miR-Intess™

confident novel miRNAs

novel_cloningOK_randfoldOK (12 loci)

block182672_novel

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block182672_novel 5arm	0.500	1	0	0	0	1	0	0	0.500	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block182672_novel 5arm	0.000	0.000	0	0	0	0.000	0	0	0.000	0

block182672 [novel_cloningOK_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

0.61/0.67

20/23/1.00

0.5

0.7

12

0

4

0

31

2

5arm

2

nd

0.26

2

12

4

na

na

Clusters

Located in cluster 18: block182671_novel, block182672_novel

Families

Member of family novel19 (seed GUCCCCA): block182671_novel, block182671_novel, block182672_novel, block182672_novel, sblock3519_cand

		reads	miRBase family seed
seed	--------------------------------------------------------------------UCCCCAC----------------------------------------	3	novel
seed	-------------------------------------------------------------------GUCCCCA-----------------------------------------	3	novel
seed	---------------------------------UCCCCAC---------------------------------------------------------------------------	3	novel
seed	--------------------------------GUCCCCA----------------------------------------------------------------------------	3	novel
		len	cloning frequencies
			T1S1	T1S2	T3S2	T5S1
	--------------------------------GTCCCCACCGTGGTTGCAGA---------------------------------------------------------------	20	-	2	-	-
	-------------------------------------------------------------------GTCCCCACCGTGGTTGCAGA----------------------------	20	-	2	-	-
	-------------------------------TGTCCCCACCGTGGTTGCAGACA-------------------------------------------------------------	23	1	-	-	-
	--------------------------------GTCCCCACCGTGGTTGCAGAC--------------------------------------------------------------	21	-	-	-	1
	------------------------------------------------------------------TGTCCCCACCGTGGTTGCAGA----------------------------	21	-	-	1	-
	------------------------------------------------------------------TGTCCCCACCGTGGTTGCAGACA--------------------------	23	1	-	-	-
	-------------------------------------------------------------------GTCCCCACCGTGGTTGCAGAC---------------------------	21	-	-	-	1
	-------------------------------TGTCCCCACCGTGGTTGCAGAC--------------------------------------------------------------	22	-	-	1	-
	-------------------------------TGTCCCCACCGTGGTTGCAGA---------------------------------------------------------------	21	-	-	1	-
	------------------------------------------------------------------TGTCCCCACCGTGGTTGCAGAC---------------------------	22	-	-	1	-
rat	cccaccatggttgcagacatgtgctacgtgcTGTCCCCACCGTGGTTGCAGACAtgtgctacgtgcTGTCCCCACCGTGGTTGCAGACAtgtgctatgtgctgtccccactgtgg
	*******************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000001412 ENSRNOG00000001065 Pscd3
rat	.((((..(((..(((((((((.((.(((((((((..((((.((((..((((.((((.....))))))))..)))).))))..)))).)))))))))))).))))..)))..))))	1.000 -57.10

rat

chromosome:12:11178280:11178394:-1

Same_strand|Intronic_coding|ENSRNOT00000001412|ENSRNOG00000001065 ## ENSRNOG00000001065|protein_coding|Pscd3|Cytohesin-3 (PH, SEC7 and coiled-coil domain-containing protein 3) (SEC7 homolog C) (rSec7-3). [Source:UniProtKB/Swiss-Prot;Acc:P97696] ## {Repeats: trf 87 110 0 class=trf}

block283058_novel

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block283058_novel 3arm	0	0	0	0	3	1	3	3	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block283058_novel 3arm	0	0	0	0	0.000	0.000	0.000	0.000	0	0

block283058 [novel_cloningOK_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

0.55/0.60

18/22/0.90

0.1

0.5

10

0

4

0

13

11

3arm

1

nd

0.10

1

10

4

na

na

		reads	miRBase family seed
seed	-------------------------------------------------------------------ACCUCCA---------------------------	9	novel
seed	--------------------------------------------------------------------CCUCCAG--------------------------	1	novel
		len	cloning frequencies
			T3S1	T3S2	T4S1	T4S2
	------------------------------------------------------------------TACCTCCAGAGCAGGAAGTGG--------------	21	2	1	1	2
	------------------------------------------------------------------TACCTCCAGAGCAGGAAG-----------------	18	-	-	1	-
	------------------------------------------------------------------TACCTCCAGAGCAGGAAGTG---------------	20	1	-	-	-
	------------------------------------------------------------------TACCTCCAGAGCAGGAAGTGGA-------------	22	-	-	-	1
	-------------------------------------------------------------------ACCTCCAGAGCAGGAAGTGG--------------	20	-	-	1	-
rat	agcagccttccccgtagccttctcacttcctgctgtggaggcagctagctcgctaggctcagttgcTACCTCCAGAGCAGGAAGTGGAggtgtgcgtgctc
	*****************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000004783 ENSRNOG00000003583 Smyd2
rat	((((........((((..((((.(((((((((((.(((((((((((((((.....)))).))))))...))))).)))))))))))))))..)))))))).	1.000 -51.90

rat

chromosome:13:106191144:106191244:-1

Same_strand|Intronic_coding|ENSRNOT00000004783|ENSRNOG00000003583 ## ENSRNOG00000003583|protein_coding|Smyd2|SET and MYND domain-containing protein 2. [Source:UniProtKB/Swiss-Prot;Acc:Q7M6Z3]

novel_cloningOK_mirtron_randfoldOK (7 loci)

block440715_novel

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block440715_novel 3arm	0	0	0	0	0	0	30	6	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block440715_novel 3arm	0	0	0	0	0	0	0.002	0.000	0	0

block440715 [novel_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

0.60/0.65

18/22/0.81

0.2

0.7

23

0

2

0

18

3

3arm

1

0

0.18

2

36

2

na

na

		reads	miRBase family seed
seed	----------------------------------------------------------------CGAUGCC-------------------------------	25	novel
seed	---------------------------------------------------------------UCGAUGC--------------------------------	10	novel
seed	-------------------------------------------------------------CCUCGAU----------------------------------	1	novel
		len	cloning frequencies
			T4S1	T4S2
	---------------------------------------------------------------TCGATGCCCACCTCTTCCCA-------------------	20	8	1
	---------------------------------------------------------------TCGATGCCCACCTCTTCCCAG------------------	21	8	1
	---------------------------------------------------------------TCGATGCCCACCTCTTCCC--------------------	19	3	1
	--------------------------------------------------------------CTCGATGCCCACCTCTTCCCAG------------------	22	4	-
	--------------------------------------------------------------CTCGATGCCCACCTCTTCCCA-------------------	21	1	2
	---------------------------------------------------------------TCGATGCCCACCTCTTCC---------------------	18	2	-
	--------------------------------------------------------------CTCGATGCCCACCTCTTCCC--------------------	20	1	1
	---------------------------------------------------------------TCGATGCCCACCTCTTCCCAGG-----------------	22	1	-
	------------------------------------------------------------TCCTCGATGCCCACCTCTTC----------------------	20	1	-
	--------------------------------------------------------------CTCGATGCCCACCTCTTCC---------------------	19	1	-
rat	ggccaagggagcatgctgggcctggggtaaggggatggcagaggagaaagctgatccacttcCTCGATGCCCACCTCTTCCCAGgccaagaatgccctggcc
	******************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000024186 ENSRNOG00000016983 Myh7
rat	((((..(((.((((.((.(((((((((..(((((..((((((((((.............))))))..))))..)))))))))))))).)).)))))))))))	1.000 -53.62

rat

chromosome:15:33078393:33078494:-1

Same_strand|Boundary_coding|ENSRNOT00000024186|ENSRNOG00000016983 ## ENSRNOG00000016983|protein_coding|Myh7|Myosin-7 (Myosin heavy chain 7) (Myosin heavy chain, cardiac muscle beta isoform) (MyHC-beta) (Myosin heavy chain slow isoform) (MyHC- slow). [Source:UniProtKB/Swiss-Prot;Acc:P02564]

block913509_novel

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block913509_novel 3arm	9	8	0	0	0	0	0	0	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block913509_novel 3arm	0.000	0.000	0	0	0	0	0	0	0	0

block913509 [novel_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

0.50/0.53

18/22/0.82

0.0

1.1

13

0

2

0

22

7

3arm

1

0

0.17

2

17

2

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------CACCAUU------------------------------------	17	novel
		len	cloning frequencies
			T1S1	T1S2
	----------------------------------------------------------------------------TCACCATTTCCACCTTCCCAGT----------------------	22	5	1
	----------------------------------------------------------------------------TCACCATTTCCACCTTCCCAG-----------------------	21	3	3
	----------------------------------------------------------------------------TCACCATTTCCACCTTCC--------------------------	18	-	2
	----------------------------------------------------------------------------TCACCATTTCCACCTTCCCA------------------------	20	1	1
	----------------------------------------------------------------------------TCACCATTTCCACCTTCCC-------------------------	19	-	1
rat	tggggcttaggtgggcagagaacatgggagggagtgaagtgcatgcattctgagtaaggaaaacagaaagttgaccTCACCATTTCCACCTTCCCAGTgtcctaatctacctgggctttg
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000027119 ENSRNOG00000020009 Npas4
rat	.((((((((((((((...((.(((((((((((...((((((............((.(((..(((.....)))..))).))))))))..)))))))).))).))..)))))))))))))).	0.400 -43.60

rat

chromosome:1:207600547:207600666:-1

Same_strand|Boundary_coding|ENSRNOT00000027119|ENSRNOG00000020009 ## ENSRNOG00000020009|protein_coding|Npas4|Neuronal PAS domain-containing protein 4 (Neuronal PAS4) (HLH-PAS transcription factor NXF). [Source:UniProtKB/Swiss-Prot;Acc:Q8CJH6]

block1030047_novel

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1030047_novel 3arm	0	0	0	2	0	1	0	0	10	12
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1030047_novel 3arm	0	0	0	0.000	0	0.000	0	0	0.001	0.001

block1030047 [novel_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

0.009

no

no

0.67/0.75

18/23/0.80

0.0

0.8

12

0

4

0

24

6

3arm

1

0

0.18

1

25

4

na

na

		reads	miRBase family seed
seed	--------------------------------------------------------------------UGGCCUC--------------------------------------	18	novel
seed	-------------------------------------------------------------------UUGGCCU---------------------------------------	5	novel
seed	---------------------------------------------------------------------GGCCUCG-------------------------------------	1	novel
seed	----------------------------------------------------------------------GCCUCGG------------------------------------	1	novel
		len	cloning frequencies
			T2S2	T3S2	T5S1	T5S2
	-------------------------------------------------------------------TTGGCCTCGGCTCTCCTCCCAG------------------------	22	-	1	4	4
	-------------------------------------------------------------------TTGGCCTCGGCTCTCCTCCCA-------------------------	21	-	-	2	1
	-------------------------------------------------------------------TTGGCCTCGGCTCTCCTC----------------------------	18	1	-	-	2
	-------------------------------------------------------------------TTGGCCTCGGCTCTCCTCCC--------------------------	20	-	-	1	1
	------------------------------------------------------------------CTTGGCCTCGGCTCTCCTCCCA-------------------------	22	-	-	1	1
	--------------------------------------------------------------------TGGCCTCGGCTCTCCTCCCA-------------------------	20	1	-	-	-
	------------------------------------------------------------------CTTGGCCTCGGCTCTCCTCCC--------------------------	21	-	-	-	1
	---------------------------------------------------------------------GGCCTCGGCTCTCCTCCCAG------------------------	20	-	-	-	1
	------------------------------------------------------------------CTTGGCCTCGGCTCTCCTCCCAG------------------------	23	-	-	-	1
	------------------------------------------------------------------CTTGGCCTCGGCTCTCCTC----------------------------	19	-	-	1	-
	-------------------------------------------------------------------TTGGCCTCGGCTCTCCTCC---------------------------	19	-	-	1	-
rat	ctccttggcaagagtagggttaccctcctgggggagcgtgggggcagaggtcacagcctcagcaaccTTGGCCTCGGCTCTCCTCCCAGgaccacgactttgagccgctgagg
	*****************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000024112 ENSRNOG00000017901 Acy3
rat	(((..((((.(((((..((......(((((((((((.((.(((((.(((((....((....)).))))).))))).)).)))).)))))))))...)))))..))))..))).	0.690 -54.30

rat

chromosome:1:206572373:206572485:1

Same_strand|Intronic_coding|ENSRNOT00000024112|ENSRNOG00000017901 ## ENSRNOG00000017901|protein_coding|Acy3|aspartoacylase-3 [Source:RefSeq_peptide;Acc:NP_001009603]

block1837880_novel

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1837880_novel 3arm	4	0	0	1	3	2	0	1	4	0.500
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1837880_novel 3arm	0.000	0	0	0.000	0.000	0.000	0	0.000	0.000	0.000

block1837880 [novel_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

0.33/0.45

18/22/0.94

0.1

0.7

16

0

7

0

28

6

3arm

2

0

0.10

2

16

7

na

na

		reads	miRBase family seed
seed	----------------------------------------------------------------UACCAUU------------------------------------------	15	novel
seed	------------------------------------------------------------------CCAUUUA----------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T2S2	T3S1	T3S2	T4S2	T5S1	T5S2
	---------------------------------------------------------------ATACCATTTACCTTTCTCCCA-----------------------------	21	3	1	-	-	-	3	-
	---------------------------------------------------------------ATACCATTTACCTTTCTCCCAG----------------------------	22	-	-	3	2	1	-	-
	-----------------------------------------------------------------ACCATTTACCTTTCTCCCAG----------------------------	20	1	-	-	-	-	-	-
	---------------------------------------------------------------ATACCATTTACCTTTCTC--------------------------------	18	-	-	-	-	-	-	1
	---------------------------------------------------------------ATACCATTTACCTTTCTCCC------------------------------	20	-	-	-	-	-	1	-
rat	gtcaggtgagcgattagtggtggtttctgggagtggagtagatgggaggctgcaggagtaaccATACCATTTACCTTTCTCCCAGaacaacagctggtgcagctgacccaaca
	*****************************************************************************************************************
	>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000023411 ENSRNOG00000017253 NP_001101427.1
rat	((..(((.(((.((((((.((...(((((((((.((.((((((((..((.(((....))).))...))))))))))..)))))))))..)).))))))...))).)))..)).	1.000 -48.00

rat

chromosome:5:59974635:59974747:1

Same_strand|Intronic_coding|ENSRNOT00000023411|ENSRNOG00000017253 ## ENSRNOG00000017253|protein_coding|NP_001101427.1|

block2150313_novel

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block2150313_novel 3arm	2	0	4	2	2	0	1	0	12	10
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block2150313_novel 3arm	0.000	0	0.000	0.000	0.000	0	0.000	0	0.001	0.001

block2150313 [novel_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

0.010

no

no

0.50/0.55

18/22/0.70

0.0

0.3

18

0

7

0

24

8

3arm

1

0

0.05

1

33

7

na

na

		reads	miRBase family seed
seed	-------------------------------------------------------------------GCUGAUC-------------------------------------	32	novel
seed	---------------------------------------------------------------------UGAUCAC-----------------------------------	1	novel
		len	cloning frequencies
			T1S1	T2S1	T2S2	T3S1	T4S1	T5S1	T5S2
	------------------------------------------------------------------AGCTGATCACTCTCCCTACAG------------------------	21	1	3	-	-	1	7	5
	------------------------------------------------------------------AGCTGATCACTCTCCCTAC--------------------------	19	-	1	-	1	-	3	2
	------------------------------------------------------------------AGCTGATCACTCTCCCTACA-------------------------	20	1	-	1	-	-	1	2
	------------------------------------------------------------------AGCTGATCACTCTCCCTA---------------------------	18	-	-	-	-	-	1	1
	--------------------------------------------------------------------CTGATCACTCTCCCTACAG------------------------	19	-	-	-	1	-	-	-
	------------------------------------------------------------------AGCTGATCACTCTCCCTACAGG-----------------------	22	-	-	1	-	-	-	-
rat	ccctggtgtgagtgccctgcgctgaatgtgtagggagagtggggtggcccaggcggtccgctgtggAGCTGATCACTCTCCCTACAGgtgccacttctgcaggtgtcgggg
	***************************************************************************************************************
	>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000010637 ENSRNOG00000007939 Naprt1
rat	(((((........((((((((.((.((.((((((((((((((..(((((((((((...)))).))).)))).)))))))))))))).))..))....)))))).)))))))	0.750 -53.30

rat

chromosome:7:113868033:113868143:-1

Same_strand|Boundary_coding|ENSRNOT00000010637|ENSRNOG00000007939 ## ENSRNOG00000007939|protein_coding|Naprt1|Nicotinate phosphoribosyltransferase (EC 2.4.2.11) (NAPRTase) (Nicotinate phosphoribosyltransferase domain-containing protein 1). [Source:UniProtKB/Swiss-Prot;Acc:Q6XQN1]

block2150508_novel

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block2150508_novel 3arm	9	9	1	1	3	4	6	2	7	2
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block2150508_novel 3arm	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000

block2150508 [novel_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

0.009

no

no

0.55/0.60

18/22/0.73

0.0

0.6

25

0

10

0

24

4

3arm

1

0

0.11

1

44

10

na

na

Families

Member of family novel80 (seed CUGACUC): block2150508_novel, block20878_cand

		reads	miRBase family seed
seed	-------------------------------------------------------------CUGACUC--------------------------------------	39	novel
seed	--------------------------------------------------------------UGACUCU-------------------------------------	4	novel
seed	-----------------------------------------------------------CUCUGAC----------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	------------------------------------------------------------TCTGACTCTTGCCTCCCACAG-------------------------	21	3	6	-	1	1	1	4	-	4	1
	------------------------------------------------------------TCTGACTCTTGCCTCCCAC---------------------------	19	-	-	-	-	2	2	1	-	-	1
	------------------------------------------------------------TCTGACTCTTGCCTCCCA----------------------------	18	2	1	1	-	-	-	1	-	1	-
	-------------------------------------------------------------CTGACTCTTGCCTCCCACAG-------------------------	20	1	1	-	-	-	-	-	1	-	-
	------------------------------------------------------------TCTGACTCTTGCCTCCCACA--------------------------	20	1	1	-	-	-	-	-	1	-	-
	------------------------------------------------------------TCTGACTCTTGCCTCCCACAGA------------------------	22	2	-	-	-	-	-	-	-	1	-
	----------------------------------------------------------TCTCTGACTCTTGCCTCCCAC---------------------------	21	-	-	-	-	-	1	-	-	-	-
	-------------------------------------------------------------CTGACTCTTGCCTCCCACAGA------------------------	21	-	-	-	-	-	-	-	-	1	-
rat	GGTTGCTCTTGGCTCAGCCTTGAATGGTGGGTGGGTGAAGTAGAGAGACCAGCATGGGTCTCTGACTCTTGCCTCCCACAGAAGACCCTGGACAGCAGAGCAGTCC
mouse	---TGCTGTTGGCTGGGCCCTGAATGGTGGGC-GGTGAAACAGAGAGCTTAGCATGGGTCTCTGACTC-TGCCTCCCACAGAAGACGCTGGACAGCAGAGC-----
	**** ******  *** ***********  ******  ******   ****************** ***************** **************
	>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000045280 ENSRNOG00000032574 RGD1565055_predicted
	>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000052080 ENSRNOG00000032574 RGD1565055_predicted
	>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000047338 ENSRNOG00000032574 RGD1565055_predicted
rat	(((((((((..((((((..((.....(((((.(((((((((..(((((((......))))))).))).)))))))))))....))..)))...)))))))))).))	0.960 -42.80
mouse	((((((((((......(((..(((..((( ((.....((((((.((......)).))))))...) ))))..)))))).....)))).))))))....	0.802 -36.90

rat	chromosome:7:114095545:114095650:-1	Same_strand|Boundary_coding|ENSRNOT00000052080|ENSRNOG00000032574 ## ENSRNOG00000032574|protein_coding|RGD1565055_predicted|
mouse	chromosome:15:75895238:75895333:-1	Same_strand|Boundary_coding|ENSMUST00000063747|ENSMUSG00000022568|protein_coding|scribbled homolog (Drosophila) Gene [Source:MGI (curated);Acc:Scrib-003]

block2664282_novel

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block2664282_novel 3arm	2	1	0	1	1	4	0	4	0	1
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block2664282_novel 3arm	0.000	0.000	0	0.000	0.000	0.000	0	0.000	0	0.000

block2664282 [novel_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

0.50/0.52

18/23/0.93

0.0

1.2

14

0

7

0

27

8

3arm

1

0

0.17

2

14

7

na

na

		reads	miRBase family seed
seed	---------------------------------------------------------------------CUACCCA------------------------------------------	14	novel
		len	cloning frequencies
			T1S1	T1S2	T2S2	T3S1	T3S2	T4S2	T5S2
	--------------------------------------------------------------------ACTACCCACTTCCATCTCCACAG---------------------------	23	-	-	-	-	3	2	-
	--------------------------------------------------------------------ACTACCCACTTCCATCTCCACA----------------------------	22	1	-	1	-	-	2	1
	--------------------------------------------------------------------ACTACCCACTTCCATCTCCAC-----------------------------	21	1	-	-	-	1	-	-
	--------------------------------------------------------------------ACTACCCACTTCCATCTC--------------------------------	18	-	1	-	-	-	-	-
	--------------------------------------------------------------------ACTACCCACTTCCATCTCCA------------------------------	20	-	-	-	1	-	-	-
rat	GAGTGAGCCTTATATCTTAGAGAGTTGGGGAGGTGGGAGGGAGAGCTGAAATAGTCTCCAGATAATTCACTACCCACTTCCATCTCCACAGCTACCTCCACGCCAAGAACATCATTCA
mouse	-------------------------TGGGGAGGTGGGAGGGATAGCTGAAATAGTCTCCAGACAATTCACTACCCACTTCCATCTCCACA----------------------------
	***************** ******************* ***************************
	>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000039911 ENSRNOG00000010838 Araf
	>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000049528 ENSRNOG00000010838 Araf
	>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000015559 ENSRNOG00000010838 Araf
rat	((((((.............((((((((.(((((((((((((..((.((((...(((....)))..))))))..)).))))))))))).)))))..))).............)))))).	0.870 -40.67
mouse	...(((((((((((((.(((.((((...(((....)))..))))))).)).)))))))))))...	1.000 -29.30

rat	chromosome:X:12559544:12559661:-1	Same_strand|Intronic_coding|ENSRNOT00000015559|ENSRNOG00000010838 ## ENSRNOG00000010838|protein_coding|Araf|A-Raf proto-oncogene serine/threonine-protein kinase (EC 2.7.11.1). [Source:UniProtKB/Swiss-Prot;Acc:P14056]
mouse	chromosome:X:20434893:20435050:1	Same_strand|Boundary_non-coding|ENSMUST00000120356|ENSMUSG00000001127|protein_coding|v-raf murine sarcoma 3611 viral oncogene homolog Gene [Source:MGI (curated);Acc:Araf-001] ## Same_strand|Boundary_coding|ENSMUST00000001155|ENSMUSG00000001127|protein_coding|v-raf murine sarcoma 3611 viral oncogene homolog Gene [Source:MGI (curated);Acc:Araf-001]

novel_multiarm_DicerOK_randfoldOK (7 loci)

sblock10772_novel

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock10772_novel 5arm	0	0	0	0	1	0	0	0	0	0
sblock10772_novel 3arm	0	0	2	0	0	0	0	0	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock10772_novel 5arm	0	0	0	0	0.000	0	0	0	0	0
sblock10772_novel 3arm	0	0	0.000	0	0	0	0	0	0	0

sblock10772 [novel_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

0.48/0.50

21/22/1.00

0.0 0.0

0.0 0.0

1 2

0 0

1 1

0 0

23 21

6 13

5arm 3arm

1 1

nd nd

0.18 0.19

2 2

3

2

3

2

		reads	miRBase family seed
seed	--------------------------------------------------------------------AUCCAGG----------------------------------	2	novel
seed	------------------------CUGUGUC------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T3S1
	-------------------------------------------------------------------TATCCAGGGTAGACACTCAGA---------------------	21	2	-
	-----------------------ACTGTGTCAATCCAGGGTAGAC----------------------------------------------------------------	22	-	1
rat	agggcagacactcagaacctgagACTGTGTCAATCCAGGGTAGACactcagaacctgagactgtgtcTATCCAGGGTAGACACTCAGAacctgaggcagcatatgtcct
	*************************************************************************************************************
rat	((((((....(((((...((((....(((((.((((.((((((((((((((...))))....)))))))))).)))).)))))))))...)))))........))))))	0.970 -45.20

rat

chromosome:7:22452263:22452371:-1

intergenic ## {Repeats: trf 12 33 0 class=trf,trf 6 27 0 class=trf,trf 55 77 0 class=trf,trf 49 71 0 class=trf}

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confident novel miRNAs:

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