miR-Intess™

candidate novel miRNAs

novel_lenNOK_cloningHIGH_multiarm_DicerOK (2 loci)

sblock3624_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock3624_cand 5arm	0	0.500	0	0	0	0	0	0	28.167	1
sblock3624_cand 3arm	0	0	0	0	0	0	0	0	5.333	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock3624_cand 5arm	0	0.000	0	0	0	0	0	0	0.002	0.000
sblock3624_cand 3arm	0	0	0	0	0	0	0	0	0.000	0

sblock3624 [novel_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

no

0.166

no

no

0.56/0.67

18/25/0.32

0.0 0.8 0.0 1.4

0.3 2.0 0.3 0.5

34 5 3 8

0 0 0 0

3 1 1 1

0 0 0 0

10 15 14 5

22 13 4 8

5arm 5arm 3arm 3arm

3 3 3 3

nd nd nd nd

0.16 0.22 0.22 0.26

2 2 2 4

74

3

3

3

Families

Member of family novel213 (seed GCAGAUG): sblock3311_cand, sblock3624_cand

		reads	miRBase family seed
seed	-----------GCAGAUG----------------------------------------------------------------------------	55	novel
seed	----------------------------------------------------------------------CCAGACA-----------------	3	novel
seed	--------------------------------------------------------------GCCUGCU-------------------------	3	novel
seed	---------------------------------------------------------------------UCCAGAC------------------	3	novel
seed	----------------UGGACUG-----------------------------------------------------------------------	2	novel
seed	------------CAGAUGG---------------------------------------------------------------------------	2	novel
seed	------------------------------------------------------------------GCUUCCA---------------------	2	novel
seed	-----------------GGACUGG----------------------------------------------------------------------	2	novel
seed	------------------GACUGGA---------------------------------------------------------------------	1	novel
seed	---------AUGCAGA------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T5S1	T5S2
	----------TGCAGATGGACTGGAAGGG-----------------------------------------------------------------	19	1	24	2
	----------TGCAGATGGACTGGAAGG------------------------------------------------------------------	18	-	10	-
	----------TGCAGATGGACTGGAAGGGG----------------------------------------------------------------	20	-	6	-
	----------TGCAGATGGACTGGAAGGGGCA--------------------------------------------------------------	22	-	5	-
	----------TGCAGATGGACTGGAAGGGGCAG-------------------------------------------------------------	23	-	3	-
	---------------------------------------------------------------------TCCAGACATGGGGTGCAGCA-----	20	-	3	-
	--------------------------------------------------------------------TTCCAGACATGGGGTGCAG-------	19	-	2	-
	---------------ATGGACTGGAAGGGGCAG-------------------------------------------------------------	18	-	2	-
	----------TGCAGATGGACTGGAAGGGGC---------------------------------------------------------------	21	-	2	-
	-----------------------------------------------------------------TGCTTCCAGACATGGGGTGCAGCA-----	24	-	2	-
	----------TGCAGATGGACTGGAAGGGGCAGCA-----------------------------------------------------------	25	-	2	-
	-----------GCAGATGGACTGGAAGGGG----------------------------------------------------------------	19	-	2	-
	-------------------------------------------------------------TGCCTGCTTCCAGACATGG--------------	19	-	2	-
	--------TATGCAGATGGACTGGAAGGGGCAG-------------------------------------------------------------	25	-	1	-
	--------------------------------------------------------------------TTCCAGACATGGGGTGCAGCA-----	21	-	1	-
	-------------------------------------------------------------TGCCTGCTTCCAGACATG---------------	18	-	1	-
	----------------TGGACTGGAAGGGGCAGCATGG--------------------------------------------------------	22	-	1	-
	----------------TGGACTGGAAGGGGCAGC------------------------------------------------------------	18	-	1	-
	-----------------GGACTGGAAGGGGCAGCATG---------------------------------------------------------	20	-	1	-
rat	GCAGGGAGTATGCAGATGGACTGGAAGGGGCAGCATGGGGAAGGAGAGGGCAGGACAGCCATGCCTGCTTCCAGACATGGGGTGCAGCAGCTGT
mouse	----------TGCAGATGGGCTGGAGGGGGTGT--GGGGGAACGAGAGGGCAGGGCAGCCATGCTTGCTTCCAGACATGGGATGCA--------
	********* ***** ****      ****** *********** ********* **************** ****
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000056932 ENSRNOG00000037566 RGD1560398_predicted
rat	((((...((.((((.(((..((((((((((((................(((......))).))))).))))))).)))....))))))..))))	0.500 -28.03
mouse	.(((.(((..(((((((((((((  ((.....................)))))))).))))))).)))....))).	0.681 -22.40

rat	chromosome:12:43049519:43049612:1	Same_strand|Intronic_non-coding|ENSRNOT00000056932|ENSRNOG00000037566 ## ENSRNOG00000037566|protein_coding|RGD1560398_predicted|
mouse	chromosome:5:115268847:115268980:-1	intergenic

novel_lenNOK_cloningOK_multiarm_DicerOK_mirtron (2 loci)

sblock2501_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock2501_cand 5arm	0	2	0	0	0	0	0	0	0	0
sblock2501_cand 3arm	3	4	0	1	0	0	0	0	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock2501_cand 5arm	0	0.000	0	0	0	0	0	0	0	0
sblock2501_cand 3arm	0.000	0.000	0	0.000	0	0	0	0	0	0

sblock2501 [novel_lenNOK_cloningOK_multiarm_DicerOK_mirtron]

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

0.070

no

no

0.59/0.64

18/22/0.50

0.0 0.9

0.0 1.9

2 8

0 0

1 3

0 0

8 6

5 7

5arm 3arm

1 1

46 0

0.10 0.17

1 1

10

3

1

1

		reads	miRBase family seed
seed	------------------------------------------------------CUCCUCU--------------------	7	novel
seed	---------UGGGUGC-----------------------------------------------------------------	2	novel
seed	-----------------------------------------------------CCUCCUC---------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S2
	-----------------------------------------------------CCTCCTCTCCTCGTACCT----------	18	1	1	1
	-----------------------------------------------------CCTCCTCTCCTCGTACCTG---------	19	1	1	-
	--------TTGGGTGCAGGGCAGGATGTC----------------------------------------------------	21	-	2	-
	-----------------------------------------------------CCTCCTCTCCTCGTACCTGCAG------	22	1	1	-
	----------------------------------------------------ACCTCCTCTCCTCGTACCTGCA-------	22	-	1	-
rat	tggggaacTTGGGTGCAGGGCAGGATGTCtagtgtcccaagagcccacggagACCTCCTCTCCTCGTACCTGCAGaaacca
	*********************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>	ENSRNOT00000034401 ENSRNOG00000002919 Gfap
rat	..((...(((((((((((((.((((.((((.(((...........)))..)))).)))).)))).))))))).))...)).	0.780 -28.90

rat

chromosome:10:92061905:92061985:-1

Same_strand|Boundary_non-coding|ENSRNOT00000003948|ENSRNOG00000002919 ## Same_strand|Intronic_coding|ENSRNOT00000034401|ENSRNOG00000002919 ## ENSRNOG00000002919|protein_coding|Gfap|Glial fibrillary acidic protein (GFAP). [Source:UniProtKB/Swiss-Prot;Acc:P47819]

sblock3971_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock3971_cand 5arm	5	0	4	0	1	1	0	0	1	0
sblock3971_cand 3arm	3	1	0	1	2	2	0	0	0	1
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock3971_cand 5arm	0.000	0	0.000	0	0.000	0.000	0	0	0.000	0
sblock3971_cand 3arm	0.000	0.000	0	0.000	0.000	0.000	0	0	0	0.000

sblock3971 [novel_lenNOK_cloningOK_multiarm_DicerOK_mirtron]

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

0.098

no

no

0.47/0.56

18/24/0.68

0.2 0.1

1.1 1.6

12 10

0 0

5 6

0 0

22 10

4 3

5arm 3arm

1 1

33 0

0.17 0.09

2 2

22

8

2

3

		reads	miRBase family seed
seed	-----------------------UUGGAGA-------------------------------------------------------------	9	novel
seed	----------------------------------------------------------CAGGUCU--------------------------	9	novel
seed	------------------------UGGAGAG------------------------------------------------------------	3	novel
seed	-----------------------------------------------------------AGGUCUU-------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T5S1	T5S2
	----------------------ATTGGAGAGCAAGGGCTTCTG------------------------------------------------	21	-	-	3	-	-	-	1	-
	---------------------------------------------------------ACAGGTCTTCTTCTCTCCA---------------	19	1	1	-	-	-	1	-	-
	---------------------------------------------------------ACAGGTCTTCTTCTCTCCAC--------------	20	-	-	-	1	1	-	-	1
	----------------------ATTGGAGAGCAAGGGCTTC--------------------------------------------------	19	1	-	1	-	-	-	-	-
	-----------------------TTGGAGAGCAAGGGCTTCTG------------------------------------------------	20	2	-	-	-	-	-	-	-
	-----------------------TTGGAGAGCAAGGGCTTC--------------------------------------------------	18	1	-	-	-	-	-	-	-
	---------------------------------------------------------ACAGGTCTTCTTCTCTCCACAGCC----------	24	-	-	-	-	-	1	-	-
	----------------------ATTGGAGAGCAAGGGCTTCTGG-----------------------------------------------	22	1	-	-	-	-	-	-	-
	---------------------------------------------------------ACAGGTCTTCTTCTCTCCACAG------------	22	1	-	-	-	-	-	-	-
	----------------------ATTGGAGAGCAAGGGCTT---------------------------------------------------	18	-	-	-	-	-	1	-	-
	---------------------------------------------------------ACAGGTCTTCTTCTCTCCACA-------------	21	-	-	-	-	1	-	-	-
	----------------------------------------------------------CAGGTCTTCTTCTCTCCACAG------------	21	1	-	-	-	-	-	-	-
	----------------------ATTGGAGAGCAAGGGCTTCTGGGA---------------------------------------------	24	-	-	-	-	1	-	-	-
rat	ttaaagcatatgctgactgctcATTGGAGAGCAAGGGCTTCTGGGAggagtcagctcACAGGTCTTCTTCTCTCCACAGCCactggtttag
	*******************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>	ENSRNOT00000050856 ENSRNOG00000002512 Gpatc2
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000003396 ENSRNOG00000002512 Gpatc2
rat	.((((.((...((((.........(((((((.(((((..((((....(((....))).))))..))))))))))))))))...)).)))).	0.490 -28.60

rat

chromosome:13:103458770:103458860:1

Same_strand|Intronic_coding|ENSRNOT00000003396|ENSRNOG00000002512 ## Same_strand|Boundary_coding|ENSRNOT00000050856|ENSRNOG00000002512 ## Same_strand|Boundary_non-coding|ENSRNOT00000040543|ENSRNOG00000002512 ## ENSRNOG00000002512|protein_coding|Gpatc2|G patch domain containing 2 [Source:RefSeq_peptide;Acc:NP_001011909]

novel_lenNOK_cloningOK_multiarm_DicerOK_mirtron_randfoldOK (2 loci)

sblock10564_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock10564_cand 5arm	1	4	0	0	0	1	0	0	0	0
sblock10564_cand 3arm	5.500	7	0	0	0	0	0	0	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock10564_cand 5arm	0.000	0.000	0	0	0	0.000	0	0	0	0
sblock10564_cand 3arm	0.000	0.000	0	0	0	0	0	0	0	0

sblock10564 [novel_lenNOK_cloningOK_multiarm_DicerOK_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

0.004

no

no

0.59/0.74

18/24/0.67

0.0 0.3

0.7 3.0

6 15

0 0

3 2

0 0

28 28

4 8

5arm 3arm

1 2

42 0

0.19 0.29

2 2

21

3

1

3

		reads	miRBase family seed
seed	---------------------------------------------------------------------UGAUGCC--------------------------------------------	11	novel
seed	-----------------------------GGGGGGC------------------------------------------------------------------------------------	6	novel
seed	----------------------------------------------------------------------GAUGCCA-------------------------------------------	2	novel
seed	-------------------------------------------------------------------CCUGAUG----------------------------------------------	1	novel
seed	--------------------------------------------------------------------CUGAUGC---------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T3S2
	----------------------------TGGGGGGCAGGCAGCACAGGAC----------------------------------------------------------------------	22	-	3	1
	--------------------------------------------------------------------CTGATGCCACCAACCCTC----------------------------------	18	-	3	-
	--------------------------------------------------------------------CTGATGCCACCAACCCTCCCACAG----------------------------	24	2	1	-
	--------------------------------------------------------------------CTGATGCCACCAACCCTCCCAC------------------------------	22	2	1	-
	---------------------------------------------------------------------TGATGCCACCAACCCTCCCACA-----------------------------	22	-	1	-
	--------------------------------------------------------------------CTGATGCCACCAACCCTCCCA-------------------------------	21	-	1	-
	--------------------------------------------------------------------CTGATGCCACCAACCCTCC---------------------------------	19	-	1	-
	------------------------------------------------------------------TCCTGATGCCACCAACCC------------------------------------	18	1	-	-
	-------------------------------------------------------------------CCTGATGCCACCAACCCTC----------------------------------	19	1	-	-
	----------------------------TGGGGGGCAGGCAGCACAGGA-----------------------------------------------------------------------	21	1	-	-
	---------------------------------------------------------------------TGATGCCACCAACCCTCCCAC------------------------------	21	-	1	-
	----------------------------TGGGGGGCAGGCAGCACAG-------------------------------------------------------------------------	19	-	1	-
rat	ggatatatccccaggggtgggggtagggTGGGGGGCAGGCAGCACAGGACagagaggcctcaggggTCCTGATGCCACCAACCCTCCCACAGaccacctcgtccaccctgaagggtgcca
	************************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000061159 ENSRNOG00000020577 Pip5k1c
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000027890 ENSRNOG00000020577 Pip5k1c
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000061156 ENSRNOG00000020577 Pip5k1c
rat	((......(((..(((((((((((.((((((((((..((..(((((((((.(((....)))....)))))).)))..))..))).)))))...))))))...)))))))...)))..)).	0.970 -58.20

rat

chromosome:7:9895777:9895896:-1

Same_strand|Intronic_coding|ENSRNOT00000061156|ENSRNOG00000020577 ## ENSRNOG00000020577|protein_coding|Pip5k1c|Phosphatidylinositol-4-phosphate 5-kinase type-1 gamma (EC 2.7.1.68) (Phosphatidylinositol-4-phosphate 5-kinase type I gamma) (PtdIns(4)P- 5-kinase gamma) (PtdInsPKIgamma) (PIP5KIgamma). [Source:UniProtKB/Swiss-Prot;Acc:Q5I6B8] ## {Repeats: dust 9895862 9895869 0 class=dust}

sblock4299_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock4299_cand 5arm	0	0	0	0	1	0	0	0	0	0
sblock4299_cand 3arm	5	1	1	0	1	0	1	0	1	1
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock4299_cand 5arm	0	0	0	0	0.000	0	0	0	0	0
sblock4299_cand 3arm	0.000	0.000	0.000	0	0.000	0	0.000	0	0.000	0.000

sblock4299 [novel_lenNOK_cloningOK_multiarm_DicerOK_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

0.005

no

no

0.52/0.59

18/22/0.17

0.0 1.0

0.0 1.1

1 11

0 0

1 7

0 0

25 29

4 5

5arm 3arm

1 1

40 0

0.14 0.19

2 3

12

7

2

1

Families

Member of family novel224 (seed GAGUAGG): block1115796_cand, sblock4299_cand

		reads	miRBase family seed
seed	-------------------------------------------------------------------ACCCAUC------------------------------------------	6	novel
seed	-----------------------------------------------------------------GUACCCA--------------------------------------------	4	novel
seed	----------------------------------------------------------------AGUACCC---------------------------------------------	1	novel
seed	--------------------------GAGUAGG-----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S1	T4S1	T5S1	T5S2
	------------------------------------------------------------------TACCCATCTGTCCCTGCT--------------------------------	18	2	-	-	1	-	-	-
	----------------------------------------------------------------AGTACCCATCTGTCCCTGC---------------------------------	19	1	-	-	-	1	-	1
	------------------------------------------------------------------TACCCATCTGTCCCTGCTT-------------------------------	19	-	1	-	-	-	1	-
	-------------------------TGAGTAGGGCAGCAGGTGCTAG---------------------------------------------------------------------	22	-	-	-	1	-	-	-
	---------------------------------------------------------------CAGTACCCATCTGTCCCTG----------------------------------	19	1	-	-	-	-	-	-
	------------------------------------------------------------------TACCCATCTGTCCCTGCTTAG-----------------------------	21	-	-	1	-	-	-	-
	----------------------------------------------------------------AGTACCCATCTGTCCCTG----------------------------------	18	1	-	-	-	-	-	-
rat	ggcctggttgaaacctcctgacagcTGAGTAGGGCAGCAGGTGCTAGgcgtgtggcaaatgacCAGTACCCATCTGTCCCTGCTTAGctcagactacgaggagatcaccatcgacc
	********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000052002 ENSRNOG00000025923 RGD1309256
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000035505 ENSRNOG00000025923 RGD1309256
rat	....(((.(((..((((((((..((((((((((((((..((((((.(((((.......))).))))))))...))).))))))))))))))).....))))...))))))......	0.910 -46.80

rat

chromosome:14:87151083:87151198:1

Same_strand|Intronic_coding|ENSRNOT00000035505|ENSRNOG00000025923 ## ENSRNOG00000025923|protein_coding|RGD1309256|RGD1309256 protein (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q68FR4]

miRNAunknown_cloningHIGH_Multihit_randfoldOK (1 loci)

block1705997_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1705997_cand 5arm	0.039	0.030	0.070	0.082	0.170	0.106	0.124	0.118	0.046	0.027
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1705997_cand 5arm	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000

block1705997 (miRNA) [miRNAunknown_cloningHIGH_Multihit_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

Ensembl miRNA

0.001

no

no

0.48/0.52

22/26/0.96

0.0

0.6

171

0

10

0

14

2

5arm

331

nd

0.27

3

268

10

na

na

		reads	miRBase family seed
seed	---------------GAGUGUG-------------------------------------------------------------------------------	265	novel
seed	----------------AGUGUGU------------------------------------------------------------------------------	3	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--------------TGAGTGTGTGTGTGTGAGTGTGTG---------------------------------------------------------------	24	4	5	11	13	29	18	18	21	4	7
	--------------TGAGTGTGTGTGTGTGAGTGTG-----------------------------------------------------------------	22	7	3	5	8	17	12	11	10	4	1
	--------------TGAGTGTGTGTGTGTGAGTGTGT----------------------------------------------------------------	23	1	1	3	5	7	4	11	8	5	-
	--------------TGAGTGTGTGTGTGTGAGTGTGTGT--------------------------------------------------------------	25	1	-	2	1	2	1	-	-	2	1
	--------------TGAGTGTGTGTGTGTGAGTGTGTGTG-------------------------------------------------------------	26	-	1	1	-	-	-	-	-	-	-
	---------------GAGTGTGTGTGTGTGAGTGTGTG---------------------------------------------------------------	23	-	-	1	-	1	-	-	-	-	-
	---------------GAGTGTGTGTGTGTGAGTGTGTGT--------------------------------------------------------------	24	-	-	-	-	-	-	1	-	-	-
rat	agtttgtgtgtgtgTGAGTGTGTGTGTGTGAGTGTGTGtgagtgtgagtgtgagtgtgtgtgtgtgtgtacactaatgggtacactcaccacacacaggct
	*****************************************************************************************************
	---------------------------------------------------------------------------------------------------------------	ENSRNOT00000020729 ENSRNOG00000027869 LOC312831
	---------------------------------------------------------------------------------------------------------------	ENSRNOT00000020512 ENSRNOG00000027869 LOC312831
	.......................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>..........	ENSRNOT00000063289 ENSRNOG00000041536
rat	((((((((((((.(((((((((..(((...((((((..((........................))..)))))).)))..)))))))))))))))))))))	1.000 -38.76

rat

chromosome:4:180451416:180451516:1

Opposite_strand|Intronic_coding|ENSRNOT00000020512|ENSRNOG00000027869 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000055542|ENSRNOG00000027869 ## Same_strand|Boundary_non-coding|ENSRNOT00000063289|ENSRNOG00000041536 ## ENSRNOG00000041536|miRNA|| ## ENSRNOG00000027869|protein_coding|LOC312831|Sry-related transcription factor Sox5 (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q91WY4] ## {Repeats: trf 30 56 0 class=trf,dust 180451365 180451391 0 class=dust,(TG)n 114 140 1 class=Simple_repeat,(TG)n 2 169 1 class=Simple_repeat}

miRNAunknown_cloningOK_multiarm_DicerNOK_randfoldOK (1 loci)

sblock9475_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock9475_cand 5arm	0	0	0	0	0.200	0	0.333	0	0	0
sblock9475_cand 3arm	0	0	2	0	9	0	0	2	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock9475_cand 5arm	0	0	0	0	0.000	0	0.000	0	0	0
sblock9475_cand 3arm	0	0	0.000	0	0.000	0	0	0.000	0	0

sblock9475 (miRNA) [miRNAunknown_cloningOK_multiarm_DicerNOK_randfoldOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

Ensembl miRNA

0.001

no

no

0.44/0.48

18/23/0.88

0.0 0.0

1.0 0.0

2 7

0 0

2 3

0 0

34 19

-5 14

5arm_loop_3arm 3arm

5 5

nd nd

0.30 0.23

4 2

16

4

15

0

Families

Member of family novel18 (seed GUGUGUG): sblock9475_cand, block78156_cand, block280302_cand, block1091454_cand, block2143793_cand

		reads	miRBase family seed
seed	-----------------------------------------------------------------------UGACAGA---------------------------------	14	novel
seed	-----------------------------------GUGUGUG---------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T2S1	T3S1	T4S1	T4S2
	----------------------------------------------------------------------CTGACAGACATGTACACACACA-------------------	22	1	7	-	-
	----------------------------------------------------------------------CTGACAGACATGTACACACAC--------------------	21	-	2	-	2
	----------------------------------------------------------------------CTGACAGACATGTACACA-----------------------	18	2	-	-	-
	----------------------------------TGTGTGTGTGTGTCTGTCTTC--------------------------------------------------------	21	-	1	-	-
	----------------------------------TGTGTGTGTGTGTCTGTCTTCTG------------------------------------------------------	23	-	-	1	-
rat	gtcctgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtctgtcttctggccaccatgcacaCTGACAGACATGTACACACACAtgcaggcacacgtaaggac
	***************************************************************************************************************
	.........<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<......................	ENSRNOT00000063259 ENSRNOG00000041506
rat	(((((..((((((.((((((((((((((..(((.((((((((((((...(((....)))...)))))))))..))).)))..)))))))))))))).))))))...)))))	1.000 -64.00

rat

chromosome:5:121903146:121903256:-1

Opposite_strand|Exonic_non-coding|ENSRNOT00000063259|ENSRNOG00000041506 ## ENSRNOG00000041506|miRNA|| ## {Repeats: (CA)n 2 48 -1 class=Simple_repeat,dust 121903210 121903223 0 class=dust,trf 1 18 0 class=trf,(CA)n 2 19 -1 class=Simple_repeat}

miRNAunknown_cloningOK_randfoldOK_bulgeHIGH (1 loci)

block2225001_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block2225001_cand 5arm	1	1	0	0	1	1	1	3	2	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block2225001_cand 5arm	0.000	0.000	0	0	0.000	0.000	0.000	0.000	0.000	0

block2225001 (miRNA) [miRNAunknown_cloningOK_randfoldOK_bulgeHIGH]

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

Ensembl miRNA

0.001

no

no

0.50/0.55

20/22/1.00

0.2

0.3

10

0

7

0

22

3

5arm

1

nd

0.27

4

10

7

na

na

Families

Member of family novel56 (seed CAGCCUC): block2225001_cand, block106348_cand, block1418222_cand

		reads	miRBase family seed
seed	-----------------------CAGCCUC------------------------------------------------------------------------	8	novel
seed	------------------------AGCCUCA-----------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1	T3S2	T4S1	T4S2	T5S1
	----------------------GCAGCCTCAGTGTTTTCAGGTG----------------------------------------------------------	22	-	-	1	1	-	3	2
	-----------------------CAGCCTCAGTGTTTTCAGGTGA---------------------------------------------------------	22	-	-	-	-	1	-	-
	-----------------------CAGCCTCAGTGTTTTCAGGTG----------------------------------------------------------	21	-	1	-	-	-	-	-
	----------------------GCAGCCTCAGTGTTTTCAGG------------------------------------------------------------	20	1	-	-	-	-	-	-
rat	GGAAGCTGATGTTCAGTGGGACGCAGCCTCAGTGTTTTCAGGTGATTTGAATGAACACCTGATAAAACTGAGGTATAGTACCACAGAACTTGGAATGCTCCC
mouse	----------------------TCAGCCTCAGTGTTTTCCCTATTTCCACACGGGAACCTG----AGCTGAGGCTCA-------------------------
	****************      *    * *   *****    * ******   *
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000014703 ENSRNOG00000010865 Cohh1_predicted
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000033021 ENSRNOG00000010865 Cohh1_predicted
	..............<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<....................	ENSRNOT00000063101 ENSRNOG00000041348
rat	((.(((....((((.((((.((...((((((((....(((((((.(((....))))))))))....))))))))...)).)))).)))).......))))).	0.990 -41.70
mouse	..(((((((((...(((((...........)))))....    .)))))))))..	1.000 -21.00

rat	chromosome:7:71189228:71189329:1	Opposite_strand|Exonic_non-coding|ENSRNOT00000063101|ENSRNOG00000041348 ## Same_strand|Intronic_coding|ENSRNOT00000033021|ENSRNOG00000010865 ## Same_strand|Boundary_non-coding|ENSRNOT00000014768|ENSRNOG00000010865 ## Same_strand|Intronic_non-coding|ENSRNOT00000014703|ENSRNOG00000010865 ## ENSRNOG00000010865|protein_coding|Cohh1_predicted| ## ENSRNOG00000041348|miRNA||
mouse	chromosome:11:58454339:58454480:-1	Opposite_strand|Boundary_coding|ENSMUST00000075084|ENSMUSG00000037124|protein_coding|tripartite motif-containing 58 Gene [Source:MGI (curated);Acc:Trim58-001]

miRNAunknown_lenNOK_cloningOK_randfoldOK (1 loci)

block875685_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block875685_cand 3arm	6	10	0	0	0	0	0	0	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block875685_cand 3arm	0.000	0.000	0	0	0	0	0	0	0	0

block875685 (miRNA) [miRNAunknown_lenNOK_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

Ensembl miRNA

0.001

no

no

0.50/0.53

18/22/0.69

0.0

1.2

13

0

2

0

8

7

3arm

1

nd

0.10

1

16

2

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------AUAUAGC----------------------------------------	16	novel
		len	cloning frequencies
			T1S1	T1S2
	----------------------------------------------------GATATAGCCAAAGCCCGACTGA--------------------------	22	-	7
	----------------------------------------------------GATATAGCCAAAGCCCGAC-----------------------------	19	3	1
	----------------------------------------------------GATATAGCCAAAGCCCGACT----------------------------	20	3	-
	----------------------------------------------------GATATAGCCAAAGCCCGACTG---------------------------	21	-	1
	----------------------------------------------------GATATAGCCAAAGCCCGA------------------------------	18	-	1
rat	GAGATCTGATCAGTCAGGCTACTGGCTATATTCCAGGACCTATCTGGTCCTGGATATAGCCAAAGCCCGACTGAATGGTGTT------------------
mouse	---------TCAGTCAGGCTGCTGGCTA---TCCATGTCTTGTCTAGTCCTGCATATAGCCAAAGCCAGACTGAATGGTGATAAAGATGTGGGAGAGTAC
	*********** *******   **** * * * *** ****** ************** ************ *
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>                  >>>>>	ENSRNOT00000063156 ENSRNOG00000041403
rat	((.(((...((((((.((((..((((((((.(((((((((.....))))))))))))))))).)))).))))))..))).))	1.000 -47.10
mouse	((((((.((((..((((((   (..((((.............))))))))))).)))).))))))..........................	0.843 -25.52

rat	chromosome:1:115321251:115321332:-1	Same_strand|Exonic_non-coding|ENSRNOT00000063156|ENSRNOG00000041403 ## ENSRNOG00000041403|miRNA||
mouse	chromosome:7:68839337:68839424:-1	intergenic

miRNAunknown_randfoldOK (1 loci)

block969943_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block969943_cand 3arm	0	0	0	3	0	0	0	0	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block969943_cand 3arm	0	0	0	0.000	0	0	0	0	0	0

block969943 (miRNA) [miRNAunknown_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

Ensembl miRNA

0.001

no

no

0.41/0.41

22/22/1.00

0.0

0.0

3

0

1

0

19

7

3arm

1

nd

0.23

3

3

1

na

na

Clusters

Located in cluster 8: block969943_cand, rno-mir-292

Families

Member of family novel79 (seed GUGUCAC): block969943_cand, block2585263_cand

		reads	miRBase family seed
seed	-----------------------------------------------------------GUGUCAC---------------------------------	3	novel
		len	cloning frequencies
			T2S2
	----------------------------------------------------------AGTGTCACACAGTTTGAGTATC-------------------	22	3
rat	gcagttttctccatcggtaacactgcaaactttgcggcacttcttccaaaagaaacaaAGTGTCACACAGTTTGAGTATCacaggtggaaacacttgca
	***************************************************************************************************
	.............<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<..............	ENSRNOT00000062153 ENSRNOG00000040400
rat	(((((.((.((((((.((...(((.((((((.((.(((((((.(((.....)))...))))))).)).)))))))))...)).)))))))).))).)).	0.980 -30.90

rat

chromosome:1:64273316:64273414:1

Opposite_strand|Exonic_non-coding|ENSRNOT00000062153|ENSRNOG00000040400 ## ENSRNOG00000040400|miRNA||

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candidate novel miRNAs:

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