	1	2	-	2	2	5	4
	------------------------------------------------------CCTGAACTAGGGGTCTGG------------------------	18	2	2	-	-	2	-	4	4	7	4
	-----------------------------------------------------CCCTGAACTAGGGGTCTGGA-----------------------	20	2	1	1	1	2	2	2	-	4	6
	------------------TGACCCCTAGTCCAGTGCTTGT--------------------------------------------------------	22	6	1	-	-	1	1	-	5	1	5
	------------------TGACCCCTAGTCCAGTGC------------------------------------------------------------	18	1	2	1	3	1	-	1	1	6	2
	-----------------------------------------------------CCCTGAACTAGGGGTCTGG------------------------	19	1	2	1	-	1	1	-	2	1	4
	------------------TGACCCCTAGTCCAGTGCT-----------------------------------------------------------	19	3	-	-	-	2	1	-	1	4	-
	-----------------------------------------------------CCCTGAACTAGGGGTCTG-------------------------	18	4	2	1	1	-	-	-	1	1	1
	------------------TGACCCCTAGTCCAGTGCTT----------------------------------------------------------	20	3	2	-	-	1	-	-	4	-	-
	------------------TGACCCCTAGTCCAGTGCTTG---------------------------------------------------------	21	-	-	-	-	-	-	-	1	4	1
rno-miR-345-3p	-----------------------------------------------------CCCTGAACTAGGGGTCTGGAGA---------------------	22	2	-	1	-	-	-	1	-	-	2
	-------------------GACCCCTAGTCCAGTGCT-----------------------------------------------------------	18	-	-	-	2	-	-	-	-	-	1
	-----------------------------------------------------CCCTGAACTAGGGGTCTGGAGAC--------------------	23	-	-	-	-	-	-	1	-	-	1
	------------------TGACCCCTAGTCCAGTGCTTGTG-------------------------------------------------------	23	-	-	-	-	1	-	-	-	-	1
	-------------------GACCCCTAGTCCAGTGCTTGT--------------------------------------------------------	21	-	-	-	-	1	-	-	-	-	-
	------------------------------CAGTGCTTGTGGTGGCTACTG---------------------------------------------	21	-	-	1	-	-	-	-	-	-	-
	------------------------------------------------------CCTGAACTAGGGGTCTGGAGACC-------------------	23	-	-	-	-	1	-	-	-	-	-
	--------------------------------------------------------------------------ACCTGGGTTTGATCTCCACAG-	21	-	-	-	-	-	-	-	-	1	-
	--------------CTGCTGACCCCTAGTCCAGTGC------------------------------------------------------------	22	-	-	-	-	-	-	-	-	1	-
	--------------------------------------------------------TGAACTAGGGGTCTGGAG----------------------	18	-	-	-	-	1	-	-	-	-	-
	-----------------CTGACCCCTAGTCCAGTGCT-----------------------------------------------------------	20	-	-	-	-	1	-	-	-	-	-
	----------------GCTGACCCCTAGTCCAGTGCTTGT--------------------------------------------------------	24	-	-	-	-	-	-	-	1	-	-
	-------------------------------------------------------CTGAACTAGGGGTCTGGAGA---------------------	20	-	-	-	-	-	-	-	-	1	-
rat	ACCCAAGTCCAGGCCTGCTGACCCCTAGTCCAGTGCTTGTGGTGGCTACTGGGCCCTGAACTAGGGGTCTGGAGACCTGGGTTTGATCTCCACAGG
mouse	---CAAGTCCAGGCCTGCTGACCCCTAGTCCAGTGCTTGTGGTGGCTACTGGGCCCTGAACTAGGGGTCTGGAGACCTGGGTTTGATCTCCA----
	*****************************************************************************************
	.....>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.....	ENSRNOT00000053741 ENSRNOG00000035618 rno-mir-345
rat	...(((..(((((.((.(.((((((((((.(((.((((((((...)))).)))).))).)))))))))).).)).)))))..)))...........	1.000 -47.60
mouse	(((..(((((.((.((((((((((((.(((.((((((((...)))).)))).))).)))))))))).)))).)))))..))).......	0.999 -45.00

rat	chromosome:6:133178806:133178901:1	Same_strand|Exonic_non-coding|ENSRNOT00000053741|ENSRNOG00000035618 ## ENSRNOG00000035618|miRNA|rno-mir-345|rno-mir-345 [Source:miRBase;Acc:MI0000631] ## {MIR: rno-mir-345}
mouse	chromosome:12:110075186:110075274:1	Same_strand|Exonic_non-coding|ENSMUST00000083495|ENSMUSG00000065429|miRNA|mmu-mir-345 [Source:miRBase;Acc:MI0000632] ## {MIR: mmu-mir-345}

rno-mir-337

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-337 5arm	1371	1031	25	17	36	34	14	9	1	14
rno-mir-337 3arm	1829.500	1635.500	21.500	10	41.500	44.500	27	29.500	5	15
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-337 5arm	0.046	0.045	0.001	0.001	0.002	0.003	0.001	0.000	0.000	0.001
rno-mir-337 3arm	0.061	0.071	0.001	0.001	0.002	0.003	0.002	0.002	0.000	0.001

sblock10439 (miRBase rno-mir-337) [miRNAknown_cloningHIGH_multiarm_DicerOK_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-337

0.001

no

no

0.38/0.67

18/24/0.73

0.0 0.0 0.2

1.0 0.0 1.5

1785 1 2836

0 0 0

10 1 10

0 0 0

28 50 14

1 -18 2

5arm_loop 5arm_loop_3arm 3arm

1 1 1

nd nd nd

0.05 0.42 0.10

1 6 1

6264

10

1

3

Clusters

Located in cluster 65: rno-mir-337, rno-mir-540, hsa-mir-665

		reads	miRBase family seed
seed	----------------------------------------------------------------------------CAGCUCC-------------------------------------------------	2713	novel
seed	--------------------------------------------GGCGUCA---------------------------------------------------------------------------------	2116	novel
seed	---------------------------------------------------------------------------UCAGCUC--------------------------------------------------	832	miR-337
seed	-----------------------------------------AACGGCG------------------------------------------------------------------------------------	217	novel
seed	------------------------------------------ACGGCGU-----------------------------------------------------------------------------------	148	novel
seed	------------------------------------------------------------------------------GCUCCUA-----------------------------------------------	142	novel
seed	----------------------------------------GAACGGC-------------------------------------------------------------------------------------	36	novel
seed	-----------------------------------------------------------------------------AGCUCCU------------------------------------------------	20	novel
seed	-------------------------------------------CGGCGUC----------------------------------------------------------------------------------	17	novel
seed	---------------------------------------------GCGUCAU--------------------------------------------------------------------------------	17	novel
seed	---------------------------------------------------------------------------------CCUAUAU--------------------------------------------	2	novel
seed	--------------------------------------------------------------------------------UCCUAUA---------------------------------------------	2	novel
seed	------------------------------------------------------------------CACAGCC-----------------------------------------------------------	1	novel
seed	----------------------------------------------------------------------GCCAUUC-------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	---------------------------------------------------------------------------TCAGCTCCTATATGATGCCT-------------------------------------	20	413	383	5	2	15	8	7	12	2	3
	---------------------------------------------------------------------------TCAGCTCCTATATGATGCC--------------------------------------	19	413	326	7	3	14	11	5	6	1	9
	---------------------------------------------------------------------------TCAGCTCCTATATGATGCCTTTC----------------------------------	23	368	346	3	3	8	15	8	8	1	2
	-------------------------------------------CGGCGTCATGCAGGAGTTGA---------------------------------------------------------------------	20	342	243	11	5	14	6	5	3	-	6
	--------------------------------------------------------------------------TTCAGCTCCTATATGATGCCT-------------------------------------	21	305	282	2	-	2	2	3	2	-	-
	-------------------------------------------CGGCGTCATGCAGGAGTTGAT--------------------------------------------------------------------	21	297	233	3	2	3	8	3	2	-	1
	-------------------------------------------CGGCGTCATGCAGGAGTTGATT-------------------------------------------------------------------	22	265	168	6	3	9	11	5	1	-	6
	-------------------------------------------CGGCGTCATGCAGGAGTT-----------------------------------------------------------------------	18	127	97	2	1	7	4	-	2	1	1
	-------------------------------------------CGGCGTCATGCAGGAGTTG----------------------------------------------------------------------	19	110	85	3	5	-	-	1	-	-	-
	---------------------------------------------------------------------------TCAGCTCCTATATGATGCCTT------------------------------------	21	76	78	2	-	1	1	1	-	-	1
	--------------------------------------------------------------------------TTCAGCTCCTATATGATGCC--------------------------------------	20	70	55	1	-	-	3	-	1	-	-
	---------------------------------------------------------------------------TCAGCTCCTATATGATGC---------------------------------------	18	61	37	1	2	1	3	-	1	-	-
	-----------------------------------------------------------------------------AGCTCCTATATGATGCCT-------------------------------------	18	56	49	1	-	-	-	-	-	-	-
	----------------------------------------GAACGGCGTCATGCAGGAGT------------------------------------------------------------------------	20	29	27	-	-	-	1	-	-	-	-
	--------------------------------------------------------------------------TTCAGCTCCTATATGATGC---------------------------------------	19	28	25	-	-	-	1	1	-	-	-
	----------------------------------------GAACGGCGTCATGCAGGAGTTG----------------------------------------------------------------------	22	31	23	-	-	-	-	-	-	-	-
	-----------------------------------------AACGGCGTCATGCAGGAGTTG----------------------------------------------------------------------	21	25	15	-	1	-	-	-	-	-	-
	----------------------------------------GAACGGCGTCATGCAGGAG-------------------------------------------------------------------------	19	16	24	-	-	-	-	-	-	-	-
	---------------------------------------------------------------------------TCAGCTCCTATATGATGCCTTT-----------------------------------	22	15	23	-	1	-	1	-	-	-	-
	-----------------------------------------AACGGCGTCATGCAGGAGT------------------------------------------------------------------------	19	14	17	-	-	-	1	-	-	-	-
	-----------------------------------------AACGGCGTCATGCAGGAGTT-----------------------------------------------------------------------	20	15	12	-	-	-	-	-	1	-	-
	----------------------------------------GAACGGCGTCATGCAGGAGTT-----------------------------------------------------------------------	21	19	8	-	-	-	-	-	-	-	-
	-----------------------------------------AACGGCGTCATGCAGGAGTTGA---------------------------------------------------------------------	22	15	8	-	-	1	1	-	-	-	-
	----------------------------------------GAACGGCGTCATGCAGGAGTTGA---------------------------------------------------------------------	23	11	12	-	-	-	1	-	-	-	-
	-----------------------------------------AACGGCGTCATGCAGGAG-------------------------------------------------------------------------	18	8	14	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------------TTCAGCTCCTATATGATG----------------------------------------	18	9	7	-	-	-	-	1	-	-	-
	--------------------------------------------------------------------------TTCAGCTCCTATATGATGCCTT------------------------------------	22	8	7	-	-	-	1	-	-	-	-
	---------------------------------------GGAACGGCGTCATGCAGGAGT------------------------------------------------------------------------	21	8	7	-	-	-	-	-	-	-	-
	----------------------------------------GAACGGCGTCATGCAGGA--------------------------------------------------------------------------	18	5	10	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------------------AGCTCCTATATGATGCCTTTCT---------------------------------	22	9	5	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------------TTCAGCTCCTATATGATGCCTTTC----------------------------------	24	8	4	-	-	-	-	-	-	-	-
	---------------------------------------GGAACGGCGTCATGCAGGAGTT-----------------------------------------------------------------------	22	8	3	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------------------AGCTCCTATATGATGCCTT------------------------------------	19	5	5	-	-	-	-	1	-	-	-
	-------------------------------------------CGGCGTCATGCAGGAGTTGATTGC-----------------------------------------------------------------	24	5	2	-	-	1	-	-	-	-	-
	----------------------------------------------------------------------------CAGCTCCTATATGATGCCTTTC----------------------------------	22	1	6	-	-	1	-	-	-	-	-
	------------------------------------------ACGGCGTCATGCAGGAGTTGA---------------------------------------------------------------------	21	2	2	-	-	1	1	-	-	-	-
	------------------------------------------ACGGCGTCATGCAGGAGT------------------------------------------------------------------------	18	2	4	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------------------AGCTCCTATATGATGCCTTTC----------------------------------	21	3	3	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------------CAGCTCCTATATGATGCC--------------------------------------	18	2	4	-	-	-	-	-	-	-	-
	---------------------------------------GGAACGGCGTCATGCAGGAG-------------------------------------------------------------------------	20	3	2	-	-	-	-	-	-	-	-
	--------------------------------------------GGCGTCATGCAGGAGTTG----------------------------------------------------------------------	18	-	4	-	-	-	-	-	-	-	-
	---------------------------------------GGAACGGCGTCATGCAGG---------------------------------------------------------------------------	18	4	-	-	-	-	-	-	-	-	-
rno-miR-337	--------------------------------------------------------------------------TTCAGCTCCTATATGATGCCTTT-----------------------------------	23	3	1	-	-	-	-	-	-	-	-
	--------------------------------------------GGCGTCATGCAGGAGTTGAT--------------------------------------------------------------------	20	2	2	-	-	-	-	-	-	-	-
	--------------------------------------------GGCGTCATGCAGGAGTTGA---------------------------------------------------------------------	19	2	2	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------------CAGCTCCTATATGATGCCTT------------------------------------	20	2	1	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------------------AGCTCCTATATGATGCCTTT-----------------------------------	20	-	2	-	-	-	-	-	-	1	-
	------------------------------------------ACGGCGTCATGCAGGAGTTG----------------------------------------------------------------------	20	1	2	-	-	-	-	-	-	-	-
	--------------------------------------------GGCGTCATGCAGGAGTTGATT-------------------------------------------------------------------	21	1	2	-	-	-	-	-	-	-	-
	------------------------------------------ACGGCGTCATGCAGGAGTT-----------------------------------------------------------------------	19	1	1	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------------------TCCTATATGATGCCTTTCTTC-------------------------------	21	-	2	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------------CAGCTCCTATATGATGCCT-------------------------------------	19	2	-	-	-	-	-	-	-	-	-
	---------------------------------------------------------------------AGCCATTCAGCTCCTATATGAT-----------------------------------------	22	1	-	-	-	-	-	-	-	-	-
	--------------------------------------------GGCGTCATGCAGGAGTTGATTG------------------------------------------------------------------	22	1	-	-	-	-	-	-	-	-	-
	-------------------------------------------------------------------------------CTCCTATATGATGCCTTTCTTC-------------------------------	22	1	-	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------------------AGCTCCTATATGATGCCTTTCTTC-------------------------------	24	1	-	-	-	-	-	-	-	-	-
	-------------------------------------------CGGCGTCATGCAGGAGTTGATTG------------------------------------------------------------------	23	-	1	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------GCACAGCCATTCAGCTCCT------------------------------------------------	19	-	1	-	-	-	-	-	-	-	-
	---------------------------------------GGAACGGCGTCATGCAGGA--------------------------------------------------------------------------	19	1	-	-	-	-	-	-	-	-	-
	-------------------------------------------------------------------------------CTCCTATATGATGCCTTTC----------------------------------	19	-	1	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------------CAGCTCCTATATGATGCCTTT-----------------------------------	21	-	1	-	-	-	-	-	-	-	-
	--------------------------------------------GGCGTCATGCAGGAGTTGATTGC-----------------------------------------------------------------	23	1	-	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------------------AGCTCCTATATGATGCCTTTCTT--------------------------------	23	-	1	-	-	-	-	-	-	-	-
rat	---------------AGTGTAGTGAGAAGTTGGGGGGTGGGAACGGCGTCATGCAGGAGTTGATTGCACAGCCATTCAGCTCCTATATGATGCCTTTCTTCACCCCCTTCAA--------------------
mouse	GGAGAGGAGGGTCCCAGTGTAGTGAGAAGTTGGGGGGTGGGAACGGCGTCATGCAGGAGTTGATTGCACAGCCATTCAGCTCCTATATGATGCCTTTCTTCACCCCCTTCAACCGCGTGAGGCCTCCGGACC
	*************************************************************************************************
	.....               >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>                    .....	ENSRNOT00000053650 ENSRNOG00000035527 rno-mir-337
rat	.............(..((((((((((((.(((((((((.(((((((((.((......)).))))))))).))))))))).))).))))))))).)..	1.000 -49.60
mouse	((...(((((..(((((((...(((......((((((((((((.(((((((((.(((((((((.((......)).))))))))).))))))))).)))).)))))))))))..))).)).)))))))...))	0.999 -64.70

rat	chromosome:6:134176751:134176847:1	Same_strand|Exonic_non-coding|ENSRNOT00000053650|ENSRNOG00000035527 ## ENSRNOG00000035527|miRNA|rno-mir-337|rno-mir-337 [Source:miRBase;Acc:MI0000614] ## {MIR: rno-mir-337}
mouse	chromosome:12:110823985:110824116:1	Same_strand|Boundary_non-coding|ENSMUST00000083592|ENSMUSG00000065526|miRNA|mmu-mir-337 [Source:miRBase;Acc:MI0000615] ## {MIR: mmu-mir-337}

rno-mir-434

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-434 5arm	3501	2775	17	8	28	30	8	13	10	14
rno-mir-434 3arm	14670	11422	105	30	83	94	66	77	41	45
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-434 5arm	0.116	0.121	0.001	0.000	0.001	0.002	0.001	0.001	0.001	0.001
rno-mir-434 3arm	0.488	0.498	0.006	0.002	0.004	0.007	0.005	0.004	0.003	0.003

sblock10444 (miRBase rno-mir-434) [miRNAknown_cloningHIGH_multiarm_DicerOK_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-434

0.002

no

no

0.42/0.56

18/25/0.70

0.1 0.0

1.1 1.4

4211 20762

0 0

10 10

0 0

11 10

3 7

5arm 3arm

1 1

nd nd

0.22 0.22

2 2

33037

10

3

3

Clusters

Located in cluster 67: rno-mir-434, rno-mir-136

		reads	miRBase family seed
seed	--------------------------------------------------UUGAACC------------------------	25769	miR-434
seed	------------GCUCGAC--------------------------------------------------------------	4923	novel
seed	-------------CUCGACU-------------------------------------------------------------	1478	novel
seed	---------------------------------------------------UGAACCA-----------------------	687	novel
seed	-------------------------------------------------UUUGAAC-------------------------	153	novel
seed	----------------------------------------------------GAACCAU----------------------	11	novel
seed	-----------------------------------------------------AACCAUC---------------------	11	novel
seed	--------------UCGACUC------------------------------------------------------------	3	novel
seed	------------------------------------------------------ACCAUCA--------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-miR-434	-------------------------------------------------TTTGAACCATCACTCGACTCCT----------	22	7454	5936	42	11	44	34	34	36	21	25
	-------------------------------------------------TTTGAACCATCACTCGAC--------------	18	4154	3218	38	10	21	23	13	26	9	11
	-------------------------------------------------TTTGAACCATCACTCGACTCC-----------	21	1729	1347	15	5	8	20	14	9	5	2
	-----------AGCTCGACTCATGGTTTGAACC------------------------------------------------	22	854	659	8	2	8	8	1	3	2	5
	-----------AGCTCGACTCATGGTTTGAACCA-----------------------------------------------	23	818	626	1	1	2	1	-	-	2	1
	-----------AGCTCGACTCATGGTTTGA---------------------------------------------------	19	517	422	1	2	4	2	1	5	1	1
	-------------------------------------------------TTTGAACCATCACTCGACTC------------	20	494	369	5	2	2	9	3	2	1	1
	------------GCTCGACTCATGGTTTGAACCA-----------------------------------------------	22	315	227	1	-	4	7	1	-	2	2
	--------------------------------------------------TTGAACCATCACTCGACTCCT----------	21	311	218	1	-	-	-	1	2	2	1
	------------GCTCGACTCATGGTTTGAACC------------------------------------------------	21	250	207	3	1	2	7	1	2	-	-
	-------------------------------------------------TTTGAACCATCACTCGACT-------------	19	288	151	3	1	5	7	1	2	1	4
	-----------AGCTCGACTCATGGTTTG----------------------------------------------------	18	230	205	-	-	4	3	2	2	1	2
	-----------AGCTCGACTCATGGTTTGAAC-------------------------------------------------	21	169	160	1	-	2	1	-	-	-	-
	------------GCTCGACTCATGGTTTGA---------------------------------------------------	18	105	84	1	1	1	-	-	-	-	1
	-----------AGCTCGACTCATGGTTTGAA--------------------------------------------------	20	105	72	-	-	-	1	1	1	1	1
	------------GCTCGACTCATGGTTTGAAC-------------------------------------------------	20	82	67	-	1	1	-	1	-	1	-
	--------------------------------------------------TTGAACCATCACTCGACTCC-----------	20	55	51	1	-	1	-	-	-	-	-
	------------GCTCGACTCATGGTTTGAA--------------------------------------------------	19	53	45	1	-	-	-	-	-	-	1
	-------------------------------------------------TTTGAACCATCACTCGACTCCTG---------	23	57	35	-	-	-	1	-	-	1	-
	------------------------------------------------GTTTGAACCATCACTCGACTCC-----------	22	38	21	-	-	-	-	-	-	-	1
	------------------------------------------------GTTTGAACCATCACTCGAC--------------	19	20	22	-	1	-	-	-	-	-	-
	------------------------------------------------GTTTGAACCATCACTCGACTCCT----------	23	21	12	-	-	-	-	-	-	-	-
	--------------------------------------------------TTGAACCATCACTCGACTC------------	19	14	12	-	-	-	-	-	-	1	-
	--------------------------------------------------TTGAACCATCACTCGACT-------------	18	7	9	-	-	-	-	-	-	-	-
	------------------------------------------------GTTTGAACCATCACTCGACTC------------	21	2	5	-	-	2	-	-	-	-	-
	----------------------------------------------------GAACCATCACTCGACTCCT----------	19	4	5	-	-	-	-	-	-	-	-
	-------------------------------------------------TTTGAACCATCACTCGACTCCTGG--------	24	8	1	-	-	-	-	-	-	-	-
	---------------------------------------------------TGAACCATCACTCGACTCCT----------	20	3	3	-	-	-	-	-	-	-	-
	------------------------------------------------GTTTGAACCATCACTCGACT-------------	20	2	3	-	-	-	-	-	-	-	-
	---------------------------------------------------TGAACCATCACTCGACTCC-----------	19	3	1	-	-	-	-	-	-	-	-
	-----------------------------------------------------AACCATCACTCGACTCCT----------	18	-	2	-	-	-	-	-	-	-	-
	----------------------------------------------------GAACCATCACTCGACTCC-----------	18	1	1	-	-	-	-	-	-	-	-
	-------------CTCGACTCATGGTTTGAACCA-----------------------------------------------	21	2	-	-	-	-	-	-	-	-	-
	------------------------------------------------GTTTGAACCATCACTCGA---------------	18	2	-	-	-	-	-	-	-	-	-
	-------------------------------------------------TTTGAACCATCACTCGACTCCTGGT-------	25	1	-	-	-	-	-	-	-	-	-
	---------------------------------------------------TGAACCATCACTCGACTC------------	18	1	-	-	-	-	-	-	-	-	-
	-------------CTCGACTCATGGTTTGAACC------------------------------------------------	20	1	-	-	-	-	-	-	-	-	-
	-----------AGCTCGACTCATGGTTTGAACCAT----------------------------------------------	24	-	1	-	-	-	-	-	-	-	-
	------------------------------------------------GTTTGAACCATCACTCGACTCCTG---------	24	1	-	-	-	-	-	-	-	-	-
rat	GTTTGAACCACAGCTCGACTCATGGTTTGAACCATTGTCAAACTCGTGGTTTGAACCATCACTCGACTCCTGGTTTGAATC
mouse	---------AAAGCTCGACTCATGGTTTGAACCATTACTTAATTCGTGGTTTGAACCATCACTCGACTCCT----------
	* *************************    ** ****************************
	.....>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.....	ENSRNOT00000062197 ENSRNOG00000040444 rno-mir-434
rat	(((..(((((.((.((((.(.((((((..((((((.(.....)..))))))..)))))).).))))))..)))))..))).	1.000 -29.80
mouse	..((.((((...((((((..((((((..........))))))..))))))...))))))...	1.000 -20.20

rat	chromosome:6:134186260:134186340:1	Same_strand|Exonic_non-coding|ENSRNOT00000062197|ENSRNOG00000040444 ## Same_strand|Boundary_non-coding|ENSRNOT00000062197|ENSRNOG00000040444 ## ENSRNOG00000040444|miRNA|rno-mir-434|rno-mir-434 [Source:miRBase;Acc:MI0006147] ## {Repeats: trf 87 109 0 class=trf,trf 22 48 0 class=trf,trf 61 85 0 class=trf} ## {MIR: rno-mir-434}
mouse	chromosome:12:110832706:110832826:1	Opposite_strand|Exonic_coding|ENSMUST00000118502|ENSMUSG00000081425|protein_coding|Retrotransposon-like protein 1 (Retrotransposon-derived protein PEG11)(Paternally expressed gene 11 protein)(Mammalian retrotransposon derived protein 1) [Source:UniProtKB/Swiss-Prot;Acc:Q7M732] ## Same_strand|Boundary_non-coding|ENSMUST00000093625|ENSMUSG00000070133|miRNA|mmu-mir-434 [Source:miRBase;Acc:MI0001526] ## {Repeats: trf 0 class=trf} ## {MIR: mmu-mir-434}

rno-mir-379

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-379 5arm	2868	1934	43	18	87	95	33	19	28	86
rno-mir-379 3arm	505	395	4	1	21	13	6	5	3	5
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-379 5arm	0.095	0.084	0.002	0.001	0.004	0.007	0.003	0.001	0.002	0.006
rno-mir-379 3arm	0.017	0.017	0.000	0.000	0.001	0.001	0.000	0.000	0.000	0.000

sblock10488 (miRBase rno-mir-379) [miRNAknown_cloningHIGH_multiarm_DicerOK_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-379

0.001

no

no

0.35/0.55

18/23/0.78

0.0 0.0

0.6 0.0

3404 515

0 0

10 10

0 0

15 12

1 5

5arm 3arm

1 1

nd nd

0.14 0.19

2 2

6169

10

3

2

		reads	miRBase family seed
seed	----------------GGUAGAC---------------------------------------------------------------	5175	miR-379
seed	------------------------------------------------------AUGUAAC-------------------------	930	novel
seed	-----------------GUAGACU--------------------------------------------------------------	35	novel
seed	-------------------------------------------------------UGUAACA------------------------	24	novel
seed	-----------------------------------------------------UAUGUAA--------------------------	2	miR-379*
seed	---------------------------------------------------------UAACAUG----------------------	2	novel
seed	--------------------GACUAUG-----------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	---------------TGGTAGACTATGGAACGTAG---------------------------------------------------	20	1129	804	19	9	30	32	14	5	9	28
rno-miR-379	---------------TGGTAGACTATGGAACGTAGG--------------------------------------------------	21	565	344	11	5	18	23	11	7	11	28
	---------------TGGTAGACTATGGAACGTAGGC-------------------------------------------------	22	562	315	1	-	22	12	1	6	1	10
	---------------TGGTAGACTATGGAACGTA----------------------------------------------------	19	314	260	4	3	13	16	5	1	6	9
	-----------------------------------------------------TATGTAACATGGTCCACTAAC------------	21	289	226	1	-	13	9	3	2	2	2
	---------------TGGTAGACTATGGAACGT-----------------------------------------------------	18	273	197	8	1	4	12	2	-	1	10
	-----------------------------------------------------TATGTAACATGGTCCACTA--------------	19	64	63	-	-	3	2	-	-	1	2
	-----------------------------------------------------TATGTAACATGGTCCACTAACTC----------	23	54	34	2	-	3	1	2	2	-	1
	-----------------------------------------------------TATGTAACATGGTCCACTAA-------------	20	41	31	1	-	1	1	1	1	-	-
	-----------------------------------------------------TATGTAACATGGTCCACT---------------	18	42	25	-	-	1	-	-	-	-	-
	------------------------------------------------------ATGTAACATGGTCCACTAAC------------	20	7	9	-	-	-	-	-	-	-	-
	----------------GGTAGACTATGGAACGTAGGC-------------------------------------------------	21	10	2	-	-	-	-	-	-	-	-
	----------------GGTAGACTATGGAACGTAG---------------------------------------------------	19	4	5	-	-	-	-	-	-	-	-
	----------------GGTAGACTATGGAACGTAGG--------------------------------------------------	20	8	1	-	-	-	-	-	-	-	-
	------------------------------------------------------ATGTAACATGGTCCACTA--------------	18	-	4	-	1	-	-	-	-	-	-
	---------------TGGTAGACTATGGAACGTAGGCG------------------------------------------------	23	1	3	-	-	-	-	-	-	-	-
	-----------------------------------------------------TATGTAACATGGTCCACTAACT-----------	22	3	1	-	-	-	-	-	-	-	-
	----------------GGTAGACTATGGAACGTA----------------------------------------------------	18	1	3	-	-	-	-	-	-	-	-
	------------------------------------------------------ATGTAACATGGTCCACTAACTC----------	22	2	1	-	-	-	-	-	-	-	-
	--------------------------------------------------------GTAACATGGTCCACTAAC------------	18	2	-	-	-	-	-	-	-	-	-
	-------------------AGACTATGGAACGTAGGC-------------------------------------------------	18	1	-	-	-	-	-	-	-	-	-
	----------------GGTAGACTATGGAACGTAGGCG------------------------------------------------	22	-	-	-	-	-	-	-	-	-	1
	----------------------------------------------------CTATGTAACATGGTCCAC----------------	18	-	1	-	-	-	-	-	-	-	-
rno-miR-379*	----------------------------------------------------CTATGTAACATGGTCCACTAAC------------	22	1	-	-	-	-	-	-	-	-	-
rat	TGGTTCCTGCAGAGGTGGTAGACTATGGAACGTAGGCGTTATG-TTTCTGACCTATGTAACATGGTCCACTAACTCTCAGTATCCA
human	---------------TGGTAGACTATGGAACGTAGGCGTTATGATTTCTGACCTATGTAACATGGTCCACTA--------------
mouse	---------------TGGTAGACTATGGAACGTAGGCGTTATG-TTTTTGACCTATGTAACATGGTCCACTA--------------
	**************************** *** ************************
	.....>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.....	ENSRNOT00000053679 ENSRNOG00000035556 rno-mir-379
rat	.((...(((.((((.((((.(((((((..(((((((((..... ....)).)))))))..))))))).)))).)))))))...)).	1.000 -33.60
human	((((.(((((((..(((((((((..........)).)))))))..))))))).))))	1.000 -21.00
mouse	((((.(((((((..(((((((((..... ....)).)))))))..))))))).))))	1.000 -21.90

rat	chromosome:6:134388198:134388282:1	Same_strand|Exonic_non-coding|ENSRNOT00000053679|ENSRNOG00000035556 ## ENSRNOG00000035556|miRNA|rno-mir-379|rno-mir-379 [Source:miRBase;Acc:MI0003541] ## {MIR: rno-mir-379}
human	chromosome:14:100558126:100558250:1	Same_strand|Boundary_non-coding|ENST00000362218|ENSG00000199088|miRNA|hsa-mir-379 [Source:miRBase;Acc:MI0000787] ## {MIR: hsa-mir-379}
mouse	chromosome:12:110947240:110947364:1	Same_strand|Boundary_non-coding|ENSMUST00000083564|ENSMUSG00000065498|miRNA|mmu-mir-379 [Source:miRBase;Acc:MI0000796] ## {MIR: mmu-mir-379}

rno-mir-411

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-411 5arm	656	95	15	7	25	24	12	7	18	41
rno-mir-411 3arm	1700	1293	6	6	45	55	18	18	20	30
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-411 5arm	0.022	0.004	0.001	0.000	0.001	0.002	0.001	0.000	0.001	0.003
rno-mir-411 3arm	0.057	0.056	0.000	0.000	0.002	0.004	0.001	0.001	0.001	0.002

sblock10489 (miRBase rno-mir-411) [miRNAknown_cloningHIGH_multiarm_DicerOK_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-411

0.007

no

no

0.40/0.53

18/24/0.71

0.4 0.0 0.0

1.0 0.0 0.7

530 1 2414

0 0 0

10 1 10

0 0 0

9 19 9

2 -3 4

5arm 3arm_loop 3arm

1 1 1

nd nd nd

0.14 0.26 0.21

1 2 1

4091

10

1

2

Clusters

Located in cluster 68: rno-mir-411, rno-mir-299

		reads	miRBase family seed
seed	------------------------------------------------------------------AUGUAAC--------------------------------------	3100	novel
seed	------------------------------UAGUAGA--------------------------------------------------------------------------	560	novel
seed	-------------------------------AGUAGAC-------------------------------------------------------------------------	296	miR-411
seed	-------------------------------------------------------------------UGUAACA-------------------------------------	70	novel
seed	--------------------------------GUAGACC------------------------------------------------------------------------	44	novel
seed	----------------------------------------------------------------GUAUGUA----------------------------------------	14	novel
seed	-----------------------------------------------------------------UAUGUAA---------------------------------------	3	miR-379*
seed	---------------------------------------------------------------------UAACACG-----------------------------------	1	novel
seed	---------------------------------------------------------------CGUAUGU-----------------------------------------	1	novel
seed	-----------------------------------------------------------GUGACGU---------------------------------------------	1	novel
seed	--------------------------------------------------------------------GUAACAC------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-----------------------------------------------------------------TATGTAACACGGTCCACTAAC-------------------------	21	582	508	2	1	17	19	2	5	8	4
	-----------------------------------------------------------------TATGTAACACGGTCCACTAACC------------------------	22	522	321	1	-	16	21	5	5	2	9
	-----------------------------------------------------------------TATGTAACACGGTCCACTA---------------------------	19	264	217	2	4	5	3	2	4	4	4
	-----------------------------------------------------------------TATGTAACACGGTCCACTAA--------------------------	20	134	101	1	1	4	7	6	2	3	5
	-----------------------------------------------------------------TATGTAACACGGTCCACT----------------------------	18	121	84	-	-	3	3	3	-	1	4
	-----------------------------ATAGTAGACCGTATAGCGT---------------------------------------------------------------	19	132	26	1	-	8	10	1	3	4	3
	-----------------------------ATAGTAGACCGTATAGCGTAC-------------------------------------------------------------	21	141	17	-	-	7	5	2	2	5	7
	------------------------------TAGTAGACCGTATAGCGTAC-------------------------------------------------------------	20	123	12	6	4	3	3	5	-	3	11
	------------------------------TAGTAGACCGTATAGCGTA--------------------------------------------------------------	19	75	2	4	-	-	1	1	-	-	6
	-----------------------------ATAGTAGACCGTATAGCG----------------------------------------------------------------	18	59	17	-	-	4	3	-	-	1	4
	-----------------------------------------------------------------TATGTAACACGGTCCACTAACCC-----------------------	23	31	24	-	-	-	1	-	1	-	1
	-----------------------------ATAGTAGACCGTATAGCGTA--------------------------------------------------------------	20	42	8	1	-	-	1	1	-	-	1
	-----------------------------ATAGTAGACCGTATAGCGTACG------------------------------------------------------------	22	27	-	-	1	1	-	1	2	1	3
	------------------------------------------------------------------ATGTAACACGGTCCACTAAC-------------------------	20	16	13	-	-	-	-	-	1	-	-
	-------------------------------AGTAGACCGTATAGCGTAC-------------------------------------------------------------	19	17	5	1	-	2	-	1	-	1	3
	------------------------------TAGTAGACCGTATAGCGT---------------------------------------------------------------	18	20	4	1	1	-	1	-	-	-	1
	------------------------------------------------------------------ATGTAACACGGTCCACTAACC------------------------	21	4	10	-	-	-	-	-	-	1	1
	------------------------------------------------------------------ATGTAACACGGTCCACTAA--------------------------	19	6	7	-	-	-	-	-	-	-	-
	------------------------------------------------------------------ATGTAACACGGTCCACTA---------------------------	18	5	5	-	-	-	-	-	-	-	-
	-------------------------------AGTAGACCGTATAGCGTA--------------------------------------------------------------	18	4	4	-	-	-	-	-	-	-	1
	-----------------------------ATAGTAGACCGTATAGCGTACGC-----------------------------------------------------------	23	5	-	1	1	-	-	-	-	-	1
rno-miR-411	------------------------------TAGTAGACCGTATAGCGTACG------------------------------------------------------------	21	5	-	-	-	-	-	-	-	2	-
	---------------------------------------------------------------CGTATGTAACACGGTCCACT----------------------------	20	4	2	-	-	-	-	-	-	-	-
	---------------------------------------------------------------CGTATGTAACACGGTCCACTA---------------------------	21	3	1	-	-	-	-	-	-	-	-
	-------------------------------AGTAGACCGTATAGCGTACG------------------------------------------------------------	20	2	-	-	-	-	-	-	-	1	-
	-------------------------------AGTAGACCGTATAGCGTACGC-----------------------------------------------------------	21	2	-	-	-	-	-	-	-	-	-
	----------------------------------------------------------------GTATGTAACACGGTCCACTAAC-------------------------	22	2	-	-	-	-	-	-	-	-	-
	------------------------------TAGTAGACCGTATAGCGTACGC-----------------------------------------------------------	22	2	-	-	-	-	-	-	-	-	-
	---------------------------------------------------------------CGTATGTAACACGGTCCA------------------------------	18	-	-	-	-	-	-	-	-	-	2
	-------------------------------------------------------------------TGTAACACGGTCCACTAACC------------------------	20	1	-	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------GTAACACGGTCCACTAACC------------------------	19	1	-	-	-	-	-	-	-	-	-
	--------------------------------------------------------------ACGTATGTAACACGGTCC-------------------------------	18	1	-	-	-	-	-	-	-	-	-
	----------------------------------------------------------------GTATGTAACACGGTCCAC-----------------------------	18	1	-	-	-	-	-	-	-	-	-
	---------------------------------------------------------------CGTATGTAACACGGTCCACTAACC------------------------	24	1	-	-	-	-	-	-	-	-	-
	------------------------------------------------------------------ATGTAACACGGTCCACTAACCC-----------------------	22	1	-	-	-	-	-	-	-	-	-
	----------------------------------------------------------TGTGACGTATGTAACACGG----------------------------------	19	-	-	-	-	-	-	-	-	1	-
	---------------------------------------------------------------CGTATGTAACACGGTCCACTAAC-------------------------	23	-	-	-	-	-	1	-	-	-	-
rat	--------------------CTTGGAGAGATAGTAGACCGTATAGCGTACGCTTTATCTGTGACGTATGTAACACGGTCCACTAACCCTCAGTATC---------------
human	CTCGGCATCTCTGTGTGGTACTTGGAGAGATAGTAGACCGTATAGCGTACGCTTTATCTGTGACGTATGTAACACGGTCCACTAACCCTCAGTATCAAATCCATCCCCGAG
mouse	CTCGGCGTCTCTGTGTGGTACTTGGAGAGATAGTAGACCGTATAGCGTACGCTTTATCTGTGACGTATGTAACACGGTCCACTAACCCTCAGTATCAAATCCATCCCCGAG
	****************************************************************************
	>>>>>                    >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>               >>>>>	ENSRNOT00000053697 ENSRNOG00000035574 rno-mir-411
rat	....(((.(.((((.((((((.(.((((((((.........).))))))).).)))))).)))).).)))......	1.000 -24.80
human	(((((..........(((((((..(((...((((.((((((...(((((((.((.......)))))))))...)))))).))))...)))))))))).........)))))	0.970 -35.41
mouse	(((((..........(((((((..(((...((((.((((((...(((((((.((.......)))))))))...)))))).))))...)))))))))).........)))))	0.995 -35.41

rat	chromosome:6:134389347:134389422:1	Same_strand|Boundary_non-coding|ENSRNOT00000053697|ENSRNOG00000035574 ## Same_strand|Exonic_non-coding|ENSRNOT00000053697|ENSRNOG00000035574 ## ENSRNOG00000035574|miRNA|rno-mir-411|rno-mir-411 [Source:miRBase;Acc:MI0006144] ## {MIR: rno-mir-411}
human	chromosome:14:100559400:100559510:1	Same_strand|Boundary_non-coding|ENST00000362239|ENSG00000199109|miRNA|hsa-mir-411 [Source:miRBase;Acc:MI0003675] ## {MIR: hsa-mir-411}
mouse	chromosome:12:110948370:110948480:1	Same_strand|Boundary_non-coding|ENSMUST00000083543|ENSMUSG00000065477|miRNA|mmu-mir-411 [Source:miRBase;Acc:MI0001163] ## {MIR: mmu-mir-411}

rno-mir-299

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-299 5arm	287.600	208.033	33.667	16	26.333	24.667	12.333	9	9.500	26
rno-mir-299 3arm	9.500	8.500	2	0	0.500	0.500	0	0	0	2
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-299 5arm	0.010	0.009	0.002	0.001	0.001	0.002	0.001	0.000	0.001	0.002
rno-mir-299 3arm	0.000	0.000	0.000	0	0.000	0.000	0	0	0	0.000

sblock10490 (miRBase rno-mir-299) [miRNAknown_cloningHIGH_multiarm_DicerOK_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-299

0.001

no

no

0.40/0.57

18/23/0.90

0.0 0.0 0.6

0.7 0.0 1.8

411 1 18

0 0 0

10 1 6

0 0 0

6 15 4

0 -7 2

5arm 3arm_loop 3arm

1 1 2

nd nd nd

0.00 0.30 0.00

0 6 0

704

10

2

2

Clusters

Located in cluster 68: rno-mir-411, rno-mir-299

Families

Member of family miR-299 (seed GGUUUAC): rno-mir-299, rno-mir-299, block89547_cand

		reads	miRBase family seed
seed	-------------------------GGUUUAC----------------------------------------------------------------	615	miR-299
seed	------------------------UGGUUUA-----------------------------------------------------------------	54	novel
seed	--------------------------------------------------------UAUGUGG---------------------------------	14	novel
seed	---------------------------------------------------------AUGUGGG--------------------------------	13	novel
seed	--------------------------GUUUACC---------------------------------------------------------------	6	novel
seed	-----------------------------------------------UUGAGUA------------------------------------------	1	novel
seed	-----------------------AUGGUUU------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-miR-299	------------------------TGGTTTACCGTCCCACATACAT--------------------------------------------------	22	138	101	11	5	18	12	3	4	4	7
	------------------------TGGTTTACCGTCCCACATAC----------------------------------------------------	20	72	49	14	3	4	3	5	2	2	6
	------------------------TGGTTTACCGTCCCACATACA---------------------------------------------------	21	51	24	3	5	2	6	4	3	-	6
	-----------------------ATGGTTTACCGTCCCACATAC----------------------------------------------------	21	11	10	1	2	-	-	-	-	1	2
	------------------------TGGTTTACCGTCCCACAT------------------------------------------------------	18	9	7	5	-	-	2	-	-	-	-
	------------------------TGGTTTACCGTCCCACATA-----------------------------------------------------	19	5	9	2	-	1	1	-	-	2	1
	-----------------------ATGGTTTACCGTCCCACATACA---------------------------------------------------	22	5	9	-	1	1	2	-	-	-	1
	--------------------------------------------------------TATGTGGGACGGTAAACCGCT-------------------	21	1	4	1	-	-	-	-	-	-	-
	-------------------------------------------------------GTATGTGGGACGGTAAACC----------------------	19	1	2	-	-	-	1	-	-	-	2
	-------------------------GGTTTACCGTCCCACATAC----------------------------------------------------	19	2	3	-	-	-	-	-	-	-	-
	------------------------TGGTTTACCGTCCCACATACATT-------------------------------------------------	23	-	-	1	-	-	-	-	-	-	3
	-------------------------------------------------------GTATGTGGGACGGTAAACCG---------------------	20	2	2	-	-	-	-	-	-	-	-
	-----------------------ATGGTTTACCGTCCCACA-------------------------------------------------------	18	3	1	-	-	-	-	-	-	-	-
	--------------------------------------------------------TATGTGGGACGGTAAACCG---------------------	19	2	-	1	-	-	-	-	-	-	-
	-------------------------------------------------------GTATGTGGGACGGTAAACCGC--------------------	21	2	-	-	-	-	-	-	-	-	1
	--------------------------------------------------------TATGTGGGACGGTAAACC----------------------	18	2	1	-	-	-	-	-	-	-	-
	-----------------------ATGGTTTACCGTCCCACAT------------------------------------------------------	19	-	-	-	-	1	-	1	-	-	-
	-----------------------ATGGTTTACCGTCCCACATA-----------------------------------------------------	20	-	2	-	-	-	-	-	-	-	-
	-------------------------GGTTTACCGTCCCACATACAT--------------------------------------------------	21	-	-	-	-	-	-	-	-	1	-
	----------------------AATGGTTTACCGTCCCACATAC----------------------------------------------------	22	1	-	-	-	-	-	-	-	-	-
	--------------------------------------------------------TATGTGGGACGGTAAACCGC--------------------	20	1	-	-	-	-	-	-	-	-	-
	----------------------------------------------TTTGAGTATGTATGTGGGAC------------------------------	20	-	1	-	-	-	-	-	-	-	-
	-------------------------------------------------------GTATGTGGGACGGTAAAC-----------------------	18	-	-	-	-	1	-	-	-	-	-
rat	------------------AAGAAATGGTTTACCGTCCCACATACATTTTGAGTATGTATGTGGGACGGTAAACCGCTTCTT---------------
human	------GTGCGGTACTTGAAGAAATGGTTTACCGTCCCACATACATTTTGAATATGTATGTGGGATGGTAAACCGCTTCTTGGTATCCAGCCC---
mouse	GCTGTCACGCGGTACTTGAAGAAATGGTTTACCGTCCCACATACATTTTGAGTATGTATGTGGGACGGTAAACCGCTTCTTGGTATCCAGCCCAGC
	********************************* ************* ***************
	.....                  >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>               .....	ENSRNOT00000053630 ENSRNOG00000035507 rno-mir-299
rat	(((((.((((((((((((((((((((((.......)))))))))))))))))))))).)))))	1.000 -42.30
human	.((.((((((..(((((.((((((((((((((((((((((.......)))))))))))))))))))))).)))))))))))))....	1.000 -47.80
mouse	((((....((((((((..(((((.((((((((((((((((((((((.......)))))))))))))))))))))).))))))))).)).)).))))	0.999 -52.60

rat	chromosome:6:134389822:134389884:1	Same_strand|Exonic_non-coding|ENSRNOT00000053630|ENSRNOG00000035507 ## ENSRNOG00000035507|miRNA|rno-mir-299|rno-mir-299 [Source:miRBase;Acc:MI0000970] ## {MIR: rno-mir-299}
human	chromosome:14:100559872:100559958:1	Same_strand|Boundary_non-coding|ENST00000385016|ENSG00000207749|miRNA|hsa-mir-299 [Source:miRBase;Acc:MI0000744] ## {MIR: hsa-mir-299}
mouse	chromosome:12:110948830:110948925:1	Same_strand|Boundary_non-coding|ENSMUST00000083616|ENSMUSG00000065550|miRNA|mmu-mir-299 [Source:miRBase;Acc:MI0000399] ## {MIR: mmu-mir-299}

rno-mir-380

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-380 5arm	142	101	0	0	1	0	0	0	0	1
rno-mir-380 3arm	683	400	0	0	1	7	6	2	1	1
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-380 5arm	0.005	0.004	0	0	0.000	0	0	0	0	0.000
rno-mir-380 3arm	0.023	0.017	0	0	0.000	0.001	0.000	0.000	0.000	0.000

sblock10491 (miRBase rno-mir-380) [miRNAknown_cloningHIGH_multiarm_DicerOK_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-380

0.001

no

no

0.36/0.48

18/23/0.80

0.0 0.0

0.2 0.0

154 718

0 0

4 8

0 0

10 10

5 6

5arm 3arm

1 1

nd nd

0.24 0.19

3 2

1346

8

1

2

Clusters

Located in cluster 69: rno-mir-380, rno-mir-323, rno-mir-758, rno-mir-329

		reads	miRBase family seed
seed	---------------------------------------------------------------AUGUAGU------------------------	1087	novel
seed	---------------------------UGGUUGA------------------------------------------------------------	244	miR-380
seed	----------------------------------------------------------------UGUAGUA-----------------------	14	novel
seed	-----------------------------GUUGACC----------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--------------------------------------------------------------TATGTAGTATGGTCCACATCT-----------	21	455	263	1	6	4	2	1	1
	--------------------------------------------------------------TATGTAGTATGGTCCACA--------------	18	110	73	-	-	-	-	-	-
	--------------------------ATGGTTGACCATAGAACATGC-----------------------------------------------	21	79	51	-	-	-	-	-	-
	--------------------------------------------------------------TATGTAGTATGGTCCACATC------------	20	73	38	-	1	1	-	-	-
	--------------------------ATGGTTGACCATAGAACATG------------------------------------------------	20	24	19	-	-	-	-	-	-
	--------------------------ATGGTTGACCATAGAACA--------------------------------------------------	18	16	16	1	-	-	-	-	1
	--------------------------------------------------------------TATGTAGTATGGTCCACAT-------------	19	16	14	-	-	-	-	-	-
	--------------------------ATGGTTGACCATAGAACAT-------------------------------------------------	19	14	7	-	-	-	-	-	-
	--------------------------------------------------------------TATGTAGTATGGTCCACATCTTC---------	23	12	7	-	-	1	-	-	-
	--------------------------ATGGTTGACCATAGAACATGCGC---------------------------------------------	23	7	8	-	-	-	-	-	-
	---------------------------------------------------------------ATGTAGTATGGTCCACATCT-----------	20	9	4	-	-	-	-	-	-
	--------------------------------------------------------------TATGTAGTATGGTCCACATCTT----------	22	7	1	-	-	-	-	-	-
rno-miR-380	--------------------------ATGGTTGACCATAGAACATGCG----------------------------------------------	22	1	-	-	-	-	-	-	-
	----------------------------GGTTGACCATAGAACATG------------------------------------------------	18	1	-	-	-	-	-	-	-
	---------------------------------------------------------------ATGTAGTATGGTCCACAT-------------	18	1	-	-	-	-	-	-	-
rat	----------------ACCTGAAAAGATGGTTGACCATAGAACATGCGCTACTTCTGTGTCGTATGTAGTATGGTCCACATCTTCTCATTATC-
mouse	ACCCTCTCTCCATGGTACCTGAAAAGATGGTTGACCATAGAACATGCGCTACTTCTGTGTCGTATGTAGTATGGTCCACATCTTCTCGTTATCA
	*********************************************************************** *****
	.....                >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .....	ENSRNOT00000053596 ENSRNOG00000035473 rno-mir-380
rat	...(((.((((((...(((((((..(((((((.(((....))).)))))))..)))))))..)))))).))).....	1.000 -30.50
mouse	............(((((..(((.((((((...(((((((..(((((((.(((....))).)))))))..)))))))..)))))).))).)))))	0.955 -32.00

rat	chromosome:6:134390988:134391064:1	Same_strand|Boundary_non-coding|ENSRNOT00000053596|ENSRNOG00000035473 ## Same_strand|Exonic_non-coding|ENSRNOT00000053596|ENSRNOG00000035473 ## ENSRNOG00000035473|miRNA|rno-mir-380|rno-mir-380 [Source:miRBase;Acc:MI0006141] ## {MIR: rno-mir-380}
mouse	chromosome:12:110949990:110950083:1	Same_strand|Boundary_non-coding|ENSMUST00000083661|ENSMUSG00000065595|miRNA|mmu-mir-380 [Source:miRBase;Acc:MI0000797] ## {MIR: mmu-mir-380}

rno-mir-494

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-494 5arm	1	4	0	0	0	0	0	0	0	2
rno-mir-494 3arm	1483	917	54	28	128	169	75	90	286	527
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-494 5arm	0.000	0.000	0	0	0	0	0	0	0	0.000
rno-mir-494 3arm	0.049	0.040	0.003	0.002	0.006	0.013	0.006	0.005	0.019	0.035

sblock10495 (miRBase rno-mir-494) [miRNAknown_cloningHIGH_multiarm_DicerOK_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-494

0.001

no

no

0.39/0.50

18/25/0.92

0.0 0.0

0.0 1.0

6 2328

0 0

3 10

0 0

15 12

0 2

5arm 3arm

1 1

nd nd

0.18 0.13

2 2

3764

10

1

2

Clusters

Located in cluster 70: rno-mir-494, mmu-mir-1193

		reads	miRBase family seed
seed	----------------------------------------------------------GAAACAU----------------------------	3718	miR-494
seed	-----------------------------------------------------------AAACAUA---------------------------	31	novel
seed	-------------------------------------------------------------ACAUACA-------------------------	7	novel
seed	-------------------------GGUUGUC-------------------------------------------------------------	7	novel
seed	---------------------------------------------------------------AUACACG-----------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	---------------------------------------------------------TGAAACATACACGGGAAACCTCT-------------	23	501	306	7	7	41	51	25	27	126	203
	---------------------------------------------------------TGAAACATACACGGGAAACCTC--------------	22	478	292	17	8	34	69	30	30	75	131
	---------------------------------------------------------TGAAACATACACGGGAAACC----------------	20	327	221	15	5	33	27	18	17	58	121
	---------------------------------------------------------TGAAACATACACGGGAAAC-----------------	19	61	30	5	4	9	6	1	6	10	26
	---------------------------------------------------------TGAAACATACACGGGAAA------------------	18	40	31	1	1	9	8	-	3	9	16
rno-miR-494	---------------------------------------------------------TGAAACATACACGGGAAACCT---------------	21	41	25	8	2	-	6	1	4	2	19
	---------------------------------------------------------TGAAACATACACGGGAAACCTCTT------------	24	14	7	-	-	2	1	-	2	2	4
	----------------------------------------------------------GAAACATACACGGGAAACCTC--------------	21	7	4	-	-	-	-	-	-	-	2
	----------------------------------------------------------GAAACATACACGGGAAACCTCT-------------	22	3	1	1	-	-	1	-	-	2	2
	------------------------AGGTTGTCCGTGTTGTCTTCTC-----------------------------------------------	22	-	4	-	-	-	-	-	-	-	2
	----------------------------------------------------------GAAACATACACGGGAAACC----------------	19	5	-	-	-	-	-	-	1	-	-
	------------------------------------------------------------AACATACACGGGAAACCTCTTT-----------	22	-	-	-	1	-	-	-	-	2	1
	------------------------------------------------------------AACATACACGGGAAACCTC--------------	19	2	-	-	-	-	-	-	-	-	1
	----------------------------------------------------------GAAACATACACGGGAAACCTCTT------------	23	2	-	-	-	-	-	-	-	-	-
	---------------------------------------------------------TGAAACATACACGGGAAACCTCTTT-----------	25	1	-	-	-	-	-	-	-	-	1
	--------------------------------------------------------------CATACACGGGAAACCTCT-------------	18	1	-	-	-	-	-	-	-	-	-
	------------------------AGGTTGTCCGTGTTGTCTTC-------------------------------------------------	20	1	-	-	-	-	-	-	-	-	-
rat	---------TGATACTTGAAGGAGAGGTTGTCCGTGTTGTCTTCTCTTTATTTATGATGAAACATACACGGGAAACCTCTTTTTTAGTATCA-
human	-----------------------GAGGTTGTCCGTGTTGTCTTCTCTTTATTTATGATGAAACATACACGGGAAACCTC--------------
mouse	AGTGCTAATTGATACTTGAAGGAGAGGTTGTCCGTGTTGTCTTCTCTTTATTTATGATGAAACATACACGGGAAACCTCTTTTTTAGTATCAA
	********************************************************
	....>         >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >....	ENSRNOT00000054367 ENSRNOG00000036244 rno-mir-494
rat	.((((((.((((((((((((..(((((((((.(((((.........)).)))))).))))))..)))))))))))))))))).	1.000 -35.80
human	((((((..(((((((((.(((((.........)).)))))).))))))..))))))	1.000 -21.10
mouse	........(((((((.(((((((((((((..(((((((((.(((((.........)).)))))).))))))..))))))))))))))))))))	0.996 -36.90

rat	chromosome:6:134394868:134394950:1	Same_strand|Exonic_non-coding|ENSRNOT00000054367|ENSRNOG00000036244 ## ENSRNOG00000036244|miRNA|rno-mir-494|rno-mir-494 [Source:miRBase;Acc:MI0003542] ## {MIR: rno-mir-494}
human	chromosome:14:100565703:100565825:1	Same_strand|Boundary_non-coding|ENST00000349529|ENSG00000194717|miRNA|hsa-mir-494 [Source:miRBase;Acc:MI0003134] ## {Repeats: dust 0 class=dust} ## {MIR: hsa-mir-494}
mouse	chromosome:12:110953520:110953612:1	Same_strand|Boundary_non-coding|ENSMUST00000093632|ENSMUSG00000070141|miRNA|mmu-mir-494 [Source:miRBase;Acc:MI0003532] ## {MIR: mmu-mir-494}

rno-mir-376b

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-376b 5arm	342.333	286.667	1.833	1	0.500	1.500	2.500	2.833	2.333	4.500
rno-mir-376b 3arm	294	230	8	7	2	3	1	1	8	25
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-376b 5arm	0.011	0.013	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
rno-mir-376b 3arm	0.010	0.010	0.000	0.000	0.000	0.000	0.000	0.000	0.001	0.002

sblock10503 (miRBase rno-mir-376b) [miRNAknown_cloningHIGH_multiarm_DicerOK_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-376b

0.001

no

no

0.33/0.47

18/25/0.71

0.0 0.0 0.0

1.2 0.0 0.3

1132 4 393

0 0 0

10 2 10

0 0 0

15 37 13

5 -13 5

5arm 5arm_loop_3arm 3arm

3 3 3

nd nd nd

0.10 0.42 0.05

1 4 1

1928

10

3

2

Clusters

Located in cluster 72: rno-mir-376c, rno-mir-376b, rno-mir-376a, rno-mir-300

		reads	miRBase family seed
seed	----------------UGGAUAU---------------------------------------------------------------	1183	miR-376b
seed	-----------------------------------------------------UCAUAGA--------------------------	565	miR-376b
seed	---------------GUGGAUA----------------------------------------------------------------	79	novel
seed	-----------------GGAUAUU--------------------------------------------------------------	77	novel
seed	----------------------------------------------------AUCAUAG---------------------------	7	novel
seed	--------------------------------------GUGCUUC-----------------------------------------	4	novel
seed	--------------GGUGGAU-----------------------------------------------------------------	3	novel
seed	---------------------------------------------------AAUCAUA----------------------------	3	novel
seed	-------------AGGUGGA------------------------------------------------------------------	3	novel
seed	-------------------------------------------------------AUAGAGG------------------------	2	novel
seed	-----------------------------------------------GGAUAAU--------------------------------	1	novel
seed	------------------------------------------------------CAUAGAG-------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-miR-376b-3p	----------------------------------------------------ATCATAGAGGAACATCCACTT-------------	21	174	163	3	2	-	3	-	1	5	14
	---------------GTGGATATTCCTTCTATGGT---------------------------------------------------	20	169	144	3	-	1	3	2	2	2	3
	---------------GTGGATATTCCTTCTATGGTT--------------------------------------------------	21	142	136	-	2	-	-	2	1	-	2
	---------------GTGGATATTCCTTCTATGG----------------------------------------------------	19	107	84	-	-	-	-	1	1	-	1
	---------------GTGGATATTCCTTCTATGGTTAC------------------------------------------------	23	99	91	-	-	-	-	-	1	1	2
	---------------GTGGATATTCCTTCTATG-----------------------------------------------------	18	92	68	1	-	-	-	-	1	1	-
	----------------------------------------------------ATCATAGAGGAACATCCAC---------------	19	56	41	4	1	-	-	1	-	2	9
	----------------------------------------------------ATCATAGAGGAACATCCACT--------------	20	35	14	-	-	2	-	-	-	-	-
	--------------GGTGGATATTCCTTCTATGGTT--------------------------------------------------	22	21	17	-	-	-	-	-	-	-	-
	----------------TGGATATTCCTTCTATGGT---------------------------------------------------	19	19	14	-	-	-	-	-	-	-	1
	----------------------------------------------------ATCATAGAGGAACATCCA----------------	18	14	6	-	-	-	-	-	-	-	-
rno-miR-376b-5p	---------------GTGGATATTCCTTCTATGGTTA-------------------------------------------------	22	12	3	-	-	-	-	-	-	-	-
	----------------------------------------------------ATCATAGAGGAACATCCACTTT------------	22	7	2	1	3	-	-	-	-	1	-
	--------------GGTGGATATTCCTTCTATGGT---------------------------------------------------	21	6	7	-	-	-	-	-	-	-	-
	----------------TGGATATTCCTTCTATGGTT--------------------------------------------------	20	7	5	-	-	-	-	-	-	-	-
	----------------TGGATATTCCTTCTATGGTTAC------------------------------------------------	22	6	4	-	-	-	-	-	-	-	-
	--------------GGTGGATATTCCTTCTATG-----------------------------------------------------	19	5	5	-	-	-	-	-	-	-	-
	----------------TGGATATTCCTTCTATGG----------------------------------------------------	18	7	3	-	-	-	-	-	-	-	-
	--------------GGTGGATATTCCTTCTATGG----------------------------------------------------	20	5	4	-	-	-	-	-	-	1	-
	----------------TGGATATTCCTTCTATGGTTACG-----------------------------------------------	23	4	2	-	-	-	-	-	-	-	-
	--------------GGTGGATATTCCTTCTAT------------------------------------------------------	18	3	2	-	-	-	-	-	-	-	-
	---------------------------------------------------AATCATAGAGGAACATCCACTT-------------	22	3	-	-	-	-	-	-	-	-	1
	-------------------------------------CGTGCTTCCTGGATAATCA------------------------------	19	2	2	-	-	-	-	-	-	-	-
	----------------TGGATATTCCTTCTATGGTTA-------------------------------------------------	21	2	2	-	-	-	-	-	-	-	-
	--------------GGTGGATATTCCTTCTATGGTTAC------------------------------------------------	24	2	1	-	-	-	-	-	-	-	-
	---------------GTGGATATTCCTTCTATGGTTACGT----------------------------------------------	25	2	1	-	-	-	-	-	-	-	-
	-------------AGGTGGATATTCCTTCTA-------------------------------------------------------	18	1	2	-	-	-	-	-	-	-	-
	------------AAGGTGGATATTCCTTCTA-------------------------------------------------------	19	2	-	-	-	-	-	-	-	-	-
	------------------------------------------------------CATAGAGGAACATCCACTT-------------	19	1	1	-	-	-	-	-	-	-	-
	--------------------------------------------------TAATCATAGAGGAACATCC-----------------	19	-	2	-	-	-	-	-	-	-	-
	---------------------------------------------------AATCATAGAGGAACATCCAC---------------	20	2	-	-	-	-	-	-	-	-	-
	------------AAGGTGGATATTCCTTCTATGGT---------------------------------------------------	23	1	-	-	-	-	-	-	-	-	-
	----------------------------------------------------ATCATAGAGGAACATCCACTTTT-----------	23	-	-	-	1	-	-	-	-	-	-
	---------------------------------------------------AATCATAGAGGAACATCCACT--------------	21	1	-	-	-	-	-	-	-	-	-
	--------------------------------------------------TAATCATAGAGGAACATCCACT--------------	22	1	-	-	-	-	-	-	-	-	-
	----------------------------------------------TGGATAATCATAGAGGAACATC------------------	22	-	1	-	-	-	-	-	-	-	-
	-----------------------------------------------------TCATAGAGGAACATCCACTT-------------	20	-	-	-	-	-	-	-	-	-	1
	----------------TGGATATTCCTTCTATGGTTACGT----------------------------------------------	24	1	-	-	-	-	-	-	-	-	-
rat	TTTGGTATTTAAAAGGTGGATATTCCTTCTATGGTTACGTGCTTCCTGGATAATCATAGAGGAACATCCACTTTTTCAGTATCAAA
human	----------AAAACGTGGATATTCCTTCTATGTTTACGTGATTCCTGGTTAATCATAGAGGAAAATCCATGTTTT----------
mouse	----------AAAAGGTGGATATTCCTTCTATGGTTACGTGCTTCCTGGATAATCATAGAGGAACATCCACTTTTT----------
	**** ****************** ******* ******* ************** *****  ****
	.....>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.....	ENSRNOT00000054598 ENSRNOG00000036490 rno-mir-376b
rat	.((((((((.(((((((((((.(((((.(((((((((....((....)).)))))))))))))).))))))))))).)))))))).	1.000 -36.20
human	(((((((((((.((((.((((((......((((.....))))..)))))))))).)))))))))))	1.000 -23.80
mouse	(((((((((((.((((.((((((((((....((....)).)))))))))))))).)))))))))))	1.000 -27.70

rat	chromosome:6:134404180:134404265:1	Same_strand|Exonic_non-coding|ENSRNOT00000054598|ENSRNOG00000036490 ## ENSRNOG00000036490|miRNA|rno-mir-376b|rno-mir-376b [Source:miRBase;Acc:MI0003544] ## {MIR: rno-mir-376b}
human	chromosome:14:100576545:100576610:1	intergenic ## {Repeats: trf 0 class=trf} ## {MIR: hsa-mir-376b}
mouse	chromosome:12:110961676:110961741:1	Same_strand|Exonic_non-coding|ENSMUST00000102052|ENSMUSG00000076006|miRNA|mmu-mir-376b [Source:miRBase;Acc:MI0001162] ## {MIR: mmu-mir-376b}

rno-mir-539

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-539 5arm	2342	1654	3	4	23	16	9	12	7	8
rno-mir-539 3arm	239	186	1	1	17	22	2	0	0	17
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-539 5arm	0.078	0.072	0.000	0.000	0.001	0.001	0.001	0.001	0.000	0.001
rno-mir-539 3arm	0.008	0.008	0.000	0.000	0.001	0.002	0.000	0	0	0.001

sblock10508 (miRBase rno-mir-539) [miRNAknown_cloningHIGH_multiarm_DicerOK_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-539

0.001

no

no

0.25/0.43

18/25/0.73

0.0 0.0

0.3 1.3

2324 263

0 0

10 8

0 0

8 6

6 8

5arm 3arm

1 1

nd nd

0.05 0.00

1 0

4563

10

1

2

Clusters

Located in cluster 73: rno-mir-381, rno-mir-381, rno-mir-487b, rno-mir-539

Families

Member of family miR-539 (seed GAGAAAU): rno-mir-539, block1861117_cand

		reads	miRBase family seed
seed	---------------------------GAGAAAU--------------------------------------------------------------------------------	4071	miR-539
seed	---------------------------------------------------------------------AUACAAG--------------------------------------	379	miR-381
seed	----------------------------------------------------------------------UACAAGG-------------------------------------	74	novel
seed	--------------------------------------------------------------------CAUACAA---------------------------------------	31	novel
seed	--------------------------GGAGAAA---------------------------------------------------------------------------------	7	novel
seed	-----------------------------------------------------------------------ACAAGGG------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--------------------------GGAGAAATTATCCTTGGTGTG-------------------------------------------------------------------	21	984	540	2	2	15	4	4	7	2	-
rno-miR-539	--------------------------GGAGAAATTATCCTTGGTGTGT------------------------------------------------------------------	22	420	380	-	1	-	2	2	2	1	5
	--------------------------GGAGAAATTATCCTTGGTG---------------------------------------------------------------------	19	294	262	-	-	2	4	-	2	1	1
	--------------------------GGAGAAATTATCCTTGGT----------------------------------------------------------------------	18	270	197	-	1	1	1	-	-	-	-
	--------------------------GGAGAAATTATCCTTGGTGT--------------------------------------------------------------------	20	176	139	-	-	-	2	1	-	1	1
	--------------------------GGAGAAATTATCCTTGGTGTGTT-----------------------------------------------------------------	23	177	113	1	-	5	1	2	1	2	1
	--------------------------------------------------------------------CATACAAGGGTAATTTCTTTTC------------------------	22	98	71	-	-	9	13	1	-	-	6
	--------------------------------------------------------------------CATACAAGGGTAATTTCTT---------------------------	19	30	26	-	1	2	4	-	-	-	4
	--------------------------------------------------------------------CATACAAGGGTAATTTCT----------------------------	18	33	31	1	-	1	-	-	-	-	-
	--------------------------------------------------------------------CATACAAGGGTAATTTCTTT--------------------------	20	24	9	-	-	3	2	-	-	-	2
	--------------------------GGAGAAATTATCCTTGGTGTGTTT----------------------------------------------------------------	24	17	20	-	-	-	1	-	-	-	-
	---------------------------------------------------------------------ATACAAGGGTAATTTCTTT--------------------------	19	15	13	-	-	-	-	-	-	-	-
	---------------------------------------------------------------------ATACAAGGGTAATTTCTTTTCG-----------------------	22	6	10	-	-	-	-	-	-	-	-
	---------------------------------------------------------------------ATACAAGGGTAATTTCTT---------------------------	18	6	5	-	-	1	1	-	-	-	2
	---------------------------------------------------------------------ATACAAGGGTAATTTCTTTTC------------------------	21	6	3	-	-	-	-	1	-	-	1
	-------------------------------------------------------------------TCATACAAGGGTAATTTCTTTTC------------------------	23	5	1	-	-	1	1	-	-	-	-
	-------------------------------------------------------------------TCATACAAGGGTAATTTCTT---------------------------	20	2	4	-	-	-	-	-	-	-	1
	-------------------------------------------------------------------TCATACAAGGGTAATTTCTTT--------------------------	21	3	3	-	-	-	-	-	-	-	1
	-------------------------------------------------------------------TCATACAAGGGTAATTTCT----------------------------	19	2	3	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------CATACAAGGGTAATTTCTTTT-------------------------	21	3	2	-	-	-	-	-	-	-	-
	-------------------------------------------------------------------TCATACAAGGGTAATTTC-----------------------------	18	3	1	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------CATACAAGGGTAATTTCTTTTCG-----------------------	23	1	2	-	-	-	-	-	-	-	-
	-------------------------AGGAGAAATTATCCTTGGTGTGT------------------------------------------------------------------	23	1	1	-	-	-	1	-	-	-	-
	---------------------------------------------------------------------ATACAAGGGTAATTTCTTTTCGA----------------------	23	1	1	-	-	-	1	-	-	-	-
	--------------------------GGAGAAATTATCCTTGGTGTGTTTG---------------------------------------------------------------	25	1	-	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------TACAAGGGTAATTTCTTTTCGA----------------------	22	-	1	-	-	-	-	-	-	-	-
	-------------------------AGGAGAAATTATCCTTGGTGTG-------------------------------------------------------------------	22	-	1	-	-	-	-	-	-	-	-
	---------------------------------------------------------------------ATACAAGGGTAATTTCTTTT-------------------------	20	1	-	-	-	-	-	-	-	-	-
	-------------------------AGGAGAAATTATCCTTGG-----------------------------------------------------------------------	18	-	1	-	-	-	-	-	-	-	-
	-------------------------AGGAGAAATTATCCTTGGT----------------------------------------------------------------------	19	1	-	-	-	-	-	-	-	-	-
	-------------------------AGGAGAAATTATCCTTGGTG---------------------------------------------------------------------	20	1	-	-	-	-	-	-	-	-	-
rat	------------------ATACTTGAGGAGAAATTATCCTTGGTGTGTTTGCTC--TTTTGGATGAATCATACAAGGGTAATTTCTTTTCGAGTAT------------------
human	-GTCCGTGCTGCTGTTTCATACTTGAGGAGAAATTATCCTTGGTGTGTTCGCTTTATTTATGATGAATCATACAAGGACAATTTCTTTTTGAGTATCAAATCTTGCCTCGGC--
mouse	CTGCTGTGCTACTGTTTCATACTTGAGGAGAAATTATCCTTGGTGTGTTGGCTC--TTTTGGATGAATCATACAAGGATAATTTCTTTTTGAGTATCAAATACTGCCCTGGTGG
	******************************* ***   ***  ****************  ********** ******
	.....                  >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>                  .....	ENSRNOT00000054596 ENSRNOG00000036488 rno-mir-539
rat	((((((((((((((((((((((((.((((((((..(  ....)..)))).))))))))))))))))))))))))))))	1.000 -35.10
human	..(((.((....((((.(((((..((((((((((.(((((.(((((((((.((.......)))))).)))))))))).))))))))))..))))).))))...))..))).	0.977 -36.40
mouse	(((((..((...(((((.(((((..((((((((((((((((.(((((.....((  .....)).....)))))))))))))))))))))..))))).)))))..))...)))))	0.991 -39.50

rat	chromosome:6:134408917:134408992:1	Same_strand|Exonic_non-coding|ENSRNOT00000054596|ENSRNOG00000036488 ## Same_strand|Boundary_non-coding|ENSRNOT00000054596|ENSRNOG00000036488 ## ENSRNOG00000036488|miRNA|rno-mir-539|rno-mir-539 [Source:miRBase;Acc:MI0003526] ## {MIR: rno-mir-539}
human	chromosome:14:100583394:100583504:1	Same_strand|Boundary_non-coding|ENST00000365690|ENSG00000202560|miRNA|hsa-mir-539 [Source:miRBase;Acc:MI0003514] ## {MIR: hsa-mir-539}
mouse	chromosome:12:110966320:110966431:1	Same_strand|Boundary_non-coding|ENSMUST00000102109|ENSMUSG00000076063|miRNA|mmu-mir-539 [Source:miRBase;Acc:MI0003520] ## {MIR: mmu-mir-539}

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confident miRBase miRNAs:

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