miR-Intess™

candidate novel miRNAs

novel_cloningOK_multiarm_DicerNOK_randfoldOK (11 loci)

MANUAL_level2 (9 loci)

block104027_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block104027_cand 3arm	102.500	80.500	19	15.500	28	10.500	25	20.500	7	10.500
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block104027_cand 3arm	0.003	0.004	0.001	0.001	0.001	0.001	0.002	0.001	0.000	0.001

block104027 [MANUAL_level2]

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

0.52/0.61

18/22/0.76

0.0

0.0

146

0

10

0

28

10

3arm

1

0

0.10

2

340

10

na

na

		reads	miRBase family seed
seed	------------------------------------------------------------------CUGUCCC-----------------------------------------	332	novel
seed	-----------------------------------------------------------------UCUGUCC------------------------------------------	4	novel
seed	-------------------------------------------------------------------UGUCCCU----------------------------------------	3	novel
seed	--------------------------------------------------------------------GUCCCUC---------------------------------------	1	miR-347
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-----------------------------------------------------------------TCTGTCCCTCTTGGCCCTTAG----------------------------	21	69	56	17	7	21	9	19	15	5	8
	-----------------------------------------------------------------TCTGTCCCTCTTGGCCCT-------------------------------	18	15	9	-	5	2	1	4	1	2	3
	-----------------------------------------------------------------TCTGTCCCTCTTGGCCCTT------------------------------	19	10	9	2	3	4	-	4	3	1	-
	-----------------------------------------------------------------TCTGTCCCTCTTGGCCCTTA-----------------------------	20	12	8	-	2	-	1	-	1	-	1
	----------------------------------------------------------------ATCTGTCCCTCTTGGCCCTTA-----------------------------	21	3	1	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------TCTGTCCCTCTTGGCCCTTAGG---------------------------	22	-	2	-	-	-	-	-	1	-	-
	------------------------------------------------------------------CTGTCCCTCTTGGCCCTTAG----------------------------	20	-	-	-	-	2	-	-	-	-	-
	------------------------------------------------------------------CTGTCCCTCTTGGCCCTT------------------------------	18	1	-	-	-	-	-	-	-	-	-
	-------------------------------------------------------------------TGTCCCTCTTGGCCCTTAG----------------------------	19	-	-	-	1	-	-	-	-	-	-
rat	acgtggtccttagtggaggtttgcttgttataggggctaagaggggccaggcgtgcctgtcatcaTCTGTCCCTCTTGGCCCTTAGgctcggcatgctacctatggcatccgta
	******************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000005684 ENSRNOG00000004032 2310067B10Rik
rat	(((.(((((.....((.(((.((((.(((.(((((((((((((((((((((....)))).........))))))))))))))))))))..)))).))).))...)).)))))).	0.970 -51.90

rat

chromosome:10:105897773:105897886:1

Same_strand|Boundary_coding|ENSRNOT00000005684|ENSRNOG00000004032 ## ENSRNOG00000004032|protein_coding|2310067B10Rik|RIKEN cDNA 2310067B10 gene Gene [Source:MGI Symbol;Acc:MGI:1919197]

block984945_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block984945_cand 3arm	0	2	0	0	3	0	0	0	15.333	16.333
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block984945_cand 3arm	0	0.000	0	0	0.000	0	0	0	0.001	0.001

block984945 [MANUAL_level2]

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

0.54/0.58

19/24/0.95

0.0

0.6

25

0

4

0

3

24

3arm

1

0

0.21

3

40

4

na

na

Families

Member of family novel74 (seed CUGCCCC): block984945_cand, block2268635_cand

		reads	miRBase family seed
seed	------------------------------------------------------------------------------CUGCCCC-------------------	39	novel
seed	-------------------------------------------------------------------------------UGCCCCA------------------	1	novel
		len	cloning frequencies
			T1S2	T3S1	T5S1	T5S2
	-----------------------------------------------------------------------------TCTGCCCCATCCTTTCCTCACAG----	23	1	2	8	7
	-----------------------------------------------------------------------------TCTGCCCCATCCTTTCCTCAC------	21	-	-	2	4
	-----------------------------------------------------------------------------TCTGCCCCATCCTTTCCTCACA-----	22	-	1	3	1
	-----------------------------------------------------------------------------TCTGCCCCATCCTTTCCTCACAGT---	24	-	-	1	3
	-----------------------------------------------------------------------------TCTGCCCCATCCTTTCCTCA-------	20	-	-	2	2
	-----------------------------------------------------------------------------TCTGCCCCATCCTTTCCTC--------	19	-	-	1	1
	------------------------------------------------------------------------------CTGCCCCATCCTTTCCTCACAGT---	23	1	-	-	-
rat	cacatgcagaggtgaggagcctttgtggggcttgagctgagggtctgaacacccaggccctgcctcttgacaacagcTCTGCCCCATCCTTTCCTCACAGTgtg
	********************************************************************************************************
	>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>	ENSRNOT00000026992 ENSRNOG00000019854 Napsa
rat	(((((...((((.(((((.......((((((..((((((((((((((......))))))))............)))))).))))))))))).))))...)))))	0.950 -50.11

rat

chromosome:1:95061089:95061192:1

Same_strand|Boundary_coding|ENSRNOT00000026992|ENSRNOG00000019854 ## ENSRNOG00000019854|protein_coding|Napsa|napsin A aspartic peptidase [Source:RefSeq_peptide;Acc:NP_113858]

block1048216_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1048216_cand 3arm	362	250	2	0	0	1	0	0	1	4
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1048216_cand 3arm	0.012	0.011	0.000	0	0	0.000	0	0	0.000	0.000

block1048216 [MANUAL_level2]

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

0.65/0.72

18/24/0.70

0.0

0.5

427

0

6

0

14

7

3arm

1

nd

0.24

3

620

6

na

na

		reads	miRBase family seed
seed	--------------------------------------------------------CUGGCUG---------------------------	606	novel
seed	---------------------------------------------------------UGGCUGC--------------------------	7	novel
seed	-------------------------------------------------------UCUGGCU----------------------------	7	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S2	T5S1	T5S2
	-------------------------------------------------------TCTGGCTGCTATGGCCCCCTC--------------	21	177	134	1	1	-	3
	-------------------------------------------------------TCTGGCTGCTATGGCCCCC----------------	19	116	49	-	-	-	-
	-------------------------------------------------------TCTGGCTGCTATGGCCCCCT---------------	20	30	36	-	-	1	1
	-------------------------------------------------------TCTGGCTGCTATGGCCCCCTCC-------------	22	15	17	1	-	-	-
	-------------------------------------------------------TCTGGCTGCTATGGCCCC-----------------	18	10	6	-	-	-	-
	-------------------------------------------------------TCTGGCTGCTATGGCCCCCTCCC------------	23	4	4	-	-	-	-
	------------------------------------------------------CTCTGGCTGCTATGGCCCCCTC--------------	22	4	-	-	-	-	-
	--------------------------------------------------------CTGGCTGCTATGGCCCCCTC--------------	20	3	1	-	-	-	-
	------------------------------------------------------CTCTGGCTGCTATGGCCCCC----------------	20	2	-	-	-	-	-
	--------------------------------------------------------CTGGCTGCTATGGCCCCCT---------------	19	-	2	-	-	-	-
	------------------------------------------------------CTCTGGCTGCTATGGCCCCCTCCC------------	24	1	-	-	-	-	-
	--------------------------------------------------------CTGGCTGCTATGGCCCCC----------------	18	-	1	-	-	-	-
rat	GTCCCTACTCTGGGAAGGTGCCATTCTGAAGGCCAGGAGTCTGAATATGAGTCACTCTGGCTGCTATGGCCCCCTCCCAGGGCTTGGGCA
human	---------CTGGGAAGGTGCCATTCTGAGGGCCAGGAGTTTGATTATGTGTCACTCTGGCTGCTATGGCCCCCTCCCAG----------
mouse	GTCCCAACTCTGGGAAGGTGCCATTCCGAGGGCCAAGAGTCTGAATATGAGTCACTCTGGCTGCTATGGCCCCCTCCCAGGGCTTGGGC-
	***************** ** ***** **** *** **** ******************************
rat	((((...((((((((.((.(((((......((((((((.((.......)).))...))))))...))))).)).))))))))...)))).	1.000 -43.00
human	((((((.((.(((((......(((((.((((..(((.....))))))))))))...))))).)).))))))	1.000 -31.80
mouse	..(((((((((((((.((.(((((......((((.(((((((.......))..)))))))))...))))).)).)))))))).))))).	1.000 -41.80

rat	chromosome:1:248574570:248574659:1	intergenic
human	chromosome:10:99625567:99625637:-1	Same_strand|Boundary_non-coding|ENST00000370591|ENSG00000095713|protein_coding|Cartilage acidic protein 1 Precursor (68 kDa chondrocyte-expressed protein)(CEP-68)(ASPIC) [Source:UniProtKB/Swiss-Prot;Acc:Q9NQ79] ## Same_strand|Intronic_coding|ENST00000298819|ENSG00000095713|protein_coding|Cartilage acidic protein 1 Precursor (68 kDa chondrocyte-expressed protein)(CEP-68)(ASPIC) [Source:UniProtKB/Swiss-Prot;Acc:Q9NQ79]
mouse	chromosome:19:42354572:42354660:-1	intergenic

block1058844_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1058844_cand 5arm	1	2	0	0	8	6	11	2	1	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1058844_cand 5arm	0.000	0.000	0	0	0.000	0.000	0.001	0.000	0.000	0

block1058844 [MANUAL_level2]

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

0.57/0.65

19/23/0.84

0.0

0.5

21

0

7

0

24

3

5arm

1

nd

0.05

1

31

7

na

na

Families

Member of family novel147 (seed ACAGUGC): block1058844_cand, block1133101_cand

		reads	miRBase family seed
seed	-------------------------ACAGUGC------------------------------------------------------------------------------------	31	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1	T3S2	T4S1	T4S2	T5S1
	------------------------CACAGTGCCCACAGCAGTGCT-----------------------------------------------------------------------	21	-	1	6	-	6	1	-
	------------------------CACAGTGCCCACAGCAGTGC------------------------------------------------------------------------	20	1	-	1	3	2	-	1
	------------------------CACAGTGCCCACAGCAGTG-------------------------------------------------------------------------	19	-	1	1	1	1	1	-
	------------------------CACAGTGCCCACAGCAGTGCTTT---------------------------------------------------------------------	23	-	-	-	2	-	-	-
	------------------------CACAGTGCCCACAGCAGTGCTT----------------------------------------------------------------------	22	-	-	-	-	2	-	-
rat	tggggagccggaggaagtgcggccCACAGTGCCCACAGCAGTGCTTTgtgagacagaaggcagtgttgttctgggcactgctgggttgcctttttctgttttcgtctgttctgcac
	********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000048985 ENSRNOG00000033581 Q62772_RAT
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000029258 ENSRNOG00000033581 Q62772_RAT
rat	((.((((((((((((((.((((((((((((((((((((((.((((((.((...)).)))))).))))))...)))))))).))))))))))))))))).........))))).)).	0.950 -62.20

rat

chromosome:20:4150063:4150178:-1

Same_strand|Intronic_coding|ENSRNOT00000029258|ENSRNOG00000033581 ## ENSRNOG00000033581|protein_coding|Q62772_RAT|Tenascin-X (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q62772]

block2683452_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block2683452_cand 5arm	75	40	0	0	0	0	0	0	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block2683452_cand 5arm	0.002	0.002	0	0	0	0	0	0	0	0

block2683452 [MANUAL_level2]

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

0.64/0.70

18/22/0.83

0.0

0.2

68

0

2

0

19

3

5arm

1

nd

0.19

3

115

2

na

na

		reads	miRBase family seed
seed	--------------------------------GGCUGCA------------------------------------------------------------------------------------------------	115	novel
		len	cloning frequencies
			T1S1	T1S2
	-------------------------------AGGCTGCAGGCCCACTTCCCT-----------------------------------------------------------------------------------	21	39	17
	-------------------------------AGGCTGCAGGCCCACTTCCC------------------------------------------------------------------------------------	20	12	10
	-------------------------------AGGCTGCAGGCCCACTTCCCTT----------------------------------------------------------------------------------	22	8	9
	-------------------------------AGGCTGCAGGCCCACTTCC-------------------------------------------------------------------------------------	19	8	3
	-------------------------------AGGCTGCAGGCCCACTTC--------------------------------------------------------------------------------------	18	8	1
rat	------------TGTGAATCCAGCTGGTTCAAGGCTGCAGGCCCACTTCCCTTGGCAGATTTTTCCATTTCAGGGAGTGGGGAAAGTGGCCCTAAACCATCAAAATGGATTATACAT------------------
mouse	TCAGATGTCTTCTGTGAATCCAGCTGGTTCAAGGCTGCAGGCCCACTTCCCTTGGCAGATTTTTCCATTTCAGGGAGTGGGGAAAGTGGCCCTAAACCATCAAAATGGATTATACATCACTCTTGACATACATGG
	*********************************************************************************************************
rat	((((((((((..(((((...((((((...(((((.((((((((.........)))....))))))))))....))))))...)))))......)))))).)))).	1.000 -37.40
mouse	.((.(((((....(((((((((..(((((...((((((...(((((.((((((((.........)))....))))))))))....))))))...)))))......)))))......))))....)))))...)).	0.991 -43.40

rat	chromosome:X:31209114:31209218:-1	intergenic
mouse	chromosome:X:143433936:143434070:1	Same_strand|Intronic_non-coding|ENSMUST00000112831|ENSMUSG00000041380|protein_coding|5-hydroxytryptamine (serotonin) receptor 2C Gene [Source:MGI (curated);Acc:Htr2c-002]

block871207_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block871207_cand 3arm	0	1	0	0	0	0	1	1	10	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block871207_cand 3arm	0	0.000	0	0	0	0	0.000	0.000	0.001	0

block871207 [MANUAL_level2]

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

0.35/0.40

20/26/0.92

0.0

0.0

9

0

4

0

9

16

3arm

1

nd

0.20

2

13

4

na

na

Clusters

Located in cluster 4: block871208_cand, block871207_cand

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------AGACAGU---------------------	12	novel
seed	------------------------------------------------------------------------------------------UCAUCAC------------	1	novel
		len	cloning frequencies
			T1S2	T4S1	T4S2	T5S1
	--------------------------------------------------------------------------------TAGACAGTATTCATCACATG---------	20	1	-	1	9
	-----------------------------------------------------------------------------------------TTCATCACATGCGATTCTGA	20	-	1	-	-
	--------------------------------------------------------------------------------TAGACAGTATTCATCACATGCGATTC---	26	-	-	-	1
rat	cttagctcgcagatacattgagaaatattgctctgtctgtacaagccaacaccaagacagtcaagttggcaagacaaaaaTAGACAGTATTCATCACATGcgattctga
	*************************************************************************************************************
rat	.((((.(((((.......(((..(((((((.(((((.(((....((((((..............))))))...)))...))))))))))))..)))..)))))..))))	1.000 -26.64

rat

chromosome:1:102926979:102927087:-1

intergenic

block1067067_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1067067_cand 5arm	1	1	0	0	0	0	0	0	18	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1067067_cand 5arm	0.000	0.000	0	0	0	0	0	0	0.001	0

block1067067 [MANUAL_level2]

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

0.008

no

no

0.52/0.59

19/24/0.90

0.0

0.0

9

0

3

0

12

19

5arm

1

nd

0.25

3

20

3

na

na

		reads	miRBase family seed
seed	-------------CCAGUAU--------------------------------------------------------------------------------------------------	15	novel
seed	---------------AGUAUGC------------------------------------------------------------------------------------------------	2	novel
seed	------------------AUGCAGG---------------------------------------------------------------------------------------------	1	novel
seed	------------UCCAGUA---------------------------------------------------------------------------------------------------	1	novel
seed	--------GCCUUCC-------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T5S1
	------------TCCAGTATGCAGGCAGTCAC--------------------------------------------------------------------------------------	20	1	-	9
	------------TCCAGTATGCAGGCAGTCA---------------------------------------------------------------------------------------	19	-	-	2
	------------TCCAGTATGCAGGCAGTCACG-------------------------------------------------------------------------------------	21	-	-	2
	-----------------TATGCAGGCAGTCACGAGGTG--------------------------------------------------------------------------------	21	-	-	1
	------------TCCAGTATGCAGGCAGTCACGAG-----------------------------------------------------------------------------------	23	-	1	-
	--------------CAGTATGCAGGCAGTCACGAGGTG--------------------------------------------------------------------------------	24	-	-	1
	-----------TTCCAGTATGCAGGCAGTCAC--------------------------------------------------------------------------------------	21	-	-	1
	-------TGCCTTCCAGTATGCAGGCA-------------------------------------------------------------------------------------------	20	-	-	1
	--------------CAGTATGCAGGCAGTCACGAGG----------------------------------------------------------------------------------	22	-	-	1
rat	aaaagcatgcctTCCAGTATGCAGGCAGTCACgaggtgccttcacgaatgcagaatgagatggagggaagcaggaggtgccctcgtgggtaccagtaagctaggaagagtcttgcttt
	**********************************************************************************************************************
rat	.((((((.((((((((((.(((.((...((((((((.((((((.....(((..................))).)))).))))))))))...)).))).))).))))).))..))))))	0.950 -42.17

rat

chromosome:20:13194673:13194790:-1

intergenic

block1848533_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1848533_cand 3arm	63	33	14	21	4	16	19	31	543	12
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1848533_cand 3arm	0.002	0.001	0.001	0.001	0.000	0.001	0.001	0.002	0.036	0.001

block1848533 [MANUAL_level2]

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

0.52/0.60

18/27/0.93

0.0 0.0

0.0 0.0

16 439

0 0

7 10

0 0

31 24

-1 5

3arm_loop 3arm

1 1

nd nd

0.20 0.14

3 2

756

10

na

na

Families

Member of family novel197 (seed CCUGAGU): block1385383_cand, block1848533_cand

		reads	miRBase family seed
seed	--------------------------------------------------------------------------CCUGAGU-------------------------------------	686	novel
seed	-----------------------------------------------------------------------------GAGUCAC----------------------------------	38	novel
seed	--------------------------------------------------------------------GGCACUC-------------------------------------------	24	novel
seed	---------------------------------------------------------------------------CUGAGUC------------------------------------	5	novel
seed	----------------------------------------------------------------------------UGAGUCA-----------------------------------	2	novel
seed	-------------------------------------------------------------------------UCCUGAG--------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-------------------------------------------------------------------------TCCTGAGTCACATCGCTCCTC------------------------	21	49	29	11	18	3	14	12	25	439	10
	----------------------------------------------------------------------------TGAGTCACATCGCTCCTCCA----------------------	20	2	1	-	-	-	-	1	1	30	-
	-------------------------------------------------------------------------TCCTGAGTCACATCGCTCCTCCATA--------------------	25	3	-	-	1	-	-	1	2	25	-
	-------------------------------------------------------------------TGGCACTCCTGAGTCACATC-------------------------------	20	1	2	2	-	-	-	1	1	16	1
	-------------------------------------------------------------------------TCCTGAGTCACATCGCTCCTCCA----------------------	23	3	-	-	-	-	1	-	-	11	-
	-------------------------------------------------------------------------TCCTGAGTCACATCGCTCCT-------------------------	20	-	-	1	1	-	-	1	-	7	1
	-------------------------------------------------------------------------TCCTGAGTCACATCGCTCC--------------------------	19	2	-	-	1	-	-	1	-	4	-
	--------------------------------------------------------------------------CCTGAGTCACATCGCTCCTC------------------------	20	-	-	-	-	-	-	2	-	3	-
	-------------------------------------------------------------------------TCCTGAGTCACATCGCTC---------------------------	18	-	1	-	-	1	1	-	1	1	-
	-------------------------------------------------------------------------TCCTGAGTCACATCGCTCCTCC-----------------------	22	1	-	-	-	-	-	-	-	1	-
	-------------------------------------------------------------------------TCCTGAGTCACATCGCTCCTCCAT---------------------	24	1	-	-	-	-	-	-	-	1	-
	---------------------------------------------------------------------------CTGAGTCACATCGCTCCTC------------------------	19	1	-	-	-	-	-	-	-	1	-
	------------------------------------------------------------------------CTCCTGAGTCACATCGCTCCTCCA----------------------	24	-	-	-	-	-	-	-	-	1	-
	----------------------------------------------------------------------------TGAGTCACATCGCTCCTCCAT---------------------	21	-	-	-	-	-	-	-	1	-	-
	-------------------------------------------------------------------------TCCTGAGTCACATCGCTCCTCCATAGA------------------	27	-	-	-	-	-	-	-	-	1	-
	----------------------------------------------------------------------------TGAGTCACATCGCTCCTC------------------------	18	-	-	-	-	-	-	-	-	1	-
	----------------------------------------------------------------------------TGAGTCACATCGCTCCTCC-----------------------	19	-	-	-	-	-	-	-	-	1	-
rat	ccttgcattggccacagcaaagccctgtctgtggttctcagaagttgtgatgtgctcagtgaccggctggcacTCCTGAGTCACATCGCTCCTCcatagacagagctctggtccaggg
	**********************************************************************************************************************
rat	(((((....(((((......(((.((((((((((........((..(((((((((((((.((((....))...))))))).))))))))..)))))))))))).))).))))))))))	0.900 -47.60

rat

chromosome:5:79247509:79247626:1

intergenic

sblock9438_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock9438_cand 5arm	0	0	0	0	0	0	0	0	1	0
sblock9438_cand 3arm	0	0	0	0	0	0	0	0	10	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock9438_cand 5arm	0	0	0	0	0	0	0	0	0.000	0
sblock9438_cand 3arm	0	0	0	0	0	0	0	0	0.001	0

sblock9438 [MANUAL_level2]

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

0.21/0.30

19/20/0.82

0.0 0.0

0.0 0.0

1 8

0 0

1 1

0 0

8 8

-1 2

5arm_loop 3arm

1 1

nd nd

0.25 0.30

2 4

11

1

3

3

Clusters

Located in cluster 59: sblock9438_cand, block1767095_cand

Families

Member of family novel172 (seed GAGAUUU): block673647_cand, sblock9438_cand

		reads	miRBase family seed
seed	---------------------------------GAGAUUU--------------------	10	novel
seed	---------AUUAUGA--------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	--------------------------------TGAGATTTGTTATAAAGTTG--------	20	8
	--------------------------------TGAGATTTGTTATAAAGTT---------	19	2
	--------TATTATGACAAGCATCAAGA--------------------------------	20	1
rat	tggctggttattatgacaagcatcaagaacctTGAGATTTGTTATAAAGTTGcaagccac
	************************************************************
rat	(((((.((..((((((((((..(((((...)))))..))))))))))....)).))))).	1.000 -20.50

rat

chromosome:5:114557736:114557795:-1

intergenic

novel_lenNOK_multiarm_DicerOK_randfoldOK (8 loci)

sblock1956_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock1956_cand 5arm	0	0	0	0	0	0	0	1	0	0
sblock1956_cand 3arm	1	2	0	0	0	0	2	0	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock1956_cand 5arm	0	0	0	0	0	0	0	0.000	0	0
sblock1956_cand 3arm	0.000	0.000	0	0	0	0	0.000	0	0	0

sblock1956 [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

0.61/0.65

18/23/0.33

0.0 0.2

0.0 1.4

1 5

0 0

1 3

0 0

22 27

3 5

5arm 3arm

1 1

nd nd

0.26 0.23

2 2

6

4

2

1

		reads	miRBase family seed
seed	-----------------------------------------------------------GAGCUGU------------------------------------------	4	novel
seed	------------------------------------------------------------AGCUGUG-----------------------------------------	1	novel
seed	-----------------------GCCCCAA------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T4S1	T4S2
	----------------------------------------------------------GGAGCTGTGTCCCTTGAGG-------------------------------	19	-	-	2	-
	----------------------------------------------------------GGAGCTGTGTCCCTTGAG--------------------------------	18	-	2	-	-
	----------------------CGCCCCAAGGACCACGGTCTCTA---------------------------------------------------------------	23	-	-	-	1
	-----------------------------------------------------------GAGCTGTGTCCCTTGAGGCAGC---------------------------	22	1	-	-	-
rat	caccagcggggtcggccctgagCGCCCCAAGGACCACGGTCTCTAtctccttaagttgGGAGCTGTGTCCCTTGAGGCAGCtttaggctcgcaagatcacagttggtg
	************************************************************************************************************
rat	(((((((..((((((((..(((((((.(((((..((((((..(((.((.....)).)))..))))))..))))).))).))))..)))).....))))...)))))))	0.990 -51.60

rat

chromosome:1:128562874:128562981:1

intergenic

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candidate novel miRNAs:

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