miR-Intess™

other hairpins

novel_lenNOK_cloningHIGH_loopOverlap_bulgeHIGH (7 loci)

block652252 [novel_lenNOK_cloningHIGH_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

0.213

no

no

0.44/0.47

18/19/0.00

0.0

0.0

147

0

10

0

20

-1

3arm_loop

1

nd

0.22

4

164

10

na

na

		reads	miRBase family seed
seed	-------------------------------------------GAGGUAG------------------------------	164	let-7a/7b/7c/7d/7e/7f/7i/miR-98
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	------------------------------------------TGAGGTAGTAACCCACTT--------------------	18	29	15	21	21	15	9	7	25	12	7
	------------------------------------------TGAGGTAGTAACCCACTTC-------------------	19	1	1	-	-	1	-	-	-	-	-
rat	gaaggacacaggtctgatataggttatctattagccctttcaTGAGGTAGTAACCCACTTccaggacagaggtttccttg
	********************************************************************************
	------------------------------------------------------------------------------------------	ENSRNOT00000046523 ENSRNOG00000014264 Phactr1
	------------------------------------------------------------------------------------------	ENSRNOT00000029196 ENSRNOG00000014264 Phactr1
	------------------------------------------------------------------------------------------	ENSRNOT00000037539 ENSRNOG00000014264 Phactr1
rat	.(((((.((..((((((....(((((.(((.....((((....))))))))))))....))..))))....)).))))).	0.500 -19.40

rat

chromosome:17:27742385:27742464:1

Opposite_strand|Intronic_coding|ENSRNOT00000046523|ENSRNOG00000014264 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000029227|ENSRNOG00000014264 ## ENSRNOG00000014264|protein_coding|Phactr1|Phosphatase and actin regulator 1. [Source:UniProtKB/Swiss-Prot;Acc:P62024]

block770582 [novel_lenNOK_cloningHIGH_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

0.131

no

no

0.14/0.17

18/22/0.01

0.0

0.1

498

0

10

0

25

-1

5arm_loop

1

nd

0.28

4

585

10

na

na

		reads	miRBase family seed
seed	--------------------------UAAUAAU------------------------------------------------------------	585	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-------------------------TTAATAATGAAAACCATT--------------------------------------------------	18	32	34	48	47	41	30	67	75	55	43
	-------------------------TTAATAATGAAAACCATTT-------------------------------------------------	19	6	3	12	7	7	4	12	26	14	16
	-------------------------TTAATAATGAAAACCATTTT------------------------------------------------	20	1	-	-	1	-	-	1	-	-	2
	-------------------------TTAATAATGAAAACCATTTTTT----------------------------------------------	22	-	-	-	-	-	-	-	1	-	-
rat	tcagagtcagaaccatgacctaataTTAATAATGAAAACCATTTtttgataatgtatttgttttcattttatgtgcaggagtgctcgcctgaa
	*********************************************************************************************
	-------------------------------------------------------------------------------------------------------	ENSRNOT00000015876 ENSRNOG00000011829 NP_001100884.1
rat	((((.((.((...(((..(((.((((....(((((((((((((.......)))).....)))))))))..))))..))).))))).)))))).	0.920 -18.00

rat

chromosome:19:16944127:16944219:-1

Opposite_strand|Intronic_coding|ENSRNOT00000015876|ENSRNOG00000011829 ## ENSRNOG00000011829|protein_coding|NP_001100884.1|similar to Fantom protein (predicted) (RGD1311099_predicted), mRNA [Source:RefSeq_dna;Acc:NM_001107414]

block1774437 [novel_lenNOK_cloningHIGH_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

0.531

no

no

0.53/0.56

18/20/0.37

0.0

0.7

51

0

10

0

50

-18

3arm_loop

1

nd

0.30

4

57

10

na

na

		reads	miRBase family seed
seed	---------------------------------------------------GCCCAUU------------------------------------------	56	novel
seed	-----------------------------------------------------CCAUUGC----------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--------------------------------------------------AGCCCATTGCCAGGGATT--------------------------------	18	2	4	3	4	1	4	6	5	2	2
	--------------------------------------------------AGCCCATTGCCAGGGATTTC------------------------------	20	2	2	1	-	2	3	5	2	1	3
	--------------------------------------------------AGCCCATTGCCAGGGATTT-------------------------------	19	-	-	-	-	-	-	-	-	1	1
	----------------------------------------------------CCCATTGCCAGGGATTTC------------------------------	18	-	-	-	-	-	-	-	-	-	1
rat	cacggagattctggtgtgtataaacaacagcttgaggaagtacggctggcAGCCCATTGCCAGGGATTTCtgtttaccagctaaagtggcgcccccgtgt
	****************************************************************************************************
rat	(((((.......((.((((....((...((((...((((((....(((((((....)))))))..)))))).......))))...)).))))))))))).	0.540 -27.91

rat

chromosome:5:129043274:129043373:-1

intergenic

novel_lenNOK_cloningHIGH_loopOverlap_randfoldOK (7 loci)

block167400 [novel_lenNOK_cloningHIGH_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

0.45/0.50

18/20/0.03

0.0

0.1

45

0

9

0

19

-1

3arm_loop

1

nd

0.17

2

61

9

na

na

		reads	miRBase family seed
seed	-------------------------------------CUGGACU------------------------------	61	miR-378
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	------------------------------------ACTGGACTTGGAGGAAGAA-------------------	19	-	1	8	3	4	9	13	3	5
	------------------------------------ACTGGACTTGGAGGAAGA--------------------	18	-	1	1	1	-	3	6	-	1
	------------------------------------ACTGGACTTGGAGGAAGAAA------------------	20	1	-	-	-	-	-	-	-	1
rat	atctccccacagtctgggctcttccaagtccggcagACTGGACTTGGAGGAAGAAaggaccatcccgatggaga
	**************************************************************************
	------------------------------------------------------------------------------------	ENSRNOT00000002447 ENSRNOG00000001795 NP_671480.2
	------------------------------------------------------------------------------------	ENSRNOT00000002446 ENSRNOG00000001795 NP_671480.2
rat	.(((((.....((((...(((((((((((((((....))))))))))))).))...)))).........)))))	0.590 -32.44

rat

chromosome:11:68659519:68659592:1

Opposite_strand|Intronic_coding|ENSRNOT00000002446|ENSRNOG00000001795 ## ENSRNOG00000001795|protein_coding|NP_671480.2|integrin, beta 5 [Source:RefSeq_peptide;Acc:NP_671480]

block365456 [novel_lenNOK_cloningHIGH_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

0.006

no

no

0.71/0.79

18/22/0.56

0.0

0.4

51

0

10

0

38

-2

3arm_loop

1

nd

0.21

3

100

10

na

na

		reads	miRBase family seed
seed	--------------------------------------------------------GUAGCCG--------------------------------------------------	97	novel
seed	---------------------------------------------------------UAGCCGU-------------------------------------------------	3	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-------------------------------------------------------TGTAGCCGTCGCCGCCGGAG--------------------------------------	20	15	15	-	2	3	2	3	4	1	2
	-------------------------------------------------------TGTAGCCGTCGCCGCCGGA---------------------------------------	19	9	7	2	-	1	1	-	1	2	5
	-------------------------------------------------------TGTAGCCGTCGCCGCCGG----------------------------------------	18	2	2	-	1	4	-	-	3	-	1
	-------------------------------------------------------TGTAGCCGTCGCCGCCGGAGA-------------------------------------	21	-	2	-	-	-	-	-	1	-	2
	-------------------------------------------------------TGTAGCCGTCGCCGCCGGAGAC------------------------------------	22	2	1	-	-	-	1	-	-	-	-
	--------------------------------------------------------GTAGCCGTCGCCGCCGGAG--------------------------------------	19	-	-	-	-	-	-	-	2	1	-
rat	acccggggcccagctgtcttgtgagttaactggcggccgcggcggcggcggctgcTGTAGCCGTCGCCGCCGGAGacggctctcgatttagtaagctcctcggtggggtaggg
	*****************************************************************************************************************
rat	.(((...((((.((((......(((((.((((.(((((((((((((((((((((...)))))))))))))))....))))...))...)))).)))))..)))).)))).)))	0.860 -60.50

rat

chromosome:14:81722737:81722849:-1

intergenic ## {SimpF: oe = 0.90 -1 CpG}

block468923 [novel_lenNOK_cloningHIGH_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

0.005

no

no

0.63/0.68

18/21/0.09

0.0

0.0

75

0

10

0

22

-1

3arm_loop

1

nd

0.05

1

127

10

na

na

		reads	miRBase family seed
seed	-------------------------------------------------UCCCAUC---------------------------------	106	novel
seed	------------------------------------------------GUCCCAU----------------------------------	15	novel
seed	-----------------------------------------------AGUCCCA-----------------------------------	4	novel
seed	--------------------------------------------------CCCAUCU--------------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	------------------------------------------------GTCCCATCTGGGGTGCCAC----------------------	19	2	-	4	6	17	41	5	2	6	17
	-----------------------------------------------AGTCCCATCTGGGGTGCCAC----------------------	20	1	-	-	2	2	3	-	-	-	-
	------------------------------------------------GTCCCATCTGGGGTGCCA-----------------------	18	2	1	1	-	1	1	-	-	-	-
	-----------------------------------------------AGTCCCATCTGGGGTGCCA-----------------------	19	1	1	-	-	-	-	1	-	-	1
	----------------------------------------------GAGTCCCATCTGGGGTGCCAC----------------------	21	-	1	1	-	-	-	-	-	-	1
	-----------------------------------------------AGTCCCATCTGGGGTGCC------------------------	18	-	-	-	-	1	1	-	-	-	1
	-------------------------------------------------TCCCATCTGGGGTGCCAC----------------------	18	-	-	-	-	-	2	-	-	-	-
	----------------------------------------------GAGTCCCATCTGGGGTGCC------------------------	19	1	-	-	-	-	-	-	-	-	-
rat	ttccaggtcactctgtgatcaccatgtggtaccataggcttgggaggaGTCCCATCTGGGGTGCCACatgttaccagggaaattggggc
	*****************************************************************************************
rat	.(((((....((((((((....(((((((((((.((((..(((((....))))))))).))))))))))))))).))))...)))))..	0.550 -37.40

rat

chromosome:15:105730561:105730649:-1

intergenic

block536943 [novel_lenNOK_cloningHIGH_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

0.60/0.67

18/20/0.01

0.0

0.0

216

0

10

0

35

-1

3arm_loop

2

nd

0.22

3

328

10

na

na

		reads	miRBase family seed
seed	------------------------------------------------------GGAGACA---------------------------------------------	328	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-----------------------------------------------------TGGAGACACCTGGCAGGG-----------------------------------	18	25	12	155	61	1	2	4	25	16	8
	-----------------------------------------------------TGGAGACACCTGGCAGGGA----------------------------------	19	-	2	10	4	-	-	-	1	-	-
	-----------------------------------------------------TGGAGACACCTGGCAGGGAA---------------------------------	20	-	-	1	-	-	-	-	-	1	-
rat	aggtttataaaggaccctgaattgtgactctgtcccacagccaggcctctgaaTGGAGACACCTGGCAGGGaatatggatggttcttagggtccctgcaaagccta
	**********************************************************************************************************
rat	((((((.....((((((((((((((.......((((...((((((.((((....))))...)))))).))))......)))))))..))))))).....)))))).	0.990 -41.92

rat

chromosome:16:47180102:47180207:-1

intergenic

block989543 [novel_lenNOK_cloningHIGH_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

0.28/0.32

18/19/0.00

0.0

0.0

35

0

10

0

42

-4

3arm_loop

2

nd

0.17

3

61

10

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------AAAGGUU----------------------------------------------------	61	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	----------------------------------------------------CAAAGGTTAAAACAAAAC------------------------------------------	18	25	6	10	1	3	2	1	2	1	5
	----------------------------------------------------CAAAGGTTAAAACAAAACC-----------------------------------------	19	2	-	1	-	-	1	-	-	1	-
rat	ctaagtaaagtctgtgacatgttttcttagaggttattttgttttctaacttCAAAGGTTAAAACAAAACctctgtatttttatctaaacatactaanacttttanacttag
	****************************************************************************************************************
rat	(((((((((((...((..((((((...(((((((...(((((((..(((((.....)))))))))))))))))))...........))))))..))..)))))...))))))	0.870 -22.84

rat

chromosome:1:105798609:105798720:1

intergenic

block1463895 [novel_lenNOK_cloningHIGH_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

0.007

no

no

0.60/0.67

18/20/0.00

0.0

0.0

340

0

10

0

18

-2

5arm_loop

3

nd

0.28

3

514

10

na

na

		reads	miRBase family seed
seed	-------------------GGGGGUU------------------------------------------------------	514	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	------------------TGGGGGTTTTTGGGGGGG--------------------------------------------	18	225	29	115	13	19	22	6	43	20	8
	------------------TGGGGGTTTTTGGGGGGGT-------------------------------------------	19	3	4	2	1	-	-	-	2	-	1
	------------------TGGGGGTTTTTGGGGGGGTA------------------------------------------	20	-	-	-	-	-	-	-	-	1	-
rat	tggatattttttgaaaccTGGGGGTTTTTGGGGGGGtattgtttttgtttttggaaactcctgattttactatatatctt
	********************************************************************************
rat	.((((((....(((((..((((((((((..((((.............))))..)))))))))).)))))....)))))).	1.000 -17.62

rat

chromosome:3:66559686:66559765:1

intergenic ## {Repeats: dust 66559708 66559728 0 class=dust}

block1653747 [novel_lenNOK_cloningHIGH_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

0.45/0.50

18/20/0.01

0.0

0.0

55

0

6

0

18

-2

3arm_loop

1

nd

0.22

1

79

6

na

na

		reads	miRBase family seed
seed	------------------------------------------CCCUGAU----------------------------	79	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S1	T4S1	T4S2
	-----------------------------------------TCCCTGATCAAAGCCAAC------------------	18	55	2	1	-	1	2
	-----------------------------------------TCCCTGATCAAAGCCAACA-----------------	19	11	5	-	1	-	-
	-----------------------------------------TCCCTGATCAAAGCCAACAA----------------	20	-	1	-	-	-	-
rat	gcccagtgggactgggcttgtggctgatctgagcaggataaTCCCTGATCAAAGCCAACaagaacaattcctaagca
	*****************************************************************************
	---------------------------------------------------------------------------------------	ENSRNOT00000012196 ENSRNOG00000009172 LOC502774
	---------------------------------------------------------------------------------------	ENSRNOT00000012332 ENSRNOG00000009172 LOC502774
rat	((....(((((.((..(((((((((....(((.((((......)))).))).))))).))))..))..))))).)).	0.940 -29.10

rat

chromosome:4:82293615:82293691:1

Opposite_strand|Intronic_coding|ENSRNOT00000012332|ENSRNOG00000009172 ## ENSRNOG00000009172|protein_coding|LOC502774|similar to Probable serine carboxypeptidase CPVL precursor (Carboxypeptidase, vitellogenic-like) (Vitellogenic carboxypeptidase-like protein) (VCP-like protein) (LOC502774), mRNA [Source:RefSeq_dna;Acc:NM_001029927]

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other hairpins:

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