miR-Intess™

candidate miRBase miRNAs

miRNAknown_lenNOK_cloningHIGH_multiarm_DicerOK (7 loci)

rno-mir-188

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-188 5arm	94	58	26	38	128	66	29	40	55	87
rno-mir-188 3arm	33	14	5	6	10	12	3	2	3	9
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-188 5arm	0.003	0.003	0.001	0.002	0.006	0.005	0.002	0.002	0.004	0.006
rno-mir-188 3arm	0.001	0.001	0.000	0.000	0.000	0.001	0.000	0.000	0.000	0.001

sblock12775 (miRBase rno-mir-188) [miRNAknown_lenNOK_cloningHIGH_multiarm_DicerOK]

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-188

0.027

no

no

0.55/0.64

18/22/0.41

0.0 0.0

0.4 0.0

402 37

0 0

10 10

0 0

10 11

5 8

5arm 3arm

1 1

nd nd

0.20 0.30

2 2

718

10

2

1

Clusters

Located in cluster 94: rno-mir-532, rno-mir-188

		reads	miRBase family seed
seed	-------------------------------AUCCCUU---------------------------------------------------------------------------------	619	miR-188
seed	----------------------------------------------------------------------UCCCACA------------------------------------------	86	novel
seed	---------------------------------------------------------------------CUCCCAC-------------------------------------------	8	miR-532
seed	-----------------------------------------------------------------------CCCACAU-----------------------------------------	2	novel
seed	--------------------------------UCCCUUG--------------------------------------------------------------------------------	2	novel
seed	--------------------------------------------------------------------CCUCCCA--------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	------------------------------CATCCCTTGCATGGTGGAG----------------------------------------------------------------------	19	42	23	13	15	53	39	11	20	27	45
	------------------------------CATCCCTTGCATGGTGGAGG---------------------------------------------------------------------	20	21	16	6	10	31	14	7	6	13	22
	------------------------------CATCCCTTGCATGGTGGA-----------------------------------------------------------------------	18	23	14	3	8	22	6	8	9	8	10
rno-miR-188	------------------------------CATCCCTTGCATGGTGGAGGG--------------------------------------------------------------------	21	6	4	1	3	18	7	2	5	7	9
	---------------------------------------------------------------------CTCCCACATGCAGGGTTTGC------------------------------	20	26	11	4	1	6	2	2	1	1	5
	---------------------------------------------------------------------CTCCCACATGCAGGGTTT--------------------------------	18	-	2	-	3	1	2	1	-	1	4
	------------------------------CATCCCTTGCATGGTGGAGGGC-------------------------------------------------------------------	22	1	1	3	2	3	-	1	-	-	1
	---------------------------------------------------------------------CTCCCACATGCAGGGTTTG-------------------------------	19	2	1	-	1	1	2	-	-	-	-
	---------------------------------------------------------------------CTCCCACATGCAGGGTTTGCA-----------------------------	21	2	-	-	1	-	3	-	-	-	-
	--------------------------------------------------------------------CCTCCCACATGCAGGGTTT--------------------------------	19	-	-	-	-	1	1	-	1	1	-
	--------------------------------------------------------------------CCTCCCACATGCAGGGTTTGC------------------------------	21	-	-	-	-	1	1	-	-	-	-
	--------------------------------------------------------------------CCTCCCACATGCAGGGTTTG-------------------------------	20	2	-	-	-	-	-	-	-	-	-
	-------------------------------ATCCCTTGCATGGTGGAG----------------------------------------------------------------------	18	-	-	-	-	1	-	-	-	-	-
	----------------------------------------------------------------------TCCCACATGCAGGGTTTG-------------------------------	18	1	-	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------TCCCACATGCAGGGTTTGCA-----------------------------	20	-	-	-	-	-	1	-	-	-	-
	-------------------------------ATCCCTTGCATGGTGGAGG---------------------------------------------------------------------	19	1	-	-	-	-	-	-	-	-	-
	-------------------------------------------------------------------TCCTCCCACATGCAGGGTTTGC------------------------------	22	-	-	1	-	-	-	-	-	-	-
rat	--------------------CCCTCTCTCACATCCCTTGCATGGTGGAGGGCGAGCTCTCTGAAAACTCCTCCCACATGCAGGGTTTGCAGGATGGTGAG-------------------
human	AGAGCAAGCCCTTCCCTGCTCCCTCTCTCACATCCCTTGCATGGTGGAGGGTGAGCTTTCTGAAAACCCCTCCCACATGCAGGGTTTGCAGGATGGCGAGCCTCAGCTTTCCTTGCTCT
mouse	AGAGTGAACCCTTCCCTGCTCCCTCTCTCACATCCCTTGCATGGTGGAGGGTGAGCTCTCTGAAAACCCCTCCCACATGCAGGGTTTGCAGGATGGTGAGCTTCAGCTTTCCTTGCTCT
	******************************* ***** ********* **************************** ***
	.....                    >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>                   .....	ENSRNOT00000053775 ENSRNOG00000035652 rno-mir-188
rat	.((..(((..((..(((((((((..((((((....(.....).....))))))..)))))))))..))..))).))....	1.000 -30.00
human	((((((((.........((((((..(((..((..(((((((((..((((((................))))))..)))))))))..))..))).)).))))..........))))))))	0.993 -49.30
mouse	(((((((..........((((((..(((..((..(((((((((..((((((................))))))..)))))))))..))..))).)).))))...........)))))))	0.862 -44.19

rat	chromosome:X:27323547:27323626:1	Same_strand|Exonic_non-coding|ENSRNOT00000053775|ENSRNOG00000035652 ## Same_strand|Boundary_non-coding|ENSRNOT00000053775|ENSRNOG00000035652 ## ENSRNOG00000035652|miRNA|rno-mir-188|rno-mir-188 [Source:miRBase;Acc:MI0006134] ## {MIR: rno-mir-188}
human	chromosome:X:49654833:49654951:1	Same_strand|Intronic_non-coding|ENST00000376091|ENSG00000171365|protein_coding|Chloride channel protein 5 (ClC-5) [Source:UniProtKB/Swiss-Prot;Acc:P51795] ## Same_strand|Boundary_non-coding|ENST00000307367|ENSG00000171365|protein_coding|Chloride channel protein 5 (ClC-5) [Source:UniProtKB/Swiss-Prot;Acc:P51795] ## {MIR: hsa-mir-188}
mouse	chromosome:X:6825089:6825207:-1	Same_strand|Boundary_non-coding|ENSMUST00000004428|ENSMUSG00000004317|protein_coding|chloride channel 5 Gene [Source:MGI (curated);Acc:Clcn5-004] ## Same_strand|Intronic_coding|ENSMUST00000115746|ENSMUSG00000004317|protein_coding|chloride channel 5 Gene [Source:MGI (curated);Acc:Clcn5-004] ## {MIR: mmu-mir-188}

rno-mir-350

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-350 5arm	0	0	0	1	0	0	0	0	0	1
rno-mir-350 3arm	434	468	153	306	379	390	154	300	68	126
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-350 5arm	0	0	0	0.000	0	0	0	0	0	0.000
rno-mir-350 3arm	0.014	0.020	0.008	0.018	0.018	0.030	0.012	0.016	0.004	0.008

sblock3801 (miRBase rno-mir-350) [miRNAknown_lenNOK_cloningHIGH_multiarm_DicerOK]

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-350

0.018

no

no

0.38/0.52

18/26/0.47

0.0 0.0

0.5 2.2

2 2002

0 0

2 10

0 0

23 15

1 2

5arm 3arm

1 1

nd nd

0.19 0.25

3 3

2780

10

1

3

		reads	miRBase family seed
seed	-------------------------------------------------------------------UCACAAA--------------------------------------------	2704	miR-350
seed	--------------------------------------------------------------------CACAAAG-------------------------------------------	65	novel
seed	----------------------------------------------------------------------CAAAGCC-----------------------------------------	6	novel
seed	------------------------------------------------------------------UUCACAA---------------------------------------------	2	novel
seed	------------------------------AAGUGCA---------------------------------------------------------------------------------	2	novel
seed	---------------------------------------------------------------------ACAAAGC------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	------------------------------------------------------------------TTCACAAAGCCCATACAC----------------------------------	18	112	131	46	81	108	106	43	88	17	33
rno-miR-350	------------------------------------------------------------------TTCACAAAGCCCATACACTTTCAC----------------------------	24	94	95	35	69	69	67	36	39	9	31
	------------------------------------------------------------------TTCACAAAGCCCATACACT---------------------------------	19	86	76	23	64	63	59	23	44	14	15
	------------------------------------------------------------------TTCACAAAGCCCATACACTTTC------------------------------	22	53	72	12	26	54	66	22	43	20	20
	------------------------------------------------------------------TTCACAAAGCCCATACACTT--------------------------------	20	44	45	10	30	44	40	10	40	6	16
	------------------------------------------------------------------TTCACAAAGCCCATACACTTTCACC---------------------------	25	32	24	18	23	16	34	15	31	1	6
	------------------------------------------------------------------TTCACAAAGCCCATACACTTT-------------------------------	21	2	3	4	2	8	8	1	5	-	2
	-------------------------------------------------------------------TCACAAAGCCCATACACTTTC------------------------------	21	2	3	1	-	4	5	-	3	-	-
	-------------------------------------------------------------------TCACAAAGCCCATACACTTTCAC----------------------------	23	4	4	3	4	1	-	1	-	-	-
	-------------------------------------------------------------------TCACAAAGCCCATACACT---------------------------------	18	-	3	-	3	3	2	-	1	-	-
	------------------------------------------------------------------TTCACAAAGCCCATACACTTTCA-----------------------------	23	1	1	-	1	1	-	2	2	1	3
	-------------------------------------------------------------------TCACAAAGCCCATACACTT--------------------------------	19	2	6	-	-	3	-	-	-	-	-
	------------------------------------------------------------------TTCACAAAGCCCATACACTTTCACCC--------------------------	26	-	-	-	3	1	2	-	2	-	-
	-------------------------------------------------------------------TCACAAAGCCCATACACTTTCACC---------------------------	24	2	2	-	-	-	-	1	-	-	-
	---------------------------------------------------------------------ACAAAGCCCATACACTTTC------------------------------	19	-	-	1	-	1	-	-	2	-	-
	-----------------------------------------------------------------GTTCACAAAGCCCATACACT---------------------------------	20	-	2	-	-	-	-	-	-	-	-
	---------------------------------------------------------------------ACAAAGCCCATACACTTTCAC----------------------------	21	-	-	-	-	1	1	-	-	-	-
	-----------------------------AAAGTGCACGTGCTTTGGGA---------------------------------------------------------------------	20	-	-	-	-	-	-	-	-	-	1
	-------------------------------------------------------------------TCACAAAGCCCATACACTTT-------------------------------	20	-	-	-	-	1	-	-	-	-	-
	-------------------------------------------------------------------TCACAAAGCCCATACACTTTCA-----------------------------	22	-	-	-	-	1	-	-	-	-	-
	-----------------------------AAAGTGCACGTGCTTTGGGAC--------------------------------------------------------------------	21	-	-	-	1	-	-	-	-	-	-
	--------------------------------------------------------------------CACAAAGCCCATACACTTTCAC----------------------------	22	-	1	-	-	-	-	-	-	-	-
rat	------AGATGCCTTGCTCCTACAAGAGTAAAGTGCACGTGCTTTGGGACAGTGAGGAAAATAATGTTCACAAAGCCCATACACTTTCACCCTTTAGGAGAGTTG-------------
mouse	ATAGATAGATGCCTTGCTCCTACAAGAGTAAAGTGCATGCGCTTTGGGACAGTGAGGAAAATAATGTTCACAAAGCCCATACACTTTCACCCTTTAGGAGAGTTGCAGCTTGCTTTAT
	******************************* * *****************************************************************
	+++++      +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++             +++++	ENSRNOT00000005467 ENSRNOG00000004127 Q91Y79_RAT
	+++++      +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++             +++++	ENSRNOT00000005532 ENSRNOG00000004127 Q91Y79_RAT
	.....      >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>             .....	ENSRNOT00000053611 ENSRNOG00000035488 rno-mir-350
rat	..........((((((.(((.((((((((...(.(((((((((((.............))))).)))))).)...)))))).)).))))))))).....	1.000 -28.02
mouse	(((((.((.(((....((((((.(((.((((((((.(((.(((((((((((.............))))).)))))).))).)))))).)).)))))))))....))).))...)))))	0.997 -36.52

rat	chromosome:13:92545075:92545173:-1	Same_strand|Intronic_coding|ENSRNOT00000005467|ENSRNOG00000004127 ## Same_strand|Boundary_non-coding|ENSRNOT00000040669|ENSRNOG00000004127 ## Same_strand|Exonic_non-coding|ENSRNOT00000053611|ENSRNOG00000035488 ## ENSRNOG00000004127|protein_coding|Q91Y79_RAT|KARP-1-binding protein 1. [Source:UniProtKB/TrEMBL;Acc:Q91Y79] ## ENSRNOG00000035488|miRNA|rno-mir-350|rno-mir-350 [Source:miRBase;Acc:MI0000639] ## {MIR: rno-mir-350}
mouse	chromosome:1:178702443:178702560:-1	Same_strand|Intronic_coding|ENSMUST00000057037|ENSMUSG00000057335|protein_coding|centrosomal protein 170 Gene [Source:MGI Symbol;Acc:MGI:1918348] ## Same_strand|Boundary_non-coding|ENSMUST00000070119|ENSMUSG00000057335|protein_coding|centrosomal protein 170 Gene [Source:MGI Symbol;Acc:MGI:1918348] ## {Repeats: trf 0 class=trf,dust 0 class=dust,(TCTA)n -1 class=Simple_repeat} ## {MIR: mmu-mir-350}

rno-mir-874

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-874 5arm	244	185	6	9	33	13	29	43	137	95
rno-mir-874 3arm	56	106	2	0	11	6	1	6	97	60
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-874 5arm	0.008	0.008	0.000	0.001	0.002	0.001	0.002	0.002	0.009	0.006
rno-mir-874 3arm	0.002	0.005	0.000	0	0.001	0.000	0.000	0.000	0.006	0.004

sblock5250 (miRBase rno-mir-874) [miRNAknown_lenNOK_cloningHIGH_multiarm_DicerOK]

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-874

0.016

no

no

0.67/0.84

18/25/0.54

0.0 0.0

1.5 2.9

439 252

0 0

10 9

0 0

9 9

3 4

5arm 3arm

1 1

nd nd

0.21 0.20

2 2

1139

10

1

2

Families

Member of family miR-874 (seed UGCCCUG): rno-mir-874, block1431105_cand

		reads	miRBase family seed
seed	--------------------------GGCCCCA--------------------------------------------------------------------------	704	novel
seed	---------------------------------------------------------------UGCCCUG-------------------------------------	337	miR-874
seed	-------------------------CGGCCCC---------------------------------------------------------------------------	58	novel
seed	----------------------------CCCCACG------------------------------------------------------------------------	21	novel
seed	---------------------------GCCCCAC-------------------------------------------------------------------------	11	novel
seed	----------------------------------------------------------------GCCCUGG------------------------------------	8	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-------------------------CGGCCCCACGCACCAGGGT---------------------------------------------------------------	19	39	52	3	6	11	3	8	10	48	31
	-------------------------CGGCCCCACGCACCAGGGTAA-------------------------------------------------------------	21	71	52	2	-	8	2	10	9	32	13
	-------------------------CGGCCCCACGCACCAGGG----------------------------------------------------------------	18	49	22	-	1	3	1	3	7	16	9
	--------------------------------------------------------------CTGCCCTGGCCCGAGGGACCGAC----------------------	23	9	39	1	-	-	2	1	2	38	15
	-------------------------CGGCCCCACGCACCAGGGTAAGA-----------------------------------------------------------	23	43	16	-	-	6	2	4	6	11	18
	--------------------------------------------------------------CTGCCCTGGCCCGAGGGA---------------------------	18	33	21	-	-	7	3	-	3	19	19
	--------------------------------------------------------------CTGCCCTGGCCCGAGGGAC--------------------------	19	7	22	-	-	-	1	-	-	21	12
	-------------------------CGGCCCCACGCACCAGGGTA--------------------------------------------------------------	20	18	12	-	1	-	3	2	2	8	7
	--------------------------------------------------------------CTGCCCTGGCCCGAGGGACC-------------------------	20	2	13	1	-	3	-	-	-	10	6
	-------------------------CGGCCCCACGCACCAGGGTAAG------------------------------------------------------------	22	1	12	-	1	1	-	1	1	3	1
	------------------------GCGGCCCCACGCACCAGGGT---------------------------------------------------------------	20	3	6	-	-	-	-	-	2	4	3
	------------------------GCGGCCCCACGCACCAGGGTAA-------------------------------------------------------------	22	5	4	-	-	1	-	1	1	3	-
	---------------------------GCCCCACGCACCAGGGTAAGA-----------------------------------------------------------	21	1	3	1	-	2	-	-	1	3	3
	--------------------------------------------------------------CTGCCCTGGCCCGAGGGACCG------------------------	21	1	5	-	-	-	-	-	1	3	2
	------------------------GCGGCCCCACGCACCAGG-----------------------------------------------------------------	18	5	3	-	-	-	1	-	1	2	-
rno-miR-874	--------------------------------------------------------------CTGCCCTGGCCCGAGGGACCGA-----------------------	22	2	3	-	-	-	-	-	-	3	4
	------------------------GCGGCCCCACGCACCAGGG----------------------------------------------------------------	19	2	2	-	-	-	-	-	-	2	1
	---------------------------------------------------------------TGCCCTGGCCCGAGGGACC-------------------------	19	1	2	-	-	-	-	-	-	1	1
	--------------------------GGCCCCACGCACCAGGGTAA-------------------------------------------------------------	20	2	-	-	-	-	-	-	1	-	2
	---------------------------GCCCCACGCACCAGGGTAA-------------------------------------------------------------	19	1	-	-	-	-	-	-	-	1	2
	------------------------GCGGCCCCACGCACCAGGGTA--------------------------------------------------------------	21	1	-	-	-	1	1	-	-	-	1
	--------------------------GGCCCCACGCACCAGGGTAAG------------------------------------------------------------	21	1	-	-	-	-	-	-	-	1	1
	--------------------------------------------------------------CTGCCCTGGCCCGAGGGACCGACT---------------------	24	-	-	-	-	1	-	-	-	2	-
	--------------------------GGCCCCACGCACCAGGGTA--------------------------------------------------------------	19	-	-	-	-	-	-	-	-	1	1
	-------------------------CGGCCCCACGCACCAGGGTAAGAGA---------------------------------------------------------	25	1	-	-	-	-	-	-	-	1	-
	------------------------GCGGCCCCACGCACCAGGGTAAG------------------------------------------------------------	23	-	1	-	-	-	-	-	-	1	-
	---------------------------GCCCCACGCACCAGGGTA--------------------------------------------------------------	18	-	-	-	-	-	-	-	2	-	-
	---------------------------GCCCCACGCACCAGGGTAAG------------------------------------------------------------	20	-	-	-	-	-	-	-	-	-	1
	-------------------------CGGCCCCACGCACCAGGGTAAGAG----------------------------------------------------------	24	1	-	-	-	-	-	-	-	-	-
	---------------------------------------------------------------TGCCCTGGCCCGAGGGACCGA-----------------------	21	1	-	-	-	-	-	-	-	-	-
	---------------------------------------------------------------TGCCCTGGCCCGAGGGACCGAC----------------------	22	-	1	-	-	-	-	-	-	-	-
	--------------------------GGCCCCACGCACCAGGGTAAGA-----------------------------------------------------------	22	-	-	-	-	-	-	-	-	-	1
	---------------------------------------------------------------TGCCCTGGCCCGAGGGACCGACT---------------------	23	-	-	-	-	-	-	-	-	-	1
rat	----------------TTAGCCCTGCGGCCCCACGCACCAGGGTAAGAGAGA--CTCGCTTCCTGCCCTGGCCCGAGGGACCGACTGGCTGGGC-------------
human	GGATGAATTGTTGGTGTTAGCCCTGCGGCCCCACGCACCAGGGTAAGAGAGACTCTCGCTTCCTGCCCTGGCCCGAGGGACCGACTGGCTGGGCCTGCCTTCTGCCC
mouse	-------------------------CGGCCCCACGCACCAGGGTAAGAGAGA--CTCACTTCCTGCCCTGGCCCGAGGGACCG------------------------
	***************************  *** *************************
	+++++                ++++++++++++++++++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++             +++++	ENSRNOT00000034856 ENSRNOG00000019533 AC142258.4
	+++++                ++++++++++++++++++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++             +++++	ENSRNOT00000026449 ENSRNOG00000019533 AC142258.4
	+++++                ++++++++++++++++++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++             +++++	ENSRNOT00000034877 ENSRNOG00000019533 AC142258.4
	+++++                ++++++++++++++++++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++             +++++	ENSRNOT00000034870 ENSRNOG00000019533 AC142258.4
	+++++                ++++++++++++++++++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++             +++++	ENSRNOT00000034887 ENSRNOG00000019533 AC142258.4
	.....                >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>             .....	ENSRNOT00000063053 ENSRNOG00000041300 rno-mir-874
rat	((((((...(((.(((.((..((((((((.(..((.  ....))..)))))))))..)).))).)))...))))))..	1.000 -37.30
human	((..(((..((.(((.((((((...(((.(((.((..(((((((.((..((.......))..)))))))))..)).))).)))...))))))))).)).)))..)).	0.994 -43.60
mouse	(((.(((.((..(((((((.((..((.  ....))..)))))))))..)).))).)))	1.000 -27.40

rat	chromosome:17:12597361:12597436:1	Same_strand|Intronic_coding|ENSRNOT00000034870|ENSRNOG00000019533 ## Same_strand|Exonic_non-coding|ENSRNOT00000063053|ENSRNOG00000041300 ## Same_strand|Boundary_non-coding|ENSRNOT00000041165|ENSRNOG00000019533 ## ENSRNOG00000041300|miRNA|rno-mir-874|rno-mir-874 [Source:miRBase;Acc:MI0006118] ## ENSRNOG00000019533|protein_coding|AC142258.4| ## {MIR: rno-mir-874}
human	chromosome:5:137011147:137011253:-1	Same_strand|Intronic_coding|ENST00000309755|ENSG00000146021|protein_coding|Kelch-like protein 3 [Source:UniProtKB/Swiss-Prot;Acc:Q9UH77] ## Same_strand|Boundary_non-coding|ENST00000401190|ENSG00000216009|miRNA|hsa-mir-874 [Source:miRBase;Acc:MI0005532] ## {MIR: hsa-mir-874}
mouse	chromosome:13:58124497:58124552:-1	Same_strand|Intronic_coding|ENSMUST00000091583|ENSMUSG00000014164|protein_coding| ## Same_strand|Exonic_non-coding|ENSMUST00000104769|ENSMUSG00000077962|miRNA|mmu-mir-874 [Source:miRBase;Acc:MI0005479] ## {MIR: mmu-mir-874}

rno-mir-27a

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-27a 5arm	10	9	0	2	25	17	5	16.333	3	8
rno-mir-27a 3arm	1692	1557.500	1452.500	2379	4132	3764.500	4624	10232	4168.500	5685
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-27a 5arm	0.000	0.000	0	0.000	0.001	0.001	0.000	0.001	0.000	0.001
rno-mir-27a 3arm	0.056	0.068	0.079	0.141	0.201	0.285	0.360	0.538	0.275	0.378

sblock5755 (miRBase rno-mir-27a) [miRNAknown_lenNOK_cloningHIGH_multiarm_DicerOK]

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-27a

0.019

no

no

0.44/0.74

18/25/0.43

0.5 0.2 0.0 0.0 0.0

0.1 1.3 0.6 0.4 2.5

12 36 23 19971 2

0 0 0 0 0

5 8 9 10 2

0 0 0 0 0

0 19 41 23 0

28 6 -15 7 28

5arm 5arm 5arm_loop_3arm 3arm 3arm

1 1 1 2 2

nd nd nd nd nd

0.50 0.15 0.43 0.15 0.61

5 2 7 2 9

43063

10

2

2

Clusters

Located in cluster 39: rno-mir-24, rno-mir-27a, rno-mir-23a

Families

Member of family miR-27a/27b (seed UCACAGU): rno-mir-27b, rno-mir-27a

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------------------------UCACAGU-----------------------------------------------	41902	miR-27a/27b
seed	--------------------------------------------------------------------------------------------------CACAGUG----------------------------------------------	761	miR-128
seed	------------------------------------------------------------------------------------------------UUCACAG------------------------------------------------	200	novel
seed	--------------------------------------------------------------------------------------------CGUGUUC----------------------------------------------------	89	novel
seed	-------------------------------------------------GGGCUUA-----------------------------------------------------------------------------------------------	51	miR-27a*
seed	-----------------------------------------------------------------------------GGUCUAC-------------------------------------------------------------------	23	novel
seed	---------------------------------------------------GCUUAGC---------------------------------------------------------------------------------------------	10	novel
seed	----CCA--------------------CUGG------------------------------------------------------------------------------------------------------------------------	6	novel
seed	---ACCA--------------------CUG-------------------------------------------------------------------------------------------------------------------------	6	novel
seed	-----------------------------------------------------------------------------------------------GUUCACA-------------------------------------------------	5	novel
seed	---------------------------------------------------------------------------------------------GUGUUCA---------------------------------------------------	3	miR-124*
seed	----------------------------------------------------------------------------------------------------------------------CCCUGGA--------------------------	2	novel
seed	-------------------------------------------------------------------------------------------UCGUGUU-----------------------------------------------------	1	novel
seed	-----------------------------------------------------------------------------------------------------AGUGGCU-------------------------------------------	1	novel
seed	----------------------------------------------------------------------------------------------UGUUCAC--------------------------------------------------	1	novel
seed	---------------------------------------------------------------------------------------------------ACAGUGG---------------------------------------------	1	novel
seed	----------------------------------------------------------------------------------------------------CAGUGGC--------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	------------------------------------------------------------------------------------------------TTCACAGTGGCTAAGTTCC------------------------------------	19	791	637	634	985	1850	1657	2215	4583	1734	2287
	------------------------------------------------------------------------------------------------TTCACAGTGGCTAAGTTCCG-----------------------------------	20	247	311	319	565	901	829	1157	2855	1039	1226
	------------------------------------------------------------------------------------------------TTCACAGTGGCTAAGTTC-------------------------------------	18	586	347	354	694	397	398	574	1394	631	1042
rno-miR-27a	------------------------------------------------------------------------------------------------TTCACAGTGGCTAAGTTCCGC----------------------------------	21	195	273	200	327	759	676	595	1396	710	989
	------------------------------------------------------------------------------------------------TTCACAGTGGCTAAGTTCCGCC---------------------------------	22	95	96	70	93	296	279	255	432	267	481
	-------------------------------------------------------------------------------------------------TCACAGTGGCTAAGTTCC------------------------------------	18	9	13	19	22	30	36	27	69	21	36
	-------------------------------------------------------------------------------------------------TCACAGTGGCTAAGTTCCG-----------------------------------	19	8	10	13	12	31	28	29	72	28	39
	------------------------------------------------------------------------------------------------TTCACAGTGGCTAAGTTCCGCCC--------------------------------	23	15	9	3	10	16	19	17	28	16	36
	-------------------------------------------------------------------------------------------------TCACAGTGGCTAAGTTCCGC----------------------------------	20	-	4	7	3	18	11	20	36	17	29
	-----------------------------------------------------------------------------------------------GTTCACAGTGGCTAAGTTC-------------------------------------	19	19	5	1	2	6	1	8	28	13	14
	-------------------------------------------------------------------------------------------------TCACAGTGGCTAAGTTCCGCC---------------------------------	21	4	-	2	-	5	9	7	10	6	15
	-----------------------------------------------------------------------------------------------GTTCACAGTGGCTAAGTT--------------------------------------	18	7	1	-	2	2	3	6	12	3	8
	-----------------------------------------------------------------------------------------------GTTCACAGTGGCTAAGTTCC------------------------------------	20	5	4	-	5	7	1	-	11	1	2
	-------------------------------------------------------------------------------------------TCGTGTTCACAGTGGCTAAGTTCC------------------------------------	24	1	4	4	-	1	9	1	2	-	1
rno-miR-27a*	------------------------------------------------AGGGCTTAGCTGCTT-GTGAGCA--------------------------------------------------------------------------------	22	2	-	-	-	10	1	1	4	1	2
	------------------------------------------------AGGGCTTAGCTGCTT-GTGAG----------------------------------------------------------------------------------	20	-	2	-	-	6	5	1	2	1	-
	-------------------------------------------------------------------------------------------TCGTGTTCACAGTGGCTAA-----------------------------------------	19	4	6	-	-	2	1	2	-	-	1
	-------------------------------------------------------------------------------------------TCGTGTTCACAGTGGCTAAGTTC-------------------------------------	23	2	6	-	-	1	1	-	3	-	-
	-------------------------------------------------------------------------------------------TCGTGTTCACAGTGGCTA------------------------------------------	18	2	3	-	-	1	1	2	-	-	4
	-------------------------------------------------------------------------------------------TCGTGTTCACAGTGGCTAAGT---------------------------------------	21	3	2	-	-	1	1	2	1	2	1
	-----------------------------------------------------------------------------------------------GTTCACAGTGGCTAAGTTCCGCC---------------------------------	23	1	-	-	-	1	-	1	6	1	1
	-------------------------------------------------------------------------------------------TCGTGTTCACAGTGGCTAAG----------------------------------------	20	1	-	1	1	3	-	-	2	2	-
	------------------------------------------------------------------------------------------------TTCACAGTGGCTAAGTTCCGCCCC-------------------------------	24	-	-	1	2	-	-	-	2	1	4
	-----------------------------------------------------------------------A-----GGTCTACAGCAAAGTCGTG-------------------------------------------------------	20	-	2	-	-	-	3	-	1	1	3
	-----------------------------------------------------------------------A-----GGTCTACAGCAAAGTCGTGT------------------------------------------------------	21	2	1	-	2	1	1	1	1	-	-
	------------------------------------------------AGGGCTTAGCTGCTT-GTGA-----------------------------------------------------------------------------------	19	-	-	-	-	-	4	-	4	-	1
	-----------------------------------------------------------------------------------------------GTTCACAGTGGCTAAGTTCCG-----------------------------------	21	-	-	-	1	2	2	-	2	-	-
	---ACCA--------------------CTGGCCT-------GTGGAGC-------------------------------------------------------------------------------------------------------	18	1	-	-	-	2	1	2	-	-	-
	-----------------------------------------------------------------------------------------------GTTCACAGTGGCTAAGTTCCGC----------------------------------	22	-	-	2	-	-	1	-	1	-	1
	--GACCA--------------------CTGGCCT-------GTGGAGC-------------------------------------------------------------------------------------------------------	19	3	-	-	-	1	-	-	-	-	1
	-------------------------------------------------------------------------------------------------TCACAGTGGCTAAGTTCCGCCC--------------------------------	22	-	1	-	2	-	1	-	1	-	-
	-----------------------------------------------------------------------A-----GGTCTACAGCAAAGTCGT--------------------------------------------------------	19	-	-	-	-	2	-	-	2	-	-
	--------------------------------------------------GGCTTAGCTGCTT-GTGAGCA--------------------------------------------------------------------------------	20	-	3	-	-	-	-	-	-	-	1
	----------------------------------------------------------------------------------------------TGTTCACAGTGGCTAAGTTCCGCC---------------------------------	24	-	-	-	-	3	-	-	-	-	-
	--------------------------------------------------GGCTTAGCTGCTT-GTGAG----------------------------------------------------------------------------------	18	1	-	-	-	-	-	-	1	-	-
	--------------------------------------------------GGCTTAGCTGCTT-GTGAGCAA-------------------------------------------------------------------------------	21	-	1	-	-	-	-	-	1	-	-
	------------------------------------------------AGGGCTTAGCTGCTT-GTGAGC---------------------------------------------------------------------------------	21	-	-	-	-	1	1	-	-	-	-
	--------------------------------------------------------------------------------------------CGTGTTCACAGTGGCTAAGT---------------------------------------	20	2	-	-	-	-	-	-	-	-	-
	--GACCA--------------------CTGGCCT-------GTGGAG--------------------------------------------------------------------------------------------------------	18	-	-	-	-	-	1	-	-	-	-
	---------------------------------------------------------------------------------------------------ACAGTGGCTAAGTTCCGC----------------------------------	18	-	-	-	-	-	-	-	1	-	-
	---------------------------------------------------------------------------------------------------------------------CCCCTGGACCC-CATCTCC---------------	18	-	-	-	-	-	1	-	-	-	-
	--------------------------------------------------GGCTTAGCTGCTT-GTGAGCAA-----GG------------------------------------------------------------------------	23	-	-	-	-	1	-	-	-	-	-
	----------------------------------------------------------------------------------------------------CAGTGGCTAAGTTCCGCC---------------------------------	18	1	-	-	-	-	-	-	-	-	-
	------------------------------------------------------------------------------------------GTCGTGTTCACAGTGGCTAAGTTCC------------------------------------	25	-	-	-	-	-	1	-	-	-	-
	------------------------------------------------AGGGCTTAGCTGCTT-GTGAGCAA-------------------------------------------------------------------------------	23	-	-	-	-	1	-	-	-	-	-
	-------------------------------------------------------------------------------------------------TCACAGTGGCTAAGTTCCGCCCCC------------------------------	24	-	-	-	-	-	-	-	1	-	-
	------------------------------------------------AGGGCTTAGCTGCTT-GTG------------------------------------------------------------------------------------	18	-	-	-	-	-	-	-	1	-	-
	-------------------------------------------------------------------------------------------TCGTGTTCACAGTGGCTAAGTT--------------------------------------	22	-	-	-	-	1	-	-	-	-	-
	---------------------------------------------------------------------------------------------GTGTTCACAGTGGCTAAGT---------------------------------------	19	-	1	-	-	-	-	-	-	-	-
	---------------------------------------------------------------------------------------------------------------------CCCCTGGACCC-CATCTCCCCAGG----------	23	-	1	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------------------------------CGTGTTCACAGTGGCTAA-----------------------------------------	18	-	-	-	1	-	-	-	-	-	-
	--------------------------------------------------------------------------------------------------CACAGTGGCTAAGTTCCGC----------------------------------	19	-	-	-	1	-	-	-	-	-	-
	----------------------------------------------------------------------------------------------TGTTCACAGTGGCTAAGTTCC------------------------------------	21	-	-	-	-	-	-	-	1	-	-
	--------------------------------------------------GGCTTAGCTGCTT-GTGAGCAA-----G-------------------------------------------------------------------------	22	1	-	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------------------------------TGTTCACAGTGGCTAAGT---------------------------------------	18	-	-	-	-	1	-	-	-	-	-
rat	--GACCA--------------------CTGGCCT-------GTGGAGCAGGGCTTAGCTGCTT-GTGAGCAA-----GGTCTACAGCAAAGTCGTGTTCACAGTGGCTAAGTTCCGCCCCCTGGACCC-CATCTCCCCAGG----------
human	--GGCAGAGAGGCCCCGAAGCCTGTGCCTGGCCT-------GAGGAGCAGGGCTTAGCTGCTT-GTGAGCAG-----GGTCCACA-CCAAGTCGTGTTCACAGTGGCTAAGTTCCGCCCCCCAGGCCCTCACCTCCTCTGGCCTTGCCGCC
mouse	CCGGCGA---------------------TGACCTCTCTAACAAGGTGCAGAGCTTAGCTGATTGGTGAACAGTGATTGGTTTCC------GCTTTGTTCACAGTGGCTAAGTTCTGCACCTGAAGAG--AAGGTGAGATGG----------
	* *                       ** ***         ** **** ********* ** **** **      ***   *      *   ******************** ** **          *  *     **
	.....  .....                    .>>>>>>       >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>     >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ............          .....	ENSRNOT00000053720 ENSRNOG00000035597 rno-mir-27a
rat	.....                    ..((((.       (.((.((.(((((((((..((. (((((((.     ((.((.......)))).)))))))))..))))))))).)).))).)).)). ............	1.000 -38.90
human	(((...((((((..((.....(((...(((((       (.((.((.(((((((((..((. (((((((.     ((...... .....)).)))))))))..))))))))).)).)).))))))..)))....)).))))))...)))	0.916 -64.30
mouse	(((....                     ..((((((((....((((((((((((((((((....((((((((....(((...))      )..))))))))..))))))))))))))))))..))))  ).)))....)))	0.998 -51.10

rat	chromosome:19:25638566:25638670:-1	Same_strand|Boundary_non-coding|ENSRNOT00000053720|ENSRNOG00000035597 ## Same_strand|Exonic_non-coding|ENSRNOT00000053720|ENSRNOG00000035597 ## ENSRNOG00000035597|miRNA|rno-mir-27a|rno-mir-27a [Source:miRBase;Acc:MI0000860] ## {MIR: rno-mir-27a}
human	chromosome:19:13808227:13808361:-1	Same_strand|Boundary_non-coding|ENST00000385073|ENSG00000207808|miRNA|hsa-mir-27a [Source:miRBase;Acc:MI0000085] ## {Repeats: dust 0 class=dust} ## {MIR: hsa-mir-27a}
mouse	chromosome:13:63401999:63402110:1	Same_strand|Intronic_coding|ENSMUST00000060660|ENSMUSG00000056199|protein_coding| ## Same_strand|Intronic_non-coding|ENSMUST00000021911|ENSMUSG00000021458|protein_coding|RIKEN cDNA 2010111I01 gene Gene [Source:MGI Symbol;Acc:MGI:1919311] ## Same_strand|Boundary_non-coding|ENSMUST00000091560|ENSMUSG00000021458|protein_coding|RIKEN cDNA 2010111I01 gene Gene [Source:MGI Symbol;Acc:MGI:1919311] ## {MIR: mmu-mir-27b}

rno-mir-210

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-210 5arm	91	82	47.500	63	16.500	19.500	107	125	68	31
rno-mir-210 3arm	1019	961	1522	1429	655	777	1454	2254	2411	2525
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-210 5arm	0.003	0.004	0.003	0.004	0.001	0.001	0.008	0.007	0.004	0.002
rno-mir-210 3arm	0.034	0.042	0.082	0.085	0.032	0.059	0.113	0.119	0.159	0.168

sblock905 (miRBase rno-mir-210) [miRNAknown_lenNOK_cloningHIGH_multiarm_DicerOK]

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-210

0.066

no

no

0.60/0.70

18/26/0.54

0.0 0.0 0.0

1.4 1.9 0.0

491 9022 1

0 0 0

10 10 1

0 0 0

27 23 3

3 6 28

5arm 3arm 3arm

1 1 1

nd nd nd

0.19 0.15 0.40

2 1 2

15669

10

3

2

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------UGUGCGU----------------------------------------------------------	14962	miR-210
seed	-----------------------------------------GCCACUG------------------------------------------------------------------------------------------------	652	novel
seed	------------------------------------------------------------------------------CUGUGCG-----------------------------------------------------------	36	novel
seed	------------------------------------------CCACUGC-----------------------------------------------------------------------------------------------	9	novel
seed	--------------------------------------------------------------------------------GUGCGUG---------------------------------------------------------	7	novel
seed	-----------------------------------------------------------------------------------CGUGUGA------------------------------------------------------	1	novel
seed	--------------------------------------------ACUGCCC---------------------------------------------------------------------------------------------	1	novel
seed	-----------------------------------------------------------------------------------------------------CUGUCCC------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-miR-210	------------------------------------------------------------------------------CTGTGCGTGTGACAGCGGCTGA--------------------------------------------	22	376	238	582	553	209	239	87	751	556	1018
	------------------------------------------------------------------------------CTGTGCGTGTGACAGCGGC-----------------------------------------------	19	262	302	381	378	161	227	625	591	614	602
	------------------------------------------------------------------------------CTGTGCGTGTGACAGCGG------------------------------------------------	18	128	202	214	203	109	131	529	293	797	340
	------------------------------------------------------------------------------CTGTGCGTGTGACAGCGGCT----------------------------------------------	20	112	122	171	175	98	121	203	329	274	276
	------------------------------------------------------------------------------CTGTGCGTGTGACAGCGGCTGATC------------------------------------------	24	84	55	114	88	46	38	-	158	67	125
	------------------------------------------------------------------------------CTGTGCGTGTGACAGCGGCTG---------------------------------------------	21	48	35	38	15	22	9	3	78	42	121
	----------------------------------------AGCCACTGCCCACAGCACACTGC---------------------------------------------------------------------------------	23	24	27	7	17	3	9	31	43	28	6
	------------------------------------------------------------------------------CTGTGCGTGTGACAGCGGCTGAT-------------------------------------------	23	6	4	18	14	8	9	1	41	44	33
	----------------------------------------AGCCACTGCCCACAGCACACT-----------------------------------------------------------------------------------	21	26	23	12	16	6	1	21	28	16	7
	----------------------------------------AGCCACTGCCCACAGCACAC------------------------------------------------------------------------------------	20	24	19	12	14	4	5	23	23	13	6
	----------------------------------------AGCCACTGCCCACAGCACACTG----------------------------------------------------------------------------------	22	12	5	15	13	3	1	25	22	7	10
	----------------------------------------AGCCACTGCCCACAGCACA-------------------------------------------------------------------------------------	19	2	6	1	-	-	2	2	6	2	1
	----------------------------------------AGCCACTGCCCACAGCAC--------------------------------------------------------------------------------------	18	4	2	1	4	1	1	5	2	2	-
	------------------------------------------------------------------------------CTGTGCGTGTGACAGCGGCTGATCT-----------------------------------------	25	-	-	2	3	-	-	-	4	4	6
	-----------------------------------------------------------------------------ACTGTGCGTGTGACAGCG-------------------------------------------------	18	-	1	2	-	1	1	-	4	2	1
	-----------------------------------------------------------------------------ACTGTGCGTGTGACAGCGGC-----------------------------------------------	20	-	-	-	-	1	2	2	1	4	-
	-----------------------------------------------------------------------------ACTGTGCGTGTGACAGCGG------------------------------------------------	19	-	2	-	-	-	-	3	1	1	1
	-----------------------------------------------------------------------------ACTGTGCGTGTGACAGCGGCTGA--------------------------------------------	23	-	-	-	-	-	-	-	1	3	-
	-----------------------------------------GCCACTGCCCACAGCACACTGC---------------------------------------------------------------------------------	22	-	-	-	-	-	1	1	-	1	-
	-------------------------------------------------------------------------------TGTGCGTGTGACAGCGGC-----------------------------------------------	18	-	-	-	-	-	-	-	2	1	-
	-----------------------------------------GCCACTGCCCACAGCACAC------------------------------------------------------------------------------------	19	1	-	-	-	-	-	-	-	-	1
	-------------------------------------------------------------------------------TGTGCGTGTGACAGCGGCT----------------------------------------------	19	2	-	-	-	-	-	-	-	-	-
	-----------------------------------------GCCACTGCCCACAGCACACTG----------------------------------------------------------------------------------	21	-	1	-	1	-	-	-	-	-	-
	-------------------------------------------------------------------------------TGTGCGTGTGACAGCGGCTGA--------------------------------------------	21	1	-	-	-	-	-	-	-	1	-
	----------------------------------------AGCCACTGCCCACAGCACACTGCGTT------------------------------------------------------------------------------	26	-	-	-	-	-	-	-	1	-	-
	-----------------------------------------GCCACTGCCCACAGCACA-------------------------------------------------------------------------------------	18	-	-	-	-	-	-	-	1	-	-
	-----------------------------------------------------------------------------ACTGTGCGTGTGACAGCGGCTG---------------------------------------------	22	-	-	-	-	-	-	-	-	1	-
	-----------------------------------------GCCACTGCCCACAGCACACT-----------------------------------------------------------------------------------	20	-	-	-	-	-	-	1	-	-	-
	-------------------------------------------CACTGCCCACAGCACACTGC---------------------------------------------------------------------------------	20	-	-	-	-	-	-	1	-	-	-
	-----------------------------------------------------------------------------ACTGTGCGTGTGACAGCGGCT----------------------------------------------	21	-	-	-	-	-	-	-	-	-	1
	----------------------------------------------------------------------------------GCGTGTGACAGCGGCTGA--------------------------------------------	18	-	-	-	-	-	-	-	-	-	1
	----------------------------------------------------------------------------------------------------TCTGTCCCTGGGCAGCGCGA------------------------	20	-	-	-	-	-	-	1	-	-	-
rat	-------------CCGGGGCAGTCCCTCCAGGCTCAGGACAGCCACTGCCCACAGCACACTGCGTTGCTCCGGACCCACTGTGCGTGTGACAGCGGCTGATCTGTCCCTGGGCAGCGCGAACC---------------------
human	GCCCGCCCACCC-----GGCAGTGCCTCCAGGCGCAGGGCAGCCCCTGCCCACCGCACACTGCGCTGCCCCAGACCCACTGTGCGTGTGACAGCGGCTGATCTGTGCCTGGGCAGCGCGACCCTCCTGGCCCCGTGTCC-GGGT
mouse	ACTTGCCCACCCGCCGGGGCAGTCCCTCCAGGCTCAGGACAGCCACTGCCCACCGCACACTGCGTTGCTCCGGACCCACTGTGCGTGTGACAGCGGCTGATCTGTCCCTGGGCAGCGCGAACC-CCTGGCCCTGTGACCAGAGT
	****** ********* **** ***** ******** ********** *** ** ********************************* ************** **
	.....             >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>                     .....	ENSRNOT00000053739 ENSRNOG00000035616 rno-mir-210
rat	..((..(.((..(.(((((..((((.(((((.(((..(((((((((.((.(((......))).)).))))).)))).))).))))).))))..))))))..))..)..))	1.000 -47.30
human	(((((..(((..     (((.((((.(((((((((((..(((((.(((..(((((((((.((..(((...)))...)).)))))).))).))).)))))..)))))))))))..))))..........)))..)))..) ))))	0.896 -72.50
mouse	((((...(((..(((((((..((...((((((..((((.(((((.(((..(((((((((.((.(((......))).)).)))))).))).))).))))).))))..))))))....))....) ))))))...)))....))))	0.982 -62.90

rat	chromosome:1:201415656:201415765:-1	Same_strand|Exonic_non-coding|ENSRNOT00000053739|ENSRNOG00000035616 ## ENSRNOG00000035616|miRNA|rno-mir-210|rno-mir-210 [Source:miRBase;Acc:MI0000950] ## {MIR: rno-mir-210}
human	chromosome:11:558069:558206:-1	Same_strand|Boundary_non-coding|ENST00000362168|ENSG00000199038|miRNA|hsa-mir-210 [Source:miRBase;Acc:MI0000286] ## {SimpF: oe = 0.88 0 CpG} ## {MIR: hsa-mir-210}
mouse	chromosome:7:148407263:148407405:-1	Same_strand|Boundary_non-coding|ENSMUST00000083617|ENSMUSG00000065551|miRNA|mmu-mir-210 [Source:miRBase;Acc:MI0000695] ## {MIR: mmu-mir-210}

miRNAknown_lenNOK_cloningHIGH_randfoldOK (4 loci)

rno-mir-194

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-194 5arm	560	172	6121	8911.667	158	148	67	119	2726	6600.667
rno-mir-194 3arm	9	3	102	69	1	0	0	0	42	45
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-194 5arm	0.019	0.008	0.332	0.528	0.008	0.011	0.005	0.006	0.180	0.439
rno-mir-194 3arm	0.000	0.000	0.006	0.004	0.000	0	0	0	0.003	0.003

block328358 (miRBase rno-mir-194-1) [miRNAknown_lenNOK_cloningHIGH_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-194-1

0.001

no

no

0.42/0.50

18/24/0.62

0.0

1.6

16087

0

10

0

14

2

5arm

2

nd

0.13

2

20478

10

na

na

Clusters

Located in cluster 21: rno-mir-194, rno-mir-215

Families

Member of family miR-194 (seed GUAACAG): rno-mir-194, rno-mir-194

		reads	miRBase family seed
seed	----------------------------GUAACAG---------------------------------------------------------------------------------	20269	miR-194
seed	-----------------------------UAACAGC--------------------------------------------------------------------------------	205	novel
seed	------------------------------AACAGCA-------------------------------------------------------------------------------	2	miR-21*
seed	---------------------------UGUAACA----------------------------------------------------------------------------------	1	novel
seed	-------------------------------ACAGCAA------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	---------------------------TGTAACAGCAACTCCATGTG---------------------------------------------------------------------	20	134	43	1982	2130	31	34	22	30	674	1401
	---------------------------TGTAACAGCAACTCCATG-----------------------------------------------------------------------	18	118	48	1298	2161	43	29	13	33	703	1306
	---------------------------TGTAACAGCAACTCCATGTGG--------------------------------------------------------------------	21	138	26	747	1074	31	28	11	16	143	1184
	---------------------------TGTAACAGCAACTCCATGT----------------------------------------------------------------------	19	58	7	499	661	14	10	-	14	256	451
	---------------------------TGTAACAGCAACTCCATGTGGAC------------------------------------------------------------------	23	29	11	325	367	11	13	1	5	126	766
rno-miR-194	---------------------------TGTAACAGCAACTCCATGTGGA-------------------------------------------------------------------	22	11	7	207	410	7	5	1	4	124	214
	----------------------------GTAACAGCAACTCCATGTG---------------------------------------------------------------------	19	2	-	33	26	-	-	1	-	6	21
	----------------------------GTAACAGCAACTCCATGTGG--------------------------------------------------------------------	20	1	-	15	16	-	-	-	-	-	23
	----------------------------GTAACAGCAACTCCATGTGGAC------------------------------------------------------------------	22	-	-	10	4	-	-	-	-	-	13
	---------------------------TGTAACAGCAACTCCATGTGGACT-----------------------------------------------------------------	24	-	-	3	11	-	-	1	-	6	3
	----------------------------GTAACAGCAACTCCATGT----------------------------------------------------------------------	18	1	-	11	3	-	-	-	-	1	5
	----------------------------GTAACAGCAACTCCATGTGGA-------------------------------------------------------------------	21	-	-	3	5	1	-	-	-	1	3
	-----------------------------TAACAGCAACTCCATGTGG--------------------------------------------------------------------	19	-	-	-	1	-	-	-	-	-	1
	--------------------------GTGTAACAGCAACTCCAT------------------------------------------------------------------------	18	-	-	1	-	-	-	-	-	-	-
	------------------------------AACAGCAACTCCATGTGGAC------------------------------------------------------------------	20	-	-	1	-	-	-	-	-	-	-
rat	-------------ATGGAGTCATCACGTGTAACAGCAACTCCATGTGGACTGTGCACAGA-TCCCAGTGGAGCTGCTGTTACTTTTGATGGCCTCCA-------------------
human	CCTTATATGTTTAATGGTGTTATCAAGTGTAACAGCAACTCCATGTGGACTGTGTACCAATTTCCAGTGGAGATGCTGTTACTTTTGATGGTTACCAACTTGCTACAATATAAAGG
mouse	---------------------------TGTAACAGCAACTCCATGTGGACTGTGCTCGGA-TTCCAGTGGAGCTGCTGTTACT---------------------------------
	***************************  *  * * ********* **********
	-----             ----------------------------------------------- ------------------------------------                   -----	ENSRNOT00000057395 ENSRNOG00000002368 Iars2
	-----             ----------------------------------------------- ------------------------------------                   -----	ENSRNOT00000057394 ENSRNOG00000002368 Iars2
	-----             ----------------------------------------------- ------------------------------------                   -----	ENSRNOT00000057393 ENSRNOG00000002368 Iars2
	-----             ----------------------------------------------- ------------------------------------                   -----	ENSRNOT00000003222 ENSRNOG00000002368 Iars2
	-----             ----------------------------------------------- ------------------------------------                   -----	ENSRNOT00000057392 ENSRNOG00000002368 Iars2
	.....             >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>                   .....	ENSRNOT00000053605 ENSRNOG00000035482 rno-mir-194-1
rat	.(((((((((((...(((((((((.((((((..((((((....))). )))..)))))).)))))))))...)))))).)))))	1.000 -44.70
human	((((((((((.((((((((..((((((.(((((((((.((((((.((((..((......)).)))))))))).))))))))).))))))...)))))..)))..))).))))).))	0.993 -40.40
mouse	.(((((((((.((((((.(((((((....))). .)))))))))).))))))))).	1.000 -28.40

rat	chromosome:13:101312447:101312529:1	Opposite_strand|Intronic_coding|ENSRNOT00000003222|ENSRNOG00000002368 ## Same_strand|Exonic_non-coding|ENSRNOT00000053605|ENSRNOG00000035482 ## ENSRNOG00000002368|protein_coding|Iars2|isoleucine-tRNA synthetase 2, mitochondrial Gene [Source:MGI (curated);Acc:Iars2-001] ## ENSRNOG00000035482|miRNA|rno-mir-194-1|rno-mir-194-1 [Source:miRBase;Acc:MI0000937] ## {MIR: rno-mir-194-1}
human	chromosome:1:218358104:218358219:-1	Opposite_strand|Intronic_coding|ENST00000302637|ENSG00000067704|protein_coding|Isoleucyl-tRNA synthetase, mitochondrial Precursor (EC 6.1.1.5)(Isoleucine--tRNA ligase)(IleRS) [Source:UniProtKB/Swiss-Prot;Acc:Q9NSE4] ## Same_strand|Boundary_non-coding|ENST00000384892|ENSG00000207624|miRNA|hsa-mir-194-1 [Source:miRBase;Acc:MI0000488] ## {MIR: hsa-mir-194-1}
mouse	chromosome:1:187137170:187137292:1	Opposite_strand|Intronic_coding|ENSMUST00000027921|ENSMUSG00000026618|protein_coding|isoleucine-tRNA synthetase 2, mitochondrial Gene [Source:MGI (curated);Acc:Iars2-001] ## Same_strand|Boundary_non-coding|ENSMUST00000083647|ENSMUSG00000065581|miRNA|mmu-mir-194-1 [Source:miRBase;Acc:MI0000236] ## {MIR: mmu-mir-194-1}

rno-mir-880

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-880 3arm	5	7	2	0	0	1	0	0	35	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-880 3arm	0.000	0.000	0.000	0	0	0.000	0	0	0.002	0

block2895941 (miRBase rno-mir-880) [miRNAknown_lenNOK_cloningHIGH_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-880

0.002

no

no

0.35/0.40

18/22/0.59

0.0

1.8

38

0

5

0

10

2

3arm

1

nd

0.21

3

50

5

na

na

Families

Member of family miR-880 (seed ACUCCAU): rno-mir-880, block299725_cand

		reads	miRBase family seed
seed	------------------------------------------------------------------ACUCCAU----------------------------------------	49	miR-880
seed	-------------------------------------------------------------------CUCCAUU---------------------------------------	1	miR-136
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S2	T5S1
	-----------------------------------------------------------------TACTCCATTCATTCTGAG------------------------------	18	-	-	2	1	13
	-----------------------------------------------------------------TACTCCATTCATTCTGAGTAG---------------------------	21	2	2	-	-	8
rno-miR-880	-----------------------------------------------------------------TACTCCATTCATTCTGAGTAGA--------------------------	22	-	4	-	-	4
	-----------------------------------------------------------------TACTCCATTCATTCTGAGTA----------------------------	20	3	-	-	-	5
	-----------------------------------------------------------------TACTCCATTCATTCTGAGT-----------------------------	19	-	1	-	-	4
	------------------------------------------------------------------ACTCCATTCATTCTGAGTAG---------------------------	20	-	-	-	-	1
rat	-------------------TGCACTGCAATACTCAGATTGGTATGAGTCACTTCCTAAAACATGTTACTCCATTCATTCTGAGTAGAGCAAGGCACA----------------
mouse	CATCACTGAACAAACTGTGTGCACTGCAATACTCAGATTGATATGAGTCACTTCCTATTGCATGTTACTCCATCCTCTCTGAGTAGAGTAAGGCACACCAATCACCAGTTTTG
	********************* ****************   ************* *  *********** ********
	.....                   >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>                .....	ENSRNOT00000062963 ENSRNOG00000041210 rno-mir-880
rat	(((..(((..((((((((.(((...((((.((............)).))))...))).))))))))..)))..)))..	1.000 -26.80
mouse	((..((((........((((((..(((..((((((((..(((..((((.((............)).)))).)))...))))))))..)))..)))))).......))))..))	0.995 -31.76

rat	chromosome:X:152850266:152850343:-1	Same_strand|Exonic_non-coding|ENSRNOT00000062963|ENSRNOG00000041210 ## ENSRNOG00000041210|miRNA|rno-mir-880|rno-mir-880 [Source:miRBase;Acc:MI0006122] ## {MIR: rno-mir-880}
mouse	chromosome:X:64053689:64053801:-1	Same_strand|Boundary_non-coding|ENSMUST00000104809|ENSMUSG00000078002|miRNA|mmu-mir-880 [Source:miRBase;Acc:MI0005473] ## {MIR: mmu-mir-880}

rno-mir-196a

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-196a 5arm	5	0	1	0	0	3	1	1	1058	1408
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-196a 5arm	0.000	0	0.000	0	0	0.000	0.000	0.000	0.070	0.094

sblock11521 (miRBase rno-mir-196a) [miRNAknown_lenNOK_cloningHIGH_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-196a

0.001

no

no

0.32/0.56

18/23/0.56

0.0 0.3

2.1 1.2

2444 11

0 0

7 2

0 0

24 60

4 -33

5arm loop

1 1

nd nd

0.05 0.04

1 1

2488

7

na

na

Families

Member of family miR-196a/196b/196c (seed AGGUAGU): rno-mir-196c, rno-mir-196a, rno-mir-196b

		reads	miRBase family seed
seed	------------------------------AGGUAGU-------------------------------------------------------------------------------	2455	miR-196a/196b/196c
seed	-------------------------------GGUAGUU------------------------------------------------------------------------------	22	novel
seed	------------------------------------------------------------------CGGCAAC-------------------------------------------	8	miR-196a*
seed	-------------------------------------------------------------------GGCAACA------------------------------------------	3	novel
		len	cloning frequencies
			T1S1	T2S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-----------------------------TAGGTAGTTTCATGTTGT---------------------------------------------------------------------	18	-	-	1	-	-	260	309
	-----------------------------TAGGTAGTTTCATGTTGTT--------------------------------------------------------------------	19	-	-	-	-	1	304	205
	-----------------------------TAGGTAGTTTCATGTTGTTG-------------------------------------------------------------------	20	-	-	1	-	-	181	246
rno-miR-196a	-----------------------------TAGGTAGTTTCATGTTGTTGGG-----------------------------------------------------------------	22	-	1	-	-	-	108	247
	-----------------------------TAGGTAGTTTCATGTTGTTGG------------------------------------------------------------------	21	2	-	1	-	-	95	251
	-----------------------------TAGGTAGTTTCATGTTGTTGGGA----------------------------------------------------------------	23	3	-	-	1	-	98	140
	------------------------------AGGTAGTTTCATGTTGTTGGG-----------------------------------------------------------------	21	-	-	-	-	-	2	6
	------------------------------AGGTAGTTTCATGTTGTTGGGA----------------------------------------------------------------	22	-	-	-	-	-	5	-
	------------------------------AGGTAGTTTCATGTTGTT--------------------------------------------------------------------	18	-	-	-	-	-	4	1
	-----------------------------------------------------------------TCGGCAACAAGAAACTGCCTG------------------------------	21	-	-	-	-	-	3	1
	------------------------------AGGTAGTTTCATGTTGTTG-------------------------------------------------------------------	19	-	-	-	-	-	1	1
	-----------------------------------------------------------------TCGGCAACAAGAAACTGCC--------------------------------	19	-	-	-	-	-	-	2
	------------------------------AGGTAGTTTCATGTTGTTGG------------------------------------------------------------------	20	-	-	-	-	-	-	2
rno-miR-196a*	-----------------------------------------------------------------TCGGCAACAAGAAACTGCCTGA-----------------------------	22	-	-	-	-	-	-	2
	------------------------------------------------------------------CGGCAACAAGAAACTGCC--------------------------------	18	-	-	-	-	-	1	1
	------------------------------------------------------------------CGGCAACAAGAAACTGCCTGAGT---------------------------	23	-	-	-	-	-	-	1
rat	-----TGTTTGCTCAGCTGATCTGTGGCTTAGGTAGTTTCATGTTGTTGGGATTGAGTTTTGAACTCGGCAACAAGAAACTGCCTGAGTTACATCAGTCGGTTTTCGTCGAGGGC-
human	-GCCCTGCTCGCTCAGCTGATCTGTGGCTTAGGTAGTTTCATGTTGTTGGGATTGAGTTTTGAACTCGGCAACAAGAAACTGCCTGAGTTACATCAGTCGGTTTTCGTCGAGGGC-
mouse	GGCCCTGCTTGCTCAGCTGATCTGTGGCTTAGGTAGTTTCATGTTGTTGGGATTGAGTTTTGAACTCGGCAACAAGAAACTGCCTGAGTTACATCAGTCGGTTTTCGTCGAGGGCC
	** * *********************************************************************************************************
	.....     >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .....	ENSRNOT00000053737 ENSRNOG00000035614 rno-mir-196a
rat	.....((((.(((((..((((((((((((((((((.((((((((((.(..(...)..).)))))))))).)))))))))))))))))))))))(((......))).))))	1.000 -48.80
human	(((((...((...(((((((.((((((((((((((((((.((((((((((.((.......)).)))))))))).))))))))))))))))))...)))))))..))...)))))	0.995 -55.10
mouse	((((((...((...(((((((.((((((((((((((((((.((((((((((.((.......)).)))))))))).))))))))))))))))))...)))))))..))...))))))	0.973 -56.70

rat	chromosome:7:141736759:141736868:1	Same_strand|Exonic_non-coding|ENSRNOT00000053737|ENSRNOG00000035614 ## ENSRNOG00000035614|miRNA|rno-mir-196a|rno-mir-196a [Source:miRBase;Acc:MI0000940] ## {MIR: rno-mir-196a}
human	chromosome:12:52671785:52671898:1	Same_strand|Boundary_non-coding|ENST00000385189|ENSG00000207924|miRNA|hsa-mir-196a-2 [Source:miRBase;Acc:MI0000279] ## {MIR: hsa-mir-196a-2}
mouse	chromosome:15:102803767:102803882:1	Same_strand|Boundary_non-coding|ENSMUST00000083554|ENSMUSG00000065488|miRNA|mmu-mir-196a-2 [Source:miRBase;Acc:MI0000553] ## {MIR: mmu-mir-196a-2}

rno-mir-219

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-219 5arm	749	585	6	10	10	32	3	7	10	14
rno-mir-219 3arm	9783	8272	6	5	2	2	6	5	35	20
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-219 5arm	0.025	0.026	0.000	0.001	0.000	0.002	0.000	0.000	0.001	0.001
rno-mir-219 3arm	0.325	0.361	0.000	0.000	0.000	0.000	0.000	0.000	0.002	0.001

sblock7099 (miRBase rno-mir-219-1) [miRNAknown_lenNOK_cloningHIGH_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-219-1

0.001

no

no

0.37/0.64

18/24/0.56

0.0 0.0

1.5 1.6

688 17

0 0

10 10

0 0

20 61

5 -38

5arm loop

2 2

nd nd

0.09 0.11

1 1

868

10

na

na

Families

Member of family miR-219 (seed GAUUGUC): rno-mir-219, rno-mir-219

		reads	miRBase family seed
seed	----------------------------------------GAUUGUC----------------------------------------------------------------------------------------------------	827	miR-219
seed	---------------------------------------------------------------------------------GAGUUGC-----------------------------------------------------------	32	miR-219
seed	-----------------------------------------AUUGUCC---------------------------------------------------------------------------------------------------	5	novel
seed	-------------------------------------------UGUCCAA-------------------------------------------------------------------------------------------------	2	novel
seed	--------------------------------------------GUCCAAA------------------------------------------------------------------------------------------------	1	novel
seed	------------------------------------------UUGUCCA--------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	---------------------------------------TGATTGTCCAAACGCAAT------------------------------------------------------------------------------------------	18	179	128	3	4	7	6	1	3	3	-
	---------------------------------------TGATTGTCCAAACGCAATTC----------------------------------------------------------------------------------------	20	85	70	-	2	1	6	-	1	1	5
rno-miR-219-5p	---------------------------------------TGATTGTCCAAACGCAATTCT---------------------------------------------------------------------------------------	21	87	73	1	3	-	1	1	-	1	-
	---------------------------------------TGATTGTCCAAACGCAATTCTC--------------------------------------------------------------------------------------	22	66	41	2	-	1	8	1	2	1	-
	---------------------------------------TGATTGTCCAAACGCAATT-----------------------------------------------------------------------------------------	19	6	15	-	1	-	1	-	1	-	-
rno-miR-219-1-3p	--------------------------------------------------------------------------------AGAGTTGCGTCTGGACGTCCCG---------------------------------------------	22	4	1	-	1	1	1	-	1	1	2
	--------------------------------------------------------------------------------AGAGTTGCGTCTGGACGTC------------------------------------------------	19	2	-	4	1	-	-	-	1	1	3
	---------------------------------------TGATTGTCCAAACGCAATTCTCG-------------------------------------------------------------------------------------	23	1	2	-	-	-	2	-	-	1	3
	--------------------------------------------------------------------------------AGAGTTGCGTCTGGACGTCCC----------------------------------------------	21	-	-	1	-	-	-	-	1	-	1
	--------------------------------------------------------------------------------AGAGTTGCGTCTGGACGT-------------------------------------------------	18	-	-	-	-	1	1	1	-	-	-
	----------------------------------------GATTGTCCAAACGCAATT-----------------------------------------------------------------------------------------	18	1	1	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------------------AGAGTTGCGTCTGGACGTCCCGAG-------------------------------------------	24	-	-	-	-	-	-	2	-	-	-
	----------------------------------------GATTGTCCAAACGCAATTCT---------------------------------------------------------------------------------------	20	1	1	-	-	-	-	-	-	-	-
	------------------------------------------TTGTCCAAACGCAATTCTC--------------------------------------------------------------------------------------	19	-	1	-	-	-	-	-	-	-	1
	----------------------------------------GATTGTCCAAACGCAATTCTC--------------------------------------------------------------------------------------	21	-	-	-	-	-	-	-	-	-	1
	-------------------------------------------TGTCCAAACGCAATTCTC--------------------------------------------------------------------------------------	18	1	-	-	-	-	-	-	-	-	-
	-----------------------------------------ATTGTCCAAACGCAATTC----------------------------------------------------------------------------------------	18	1	-	-	-	-	-	-	-	-	-
rat	-------------------CTGTCCCGGGCCGCGGCTCCTGATTGTCCAAACGCAATTCTCGAGTCTCTGGCTCCGGCCGAGAGTTGCGTCTGGACGTCCCGAGCCGCCGCCCCCAAACCTCGAGGGGG------------------
human	--GCGCCTCCCTCCCTTCCCCGCCCCGGGCCGCGGCTCCTGATTGTCCAAACGCAATTCTCGAGTCTATGGCTCCGGCCGAGAGTTGAGTCTGGACGTCCCGAGCCGCCGCCCCCAAACCTCGAGCGGGAGA-GCGGGTCGGAGGGT
mouse	CTCCGATGCGCTTCTCTCCCCGTCCCGGGCCGCGGCTCCTGATTGTCCAAACGCAATTCTCGAGTCTCTGGCTCCGGCCGAGAGTTGCGTCTGGACGTCCCGAGCCGCCGCCCCCAAACCTCGAGGGGGAGAGGCCGGGCGGAG---
	* * ******************************************** ******************* ************************************* ***
	.....                   >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>                  .....	ENSRNOT00000053776 ENSRNOG00000035653 rno-mir-219-1
rat	.......((((.(((((((..(((.(((((.((((((((((((.(((.........))))))))))))))).))))))))..))))))).)))).....(((....))).	1.000 -60.00
human	...(((((..(((((((((((...((((.(((((((..((.((((((.((.(((((((((.(((.........)))))))))))).)).))))))))..))))))).))))...........))))).)) ).)))..)))))..	0.986 -76.54
mouse	(((((.((.(((((((((((((....((((.(((((((..((.((((((.((((((((((((.(((.........))))))))))))))).))))))))..))))))).))))........)).)))))))))))))..)))))	1.000 -86.60

rat	chromosome:20:4967801:4967910:1	Same_strand|Exonic_non-coding|ENSRNOT00000053776|ENSRNOG00000035653 ## ENSRNOG00000035653|miRNA|rno-mir-219-1|rno-mir-219-1 [Source:miRBase;Acc:MI0000959] ## {SimpF: oe = 0.97 1 CpG} ## {MIR: rno-mir-219-1}
human	chromosome:6:33283573:33283716:1	Same_strand|Boundary_non-coding|ENST00000362166|ENSG00000199036|miRNA|hsa-mir-219-1 [Source:miRBase;Acc:MI0000296] ## {SimpF: rank = 1 -1 FirstEF,oe = 1.00 0 CpG} ## {MIR: hsa-mir-219-1}
mouse	chromosome:17:34161913:34162056:-1	Same_strand|Boundary_non-coding|ENSMUST00000083621|ENSMUSG00000065555|miRNA|mmu-mir-219-1 [Source:miRBase;Acc:MI0000702] ## {SimpF: oe = 0.97 -1 CpG, 1 Eponine} ## {MIR: mmu-mir-219-1}

miRNAknown_rep_cloningHIGH_multiarm_DicerOK_randfoldOK (4 loci)

rno-mir-493

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-493 5arm	153	101	4	2	0	3	0	2	2	0
rno-mir-493 3arm	11	8	0	0	0	0	0	0	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-493 5arm	0.005	0.004	0.000	0.000	0	0.000	0	0.000	0.000	0
rno-mir-493 3arm	0.000	0.000	0	0	0	0	0	0	0	0

sblock10438 (miRBase rno-mir-493) [miRNAknown_rep_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-493

0.001

no

LINE,LINE/L2,SINE,SINE/MIR

0.36/0.58

18/24/0.82

0.0 0.0

1.5 1.0

179 16

0 0

7 2

0 0

13 10

5 8

5arm 3arm

1 1

nd nd

0.05 0.05

1 1

286

7

3

1

		reads	miRBase family seed
seed	----------------UGUACAU-------------------------------------------------------------------	264	novel
seed	---------------------------------------------------------GAAGGU-C-------------------------	19	miR-493
seed	-----------------GUACAUG------------------------------------------------------------------	3	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S2	T4S2	T5S1
	---------------TTGTACATGGTAGGCTTTCA-------------------------------------------------------	20	58	34	-	-	1	2	-
	---------------TTGTACATGGTAGGCTTTCATTC----------------------------------------------------	23	50	37	1	-	1	-	1
	---------------TTGTACATGGTAGGCTTT---------------------------------------------------------	18	17	12	3	1	1	-	1
	---------------TTGTACATGGTAGGCTTTCAT------------------------------------------------------	21	12	7	-	1	-	-	-
	---------------TTGTACATGGTAGGCTTTC--------------------------------------------------------	19	8	5	-	-	-	-	-
	---------------TTGTACATGGTAGGCTTTCATT-----------------------------------------------------	22	8	3	-	-	-	-	-
rno-miR-493	--------------------------------------------------------TGAAGGT-CTACTGTGTGCCAG------------	21	5	3	-	-	-	-	-
	--------------------------------------------------------TGAAGGT-CTACTGTGTGCCA-------------	20	1	3	-	-	-	-	-
	--------------------------------------------------------TGAAGGT-CTACTGTGTGC---------------	18	3	-	-	-	-	-	-
	----------------TGTACATGGTAGGCTTTCAT------------------------------------------------------	20	-	2	-	-	-	-	-
	--------------------------------------------------------TGAAGGT-CTACTGTGTGCC--------------	19	-	2	-	-	-	-	-
	--------------------------------------------------------TGAAGGT-CTACTGTGTGCCAGGCC---------	24	1	-	-	-	-	-	-
	--------------------------------------------------------TGAAGGT-CTACTGTGTGCCAGG-----------	22	1	-	-	-	-	-	-
	----------------TGTACATGGTAGGCTTTCATT-----------------------------------------------------	21	-	1	-	-	-	-	-
rat	--GGCCTCCAGGGCCTTGTACATGGTAGGCTTTCATTCATT-GTTTGCACATTCGGTGAAGGT-CTACTGTGTGCCAGGCCCTGTGCC--
human	CTGGCCTCCAGGGCTTTGTACATGGTAGGCTTTCATTCATTCGTTTGCACATTCGGTGAAGGT-CTACTGTGTGCCAGGCCCTGTGCCAG
mouse	---------------TTGTACATGGTAGGCTTTCATTCATT-TTTTGCACATTCGGTGAAGGTCCTACTGTGTGCCA-------------
	**************************  ******************** *************
	.....  >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>  .....	ENSRNOT00000054366 ENSRNOG00000036243 rno-mir-493
rat	(((...((((((((.((((((((((((((((((((...( ((....)))...))))))))) ))))))))))).)))))))).)))	1.000 -49.20
human	(((((...((((((((.((((((((((((((((((((.....((....))....))))))))) ))))))))))).)))))))).)))))	1.000 -47.70
mouse	..((((((((((((((((((((.... ............)))))))).))))))))))))..	1.000 -23.39

rat	chromosome:6:134170340:134170423:1	Same_strand|Exonic_non-coding|ENSRNOT00000054366|ENSRNOG00000036243 ## ENSRNOG00000036243|miRNA|rno-mir-493|rno-mir-493 [Source:miRBase;Acc:MI0003540] ## {Repeats: L2 3265 3271 -1 class=LINE/L2,L2 3224 3248 -1 class=LINE/L2,L2 -1 3377 -1 class=LINE,THER1_MD -29 245 -1 class=SINE} ## {MIR: rno-mir-493}
human	chromosome:14:100405150:100405238:1	Same_strand|Exonic_non-coding|ENST00000385254|ENSG00000207989|miRNA|hsa-mir-493 [Source:miRBase;Acc:MI0003132] ## {Repeats: L2 -1 class=LINE/L2} ## {MIR: hsa-mir-493}
mouse	chromosome:12:110818420:110818543:1	Same_strand|Boundary_non-coding|ENSMUST00000103837|ENSMUSG00000077025|miRNA|mmu-mir-493 [Source:miRBase;Acc:MI0005514] ## {Repeats: MIRm -1 class=SINE/MIR} ## {MIR: mmu-mir-493}

Back to summary page

candidate miRBase miRNAs:

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