miR-Intess™

candidate novel miRNAs

novel_lenNOK_multiarm_DicerOK_randfoldOK (8 loci)

sblock3211_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock3211_cand 5arm	1	0	0	0	0	0	0	0	0	0
sblock3211_cand 3arm	1	0	0	0	0	0	0	0	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock3211_cand 5arm	0.000	0	0	0	0	0	0	0	0	0
sblock3211_cand 3arm	0.000	0	0	0	0	0	0	0	0	0

sblock3211 [novel_lenNOK_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

no

0.004

no

no

0.61/0.61

18/18/0.00

0.0 0.0

0.0 0.0

1 1

0 0

1 1

0 0

22 9

21 24

5arm 3arm

1 1

nd nd

0.33 0.11

4 1

2

1

3

2

Families

Member of family novel169 (seed CCAUGGC): block304777_cand, sblock3211_cand

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------------------CCAUGGC-------------------	1	novel
seed	-----------------------GCAGCCU---------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	----------------------AGCAGCCTGCCTGGGATT-----------------------------------------------------------------------------	18	1
	------------------------------------------------------------------------------------------ACCATGGCAGGAGCACTG---------	18	1
rat	tacctggagtcaatgttcagatAGCAGCCTGCCTGGGATTagggttctgcatgacagtggatggctttcaaatacaaatggcaggcctgaACCATGGCAGGAGCACTGacccaggtg
	*********************************************************************************************************************
	-------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000038143 ENSRNOG00000000999 RGD1309707_predicted
rat	(((((((.((((.((((..........(((((((((..(((((..(((((.((....((((.....))))....))....)))))))))).))).)))))))))).)))))))))))	0.800 -45.10

rat

chromosome:12:9991361:9991477:-1

Opposite_strand|Intronic_non-coding|ENSRNOT00000038143|ENSRNOG00000000999 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000031901|ENSRNOG00000000999 ## ENSRNOG00000000999|protein_coding|RGD1309707_predicted|similar to Smad ubiquitination regulatory factor 1 isoform 2 (LOC690516), mRNA [Source:RefSeq_dna;Acc:NM_001109598]

sblock4307_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock4307_cand 5arm	0	0	1	0	0	0	0	0	0	0
sblock4307_cand 3arm	0	0	0	1	0	0	0	0	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock4307_cand 5arm	0	0	0.000	0	0	0	0	0	0	0
sblock4307_cand 3arm	0	0	0	0.000	0	0	0	0	0	0

sblock4307 [novel_lenNOK_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

no

0.001

no

no

0.50/0.62

18/21/0.50

0.0 0.0

0.0 0.0

1 1

0 0

1 1

0 0

23 24

0 3

5arm 3arm

1 1

nd nd

0.10 0.06

1 1

2

2

3

1

		reads	miRBase family seed
seed	------------------------GAGCUGC----------------------------------------------------------------	1	novel
seed	------------------------------------------------------UGGUUCU----------------------------------	1	novel
		len	cloning frequencies
			T2S1	T2S2
	-----------------------------------------------------TTGGTTCTAGCAGCTCTG------------------------	18	-	1
	-----------------------AGAGCTGCCTGGAGCCAACTG---------------------------------------------------	21	1	-
rat	CTTGCCCGTAGCGTGTATTACACAGAGCTGCCTGGAGCCAACTGACCAGACAGTTGGTTCTAGCAGCTCTGCATCAAGACACTTCCATGGCAAGA
human	-----------------------CGAGCTGCCTGGAGCC----------------------------TCTGCG---AGGGGCCAGTTCGGCCTCC
mouse	-----------------------AGAGCTGCCTGGAGCC--------------CCACCTCAGAAGGTGCGGGATATGGGTGCTAG----------
	***************                             * *      *   *
rat	((((((......((((......((((((((.(((((((((((((......))))))))))))))))))))).......))))......)))))).	1.000 -48.82
human	.((((((.((((..((                            ((...)   )))..))))..)))).)).	0.992 -16.30
mouse	..(((.(((((...((              ((((((....))))).)))...))))))))..	1.000 -21.20

rat	chromosome:14:97788241:97788335:1	intergenic
human	chromosome:6:18385740:18385874:1	intergenic ## {SimpF: oe = 0.86 0 CpG,rank = 1 -1 FirstEF}
mouse	chromosome:1:36373237:36373371:1	Same_strand|Intronic_non-coding|ENSMUST00000115029|ENSMUSG00000037447|protein_coding|AT rich interactive domain 5A (MRF1-like) Gene [Source:MGI (curated);Acc:Arid5a-002] ## Same_strand|Intronic_coding|ENSMUST00000097778|ENSMUSG00000037447|protein_coding|AT rich interactive domain 5A (MRF1-like) Gene [Source:MGI (curated);Acc:Arid5a-002]

sblock6133_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock6133_cand 5arm	0	0	0	0	0	3	0	0	0	0
sblock6133_cand 3arm	0	0	0	0	4	1	0	1	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock6133_cand 5arm	0	0	0	0	0	0.000	0	0	0	0
sblock6133_cand 3arm	0	0	0	0	0.000	0.000	0	0.000	0	0

sblock6133 [novel_lenNOK_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

no

0.001

no

no

0.52/0.60

18/23/0.44

0.0 0.0

2.0 1.2

3 6

0 0

1 3

0 0

14 17

2 3

5arm 3arm

1 1

nd nd

0.05 0.05

1 1

9

3

1

2

		reads	miRBase family seed
seed	-----------------------------------------------------------CUGUCAA--------------------------------	6	novel
seed	---------------GCAGCUG----------------------------------------------------------------------------	3	novel
		len	cloning frequencies
			T3S1	T3S2	T4S2
	----------------------------------------------------------ACTGTCAAGCTGCCAGCTGC--------------------	20	2	-	-
	----------------------------------------------------------ACTGTCAAGCTGCCAGCTG---------------------	19	1	1	-
	--------------TGCAGCTGGTAGCTTGTG------------------------------------------------------------------	18	-	1	-
	----------------------------------------------------------ACTGTCAAGCTGCCAGCT----------------------	18	-	-	1
	--------------TGCAGCTGGTAGCTTGTGC-----------------------------------------------------------------	19	-	1	-
	----------------------------------------------------------ACTGTCAAGCTGCCAGCTGCTAT-----------------	23	1	-	-
	--------------TGCAGCTGGTAGCTTGTGCACTG-------------------------------------------------------------	23	-	1	-
rat	GGTCCCTCTCTACCTGCAGCTGGTAGCTTGTGCACTGACAGTAGAACATGAGAAAGTCACTGTCAAGCTGCCAGCTGCTATTTAAAAGATAGTTACTA
mouse	-------------CTGCCACTGGCAGCTTGCAGACTGATGGCAGAACATGAGAAAGTCACTGTCAAGTTGCCAGCTGCTA------------------
	****  **** ******   *****  * ************************* ************
rat	(((..((.(((....(((((((((((((((.(((.((((................)))).))))))))))))))))))........))).))..))).	0.940 -38.49
mouse	..((..((((((((((((((..((((..((.....)).....))))))).)))))))))))..))..	0.929 -26.40

rat	chromosome:2:175823362:175823459:-1	intergenic
mouse	chromosome:3:83872899:83873036:-1	intergenic

sblock6576_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock6576_cand 5arm	0	0	0	0	0	1	0	0	0	0
sblock6576_cand 3arm	0	0	0	0	0	0.333	0	0	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock6576_cand 5arm	0	0	0	0	0	0.000	0	0	0	0
sblock6576_cand 3arm	0	0	0	0	0	0.000	0	0	0	0

sblock6576 [novel_lenNOK_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

no

0.003

no

no

0.56/0.67

18/18/0.00

0.0 0.0

0.0 0.0

1 1

0 0

1 1

0 0

36 21

4 5

5arm 3arm

1 3

nd nd

0.28 0.22

2 2

2

1

1

3

		reads	miRBase family seed
seed	-------------------------------------GGUCCAC---------------------------------------------------------------	1	novel
seed	---------------------------------------------------------------------CAGGAUG-------------------------------	1	novel
		len	cloning frequencies
			T3S2
	--------------------------------------------------------------------TCAGGATGTGACCCAGGA---------------------	18	1
	------------------------------------TGGTCCACAACCTGGGGG-----------------------------------------------------	18	1
rat	ggggcttctgctccccccacacacccccaaagatgcTGGTCCACAACCTGGGGGaggcacagggcctcTCAGGATGTGACCCAGGAtgtggggacctgcaggctcct
	***********************************************************************************************************
rat	(((((..((((...((((((............((.((((..((((.((((..((((((.....)))))))))).))))..)))).))))))))....))))))))).	0.590 -51.10

rat

chromosome:2:203128363:203128469:1

intergenic

sblock7818_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock7818_cand 5arm	0	0	0	1	2	1	0	1	0	0
sblock7818_cand 3arm	0	0	3	0	1	0	0	0	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock7818_cand 5arm	0	0	0	0.000	0.000	0.000	0	0.000	0	0
sblock7818_cand 3arm	0	0	0.000	0	0.000	0	0	0	0	0

sblock7818 [novel_lenNOK_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

no

0.001

no

no

0.42/0.59

18/22/0.44

0.0 0.5 0.0

0.0 1.0 1.0

1 4 4

0 0 0

1 3 2

0 0 0

16 27 34

16 4 7

5arm 5arm 3arm

1 1 1

nd nd nd

0.05 0.05 0.05

1 1 1

9

5

3

2

Families

Member of family novel230 (seed UCCCCAA): block853285_cand, sblock7818_cand

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------------AAGCUUA------------------------------------------------	4	novel
seed	-----------------------------CCCCAAC------------------------------------------------------------------------------------------------------------------	2	novel
seed	----------------------------UCCCCAA-------------------------------------------------------------------------------------------------------------------	2	novel
seed	-----------------UGCCCAA------------------------------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T2S2	T3S1	T3S2	T4S2
	----------------------------------------------------------------------------------------------CAAGCTTAAAGGTTGAGGA-------------------------------------	19	2	-	-	-	-
	---------------------------GTCCCCAACCTTTAAGCTT--------------------------------------------------------------------------------------------------------	19	-	-	1	1	-
	----------------------------TCCCCAACCTTTAAGCTT--------------------------------------------------------------------------------------------------------	18	-	-	1	-	-
	----------------ATGCCCAAGGAGTCCCCAACCT----------------------------------------------------------------------------------------------------------------	22	-	-	-	-	1
	----------------------------TCCCCAACCTTTAAGCTTGTGC----------------------------------------------------------------------------------------------------	22	-	1	-	-	-
	----------------------------------------------------------------------------------------------CAAGCTTAAAGGTTGAGGACTC----------------------------------	22	1	-	-	-	-
	----------------------------------------------------------------------------------------------CAAGCTTAAAGGTTGAGGAC------------------------------------	20	-	-	1	-	-
rat	GCTAGGAACAGTCTGGATGCCCAAGGAGTCCCCAACCTTTAAGCTTGTGCTGAGCCTCTGGG------------------------------CACAAGCTTAAAGGTTGAGGACTCCTTGGGCAATCTAAATACATTTGTTCACCCTAGG
mouse	-----------------TGCCCAAGGAGGCCCCAGTCTTTAAGCTTCTGCTGAGCCTCTGGGTCTTGCTATTGAGAAAATCCACAGGCTCAACACAAGCTTAAAGGTTGGGGACTCCTTGGGCA--------------------------
	*********** *****  ********** ***************                              ***************** **************
	-------------------------------------------------------------------                              ---------------------------------------------------------------	ENSRNOT00000024352 ENSRNOG00000017983 Ubadc1
rat	.((((((((((..((((((((((((((((((.(((((((((((((((((((.((...)).))                              ))))))))))))))))).)))))))))))))).)))).......)))))...))))).	0.930 -74.00
mouse	.((((((((((.(((((..((((((((((.((.(((((((.((((((((......))))...)))).))))))).)).))))))))))..))))).)))))))))).	1.000 -69.70

rat	chromosome:3:4200057:4200176:1	Opposite_strand|Intronic_coding|ENSRNOT00000024352|ENSRNOG00000017983 ## ENSRNOG00000017983|protein_coding|Ubadc1|Ubiquitin-associated domain-containing protein 1 (UBA domain- containing protein 1) (E3 ubiquitin-protein ligase subunit KPC2) (Kip1 ubiquitination-promoting complex protein 2). [Source:UniProtKB/Swiss-Prot;Acc:Q5XIR9]
mouse	chromosome:2:25875691:25875797:1	Opposite_strand|Intronic_coding|ENSMUST00000114161|ENSMUSG00000036352|protein_coding|ubiquitin associated domain containing 1 Gene [Source:MGI (curated);Acc:Ubac1-001]

sblock8126_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock8126_cand 5arm	1	0	0	0	0	0	0	0	0	0
sblock8126_cand 3arm	1	0	0	0	0	0	0	0	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock8126_cand 5arm	0.000	0	0	0	0	0	0	0	0	0
sblock8126_cand 3arm	0.000	0	0	0	0	0	0	0	0	0

sblock8126 [novel_lenNOK_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

no

0.001

no

no

0.65/0.68

19/20/0.50

0.0 0.0

0.0 0.0

1 1

0 0

1 1

0 0

16 8

2 3

5arm 3arm

1 1

nd nd

0.26 0.15

2 1

2

1

1

3

		reads	miRBase family seed
seed	-----------------------------------------------CCUGGAG--------------------	1	novel
seed	-----------------GCUCCAG--------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	----------------------------------------------TCCTGGAGCGCTTAGCCGAG--------	20	1
	----------------GGCTCCAGCACTCCAGAGC---------------------------------------	19	1
rat	agtatgaacctcacagGGCTCCAGCACTCCAGAGCtttcctttgagTCCTGGAGCGCTTAGCCGAGgtggagac
	**************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000019215 ENSRNOG00000014230 Mtap1a
rat	.((....(((((....((((..(((.((((((..(((......)))..)))))).))).)))))))))....))	1.000 -31.10

rat

chromosome:3:108096111:108096184:1

Same_strand|Boundary_non-coding|ENSRNOT00000019320|ENSRNOG00000014230 ## Same_strand|Intronic_coding|ENSRNOT00000019215|ENSRNOG00000014230 ## ENSRNOG00000014230|protein_coding|Mtap1a|Microtubule-associated protein 1A (MAP 1A) [Contains: MAP1 light chain LC2]. [Source:UniProtKB/Swiss-Prot;Acc:P34926]

sblock8483_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock8483_cand 5arm	1	0	0	0	0	0	0	0	0	0
sblock8483_cand 3arm	0	0	0	0	0	0	1	0	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock8483_cand 5arm	0.000	0	0	0	0	0	0	0	0	0
sblock8483_cand 3arm	0	0	0	0	0	0	0.000	0	0	0

sblock8483 [novel_lenNOK_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

no

0.003

no

no

0.53/0.57

19/23/0.50

0.0 0.0

0.0 0.0

1 1

0 0

1 1

0 0

31 24

8 8

5arm 3arm

1 1

nd nd

0.21 0.35

3 3

2

2

1

2

		reads	miRBase family seed
seed	-----------------------------------------------------------------------AACAGAG---------------------------------------	1	novel
seed	--------------------------------CCAGAUG------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T4S1
	-------------------------------CCCAGATGGGCTCATATCT-------------------------------------------------------------------	19	1	-
	----------------------------------------------------------------------GAACAGAGACCAGGTCTGGAGGA------------------------	23	-	1
rat	GCTGTGCCAGGCCCCTCTGCCACAAGCCCTCCCCAGATGGGCTCATATCTCTTATTCCCAATGGAAGTGAGAACAGAGACCAGGTCTGGAGGAACCAGAGGGACCATGGTGACCGTG
mouse	-------------------------------CCCAGATGGGCTCAGATCTCTTGTTCACAATGGAAGTGAGACCAGAGACCAGGTCTGGAG--------------------------
	************** ******* *** ************** ******************
rat	((.((((((((.(((((((..........(((((((((.(((((...((((...((((....))))..))))...))).))..)))))).)))..))))))).)).)))).)).)).	0.670 -46.80
mouse	.((((((.(((((...((((...(((.....)))...))))...))).))..))))))..	0.994 -20.80

rat	chromosome:4:118404485:118404601:-1	intergenic
mouse	chromosome:6:84193327:84193483:-1	intergenic

novel_lenNOK_cloningOK_mirtron_randfoldOK (5 loci)

block448483_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block448483_cand 3arm	6	3	0	0	5	1	3	1	1	1
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block448483_cand 3arm	0.000	0.000	0	0	0.000	0.000	0.000	0.000	0.000	0.000

block448483 [novel_lenNOK_cloningOK_mirtron_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

no

0.001

no

no

0.67/0.78

18/22/0.62

0.7

1.6

21

0

8

0

8

5

3arm

1

0

0.28

2

21

8

na

na

Families

Member of family novel199 (seed CUCCCUG): block448483_cand, block796693_cand

		reads	miRBase family seed
seed	---------------------------------------------------UCCCUGU-----------------------	11	novel
seed	----------------------------------------------------CCCUGUC----------------------	8	miR-339
seed	--------------------------------------------------CUCCCUG------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--------------------------------------------------CTCCCTGTCCACCGCCCC-------------	18	1	2	-	1	-	-	-	-
	---------------------------------------------------TCCCTGTCCACCGCCCCTACA---------	21	-	1	2	-	-	-	1	-
	---------------------------------------------------TCCCTGTCCACCGCCCCT------------	18	3	-	-	-	-	-	-	-
	--------------------------------------------------CTCCCTGTCCACCGCCCCTAC----------	21	1	-	2	-	-	-	-	-
	--------------------------------------------------CTCCCTGTCCACCGCCCCTA-----------	20	-	-	-	-	2	-	-	-
	-------------------------------------------------CCTCCCTGTCCACCGCCCCTAC----------	22	1	-	-	-	-	-	-	-
	--------------------------------------------------CTCCCTGTCCACCGCCCCTACA---------	22	-	-	1	-	-	-	-	-
	-------------------------------------------------CCTCCCTGTCCACCGCCCCTA-----------	21	-	-	-	-	1	-	-	-
	--------------------------------------------------CTCCCTGTCCACCGCCCCT------------	19	-	-	-	-	-	-	-	1
	---------------------------------------------------TCCCTGTCCACCGCCCCTACAG--------	22	-	-	-	-	-	1	-	-
rat	gcagggacatttggggctgtgggcggcctctgggttcatattctgacccCCTCCCTGTCCACCGCCCCTACAGgctctgcc
	*********************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>	ENSRNOT00000022706 ENSRNOG00000016777 R3hcc1_predicted
rat	((((((......(((((.((((((((.....(((((........))))).....)))))))).)))))......)))))).	1.000 -41.10

rat

chromosome:15:50079598:50079678:-1

Same_strand|Intronic_coding|ENSRNOT00000022706|ENSRNOG00000016777 ## ENSRNOG00000016777|protein_coding|R3hcc1_predicted|

block668798_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block668798_cand 5arm	2	2	2	2	0	0	3	0	3	2
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block668798_cand 5arm	0.000	0.000	0.000	0.000	0	0	0.000	0	0.000	0.000

block668798 [novel_lenNOK_cloningOK_mirtron_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

no

0.003

no

no

0.44/0.47

18/19/0.00

0.1

0.1

16

0

7

0

22

17

5arm

1

4

0.26

3

16

7

na

na

		reads	miRBase family seed
seed	-----------------------CUGUCAU---------------------------------------------------------------------------------------	15	novel
seed	------------------------UGUCAUU--------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T4S1	T5S1	T5S2
	----------------------CCTGTCATTTCCAGGATA-----------------------------------------------------------------------------	18	2	2	2	2	2	3	1
	----------------------CCTGTCATTTCCAGGATAC----------------------------------------------------------------------------	19	-	-	-	-	1	-	-
	-----------------------CTGTCATTTCCAGGATAC----------------------------------------------------------------------------	18	-	-	-	-	-	-	1
rat	ttgcttttcttagtaataattgCCTGTCATTTCCAGGATACagctggtcaagaaaggttcagaacattaactcccagctattatagaggtgcacagggagttatattaggtaagtaa
	*********************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++	ENSRNOT00000025828 ENSRNOG00000018972 Rab18
rat	.(((((..((((((.((((((.(((((((((((...(((..((((((.........((.....))........)))))))))...)))))).))))).)))))))))))).))))).	0.980 -34.53

rat

chromosome:17:63522941:63523057:1

Same_strand|Boundary_coding|ENSRNOT00000025828|ENSRNOG00000018972 ## ENSRNOG00000018972|protein_coding|Rab18|Ras-related protein Rab-18. [Source:UniProtKB/Swiss-Prot;Acc:Q5EB77]

block749566_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block749566_cand 3arm	0	0	0	0	10	0	2	0	3	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block749566_cand 3arm	0	0	0	0	0.000	0	0.000	0	0.000	0

block749566 [novel_lenNOK_cloningOK_mirtron_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

no

0.002

no

no

0.39/0.48

18/24/0.60

0.7

3.3

15

0

3

0

22

5

3arm

1

0

0.13

2

15

3

na

na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------UUGUGUU--------------------------------------	11	novel
seed	--------------------------------------------------------------------------CUUGUGU---------------------------------------	4	novel
		len	cloning frequencies
			T3S1	T4S1	T5S1
	--------------------------------------------------------------------------CTTGTGTTTCTCTTCCTTCCCA------------------------	22	2	1	-
	-------------------------------------------------------------------------ACTTGTGTTTCTCTTCCT-----------------------------	18	1	-	2
	--------------------------------------------------------------------------CTTGTGTTTCTCTTCCTTCCC-------------------------	21	2	-	1
	--------------------------------------------------------------------------CTTGTGTTTCTCTTCCTTC---------------------------	19	2	-	-
	--------------------------------------------------------------------------CTTGTGTTTCTCTTCCTTCCCAGT----------------------	24	-	1	-
	-------------------------------------------------------------------------ACTTGTGTTTCTCTTCCTTCCCA------------------------	23	1	-	-
	--------------------------------------------------------------------------CTTGTGTTTCTCTTCCTT----------------------------	18	1	-	-
	--------------------------------------------------------------------------CTTGTGTTTCTCTTCCTTCCCAG-----------------------	23	1	-	-
rat	gggcttgactgctctacagttctaagagattgggaggaggtggggacaacaaactgataacccagatgtatcaACTTGTGTTTCTCTTCCTTCCCAGTgttcttgtgaagacagaagcca
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000025344 ENSRNOG00000018735 Cd74
rat	.(((((..(((.(((.((....((((((((((((((((((.((..((.((((..(((((.........)))))..))))))..)))))))).)))))).)))))))).))))))))))).	0.910 -43.20

rat

chromosome:18:56765150:56765269:1

Same_strand|Boundary_non-coding|ENSRNOT00000025354|ENSRNOG00000018735 ## Same_strand|Boundary_coding|ENSRNOT00000025344|ENSRNOG00000018735 ## ENSRNOG00000018735|protein_coding|Cd74|H-2 class II histocompatibility antigen gamma chain (MHC class II- associated invariant chain) (Ia antigen-associated invariant chain) (Ii) (CD74 antigen). [Source:UniProtKB/Swiss-Prot;Acc:P10247]

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candidate novel miRNAs:

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