miR-Intess: classification

other miRBase miRNAs

miRNAknown_rep_lenNOK_cloningHIGH_multiarm_DicerNOK_randfoldOK (7 loci)

rno-mir-370

Cloning frequencies
absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-370 5arm	104	65	4	0	0	3	4	0	0	0
rno-mir-370 3arm	240	191	0	0	2	2	1	2	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-370 5arm	0.003	0.003	0.000	0	0	0.000	0.000	0	0	0
rno-mir-370 3arm	0.008	0.008	0	0	0.000	0.000	0.000	0.000	0	0

sblock10448 (miRBase rno-mir-370) [miRNAknown_rep_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-370	0.001	no	SINE,SINE/MIR	0.48/0.72	18/25/0.69	1.5 0.0 0.0	1.8 0.0 1.7	108 1 388	0 0 0	5 1 6	0 0 0	8 30 10	1 -14 5	5arm 5arm_loop_3arm 3arm	1 1 1	nd nd nd	0.24 0.38 0.27	2 5 2	618	7	4	2

Families
Member of family miR-370 (seed CCUGCUG): rno-mir-370, rno-mir-24-1, rno-mir-24-2, block638635_cand

		reads	miRBase family seed
seed	---------------------------------------------------------------CCUGCUG------------------------------------------	405	miR-370
seed	----------------------------AGGUCAC-----------------------------------------------------------------------------	98	novel
seed	------------------------GACCAGG---------------------------------------------------------------------------------	72	novel
seed	--------------------------------------------------------------GCCUGCU-------------------------------------------	21	novel
seed	----------------------------------------------------------------CUGCUGG-----------------------------------------	11	novel
seed	---------------------------CAGGUCA------------------------------------------------------------------------------	9	novel
seed	-------------------------------------------------------------------CUGGGGU--------------------------------------	1	novel
seed	----------------------------------------------UACACAG-----------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S1	T3S2	T4S1	T4S2
	--------------------------------------------------------------GCCTGCTGGGGTGGAACCTG------------------------------	20	67	58	-	-	1	-	1
	--------------------------------------------------------------GCCTGCTGGGGTGGAACCTGGT----------------------------	22	68	43	-	-	-	-	-
	--------------------------------------------------------------GCCTGCTGGGGTGGAACCT-------------------------------	19	30	31	-	-	-	-	1
	--------------------------------------------------------------GCCTGCTGGGGTGGAACC--------------------------------	18	23	21	-	1	1	1	-
	--------------------------------------------------------------GCCTGCTGGGGTGGAACCTGG-----------------------------	21	26	21	-	-	-	-	-
	---------------------------CAGGTCACGTCTCTGCAGT------------------------------------------------------------------	19	21	10	-	-	-	1	-
	---------------------------CAGGTCACGTCTCTGCAGTTACAC-------------------------------------------------------------	24	12	12	-	-	-	-	-
	-----------------------AGACCAGGTCACGTCTCTGCAG-------------------------------------------------------------------	22	7	10	-	-	3	-	-
	---------------------------CAGGTCACGTCTCTGCAG-------------------------------------------------------------------	18	13	4	-	-	-	-	-
	-----------------------AGACCAGGTCACGTCTCTGCA--------------------------------------------------------------------	21	8	5	-	-	-	1	-
	-----------------------AGACCAGGTCACGTCTCTGCAGT------------------------------------------------------------------	23	8	4	-	-	-	-	-
	-----------------------AGACCAGGTCACGTCTCT-----------------------------------------------------------------------	18	6	4	-	-	-	-	-
	-------------------------------------------------------------TGCCTGCTGGGGTGGAACCTG------------------------------	21	7	3	-	-	-	-	-
	---------------------------CAGGTCACGTCTCTGCAGTT-----------------------------------------------------------------	20	3	4	3	-	-	-	-
	-----------------------AGACCAGGTCACGTCTCTG----------------------------------------------------------------------	19	7	1	1	-	-	-	-
	---------------------------CAGGTCACGTCTCTGCAGTTAC---------------------------------------------------------------	22	2	5	-	-	-	2	-
rno-miR-370	--------------------------------------------------------------GCCTGCTGGGGTGGAACCTGGTT---------------------------	23	5	4	-	-	-	-	-
	---------------------------------------------------------------CCTGCTGGGGTGGAACCTG------------------------------	19	2	3	-	-	-	-	-
	---------------------------------------------------------------CCTGCTGGGGTGGAACCTGG-----------------------------	20	3	2	-	-	-	-	-
	-------------------------------------------------------------TGCCTGCTGGGGTGGAACCT-------------------------------	20	4	-	-	-	-	-	-
	-----------------------AGACCAGGTCACGTCTCTGCAGTT-----------------------------------------------------------------	24	3	1	-	-	-	-	-
	---------------------------CAGGTCACGTCTCTGCAGTTA----------------------------------------------------------------	21	2	1	-	-	-	-	-
	-------------------------------------------------------------TGCCTGCTGGGGTGGAACC--------------------------------	19	-	3	-	-	-	-	-
	-------------------------------------------------------------TGCCTGCTGGGGTGGAAC---------------------------------	18	1	1	-	1	-	-	-
	--------------------------CCAGGTCACGTCTCTGCAG-------------------------------------------------------------------	19	2	1	-	-	-	-	-
	-----------------------AGACCAGGTCACGTCTCTGC---------------------------------------------------------------------	20	3	-	-	-	-	-	-
	--------------------------CCAGGTCACGTCTCTGCAGT------------------------------------------------------------------	20	2	-	-	-	-	-	-
	--------------------------CCAGGTCACGTCTCTGCA--------------------------------------------------------------------	18	1	1	-	-	-	-	-
	--------------------------CCAGGTCACGTCTCTGCAGTT-----------------------------------------------------------------	21	1	1	-	-	-	-	-
	--------------------------------------------------------------GCCTGCTGGGGTGGAACCTGGTTT--------------------------	24	2	-	-	-	-	-	-
	---------------------------CAGGTCACGTCTCTGCAGTTACA--------------------------------------------------------------	23	2	-	-	-	-	-	-
	-------------------------------------------------------------TGCCTGCTGGGGTGGAACCTGGT----------------------------	23	1	-	-	-	-	-	-
	------------------------------------------------------------------GCTGGGGTGGAACCTGGTTT--------------------------	20	-	1	-	-	-	-	-
	---------------------------------------------------------------CCTGCTGGGGTGGAACCTGGT----------------------------	21	1	-	-	-	-	-	-
	---------------------------CAGGTCACGTCTCTGCAGTTACACA------------------------------------------------------------	25	1	-	-	-	-	-	-
	---------------------------------------------TTACACAGCTCATGAGTGCCT----------------------------------------------	21	-	1	-	-	-	-	-
rat	---------------AGACAGAGAGACCAGGTCACGTCTCTGCAGTTACACAGCTCATGAGTGCCTGCTGGGGTGGAACCTGGTTTGTCTGTCT------------------
human	-------------------------GCCAGGTCACGTCTCTGCAGTTACACAGCTCACGAGTGCCTGCTGGGGTGGAACCTGGT----------------------------
mouse	CGAGTCCGGGGCCTAAGACGGAGAGACCAGGTCACGTCTCTGCAGTTACACAGCTCATGAGTGCCTGCTGGGGTGGAACCTGGTTTGTCTGTCTGTCTGTCACCATCGCTCG
	***************************** ************************
	..... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .....	ENSRNOT00000053738 ENSRNOG00000035615 rno-mir-370
rat	(((((((.(((((((((..(..(((.((((.(((.((.....)).))).)))).)))..)..))))))))).)))))))	1.000 -43.10
human	(((((((..((((((.((((.(((...........))).)))).))))))..)))))))	1.000 -24.70
mouse	(((((..(((((...(((((((.(((((((((..((((((.((((.(((.((.....)).))).)))).))))))..))))))))).)))))))....))).))...)))))	1.000 -53.00

rat	chromosome:6:134210194:134210272:1	Same_strand\|Boundary_non-coding\|ENSRNOT00000053738\|ENSRNOG00000035615 ## Same_strand\|Exonic_non-coding\|ENSRNOT00000053738\|ENSRNOG00000035615 ## ENSRNOG00000035615\|miRNA\|rno-mir-370\|rno-mir-370 [Source:miRBase;Acc:MI0003486] ## {Repeats: MIR 44 69 -1 class=SINE/MIR,MIR 64 85 -1 class=SINE/MIR,MIR 102 123 -1 class=SINE/MIR,MIR_Mars -85 178 -1 class=SINE,MIR 78 107 -1 class=SINE/MIR} ## {MIR: rno-mir-370}
human	chromosome:14:100447209:100447327:1	Same_strand\|Boundary_non-coding\|ENST00000362135\|ENSG00000199005\|miRNA\|hsa-mir-370 [Source:miRBase;Acc:MI0000778] ## {Repeats: MIR_Mars -1 class=SINE/MIR} ## {MIR: hsa-mir-370}
mouse	chromosome:12:110856453:110856564:1	Same_strand\|Boundary_non-coding\|ENSMUST00000083499\|ENSMUSG00000065433\|miRNA\|mmu-mir-370 [Source:miRBase;Acc:MI0001165] ## {MIR: mmu-mir-370}

rno-mir-652

Cloning frequencies
absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-652 5arm	94	43	5	10	45	43	18	18	65	35
rno-mir-652 3arm	554	157	42	40	367	150	68	88	43	140
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-652 5arm	0.003	0.002	0.000	0.001	0.002	0.003	0.001	0.001	0.004	0.002
rno-mir-652 3arm	0.018	0.007	0.002	0.002	0.018	0.011	0.005	0.005	0.003	0.009

sblock12654 (miRBase rno-mir-652) [miRNAknown_rep_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-652	0.001	no	DNA,DNA/Tip100	0.55/0.72	18/24/0.31	0.2 0.0	0.4 0.3	104 791	0 0	10 10	0 0	9 10	8 6	5arm 3arm	1 1	nd nd	0.23 0.05	5 1	2025	10	-2	1

		reads	miRBase family seed
seed	------------------------------------------------------AUGGCGC--------------------------	1623	miR-652
seed	-------------CAACCCU-------------------------------------------------------------------	236	novel
seed	--------------AACCCUA------------------------------------------------------------------	139	novel
seed	-------------------------------------------------------UGGCGCC-------------------------	19	novel
seed	----------------------------------------------------GAAUGGC----------------------------	5	novel
seed	-----------------------------------------------------AAUGGCG---------------------------	2	novel
seed	----------------CCCUAGG----------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-----------------------------------------------------AATGGCGCCACTAGGGTTG---------------	19	324	100	25	25	244	92	50	57	32	81
rno-miR-652	-----------------------------------------------------AATGGCGCCACTAGGGTTGTG-------------	21	123	10	4	2	56	14	1	9	1	14
	-----------------------------------------------------AATGGCGCCACTAGGGTT----------------	18	56	25	10	10	42	28	10	15	6	23
	------------ACAACCCTAGGAGGGGGTGCCA-----------------------------------------------------	22	51	11	2	5	8	16	10	13	18	9
	-----------------------------------------------------AATGGCGCCACTAGGGTTGT--------------	20	33	18	1	3	16	13	6	6	3	21
	-------------CAACCCTAGGAGGGGGTGC-------------------------------------------------------	19	10	11	1	2	12	7	3	2	19	14
	------------ACAACCCTAGGAGGGGGTGCCAT----------------------------------------------------	23	11	5	-	1	6	6	1	-	4	3
	------------ACAACCCTAGGAGGGGGTG--------------------------------------------------------	19	8	3	2	-	3	2	2	-	6	1
	-------------CAACCCTAGGAGGGGGTGCCA-----------------------------------------------------	21	3	2	-	-	6	-	-	-	3	3
	-------------CAACCCTAGGAGGGGGTGCCAT----------------------------------------------------	22	-	2	-	-	4	6	-	-	3	1
	------------ACAACCCTAGGAGGGGGT---------------------------------------------------------	18	1	5	-	-	-	3	-	1	4	-
	------------------------------------------------------ATGGCGCCACTAGGGTTG---------------	18	4	-	1	-	3	3	-	-	1	-
	------------ACAACCCTAGGAGGGGGTGCC------------------------------------------------------	21	5	1	-	-	3	1	-	-	-	2
	-----------------------------------------------------AATGGCGCCACTAGGGTTGTGC------------	22	7	1	-	-	3	-	-	1	-	-
	-------------CAACCCTAGGAGGGGGTGCCATTC--------------------------------------------------	24	3	1	-	2	-	1	1	-	1	-
	-------------CAACCCTAGGAGGGGGTGCCATT---------------------------------------------------	23	-	1	-	-	-	1	1	1	3	1
	-------------CAACCCTAGGAGGGGGTGCC------------------------------------------------------	20	1	1	-	-	1	-	-	-	2	1
	------------------------------------------------------ATGGCGCCACTAGGGTTGTG-------------	20	3	1	-	-	-	-	1	-	-	-
	---------------------------------------------------TGAATGGCGCCACTAGGGT-----------------	19	-	1	1	-	1	-	-	-	-	-
	------------ACAACCCTAGGAGGGGGTGC-------------------------------------------------------	20	-	-	-	-	-	-	-	1	2	-
	-------------CAACCCTAGGAGGGGGTG--------------------------------------------------------	18	1	-	-	-	1	-	-	-	-	-
	------------------------------------------------------ATGGCGCCACTAGGGTTGT--------------	19	1	-	-	-	1	-	-	-	-	-
	-----------------------------------------------------AATGGCGCCACTAGGGTTGTGCA-----------	23	2	-	-	-	-	-	-	-	-	-
	---------------------------------------------------TGAATGGCGCCACTAGGGTTG---------------	21	-	-	-	-	-	-	-	-	-	1
	---------------------------------------------------TGAATGGCGCCACTAGGG------------------	18	1	-	-	-	-	-	-	-	-	-
	---------------ACCCTAGGAGGGGGTGCC------------------------------------------------------	18	-	-	-	-	1	-	-	-	-	-
	----------------------------------------------------GAATGGCGCCACTAGGGTTGT--------------	21	-	1	-	-	-	-	-	-	-	-
	----------------------------------------------------GAATGGCGCCACTAGGGTTG---------------	20	-	-	-	-	1	-	-	-	-	-
rat	---ATGCACTGCACAACCCTAGGAGGGGGTGCCATTCACATAGACTATAATTGAATGGCGCCACTAGGGTTGTGCAGTGTACAA---
human	----TGCACTGCACAACCCTAGGAGAGGGTGCCATTCACATAGACTATAATTGAATGGCGCCACTAGGGTTGTGCAGTGCACAACCT
mouse	GCTATGTACTGCACAACCCTAGGAGGGGGTGCCATTCACATAGAGTATAATTGAATGGCGCCACTAGGGTTGTGCAGTGTACAGC--
	************** ************** ****************************** *
	+++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	ENSRNOT00000005633 ENSRNOG00000012787 NP_001102484.1
	..... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .....	ENSRNOT00000062211 ENSRNOG00000040458 rno-mir-652
rat	.((((((((((((((((((.....(((((((((((..((.....))..))))))))))).))))))))))))))))))...	1.000 -51.70
human	((((((((((((((((((.....(((((((((((..((.....))..))))))))))).))))))))))))))))))......	1.000 -53.40
mouse	(((.((((((((((((((((((.....(((((((((((..((.....))..))))))))))).)))))))))))))))))).)))	1.000 -50.30

rat	chromosome:X:35821324:35821404:-1	Same_strand\|Intronic_coding\|ENSRNOT00000005633\|ENSRNOG00000012787 ## Same_strand\|Exonic_non-coding\|ENSRNOT00000062211\|ENSRNOG00000040458 ## Same_strand\|Boundary_non-coding\|ENSRNOT00000062211\|ENSRNOG00000040458 ## ENSRNOG00000012787\|protein_coding\|NP_001102484.1\| ## ENSRNOG00000040458\|miRNA\|rno-mir-652\|rno-mir-652 [Source:miRBase;Acc:MI0006169] ## {Repeats: MER91C 16 41 -1 class=DNA/Tip100,MER91C 1 115 -1 class=DNA,MER91C 78 103 -1 class=DNA/Tip100,MER91C 39 64 -1 class=DNA/Tip100,MER91C 101 115 -1 class=DNA/Tip100} ## {MIR: rno-mir-652}
human	chromosome:X:109185224:109185306:1	Same_strand\|Intronic_coding\|ENST00000288381\|ENSG00000157600\|protein_coding\|Transmembrane protein 164 [Source:UniProtKB/Swiss-Prot;Acc:Q5U3C3] ## Same_strand\|Exonic_non-coding\|ENST00000385278\|ENSG00000208013\|miRNA\|hsa-mir-652 [Source:miRBase;Acc:MI0003667] ## {Repeats: MER91C 1 class=DNA/Tip100} ## {MIR: hsa-mir-652}
mouse	chromosome:X:139173550:139173634:1	Same_strand\|Boundary_non-coding\|ENSMUST00000112888\|ENSMUSG00000047045\|protein_coding\|transmembrane protein 164 Gene [Source:MGI (curated);Acc:Tmem164-003] ## Same_strand\|Intronic_non-coding\|ENSMUST00000054263\|ENSMUSG00000047045\|protein_coding\|transmembrane protein 164 Gene [Source:MGI (curated);Acc:Tmem164-003] ## Same_strand\|Intronic_coding\|ENSMUST00000087333\|ENSMUSG00000047045\|protein_coding\|transmembrane protein 164 Gene [Source:MGI (curated);Acc:Tmem164-003] ## Same_strand\|Exonic_non-coding\|ENSMUST00000102057\|ENSMUSG00000076011\|miRNA\|mmu-mir-652 [Source:miRBase;Acc:MI0004965] ## {Repeats: MER91C -1 class=DNA/Tip100} ## {MIR: mmu-mir-652}

rno-mir-421

Cloning frequencies
absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-421 5arm	116.333	94	3	3	34	23	6	11	30	23
rno-mir-421 3arm	1223	638	71	69	269	279	114	174	269	423
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-421 5arm	0.004	0.004	0.000	0.000	0.002	0.002	0.000	0.001	0.002	0.002
rno-mir-421 3arm	0.041	0.028	0.004	0.004	0.013	0.021	0.009	0.009	0.018	0.028

sblock12685 (miRBase rno-mir-421) [miRNAknown_rep_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-421	0.001	no	LINE,LINE/L2	0.26/0.53	18/25/0.32	0.0 0.7	1.4 1.1	172 1400	0 0	10 10	0 0	9 9	4 2	5arm 3arm	1 1	nd nd	0.14 0.16	3 3	3873	10	-1	-4

Clusters
Located in cluster 84: rno-mir-421, rno-mir-374

		reads	miRBase family seed
seed	--------------------------------------------------------------UCAACAG---------------------------------------	2213	novel
seed	------------------------------------------------------------------CAGACAU-----------------------------------	677	novel
seed	-----------------------------------------------------------------ACAGACA------------------------------------	476	novel
seed	-------------------------GCCUCAU----------------------------------------------------------------------------	342	miR-421
seed	---------------------------------------------------------------CAACAGA--------------------------------------	148	novel
seed	----------------------------------------------------------------AACAGAC-------------------------------------	13	novel
seed	--------------------------------------------------------------------GACAUUA---------------------------------	1	novel
seed	-------------------------------------------------------------------AGACAUU----------------------------------	1	novel
seed	----------------------------UCAUUAA-------------------------------------------------------------------------	1	novel
seed	---------------------------CUCAUUA--------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-------------------------------------------------------------ATCAACAGACATTAATTGG----------------------------	19	321	159	31	25	97	92	38	68	118	102
	-------------------------------------------------------------ATCAACAGACATTAATTG-----------------------------	18	212	103	16	9	55	49	35	41	96	78
	-----------------------------------------------------------------ACAGACATTAATTGGGCGCC-----------------------	20	168	89	6	9	23	25	5	15	2	65
	----------------------------------------------------------------AACAGACATTAATTGGGCG-------------------------	19	120	53	2	7	16	22	11	8	8	44
	-------------------------------------------------------------ATCAACAGACATTAATTGGGC--------------------------	21	92	60	2	3	17	38	10	14	7	32
	-------------------------------------------------------------ATCAACAGACATTAATTGGG---------------------------	20	55	28	2	7	20	9	4	10	25	15
	----------------------------------------------------------------AACAGACATTAATTGGGC--------------------------	18	52	39	5	2	12	9	4	-	4	19
	-----------------------------------------------------------------ACAGACATTAATTGGGCGC------------------------	19	57	23	1	3	8	13	1	6	2	29
	------------------------GGCCTCATTAAATGTTTGTTGA--------------------------------------------------------------	22	41	23	1	1	6	7	3	4	11	7
rno-miR-421	------------------------GGCCTCATTAAATGTTTGTTG---------------------------------------------------------------	21	31	16	1	2	12	7	-	1	9	9
	--------------------------------------------------------------TCAACAGACATTAATTGG----------------------------	18	33	25	3	1	1	2	3	4	1	10
	------------------------GGCCTCATTAAATGTTTGT-----------------------------------------------------------------	19	21	26	-	-	5	1	1	5	4	3
	-----------------------------------------------------------------ACAGACATTAATTGGGCG-------------------------	18	31	14	1	2	6	2	-	2	3	3
	--------------------------------------------------------------TCAACAGACATTAATTGGG---------------------------	19	21	8	-	-	4	5	-	2	-	4
	-----------------------------------------------------------------ACAGACATTAATTGGGCGCCTG---------------------	22	18	10	-	1	-	4	1	1	-	7
	------------------------GGCCTCATTAAATGTTTG------------------------------------------------------------------	18	11	14	-	-	5	5	1	1	2	3
	----------------------------------------------------------------AACAGACATTAATTGGGCGCC-----------------------	21	14	7	-	-	7	2	-	-	-	4
	------------------------GGCCTCATTAAATGTTTGTTGAA-------------------------------------------------------------	23	10	4	1	-	6	3	-	-	1	-
	------------------------GGCCTCATTAAATGTTTGTT----------------------------------------------------------------	20	1	11	-	-	-	-	1	-	3	1
	--------------------------------------------------------------TCAACAGACATTAATTGGGC--------------------------	20	7	7	-	-	1	2	-	-	-	-
	-------------------------------------------------------------ATCAACAGACATTAATTGGGCG-------------------------	22	3	3	1	-	1	1	1	-	1	1
	-----------------------------------------------------------------ACAGACATTAATTGGGCGCCT----------------------	21	8	2	-	-	-	2	-	-	-	-
	---------------------------------------------------------------CAACAGACATTAATTGGGC--------------------------	19	2	2	-	-	-	-	-	-	1	3
	-------------------------------------------------------------ATCAACAGACATTAATTGGGCGC------------------------	23	-	2	-	-	-	-	1	1	1	1
	---------------------------------------------------------------CAACAGACATTAATTGGG---------------------------	18	2	-	-	-	-	1	-	1	-	1
	-----------------------------------------------------------------ACAGACATTAATTGGGCGCCTGC--------------------	23	1	1	-	-	-	1	-	-	-	2
	----------------------------------------------------------------AACAGACATTAATTGGGCGC------------------------	20	2	1	-	-	-	-	-	-	-	1
	-----------------------------------------------------------------ACAGACATTAATTGGGCGCCTGCTC------------------	25	-	1	-	-	-	-	-	-	-	2
	--------------------------------------------------------------TCAACAGACATTAATTGGGCG-------------------------	21	-	-	-	-	1	-	-	1	-	-
	--------------------------------------------------------------TCAACAGACATTAATTGGGCGC------------------------	22	2	-	-	-	-	-	-	-	-	-
	-------------------------------------------------------------------AGACATTAATTGGGCGCC-----------------------	18	1	-	-	-	-	-	-	-	-	-
	--------------------------CCTCATTAAATGTTTGTTGAA-------------------------------------------------------------	21	1	-	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------ACAGACATTAATTGGGCGCCTGCT-------------------	24	-	1	-	-	-	-	-	-	-	-
	---------------------------CTCATTAAATGTTTGTTGA--------------------------------------------------------------	19	1	-	-	-	-	-	-	-	-	-
	------------------------------------------------------------------CAGACATTAATTGGGCGCC-----------------------	19	-	-	1	-	-	-	-	-	-	-
	----------------------------------------------------------------AACAGACATTAATTGGGCGCCT----------------------	22	1	-	-	-	-	-	-	-	-	-
rat	---------------CACACTGTAGGCCTCATTAAATGTTTGTTGAATGAAAAAATGAATCATCAACAGACATTAATTGGGCGCCTGCTCTGTG--------------
human	GTGCCTAATCCGGTGCACATTGTAGGCCTCATTAAATGTTTGTTGAATGAAAAAATGAATCATCAACAGACATTAATTGGGCGCCTGCTCTGTGATCTCCATGGGCTC
mouse	GTGCCTAATCCGGTGCACATTGTAGGCCTCATTAAATGTTTGTTGAATGAAAAAATGAATCATCAACAGACATTAATTGGGCGCCTGCTCTGTGATCTCCATGGGCTC
	** ************************************************************************
	..... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .....	ENSRNOT00000053669 ENSRNOG00000035546 rno-mir-421
rat	((((..((((((((((...((((((((((((.(((.........)))))))))))))))...)))).))))))..))))	1.000 -33.90
human	..(((((....(((.((((..((((((((((...(((((((((((.((((.........)))))))))))))))...)))).))))))..)))))))....)))))..	1.000 -43.40
mouse	..(((((....(((.((((..((((((((((...(((((((((((.((((.........)))))))))))))))...)))).))))))..)))))))....)))))..	1.000 -43.40

rat	chromosome:X:91563416:91563494:-1	Same_strand\|Exonic_non-coding\|ENSRNOT00000053669\|ENSRNOG00000035546 ## Same_strand\|Boundary_non-coding\|ENSRNOT00000053669\|ENSRNOG00000035546 ## ENSRNOG00000035546\|miRNA\|rno-mir-421\|rno-mir-421 [Source:miRBase;Acc:MI0001423] ## {Repeats: L2 3216 3239 1 class=LINE/L2,L2 0 3378 1 class=LINE,L2 3337 3368 -1 class=LINE,L2 3200 3218 1 class=LINE/L2,L2 3235 3262 -1 class=LINE/L2} ## {MIR: rno-mir-421}
human	chromosome:X:73354928:73355035:-1	Same_strand\|Boundary_non-coding\|ENST00000365696\|ENSG00000202566\|miRNA\|hsa-mir-421 [Source:miRBase;Acc:MI0003685] ## {Repeats: L2 -1 class=LINE/L2,L2 1 class=LINE/L2} ## {MIR: hsa-mir-421}
mouse	chromosome:X:100768245:100768352:-1	Same_strand\|Boundary_non-coding\|ENSMUST00000083575\|ENSMUSG00000065509\|miRNA\|mmu-mir-421 [Source:miRBase;Acc:MI0005496] ## {Repeats: L2 -1 class=LINE/L2,L2 1 class=LINE/L2} ## {MIR: mmu-mir-421}

rno-mir-708

Cloning frequencies
absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-708 5arm	1632.333	1008.750	1.250	3	60	29.250	35.500	52.500	224.083	73.750
rno-mir-708 3arm	59	21	0	0	0	0	0	0	3	9
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-708 5arm	0.054	0.044	0.000	0.000	0.003	0.002	0.003	0.003	0.015	0.005
rno-mir-708 3arm	0.002	0.001	0	0	0	0	0	0	0.000	0.001

sblock2035 (miRBase rno-mir-708) [miRNAknown_rep_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-708	0.001	no	LINE,LINE/L2	0.39/0.52	18/26/0.50	0.0 0.0 0.0	0.6 0.0 0.2	1970 1 49	0 0 0	10 1 4	0 0 0	10 31 12	10 -12 10	5arm 5arm_loop_3arm 3arm	4 4 4	nd nd nd	0.11 0.50 0.11	1 5 1	4870	10	0	-1

Families
Member of family miR-28/708 (seed AGGAGCU): rno-mir-708, rno-mir-28

		reads	miRBase family seed
seed	----------------------------AGGAGCU----------------------------------------------------------------------------------	4680	miR-28/708
seed	--------------------------------------------------------------------------AACUAGA------------------------------------	76	miR-708*
seed	-----------------------------GGAGCUU---------------------------------------------------------------------------------	68	novel
seed	---------------------------------------------------------------------------ACUAGAC-----------------------------------	17	novel
seed	---------------------------AAGGAGC-----------------------------------------------------------------------------------	14	novel
seed	-------------------------------AGCUUAC-------------------------------------------------------------------------------	9	novel
seed	----------------------------------------------------------------------------CUAGACU----------------------------------	2	novel
seed	------------------------------GAGCUUA--------------------------------------------------------------------------------	2	novel
seed	-------------------------------------------------GGGUAGA-------------------------------------------------------------	1	novel
seed	-----------------------------------------------------------------------CACAACU---------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	---------------------------AAGGAGCTTACAATCTAG------------------------------------------------------------------------	18	853	710	1	2	40	35	35	44	127	39
	---------------------------AAGGAGCTTACAATCTAGCTG---------------------------------------------------------------------	21	407	233	1	-	17	4	5	8	65	14
	---------------------------AAGGAGCTTACAATCTAGCT----------------------------------------------------------------------	20	214	182	-	-	11	4	3	10	34	15
	---------------------------AAGGAGCTTACAATCTAGC-----------------------------------------------------------------------	19	205	159	-	1	6	3	7	9	40	12
	---------------------------AAGGAGCTTACAATCTAGCTGG--------------------------------------------------------------------	22	230	122	-	-	10	2	8	5	34	3
	---------------------------AAGGAGCTTACAATCTAGCTGGGG------------------------------------------------------------------	24	203	100	-	-	6	3	5	6	21	10
rno-miR-708	---------------------------AAGGAGCTTACAATCTAGCTGGG-------------------------------------------------------------------	23	191	71	-	1	3	5	2	7	9	9
	-------------------------------------------------------------------------CAACTAGACTGTGAGCTTCT------------------------	20	30	10	-	-	-	-	-	-	-	4
	---------------------------AAGGAGCTTACAATCTAGCTGGGGG-----------------------------------------------------------------	25	17	7	-	-	-	1	-	1	4	5
	---------------------------AAGGAGCTTACAATCTAGCTGGGGGT----------------------------------------------------------------	26	8	11	-	1	-	-	-	-	3	1
	----------------------------AGGAGCTTACAATCTAGCTG---------------------------------------------------------------------	20	9	6	-	-	-	-	-	-	-	-
	----------------------------AGGAGCTTACAATCTAGCTGGG-------------------------------------------------------------------	22	11	2	-	-	-	-	-	-	-	-
	----------------------------AGGAGCTTACAATCTAGCTGGGG------------------------------------------------------------------	23	7	5	-	-	-	-	-	-	-	-
	-------------------------------------------------------------------------CAACTAGACTGTGAGCTTC-------------------------	19	9	2	-	-	-	-	-	-	1	-
	----------------------------AGGAGCTTACAATCTAGC-----------------------------------------------------------------------	18	7	3	-	-	-	-	1	-	-	-
	-------------------------------------------------------------------------CAACTAGACTGTGAGCTTCTA-----------------------	21	8	2	-	-	-	-	-	-	1	-
	--------------------------CAAGGAGCTTACAATCTA-------------------------------------------------------------------------	18	2	6	-	-	-	-	-	-	-	-
	----------------------------AGGAGCTTACAATCTAGCT----------------------------------------------------------------------	19	3	3	-	-	-	-	-	-	1	1
	--------------------------CAAGGAGCTTACAATCTAG------------------------------------------------------------------------	19	1	3	-	-	-	-	-	-	1	-
	--------------------------------------------------------------------------AACTAGACTGTGAGCTTCT------------------------	19	3	2	-	-	-	-	-	-	-	-
	-------------------------------------------------------------------------CAACTAGACTGTGAGCTTCTAGA---------------------	23	3	-	-	-	-	-	-	-	-	2
	----------------------------AGGAGCTTACAATCTAGCTGG--------------------------------------------------------------------	21	3	2	-	-	-	-	-	-	-	-
	------------------------------GAGCTTACAATCTAGCTGGG-------------------------------------------------------------------	20	5	-	-	-	-	-	-	-	-	-
	----------------------------AGGAGCTTACAATCTAGCTGGGGGT----------------------------------------------------------------	25	2	2	-	-	-	-	-	-	-	-
rno-miR-708*	-------------------------------------------------------------------------CAACTAGACTGTGAGCTTCTAG----------------------	22	1	1	-	-	-	-	-	-	1	1
	--------------------------------------------------------------------------AACTAGACTGTGAGCTTCTA-----------------------	20	2	2	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------------AACTAGACTGTGAGCTTCTAGA---------------------	22	1	1	-	-	-	-	-	-	-	1
	------------------------------GAGCTTACAATCTAGCTGG--------------------------------------------------------------------	19	-	2	-	-	-	-	-	-	1	-
	--------------------------------------------------------------------------AACTAGACTGTGAGCTTC-------------------------	18	3	-	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------------AACTAGACTGTGAGCTTCTAG----------------------	21	-	1	-	-	-	-	-	-	-	1
	------------------------------GAGCTTACAATCTAGCTGGGGGT----------------------------------------------------------------	23	1	-	-	-	-	-	-	-	-	-
	-----------------------------GGAGCTTACAATCTAGCT----------------------------------------------------------------------	18	-	1	-	-	-	-	-	-	-	-
	---------------------------------------------------------------------------ACTAGACTGTGAGCTTCTAG----------------------	20	1	-	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------ACACAACTAGACTGTGAGCTTC-------------------------	22	1	-	-	-	-	-	-	-	-	-
	-----------------------------GGAGCTTACAATCTAGCTG---------------------------------------------------------------------	19	1	-	-	-	-	-	-	-	-	-
	--------------------------CAAGGAGCTTACAATCTAGC-----------------------------------------------------------------------	20	1	-	-	-	-	-	-	-	-	-
	---------------------------------------------------------------------------ACTAGACTGTGAGCTTCTAGAG--------------------	22	-	1	-	-	-	-	-	-	-	-
	------------------------------------------------GGGGTAGATGACTTGCACTTGA-----------------------------------------------	22	1	-	-	-	-	-	-	-	-	-
rat	-----------------GACTGCCCTCAAGGAGCTTACAATCTAGCTGGGGGTAGATGACTTGCACTTGAACACAACTAGACTGTGAGCTTCTAGAGGGCAGGGG------------
human	GCTGTGTGTGAAATGGTAACTGCCCTCAAGGAGCTTACAATCTAGCTGGGGGTAAATGACTTGCACATGAACACAACTAGACTGTGAGCTTCTAGAGGGCAGGGACCTTACCCTAGT
mouse	---------------------------AAGGAGCTTACAATCTAGCTGGGGGTAGATGACTTGCACTTGAACACAACTAGACTGTGAGCTTCTA-----------------------
	************************* ******* *************************
	..... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .....	ENSRNOT00000062200 ENSRNOG00000040447 rno-mir-708
rat	..((((((((.(((((((((((.(((((.((.(..(((.((.....)).)))..).)).))))).))))))))))).))))))))...	1.000 -44.10
human	((((...((((...(((..((((((((.(((((((((((.(((((.((...((..(((.......)))..)).)).))))).))))))))))).))))))))..)))))))..))))	0.969 -51.60
mouse	.(((((((((((.(((((.((....((..((.....))..))....)).))))).))))))))))).	0.920 -23.70

rat	chromosome:1:153476669:153476756:1	Same_strand\|Exonic_non-coding\|ENSRNOT00000062200\|ENSRNOG00000040447 ## ENSRNOG00000040447\|miRNA\|rno-mir-708\|rno-mir-708 [Source:miRBase;Acc:MI0006160] ## {Repeats: L2 -97 3281 -1 class=LINE,L2 3132 3147 -1 class=LINE/L2,L2 3142 3169 -1 class=LINE/L2} ## {MIR: rno-mir-708}
human	chromosome:11:78790702:78790818:-1	Same_strand\|Boundary_non-coding\|ENST00000390708\|ENSG00000211997\|miRNA\|hsa-mir-708 [Source:miRBase;Acc:MI0005543] ## {Repeats: L2 1 class=LINE/L2,L2 -1 class=LINE/L2} ## {MIR: hsa-mir-708}
mouse	chromosome:7:103397930:103398057:1	Same_strand\|Intronic_non-coding\|ENSMUST00000084996\|ENSMUSG00000048078\|protein_coding\|odd Oz/ten-m homolog 4 (Drosophila) Gene [Source:MGI (curated);Acc:Odz4-001] ## Same_strand\|Boundary_non-coding\|ENSMUST00000102189\|ENSMUSG00000076143\|miRNA\|mmu-mir-708 [Source:miRBase;Acc:MI0004692] ## {Repeats: L2 -1 class=LINE/L2} ## {MIR: mmu-mir-708}

miRNAknown_rep_lenNOK_cloningHIGH_multiarm_DicerOK_randfoldOK (5 loci)

rno-mir-130b

Cloning frequencies
absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-130b 5arm	34	24	9	5	263	140	14	21	22	23
rno-mir-130b 3arm	20	15	11	12	306	179	20	19	19	56
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-130b 5arm	0.001	0.001	0.000	0.000	0.013	0.011	0.001	0.001	0.001	0.002
rno-mir-130b 3arm	0.001	0.001	0.001	0.001	0.015	0.014	0.002	0.001	0.001	0.004

sblock3193 (miRBase rno-mir-130b) [miRNAknown_rep_lenNOK_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-130b	0.005	no	SINE/MIR	0.42/0.50	18/24/0.56	0.0 0.0	1.2 1.2	333 379	0 0	10 10	0 0	12 10	7 5	5arm 3arm	1 1	nd nd	0.11 0.11	2 2	1212	10	2	2

Clusters
Located in cluster 17: rno-mir-301b, rno-mir-130b

Families
Member of family miR-130a/130b/301a/301b (seed AGUGCAA): rno-mir-301a, rno-mir-130a, rno-mir-301b, rno-mir-130b, sblock2545_novel

		reads	miRBase family seed
seed	----------------------------------------------------------------------AGUGCAA-----------------------------------------	643	miR-130a/130b/301a/301b
seed	--------------------------------CUCUUUC-------------------------------------------------------------------------------	534	novel
seed	------------------------------CACUCUU---------------------------------------------------------------------------------	15	novel
seed	-----------------------------------------------------------------------GUGCAAU----------------------------------------	13	novel
seed	-------------------------------ACUCUUU--------------------------------------------------------------------------------	6	novel
seed	-------------------------------------------------------------------------GCAAUGA--------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	---------------------------------------------------------------------CAGTGCAATGATGAAAGGG------------------------------	19	5	7	4	5	87	64	6	7	7	16
	-------------------------------ACTCTTTCCCTGTTGCACTACT-----------------------------------------------------------------	22	17	13	2	-	66	47	5	6	5	6
	-------------------------------ACTCTTTCCCTGTTGCACTAC------------------------------------------------------------------	21	9	6	2	-	74	32	5	10	9	6
	---------------------------------------------------------------------CAGTGCAATGATGAAAGG-------------------------------	18	6	1	1	-	79	34	5	3	5	14
rno-miR-130b	---------------------------------------------------------------------CAGTGCAATGATGAAAGGGCAT---------------------------	22	4	2	1	4	78	37	4	2	3	10
	-------------------------------ACTCTTTCCCTGTTGCACT--------------------------------------------------------------------	19	2	4	2	-	54	19	-	2	-	5
	-------------------------------ACTCTTTCCCTGTTGCAC---------------------------------------------------------------------	18	3	1	2	4	36	24	2	1	4	2
	---------------------------------------------------------------------CAGTGCAATGATGAAAGGGCA----------------------------	21	1	1	2	2	26	13	2	1	2	8
	---------------------------------------------------------------------CAGTGCAATGATGAAAGGGCATC--------------------------	23	-	-	1	-	13	20	2	4	1	5
	-------------------------------ACTCTTTCCCTGTTGCACTA-------------------------------------------------------------------	20	3	-	1	1	21	11	2	1	1	4
	---------------------------------------------------------------------CAGTGCAATGATGAAAGGGC-----------------------------	20	4	1	1	-	15	4	-	-	1	2
	---------------------------------------------------------------------CAGTGCAATGATGAAAGGGCATCC-------------------------	24	-	2	1	1	3	1	-	1	-	1
	----------------------------------------------------------------------AGTGCAATGATGAAAGGGCA----------------------------	20	-	-	-	-	1	3	1	-	-	-
	-----------------------------ACACTCTTTCCCTGTTGCACT--------------------------------------------------------------------	21	-	-	-	-	4	1	-	-	-	-
	-----------------------------ACACTCTTTCCCTGTTGCAC---------------------------------------------------------------------	20	-	-	-	-	1	1	-	-	2	-
	------------------------------CACTCTTTCCCTGTTGCACT--------------------------------------------------------------------	20	-	-	-	-	1	1	-	1	-	-
	----------------------------------------------------------------------AGTGCAATGATGAAAGGGC-----------------------------	19	-	-	-	-	2	1	-	-	-	-
	-----------------------------ACACTCTTTCCCTGTTGC-----------------------------------------------------------------------	18	-	-	-	-	2	-	-	-	-	-
	-----------------------------ACACTCTTTCCCTGTTGCACTAC------------------------------------------------------------------	23	-	-	-	-	1	1	-	-	-	-
	----------------------------------------------------------------------AGTGCAATGATGAAAGGGCAT---------------------------	21	-	1	-	-	-	1	-	-	-	-
	------------------------------CACTCTTTCCCTGTTGCA----------------------------------------------------------------------	18	-	-	-	-	-	1	-	-	1	-
	----------------------------------------------------------------------AGTGCAATGATGAAAGGGCATC--------------------------	22	-	-	-	-	-	1	-	1	-	-
	-------------------------------ACTCTTTCCCTGTTGCACTACTG----------------------------------------------------------------	23	-	-	-	-	1	1	-	-	-	-
	-----------------------------ACACTCTTTCCCTGTTGCACTA-------------------------------------------------------------------	22	-	-	-	-	1	-	-	-	-	-
	----------------------------------------------------------------------AGTGCAATGATGAAAGGG------------------------------	18	-	-	-	-	1	-	-	-	-	-
	------------------------------CACTCTTTCCCTGTTGCACTAC------------------------------------------------------------------	22	-	-	-	-	-	1	-	-	-	-
	------------------------------------------------------------------------TGCAATGATGAAAGGGCAT---------------------------	19	-	-	-	-	1	-	-	-	-	-
	-----------------------------ACACTCTTTCCCTGTTGCA----------------------------------------------------------------------	19	-	-	-	-	1	-	-	-	-	-
rat	-------------------GGCTTGCTGGACACTCTTTCCCTGTTGCACTACTGTGGGCCTCTGGGAAGCAGTGCAATGATGAAAGGGCATCCGTCAGGCC-----------------
human	CCTGGGGGAGGCACTGGCAGGCCTGCCCGACACTCTTTCCCTGTTGCACTACTATAGGCCGCTGGGAAGCAGTGCAATGATGAAAGGGCATCGGTCAGGTCCAGCCTGCTACCCTGGG
mouse	-----------------------------ACACTCTTTCCCTGTTGCACTACTGTGGGCCTCTGGGAAGCAGTGCAATGATGAAAGGGCAT---------------------------
	************************ * ** ****************************
	>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>	ENSRNOT00000046664 ENSRNOG00000026918 RGD1308065_predicted
	..... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .....	ENSRNOT00000053664 ENSRNOG00000035541 rno-mir-130b
rat	((((((.((((..(((((((..(((((((((.((.....((....)).)).)))))))))..)))))))..)))).))))))	1.000 -35.80
human	((..(((..((((..(((.((((((.((((..(((((((..(((((((((.((.(((....)))...)).)))))))))..)))))))..)))).))))))..))))))).)))..))	0.984 -57.60
mouse	...(((((((..(((((((((.((.....((....)).)).)))))))))..)))))))...	1.000 -20.80

rat	chromosome:11:85885595:85885676:1	Same_strand\|Exonic_non-coding\|ENSRNOT00000053664\|ENSRNOG00000035541 ## ENSRNOG00000026918\|protein_coding\|RGD1308065_predicted\| ## ENSRNOG00000035541\|miRNA\|rno-mir-130b\|rno-mir-130b [Source:miRBase;Acc:MI0000904] ## {MIR: rno-mir-130b}
human	chromosome:22:20337574:20337691:1	Same_strand\|Boundary_non-coding\|ENST00000385018\|ENSG00000207751\|miRNA\|hsa-mir-130b [Source:miRBase;Acc:MI0000748] ## {Repeats: MIRm -1 class=SINE/MIR} ## {SimpF: rank = 1 1 FirstEF} ## {MIR: hsa-mir-130b}
mouse	chromosome:16:17124134:17124255:-1	Same_strand\|Intronic_non-coding\|ENSMUST00000115714\|ENSMUSG00000049916\|protein_coding\|RIKEN cDNA 2610318N02 gene Gene [Source:MGI Symbol;Acc:MGI:1917708] ## Same_strand\|Boundary_non-coding\|ENSMUST00000083638\|ENSMUSG00000065572\|miRNA\|mmu-mir-130b [Source:miRBase;Acc:MI0000408] ## {MIR: mmu-mir-130b}

rno-mir-31

Cloning frequencies
absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-31 5arm	4695	2687	21751	13969	493	276	1048	1699	4082	2148
rno-mir-31 3arm	286	151	1775	1272	39	31	72	89	251	70
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-31 5arm	0.156	0.117	1.178	0.828	0.024	0.021	0.082	0.089	0.269	0.143
rno-mir-31 3arm	0.010	0.007	0.096	0.075	0.002	0.002	0.006	0.005	0.017	0.005

sblock9372 (miRBase rno-mir-31) [miRNAknown_rep_lenNOK_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-31	0.001	no	LINE/L2	0.37/0.58	18/25/0.61	0.0 0.0	1.7 0.8	36221 2027	0 0	10 10	0 0	27 19	2 4	5arm 3arm	1 1	nd nd	0.11 0.17	1 2	56884	10	1	3

Families
Member of family miR-31 (seed GGCAAGA): rno-mir-31, block131510_cand, block871208_cand

		reads	miRBase family seed
seed	-------------------------------------------GGCAAGA-------------------------------------------------------------------------------------------	52802	miR-31
seed	-------------------------------------------------------------------------------GCUAUGC-------------------------------------------------------	3421	novel
seed	--------------------------------------------------------------------------------CUAUGCC------------------------------------------------------	337	novel
seed	----------------------------------------------------------------------------------AUGCCAA----------------------------------------------------	201	novel
seed	---------------------------------------------------------------------------------UAUGCCA-----------------------------------------------------	71	novel
seed	--------------------------------------------GCAAGAU------------------------------------------------------------------------------------------	26	novel
seed	------------------------------------------AGGCAAG--------------------------------------------------------------------------------------------	14	novel
seed	---------------------------------------------CAAGAUG-----------------------------------------------------------------------------------------	5	novel
seed	-----------------------------------------------------------------------------------UGCCAAC---------------------------------------------------	2	novel
seed	-----------------------------------------------------------------------------CUGCUAU---------------------------------------------------------	2	novel
seed	-----------------------------------------GAGGCAA---------------------------------------------------------------------------------------------	1	novel
seed	--------------------------------------------------------------------------AACCUGC------------------------------------------------------------	1	novel
seed	------------------------------------------------------------------------------UGCUAUG--------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	------------------------------------------AGGCAAGATGCTGGCATA---------------------------------------------------------------------------------	18	890	573	6277	4185	105	65	265	419	1222	574
	------------------------------------------AGGCAAGATGCTGGCATAGCT------------------------------------------------------------------------------	21	2094	1079	5089	3078	150	101	355	570	960	723
	------------------------------------------AGGCAAGATGCTGGCATAGC-------------------------------------------------------------------------------	20	809	469	5075	3238	113	41	238	332	770	369
	------------------------------------------AGGCAAGATGCTGGCATAG--------------------------------------------------------------------------------	19	424	307	3068	2130	83	48	144	262	482	249
rno-miR-31	------------------------------------------AGGCAAGATGCTGGCATAGCTG-----------------------------------------------------------------------------	22	416	241	1987	1197	31	18	42	105	607	158
	------------------------------------------------------------------------------TGCTATGCCAACATATTGCCATC----------------------------------------	23	112	39	489	318	13	11	23	28	53	14
	------------------------------------------------------------------------------TGCTATGCCAACATATTGCCAT-----------------------------------------	22	53	47	326	260	5	7	11	20	82	18
	------------------------------------------------------------------------------TGCTATGCCAACATATTGCCA------------------------------------------	21	58	40	246	229	7	7	18	23	62	16
	------------------------------------------AGGCAAGATGCTGGCATAGCTGT----------------------------------------------------------------------------	23	56	15	204	112	11	2	4	9	36	68
	------------------------------------------------------------------------------TGCTATGCCAACATATTGCCATCT---------------------------------------	24	7	2	159	110	2	1	1	-	8	1
	------------------------------------------------------------------------------TGCTATGCCAACATATTGC--------------------------------------------	19	9	7	81	86	2	1	5	7	9	3
	-------------------------------------------------------------------------------GCTATGCCAACATATTGCCATC----------------------------------------	22	7	2	82	60	2	-	4	2	16	6
	------------------------------------------------------------------------------TGCTATGCCAACATATTGCC-------------------------------------------	20	8	2	124	27	3	-	1	1	5	3
	------------------------------------------------------------------------------TGCTATGCCAACATATTG---------------------------------------------	18	5	6	35	41	2	1	4	5	3	5
	-------------------------------------------------------------------------------GCTATGCCAACATATTGCCA------------------------------------------	20	10	1	39	36	3	3	-	1	7	1
	---------------------------------------------------------------------------------TATGCCAACATATTGCCATCT---------------------------------------	21	4	1	35	30	-	-	-	1	2	1
	---------------------------------------------------------------------------------TATGCCAACATATTGCCATC----------------------------------------	20	3	1	37	25	-	-	3	-	-	-
	------------------------------------------AGGCAAGATGCTGGCATAGCTGTT---------------------------------------------------------------------------	24	1	2	29	16	-	-	-	1	4	2
	---------------------------------------------------------------------------------TATGCCAACATATTGCCA------------------------------------------	18	-	-	37	6	-	-	1	-	2	-
	--------------------------------------------------------------------------------CTATGCCAACATATTGCCATC----------------------------------------	21	2	1	9	14	-	-	-	-	-	1
	-------------------------------------------------------------------------------GCTATGCCAACATATTGCC-------------------------------------------	19	-	-	19	2	-	-	-	-	-	-
	--------------------------------------------------------------------------------CTATGCCAACATATTGCCATCT---------------------------------------	22	4	-	12	4	-	-	-	-	-	1
	-------------------------------------------------------------------------------GCTATGCCAACATATTGCCATCT---------------------------------------	23	-	1	13	6	-	-	-	-	-	-
	--------------------------------------------------------------------------------CTATGCCAACATATTGCCA------------------------------------------	19	2	-	8	6	-	-	1	1	1	-
	-------------------------------------------GGCAAGATGCTGGCATAGC-------------------------------------------------------------------------------	19	3	1	5	3	-	1	-	-	-	-
	---------------------------------------------------------------------------------TATGCCAACATATTGCCAT-----------------------------------------	19	1	1	7	3	-	-	-	-	-	-
	-------------------------------------------------------------------------------GCTATGCCAACATATTGCCAT-----------------------------------------	21	1	-	8	3	-	-	-	-	-	-
	-----------------------------------------GAGGCAAGATGCTGGCATAG--------------------------------------------------------------------------------	20	1	-	4	-	-	-	-	-	-	-
	-------------------------------------------GGCAAGATGCTGGCATAGCT------------------------------------------------------------------------------	20	-	-	4	1	-	-	-	-	-	-
	-----------------------------------------GAGGCAAGATGCTGGCATAGCT------------------------------------------------------------------------------	22	-	-	3	1	-	-	-	-	-	-
	------------------------------------------------------------------------------TGCTATGCCAACATATTGCCATCTT--------------------------------------	25	-	-	2	2	-	-	-	-	-	-
	-------------------------------------------GGCAAGATGCTGGCATAGCTG-----------------------------------------------------------------------------	21	1	-	-	1	-	-	-	1	-	-
	--------------------------------------------------------------------------------CTATGCCAACATATTGCCAT-----------------------------------------	20	-	-	2	-	-	-	-	-	1	-
	-----------------------------------------GAGGCAAGATGCTGGCATA---------------------------------------------------------------------------------	19	-	-	2	1	-	-	-	-	-	-
	-------------------------------------------GGCAAGATGCTGGCATAG--------------------------------------------------------------------------------	18	-	-	1	2	-	-	-	-	-	-
	------------------------------------------AGGCAAGATGCTGGCATAGCTGTTG--------------------------------------------------------------------------	25	-	-	-	2	-	-	-	-	1	-
	-----------------------------------------GAGGCAAGATGCTGGCATAGC-------------------------------------------------------------------------------	21	-	-	2	-	-	-	-	-	-	-
	--------------------------------------------GCAAGATGCTGGCATAGC-------------------------------------------------------------------------------	18	-	-	-	1	-	-	-	-	-	1
	-------------------------------------------------------------------------------GCTATGCCAACATATTGC--------------------------------------------	18	-	-	1	1	-	-	-	-	-	-
	----------------------------------------------------------------------------CCTGCTATGCCAACATATTGCC-------------------------------------------	22	-	-	-	2	-	-	-	-	-	-
	----------------------------------------------------------------------------------ATGCCAACATATTGCCATC----------------------------------------	19	-	-	1	1	-	-	-	-	-	-
	-------------------------------------------GGCAAGATGCTGGCATAGCTGT----------------------------------------------------------------------------	22	-	-	-	-	-	-	-	-	-	2
	--------------------------------------------GCAAGATGCTGGCATAGCTG-----------------------------------------------------------------------------	20	-	-	-	-	-	-	-	-	-	1
	-----------------------------------------------------------------------------CTGCTATGCCAACATATTGCCA------------------------------------------	22	-	-	1	-	-	-	-	-	-	-
	--------------------------------------------------------------------------------CTATGCCAACATATTGCC-------------------------------------------	18	-	-	1	-	-	-	-	-	-	-
	--------------------------------------------GCAAGATGCTGGCATAGCT------------------------------------------------------------------------------	19	-	-	-	-	-	-	-	-	-	1
	--------------------------------------------GCAAGATGCTGGCATAGCTGT----------------------------------------------------------------------------	21	-	-	-	1	-	-	-	-	-	-
	----------------------------------------GGAGGCAAGATGCTGGCATA---------------------------------------------------------------------------------	20	-	-	1	-	-	-	-	-	-	-
	-------------------------------------------------------------------------GAACCTGCTATGCCAACAT-------------------------------------------------	19	-	-	1	-	-	-	-	-	-	-
rat	---------------TGCTCCTGAAACTTGGAACTGGAGAGGAGGCAAGATGCTGGCATAGCTGTTGAACTGAGAACCTGCTATGCCAACATATTGCCATCTTTCCTGTCTGACAGCAGCT--------------------
human	-----------------------------------GGAGAGGAGGCAAGATGCTGGCATAGCTGTTGAACTGGGAACCTGCTATGCCAACATATTGCCATCTTTCCTGTCTGAC---------------------------
mouse	GAAGAGGGATGGTATTGCTCCTGTAACTCGGAACTGGAGAGGAGGCAAGATGCTGGCATAGCTGTTGAACTGAGAACCTGCTATGCCAACATATTGCCATCTTTCCTGTCTGACAGCAGCTTGGCTACCTCCGTCCTGTTC
	*********************************** ***************************************
	..... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .....	ENSRNOT00000053729 ENSRNOG00000035606 rno-mir-31
rat	.(((.(((....(..((...((((((..(((((.(((.(((((((((.(((........)))..))))))))).))).)))))..))))))..))..)))).))).	1.000 -46.40
human	((((((..(((((.(((.(((((((((.(((........)))..))))))))).))).)))))..))))))........	0.997 -37.20
mouse	(((..(((((((....(((.((((...(((((...((((((..(((((.(((.(((((((((.(((........)))..))))))))).))).)))))..))))))..)))))..))))...))).....))))))).)))	0.990 -61.60

rat	chromosome:5:108497649:108497754:-1	Same_strand\|Exonic_non-coding\|ENSRNOT00000053729\|ENSRNOG00000035606 ## ENSRNOG00000035606\|miRNA\|rno-mir-31\|rno-mir-31 [Source:miRBase;Acc:MI0000872] ## {MIR: rno-mir-31}
human	chromosome:9:21502106:21502184:-1	Same_strand\|Intronic_non-coding\|ENST00000304425\|ENSG00000171889\|protein_coding\|Putative uncharacterized protein LOC554202 [Source:UniProtKB/Swiss-Prot;Acc:Q8WTY6] ## Same_strand\|Boundary_non-coding\|ENST00000362307\|ENSG00000199177\|miRNA\|hsa-mir-31 [Source:miRBase;Acc:MI0000089] ## {MIR: hsa-mir-31}
mouse	chromosome:4:88556441:88556581:-1	Same_strand\|Boundary_non-coding\|ENSMUST00000083474\|ENSMUSG00000065408\|miRNA\|mmu-mir-31 [Source:miRBase;Acc:MI0000579] ## {Repeats: L2 1 class=LINE/L2} ## {MIR: mmu-mir-31}

rno-mir-148b

Cloning frequencies
absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-148b 5arm	53	53	21	12	47	35	14	22	51	33
rno-mir-148b 3arm	595	319	173	255	279	451	116	194	263	656
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-148b 5arm	0.002	0.002	0.001	0.001	0.002	0.003	0.001	0.001	0.003	0.002
rno-mir-148b 3arm	0.020	0.014	0.009	0.015	0.014	0.034	0.009	0.010	0.017	0.044

sblock11523 (miRBase rno-mir-148b) [miRNAknown_rep_lenNOK_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-148b	0.001	no	LINE,LINE/L2	0.32/0.45	18/25/0.66	0.0 0.0	2.0 1.4	189 1300	0 0	10 10	0 0	23 14	0 10	5arm 3arm	1 1	nd nd	0.10 0.22	1 2	3642	10	3	3

Families
Member of family miR-148b/152 (seed CAGUGCA): rno-mir-152, rno-mir-148b

		reads	miRBase family seed
seed	---------------------------------------------------------------CAGUGCA-----------------------------	3262	miR-148b/152
seed	------------------------AAGUUCU--------------------------------------------------------------------	332	miR-148b
seed	----------------------------------------------------------------AGUGCAU----------------------------	34	novel
seed	-------------------------AGUUCUG-------------------------------------------------------------------	7	novel
seed	-----------------------------------------------------------------GUGCAUC---------------------------	3	novel
seed	-----------------------GAAGUUC---------------------------------------------------------------------	2	novel
seed	------------------------------------------------------------------UGCAUCA--------------------------	1	novel
seed	-------------------------------------------------------------------GCAUCAC-------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--------------------------------------------------------------TCAGTGCATCACAGAACTTTGTC--------------	23	172	107	29	58	86	133	44	62	89	287
	--------------------------------------------------------------TCAGTGCATCACAGAACT-------------------	18	126	42	35	46	57	79	19	37	45	115
	--------------------------------------------------------------TCAGTGCATCACAGAACTT------------------	19	88	51	35	43	34	61	14	41	36	77
rno-miR-148b-3p	--------------------------------------------------------------TCAGTGCATCACAGAACTTTGT---------------	22	61	36	38	47	39	91	17	20	37	64
	--------------------------------------------------------------TCAGTGCATCACAGAACTTTG----------------	21	92	59	24	42	36	49	14	23	35	68
	--------------------------------------------------------------TCAGTGCATCACAGAACTTT-----------------	20	46	19	8	17	22	28	6	8	17	44
	-----------------------GAAGTTCTGTTATACACTCAG-------------------------------------------------------	21	18	12	8	1	8	7	5	5	9	12
	-----------------------GAAGTTCTGTTATACACT----------------------------------------------------------	18	9	12	-	2	22	6	2	6	9	1
	-----------------------GAAGTTCTGTTATACACTC---------------------------------------------------------	19	5	8	4	2	3	3	1	3	10	9
	-----------------------GAAGTTCTGTTATACACTCAGGC-----------------------------------------------------	23	6	9	4	1	3	6	3	1	11	3
	-----------------------GAAGTTCTGTTATACACTCA--------------------------------------------------------	20	9	7	1	2	3	5	1	2	6	4
	-----------------------GAAGTTCTGTTATACACTCAGGCT----------------------------------------------------	24	3	1	2	3	5	2	1	-	5	-
rno-miR-148b-5p	-----------------------GAAGTTCTGTTATACACTCAGG------------------------------------------------------	22	1	2	2	1	-	6	1	3	1	4
	---------------------------------------------------------------CAGTGCATCACAGAACTTTGTC--------------	22	2	1	2	1	1	3	-	1	-	-
	---------------------------------------------------------------CAGTGCATCACAGAACTT------------------	18	4	1	-	-	1	-	-	-	1	-
	--------------------------------------------------------------TCAGTGCATCACAGAACTTTGTCTC------------	25	-	-	-	-	3	4	-	-	-	-
	---------------------------------------------------------------CAGTGCATCACAGAACTTT-----------------	19	3	-	2	-	-	1	-	-	-	-
	---------------------------------------------------------------CAGTGCATCACAGAACTTTGT---------------	21	-	1	-	1	-	-	1	2	1	-
	---------------------------------------------------------------CAGTGCATCACAGAACTTTG----------------	20	1	2	-	-	-	-	-	-	-	1
	------------------------AAGTTCTGTTATACACTCA--------------------------------------------------------	19	1	-	-	-	1	-	-	2	-	-
	----------------------------------------------------------------AGTGCATCACAGAACTTTGTC--------------	21	-	-	-	-	-	1	-	-	2	-
	----------------------TGAAGTTCTGTTATACACTC---------------------------------------------------------	20	-	-	-	-	2	-	-	-	-	-
	------------------------------------------------------------------TGCATCACAGAACTTTGTC--------------	19	-	-	-	-	-	1	-	-	-	-
	-----------------------------------------------------------------GTGCATCACAGAACTTTGTC--------------	20	-	-	-	-	-	-	1	-	-	-
	------------------------AAGTTCTGTTATACACTC---------------------------------------------------------	18	1	-	-	-	-	-	-	-	-	-
	------------------------AAGTTCTGTTATACACTCAGG------------------------------------------------------	21	-	1	-	-	-	-	-	-	-	-
	------------------------AAGTTCTGTTATACACTCAG-------------------------------------------------------	20	-	1	-	-	-	-	-	-	-	-
rat	CAGGCACTCTTAGCATTTGAGGTGAAGTTCTGTTATACACTCAGGCTGTGG--CTCTGAAAGTCAGTGCATCACAGAACTTTGTCTCGAAAGCTTTCTA
human	---------------------GTGAAGTTCTGTTATACACTCAGGCTGTGGCTCTCTGAAAGTCAGTGCATCACAGAACTTTGT---------------
mouse	-----------AGCATTTGAGGTGAAGTTCTGTTATACACTCAGGCTGTGG--CTCTGAAAGTCAGTGCATCACAGAACTTTGTCTCGAAAGCT-----
	**************************** *****************************
	.....>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.....	ENSRNOT00000053648 ENSRNOG00000035525 rno-mir-148b
rat	...........(((.(((((((..(((((((((.((.(((((((((....) ).))))......))).)).)))))))))..))))))).))).....	1.000 -34.60
human	..((((((((((.((.((((..((((.............)))))))).)).))))))))))..	0.910 -18.72
mouse	(((.(((((((..(((((((((.((.(((((((((....) ).))))......))).)).)))))))))..))))))).)))	0.841 -34.30

rat	chromosome:7:142195694:142195790:1	Same_strand\|Exonic_non-coding\|ENSRNOT00000053648\|ENSRNOG00000035525 ## ENSRNOG00000035525\|miRNA\|rno-mir-148b\|rno-mir-148b [Source:miRBase;Acc:MI0000616] ## {Repeats: L2 2711 2736 1 class=LINE/L2,L2 2814 2912 1 class=LINE} ## {MIR: rno-mir-148b}
human	chromosome:12:53017249:53017385:1	Same_strand\|Intronic_coding\|ENST00000262061\|ENSG00000111481\|protein_coding\|Coatomer subunit zeta-1 (Zeta-1-coat protein)(Zeta-1 COP) [Source:UniProtKB/Swiss-Prot;Acc:P61923] ## Same_strand\|Boundary_non-coding\|ENST00000362252\|ENSG00000199122\|miRNA\|hsa-mir-148b [Source:miRBase;Acc:MI0000811] ## {MIR: hsa-mir-148b}
mouse	chromosome:15:103115567:103115647:1	Same_strand\|Boundary_non-coding\|ENSMUST00000072242\|ENSMUSG00000060992\|protein_coding\|coatomer protein complex, subunit zeta 1 Gene [Source:MGI Symbol;Acc:MGI:1929063] ## Same_strand\|Intronic_coding\|ENSMUST00000100162\|ENSMUSG00000060992\|protein_coding\|coatomer protein complex, subunit zeta 1 Gene [Source:MGI Symbol;Acc:MGI:1929063] ## Same_strand\|Exonic_non-coding\|ENSMUST00000083626\|ENSMUSG00000065560\|miRNA\|mmu-mir-148b [Source:miRBase;Acc:MI0000617] ## {MIR: mmu-mir-148b}

rno-mir-28

Cloning frequencies
absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-28 5arm	212.500	115	269.500	345	483	391	284.500	500.500	502	425
rno-mir-28 3arm	89.500	73	471	511	401.500	241.500	288	449.500	603	335
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-28 5arm	0.007	0.005	0.015	0.020	0.024	0.030	0.022	0.026	0.033	0.028
rno-mir-28 3arm	0.003	0.003	0.026	0.030	0.020	0.018	0.022	0.024	0.040	0.022

sblock2989 (miRBase rno-mir-28) [miRNAknown_rep_lenNOK_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-28	0.001	no	LINE,LINE/L2	0.42/0.56	18/25/0.68	0.0 0.0	0.6 1.8	2166 2440	0 0	10 10	0 0	13 11	4 8	5arm 3arm	1 1	nd nd	0.10 0.11	2 2	6999	10	1	2

Families
Member of family miR-28/708 (seed AGGAGCU): rno-mir-708, rno-mir-28

		reads	miRBase family seed
seed	------------------AGGAGCU------------------------------------------------------------------	3510	miR-28/708
seed	----------------------------------------------------------ACUAGAU--------------------------	3283	miR-28*
seed	-----------------------------------------------------------CUAGAUU-------------------------	81	novel
seed	---------------------------------------------------------CACUAGA---------------------------	52	novel
seed	------------------------------------------------------------UAGAUUG------------------------	47	novel
seed	-----------------AAGGAGC-------------------------------------------------------------------	21	novel
seed	--------------------GAGCUCA----------------------------------------------------------------	2	novel
seed	-------------------------------------------------------------AGAUUGU-----------------------	1	novel
seed	--------------------------------------------------------------GAUUGUG----------------------	1	novel
seed	--------------------------------------------------------CCACUAG----------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-----------------AAGGAGCTCACAGTCTATTGA-----------------------------------------------------	21	98	53	121	113	227	193	140	228	248	248
rno-miR-28*	---------------------------------------------------------CACTAGATTGTGAGCTCCTGGA------------	22	19	30	154	192	128	60	79	144	188	80
	-----------------AAGGAGCTCACAGTCTAT--------------------------------------------------------	18	37	19	54	77	104	73	55	122	75	66
	---------------------------------------------------------CACTAGATTGTGAGCTCC----------------	18	23	12	74	108	76	52	52	81	114	70
	---------------------------------------------------------CACTAGATTGTGAGCTCCTG--------------	20	8	8	103	81	69	45	55	82	122	52
	---------------------------------------------------------CACTAGATTGTGAGCTCCT---------------	19	20	11	71	67	57	35	61	70	98	68
	-----------------AAGGAGCTCACAGTCTATTG------------------------------------------------------	20	25	16	52	62	87	55	40	85	66	49
	---------------------------------------------------------CACTAGATTGTGAGCTCCTGG-------------	21	7	11	50	44	46	27	25	46	48	27
	-----------------AAGGAGCTCACAGTCTATT-------------------------------------------------------	19	26	15	23	41	37	32	27	34	48	23
rno-miR-28	-----------------AAGGAGCTCACAGTCTATTGAG----------------------------------------------------	22	25	10	11	36	25	21	20	18	49	32
	-----------------AAGGAGCTCACAGTCTATTGAGT---------------------------------------------------	23	-	1	7	12	2	13	1	11	12	5
	---------------------------------------------------------CACTAGATTGTGAGCTCCTGGAG-----------	23	3	-	3	3	3	5	1	2	5	5
	----------------------------------------------------------ACTAGATTGTGAGCTCCTGGA------------	21	1	-	1	6	2	4	4	5	3	3
	----------------------------------------------------------ACTAGATTGTGAGCTCCTGGAG-----------	22	-	-	1	2	3	-	-	6	8	3
	-----------------------------------------------------------CTAGATTGTGAGCTCCTGGAG-----------	21	2	-	1	-	3	1	-	3	2	7
	--------------------------------------------------------CCACTAGATTGTGAGCTCCTG--------------	21	1	-	2	1	5	3	1	2	1	1
	----------------------------------------------------------ACTAGATTGTGAGCTCCTG--------------	19	-	-	2	-	1	3	1	-	3	4
	--------------------------------------------------------CCACTAGATTGTGAGCTCCTGG-------------	22	-	-	2	2	2	1	-	1	-	5
	-----------------------------------------------------------CTAGATTGTGAGCTCCTGG-------------	19	-	-	1	-	-	1	2	3	2	3
	--------------------------------------------------------CCACTAGATTGTGAGCTCC----------------	19	2	-	1	2	-	1	1	-	1	1
	----------------CAAGGAGCTCACAGTCTA---------------------------------------------------------	18	3	-	1	-	-	2	-	3	-	-
	-----------------------------------------------------------CTAGATTGTGAGCTCCTGGA------------	20	2	1	1	-	1	1	1	-	2	-
	--------------------------------------------------------CCACTAGATTGTGAGCTCCT---------------	20	-	-	2	1	2	-	-	1	-	2
	----------------------------------------------------------ACTAGATTGTGAGCTCCTGG-------------	20	-	-	-	-	1	-	1	2	1	2
	----------------------------------------------------------ACTAGATTGTGAGCTCCT---------------	18	1	-	-	2	1	1	-	1	-	-
	-----------------------------------------------------------CTAGATTGTGAGCTCCTG--------------	18	1	-	-	-	1	1	-	-	2	1
	-----------------AAGGAGCTCACAGTCTATTGAGTT--------------------------------------------------	24	-	-	-	1	-	-	1	1	1	1
	----------------CAAGGAGCTCACAGTCTATTGA-----------------------------------------------------	22	-	1	-	-	1	1	-	-	-	1
	--------------------------------------------------------CCACTAGATTGTGAGCTCCTGGA------------	23	-	-	-	-	-	1	1	-	2	-
	----------------CAAGGAGCTCACAGTCTATT-------------------------------------------------------	20	-	-	-	2	-	2	-	-	-	-
	----------------CAAGGAGCTCACAGTCTAT--------------------------------------------------------	19	-	-	1	1	-	-	-	-	1	-
	----------------------------------------------------------ACTAGATTGTGAGCTCCTGGAGG----------	23	-	-	-	-	-	-	-	1	1	-
	---------------------------------------------------------CACTAGATTGTGAGCTCCTGGAGG----------	24	-	-	1	1	-	-	-	-	-	-
	--------------------------------------------------------CCACTAGATTGTGAGCTC-----------------	18	-	-	-	-	-	-	1	-	-	-
	-------------------------------------------------------CCCACTAGATTGTGAGCTCC----------------	20	-	-	-	-	-	-	1	-	-	-
	-------------------GGAGCTCACAGTCTATTGA-----------------------------------------------------	19	-	-	-	-	-	-	1	-	-	-
	-------------------------------------------------------------AGATTGTGAGCTCCTGGA------------	18	-	-	-	-	1	-	-	-	-	-
	-----------------------------------------------------------CTAGATTGTGAGCTCCTGGAGG----------	22	-	-	-	-	-	-	-	-	-	1
	---------------------------------------------------------CACTAGATTGTGAGCTCCTGGAGGG---------	25	-	-	-	-	-	-	1	-	-	-
	----------------CAAGGAGCTCACAGTCTATTG------------------------------------------------------	21	-	-	-	-	-	-	-	-	1	-
	-------------------GGAGCTCACAGTCTATTGAG----------------------------------------------------	20	-	-	-	-	-	-	-	-	1	-
	------------------------------------------------------------TAGATTGTGAGCTCCTGGA------------	19	-	-	1	-	-	-	-	-	-	-
rat	----GGTCCCTACCCGCAAGGAGCTCACAGTCTATTGAGTTCCTTTTCTGATTCTCCCACTAGATTGTGAGCTCCTGGAGGGCAGGCACT-
human	----GGTCCTTGCCCTCAAGGAGCTCACAGTCTATTGAGTTACCTTTCTGACTTTCCCACTAGATTGTGAGCTCCTGGAGGGCAGGCACT-
mouse	AGGTGGTCCCTACCTTCAAGGAGCTCACAGTCTATTGAGTTGCCTTTCTGATTCTCCCACTAGATTGTGAGCTGCTGGAGGGCAGGCACTT
	***** * *********************** * ******* * ***************** **************
	+++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	ENSRNOT00000044279 ENSRNOG00000031669 Lpp
	+++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	ENSRNOT00000050389 ENSRNOG00000031669 Lpp
	..... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .....	ENSRNOT00000053659 ENSRNOG00000035536 rno-mir-28
rat	(((.(((.(((...((((((((((((((((..(((.((.......))..)))....))))))))))))))))...))).))).)))	1.000 -41.20
human	(((.(((((((((.((((((((((((((((.(((((((......)))))....)).)))))))))))))))).))))))))).)))	1.000 -50.60
mouse	(((((...(((.(((((.((.(((((((((((((..(((((........)))))......))))))))))))).)).))))).))))))))	0.998 -38.70

rat	chromosome:11:78139669:78139754:-1	Same_strand\|Intronic_coding\|ENSRNOT00000050389\|ENSRNOG00000031669 ## Same_strand\|Boundary_non-coding\|ENSRNOT00000044501\|ENSRNOG00000031669 ## Same_strand\|Exonic_non-coding\|ENSRNOT00000053659\|ENSRNOG00000035536 ## ENSRNOG00000031669\|protein_coding\|Lpp\|Lipoma-preferred partner homolog. [Source:UniProtKB/Swiss-Prot;Acc:Q5XI07] ## ENSRNOG00000035536\|miRNA\|rno-mir-28\|rno-mir-28 [Source:miRBase;Acc:MI0000861] ## {Repeats: L2 -92 3286 1 class=LINE,L2 3148 3173 -1 class=LINE/L2,L2 3145 3172 1 class=LINE/L2,L2 3252 3376 -1 class=LINE} ## {MIR: rno-mir-28}
human	chromosome:3:189889263:189889348:1	Same_strand\|Intronic_coding\|ENST00000312675\|ENSG00000145012\|protein_coding\|Lipoma-preferred partner (LIM domain-containing preferred translocation partner in lipoma) [Source:UniProtKB/Swiss-Prot;Acc:Q93052] ## Same_strand\|Exonic_non-coding\|ENST00000384918\|ENSG00000207651\|miRNA\|hsa-mir-28 [Source:miRBase;Acc:MI0000086] ## {Repeats: L2 -1 class=LINE/L2,L2 1 class=LINE/L2} ## {MIR: hsa-mir-28}
mouse	chromosome:16:24827937:24828027:1	Same_strand\|Intronic_coding\|ENSMUST00000115314\|ENSMUSG00000033306\|protein_coding\|LIM domain containing preferred translocation partner in lipoma Gene [Source:MGI Symbol;Acc:MGI:2441849] ## Same_strand\|Boundary_non-coding\|ENSMUST00000083560\|ENSMUSG00000065494\|miRNA\|mmu-mir-28 [Source:miRBase;Acc:MI0000690] ## {Repeats: L2 -1 class=LINE/L2,L2 1 class=LINE/L2} ## {MIR: mmu-mir-28}

rno-mir-339

Cloning frequencies
absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-339 5arm	861	541.500	2843	3123.500	2708	2555.500	937	1234.500	2484	2582.500
rno-mir-339 3arm	29	3	112	70	125	77	67	92	92	84
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-339 5arm	0.029	0.024	0.154	0.185	0.132	0.194	0.073	0.065	0.164	0.172
rno-mir-339 3arm	0.001	0.000	0.006	0.004	0.006	0.006	0.005	0.005	0.006	0.006

sblock3512 (miRBase rno-mir-339) [miRNAknown_rep_lenNOK_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-339	0.003	no	SINE,SINE/MIR	0.62/0.71	18/25/0.69	0.0 0.4	1.5 1.5	16123 373	0 0	10 10	0 0	15 23	3 6	5arm 3arm	2 2	nd nd	0.18 0.21	1 1	23768	10	1	2

Families
Member of family miR-339 (seed CCCUGUC): rno-mir-339, rno-mir-151, block1084584_cand, block2837956_cand

		reads	miRBase family seed
seed	----------------CCCUGUC-------------------------------------------------------------------------	22881	miR-339
seed	---------------------------------------------------GAGCGCC--------------------------------------	524	miR-339
seed	-----------------------------------------------------GCGCCUC------------------------------------	179	novel
seed	-----------------CCUGUCC------------------------------------------------------------------------	123	novel
seed	----------------------------------------------------AGCGCCU-------------------------------------	47	novel
seed	---------------UCCCUGU--------------------------------------------------------------------------	10	novel
seed	------------------CUGUCCU-----------------------------------------------------------------------	3	novel
seed	---------------------------------------------------------CUCGACG--------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	---------------TCCCTGTCCTCCAGGAGCTCAC-----------------------------------------------------------	22	380	223	929	1157	1155	1213	421	503	1169	1231
	---------------TCCCTGTCCTCCAGGAGC---------------------------------------------------------------	18	274	193	762	847	898	899	326	401	784	909
	---------------TCCCTGTCCTCCAGGAGCTCA------------------------------------------------------------	21	147	98	873	775	445	306	185	265	372	300
	---------------TCCCTGTCCTCCAGGAGCTC-------------------------------------------------------------	20	85	68	249	290	298	260	63	100	226	274
	---------------TCCCTGTCCTCCAGGAGCTCACGT---------------------------------------------------------	24	48	25	218	227	146	139	64	73	151	127
rno-miR-339-5p	---------------TCCCTGTCCTCCAGGAGCTCACG----------------------------------------------------------	23	22	13	79	106	104	108	25	37	91	115
	---------------TCCCTGTCCTCCAGGAGCT--------------------------------------------------------------	19	33	16	90	114	88	67	11	49	65	77
	--------------------------------------------------TGAGCGCCTCGACGACAGA---------------------------	19	11	-	38	32	43	23	13	25	23	24
	----------------------------------------------------AGCGCCTCGACGACAGAGCCA-----------------------	21	4	-	15	3	8	10	16	13	21	17
rno-miR-339-3p	--------------------------------------------------TGAGCGCCTCGACGACAGAGCCA-----------------------	23	-	-	15	2	15	9	10	13	9	8
	--------------------------------------------------TGAGCGCCTCGACGACAGAG--------------------------	20	1	-	8	6	14	9	3	9	7	7
	----------------CCCTGTCCTCCAGGAGCTCAC-----------------------------------------------------------	21	4	1	7	12	10	4	4	4	10	3
	--------------------------------------------------TGAGCGCCTCGACGACAGAGCC------------------------	22	-	1	2	10	13	3	4	9	8	8
	--------------------------------------------------TGAGCGCCTCGACGACAG----------------------------	18	2	2	2	4	10	8	3	7	6	4
	----------------------------------------------------AGCGCCTCGACGACAGAGCC------------------------	20	-	-	4	3	3	2	7	5	3	2
	----------------CCCTGTCCTCCAGGAGCTCA------------------------------------------------------------	20	3	1	4	5	3	1	-	1	3	1
	---------------------------------------------------GAGCGCCTCGACGACAGAGCCA-----------------------	22	-	-	5	-	2	2	3	2	3	3
	----------------------------------------------------AGCGCCTCGACGACAGAGC-------------------------	19	2	-	5	1	2	2	1	4	1	1
	--------------------------------------------------TGAGCGCCTCGACGACAGAGCCAGA---------------------	25	2	-	2	-	10	1	2	-	-	2
	----------------------------------------------------AGCGCCTCGACGACAGAGCCAG----------------------	22	1	-	4	5	-	1	-	-	1	2
	----------------CCCTGTCCTCCAGGAGCTC-------------------------------------------------------------	19	1	-	1	4	3	2	-	2	1	-
	--------------------------------------------------TGAGCGCCTCGACGACAGAGC-------------------------	21	3	-	3	-	3	-	-	1	1	2
	----------------CCCTGTCCTCCAGGAGCTCACG----------------------------------------------------------	22	1	-	1	4	4	-	-	-	2	-
	----------------CCCTGTCCTCCAGGAGCT--------------------------------------------------------------	18	-	-	5	3	-	1	1	-	1	-
	---------------------------------------------------GAGCGCCTCGACGACAGA---------------------------	18	-	-	3	1	2	-	-	1	3	1
	--------------------------------------------------TGAGCGCCTCGACGACAGAGCCAG----------------------	24	-	-	1	1	-	3	1	2	1	-
	---------------------------------------------------GAGCGCCTCGACGACAGAGCCAGA---------------------	24	2	-	-	1	-	-	1	-	-	2
	--------------GTCCCTGTCCTCCAGGAGC---------------------------------------------------------------	19	-	-	4	-	-	2	-	-	-	-
	----------------------------------------------------AGCGCCTCGACGACAGAGCCAGA---------------------	23	1	-	1	-	-	1	2	-	1	-
	---------------------------------------------------GAGCGCCTCGACGACAGAGCC------------------------	21	-	-	-	-	-	2	-	1	2	-
	---------------------------------------------------GAGCGCCTCGACGACAGAG--------------------------	19	-	-	3	-	-	-	-	-	1	-
	----------------------------------------------------AGCGCCTCGACGACAGAG--------------------------	18	-	-	1	-	-	1	1	-	1	-
	--------------GTCCCTGTCCTCCAGGAGCTCAC-----------------------------------------------------------	23	-	-	-	1	2	-	-	-	-	-
	----------------CCCTGTCCTCCAGGAGCTCACGT---------------------------------------------------------	23	-	-	1	2	-	-	-	-	-	-
	----------------CCCTGTCCTCCAGGAGCTCACGTA--------------------------------------------------------	24	-	-	1	-	1	-	-	-	-	-
	-----------------CCTGTCCTCCAGGAGCTCAC-----------------------------------------------------------	20	-	-	-	-	-	2	-	-	-	-
	---------------------------------------------------GAGCGCCTCGACGACAGAGCCAG----------------------	23	-	-	-	1	-	-	-	-	-	-
	-----------------CCTGTCCTCCAGGAGCTCA------------------------------------------------------------	19	-	-	-	-	-	1	-	-	-	-
	--------------GTCCCTGTCCTCCAGGAGCTCA------------------------------------------------------------	22	-	-	-	-	-	-	-	-	1	-
	--------------------------------------------------------CCTCGACGACAGAGCCAG----------------------	18	-	-	-	-	-	-	-	-	-	1
rat	ACGGGGTGGACACCGTCCCTGTCCTCCAGGAGCTCACGTATGCCTGCCTGTGAGCGCCTCGACGACAGAGCCAGAGTCCACCCCTGCACTGCCCAA
mouse	---------------TCCCTGTCCTCCAGGAGCTCACGTATGCCTGCCTGTGAGCGCCTCGGCGACAGAGC-------------------------
	******************************************** *******
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000001734 ENSRNOG00000001289 LOC498154
	.....>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.....	ENSRNOT00000053602 ENSRNOG00000035479 rno-mir-339
rat	..(((((((((.(.(.(.(((((.((.(((.(((((((((....)))..)))))).))).)).))))).).).).)))))))))............	1.000 -44.20
mouse	...(((((..(((((.(((((((((....)))..)))))).))).)).)))))...	1.000 -22.70

rat	chromosome:12:15778323:15778418:1	Same_strand\|Boundary_non-coding\|ENSRNOT00000053602\|ENSRNOG00000035479 ## Same_strand\|Exonic_non-coding\|ENSRNOT00000053602\|ENSRNOG00000035479 ## Same_strand\|Intronic_coding\|ENSRNOT00000001734\|ENSRNOG00000001289 ## ENSRNOG00000035479\|miRNA\|rno-mir-339\|rno-mir-339 [Source:miRBase;Acc:MI0000620] ## ENSRNOG00000001289\|protein_coding\|LOC498154\|Uncharacterized protein C7orf50 homolog. [Source:UniProtKB/Swiss-Prot;Acc:Q5I0E3] ## {Repeats: MIRm 162 184 -1 class=SINE/MIR,MIRm -68 208 -1 class=SINE,MIRm 183 202 -1 class=SINE/MIR} ## {MIR: rno-mir-339}
mouse	chromosome:5:139845584:139845719:-1	Same_strand\|Intronic_coding\|ENSMUST00000066052\|ENSMUSG00000053553\|protein_coding\|RIKEN cDNA 3110082I17 gene Gene [Source:MGI Symbol;Acc:MGI:1920462] ## Same_strand\|Boundary_non-coding\|ENSMUST00000083659\|ENSMUSG00000065593\|miRNA\|mmu-mir-339 [Source:miRBase;Acc:MI0000621] ## {Repeats: MIRm -1 class=SINE/MIR} ## {MIR: mmu-mir-339}

miRNAknown_cloningHIGH_multiarm_DicerNOK_loopOverlap_randfoldOK (3 loci)

rno-mir-409

Cloning frequencies
absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-409 5arm	1540	1173	12	3	11	23	2	4	17	31
rno-mir-409 3arm	1717	1214	11	4	35	33	16	11	50	80
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-409 5arm	0.051	0.051	0.001	0.000	0.001	0.002	0.000	0.000	0.001	0.002
rno-mir-409 3arm	0.057	0.053	0.001	0.000	0.002	0.003	0.001	0.001	0.003	0.005

sblock10519 (miRBase rno-mir-409) [miRNAknown_cloningHIGH_multiarm_DicerNOK_loopOverlap_randfoldOK]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
miRBase rno-mir-409	0.001	no	no	0.47/0.61	18/25/0.75	0.0 0.2	2.8 0.3	2270 2021	0 0	10 10	0 0	13 10	-3 3	5arm_loop 3arm	1 1	nd nd	0.11 0.18	2 2	5987	10	5	2

Clusters
Located in cluster 76: rno-mir-541, rno-mir-409, rno-mir-412, rno-mir-369, rno-mir-410

		reads	miRBase family seed
seed	--------------------------GGUUACC---------------------------------------------------------------------------	2813	miR-409
seed	----------------------------------------------------------AAUGUUG-------------------------------------------	1916	novel
seed	-----------------------------------------------------------AUGUUGC------------------------------------------	865	miR-409
seed	---------------------------------------------------------GAAUGUU--------------------------------------------	376	novel
seed	--------------------------------------------------------CGAAUGU---------------------------------------------	4	novel
seed	-----------------------------------------------------GGACGAA------------------------------------------------	4	novel
seed	-------------------------------------------------------------GUUGCUC----------------------------------------	3	novel
seed	---------------------------GUUACCC--------------------------------------------------------------------------	2	novel
seed	------------------------------------------------------------UGUUGCU-----------------------------------------	2	novel
seed	----------------------------UUACCCG-------------------------------------------------------------------------	1	novel
seed	--------------------------------------------------------------UUGCUCG---------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	---------------------------------------------------------GAATGTTGCTCGGTGAACCCCT-----------------------------	22	578	413	4	1	8	11	6	5	13	12
	-------------------------AGGTTACCCGAGCAACTTTGCATC-----------------------------------------------------------	24	510	316	3	-	2	3	1	1	2	6
	-------------------------AGGTTACCCGAGCAACTTT----------------------------------------------------------------	19	395	325	3	1	6	9	1	2	6	8
	---------------------------------------------------------GAATGTTGCTCGGTGAACCCC------------------------------	21	330	203	-	-	5	8	4	1	7	6
	-------------------------AGGTTACCCGAGCAACTTTGC--------------------------------------------------------------	21	273	264	4	1	-	1	-	-	4	6
	----------------------------------------------------------AATGTTGCTCGGTGAACCCCT-----------------------------	21	267	230	-	-	6	2	2	-	5	8
	-------------------------AGGTTACCCGAGCAACTT-----------------------------------------------------------------	18	187	129	1	1	3	6	-	1	1	7
rno-miR-409-3p	----------------------------------------------------------AATGTTGCTCGGTGAACCCC------------------------------	20	127	75	-	-	3	-	-	-	2	6
	--------------------------------------------------------CGAATGTTGCTCGGTGAACCCCT-----------------------------	23	78	71	1	1	2	4	1	-	10	23
rno-miR-409-5p	-------------------------AGGTTACCCGAGCAACTTTG---------------------------------------------------------------	20	78	86	-	-	-	1	-	-	2	1
	---------------------------------------------------------GAATGTTGCTCGGTGAACC--------------------------------	19	79	55	-	-	4	1	1	1	1	-
	-------------------------AGGTTACCCGAGCAACTTTGCA-------------------------------------------------------------	22	74	45	1	-	-	-	-	-	2	2
	--------------------------------------------------------CGAATGTTGCTCGGTGAACCCC------------------------------	22	49	34	2	-	2	3	-	1	6	8
	---------------------------------------------------------GAATGTTGCTCGGTGAACCC-------------------------------	20	42	32	1	-	-	1	-	1	1	4
	---------------------------------------------------------GAATGTTGCTCGGTGAAC---------------------------------	18	36	24	-	-	1	3	-	-	-	-
	----------------------------------------------------------AATGTTGCTCGGTGAACCC-------------------------------	19	37	22	-	-	-	-	-	-	-	1
	----------------------------------------------------------AATGTTGCTCGGTGAACC--------------------------------	18	20	17	1	-	1	-	1	-	-	-
	-------------------------AGGTTACCCGAGCAACTTTGCATCT----------------------------------------------------------	25	20	4	-	-	-	3	-	-	-	-
	--------------------------------------------------------CGAATGTTGCTCGGTGAAC---------------------------------	19	13	5	-	1	-	-	-	-	2	3
	--------------------------------------------------------CGAATGTTGCTCGGTGAACCC-------------------------------	21	11	6	2	-	-	-	1	-	-	1
	--------------------------------------------------------CGAATGTTGCTCGGTGAACC--------------------------------	20	8	7	-	-	-	-	-	-	2	2
	----------------------------------------------------------AATGTTGCTCGGTGAACCCCTT----------------------------	22	11	7	-	1	-	-	-	-	-	-
	----------------------------------------------------------AATGTTGCTCGGTGAACCCCTTT---------------------------	23	8	1	-	-	1	-	-	-	-	2
	--------------------------------------------------------CGAATGTTGCTCGGTGAA----------------------------------	18	6	3	-	-	-	-	-	-	1	2
	---------------------------------------------------------GAATGTTGCTCGGTGAACCCCTT----------------------------	23	5	2	-	-	1	-	-	2	-	1
	-------------------------AGGTTACCCGAGCAACTTTGCAT------------------------------------------------------------	23	2	2	-	-	-	-	-	-	-	1
	--------------------------------------------------------CGAATGTTGCTCGGTGAACCCCTT----------------------------	24	1	1	-	-	-	-	-	-	-	1
	---------------------------------------------------------GAATGTTGCTCGGTGAACCCCTTT---------------------------	24	2	-	-	-	-	-	-	-	-	-
	----------------------------------------------------AGGACGAATGTTGCTCGGT-------------------------------------	19	2	-	-	-	-	-	-	-	-	-
	----------------------------------------------------AGGACGAATGTTGCTCGGTGA-----------------------------------	21	-	2	-	-	-	-	-	-	-	-
	------------------------------------------------------------TGTTGCTCGGTGAACCCCT-----------------------------	19	2	-	-	-	-	-	-	-	-	-
	--------------------------GGTTACCCGAGCAACTTTGC--------------------------------------------------------------	20	-	2	-	-	-	-	-	-	-	-
	-----------------------------------------------------------ATGTTGCTCGGTGAACCCCT-----------------------------	20	-	-	-	-	1	-	-	-	-	-
	-----------------------------------------------------------ATGTTGCTCGGTGAACCCC------------------------------	19	-	1	-	-	-	-	-	-	-	-
	-------------------------------------------------------ACGAATGTTGCTCGGTGAACC--------------------------------	21	1	-	-	-	-	-	-	-	-	-
	--------------------------------------------------------CGAATGTTGCTCGGTGAACCCCTTT---------------------------	25	1	-	-	-	-	-	-	-	-	-
	-------------------------------------------------------ACGAATGTTGCTCGGTGAACCC-------------------------------	22	-	1	-	-	-	-	-	-	-	-
	-------------------------------------------------------ACGAATGTTGCTCGGTGAA----------------------------------	19	-	1	-	-	-	-	-	-	-	-
	-------------------------------------------------------ACGAATGTTGCTCGGTGA-----------------------------------	18	-	1	-	-	-	-	-	-	-	-
	----------------------------------------------------------AATGTTGCTCGGTGAACCCCTTTTC-------------------------	25	1	-	-	-	-	-	-	-	-	-
	---------------------------GTTACCCGAGCAACTTTGCATC-----------------------------------------------------------	22	1	-	-	-	-	-	-	-	-	-
	------------------------------------------------------------TGTTGCTCGGTGAACCCC------------------------------	18	1	-	-	-	-	-	-	-	-	-
	-------------------------------------------------------------GTTGCTCGGTGAACCCCT-----------------------------	18	1	-	-	-	-	-	-	-	-	-
rat	------------GGTACTCGGAGAGAGGTTACCCGAGCAACTTTGCATCTGGAGGACGAATGTTGCTCGGTGAACCCCTTTTCGGTATC-------------------
human	GAGCCTCTCCATGGTACTCGGGGAGAGGTTACCCGAGCAACTTTGCATCTGGACGACGAATGTTGCTCGGTGAACCCCTTTTCGGTATCAAATTCCACCAGGGAGGCC
mouse	GAGCCTCTCCGTGGTACTCGGAGAGAGGTTACCCGAGCAACTTTGCATCTGGAGGACGAATGTTGCTCGGTGAACCCCTTTTCGGTATCAAATCCCTCCAGGGAGGCC
	******* *************************** *********************************
	....> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >....	ENSRNOT00000053696 ENSRNOG00000035573 rno-mir-409
rat	(((((.(((((((.((((..((((((((((((((........).)))).)))))))))..)))).))))))))))))	1.000 -36.40
human	..(((((((..((((((.((..(((.((((..(((((((((((((..((.....)))))).)))))))))..)))).)))..))))))))..........))))))).	0.845 -47.50
mouse	..(((((.((.((((((.(((((((.((((..(((((((((((((..((.....)))))).)))))))))..)))).)))))))))))))..........))))))).	0.836 -49.30

rat	chromosome:6:134424504:134424580:1	Same_strand\|Exonic_non-coding\|ENSRNOT00000053696\|ENSRNOG00000035573 ## ENSRNOG00000035573\|miRNA\|rno-mir-409\|rno-mir-409 [Source:miRBase;Acc:MI0003550] ## {MIR: rno-mir-409}
human	chromosome:14:100601379:100601486:1	Same_strand\|Boundary_non-coding\|ENST00000362237\|ENSG00000199107\|miRNA\|hsa-mir-409 [Source:miRBase;Acc:MI0001735] ## {SimpF: oe = 0.96 0 CpG} ## {MIR: hsa-mir-409}
mouse	chromosome:12:110981357:110981464:1	Same_strand\|Boundary_non-coding\|ENSMUST00000083544\|ENSMUSG00000065478\|miRNA\|mmu-mir-409 [Source:miRBase;Acc:MI0001160] ## {MIR: mmu-mir-409}

Back to summary page

other miRBase miRNAs:

Page 1

Page 6

Page 11

miR-Intess™

rno-mir-370

sblock10448 (miRBase rno-mir-370) [miRNAknown_rep_lenNOK_cloningHIGH_multiarm_DicerNOK_randfoldOK]

rno-mir-652

sblock12654 (miRBase rno-mir-652) [miRNAknown_rep_lenNOK_cloningHIGH_multiarm_DicerNOK_randfoldOK]

rno-mir-421

sblock12685 (miRBase rno-mir-421) [miRNAknown_rep_lenNOK_cloningHIGH_multiarm_DicerNOK_randfoldOK]

rno-mir-708

sblock2035 (miRBase rno-mir-708) [miRNAknown_rep_lenNOK_cloningHIGH_multiarm_DicerNOK_randfoldOK]

rno-mir-130b

sblock3193 (miRBase rno-mir-130b) [miRNAknown_rep_lenNOK_cloningHIGH_multiarm_DicerOK_randfoldOK]

rno-mir-31

sblock9372 (miRBase rno-mir-31) [miRNAknown_rep_lenNOK_cloningHIGH_multiarm_DicerOK_randfoldOK]

rno-mir-148b

sblock11523 (miRBase rno-mir-148b) [miRNAknown_rep_lenNOK_cloningHIGH_multiarm_DicerOK_randfoldOK]

rno-mir-28

sblock2989 (miRBase rno-mir-28) [miRNAknown_rep_lenNOK_cloningHIGH_multiarm_DicerOK_randfoldOK]

rno-mir-339

sblock3512 (miRBase rno-mir-339) [miRNAknown_rep_lenNOK_cloningHIGH_multiarm_DicerOK_randfoldOK]

rno-mir-409

sblock10519 (miRBase rno-mir-409) [miRNAknown_cloningHIGH_multiarm_DicerNOK_loopOverlap_randfoldOK]