miR-Intess™

other hairpins

novel_lenNOK_cloningOK_multiarm_DicerOK_Multihit_bulgeHIGH (9 loci)

novel_lenNOK_cloningOK_shortStem_loopOverlap (9 loci)

block398160 [novel_lenNOK_cloningOK_shortStem_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

0.094

no

no

0.50/0.53

18/19/0.00

0.0

0.0

40

0

8

0

1

-1

3arm_loop

1

nd

0.22

2

44

8

na

na

		reads	miRBase family seed
seed	-------------------------GGCUUAU-----------	44	novel
		len	cloning frequencies
			T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	------------------------TGGCTTATCAGACTGAGG-	18	5	7	11	13	1	1	4	1
	------------------------TGGCTTATCAGACTGAGGG	19	-	-	1	-	-	-	-	-
rat	ttttccatttgaaagtcttatatgTGGCTTATCAGACTGAGGg
	*******************************************
	-----------------------------------------------------	ENSRNOT00000002883 ENSRNOG00000026504 RGD1309701_predicted
	-----------------------------------------------------	ENSRNOT00000059132 ENSRNOG00000026504 RGD1309701_predicted
	-----------------------------------------------------	ENSRNOT00000059131 ENSRNOG00000026504 RGD1309701_predicted
	-----------------------------------------------------	ENSRNOT00000059130 ENSRNOG00000026504 RGD1309701_predicted
rat	.((((..((((((((((........))))).)))))..)))).	1.000 -9.10

rat

chromosome:14:45984402:45984444:1

Opposite_strand|Intronic_coding|ENSRNOT00000059130|ENSRNOG00000026504 ## ENSRNOG00000026504|protein_coding|RGD1309701_predicted|

block1179415 [novel_lenNOK_cloningOK_shortStem_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

0.290

no

no

0.50/0.50

18/18/0.00

0.0

0.0

6

0

5

0

2

-1

3arm_loop

3

nd

0.17

2

10

5

na

na

		reads	miRBase family seed
seed	------------------------------------AGCAAUG------------	10	novel
		len	cloning frequencies
			T2S1	T3S1	T3S2	T4S2	T5S1
	-----------------------------------GAGCAATGGCAGTTTTGG--	18	1	1	1	1	6
rat	atctgaagaatatttatgtcatttattgttaacctGAGCAATGGCAGTTTTGGat
	*******************************************************
rat	(((..(((........((((((....((((......)))))))))).)))..)))	0.990 -8.50

rat

chromosome:2:136120887:136120941:-1

intergenic

block1179429 [novel_lenNOK_cloningOK_shortStem_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

0.290

no

no

0.50/0.50

18/18/0.00

0.0

0.0

6

0

5

0

2

-1

3arm_loop

3

nd

0.17

2

10

5

na

na

		reads	miRBase family seed
seed	------------------------------------AGCAAUG------------	10	novel
		len	cloning frequencies
			T2S1	T3S1	T3S2	T4S2	T5S1
	-----------------------------------GAGCAATGGCAGTTTTGG--	18	1	1	1	1	6
rat	atctgaagaatatttatgtcatttattgttaacctGAGCAATGGCAGTTTTGGat
	*******************************************************
rat	(((..(((........((((((....((((......)))))))))).)))..)))	0.990 -8.50

rat

chromosome:2:136338475:136338529:-1

intergenic

block1257786 [novel_lenNOK_cloningOK_shortStem_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

0.145

no

no

0.45/0.50

18/22/0.08

0.4

0.5

22

0

2

0

4

-5

5arm_loop

2

nd

0.28

3

26

2

na

na

		reads	miRBase family seed
seed	-----GACAGUC------------------------------------------------	18	novel
seed	-------CAGUCUA----------------------------------------------	8	novel
		len	cloning frequencies
			T1S1	T1S2
	----TGACAGTCTACAGCCATG--------------------------------------	18	12	6
	------ACAGTCTACAGCCATGTTC-----------------------------------	19	2	4
	------ACAGTCTACAGCCATGTTCTCC--------------------------------	22	1	-
	------ACAGTCTACAGCCATGTTCT----------------------------------	20	-	1
rat	tgctTGACAGTCTACAGCCATGTTCtccctctggtccatgtagcacacaacatcaggtac
	************************************************************
	----------------------------------------------------------------------	ENSRNOT00000033627 ENSRNOG00000026842 Nnt
	----------------------------------------------------------------------	ENSRNOT00000037049 ENSRNOG00000026842 Nnt
rat	(((((((..(((((((((((...........))))...))))).))......))))))).	1.000 -11.60

rat

chromosome:2:51508869:51508928:1

Opposite_strand|Intronic_coding|ENSRNOT00000037049|ENSRNOG00000026842 ## ENSRNOG00000026842|protein_coding|Nnt|nicotinamide nucleotide transhydrogenase [Source:RefSeq_peptide;Acc:NP_001013175]

block1306473 [novel_lenNOK_cloningOK_shortStem_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

0.552

no

no

0.50/0.58

18/19/0.00

0.0

0.0

25

0

10

0

3

-1

5arm_loop

2

nd

0.22

2

38

10

na

na

		reads	miRBase family seed
seed	----CAUUGCC-------------------------------------------------------	29	novel
seed	---ACAUUGC--------------------------------------------------------	8	novel
seed	------UUGCCAG-----------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	---ACATTGCCAGGGATTTCC---------------------------------------------	18	3	3	1	-	3	1	6	10	1	1
	--GACATTGCCAGGGATTTCC---------------------------------------------	19	1	1	-	1	-	-	1	2	-	-
	--GACATTGCCAGGGATTTC----------------------------------------------	18	1	-	-	-	1	-	-	-	-	-
	-----ATTGCCAGGGATTTCCGCC------------------------------------------	19	-	-	-	1	-	-	-	-	-	-
rat	gcgACATTGCCAGGGATTTCCgccattacccacttcctaaatccaagagatcttagcggatgtgca
	******************************************************************
rat	((.(((((((..((((((((..........................)))))))).))).)))))).	0.920 -12.07

rat

chromosome:2:171659360:171659425:1

intergenic

block1435080 [novel_lenNOK_cloningOK_shortStem_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

0.063

no

no

0.53/0.56

18/19/0.00

0.0

0.1

14

0

8

0

3

-3

5arm_loop

1

nd

0.28

3

14

8

na

na

		reads	miRBase family seed
seed	----CCAGUUG-----------------------------------------	14	novel
		len	cloning frequencies
			T1S2	T2S1	T2S2	T3S1	T3S2	T4S2	T5S1	T5S2
	---CCCAGTTGGACTCAGCAA-------------------------------	18	2	1	1	3	1	-	3	2
	---CCCAGTTGGACTCAGCAAA------------------------------	19	-	-	-	-	-	1	-	-
rat	ttgCCCAGTTGGACTCAGCAAActgttggtggccagttttttactgtggcag
	****************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000012289 ENSRNOG00000009239 Entpd8
rat	.(((((((((((..(((((.....)))))...))).......)))).)))).	0.990 -16.01

rat

chromosome:3:5229571:5229622:1

Same_strand|Intronic_coding|ENSRNOT00000012289|ENSRNOG00000009239 ## ENSRNOG00000009239|protein_coding|Entpd8|Ectonucleoside triphosphate diphosphohydrolase 8 (EC 3.6.1.5) (NTPDase 8) (NTPDase8) (E-NTPDase 8). [Source:UniProtKB/Swiss-Prot;Acc:Q5DRK1]

block1967520 [novel_lenNOK_cloningOK_shortStem_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

0.016

no

no

0.56/0.56

18/18/0.00

0.0

0.0

19

0

2

0

1

-1

3arm

5

nd

0.22

3

19

2

na

na

		reads	miRBase family seed
seed	----------------------------------GGAGGUG-----------	19	novel
		len	cloning frequencies
			T2S1	T2S2
	---------------------------------TGGAGGTGTGTGGCAATG-	18	12	7
rat	cgcatgtgacagccactctcctctttgacttccTGGAGGTGTGTGGCAATGc
	****************************************************
rat	.((((......(((((...(((((..........)))))...))))).))))	0.980 -17.20

rat

chromosome:6:111829578:111829629:-1

intergenic

block2111523 [novel_lenNOK_cloningOK_shortStem_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

0.524

no

no

0.42/0.44

18/19/0.00

0.0

0.0

19

0

8

0

3

-1

5arm_loop

1

nd

0.22

2

29

8

na

na

		reads	miRBase family seed
seed	----GAGGUAG----------------------------------------------------	29	let-7a/7b/7c/7d/7e/7f/7i/miR-98
		len	cloning frequencies
			T1S1	T1S2	T2S2	T3S2	T4S1	T4S2	T5S1	T5S2
	---TGAGGTAGGAGGAACATA------------------------------------------	18	4	7	2	2	4	1	4	2
	---TGAGGTAGGAGGAACATAA-----------------------------------------	19	1	1	-	-	1	-	-	-
rat	gctTGAGGTAGGAGGAACATAatcaaaagctaccacatgttaaaccagcctgtgtcctaaagc
	***************************************************************
rat	((((.(((((((.(((((((................)))))...))..))))...))).))))	0.640 -9.89

rat

chromosome:7:50773916:50773978:-1

intergenic

block2140352 [novel_lenNOK_cloningOK_shortStem_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

0.103

no

no

0.44/0.52

18/26/0.50

0.0

2.8

13

0

4

0

0

-7

5arm_loop

1

nd

0.17

1

18

4

na

na

		reads	miRBase family seed
seed	-CCAAGGU----------------------------------------------------------	15	novel
seed	---------CUGAUAA--------------------------------------------------	3	novel
		len	cloning frequencies
			T1S1	T3S1	T4S2	T5S1
	GCCAAGGTTCTGATAACAGCACCAAC----------------------------------------	26	-	-	-	4
	GCCAAGGTTCTGATAACAGCACCA------------------------------------------	24	-	-	-	3
	GCCAAGGTTCTGATAACA------------------------------------------------	18	-	2	-	1
	GCCAAGGTTCTGATAACAGCACC-------------------------------------------	23	-	-	-	2
	GCCAAGGTTCTGATAACAGCAC--------------------------------------------	22	-	-	-	2
	GCCAAGGTTCTGATAACAGCACCAA-----------------------------------------	25	1	-	-	-
	--------TCTGATAACAGCACCAACCCTT------------------------------------	22	-	-	-	1
	--------TCTGATAACAGCACCAAC----------------------------------------	18	-	-	-	1
	--------TCTGATAACAGCACCAACCC--------------------------------------	20	-	-	1	-
rat	GCCAAGGTTCTGATAACAGCACCAACccttataaattcttttttcccctgttttttgaaccagtgg
	******************************************************************
rat	.(((.(((((.((.(((((............................))))).)).)))))..)))	0.980 -11.09

rat

chromosome:7:96037381:96037446:-1

intergenic

novel_lenNOK_cloningOK_shortStem_randfoldOK_nonpairedHIGH_bulgeHIGH (9 loci)

block154129 [novel_lenNOK_cloningOK_shortStem_randfoldOK_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

0.008

no

no

0.47/0.50

18/19/0.00

0.0

0.0

6

0

6

0

3

1

3arm

1

nd

0.33

4

10

6

na

na

		reads	miRBase family seed
seed	-----------------------------GGGGGUU-------------	10	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S1	T3S2	T4S1
	----------------------------TGGGGGTTTTTTGTTGGG---	18	1	1	4	-	2	1
	----------------------------TGGGGGTTTTTTGTTGGGT--	19	-	-	-	1	-	-
rat	tgagctaatgcctcaactcccaaattctTGGGGGTTTTTTGTTGGGttt
	*************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000049373 ENSRNOG00000026236 NP_001100579.1
rat	.(((((...((...(((((((((....)))))))))....))..)))))	0.980 -14.60

rat

chromosome:11:34074830:34074878:1

Same_strand|Intronic_coding|ENSRNOT00000049373|ENSRNOG00000026236 ## ENSRNOG00000026236|protein_coding|NP_001100579.1|microrchidia 3 [Source:RefSeq_peptide;Acc:NP_001100579] ## {Repeats: dust 34074878 34074891 0 class=dust}

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