miR-Intess™

other hairpins

novel_multiarm_DicerNOK_Multihit_nonpairedHIGH (16 loci)

sblock3018 [novel_multiarm_DicerNOK_Multihit_nonpairedHIGH]

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

0.011

no

no

0.52/0.55

20/21/1.00

0.0 0.0

0.0 0.0

2 2

0 0

1 1

0 0

30 9

8 25

5arm 3arm

455 455

nd nd

0.50 0.38

4 3

4

2

0

-2

		reads	miRBase family seed
seed	----------------------------------------------------------------------------------------GGGGUUG----------------------	2	novel
seed	-------------------------------AGCAGAC-------------------------------------------------------------------------------	1	novel
seed	--------------------------------------------------------------------AGCAGAC------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T4S1
	---------------------------------------------------------------------------------------TGGGGTTGGTAACAATGGAGC---------	21	2	-
	------------------------------GAGCAGACTGCAGGAGATGA-------------------------------------------------------------------	20	-	1
	-------------------------------------------------------------------GAGCAGACTGCAGGAGATGA------------------------------	20	-	1
rat	ctgcaggagatgacggggttggtaacaatgGAGCAGACTGCAGGAGATGAcggggttggtaacaatgGAGCAGACTGCAGGAGATGATGGGGTTGGTAACAATGGAGCagactgcag
	*********************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000058274 ENSRNOG00000001764 RGD1309443_predicted
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000029255 ENSRNOG00000001764 RGD1309443_predicted
rat	((((((....((.((..((((.((((..((...((..((((((....((.....((((....))))....))..))))))....)).))..)))).))))..))...))..))))))	1.000 -32.50

rat

chromosome:11:81738791:81738907:-1

Same_strand|Boundary_non-coding|ENSRNOT00000058276|ENSRNOG00000001764 ## Same_strand|Intronic_coding|ENSRNOT00000029255|ENSRNOG00000001764 ## ENSRNOG00000001764|protein_coding|RGD1309443_predicted| ## {Repeats: trf 8071 8092 0 class=trf,trf 8034 8055 0 class=trf,trf 8092 8112 0 class=trf,trf 7886 7907 0 class=trf,trf 7812 7833 0 class=trf,trf 8166 8186 0 class=trf,trf 7944 7964 0 class=trf,trf 8129 8149 0 class=trf,trf 7870 7890 0 class=trf,trf 7981 8001 0 class=trf,trf 8203 8223 0 class=trf,trf 7960 7981 0 class=trf,trf 7923 7944 0 class=trf,trf 8055 8075 0 class=trf,trf 7907 7927 0 class=trf}

sblock3021 [novel_multiarm_DicerNOK_Multihit_nonpairedHIGH]

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

0.201

no

no

0.52/0.55

20/21/1.00

0.0 0.0

0.0 0.0

2 2

0 0

1 1

0 0

5 24

28 1

5arm 3arm

455 455

nd nd

0.35 0.33

4 3

4

2

0

-2

		reads	miRBase family seed
seed	---------------------------------------------------------------GGGGUUG-------------------------------------	2	novel
seed	--------------------------------------------------------------------------------AGCAGAC--------------------	1	novel
seed	------AGCAGAC----------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T4S1
	--------------------------------------------------------------TGGGGTTGGTAACAATGGAGC------------------------	21	2	-
	-----GAGCAGACTGCAGGAGATGA----------------------------------------------------------------------------------	20	-	1
	-------------------------------------------------------------------------------GAGCAGACTGCAGGAGATGA--------	20	-	1
rat	taatgGAGCAGACTGCAGGAGATGAcggggttggtaacaatggagcagactgcaggagatggTGGGGTTGGTAACAATGGAGCAGACTGCAGGAGATGActgagtta
	***********************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000058274 ENSRNOG00000001764 RGD1309443_predicted
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000029255 ENSRNOG00000001764 RGD1309443_predicted
rat	((((..((((..((((((....((.((..((((.((((...........((((........)))).)))).))))..))...))..))))))....)).))..))))	0.420 -23.00

rat

chromosome:11:81740922:81741028:-1

Same_strand|Boundary_non-coding|ENSRNOT00000058276|ENSRNOG00000001764 ## Same_strand|Intronic_coding|ENSRNOT00000029255|ENSRNOG00000001764 ## ENSRNOG00000001764|protein_coding|RGD1309443_predicted| ## {Repeats: trf 10016 10036 0 class=trf,trf 10217 10238 0 class=trf,trf 10164 10184 0 class=trf,trf 10053 10073 0 class=trf,trf 10127 10147 0 class=trf,trf 10090 10110 0 class=trf,trf 10201 10221 0 class=trf}

sblock3028 [novel_multiarm_DicerNOK_Multihit_nonpairedHIGH]

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

0.016

no

no

0.52/0.55

20/21/1.00

0.0 0.0

0.0 0.0

2 2

0 0

1 1

0 0

30 10

8 25

5arm 3arm

455 455

nd nd

0.50 0.38

4 3

4

2

0

-2

		reads	miRBase family seed
seed	----------------------------------------------------------------------------------------GGGGUUG-----------------------	2	novel
seed	-------------------------------AGCAGAC--------------------------------------------------------------------------------	1	novel
seed	--------------------------------------------------------------------AGCAGAC-------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T4S1
	---------------------------------------------------------------------------------------TGGGGTTGGTAACAATGGAGC----------	21	2	-
	-------------------------------------------------------------------GAGCAGACTGCAGGAGATGA-------------------------------	20	-	1
	------------------------------GAGCAGACTGCAGGAGATGA--------------------------------------------------------------------	20	-	1
rat	ctgcaggagatgacggngttagtaataatgGAGCAGACTGCAGGAGATGAcggagttagtaataatgGAGCAGACTGCAGGAGATGATGGGGTTGGTAACAATGGAGCagactgcagg
	**********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000058274 ENSRNOG00000001764 RGD1309443_predicted
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000029255 ENSRNOG00000001764 RGD1309443_predicted
rat	((((((....((.((..((((.((((..((...((..((((((....((.....((((....))))....))..))))))....)).))..)))).))))..))...))..)))))).	0.900 -29.50

rat

chromosome:11:81743222:81743339:-1

Same_strand|Boundary_non-coding|ENSRNOT00000058276|ENSRNOG00000001764 ## Same_strand|Intronic_coding|ENSRNOT00000029255|ENSRNOG00000001764 ## ENSRNOG00000001764|protein_coding|RGD1309443_predicted| ## {Repeats: trf 12746 12766 0 class=trf,trf 12635 12655 0 class=trf,trf 12561 12581 0 class=trf,trf 13042 13062 0 class=trf,trf 12968 12988 0 class=trf,trf 12857 12877 0 class=trf,trf 12672 12692 0 class=trf,trf 12894 12914 0 class=trf,trf 12783 12803 0 class=trf,trf 12503 12524 0 class=trf,trf 13005 13025 0 class=trf,trf 12709 12729 0 class=trf,trf 12598 12618 0 class=trf,trf 12524 12544 0 class=trf,trf 12820 12840 0 class=trf}

sblock3030 [novel_multiarm_DicerNOK_Multihit_nonpairedHIGH]

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

0.015

no

no

0.52/0.55

20/21/1.00

0.0 0.0

0.0 0.0

2 2

0 0

1 1

0 0

30 10

8 25

5arm 3arm

455 455

nd nd

0.50 0.38

4 3

4

2

0

-2

		reads	miRBase family seed
seed	----------------------------------------------------------------------------------------GGGGUUG-----------------------	2	novel
seed	-------------------------------AGCAGAC--------------------------------------------------------------------------------	1	novel
seed	--------------------------------------------------------------------AGCAGAC-------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T4S1
	---------------------------------------------------------------------------------------TGGGGTTGGTAACAATGGAGC----------	21	2	-
	-------------------------------------------------------------------GAGCAGACTGCAGGAGATGA-------------------------------	20	-	1
	------------------------------GAGCAGACTGCAGGAGATGA--------------------------------------------------------------------	20	-	1
rat	ctgcaggagatgactgagttagtaacaatgGAGCAGACTGCAGGAGATGAcagagttagtaataatgGAGCAGACTGCAGGAGATGATGGGGTTGGTAACAATGGAGCagactgcagg
	**********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000058274 ENSRNOG00000001764 RGD1309443_predicted
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000029255 ENSRNOG00000001764 RGD1309443_predicted
rat	((((((....((.((..((((.((((..((...((..((((((....((.....((((....))))....))..))))))....)).))..)))).))))...))..))..)))))).	0.960 -31.00

rat

chromosome:11:81745145:81745262:-1

Same_strand|Boundary_non-coding|ENSRNOT00000058276|ENSRNOG00000001764 ## Same_strand|Intronic_coding|ENSRNOT00000029255|ENSRNOG00000001764 ## ENSRNOG00000001764|protein_coding|RGD1309443_predicted| ## {Repeats: trf 14114 14134 0 class=trf,trf 14410 14430 0 class=trf,trf 14521 14541 0 class=trf,trf 13929 13949 0 class=trf,trf 14299 14319 0 class=trf,trf 14003 14023 0 class=trf,trf 14336 14356 0 class=trf,trf 13966 13986 0 class=trf,trf 14373 14393 0 class=trf,trf 14077 14097 0 class=trf,trf 14225 14245 0 class=trf,trf 14188 14208 0 class=trf,trf 14447 14467 0 class=trf,trf 13892 13912 0 class=trf,trf 14484 14504 0 class=trf,trf 14426 14447 0 class=trf,trf 14262 14282 0 class=trf,trf 13818 13838 0 class=trf,trf 13855 13875 0 class=trf,trf 14151 14171 0 class=trf,trf 14040 14060 0 class=trf}

sblock3856 [novel_multiarm_DicerNOK_Multihit_nonpairedHIGH]

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

0.224

no

no

0.36/0.55

20/22/1.00

0.0 0.0

0.0 0.0

2 1

0 0

1 1

0 0

16 16

25 17

5arm 3arm

48 153

nd nd

0.35 0.32

5 3

3

2

-6

-1

		reads	miRBase family seed
seed	-----------------ACCAGGU------------------------------------------------------------------------------------------------	2	novel
seed	-----------------------------------------------------------------------------------UGCUCUC------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S1
	----------------GACCAGGTTGTCTCCTGTGA------------------------------------------------------------------------------------	20	-	2
	----------------------------------------------------------------------------------TTGCTCTCAATGACAACTTTGT----------------	22	1	-
rat	cctgggctacactgagGACCAGGTTGTCTCCTGTGActtcaacagcagctctcactcttcacctttgatgctggggctggcaTTGCTCTCAATGACAACTTTGTaaaactcatttcctgg
	************************************************************************************************************************
rat	.(((((......((((.((.((((((((.....(((...(((...((((.((((....(((....)))...))))))))...)))...)))..)))))))).))....))))...)))))	0.420 -29.30

rat

chromosome:13:43443729:43443848:1

intergenic

sblock472 [novel_multiarm_DicerNOK_Multihit_nonpairedHIGH]

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

0.484

no

no

0.35/0.40

20/20/1.00

0.0 0.0

0.0 0.0

1 1

0 0

1 1

0 0

23 10

12 25

5arm 3arm

7 41

nd nd

0.35 0.35

3 4

2

2

8

7

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------GAUAAAC----------------------	1	novel
seed	------------------------GGAAGAU---------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	-----------------------TGGAAGATTTCATGAGCTCA---------------------------------------------------------------------------	20	1	-
	----------------------------------------------------------------------------------------TGATAAACTTCAGGTGAATG----------	20	-	1
rat	tgtgtgctaggaccactaacctaTGGAAGATTTCATGAGCTCAtaccactctgcacctcactttgtggaagctggtgtttttagaatgTGATAAACTTCAGGTGAATGgatgcattca
	**********************************************************************************************************************
	--------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000041486 ENSRNOG00000033456 LOC308198
rat	((.((((.....(((...((((...((((...(((((..((.(((((((((((((........))))).)).))))))....))..)))))....))))))))...)))..)))).))	0.910 -26.50

rat

chromosome:1:52396195:52396312:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000044415|ENSRNOG00000033456 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000041486|ENSRNOG00000033456 ## ENSRNOG00000033456|protein_coding|LOC308198|

sblock7838 [novel_multiarm_DicerNOK_Multihit_nonpairedHIGH]

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

0.36/0.55

20/22/1.00

0.0 0.0

0.0 0.0

2 1

0 0

1 1

0 0

4 8

25 17

5arm 3arm

48 153

nd nd

0.35 0.32

5 3

3

2

-6

-1

		reads	miRBase family seed
seed	-----ACCAGGU----------------------------------------------------------------------------------------	2	novel
seed	-----------------------------------------------------------------------UGCUCUC----------------------	1	novel
		len	cloning frequencies
			T1S2	T2S1
	----GACCAGGTTGTCTCCTGTGA----------------------------------------------------------------------------	20	-	2
	----------------------------------------------------------------------TTGCTCTCAATGACAACTTTGT--------	22	1	-
rat	tgagGACCAGGTTGTCTCCTGTGActtcaacagcagctctcactcttcacctttgatgctggggctggcaTTGCTCTCAATGACAACTTTGTaaaattca
	****************************************************************************************************
rat	.(((.((.((((((((.....(((...(((...((((.((((....(((....)))...))))))))...)))...)))..)))))))).))....))).	0.420 -23.80

rat

chromosome:3:9272009:9272108:1

intergenic

novel_shortStem_5varHIGH_nonpairedHIGH_bulgeHIGH (16 loci)

block385485 [novel_shortStem_5varHIGH_nonpairedHIGH_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

0.558

no

no

0.62/0.75

20/24/1.00

2.6

1.0

5

0

2

0

2

21

5arm

1

nd

0.42

5

5

2

na

na

		reads	miRBase family seed
seed	---CGGCCCU-------------------------------------------------------------------------------------------------	2	novel
seed	------CCCUCGG----------------------------------------------------------------------------------------------	1	novel
seed	-------CCUCGGG---------------------------------------------------------------------------------------------	1	novel
seed	---------UCGGGGU-------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T3S2
	--CCGGCCCTCGGGGTTGTGAGCGTG---------------------------------------------------------------------------------	24	2	-
	-----GCCCTCGGGGTTGTGAGCGTGTG-------------------------------------------------------------------------------	23	-	1
	--------CTCGGGGTTGTGAGCGTGTGT------------------------------------------------------------------------------	21	-	1
	------CCCTCGGGGTTGTGAGCGTG---------------------------------------------------------------------------------	20	1	-
rat	ccCCGGCCCTCGGGGTTGTGAGCGTGTGTgaattagagcgaaggcaccgaaagctcgcgtctctcttctctccctgtctttctctctctgctcggccccggcctcgg
	***********************************************************************************************************
rat	((..((((...(((((((.(((.......((....(((.(((((.(((((....))).))...))))).)))....)).......)))....)))))))))))..))	0.940 -32.54

rat

chromosome:14:14923870:14923976:1

intergenic ## {SimpF: oe = 0.90 0 CpG}

block728877 [novel_shortStem_5varHIGH_nonpairedHIGH_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

0.152

no

no

0.45/0.48

21/22/1.00

1.5

1.0

2

0

2

0

4

12

5arm

2

nd

0.50

4

2

2

na

na

		reads	miRBase family seed
seed	--------UCCGGAA-------------------------------------------------------------	1	novel
seed	-----ACAUCCG----------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S2	T4S1
	-------ATCCGGAACATGTCAGTCATC------------------------------------------------	21	1	-
	----AACATCCGGAACATGTCAGTCA--------------------------------------------------	22	-	1
rat	agccAACATCCGGAACATGTCAGTCATCgctcacgtggaccacagtaagtccacgctgaccgactcccttgtgtgc
	****************************************************************************
rat	.((..(((...(((....(((((..........(((((((........))))))))))))....)))..)))..))	0.770 -20.20

rat

chromosome:18:12706539:12706614:1

intergenic

block818778 [novel_shortStem_5varHIGH_nonpairedHIGH_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

0.387

no

no

0.58/0.67

21/24/1.00

4.0

2.5

2

0

2

0

4

2

5arm

1

nd

0.33

4

2

2

na

na

		reads	miRBase family seed
seed	-------------GACCCUC------------------------------------------------------------	1	novel
seed	-----UCAGCAG--------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S1	T5S1
	------------TGACCCTCACCTCCAGCCCTG-----------------------------------------------	21	-	1
	----ATCAGCAGTGACCCTCACCTCCAG----------------------------------------------------	24	1	-
rat	tcccATCAGCAGTGACCCTCACCTCCAGCCCTGtgcccatcgatcacggcagctgtggccccggtctccagctcccagga
	********************************************************************************
	------------------------------------------------------------------------------------------	ENSRNOT00000018145 ENSRNOG00000013376 Mvd
rat	(((....(((...((((....((..((((.(((((.........)))))..)))).))....))))....)))....)))	0.880 -20.20

rat

chromosome:19:52731895:52731974:1

Opposite_strand|Intronic_coding|ENSRNOT00000018145|ENSRNOG00000013376 ## ENSRNOG00000013376|protein_coding|Mvd|Diphosphomevalonate decarboxylase (EC 4.1.1.33) (Mevalonate pyrophosphate decarboxylase) (Mevalonate (diphospho)decarboxylase). [Source:UniProtKB/Swiss-Prot;Acc:Q62967]

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other hairpins:

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