miR-Intess™

other hairpins

novel_lenNOK_shortStem_5varHIGH_loopOverlap (22 loci)

block1674152 [novel_lenNOK_shortStem_5varHIGH_loopOverlap]

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

0.177

no

no

0.50/0.50

18/22/0.67

4.0

2.0

3

0

3

0

0

-16

3arm_loop

2

nd

0.26

3

3

3

na

na

		reads	miRBase family seed
seed	-----------------------GCUCAGA------------	2	novel
seed	-----------------UACUGUG------------------	1	novel
		len	cloning frequencies
			T1S1	T4S2	T5S2
	----------------------TGCTCAGATCTGTGACTC--	18	-	1	-
	----------------CTACTGTGCTCAGATCTGTGAC----	22	1	-	-
	----------------------TGCTCAGATCTGTGACTCCT	20	-	-	1
rat	gggagcccattccagaCTACTGTGCTCAGATCTGTGACTCCT
	******************************************
rat	(((((.....((((((...(((....))).)))).)))))))	0.990 -10.10

rat

chromosome:4:122924358:122924399:1

intergenic

block1695774 [novel_lenNOK_shortStem_5varHIGH_loopOverlap]

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

0.079

no

no

0.41/0.47

19/25/0.43

6.0

4.9

14

0

1

0

0

-2

3arm

1

nd

0.22

3

14

1

na

na

		reads	miRBase family seed
seed	--------------------------------------GAGUACA------------------------	3	novel
seed	-----------------------------------AAGGAGU---------------------------	3	novel
seed	-----------------------------------------UACAGAG---------------------	2	novel
seed	----------------------------------------------AGAAUGC----------------	1	novel
seed	--------------------------------------------AGAGAAU------------------	1	novel
seed	---------------------------------------------------GCAGAUA-----------	1	novel
seed	-----------------------------------------------GAAUGCA---------------	1	novel
seed	------------------------------------------------AAUGCAG--------------	1	novel
seed	-------------------------------------GGAGUAC-------------------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------------------TAAGGAGTACAGAGAATGCAGA-------------	22	3
	-------------------------------------GGAGTACAGAGAATGCAGA-------------	19	3
	----------------------------------------GTACAGAGAATGCAGATATTGCCCT----	25	2
	-------------------------------------------CAGAGAATGCAGATATTGCCCT----	22	1
	-----------------------------------------------GAATGCAGATATTGCCCTA---	19	1
	------------------------------------AGGAGTACAGAGAATGCAGA-------------	20	1
	----------------------------------------------AGAATGCAGATATTGCCCT----	19	1
	--------------------------------------------------TGCAGATATTGCCCTAAGC	19	1
	---------------------------------------------GAGAATGCAGATATTGCCCT----	20	1
rat	cttggtggcaaggcctgtaggtaaagctgaggagTAAGGAGTACAGAGAATGCAGATATTGCCCTAAGC
	*********************************************************************
rat	(((((.(((((...(((((.(((...((........))...)))......)))))...)))))))))).	0.960 -18.40

rat

chromosome:4:164246443:164246511:1

intergenic

block1695969 [novel_lenNOK_shortStem_5varHIGH_loopOverlap]

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

0.017

no

no

0.47/0.57

18/21/0.40

3.0

3.4

5

0

1

0

0

-18

3arm_loop

1

nd

0.30

3

5

1

na

na

		reads	miRBase family seed
seed	-----------------GUAACCU---------------	2	novel
seed	--------------GUGGUAA------------------	1	novel
seed	-------------------AACCUUA-------------	1	novel
seed	------------------UAACCUU--------------	1	novel
		len	cloning frequencies
			T5S1
	------------------TAACCTTAGGAGAGCCAGGCC	21	1
	-----------------GTAACCTTAGGAGAGCCA----	18	1
	----------------GGTAACCTTAGGAGAGCCA----	19	1
	----------------GGTAACCTTAGGAGAGCCAG---	20	1
	-------------TGTGGTAACCTTAGGAGAG-------	19	1
rat	gcttaggcatctcTGTGGTAACCTTAGGAGAGCCAGGCC
	***************************************
rat	((((.(((.(((((..((...))...)))))))))))).	1.000 -15.60

rat

chromosome:4:164252973:164253011:1

intergenic

block1767204 [novel_lenNOK_shortStem_5varHIGH_loopOverlap]

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

0.017

no

no

0.26/0.32

19/23/0.67

1.2

2.5

6

0

2

0

3

-6

3arm_loop

1

nd

0.22

2

6

2

na

na

		reads	miRBase family seed
seed	------------------------------CUCAUCU------------------	3	novel
seed	---------------------------UUCCUCA---------------------	2	novel
seed	-----------------------------CCUCAUC-------------------	1	novel
		len	cloning frequencies
			T4S2	T5S1
	-----------------------------CCTCATCTGAAATTTTTTAAAGT---	23	-	3
	--------------------------CTTCCTCATCTGAAATTTT----------	19	1	1
	----------------------------TCCTCATCTGAAATTTTTTAAAG----	23	-	1
rat	attaatttaacatagtgttcagatgtCTTCCTCATCTGAAATTTTTTAAAGTaat
	*******************************************************
rat	((((.(((((...(((.((((((((.......)))))))))))..))))).))))	0.990 -9.90

rat

chromosome:5:114562945:114562999:-1

intergenic

block2172187 [novel_lenNOK_shortStem_5varHIGH_loopOverlap]

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

0.665

no

no

0.68/0.75

19/20/0.50

2.0

1.5

2

0

2

0

1

-5

3arm

2

nd

0.16

2

2

2

na

na

		reads	miRBase family seed
seed	------------------------------------------CCGAGCG------------	1	novel
seed	--------------------------------------CCGACCG----------------	1	novel
		len	cloning frequencies
			T1S2	T2S1
	-------------------------------------ACCGACCGAGCGCACCGACC----	20	1	-
	-----------------------------------------ACCGAGCGCACCGACCATG-	19	-	1
rat	ctattggttcatgcaaaaaataagaatgagggcacggACCGACCGAGCGCACCGACCATGg
	*************************************************************
rat	(((.(((((..(((.................((.(((.....))).)))))..))))))))	0.470 -11.02

rat

chromosome:7:139657967:139658027:-1

intergenic

block2251707 [novel_lenNOK_shortStem_5varHIGH_loopOverlap]

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

0.319

no

no

0.36/0.48

25/25/0.00

4.5

4.5

2

0

1

0

2

-23

3arm

1

nd

0.20

2

2

1

na

na

		reads	miRBase family seed
seed	-----------------------------------------AUCCUUG-------------------	1	novel
seed	--------------------------------ACCUAAC----------------------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------------------------TATCCTTGAATGTCAGCCCTGTGTG--	25	1
	-------------------------------TACCTAACATATCCTTGAATGTCAG-----------	25	1
rat	gcccagaggtgccttttcagtggctcaggcaTACCTAACATATCCTTGAATGTCAGCCCTGTGTGgc
	*******************************************************************
rat	(((((.(((.((........(((((((((.(((.......))).)))))..))))))))).)).)))	0.520 -17.30

rat

chromosome:7:116639271:116639337:1

intergenic

block2473919 [novel_lenNOK_shortStem_5varHIGH_loopOverlap]

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

0.302

no

no

0.63/0.68

19/22/0.67

1.7

0.0

3

0

2

0

3

-4

3arm

1

nd

0.21

3

3

2

na

na

		reads	miRBase family seed
seed	--------------------------------------------UCCGGCU--------------	1	novel
seed	-----------------------------------------CGUUCCG-----------------	1	novel
seed	-------------------------------------------UUCCGGC---------------	1	novel
		len	cloning frequencies
			T3S1	T5S2
	-------------------------------------------TTCCGGCTGGTCCTACCTC---	19	1	-
	----------------------------------------GCGTTCCGGCTGGTCCTACCTC---	22	-	1
	------------------------------------------GTTCCGGCTGGTCCTACCTC---	20	1	-
rat	ggacgtcaattggggccaaacatccgggtttctcacttttGCGTTCCGGCTGGTCCTACCTCgcc
	*****************************************************************
	.........................................................>>>>>>>>>>>>>>>>>>	ENSRNOT00000025769 ENSRNOG00000018998 Yipf3
rat	((.((.....((((((((.....(((((................))))).))))))))...))))	0.880 -17.69

rat

chromosome:9:10298156:10298220:-1

Same_strand|Boundary_non-coding|ENSRNOT00000025769|ENSRNOG00000018998 ## ENSRNOG00000018998|protein_coding|Yipf3|Protein YIPF3 (YIP1 family member 3) (Liver regeneration-related protein LRRGT00110). [Source:UniProtKB/Swiss-Prot;Acc:Q6TUD4]

block1060869 [novel_lenNOK_shortStem_5varHIGH_loopOverlap]

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

0.068

no

no

0.40/0.58

18/25/0.33

8.3

5.2

6

0

3

0

4

-19

3arm

1

nd

0.21

2

6

3

na

na

		reads	miRBase family seed
seed	-----------------------------------------------ACAAUGA--------------------	2	novel
seed	---------------------------------GACGCGA----------------------------------	2	novel
seed	------------------------------------------GCAUUAC-------------------------	1	novel
seed	----------------------------------------------UACAAUG---------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T5S1
	--------------------------------TGACGCGAAAGCATTACAATGAGAG-----------------	25	1	1	-
	----------------------------------------------TACAATGAGAGCTTCCCG----------	18	-	-	1
	----------------------------------------------TACAATGAGAGCTTCCCGCCCCCA----	24	-	-	1
	---------------------------------------------TTACAATGAGAGCTTCCCG----------	19	1	-	-
	-----------------------------------------AGCATTACAATGAGAGCTTC-------------	20	-	-	1
rat	ctgaggggaggtgacatatggcaggccatctgTGACGCGAAAGCATTACAATGAGAGCTTCCCGCCCCCAttgg
	**************************************************************************
rat	((((.(((.((((......((.((((..(((((((.((....)).)))))..))..))))))))))))).))))	0.710 -25.80

rat

chromosome:20:5519700:5519773:-1

intergenic

block1695800 [novel_lenNOK_shortStem_5varHIGH_loopOverlap]

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

0.110

no

no

0.50/0.65

18/22/0.30

1.2

1.8

8

0

1

0

4

-6

5arm_loop_3arm

1

nd

0.17

2

10

1

na

na

		reads	miRBase family seed
seed	-----UGAAUGG--------------------------------------------	6	novel
seed	----------GGCGAUA---------------------------------------	3	novel
seed	------GAAUGGC-------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----TTGAATGGCGATACCCAG----------------------------------	18	6
	---------TGGCGATACCCAGCACCCAG---------------------------	20	2
	-----TGAATGGCGATACCCAGCACCC-----------------------------	22	1
	---------TGGCGATACCCAGCACCCA----------------------------	19	1
rat	ggtaTTGAATGGCGATACCCAGCACCCAGcctgtctatgagccacttcagagtgcc
	********************************************************
rat	(((((((((((((.(((..((((.....)).))..)))..)))).))))..)))))	1.000 -15.80

rat

chromosome:4:164247283:164247338:1

intergenic

novel_lenNOK_Multihit_loopOverlap_bulgeHIGH (21 loci)

block396457 [novel_lenNOK_Multihit_loopOverlap_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

no

0.182

no

no

0.53/0.53

19/19/0.00

0.0

0.0

1

0

1

0

20

-3

5arm_loop

37

nd

0.26

4

1

1

na

na

		reads	miRBase family seed
seed	---------------------AGGACAC--------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	--------------------CAGGACACGGTGTGTTACT---------------------------------------------	19	1
rat	gacactgtgtgttactcctaCAGGACACGGTGTGTTACTccctacaggacactgtgtgttactccttacaggacattgtgtgtt
	************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000041793 ENSRNOG00000034200 Atp8a1
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000044017 ENSRNOG00000034200 Atp8a1
rat	(((((...(((....((((..((((((((((((.((.........)).))))))))......))))...)))))))...)))))	0.720 -21.60

rat

chromosome:14:42971884:42971967:1

Same_strand|Intronic_coding|ENSRNOT00000041793|ENSRNOG00000034200 ## ENSRNOG00000034200|protein_coding|Atp8a1|ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1 Gene [Source:MGI (curated);Acc:Atp8a1-001] ## {Repeats: trf 93 112 0 class=trf}

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other hairpins:

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