miR-Intess™

other miRBase miRNAs

miRNAknown_cloningHIGH_multiarm_DicerNOK_loopOverlap_randfoldOK (3 loci)

rno-mir-451

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-451 5arm	4893	7127	8872	8489	154310	93121	20631	16715	1853	2381
rno-mir-451 3arm	1	3	0	3	6	7	5	3	1	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-451 5arm	0.163	0.311	0.481	0.503	7.516	7.058	1.605	0.880	0.122	0.158
rno-mir-451 3arm	0.000	0.000	0	0.000	0.000	0.001	0.000	0.000	0.000	0

sblock2721 (miRBase rno-mir-451) [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-451

0.001

no

no

0.29/0.58

18/25/0.85

0.0 0.0 0.1

1.3 1.4 0.9

3 200736 29

0 0 0

2 10 8

0 0 0

1 16 5

11 -5 3

5arm 5arm_loop_3arm 3arm

1 1 1

nd nd nd

0.18 0.15 0.10

2 3 2

318421

10

4

0

Clusters

Located in cluster 14: rno-mir-144, rno-mir-451

		reads	miRBase family seed
seed	-----------------AACCGUU------------------------------------------------	318073	miR-451
seed	------------------ACCGUUA-----------------------------------------------	173	novel
seed	-------------------CCGUUAC----------------------------------------------	58	novel
seed	----------------------UUACCAU-------------------------------------------	29	novel
seed	--------------------------------------------UGGUAAU---------------------	26	novel
seed	--------------------CGUUACC---------------------------------------------	19	novel
seed	----------------AAACCGU-------------------------------------------------	17	novel
seed	---------------------GUUACCA--------------------------------------------	11	novel
seed	-------------------------CCAUUAC----------------------------------------	4	novel
seed	---------GGCGAGG--------------------------------------------------------	3	novel
seed	--UGGGAAU---------------------------------------------------------------	3	novel
seed	----------GCGAGGA-------------------------------------------------------	2	novel
seed	---------------------------------------------GGUAAUG--------------------	2	novel
seed	------------------------------------------AAUGGUA-----------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	----------------AAACCGTTACCATTACTGAGTTT---------------------------------	23	1162	1821	2588	2556	51476	28491	5707	4319	530	751
	----------------AAACCGTTACCATTACTGAG------------------------------------	20	1052	1450	1778	1632	32613	22814	4020	3215	390	455
	----------------AAACCGTTACCATTACTGAGT-----------------------------------	21	845	1121	1487	1357	27363	16701	3593	2867	308	424
rno-miR-451	----------------AAACCGTTACCATTACTGAGTT----------------------------------	22	1056	1635	1906	1765	21278	7965	4633	3815	392	359
	----------------AAACCGTTACCATTACTGA-------------------------------------	19	382	587	617	665	11896	8358	1437	1225	137	215
	----------------AAACCGTTACCATTACTG--------------------------------------	18	377	487	447	490	9106	8214	1188	1232	89	166
	----------------AAACCGTTACCATTACTGAGTTTAG-------------------------------	25	11	10	17	7	255	320	17	14	4	6
	----------------AAACCGTTACCATTACTGAGTTTA--------------------------------	24	4	8	12	5	163	182	18	10	1	4
	-----------------AACCGTTACCATTACTGAG------------------------------------	19	1	-	2	3	32	19	2	2	1	-
	-----------------AACCGTTACCATTACTGAGTTT---------------------------------	22	2	1	1	2	15	9	5	3	-	-
	-----------------AACCGTTACCATTACTGAGT-----------------------------------	20	-	-	2	2	22	7	1	3	-	-
	------------------ACCGTTACCATTACTGAGTTT---------------------------------	21	-	-	4	-	17	7	3	-	-	-
	---------------------GTTACCATTACTGAGTTT---------------------------------	18	1	1	5	2	10	5	-	2	-	-
	-----------------AACCGTTACCATTACTGAGTT----------------------------------	21	-	1	-	-	10	4	-	2	-	1
	-----------------AACCGTTACCATTACTGA-------------------------------------	18	-	-	2	-	9	3	1	1	-	-
	-------------------------------------------ATGGTAATGGTTCTCTTGC----------	19	1	2	-	2	-	2	3	1	1	-
	------------------ACCGTTACCATTACTGAGTT----------------------------------	20	-	-	1	-	3	4	-	1	-	-
	-------------------CCGTTACCATTACTGAGTTT---------------------------------	20	-	-	-	2	4	1	-	-	-	-
	------------------ACCGTTACCATTACTGAG------------------------------------	18	-	-	-	-	6	-	1	-	-	-
	-------------------CCGTTACCATTACTGAGTT----------------------------------	19	-	-	-	-	2	2	1	1	-	-
	-------------------------------------------ATGGTAATGGTTCTCTTGCT---------	20	-	-	-	-	1	1	2	2	-	-
	-------------------CCGTTACCATTACTGAGT-----------------------------------	18	-	-	-	-	2	1	2	1	-	-
	---------------GAAACCGTTACCATTACTG--------------------------------------	19	-	-	-	-	2	1	1	1	-	-
	-------------------------------------------ATGGTAATGGTTCTCTTG-----------	18	-	1	-	-	2	2	-	-	-	-
	--------------------CGTTACCATTACTGAGTTT---------------------------------	19	-	1	-	-	3	-	-	-	-	-
	--------------------CGTTACCATTACTGAGTT----------------------------------	18	-	-	-	1	2	1	-	-	-	-
	------------------ACCGTTACCATTACTGAGTTTAG-------------------------------	23	-	-	-	-	1	2	-	1	-	-
	------------------ACCGTTACCATTACTGAGT-----------------------------------	19	-	-	1	-	3	-	-	-	-	-
	---------------GAAACCGTTACCATTACTGAGTTT---------------------------------	24	-	-	-	-	2	1	-	-	-	-
	---------------GAAACCGTTACCATTACTGAG------------------------------------	21	-	-	-	-	2	1	-	-	-	-
	---------------------GTTACCATTACTGAGTTTAG-------------------------------	20	-	-	-	-	1	1	-	-	-	-
	---------------GAAACCGTTACCATTACT---------------------------------------	18	-	-	-	-	1	1	-	-	-	-
	--------------------CGTTACCATTACTGAGTTTAG-------------------------------	21	-	-	-	-	2	-	-	-	-	-
	-------------------------------------------ATGGTAATGGTTCTCTTGCTGCTC-----	24	-	-	-	1	-	1	-	-	-	-
	---------------GAAACCGTTACCATTACTGA-------------------------------------	20	-	-	-	-	2	-	-	-	-	-
	--------TGGCGAGGAAACCGTTACCATT------------------------------------------	22	-	-	2	-	-	-	-	-	-	-
	------------------------ACCATTACTGAGTTTAGT------------------------------	18	-	-	-	-	-	2	-	-	-	-
	-----------------AACCGTTACCATTACTGAGTTTA--------------------------------	23	-	-	-	-	1	1	-	-	-	-
	------------------ACCGTTACCATTACTGAGTTTA--------------------------------	22	-	-	-	-	2	-	-	-	-	-
	-TTGGGAATGGCGAGGAAACCGT-------------------------------------------------	22	-	1	-	-	-	1	-	-	-	-
	------------------------ACCATTACTGAGTTTAGTAA----------------------------	20	-	-	-	-	-	-	1	-	-	-
	---------------GAAACCGTTACCATTACTGAGT-----------------------------------	22	-	-	-	-	1	-	-	-	-	-
	-TTGGGAATGGCGAGGAAACC---------------------------------------------------	20	-	-	-	-	-	1	-	-	-	-
	--------------------------------------------TGGTAATGGTTCTCTTGC----------	18	-	-	-	-	1	-	-	-	-	-
	-----------------------------------------TAATGGTAATGGTTCTCTTG-----------	20	-	-	-	-	1	-	-	-	-	-
	------------------ACCGTTACCATTACTGAGTTTAGT------------------------------	24	-	1	-	-	-	-	-	-	-	-
	---------GGCGAGGAAACCGTTACCATTAC----------------------------------------	23	-	1	-	-	-	-	-	-	-	-
	--------TGGCGAGGAAACCGTTACC---------------------------------------------	19	-	-	-	-	-	-	-	-	1	-
	--------------------CGTTACCATTACTGAGTTTA--------------------------------	20	-	-	-	-	1	-	-	-	-	-
	------------------------ACCATTACTGAGTTTAGTA-----------------------------	19	-	-	-	-	1	-	-	-	-	-
	--------------------------------------------TGGTAATGGTTCTCTTGCTG--------	20	-	-	-	-	-	1	-	-	-	-
	---------------------GTTACCATTACTGAGTTTAGTAAT---------------------------	24	-	-	-	-	-	1	-	-	-	-
	---------GGCGAGGAAACCGTTACCA--------------------------------------------	19	-	1	-	-	-	-	-	-	-	-
	---------------GAAACCGTTACCATTACTGAGTT----------------------------------	23	-	-	-	-	1	-	-	-	-	-
	-------------------------------------------ATGGTAATGGTTCTCTTGCTG--------	21	-	-	-	-	1	-	-	-	-	-
rat	tttgggaatggcgaggAAACCGTTACCATTACTGAGTTTagtaatggtaatggttctcttgctgctcccaca
	************************************************************************
	.....>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.....	ENSRNOT00000054381 ENSRNOG00000036258 rno-mir-451
rat	..(((((..((((((..(((((((((((((((((....)))))))))))))))))..))))))..)))))..	1.000 -43.90

rat

chromosome:10:64129518:64129589:1

Same_strand|Boundary_non-coding|ENSRNOT00000054381|ENSRNOG00000036258 ## Same_strand|Exonic_non-coding|ENSRNOT00000054381|ENSRNOG00000036258 ## ENSRNOG00000036258|miRNA|rno-mir-451|rno-mir-451 [Source:miRBase;Acc:MI0001731] ## {MIR: rno-mir-451}

rno-mir-205

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-205 5arm	93	111	30	17	138	45	5	25	2058	917
rno-mir-205 3arm	0	0	0	0	0	0	0	0	0	2
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-205 5arm	0.003	0.005	0.002	0.001	0.007	0.003	0.000	0.001	0.136	0.061
rno-mir-205 3arm	0	0	0	0	0	0	0	0	0	0.000

sblock3828 (miRBase rno-mir-205) [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-205

0.001

no

no

0.45/0.58

18/25/0.76

0.0 0.0

1.9 0.5

2616 2

0 0

10 1

0 0

32 20

-2 2

5arm_loop 3arm

1 1

nd nd

0.10 0.15

1 2

3441

10

4

0

		reads	miRBase family seed
seed	----------------------------------CCUUCAU---------------------------------------------------------------------	3411	miR-205
seed	-----------------------------------CUUCAUU--------------------------------------------------------------------	28	novel
seed	-----------------------------------------------------------------------AUUUCAG--------------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	---------------------------------TCCTTCATTCCACCGGAGTCTGTC-----------------------------------------------------	24	12	16	7	3	26	5	-	1	520	245
rno-miR-205	---------------------------------TCCTTCATTCCACCGGAGTCTG-------------------------------------------------------	22	21	27	1	1	37	10	1	4	546	172
	---------------------------------TCCTTCATTCCACCGGAG-----------------------------------------------------------	18	25	27	10	7	31	12	2	9	424	205
	---------------------------------TCCTTCATTCCACCGGAGTC---------------------------------------------------------	20	20	20	3	2	24	11	1	3	294	139
	---------------------------------TCCTTCATTCCACCGGAGTCT--------------------------------------------------------	21	12	16	7	3	13	5	1	6	210	113
	---------------------------------TCCTTCATTCCACCGGAGT----------------------------------------------------------	19	1	3	1	-	5	1	-	-	29	28
	---------------------------------TCCTTCATTCCACCGGAGTCTGT------------------------------------------------------	23	2	1	1	1	1	1	-	1	15	8
	----------------------------------CCTTCATTCCACCGGAGTCTG-------------------------------------------------------	21	-	1	-	-	1	-	-	-	4	2
	----------------------------------CCTTCATTCCACCGGAGTC---------------------------------------------------------	19	-	-	-	-	-	-	-	1	6	-
	----------------------------------CCTTCATTCCACCGGAGTCT--------------------------------------------------------	20	-	-	-	-	-	-	-	-	5	2
	----------------------------------CCTTCATTCCACCGGAGTCTGTC-----------------------------------------------------	23	-	-	-	-	-	-	-	-	5	1
	---------------------------------TCCTTCATTCCACCGGAGTCTGTCT----------------------------------------------------	25	-	-	-	-	-	-	-	-	-	2
	----------------------------------------------------------------------GATTTCAGTGGAGTGAAGCT--------------------	20	-	-	-	-	-	-	-	-	-	1
	----------------------------------------------------------------------GATTTCAGTGGAGTGAAGC---------------------	19	-	-	-	-	-	-	-	-	-	1
rat	AAACAGCCCCAGACAATCCATGGG-TCCTCCTGTCCTTCATTCCACCGGAGTCTGTCTTATG-CCAACCAGATTTCAGTGGAGTGAAGCTCAGGAGGCATGGAGCTGCCA
human	----------------TCCATGTGCTTCTCTTGTCCTTCATTCCACCGGAGTCTGTCTCATACCCAACCAGATTTCAGTGGAGTGAAGTTCAGGAGGCATGGA-------
mouse	----------------TCCATGGG-TCCTCTTGTCCTTCATTCCACCGGAGTCTGTCTTATG-CCAACCAGATTTCAGTGGAGTGAAGCTCAGGAGGCATGGA-------
	****** * * *** *************************** **  ************************* **************
	.....>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.....	ENSRNOT00000053643 ENSRNOG00000035520 rno-mir-205
rat	...((((.........((((((.. .(((((((..(((((((((((.((((((((....... .....)))))))).)))))))))))..)))))))))))))))))...	1.000 -50.90
human	(((((((....((((((..(((((((((((.((((((((.............)))))))).)))))))))))..)))))))))))))	1.000 -43.62
mouse	((((((.. .(((((((..(((((((((((.((((((((....... .....)))))))).)))))))))))..)))))))))))))	1.000 -44.50

rat	chromosome:13:109352371:109352478:-1	Same_strand|Exonic_non-coding|ENSRNOT00000053643|ENSRNOG00000035520 ## ENSRNOG00000035520|miRNA|rno-mir-205|rno-mir-205 [Source:miRBase;Acc:MI0000947] ## {MIR: rno-mir-205}
human	chromosome:1:207672117:207672203:1	Same_strand|Exonic_non-coding|ENST00000384891|ENSG00000207623|miRNA|hsa-mir-205 [Source:miRBase;Acc:MI0000285] ## {MIR: hsa-mir-205}
mouse	chromosome:1:195333650:195333734:-1	Same_strand|Boundary_non-coding|ENSMUST00000083599|ENSMUSG00000065533|miRNA|mmu-mir-205 [Source:miRBase;Acc:MI0000248] ## {MIR: mmu-mir-205}

miRNAknown_lenNOK_cloningHIGH_multiarm_DicerNOK_shortStem_randfoldOK (3 loci)

rno-mir-381

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-381 5arm	62	34	2	0	0	3	0	0	0	1
rno-mir-381 3arm	63	25	0	0	1	3	1	1	1	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-381 5arm	0.002	0.001	0.000	0	0	0.000	0	0	0	0.000
rno-mir-381 3arm	0.002	0.001	0	0	0.000	0.000	0.000	0.000	0.000	0

sblock10506 (miRBase rno-mir-381) [miRNAknown_lenNOK_cloningHIGH_multiarm_DicerNOK_shortStem_randfoldOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

miRBase rno-mir-381

0.001

no

no

0.43/0.56

18/24/0.52

0.0 0.0

1.9 0.6

80 71

0 0

5 7

0 0

0 0

4 9

5arm 3arm

1 1

nd nd

0.14 0.11

1 1

196

9

3

0

Clusters

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

Families

Member of family miR-381 (seed AUACAAG): rno-mir-381, rno-mir-381

		reads	miRBase family seed
seed	--------------GCGAGGU------------------------------------------------------------------	101	novel
seed	-------------------------------------------------------AUACAAG-------------------------	91	miR-381
seed	------------------------------------------------------UAUACAA--------------------------	3	let-7b*
seed	----------------GAGGUUG----------------------------------------------------------------	1	miR-672
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-miR-381	------------------------------------------------------TATACAAGGGCAAGCTCTC--------------	19	25	18	-	1	3	-	1	-	-
	-------------AGCGAGGTTGCCCTTTGTATAT----------------------------------------------------	22	22	13	1	-	2	-	-	-	1
	------------------------------------------------------TATACAAGGGCAAGCTCTCT-------------	20	28	4	-	-	-	1	-	1	-
	-------------AGCGAGGTTGCCCTTTGTA-------------------------------------------------------	19	22	9	1	-	-	-	-	-	-
	-------------AGCGAGGTTGCCCTTTGTATA-----------------------------------------------------	21	6	7	-	-	-	-	-	-	-
	------------------------------------------------------TATACAAGGGCAAGCTCT---------------	18	6	3	-	-	-	-	-	-	-
	-------------AGCGAGGTTGCCCTTTGTATATTC--------------------------------------------------	24	7	-	-	-	-	-	-	-	-
	-------------AGCGAGGTTGCCCTTTGTAT------------------------------------------------------	20	1	3	-	-	-	-	-	-	-
	-------------AGCGAGGTTGCCCTTTGT--------------------------------------------------------	18	4	-	-	-	-	-	-	-	-
	-----------------------------------------------------ATATACAAGGGCAAGCTCTCT-------------	21	2	-	-	-	-	-	-	-	-
	-------------AGCGAGGTTGCCCTTTGTATATT---------------------------------------------------	23	-	1	-	-	1	-	-	-	-
	-----------------------------------------------------ATATACAAGGGCAAGCTCTC--------------	20	1	-	-	-	-	-	-	-	-
	---------------CGAGGTTGCCCTTTGTATAT----------------------------------------------------	20	-	1	-	-	-	-	-	-	-
rat	-------------AGCGAGGTTGCCCTTTGTATATTCGGTTTATTGACATGGGATATACAAGGGCAAGCTCTCT-------------
human	GTTTGGTACTTAAAGCGAGGTTGCCCTTTGTATATTCGGTTTATTGACATGGAATATACAAGGGCAAGCTCTCTGTGAGTATCAAAC
mouse	GTTTGGTACTTAAAGCGAGGTTGCCCTTTGTATATTCGGTTTATTGACATGGAATATACAAGGGCAAGCTCTCTGTGAGTATCAAAC
	*************************************** *********************
	.....             >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>             .....	ENSRNOT00000053616 ENSRNOG00000035493 rno-mir-381
rat	((.(((.((((((((.((((((((.(((....)))...)))))))))))))))).))).))	1.000 -28.30
human	((((((((((((.((.(((.((((((.((((((((((.(((....)))...)))))))))))))))).))).)).))))))))))))	1.000 -44.50
mouse	((((((((((((.((.(((.((((((.((((((((((.(((....)))...)))))))))))))))).))).)).))))))))))))	1.000 -44.50

rat	chromosome:6:134407700:134407760:1	Same_strand|Exonic_non-coding|ENSRNOT00000053616|ENSRNOG00000035493 ## Same_strand|Boundary_non-coding|ENSRNOT00000053616|ENSRNOG00000035493 ## ENSRNOG00000035493|miRNA|rno-mir-381|rno-mir-381 [Source:miRBase;Acc:MI0003546] ## {MIR: rno-mir-381}
human	chromosome:14:100582004:100582090:1	Same_strand|Boundary_non-coding|ENST00000362150|ENSG00000199020|miRNA|hsa-mir-381 [Source:miRBase;Acc:MI0000789] ## {MIR: hsa-mir-381}
mouse	chromosome:12:110965026:110965112:1	Same_strand|Boundary_non-coding|ENSMUST00000083632|ENSMUSG00000065566|miRNA|mmu-mir-381 [Source:miRBase;Acc:MI0000798] ## {MIR: mmu-mir-381}

rno-mir-499

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-499 5arm	19	4	2	11	5	8	744.500	1239.500	58	147
rno-mir-499 3arm	8	12	1	4	0	1	241	415	36	33
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-499 5arm	0.001	0.000	0.000	0.001	0.000	0.001	0.058	0.065	0.004	0.010
rno-mir-499 3arm	0.000	0.001	0.000	0.000	0	0.000	0.019	0.022	0.002	0.002

sblock8270 (miRBase rno-mir-499) [miRNAknown_lenNOK_cloningHIGH_multiarm_DicerNOK_shortStem_randfoldOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

miRBase rno-mir-499

0.001

no

no

0.32/0.52

18/25/0.45

0.0 0.5 0.4

1.5 2.0 1.4

1420 2 553

0 0 0

10 1 9

0 0 0

4 25 2

3 -23 2

5arm 5arm_loop_3arm 3arm

1 1 1

nd nd nd

0.14 0.44 0.11

2 10 1

2990

10

0

2

		reads	miRBase family seed
seed	---------------------UAAGACU--------------------------------------------------------------------	1800	miR-499
seed	----------------------AAGACUU-------------------------------------------------------------------	429	novel
seed	----------------------------------------------------------ACAUCAC-------------------------------	377	novel
seed	---------------------------------------------------------AACAUCA--------------------------------	374	novel
seed	-----------------------AGACUUG------------------------------------------------------------------	8	novel
seed	------------------------------------------GCUCCUC-----------------------------------------------	1	novel
seed	-------------------------------------------CUCCUCU----------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-miR-499	--------------------TTAAGACTTGCAGTGATGTTT-------------------------------------------------------	21	6	-	1	1	3	3	223	337	14	48
	--------------------TTAAGACTTGCAGTGATG----------------------------------------------------------	18	-	-	1	4	-	1	174	295	5	16
	--------------------TTAAGACTTGCAGTGATGT---------------------------------------------------------	19	3	1	-	3	-	3	139	252	14	32
	---------------------TAAGACTTGCAGTGATGTT--------------------------------------------------------	19	-	1	-	2	1	1	60	83	8	20
	---------------------------------------------------------AACATCACAGCAAGTCTG---------------------	18	1	4	-	1	-	1	42	79	3	9
	--------------------------------------------------------GAACATCACAGCAAGTCT----------------------	18	3	1	-	1	-	-	27	77	2	3
	--------------------TTAAGACTTGCAGTGATGTTTA------------------------------------------------------	22	-	-	-	1	1	-	28	77	-	5
	---------------------------------------------------------AACATCACAGCAAGTCTGTGCT-----------------	22	-	2	-	-	-	-	42	54	8	4
	--------------------TTAAGACTTGCAGTGATGTT--------------------------------------------------------	20	3	-	-	-	-	-	30	57	4	5
	--------------------------------------------------------GAACATCACAGCAAGTCTG---------------------	19	1	4	-	1	-	-	30	41	6	7
	---------------------TAAGACTTGCAGTGATGT---------------------------------------------------------	18	2	-	-	-	-	-	32	41	4	4
	---------------------------------------------------------AACATCACAGCAAGTCTGT--------------------	19	1	-	-	-	-	-	32	39	4	1
	--------------------------------------------------------GAACATCACAGCAAGTCTGTGCT-----------------	23	-	-	1	-	-	-	21	35	4	1
	---------------------TAAGACTTGCAGTGATGTTTAGC----------------------------------------------------	23	-	-	-	-	-	-	10	28	3	9
	--------------------------------------------------------GAACATCACAGCAAGTCTGT--------------------	20	1	1	-	1	-	-	15	31	1	-
	---------------------TAAGACTTGCAGTGATGTTTAG-----------------------------------------------------	22	1	1	-	-	-	-	25	16	2	2
	---------------------TAAGACTTGCAGTGATGTTT-------------------------------------------------------	20	-	1	-	-	-	-	13	22	2	3
	---------------------------------------------------------AACATCACAGCAAGTCTGTG-------------------	20	-	-	-	-	-	-	11	24	1	-
	--------------------------------------------------------GAACATCACAGCAAGTCTGTG-------------------	21	-	-	-	-	-	-	4	16	5	7
	--------------------------------------------------------GAACATCACAGCAAGTCTGTGC------------------	22	-	-	-	-	-	-	11	12	2	-
	---------------------TAAGACTTGCAGTGATGTTTA------------------------------------------------------	21	-	-	-	-	-	-	3	14	1	3
	---------------------------------------------------------AACATCACAGCAAGTCTGTGC------------------	21	1	-	-	-	-	-	6	6	-	1
	---------------------TAAGACTTGCAGTGATGTTTAGCTC--------------------------------------------------	25	4	-	-	-	-	-	1	5	1	-
	--------------------TTAAGACTTGCAGTGATGTTTAG-----------------------------------------------------	23	-	-	-	-	-	-	3	4	-	-
	----------------------AAGACTTGCAGTGATGTTTAGC----------------------------------------------------	22	-	-	-	-	-	-	1	2	-	-
	--------------------TTAAGACTTGCAGTGATGTTTAGC----------------------------------------------------	24	-	-	-	-	-	-	1	2	-	-
	----------------------AAGACTTGCAGTGATGTTTA------------------------------------------------------	20	-	-	-	-	-	-	1	2	-	-
	----------------------AAGACTTGCAGTGATGTT--------------------------------------------------------	18	-	-	-	-	-	-	1	1	-	-
	-----------------------------------------AGCTCCTCTCCATGTGAACATC---------------------------------	22	-	-	-	-	-	-	-	1	-	-
	------------------------------------------GCTCCTCTCCATGTGAACATCACAG-----------------------------	25	-	-	-	-	-	-	-	1	-	-
	--------------------------------------------------------GAACATCACAGCAAGTCTGTGCTG----------------	24	-	-	-	-	-	-	-	1	-	-
rat	----------------GCTGTTAAGACTTGCAGTGATGTTTAGCTCCTCTCCATGTGAACATCACAGCAAGTCTGTGCTGC---------------
human	GTGCCTTGGGCGGGCGGCTGTTAAGACTTGCAGTGATGTTTAACTCCTCTCCACGTGAACATCACAGCAAGTCTGTGCTGCTTCCCGTCCCTACGC
mouse	GTGTCTTGGGTGGGCAGCTGTTAAGACTTGCAGTGATGTTTAGCTCCTCTGCATGTGAACATCACAGCAAGTCTGTGCTGCTGCCTGCCCCCATGC
	************************** ******* ** ***************************
	+++++                +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++               +++++	ENSRNOT00000025859 ENSRNOG00000018997 NP_001101264.1
	+++++                +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++               +++++	ENSRNOT00000049530 ENSRNOG00000018997 NP_001101264.1
	+++++                +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++               +++++	ENSRNOT00000004246 ENSRNOG00000018997 NP_001101264.1
	+++++                +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++               +++++	ENSRNOT00000055257 ENSRNOG00000018997 NP_001101264.1
	+++++                +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++               +++++	ENSRNOT00000037254 ENSRNOG00000018997 NP_001101264.1
	+++++                +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++               +++++	ENSRNOT00000051987 ENSRNOG00000018997 NP_001101264.1
	+++++                +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++               +++++	ENSRNOT00000040338 ENSRNOG00000018997 NP_001101264.1
	.....                >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>               .....	ENSRNOT00000054554 ENSRNOG00000036443 rno-mir-499
rat	((.((..((((((((.((((((((((.(..........))))))))))).))))))))..)).))	1.000 -26.10
human	(((....(((((((.(((.((..((((((((.((((((((((.............)))))))))).))))))))..)).))).)))))))...)))	1.000 -44.22
mouse	.......(((..((((((.((..((((((((.((((((((((((......))...)))))))))).))))))))..)).))))))..)))......	1.000 -51.20

rat	chromosome:3:146127959:146128023:1	Same_strand|Intronic_coding|ENSRNOT00000040338|ENSRNOG00000018997 ## Same_strand|Exonic_non-coding|ENSRNOT00000054554|ENSRNOG00000036443 ## Same_strand|Boundary_non-coding|ENSRNOT00000054554|ENSRNOG00000036443 ## ENSRNOG00000036443|miRNA|rno-mir-499|rno-mir-499 [Source:miRBase;Acc:MI0003721] ## ENSRNOG00000018997|protein_coding|NP_001101264.1|myosin, heavy polypeptide 7B, cardiac muscle, beta [Source:RefSeq_peptide;Acc:NP_001101264] ## {MIR: rno-mir-499}
human	chromosome:20:33041852:33041947:1	Same_strand|Intronic_coding|ENST00000374615|ENSG00000078814|protein_coding|Myosin-7B (Myosin heavy chain 7B, cardiac muscle beta isoform)(Myosin cardiac muscle beta chain)(Antigen MLAA-21)(Slow A MYH14) [Source:UniProtKB/Swiss-Prot;Acc:A7E2Y1] ## Same_strand|Exonic_non-coding|ENST00000384903|ENSG00000207635|miRNA|hsa-mir-499 [Source:miRBase;Acc:MI0003183] ## {MIR: hsa-mir-499}
mouse	chromosome:2:155448609:155448704:1	Same_strand|Intronic_coding|ENSMUST00000092995|ENSMUSG00000074652|protein_coding|myosin, heavy chain 7B, cardiac muscle, beta Gene [Source:MGI (curated);Acc:Myh7b-001] ## Same_strand|Boundary_non-coding|ENSMUST00000102357|ENSMUSG00000076312|miRNA|mmu-mir-499 [Source:miRBase;Acc:MI0004676] ## {MIR: mmu-mir-499}

rno-mir-200c

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-200c 5arm	4	0	0	0	0	3	0	0	7	1
rno-mir-200c 3arm	118	4	13	22	83	74	11	4	340	531
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-200c 5arm	0.000	0	0	0	0	0.000	0	0	0.000	0.000
rno-mir-200c 3arm	0.004	0.000	0.001	0.001	0.004	0.006	0.001	0.000	0.022	0.035

sblock8713 (miRBase rno-mir-200c) [miRNAknown_lenNOK_cloningHIGH_multiarm_DicerNOK_shortStem_randfoldOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

miRBase rno-mir-200c

0.001

no

no

0.40/0.56

18/25/0.48

0.5 0.0

0.8 0.7

10 566

0 0

4 10

0 0

4 4

6 6

5arm 3arm

1 1

nd nd

0.10 0.11

1 1

1215

10

1

0

Clusters

Located in cluster 54: rno-mir-141, rno-mir-200c

Families

Member of family miR-200b/200c/429 (seed AAUACUG): rno-mir-429, rno-mir-200b, rno-mir-200c

		reads	miRBase family seed
seed	--------------------------------------------------------------AAUACUG------------------------------------	1079	miR-200b/200c/429
seed	-------------------------------------------------------------UAAUACU-------------------------------------	90	novel
seed	---------------------------------------------------------------AUACUGC-----------------------------------	28	novel
seed	----------------------GUCUUAC----------------------------------------------------------------------------	9	novel
seed	-----------------------UCUUACC---------------------------------------------------------------------------	5	novel
seed	----------------------------------------------------------------UACUGCC----------------------------------	2	novel
seed	---------------------CGUCUUA-----------------------------------------------------------------------------	1	novel
seed	------------------------------------------------------------------CUGCCGG--------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-------------------------------------------------------------TAATACTGCCGGGTAATGA-------------------------	19	42	1	5	11	28	31	5	2	129	206
	-------------------------------------------------------------TAATACTGCCGGGTAATGATG-----------------------	21	16	-	3	5	19	12	-	-	67	101
	-------------------------------------------------------------TAATACTGCCGGGTAATGAT------------------------	20	25	1	3	2	7	7	-	-	33	60
rno-miR-200c	-------------------------------------------------------------TAATACTGCCGGGTAATGATGG----------------------	22	8	1	-	2	13	8	1	-	39	55
	-------------------------------------------------------------TAATACTGCCGGGTAATG--------------------------	18	7	1	1	2	10	11	2	2	26	63
	------------------------------------------------------------CTAATACTGCCGGGTAATGATG-----------------------	22	5	-	1	-	1	-	-	-	8	14
	------------------------------------------------------------CTAATACTGCCGGGTAATGA-------------------------	20	7	-	-	-	-	-	-	-	12	5
	------------------------------------------------------------CTAATACTGCCGGGTAAT---------------------------	18	1	-	-	-	-	-	-	-	8	4
	------------------------------------------------------------CTAATACTGCCGGGTAATGAT------------------------	21	2	-	-	-	1	1	-	-	6	2
	------------------------------------------------------------CTAATACTGCCGGGTAATG--------------------------	19	2	-	-	-	-	2	-	-	1	4
	--------------------------------------------------------------AATACTGCCGGGTAATGATG-----------------------	20	-	-	-	-	-	2	1	-	1	4
	--------------------------------------------------------------AATACTGCCGGGTAATGATGG----------------------	21	1	-	-	-	-	-	1	-	1	5
	--------------------------------------------------------------AATACTGCCGGGTAATGA-------------------------	18	-	-	-	-	-	-	-	-	3	3
	---------------------CGTCTTACCCAGCAGTGTTTG---------------------------------------------------------------	21	-	-	-	-	-	1	-	-	5	-
	--------------------------------------------------------------AATACTGCCGGGTAATGAT------------------------	19	1	-	-	-	2	-	-	-	1	1
	------------------------------------------------------------CTAATACTGCCGGGTAATGATGG----------------------	23	-	-	-	-	-	-	-	-	2	1
	-------------------------------------------------------------TAATACTGCCGGGTAATGATGGAG--------------------	24	-	-	-	-	1	-	-	-	-	2
	----------------------GTCTTACCCAGCAGTGTT-----------------------------------------------------------------	18	3	-	-	-	-	-	-	-	-	-
	---------------------CGTCTTACCCAGCAGTGTTTGG--------------------------------------------------------------	22	-	-	-	-	-	1	-	-	-	1
	----------------------GTCTTACCCAGCAGTGTTT----------------------------------------------------------------	19	-	-	-	-	-	-	-	-	2	-
	---------------------------------------------------------------ATACTGCCGGGTAATGATG-----------------------	19	-	-	-	-	-	-	1	-	-	1
	-------------------------------------------------------------TAATACTGCCGGGTAATGATGGA---------------------	23	-	-	-	-	-	-	-	-	2	-
	-------------------------------------------------------------TAATACTGCCGGGTAATGATGGAGG-------------------	25	-	-	-	-	-	-	-	-	1	-
	--------------------TCGTCTTACCCAGCAGTG-------------------------------------------------------------------	18	-	-	-	-	-	1	-	-	-	-
	-----------------------------------------------------------------ACTGCCGGGTAATGATGGA---------------------	19	-	-	-	-	1	-	-	-	-	-
	--------------------------------------------------------------AATACTGCCGGGTAATGATGGA---------------------	22	1	-	-	-	-	-	-	-	-	-
	---------------------CGTCTTACCCAGCAGTGTT-----------------------------------------------------------------	19	1	-	-	-	-	-	-	-	-	-
rat	-----------------CCCTCGTCTTACCCAGCAGTGTTTGGGTGCTGGTTGGGAGTCTCTAATACTGCCGGGTAATGATGGAGG-------------------
human	-GCGGGCTGGGCGGGGGCCCTCGTCTTACCCAGCAGTGTTTGGGTGC-GGTTGGGAGTCTCTAATACTGCCGGGTAATGATGGAGGCCCCTGTCCCTGTGTCAGC
mouse	GACTGGTTGGGTAGGGGCCCTCGTCTTACCCAGCAGTGTTTGGGTGCTGGTTGGGAGTCTCTAATACTGCCGGGTAATGATGGAGGCCCCTGTCCCAGTGTC---
	****************************** **************************************
	-----                 ---------------------------------------------------------------------                   -----	ENSRNOT00000056049 ENSRNOG00000037145
	-----                 ---------------------------------------------------------------------                   -----	ENSRNOT00000056039 ENSRNOG00000037143
	.....                 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>                   .....	ENSRNOT00000053710 ENSRNOG00000035587 rno-mir-200c
rat	((..((((((((((.((((((((.(((.(((.......)))))).)))))))).)))))).))))..))	1.000 -31.60
human	((.(((.(((((((((((..((((((((((.((((((((.(((.(( ........))))).)))))))).)))))).))))..)))))))).)))...))).))	1.000 -60.00
mouse	(((...(((((((((((((..((((((((((.((((((((.(((.(((.......)))))).)))))))).)))))).))))..)))))))).))))).)))	1.000 -57.90

rat	chromosome:4:160841344:160841412:-1	Opposite_strand|Intronic_coding|ENSRNOT00000056049|ENSRNOG00000037145 ## Same_strand|Exonic_non-coding|ENSRNOT00000053710|ENSRNOG00000035587 ## ENSRNOG00000035587|miRNA|rno-mir-200c|rno-mir-200c [Source:miRBase;Acc:MI0000942] ## ENSRNOG00000037145|protein_coding|| ## ENSRNOG00000037143|protein_coding|| ## {MIR: rno-mir-200c}
human	chromosome:12:6943107:6943209:1	Same_strand|Boundary_non-coding|ENST00000384980|ENSG00000207713|miRNA|hsa-mir-200c [Source:miRBase;Acc:MI0000650] ## {MIR: hsa-mir-200c}
mouse	chromosome:6:124668324:124668425:-1	Same_strand|Boundary_non-coding|ENSMUST00000083528|ENSMUSG00000065462|miRNA|mmu-mir-200c [Source:miRBase;Acc:MI0000694] ## {MIR: mmu-mir-200c}

miRNAknown_rep_cloningHIGH_multiarm_DicerNOK_randfoldOK (3 loci)

rno-mir-330

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-330 5arm	134.750	111.250	2	1	12	27	0	2	0	24
rno-mir-330 3arm	4518.500	2125	29	40	202	101	33	1	258	266
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-330 5arm	0.004	0.005	0.000	0.000	0.001	0.002	0	0.000	0	0.002
rno-mir-330 3arm	0.150	0.093	0.002	0.002	0.010	0.008	0.003	0.000	0.017	0.018

sblock1762 (miRBase rno-mir-330) [miRNAknown_rep_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-330

0.003

no

SINE/MIR

0.48/0.67

18/25/0.73

0.0 0.0 0.6

0.0 0.0 1.7

134 2 5763

0 0 0

8 1 10

0 0 0

20 27 14

4 -8 2

5arm 3arm_loop 3arm

1 1 1

nd nd nd

0.15 0.43 0.17

2 7 2

7891

10

-1

1

Families

Member of family miR-326/330 (seed CUCUGGG): rno-mir-330, rno-mir-326

		reads	miRBase family seed
seed	-------------------------------------------------------------AAAGCAC-----------------------------	3928	novel
seed	------------------------------------------------------------CAAAGCA------------------------------	3628	miR-330*
seed	---------------------CUCUGGG---------------------------------------------------------------------	309	miR-326/330
seed	--------------------------------------------------------------AAGCACA----------------------------	11	novel
seed	----------------------UCUGGGC--------------------------------------------------------------------	8	novel
seed	---------------------------------------------------------------AGCACAG---------------------------	2	novel
seed	--------------------------------------------------AUCUAAC----------------------------------------	2	novel
seed	----------------------------------------------------------------GCACAGG--------------------------	1	novel
seed	-----------------------------------------------------------------CACAGGG-------------------------	1	novel
seed	-----------------------------------------------------------GCAAAGC-------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	------------------------------------------------------------CAAAGCACAGGGCCTGCAGAGA---------------	22	568	257	2	2	23	12	5	-	24	20
	-----------------------------------------------------------GCAAAGCACAGGGCCTGCAGA-----------------	21	537	238	3	6	24	8	4	1	27	26
rno-miR-330*	-----------------------------------------------------------GCAAAGCACAGGGCCTGCAGAGA---------------	23	596	122	1	2	32	15	4	-	26	43
	------------------------------------------------------------CAAAGCACAGGGCCTGCA-------------------	18	483	254	3	7	11	13	1	-	25	13
	------------------------------------------------------------CAAAGCACAGGGCCTGCAGAG----------------	21	402	334	2	1	12	15	2	-	16	17
	-----------------------------------------------------------GCAAAGCACAGGGCCTGCA-------------------	19	383	128	4	4	18	9	1	-	23	32
	------------------------------------------------------------CAAAGCACAGGGCCTGCAGA-----------------	20	341	207	2	-	11	6	5	-	20	10
	-----------------------------------------------------------GCAAAGCACAGGGCCTGCAGAG----------------	22	313	187	6	3	17	6	-	-	27	33
	-----------------------------------------------------------GCAAAGCACAGGGCCTGCAG------------------	20	227	104	1	2	9	2	1	-	15	23
	------------------------------------------------------------CAAAGCACAGGGCCTGCAGAGAG--------------	23	217	100	1	5	11	3	5	-	20	14
	------------------------------------------------------------CAAAGCACAGGGCCTGCAG------------------	19	219	104	2	1	12	3	3	-	10	12
	-----------------------------------------------------------GCAAAGCACAGGGCCTGC--------------------	18	136	56	1	4	16	2	-	-	11	17
	--------------------TCTCTGGGCCTGTGTCTTAG---------------------------------------------------------	20	78	56	1	-	4	13	-	2	-	11
	-----------------------------------------------------------GCAAAGCACAGGGCCTGCAGAGAG--------------	24	56	14	1	1	5	2	-	-	11	2
	--------------------TCTCTGGGCCTGTGTCTTA----------------------------------------------------------	19	20	23	-	1	3	-	-	-	-	6
	--------------------TCTCTGGGCCTGTGTCTTAGG--------------------------------------------------------	21	21	16	-	-	-	7	-	-	-	2
	------------------------------------------------------------CAAAGCACAGGGCCTGCAGAGAGG-------------	24	22	6	-	-	-	2	1	-	1	-
	------------------------------------------------------------CAAAGCACAGGGCCTGCAGAGAGGT------------	25	12	6	-	-	-	3	1	-	2	4
	--------------------TCTCTGGGCCTGTGTCTTAGGCTC-----------------------------------------------------	24	5	9	-	-	4	5	-	-	-	3
rno-miR-330	--------------------TCTCTGGGCCTGTGTCTTAGGC-------------------------------------------------------	22	4	6	1	-	1	-	-	-	-	2
	---------------------CTCTGGGCCTGTGTCTTAG---------------------------------------------------------	19	5	1	-	-	-	-	-	-	-	-
	--------------------TCTCTGGGCCTGTGTCTT-----------------------------------------------------------	18	3	1	-	-	-	-	-	-	-	-
	-------------------------------------------------------------AAAGCACAGGGCCTGCAGAGAG--------------	22	1	3	-	-	-	-	-	-	-	-
	-------------------------------------------------GATCTAACGAGCAAAGCACAG---------------------------	21	-	-	-	2	-	-	-	-	-	-
	-------------------------------------------------------------AAAGCACAGGGCCTGCAGAGAGGT------------	24	-	2	-	-	-	-	-	-	-	-
	-------------------------------------------------------------AAAGCACAGGGCCTGCAGA-----------------	19	1	1	-	-	-	-	-	-	-	-
	--------------------------------------------------------------AAGCACAGGGCCTGCAGAGA---------------	20	1	1	-	-	-	-	-	-	-	-
	-------------------------------------------------------------AAAGCACAGGGCCTGCAGAG----------------	20	1	-	-	-	1	-	-	-	-	-
	---------------------CTCTGGGCCTGTGTCTTAGGCTC-----------------------------------------------------	23	-	-	-	-	-	1	-	-	-	-
	-------------------------------------------------------------AAAGCACAGGGCCTGCAGAGA---------------	21	1	-	-	-	-	-	-	-	-	-
	---------------------CTCTGGGCCTGTGTCTTAGGC-------------------------------------------------------	21	-	-	-	-	-	1	-	-	-	-
	----------------------------------------------------------------GCACAGGGCCTGCAGAGA---------------	18	1	-	-	-	-	-	-	-	-	-
	--------------------TCTCTGGGCCTGTGTCTTAGGCT------------------------------------------------------	23	1	-	-	-	-	-	-	-	-	-
	---------------------------------------------------------------AGCACAGGGCCTGCAGAGAG--------------	20	-	1	-	-	-	-	-	-	-	-
	----------------------------------------------------------AGCAAAGCACAGGGCCTGCAGAGA---------------	24	1	-	-	-	-	-	-	-	-	-
rat	ACCCTTTGGCGATCTCTGCCTCTCTGGGCCTGTGTCTTAGGCTCTTCAAGATCTAACGAGCAAAGCACAGGGCCTGCAGAGAGGTAGCGCTCTGCTC
human	--------------------TCTCTGGGCCTGTGTCTTAGGCTCTGCAAGATCAACCGAGCAAAGCACACGGCCTGCAGAGA---------------
mouse	--------------------------GGCCTGTGTCTTAGGCTCTTCAAGATCCAACGAGCAAAGCACAGGGC------------------------
	******************* ******* * ************* ***
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000041215 ENSRNOG00000030127 Eml2
	.....>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.....	ENSRNOT00000053688 ENSRNOG00000035565 rno-mir-330
rat	.......(((((.(.(((((((((((((((((((.(((..((((.............)))).))))))).))))..))))))))))).).)).))).	1.000 -41.92
human	((((((((((((((.(((..((((.............)))).))))))).))))..))))))	1.000 -25.22
mouse	..((((((.(((..((((.............)))).)))))))))..	1.000 -16.02

rat	chromosome:1:78544318:78544414:1	Same_strand|Exonic_non-coding|ENSRNOT00000053688|ENSRNOG00000035565 ## Same_strand|Intronic_coding|ENSRNOT00000041215|ENSRNOG00000030127 ## ENSRNOG00000030127|protein_coding|Eml2|Echinoderm microtubule-associated protein-like 2 (EMAP-2). [Source:UniProtKB/Swiss-Prot;Acc:Q6P6T4] ## ENSRNOG00000035565|miRNA|rno-mir-330|rno-mir-330 [Source:miRBase;Acc:MI0000606] ## {MIR: rno-mir-330}
human	chromosome:19:50834072:50834208:-1	Same_strand|Intronic_coding|ENST00000245925|ENSG00000125746|protein_coding|Echinoderm microtubule-associated protein-like 2 (EMAP-2)(HuEMAP-2) [Source:UniProtKB/Swiss-Prot;Acc:O95834] ## Same_strand|Boundary_non-coding|ENST00000362196|ENSG00000199066|miRNA|hsa-mir-330 [Source:miRBase;Acc:MI0000803] ## {Repeats: MIRm 1 class=SINE/MIR} ## {MIR: hsa-mir-330}
mouse	chromosome:7:19766751:19766887:1	Same_strand|Intronic_coding|ENSMUST00000120595|ENSMUSG00000040811|protein_coding|echinoderm microtubule associated protein like 2 Gene [Source:MGI (curated);Acc:Eml2-001] ## Same_strand|Boundary_non-coding|ENSMUST00000083609|ENSMUSG00000065543|miRNA|mmu-mir-330 [Source:miRBase;Acc:MI0000607] ## {MIR: mmu-mir-330}

rno-mir-151

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-151 5arm	3813.500	4078.500	1658	2240	2474	1749.500	1927	2840	2032.500	1535.500
rno-mir-151 3arm	836	575	463	481	625	412	507	600	710	767
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-151 5arm	0.127	0.178	0.090	0.133	0.120	0.133	0.150	0.149	0.134	0.102
rno-mir-151 3arm	0.028	0.025	0.025	0.029	0.030	0.031	0.039	0.032	0.047	0.051

sblock10938 (miRBase rno-mir-151) [miRNAknown_rep_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-151

0.001

no

LINE,LINE/L2

0.47/0.67

18/25/0.74

0.0 0.0 0.0

0.8 0.5 0.0

16994 3831 1

0 0 0

10 10 1

0 0 0

15 24 5

3 4 25

5arm 3arm 3arm

1 1 1

nd nd nd

0.10 0.05 0.57

2 1 11

30379

10

1

4

		reads	miRBase family seed
seed	---------------------------------CGAGGAG---------------------------------------------------------------------------	23805	miR-151
seed	---------------------------------------------------------------------UAGACUG---------------------------------------	5820	miR-151*
seed	--------------------------------UCGAGGA----------------------------------------------------------------------------	302	novel
seed	----------------------------------GAGGAGC--------------------------------------------------------------------------	269	novel
seed	--------------------------------------------------------------------CUAGACU----------------------------------------	61	novel
seed	----------------------------------------------------------------------AGACUGA--------------------------------------	51	novel
seed	-------------------------------------------------------------------ACUAGAC-----------------------------------------	24	novel
seed	-----------------------------------------------------------------------GACUGAG-------------------------------------	19	novel
seed	-------------------------------CUCGAGG-----------------------------------------------------------------------------	15	novel
seed	------------------------------CCUCGAG------------------------------------------------------------------------------	8	novel
seed	-----------------------------------AGGAGCU-------------------------------------------------------------------------	4	miR-28/708
seed	------------------------------------------------------------------------------------------CAGGGAU------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-miR-151	--------------------------------TCGAGGAGCTCACAGTCTAGT--------------------------------------------------------------	21	1303	1404	561	717	793	541	579	948	636	412
	--------------------------------TCGAGGAGCTCACAGTCTAG---------------------------------------------------------------	20	1349	1005	433	628	620	452	515	809	628	593
	--------------------------------TCGAGGAGCTCACAGTCT-----------------------------------------------------------------	18	379	663	310	287	504	316	344	439	291	146
	--------------------------------TCGAGGAGCTCACAGTCTA----------------------------------------------------------------	19	434	440	103	235	246	189	239	312	195	127
	--------------------------------------------------------------------CTAGACTGAGGCTCCTTGAG---------------------------	20	270	170	180	167	231	148	199	252	314	256
	--------------------------------TCGAGGAGCTCACAGTCTAGTA-------------------------------------------------------------	22	190	360	149	190	182	153	138	189	172	129
rno-miR-151*	--------------------------------------------------------------------CTAGACTGAGGCTCCTTGAGG--------------------------	21	163	105	121	139	137	75	110	96	118	172
	--------------------------------TCGAGGAGCTCACAGTCTAGTAT------------------------------------------------------------	23	49	109	72	142	78	70	73	97	43	85
	--------------------------------------------------------------------CTAGACTGAGGCTCCTTGA----------------------------	19	148	97	48	48	90	63	62	97	77	81
	--------------------------------------------------------------------CTAGACTGAGGCTCCTTGAGGAC------------------------	23	68	76	32	14	64	48	21	23	64	141
	--------------------------------------------------------------------CTAGACTGAGGCTCCTTG-----------------------------	18	80	72	29	47	54	37	41	67	43	39
	--------------------------------------------------------------------CTAGACTGAGGCTCCTTGAGGA-------------------------	22	77	40	41	52	33	25	66	50	70	49
	---------------------------------CGAGGAGCTCACAGTCTAGT--------------------------------------------------------------	20	22	20	7	8	9	1	13	15	10	10
	-------------------------------CTCGAGGAGCTCACAGTCTAGT--------------------------------------------------------------	22	18	19	5	7	10	10	5	11	10	15
	---------------------------------CGAGGAGCTCACAGTCTAG---------------------------------------------------------------	19	12	13	8	8	5	1	8	8	4	4
	-------------------------------CTCGAGGAGCTCACAGTCT-----------------------------------------------------------------	19	12	12	1	5	5	4	3	5	10	2
	-------------------------------CTCGAGGAGCTCACAGTC------------------------------------------------------------------	18	12	8	4	7	5	2	1	6	5	4
	-------------------------------CTCGAGGAGCTCACAGTCTAG---------------------------------------------------------------	21	13	10	2	5	7	4	3	1	4	2
	---------------------------------CGAGGAGCTCACAGTCTA----------------------------------------------------------------	18	3	8	4	2	3	2	8	4	3	1
	-------------------------------------------------------------------ACTAGACTGAGGCTCCTTGAG---------------------------	21	7	2	3	-	-	3	1	7	5	4
	---------------------------------CGAGGAGCTCACAGTCTAGTA-------------------------------------------------------------	21	6	7	2	-	2	2	2	-	5	2
	-------------------------------CTCGAGGAGCTCACAGTCTA----------------------------------------------------------------	20	6	4	1	1	1	2	-	-	7	1
	--------------------------------------------------------------------CTAGACTGAGGCTCCTTGAGGACA-----------------------	24	3	1	1	3	2	-	2	2	7	1
	---------------------------------------------------------------------TAGACTGAGGCTCCTTGAGGAC------------------------	22	1	-	1	-	3	1	1	-	1	6
	---------------------------------CGAGGAGCTCACAGTCTAGTAT------------------------------------------------------------	22	6	-	-	1	1	-	-	1	3	2
	---------------------------------------------------------------------TAGACTGAGGCTCCTTGAG---------------------------	19	2	3	-	-	1	2	-	1	-	4
	-------------------------------------------------------------------ACTAGACTGAGGCTCCTTGAGG--------------------------	22	4	-	1	1	2	2	-	-	-	3
	------------------------------------------------------------------TACTAGACTGAGGCTCCTTGA----------------------------	21	4	1	1	-	-	2	-	-	2	-
	---------------------------------------------------------------------TAGACTGAGGCTCCTTGAGG--------------------------	20	1	-	1	-	1	1	-	-	2	2
	------------------------------------------------------------------TACTAGACTGAGGCTCCTTGAG---------------------------	22	2	1	-	1	-	-	1	-	-	2
	---------------------------------------------------------------------TAGACTGAGGCTCCTTGA----------------------------	18	-	1	-	3	-	-	1	-	2	-
	--------------------------------TCGAGGAGCTCACAGTCTAGTATGT----------------------------------------------------------	25	-	-	1	-	-	-	1	-	4	1
	----------------------------------------------------------------------AGACTGAGGCTCCTTGAGGAC------------------------	21	-	2	1	1	-	1	-	-	1	-
	----------------------------------------------------------------------AGACTGAGGCTCCTTGAGGA-------------------------	20	-	-	-	1	2	-	1	-	1	1
	---------------------------------------------------------------------TAGACTGAGGCTCCTTGAGGA-------------------------	21	-	-	-	1	-	1	-	1	-	2
	-------------------------------------------------------------------ACTAGACTGAGGCTCCTTGA----------------------------	20	-	-	1	-	-	-	1	2	-	1
	-------------------------------------------------------------------ACTAGACTGAGGCTCCTT------------------------------	18	3	1	-	-	-	-	-	-	-	-
	-------------------------------------------------------------------ACTAGACTGAGGCTCCTTG-----------------------------	19	1	-	-	1	1	-	-	1	-	-
	----------------------------------------------------------------------AGACTGAGGCTCCTTGAGG--------------------------	19	1	1	2	-	-	-	-	-	-	-
	------------------------------CCTCGAGGAGCTCACAGTCT-----------------------------------------------------------------	20	1	1	-	-	-	-	2	-	-	-
	---------------------------------------------------------------------TAGACTGAGGCTCCTTGAGGACA-----------------------	23	-	1	-	-	-	-	-	1	1	1
	-------------------------------CTCGAGGAGCTCACAGTCTAGTA-------------------------------------------------------------	23	1	1	-	-	-	-	-	1	-	1
	------------------------------------------------------------------TACTAGACTGAGGCTCCTTG-----------------------------	20	-	-	-	1	1	-	-	-	1	-
	------------------------------CCTCGAGGAGCTCACAGTCTA----------------------------------------------------------------	21	-	-	-	1	1	-	-	-	-	1
	------------------------------------------------------------------TACTAGACTGAGGCTCCT-------------------------------	18	-	-	-	1	-	1	-	-	1	-
	------------------------------CCTCGAGGAGCTCACAGTCTAGT--------------------------------------------------------------	23	1	2	-	-	-	-	-	-	-	-
	--------------------------------TCGAGGAGCTCACAGTCTAGTATG-----------------------------------------------------------	24	1	-	-	-	1	-	-	-	1	-
	-------------------------------------------------------------------ACTAGACTGAGGCTCCTTGAGGAC------------------------	24	1	-	-	-	2	-	-	-	-	-
	------------------------------CCTCGAGGAGCTCACAGTCTAG---------------------------------------------------------------	22	1	-	-	1	-	1	-	-	-	-
	---------------------------------CGAGGAGCTCACAGTCTAGTATGTC---------------------------------------------------------	25	-	-	-	-	2	-	-	-	-	-
	-----------------------------CCCTCGAGGAGCTCACAGTCTA----------------------------------------------------------------	22	1	-	-	-	1	-	-	-	-	-
	----------------------------------GAGGAGCTCACAGTCTAGTATGTC---------------------------------------------------------	24	-	-	-	-	-	-	-	-	2	-
	----------------------------------------------------------------------AGACTGAGGCTCCTTGAG---------------------------	18	-	-	-	-	-	-	-	-	-	2
	-----------------------------CCCTCGAGGAGCTCACAGT-------------------------------------------------------------------	19	-	-	-	-	-	-	-	-	2	-
	-----------------------------CCCTCGAGGAGCTCACAG--------------------------------------------------------------------	18	-	1	-	-	-	-	1	-	-	-
	------------------------------CCTCGAGGAGCTCACAGT-------------------------------------------------------------------	18	-	1	1	-	-	-	-	-	-	-
	----------------------------------GAGGAGCTCACAGTCTAGTA-------------------------------------------------------------	20	-	1	-	-	-	-	-	-	-	-
	---------------------------------CGAGGAGCTCACAGTCTAGTATG-----------------------------------------------------------	23	-	-	-	-	-	1	-	-	-	-
	----------------------------------------------------------------------AGACTGAGGCTCCTTGAGGACA-----------------------	22	-	-	-	-	-	1	-	-	-	-
	-------------------------------CTCGAGGAGCTCACAGTCTAGTAT------------------------------------------------------------	24	-	-	-	-	1	-	-	-	-	-
	------------------------------------------------------------------TACTAGACTGAGGCTCCTT------------------------------	19	-	1	-	-	-	-	-	-	-	-
	-----------------------------CCCTCGAGGAGCTCACAGTCT-----------------------------------------------------------------	21	-	-	-	-	1	-	-	-	-	-
	----------------------------------GAGGAGCTCACAGTCTAGT--------------------------------------------------------------	19	1	-	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------CTAGACTGAGGCTCCTTGAGGACAG----------------------	25	-	-	-	-	-	1	-	-	-	-
	-----------------------------CCCTCGAGGAGCTCACAGTCTAG---------------------------------------------------------------	23	-	-	-	-	-	-	-	-	1	-
	-----------------------------------------------------------------------------------------ACAGGGATCGTCATACTCACC-----	21	-	-	-	-	1	-	-	-	-	-
rat	-----------------AGCGCTTTCCTGCCCTCGAGGAGCTCACAGTCTAGTATGTCTCCT-CCCTACTAGACTGAGGCTCCTTGAGGACAGGGATCGTCATACTCACCTCCCG
human	GGGCAAAGATGACTAAAACACTTTTCCTGCCCTCGAGGAGCTCACAGTCTAGTATGTCTCATCCCCTACTAGACTGAAGCTCCTTGAGGACAGGGATGGTCAT------------
mouse	--------------------------------TCGAGGAGCTCACAGTCTAGTATGTCTCCT-CCCTACTAGACTGAGGCTCCTTGA----------------------------
	**************************** * ************** *********
	+++++                 +++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000011219 ENSRNOG00000007916 Ptk2
	+++++                 +++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000046362 ENSRNOG00000007916 Ptk2
	.....                 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.....	ENSRNOT00000053580 ENSRNOG00000035457 rno-mir-151
rat	.(((..((((((.((((((((((((..((((((((((.(...... .).)))))))))).)))))))))))).)))))).)))...............	1.000 -47.40
human	........(((((((........((((((.((((((((((((..((((((((((............)))))))))).)))))))))))).)))))))))))))	0.979 -49.40
mouse	((((((((((..((((((((((........ ...)))))))))).))))))))))	1.000 -28.60

rat	chromosome:7:110979296:110979392:-1	Same_strand|Boundary_non-coding|ENSRNOT00000010896|ENSRNOG00000007916 ## Same_strand|Exonic_non-coding|ENSRNOT00000053580|ENSRNOG00000035457 ## Same_strand|Intronic_coding|ENSRNOT00000046362|ENSRNOG00000007916 ## ENSRNOG00000035457|miRNA|rno-mir-151|rno-mir-151 [Source:miRBase;Acc:MI0000647] ## ENSRNOG00000007916|protein_coding|Ptk2|Focal adhesion kinase 1 (EC 2.7.10.2) (FADK 1) (pp125FAK). [Source:UniProtKB/Swiss-Prot;Acc:O35346] ## {Repeats: L2 3173 3178 -1 class=LINE/L2,L2 3180 3183 1 class=LINE/L2,L2 3255 3284 -1 class=LINE,L2 -94 3325 1 class=LINE,L2 3190 3217 1 class=LINE/L2,L2 3149 3173 -1 class=LINE/L2,L2 3213 3219 1 class=LINE/L2} ## {MIR: rno-mir-151}
human	chromosome:8:141811854:141811956:-1	Same_strand|Boundary_non-coding|ENST00000342207|ENSG00000169398|protein_coding|Focal adhesion kinase 1 (FADK 1)(EC 2.7.10.2)(pp125FAK)(Protein-tyrosine kinase 2) [Source:UniProtKB/Swiss-Prot;Acc:Q05397] ## Same_strand|Intronic_coding|ENST00000354438|ENSG00000169398|protein_coding|Focal adhesion kinase 1 (FADK 1)(EC 2.7.10.2)(pp125FAK)(Protein-tyrosine kinase 2) [Source:UniProtKB/Swiss-Prot;Acc:Q05397] ## {Repeats: L2 1 class=LINE/L2,L2 -1 class=LINE/L2} ## {MIR: hsa-mir-151}
mouse	chromosome:15:73085204:73085340:-1	Same_strand|Intronic_non-coding|ENSMUST00000068756|ENSMUSG00000022607|protein_coding|PTK2 protein tyrosine kinase 2 Gene [Source:MGI Symbol;Acc:MGI:95481] ## Same_strand|Intronic_coding|ENSMUST00000080736|ENSMUSG00000022607|protein_coding|PTK2 protein tyrosine kinase 2 Gene [Source:MGI Symbol;Acc:MGI:95481] ## Same_strand|Boundary_non-coding|ENSMUST00000083678|ENSMUSG00000065612|miRNA|mmu-mir-151 [Source:miRBase;Acc:MI0000173] ## {Repeats: L2 1 class=LINE/L2,L2 -1 class=LINE/L2} ## {MIR: mmu-mir-151}

rno-mir-598

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-598 5arm	4	2	0	0	0	0	0	0	0	0
rno-mir-598 3arm	4343.083	2511.167	37	38.250	20.667	10.667	20.333	51.667	51	83.333
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-598 5arm	0.000	0.000	0	0	0	0	0	0	0	0
rno-mir-598 3arm	0.144	0.110	0.002	0.002	0.001	0.001	0.002	0.003	0.003	0.006

sblock4623 (miRBase rno-mir-598) [miRNAknown_rep_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-598

0.005

no

SINE/MIR

0.43/0.68

18/24/0.76

0.0 0.0

0.8 1.2

6 5320

0 0

2 10

0 0

10 8

2 6

5arm 3arm

1 3

nd nd

0.11 0.21

1 3

9243

10

2

4

		reads	miRBase family seed
seed	---------------------------------------------------ACGUCAU---------------------------------	9178	miR-598
seed	----------------------------------------------------CGUCAUC--------------------------------	54	novel
seed	--------------CGGUGAU----------------------------------------------------------------------	6	miR-598
seed	--------------------------------------------------UACGUCA----------------------------------	4	novel
seed	---------------------------------------------------------UCGUCGU---------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--------------------------------------------------TACGTCATCGTCGTCATCGTTATC-----------------	24	2347	1408	28	22	10	6	14	23	27	46
	--------------------------------------------------TACGTCATCGTCGTCATC-----------------------	18	758	529	4	5	7	2	3	15	11	24
rno-miR-598-3p	--------------------------------------------------TACGTCATCGTCGTCATCGTTA-------------------	22	807	420	3	7	5	1	2	16	14	12
	--------------------------------------------------TACGTCATCGTCGTCATCGT---------------------	20	551	308	6	3	7	2	2	8	6	9
	--------------------------------------------------TACGTCATCGTCGTCATCG----------------------	19	486	316	2	7	3	1	2	3	7	10
	--------------------------------------------------TACGTCATCGTCGTCATCGTT--------------------	21	536	261	1	3	-	2	1	4	2	11
	--------------------------------------------------TACGTCATCGTCGTCATCGTTAT------------------	23	22	19	1	-	-	-	-	-	-	-
	---------------------------------------------------ACGTCATCGTCGTCATCGTTATC-----------------	23	23	6	-	1	-	-	1	-	-	-
	---------------------------------------------------ACGTCATCGTCGTCATCGTTA-------------------	21	6	5	-	-	-	-	-	-	-	-
	---------------------------------------------------ACGTCATCGTCGTCATCGTT--------------------	20	2	4	-	-	-	-	-	-	-	-
	---------------------------------------------------ACGTCATCGTCGTCATCGT---------------------	19	2	2	-	1	-	-	-	-	-	-
	-------------GCGGTGATGCCGATGGTGC-----------------------------------------------------------	19	3	-	-	-	-	-	-	-	-	-
	-------------------------------------------------CTACGTCATCGTCGTCATCGTT--------------------	22	1	1	-	-	-	-	-	-	-	-
	-------------GCGGTGATGCCGATGGTG------------------------------------------------------------	18	-	2	-	-	-	-	-	-	-	-
	-------------------------------------------------CTACGTCATCGTCGTCATCGTTA-------------------	23	-	1	-	-	-	-	-	-	-	-
	-------------------------------------------------CTACGTCATCGTCGTCATCGT---------------------	21	-	1	-	-	-	-	-	-	-	-
	---------------------------------------------------ACGTCATCGTCGTCATCG----------------------	18	1	-	-	-	-	-	-	-	-	-
	--------------------------------------------------------ATCGTCGTCATCGTTATC-----------------	18	-	1	-	-	-	-	-	-	-	-
rno-miR-598-5p	-------------GCGGTGATGCCGATGGTGCGAG--------------------------------------------------------	22	1	-	-	-	-	-	-	-	-	-
rat	---GCTGATGCTGGCGGTGATGCCGATGGTGCGAGCTGAAAATGGGCTGCTACGTCATCGTCGTCATCGTTATCATCATCAT---------
human	GCTGCTGATGCTGGCGGTGATCCCGATGGTGTGAGCTGGAAATGGGGTGCTACGTCATCGTTGTCATCGTCATCATCATCATCCGAGCAGC
	****************** ********* ****** ******* ************** ******** ***********
	.....   >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         .....	ENSRNOT00000054498 ENSRNOG00000036380 rno-mir-598
rat	(.(((((.(((((((((((.((((((.((.((((.......))))))....)))))).))))))))))).))))).)..	1.000 -33.30
human	((((((((((.((((((((((..(((((..((.(((............)))))..)))))..)))))))))).)))))........)))))	0.872 -40.00

rat	chromosome:15:42988355:42988433:1	Same_strand|Boundary_non-coding|ENSRNOT00000054498|ENSRNOG00000036380 ## Same_strand|Exonic_non-coding|ENSRNOT00000054498|ENSRNOG00000036380 ## ENSRNOG00000036380|miRNA|rno-mir-598|rno-mir-598 [Source:miRBase;Acc:MI0006155] ## {Repeats: (CAT)n 3 32 1 class=Simple_repeat,(CAT)n 3 22 1 class=Simple_repeat,(CAT)n 23 32 1 class=Simple_repeat} ## {MIR: rno-mir-598}
human	chromosome:8:10930122:10930212:-1	Same_strand|Boundary_non-coding|ENST00000297303|ENSG00000171044|protein_coding|XK-related protein 6 [Source:UniProtKB/Swiss-Prot;Acc:Q5GH73] ## Same_strand|Intronic_coding|ENST00000382461|ENSG00000171044|protein_coding|XK-related protein 6 [Source:UniProtKB/Swiss-Prot;Acc:Q5GH73] ## {Repeats: MIRb -1 class=SINE/MIR} ## {MIR: hsa-mir-598}

miRNAknown_RNA_lenNOK_cloningHIGH_multiarm_DicerNOK_shortStem_randfoldOK (2 loci)

rno-mir-664

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-664 5arm	70	52	8	2	9	6	4	7	5	18
rno-mir-664 3arm	3012	2271	228	425	425	292	403.500	717	520	624
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-664 5arm	0.002	0.002	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.001
rno-mir-664 3arm	0.100	0.099	0.012	0.025	0.021	0.022	0.031	0.038	0.034	0.042

sblock3962 (miRBase rno-mir-664-2) [miRNAknown_RNA_lenNOK_cloningHIGH_multiarm_DicerNOK_shortStem_randfoldOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

miRBase rno-mir-664-2

0.001

snoRNA

no

0.17/0.52

18/26/0.59

0.0 0.0 0.0

1.2 0.0 2.0

113 1 4947

0 0 0

10 1 10

0 0 0

0 11 0

5 -4 3

5arm 3arm_loop 3arm

1 4 4

nd nd nd

0.23 0.28 0.11

3 3 1

9095

10

-2

0

Families

Member of family miR-664 (seed AUUCAUU): rno-mir-664, rno-mir-664

		reads	miRBase family seed
seed	-------------------------------------------------------AUUCAUU------------------------------	8353	miR-664
seed	--------------------------------------------------------UUCAUUU-----------------------------	336	novel
seed	---------------------------------------------------------UCAUUUA----------------------------	191	novel
seed	------------------UGGCUGG-------------------------------------------------------------------	159	novel
seed	----------------------------------------------------------CAUUUAC---------------------------	25	novel
seed	-------------------GGCUGGG------------------------------------------------------------------	18	novel
seed	------------------------------------------------------UAUUCAU-------------------------------	7	novel
seed	-----------------------------------------------------------AUUUACU--------------------------	3	novel
seed	-----------------------------------------------------CUAUUCA--------------------------------	2	novel
seed	------------------------------------------------UUAUUCU-------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-miR-664	------------------------------------------------------TATTCATTTACTCCCCAGCCTA----------------	22	440	426	69	121	136	84	91	179	117	167
	------------------------------------------------------TATTCATTTACTCCCCAGCC------------------	20	596	555	54	66	76	60	83	141	87	92
	------------------------------------------------------TATTCATTTACTCCCCAGC-------------------	19	634	451	41	85	66	50	87	165	87	123
	------------------------------------------------------TATTCATTTACTCCCCAG--------------------	18	638	254	28	75	62	34	67	89	132	116
	------------------------------------------------------TATTCATTTACTCCCCAGCCT-----------------	21	517	436	23	58	60	41	49	91	64	90
	-------------------------------------------------------ATTCATTTACTCCCCAGCC------------------	19	46	37	3	7	4	4	4	8	8	6
	--------------------------------------------------------TTCATTTACTCCCCAGCC------------------	18	30	28	2	3	7	4	7	12	4	6
	-------------------------------------------------------ATTCATTTACTCCCCAGCCT-----------------	20	28	31	1	3	4	1	3	7	1	5
	-------------------------------------------------------ATTCATTTACTCCCCAGCCTA----------------	21	22	19	3	-	3	6	4	7	7	4
	--------------------------------------------------------TTCATTTACTCCCCAGCCT-----------------	19	15	8	1	3	2	3	3	5	6	8
	-------------------------------------------------------ATTCATTTACTCCCCAGC-------------------	18	27	8	-	3	1	-	3	2	4	2
	-----------------CTGGCTGGGGAAAATGAT---------------------------------------------------------	18	9	14	5	1	5	3	-	-	1	3
	-----------------CTGGCTGGGGAAAATGATT--------------------------------------------------------	19	20	6	-	-	1	1	3	2	2	2
	--------------------------------------------------------TTCATTTACTCCCCAGCCTA----------------	20	5	5	3	1	4	3	-	9	2	2
	-----------------CTGGCTGGGGAAAATGATTG-------------------------------------------------------	20	15	11	2	-	1	1	-	-	-	2
	-----------------CTGGCTGGGGAAAATGATTGG------------------------------------------------------	21	10	8	1	-	2	-	-	2	-	6
	-----------------CTGGCTGGGGAAAATGATTGGA-----------------------------------------------------	22	8	6	-	1	-	-	1	-	2	-
	---------------------------------------------------------TCATTTACTCCCCAGCCT-----------------	18	5	9	-	-	-	-	1	-	1	1
	---------------------------------------------------------TCATTTACTCCCCAGCCTA----------------	19	4	2	-	-	-	1	1	-	-	-
	------------------TGGCTGGGGAAAATGATTG-------------------------------------------------------	19	2	2	-	-	-	-	-	1	-	1
	------------------TGGCTGGGGAAAATGATTGG------------------------------------------------------	20	1	2	-	-	-	-	-	-	-	1
	-----------------------------------------------------CTATTCATTTACTCCCCAG--------------------	19	2	1	-	-	-	-	-	1	-	-
	------------------TGGCTGGGGAAAATGATT--------------------------------------------------------	18	1	-	-	-	-	-	-	2	-	1
	----------------------------------------------------------CATTTACTCCCCAGCCTA----------------	18	2	-	-	-	-	1	-	-	-	-
	------------------TGGCTGGGGAAAATGATTGGA-----------------------------------------------------	21	-	2	-	-	-	-	-	-	-	-
	-----------------------------------------------------CTATTCATTTACTCCCCA---------------------	18	-	-	-	-	-	-	-	-	-	2
	----------------------------------------------------TCTATTCATTTACTCCCC----------------------	18	-	-	-	-	-	-	-	1	-	-
	------------------TGGCTGGGGAAAATGATTGGAT----------------------------------------------------	22	1	-	-	-	-	-	-	-	-	-
	-----------------------------------------------------CTATTCATTTACTCCCCAGCC------------------	21	1	-	-	-	-	-	-	-	-	-
	------------------TGGCTGGGGAAAATGATTGGATAGA-------------------------------------------------	25	-	-	-	-	-	1	-	-	-	-
	----------------------------------------------------TCTATTCATTTACTCCCCAG--------------------	20	-	1	-	-	-	-	-	-	-	-
	-----------------CTGGCTGGGGAAAATGATTGGAT----------------------------------------------------	23	-	-	-	-	-	-	-	-	-	1
	-----------------------------------------------ATTATTCTATTCATTTAC---------------------------	18	-	-	-	-	-	-	1	-	-	-
	-----------------CTGGCTGGGGAAAATGATTGGATAGA-------------------------------------------------	26	1	-	-	-	-	-	-	-	-	-
rat	-----------------CTGGCTGGGGAAAATGATTGGATAGAAAACATTATTCTATTCATTTACTCCCCAGCCTA----------------
human	ACTTTGGAACATTGAAACTGGCTAGGGAAAATGATTGGATAGAAACTATTATTCTATTCATTTA-TCCCCAGCCTACAAAATGAAAAAAGGT
mouse	-----------------CTGGCTGGGGAAAATGACTGGATAGAAAACATTATTCTATTCATTTACTCCCCAGCCTA----------------
	****** ********** **********  ***************** ***********
	+++++                 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++                +++++	ENSRNOT00000034888 ENSRNOG00000002353 Rab3gap2
	+++++                 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++                +++++	ENSRNOT00000003216 ENSRNOG00000002353 Rab3gap2
	>>>>>                 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>                >>>>>	ENSRNOT00000063456 ENSRNOG00000041703 SNORA36
rat	..(((((((((...(((.(((((((((.......))))))))).))).)))))))))..	1.000 -28.50
human	.((((....((((......((((.((((...(((.(((((((((.......))))))))).))) )))).)))).....))))...))))..	1.000 -26.20
mouse	..(((((((((...(((.(((((((((.......))))))))).))).)))))))))..	1.000 -28.00

rat	chromosome:13:101253993:101254051:1	Same_strand|Boundary_non-coding|ENSRNOT00000063456|ENSRNOG00000041703 ## Same_strand|Intronic_coding|ENSRNOT00000034888|ENSRNOG00000002353 ## Same_strand|Exonic_non-coding|ENSRNOT00000063456|ENSRNOG00000041703 ## ENSRNOG00000002353|protein_coding|Rab3gap2|Rab3 GTPase-activating protein non-catalytic subunit (Rab3 GTPase- activating protein 150 kDa subunit) (Rab3-GAP p150) (Rab3-GAP regulatory subunit) (RAB3-GAP150). [Source:UniProtKB/Swiss-Prot;Acc:Q5U1Z0] ## ENSRNOG00000041703|snoRNA|SNORA36|Small nucleolar RNA SNORA36 family [Source: RFAM 9.0] ## {MIR: rno-mir-664-2}
human	chromosome:1:218440500:218440590:-1	Same_strand|Intronic_coding|ENST00000237724|ENSG00000118873|protein_coding|Rab3 GTPase-activating protein non-catalytic subunit (Rab3 GTPase-activating protein 150 kDa subunit)(Rab3-GAP p150)(RAB3-GAP150)(Rab3-GAP regulatory subunit)(RGAP-iso) [Source:UniProtKB/Swiss-Prot;Acc:Q9H2M9] ## Same_strand|Boundary_non-coding|ENST00000410438|ENSG00000222370|snoRNA| ## {MIR: hsa-mir-664}
mouse	chromosome:1:187066834:187066932:1	Same_strand|Intronic_coding|ENSMUST00000069652|ENSMUSG00000039318|protein_coding|RAB3 GTPase activating protein subunit 2 Gene [Source:MGI Symbol;Acc:MGI:1916043] ## Same_strand|Boundary_non-coding|ENSMUST00000104383|ENSMUSG00000077571|snoRNA|

sblock5667 (miRBase rno-mir-664-1) [miRNAknown_RNA_lenNOK_cloningHIGH_multiarm_DicerNOK_shortStem_randfoldOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

miRBase rno-mir-664-1

0.001

snoRNA

no

0.17/0.52

18/22/0.59

0.0 0.0 0.0

1.0 0.0 2.0

4 1 4947

0 0 0

3 1 10

0 0 0

0 11 0

6 -4 3

5arm 3arm_loop 3arm

1 4 4

nd nd nd

0.29 0.33 0.16

4 3 2

8922

10

-3

0

Families

Member of family miR-664 (seed AUUCAUU): rno-mir-664, rno-mir-664

		reads	miRBase family seed
seed	--------------------------------------AUUCAUU--------------	8353	miR-664
seed	---------------------------------------UUCAUUU-------------	336	novel
seed	----------------------------------------UCAUUUA------------	191	novel
seed	-----------------------------------------CAUUUAC-----------	25	novel
seed	-------------------------------------UAUUCAU---------------	7	novel
seed	-UGGCUGG---------------------------------------------------	4	novel
seed	------------------------------------------AUUUACU----------	3	novel
seed	------------------------------------CUAUUCA----------------	2	novel
seed	-------------------------------UUAUUCU---------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-miR-664	-------------------------------------TATTCATTTACTCCCCAGCCTA	22	440	426	69	121	136	84	91	179	117	167
	-------------------------------------TATTCATTTACTCCCCAGCC--	20	596	555	54	66	76	60	83	141	87	92
	-------------------------------------TATTCATTTACTCCCCAGC---	19	634	451	41	85	66	50	87	165	87	123
	-------------------------------------TATTCATTTACTCCCCAG----	18	638	254	28	75	62	34	67	89	132	116
	-------------------------------------TATTCATTTACTCCCCAGCCT-	21	517	436	23	58	60	41	49	91	64	90
	--------------------------------------ATTCATTTACTCCCCAGCC--	19	46	37	3	7	4	4	4	8	8	6
	---------------------------------------TTCATTTACTCCCCAGCC--	18	30	28	2	3	7	4	7	12	4	6
	--------------------------------------ATTCATTTACTCCCCAGCCT-	20	28	31	1	3	4	1	3	7	1	5
	--------------------------------------ATTCATTTACTCCCCAGCCTA	21	22	19	3	-	3	6	4	7	7	4
	---------------------------------------TTCATTTACTCCCCAGCCT-	19	15	8	1	3	2	3	3	5	6	8
	--------------------------------------ATTCATTTACTCCCCAGC---	18	27	8	-	3	1	-	3	2	4	2
	---------------------------------------TTCATTTACTCCCCAGCCTA	20	5	5	3	1	4	3	-	9	2	2
	----------------------------------------TCATTTACTCCCCAGCCT-	18	5	9	-	-	-	-	1	-	1	1
	----------------------------------------TCATTTACTCCCCAGCCTA	19	4	2	-	-	-	1	1	-	-	-
	------------------------------------CTATTCATTTACTCCCCAG----	19	2	1	-	-	-	-	-	1	-	-
	-----------------------------------------CATTTACTCCCCAGCCTA	18	2	-	-	-	-	1	-	-	-	-
	CTGGCTGGGGAAAAAGAT-----------------------------------------	18	1	1	-	-	-	-	-	-	-	-
	------------------------------------CTATTCATTTACTCCCCA-----	18	-	-	-	-	-	-	-	-	-	2
	-----------------------------------TCTATTCATTTACTCCCC------	18	-	-	-	-	-	-	-	1	-	-
	CTGGCTGGGGAAAAAGATT----------------------------------------	19	1	-	-	-	-	-	-	-	-	-
	CTGGCTGGGGAAAAAGATTGG--------------------------------------	21	-	-	-	-	-	-	-	-	-	1
	-----------------------------------TCTATTCATTTACTCCCCAG----	20	-	1	-	-	-	-	-	-	-	-
	------------------------------ATTATTCTATTCATTTAC-----------	18	-	-	-	-	-	-	1	-	-	-
	------------------------------------CTATTCATTTACTCCCCAGCC--	21	1	-	-	-	-	-	-	-	-	-
rat	CTGGCTGGGGAAAAAGATTGGATAGAAAACATTATTCTATTCATTTACTCCCCAGCCTA
mouse	CTGGCTGGGGAAAATGACTGGATAGAAAACATTATTCTATTCATTTACTCCCCAGCCTA
	************** ** *****************************************
	.....>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.....	ENSRNOT00000063047 ENSRNOG00000041294 rno-mir-664-1
rat	..(((((((((....((.(((((((((.......))))))))).))..)))))))))..	1.000 -27.20
mouse	..(((((((((...(((.(((((((((.......))))))))).))).)))))))))..	1.000 -28.00

rat	chromosome:18:47881354:47881412:1	Same_strand|Boundary_non-coding|ENSRNOT00000063047|ENSRNOG00000041294 ## ENSRNOG00000041294|miRNA|rno-mir-664-1|rno-mir-664-1 [Source:miRBase;Acc:MI0003722] ## {MIR: rno-mir-664-1}
mouse	chromosome:1:187066834:187066932:1	Same_strand|Intronic_coding|ENSMUST00000069652|ENSMUSG00000039318|protein_coding|RAB3 GTPase activating protein subunit 2 Gene [Source:MGI Symbol;Acc:MGI:1916043] ## Same_strand|Boundary_non-coding|ENSMUST00000104383|ENSMUSG00000077571|snoRNA|

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