miR-Intess™

other hairpins

novel_multiarm_DicerNOK_Multihit_loopOverlap_nonpairedHIGH_bulgeHIGH (10 loci)

miRNAunknown_lenNOK_Multihit_loopOverlap_nonpairedHIGH (9 loci)

block73558 (miRNA) [miRNAunknown_lenNOK_Multihit_loopOverlap_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

Ensembl miRNA

0.025

no

no

0.74/0.74

19/19/0.00

0.0

0.0

1

0

1

0

9

-2

5arm_loop

11

nd

0.32

3

1

1

na

na

		reads	miRBase family seed
seed	----------GCAGGGC----------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	---------GGCAGGGCCACAACCAGCG-----------------------------	19	1
rat	ccgtagggtGGCAGGGCCACAACCAGCGcagactggcgtggcccaggcatctctggg
	*********************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000038803 ENSRNOG00000032593
	...........>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000054440 ENSRNOG00000036318
rat	((.(((((..((.(((((((..((((......)))).)))))))..))..)))))))	1.000 -27.70

rat

chromosome:10:45778212:45778268:1

Same_strand|Exonic_coding|ENSRNOT00000038803|ENSRNOG00000032593 ## Same_strand|Exonic_non-coding|ENSRNOT00000054440|ENSRNOG00000036318 ## ENSRNOG00000036318|miRNA|| ## ENSRNOG00000032593|protein_coding||

block321874 (miRNA) [miRNAunknown_lenNOK_Multihit_loopOverlap_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

Ensembl miRNA

0.025

no

no

0.74/0.74

19/19/0.00

0.0

0.0

1

0

1

0

9

-2

5arm_loop

11

nd

0.32

3

1

1

na

na

		reads	miRBase family seed
seed	----------GCAGGGC----------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	---------GGCAGGGCCACAACCAGCG-----------------------------	19	1
rat	ccgtagggtGGCAGGGCCACAACCAGCGcagactggcgtggcccaggcatctctggg
	*********************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000044575 ENSRNOG00000031540
	...........>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000054482 ENSRNOG00000036362
rat	((.(((((..((.(((((((..((((......)))).)))))))..))..)))))))	1.000 -27.70

rat

chromosome:13:86732859:86732915:1

Same_strand|Exonic_non-coding|ENSRNOT00000044575|ENSRNOG00000031540 ## ENSRNOG00000036362|miRNA|| ## ENSRNOG00000031540|pseudogene||

block615069 (miRNA) [miRNAunknown_lenNOK_Multihit_loopOverlap_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

Ensembl miRNA

0.025

no

no

0.74/0.74

19/19/0.00

0.0

0.0

1

0

1

0

9

-2

5arm_loop

11

nd

0.32

3

1

1

na

na

		reads	miRBase family seed
seed	----------GCAGGGC----------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	---------GGCAGGGCCACAACCAGCG-----------------------------	19	1
rat	ccgtagggtGGCAGGGCCACAACCAGCGcagactggcgtggcccaggcatctctggg
	*********************************************************
	...........>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000054512 ENSRNOG00000036397
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000048298 ENSRNOG00000018804 RGD1306939
rat	((.(((((..((.(((((((..((((......)))).)))))))..))..)))))))	1.000 -27.70

rat

chromosome:17:47394410:47394466:-1

Same_strand|Boundary_non-coding|ENSRNOT00000025440|ENSRNOG00000018804 ## Same_strand|Exonic_non-coding|ENSRNOT00000054512|ENSRNOG00000036397 ## Same_strand|Exonic_coding|ENSRNOT00000048298|ENSRNOG00000018804 ## ENSRNOG00000036397|miRNA|| ## ENSRNOG00000018804|protein_coding|RGD1306939|similar to mKIAA0386 protein (RGD1306939), mRNA [Source:RefSeq_dna;Acc:NM_001014009]

block868019 (miRNA) [miRNAunknown_lenNOK_Multihit_loopOverlap_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

Ensembl miRNA

0.025

no

no

0.74/0.74

19/19/0.00

0.0

0.0

1

0

1

0

9

-2

5arm_loop

11

nd

0.32

3

1

1

na

na

		reads	miRBase family seed
seed	----------GCAGGGC----------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	---------GGCAGGGCCACAACCAGCG-----------------------------	19	1
rat	ccgtagggtGGCAGGGCCACAACCAGCGcagactggcgtggcccaggcatctctggg
	*********************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000028315 ENSRNOG00000020843 LOC364392
	...........>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000054422 ENSRNOG00000036301
rat	((.(((((..((.(((((((..((((......)))).)))))))..))..)))))))	1.000 -27.70

rat

chromosome:1:95929444:95929500:-1

Same_strand|Exonic_coding|ENSRNOT00000028315|ENSRNOG00000020843 ## Same_strand|Exonic_non-coding|ENSRNOT00000054422|ENSRNOG00000036301 ## ENSRNOG00000036301|miRNA|| ## ENSRNOG00000020843|protein_coding|LOC364392|Ferritin light chain 1 (Ferritin L subunit 1). [Source:UniProtKB/Swiss-Prot;Acc:P02793]

block1005545 (miRNA) [miRNAunknown_lenNOK_Multihit_loopOverlap_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

Ensembl miRNA

0.025

no

no

0.74/0.74

19/19/0.00

0.0

0.0

1

0

1

0

9

-2

5arm_loop

11

nd

0.32

3

1

1

na

na

		reads	miRBase family seed
seed	----------GCAGGGC----------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	---------GGCAGGGCCACAACCAGCG-----------------------------	19	1
rat	ccgtagggtGGCAGGGCCACAACCAGCGcagactggcgtggcccaggcatctctggg
	*********************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000035257 ENSRNOG00000022941 LOC682465
	...........>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000054418 ENSRNOG00000036296
rat	((.(((((..((.(((((((..((((......)))).)))))))..))..)))))))	1.000 -27.70

rat

chromosome:1:146506989:146507045:1

Same_strand|Exonic_non-coding|ENSRNOT00000054418|ENSRNOG00000036296 ## Same_strand|Exonic_coding|ENSRNOT00000035257|ENSRNOG00000022941 ## ENSRNOG00000036296|miRNA|| ## ENSRNOG00000022941|protein_coding|LOC682465|

block1150311 (miRNA) [miRNAunknown_lenNOK_Multihit_loopOverlap_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

Ensembl miRNA

0.025

no

no

0.74/0.74

19/19/0.00

0.0

0.0

1

0

1

0

9

-2

5arm_loop

11

nd

0.32

3

1

1

na

na

		reads	miRBase family seed
seed	----------GCAGGGC----------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	---------GGCAGGGCCACAACCAGCG-----------------------------	19	1
rat	ccgtagggtGGCAGGGCCACAACCAGCGcagactggcgtggcccaggcatctctggg
	*********************************************************
	...........>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000054544 ENSRNOG00000036432
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000049594 ENSRNOG00000039093
rat	((.(((((..((.(((((((..((((......)))).)))))))..))..)))))))	1.000 -27.70

rat

chromosome:2:61990117:61990173:-1

Same_strand|Exonic_non-coding|ENSRNOT00000054544|ENSRNOG00000036432 ## ENSRNOG00000039093|pseudogene|| ## ENSRNOG00000036432|miRNA||

block1888094 (miRNA) [miRNAunknown_lenNOK_Multihit_loopOverlap_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

Ensembl miRNA

0.025

no

no

0.74/0.74

19/19/0.00

0.0

0.0

1

0

1

0

9

-2

5arm_loop

11

nd

0.32

3

1

1

na

na

		reads	miRBase family seed
seed	----------GCAGGGC----------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	---------GGCAGGGCCACAACCAGCG-----------------------------	19	1
rat	ccgtagggtGGCAGGGCCACAACCAGCGcagactggcgtggcccaggcatctctggg
	*********************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000044711 ENSRNOG00000031506 Ftl1
	...........>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000054579 ENSRNOG00000036471
rat	((.(((((..((.(((((((..((((......)))).)))))))..))..)))))))	1.000 -27.70

rat

chromosome:5:152846605:152846661:1

Same_strand|Exonic_coding|ENSRNOT00000044711|ENSRNOG00000031506 ## Same_strand|Exonic_non-coding|ENSRNOT00000054579|ENSRNOG00000036471 ## ENSRNOG00000036471|miRNA|| ## ENSRNOG00000031506|protein_coding|Ftl1|Ferritin light chain 1 (Ferritin L subunit 1). [Source:UniProtKB/Swiss-Prot;Acc:P02793]

block2186333 (miRNA) [miRNAunknown_lenNOK_Multihit_loopOverlap_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

Ensembl miRNA

0.025

no

no

0.74/0.74

19/19/0.00

0.0

0.0

1

0

1

0

9

-2

5arm_loop

11

nd

0.32

3

1

1

na

na

		reads	miRBase family seed
seed	----------GCAGGGC----------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	---------GGCAGGGCCACAACCAGCG-----------------------------	19	1
rat	ccgtagggtGGCAGGGCCACAACCAGCGcagactggcgtggcccaggcatctctggg
	*********************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000052297 ENSRNOG00000039298 RGD1560687_predicted
	...........>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000054635 ENSRNOG00000036528
rat	((.(((((..((.(((((((..((((......)))).)))))))..))..)))))))	1.000 -27.70

rat

chromosome:7:13799804:13799860:1

Same_strand|Exonic_coding|ENSRNOT00000052297|ENSRNOG00000039298 ## Same_strand|Exonic_non-coding|ENSRNOT00000054635|ENSRNOG00000036528 ## ENSRNOG00000039298|protein_coding|RGD1560687_predicted| ## ENSRNOG00000036528|miRNA||

block519419 (miRNA) [miRNAunknown_lenNOK_Multihit_loopOverlap_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

Ensembl miRNA

0.012

no

no

0.74/0.74

19/19/0.00

0.0

0.0

2

0

1

0

38

-1

5arm_loop

71

nd

0.42

2

2

1

na

na

		reads	miRBase family seed
seed	---------------------------------------CGGUCGG------------------------------------------------------------------------	1	novel
seed	-----------------------------------------------------------CGGUCGG----------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	----------------------------------------------------------TCGGTCGGTCGGTCGGTCG-----------------------------------------	19	1
	--------------------------------------TCGGTCGGTCGGTCGGTCG-------------------------------------------------------------	19	1
rat	agagaggaagtgtgaagggcgtcttcagcattgtagagTCGGTCGGTCGGTCGGTCGgTCGGTCGGTCGGTCGGTCGgttttcgtttaccttttgcttttgacacttgatagatcttt
	**********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000026680 ENSRNOG00000019697 RGD1559931_predicted
	..........................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>..................................	ENSRNOT00000062146 ENSRNOG00000040393
rat	(((((..((((((.(((((((..........((.(((..((..((..((..(((((....)))))..))..))..))..))))).........))))))).))))))......)))))	0.880 -40.41

rat

chromosome:16:7205279:7205396:-1

Same_strand|Exonic_non-coding|ENSRNOT00000062146|ENSRNOG00000040393 ## Same_strand|Intronic_coding|ENSRNOT00000026680|ENSRNOG00000019697 ## ENSRNOG00000019697|protein_coding|RGD1559931_predicted| ## ENSRNOG00000040393|miRNA|| ## {Repeats: (ACCG)n 3 44 -1 class=Simple_repeat,dust 7205320 7205359 0 class=dust,trf 3 42 0 class=trf,(ACCG)n 5 44 -1 class=Simple_repeat}

novel_cloningOK_5varHIGH (9 loci)

block1060868 [novel_cloningOK_5varHIGH]

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

0.041

no

no

0.42/0.55

18/25/0.77

2.5

2.2

13

0

2

0

6

1

5arm

1

nd

0.24

3

13

2

na

na

		reads	miRBase family seed
seed	-------GCUGUAC----------------------------------------------------------------	4	novel
seed	------------ACAGAAG-----------------------------------------------------------	4	novel
seed	----------GUACAGA-------------------------------------------------------------	3	novel
seed	-----------------AGUUUCU------------------------------------------------------	1	novel
seed	----------------AAGUUUC-------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T5S1
	---------TGTACAGAAGTTTCTGGAGTGGAG---------------------------------------------	24	-	3
	-----------TACAGAAGTTTCTGGAGTGGAG---------------------------------------------	22	-	3
	------TGCTGTACAGAAGTTTCTGGAGTGG-----------------------------------------------	25	-	1
	----------------AAGTTTCTGGAGTGGAGC--------------------------------------------	18	-	1
	------TGCTGTACAGAAGTTTCTG-----------------------------------------------------	19	-	1
	---------------GAAGTTTCTGGAGTGGAGCG-------------------------------------------	20	-	1
	------TGCTGTACAGAAGTTTCTGGA---------------------------------------------------	21	-	1
	-----------TACAGAAGTTTCTGGAGTGG-----------------------------------------------	20	1	-
	------TGCTGTACAGAAGTTTCTGG----------------------------------------------------	20	-	1
rat	agcaggTGCTGTACAGAAGTTTCTGGAGTGGAGCGattgtcttcattctctgcagaaaatgagttgatagtacacggt
	******************************************************************************
rat	.((..(((((((.(((...((((((.((.(((..((......)).))).)).)))))).....))))))))))...))	1.000 -22.50

rat

chromosome:20:5519611:5519688:-1

intergenic

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other hairpins:

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