miR-Intess™

other hairpins

novel_Multihit_loopOverlap_randfoldOK (36 loci)

block155450 [novel_Multihit_loopOverlap_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

0.46/0.46

24/24/1.00

0.0

0.0

1

0

1

0

33

-2

3arm_loop

158

nd

0.12

1

1

1

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------GGAAUAC-------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------------------------------------------AGGAATACATGGTAGCCAGTGTGT---------------------------------	24	1
rat	acgggaatacatggcagccagtgtgttcacgggaatacatggtagccagtgtgttcacAGGAATACATGGTAGCCAGTGTGTtcacgggaatacatggtagccagtgtgttcacg
	*******************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000051546 ENSRNOG00000032380
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042801 ENSRNOG00000028216 LOC304000
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000032566 ENSRNOG00000028216 LOC304000
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000032555 ENSRNOG00000028216 LOC304000
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042063 ENSRNOG00000028216 LOC304000
rat	.((.(((((((((((.((((.(((((((.((.(((((((((((.((((.(((((((....))))))))))).)))).))))))).)).))))))))))).)))).))))))).))	1.000 -58.80

rat

chromosome:11:36739485:36739599:1

Same_strand|Intronic_coding|ENSRNOT00000042801|ENSRNOG00000028216 ## Opposite_strand|Intronic_coding|ENSRNOT00000051546|ENSRNOG00000032380 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000043924|ENSRNOG00000032380 ## ENSRNOG00000028216|protein_coding|LOC304000|immunoglobulin superfamily, member 5 [Source:RefSeq_peptide;Acc:NP_001006991] ## ENSRNOG00000032380|protein_coding|| ## {Repeats: trf 4389 4413 0 class=trf}

block155451 [novel_Multihit_loopOverlap_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

0.46/0.46

24/24/1.00

0.0

0.0

1

0

1

0

33

-2

3arm_loop

158

nd

0.12

1

1

1

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------GGAAUAC-------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------------------------------------------AGGAATACATGGTAGCCAGTGTGT---------------------------------	24	1
rat	acgggaatacatggtagccagtgtgttcacgggaatacatggtagccagtgtgttcacAGGAATACATGGTAGCCAGTGTGTtcacgggaatacatggcagccagtgtgttcacg
	*******************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000051546 ENSRNOG00000032380
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042801 ENSRNOG00000028216 LOC304000
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000032566 ENSRNOG00000028216 LOC304000
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000032555 ENSRNOG00000028216 LOC304000
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042063 ENSRNOG00000028216 LOC304000
rat	.((.(((((((((((.((((.(((((((.((.(((((((((((.((((.(((((((....))))))))))).)))).))))))).)).))))))))))).)))).))))))).))	1.000 -58.80

rat

chromosome:11:36739569:36739683:1

Same_strand|Intronic_coding|ENSRNOT00000042801|ENSRNOG00000028216 ## Opposite_strand|Intronic_coding|ENSRNOT00000051546|ENSRNOG00000032380 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000043924|ENSRNOG00000032380 ## ENSRNOG00000028216|protein_coding|LOC304000|immunoglobulin superfamily, member 5 [Source:RefSeq_peptide;Acc:NP_001006991] ## ENSRNOG00000032380|protein_coding|| ## {Repeats: trf 4305 4329 0 class=trf}

block155511 [novel_Multihit_loopOverlap_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

0.46/0.46

24/24/1.00

0.0

0.0

2

0

1

0

36

-2

3arm_loop

158

nd

0.12

1

2

1

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------GGAAUAC------------------------	1	novel
seed	-------------------------------------------------------------GGAAUAC----------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	------------------------------------------------------------AGGAATACATGGTAGCCAGTGTGT------------------------------------	24	1
	----------------------------------------------------------------------------------------AGGAATACATGGTAGCCAGTGTGT--------	24	1
rat	tcacaggaatacatggcagccagtgtgttcacgggaatacatggtagccagtgtgttcacAGGAATACATGGTAGCCAGTGTGTtcacAGGAATACATGGTAGCCAGTGTGTtcacagga
	************************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000051546 ENSRNOG00000032380
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042801 ENSRNOG00000028216 LOC304000
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000032566 ENSRNOG00000028216 LOC304000
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000032555 ENSRNOG00000028216 LOC304000
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042063 ENSRNOG00000028216 LOC304000
rat	((....(((((((((((.((((.(((((((....(((((((((((.((((.(((((((....))))))))))).)))).)))))))....))))))))))).)))).)))))))....))	0.990 -56.40

rat

chromosome:11:36743123:36743242:1

Same_strand|Intronic_coding|ENSRNOT00000042801|ENSRNOG00000028216 ## Opposite_strand|Intronic_coding|ENSRNOT00000051546|ENSRNOG00000032380 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000043924|ENSRNOG00000032380 ## ENSRNOG00000028216|protein_coding|LOC304000|immunoglobulin superfamily, member 5 [Source:RefSeq_peptide;Acc:NP_001006991] ## ENSRNOG00000032380|protein_coding|| ## {Repeats: trf 721 745 0 class=trf}

block155513 [novel_Multihit_loopOverlap_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

0.46/0.46

24/24/1.00

0.0

0.0

1

0

1

0

33

-2

3arm_loop

158

nd

0.12

1

1

1

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------GGAAUAC-------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------------------------------------------AGGAATACATGGTAGCCAGTGTGT---------------------------------	24	1
rat	acgggaatacatggtagccagtgtgttcacgggaatacatggcagccagtgtgttcacAGGAATACATGGTAGCCAGTGTGTtcacgggaatacatggtagccagtgtgttcacg
	*******************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000051546 ENSRNOG00000032380
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042801 ENSRNOG00000028216 LOC304000
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000032566 ENSRNOG00000028216 LOC304000
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000032555 ENSRNOG00000028216 LOC304000
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042063 ENSRNOG00000028216 LOC304000
rat	.((.(((((((((((.((((.(((((((.((.(((((((((((.((((.(((((((....))))))))))).)))).))))))).)).))))))))))).)))).))))))).))	1.000 -58.80

rat

chromosome:11:36743377:36743491:1

Same_strand|Intronic_coding|ENSRNOT00000042801|ENSRNOG00000028216 ## Opposite_strand|Intronic_coding|ENSRNOT00000051546|ENSRNOG00000032380 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000043924|ENSRNOG00000032380 ## ENSRNOG00000028216|protein_coding|LOC304000|immunoglobulin superfamily, member 5 [Source:RefSeq_peptide;Acc:NP_001006991] ## ENSRNOG00000032380|protein_coding|| ## {Repeats: trf 497 521 0 class=trf}

block155515 [novel_Multihit_loopOverlap_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

0.46/0.46

24/24/1.00

0.0

0.0

1

0

1

0

33

-2

3arm_loop

158

nd

0.12

1

1

1

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------GGAAUAC-------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------------------------------------------AGGAATACATGGTAGCCAGTGTGT---------------------------------	24	1
rat	acgggaatacatggcagccagtgtgttcacgggaatacatggtagccagtgtgttcacAGGAATACATGGTAGCCAGTGTGTtcacgggaatacatggtagccagtgtgttcacg
	*******************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000051546 ENSRNOG00000032380
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042801 ENSRNOG00000028216 LOC304000
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000032566 ENSRNOG00000028216 LOC304000
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000032555 ENSRNOG00000028216 LOC304000
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042063 ENSRNOG00000028216 LOC304000
rat	.((.(((((((((((.((((.(((((((.((.(((((((((((.((((.(((((((....))))))))))).)))).))))))).)).))))))))))).)))).))))))).))	1.000 -58.80

rat

chromosome:11:36743573:36743687:1

Same_strand|Intronic_coding|ENSRNOT00000042801|ENSRNOG00000028216 ## Opposite_strand|Intronic_coding|ENSRNOT00000051546|ENSRNOG00000032380 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000043924|ENSRNOG00000032380 ## ENSRNOG00000028216|protein_coding|LOC304000|immunoglobulin superfamily, member 5 [Source:RefSeq_peptide;Acc:NP_001006991] ## ENSRNOG00000032380|protein_coding|| ## {Repeats: trf 301 325 0 class=trf}

block155516 [novel_Multihit_loopOverlap_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

0.46/0.46

24/24/1.00

0.0

0.0

1

0

1

0

33

-2

3arm_loop

158

nd

0.12

1

1

1

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------GGAAUAC-------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------------------------------------------AGGAATACATGGTAGCCAGTGTGT---------------------------------	24	1
rat	acgggaatacatggtagccagtgtgttcacgggaatacatggtagccagtgtgttcacAGGAATACATGGTAGCCAGTGTGTtcacgggaatacatggcagccagtgtgttcacg
	*******************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000051546 ENSRNOG00000032380
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042801 ENSRNOG00000028216 LOC304000
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000032566 ENSRNOG00000028216 LOC304000
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000032555 ENSRNOG00000028216 LOC304000
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042063 ENSRNOG00000028216 LOC304000
rat	.((.(((((((((((.((((.(((((((.((.(((((((((((.((((.(((((((....))))))))))).)))).))))))).)).))))))))))).)))).))))))).))	1.000 -58.80

rat

chromosome:11:36743657:36743771:1

Same_strand|Intronic_coding|ENSRNOT00000042801|ENSRNOG00000028216 ## Opposite_strand|Intronic_coding|ENSRNOT00000051546|ENSRNOG00000032380 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000043924|ENSRNOG00000032380 ## ENSRNOG00000028216|protein_coding|LOC304000|immunoglobulin superfamily, member 5 [Source:RefSeq_peptide;Acc:NP_001006991] ## ENSRNOG00000032380|protein_coding|| ## {Repeats: trf 217 241 0 class=trf}

block846089 [novel_Multihit_loopOverlap_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

0.008

no

no

0.64/0.64

22/22/1.00

0.0

0.0

1

0

1

0

19

-3

3arm_loop

46

nd

0.27

2

1

1

na

na

		reads	miRBase family seed
seed	---------------------------------CUGGGAG---------------------------------	1	novel
		len	cloning frequencies
			T3S1
	--------------------------------GCTGGGAGTTAGGCTGGATGCC-------------------	22	1
rat	gggctcatccacaggcatctcacactctccctGCTGGGAGTTAGGCTGGATGCCtgctgtgtgggagctgcct
	*************************************************************************
	-----------------------------------------------------------------------------------	ENSRNOT00000059954 ENSRNOG00000039180
	-----------------------------------------------------------------------------------	ENSRNOT00000059953 ENSRNOG00000039180
rat	.(((((...((((((((((.((..(((((((....)))))..))..)))))))))).)).....)))))....	0.470 -32.50

rat

chromosome:1:50930944:50931016:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000059955|ENSRNOG00000039180 ## Opposite_strand|Intronic_coding|ENSRNOT00000059954|ENSRNOG00000039180 ## ENSRNOG00000039180|protein_coding||

novel_lenNOK_cloningOK_shortStem_randfoldOK (36 loci)

block1390 [novel_lenNOK_cloningOK_shortStem_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

0.61/0.63

18/19/0.00

0.0

0.0

11

0

6

0

1

12

3arm

1

nd

0.11

2

20

6

na

na

		reads	miRBase family seed
seed	-------------------------------------------------------ACAGCUC------------	20	miR-674
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S2	T4S1
	------------------------------------------------------CACAGCTCCCATCCTGAGG-	19	8	2	3	2	1	2
	------------------------------------------------------CACAGCTCCCATCCTGAG--	18	1	-	1	-	-	-
rat	agcctccaggatggggagaaaaaggtgttaaaatgaagcctccttctgaaagggCACAGCTCCCATCCTGAGGc
	**************************************************************************
rat	.((((.((((((.(((((......(((((.....((((....))))......)))))..)))))))))))))))	0.800 -31.70

rat

chromosome:10:2825686:2825759:-1

intergenic

block43659 [novel_lenNOK_cloningOK_shortStem_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

0.39/0.46

18/24/0.65

0.1

0.6

14

0

3

0

4

19

3arm

1

nd

0.22

2

23

3

na

na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------UAGAUGA-----------------	18	novel
seed	-------------------------------------------------------------------------GUAGAUG------------------	5	novel
		len	cloning frequencies
			T1S1	T3S1	T3S2
	-------------------------------------------------------------------------GTAGATGATGATGAGAGCTGA----	21	1	4	5
	-------------------------------------------------------------------------GTAGATGATGATGAGAGC-------	18	-	3	1
	------------------------------------------------------------------------AGTAGATGATGATGAGAGC-------	19	-	1	1
	------------------------------------------------------------------------AGTAGATGATGATGAGAGCTGA----	22	-	2	-
	------------------------------------------------------------------------AGTAGATGATGATGAGAG--------	18	-	1	-
	-------------------------------------------------------------------------GTAGATGATGATGAGAGCTGATGC-	24	-	1	-
	-------------------------------------------------------------------------GTAGATGATGATGAGAGCTGAT---	22	-	1	-
	-------------------------------------------------------------------------GTAGATGATGATGAGAGCTG-----	20	-	1	-
	-------------------------------------------------------------------------GTAGATGATGATGAGAGCT------	19	-	-	1
rat	gctgctctcagtcatcccacagtgagaactgggaaggcaggctgagtacaggtgcgagcctcccagtcctcgAGTAGATGATGATGAGAGCTGAtgct
	**************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000055176 ENSRNOG00000002818 Eftud2
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000003807 ENSRNOG00000002818 Eftud2
rat	((.(((((((((((((..((..((((.((((((.((((..((...........))..)))))))))).)))).)).))))))..)))))))....)).	1.000 -43.10

rat

chromosome:10:92041937:92042034:-1

Same_strand|Intronic_coding|ENSRNOT00000003807|ENSRNOG00000002818 ## ENSRNOG00000002818|protein_coding|Eftud2|Eftud2 protein (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q5EB83]

block48720 [novel_lenNOK_cloningOK_shortStem_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

0.72/0.74

18/19/0.00

0.0

0.2

27

0

8

0

1

34

5arm

1

nd

0.16

3

43

8

na

na

		reads	miRBase family seed
seed	--GGCUCAG------------------------------------------------------------------------------------------------------	43	miR-24
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S1	T4S1	T4S2	T5S1	T5S2
	-TGGCTCAGCCTGCCAGGG--------------------------------------------------------------------------------------------	18	1	-	1	1	5	16	2	3
	-TGGCTCAGCCTGCCAGGGG-------------------------------------------------------------------------------------------	19	2	1	-	-	2	6	3	-
rat	cTGGCTCAGCCTGCCAGGGGacatttcatgggtgggagaatgagttaagctcctgccacttgaggatgccttatctacacctgtgaactcccctcttctgggtttgagcta
	***************************************************************************************************************
rat	.(((((((((((...((((((...((((((((((..((.(((((....((((((........)))).))))))))).)))))))))).)))))).....))))).))))))	0.980 -45.20

rat

chromosome:10:102627295:102627405:-1

intergenic

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other hairpins:

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