miR-Intess™

other hairpins

novel_Multihit_shortStem_nonpairedHIGH (190 loci)

block1707527 [novel_Multihit_shortStem_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

0.169

no

no

0.55/0.55

20/20/1.00

0.0

0.0

2

0

1

0

4

27

5arm

22

nd

0.35

2

2

1

na

na

		reads	miRBase family seed
seed	-----CCCAGCU---------------------------------------------------------------------------------------------------	1	novel
seed	-------------------------------------------------------------------------------------CCCAGCU-------------------	1	novel
		len	cloning frequencies
			T3S2
	----TCCCAGCTCACAGTGTTCTC---------------------------------------------------------------------------------------	20	1
	------------------------------------------------------------------------------------TCCCAGCTCACAGTGTTCTC-------	20	1
rat	gtgtTCCCAGCTCACAGTGTTCTCggctcacagtgttcccagctcacagtgttcccagctcacagtgttcccagctcacagtgtTCCCAGCTCACAGTGTTCTCggctcac
	***************************************************************************************************************
	-------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000021306 ENSRNOG00000015910 Ifltd1_predicted
rat	(((..((.((..(((.(((..((.((..(((.(((.....(((((((.(((.........))).))).....))))))).)))..)).))..))).)))..)).))..)))	0.990 -27.90

rat

chromosome:4:183060423:183060533:1

Opposite_strand|Intronic_coding|ENSRNOT00000021306|ENSRNOG00000015910 ## ENSRNOG00000015910|protein_coding|Ifltd1_predicted| ## {Repeats: trf 855 875 0 class=trf}

block1640891 [novel_Multihit_shortStem_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

0.284

no

no

0.50/0.50

22/22/1.00

0.0

0.0

1

0

1

0

4

6

3arm

12

nd

0.36

3

1

1

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------UUGGUGG------------------	1	novel
		len	cloning frequencies
			T5S2
	----------------------------------------------------CTTGGTGGCCAAAGCTGTTTCA----	22	1
rat	cagtcgagagcagcagatggcaggcctttgttgaacctagcttgatgcttgaCTTGGTGGCCAAAGCTGTTTCAtgct
	******************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000012414 ENSRNOG00000008752 Nrf1_predicted
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000051418 ENSRNOG00000008752 Nrf1_predicted
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000011851 ENSRNOG00000008752 Nrf1_predicted
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000060167 ENSRNOG00000008752 Nrf1_predicted
rat	.(((...(((((((...((((..(((...((((.....(((.....)))))))..))).))))..)))))))...)))	0.990 -22.20

rat

chromosome:4:57003733:57003810:1

Same_strand|Intronic_coding|ENSRNOT00000012414|ENSRNOG00000008752 ## ENSRNOG00000008752|protein_coding|Nrf1_predicted|Nuclear respiratory factor 1 (NRF-1) (Alpha palindromic-binding protein) (Alpha-pal) (Fragment). [Source:UniProtKB/Swiss-Prot;Acc:Q62792]

block2033250 [novel_Multihit_shortStem_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

0.412

no

no

0.50/0.53

19/23/0.71

0.0

0.0

4

0

3

0

2

27

3arm

49

nd

0.35

3

7

3

na

na

		reads	miRBase family seed
seed	----------------------------------------------------------------------CCGUUGU--------------	4	novel
seed	-----------------------------------------------------------------------CGUUGUG-------------	2	novel
seed	---------------------------------------------------------------------UCCGUUG---------------	1	novel
		len	cloning frequencies
			T1S1	T2S2	T3S1
	---------------------------------------------------------------------TCCGTTGTGGATCTGACATG--	20	-	-	4
	----------------------------------------------------------------------CCGTTGTGGATCTGACATG--	19	1	1	-
	--------------------------------------------------------------------ATCCGTTGTGGATCTGACATGCC	23	-	-	1
rat	ggcaaggtcatcccagagctgaatgggaaactcatgggcatggccttctgtgttcctacctccagtgtaTCCGTTGTGGATCTGACATGcc
	*******************************************************************************************
rat	((((..((((((((((.((((..((((((...((.((((...))))..))..))))))....)))).......))).)))..)))).))))	0.710 -26.20

rat

chromosome:6:80063977:80064067:1

intergenic

novel_lenNOK_cloningHIGH_nonpairedHIGH_bulgeHIGH (187 loci)

block56614 [novel_lenNOK_cloningHIGH_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

0.577

no

no

0.28/0.36

18/22/0.04

0.0

0.2

42

0

10

0

14

13

5arm

3

nd

0.44

4

68

10

na

na

		reads	miRBase family seed
seed	---------------GAAAAUU----------------------------------------------------------------------------	66	novel
seed	----------------AAAAUUC---------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--------------AGAAAATTCCACATACATC-----------------------------------------------------------------	19	1	-	2	3	1	-	3	24	4	9
	--------------AGAAAATTCCACATACAT------------------------------------------------------------------	18	-	1	1	3	-	1	-	9	-	1
	---------------GAAAATTCCACATACATC-----------------------------------------------------------------	18	-	-	-	-	-	-	-	2	-	-
	--------------AGAAAATTCCACATACATCGA---------------------------------------------------------------	21	-	-	-	-	-	-	2	-	-	-
	--------------AGAAAATTCCACATACATCGAG--------------------------------------------------------------	22	-	-	-	-	-	-	-	1	-	-
rat	gcctgctaggttccAGAAAATTCCACATACATCgagtgcctattgcagccggcgattgctctgattggtgcccattaattgcctgcctacttcaggtc
	**************************************************************************************************
rat	(((((.(((((..(((..(((..(((....(((.((.((..(((((.....))))).)).)))))..)))...)))..)))...)))))...))))).	0.810 -22.20

rat

chromosome:10:6605668:6605765:1

intergenic

block57927 [novel_lenNOK_cloningHIGH_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

0.072

no

no

0.32/0.33

18/19/0.00

0.0

0.0

44

0

8

0

18

0

5arm

1

nd

0.47

4

53

8

na

na

		reads	miRBase family seed
seed	-------------------AUUCCAA------------------------------------------------------	53	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S2	T4S1	T4S2	T5S1	T5S2
	------------------AATTCCAATTACCACTACT-------------------------------------------	19	15	12	6	-	2	6	2	5
	------------------AATTCCAATTACCACTAC--------------------------------------------	18	-	2	-	1	-	-	-	2
rat	agcatttgcctagcacacAATTCCAATTACCACTACTaaaaaaaaaatcaagtcttaaagtaaagttggctataaatgca
	********************************************************************************
rat	.(((((((..((((...(((((....((((....(((.............)))......)))))))))))))))))))).	0.800 -9.72

rat

chromosome:10:10152669:10152748:1

intergenic

block59519 [novel_lenNOK_cloningHIGH_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

0.114

no

no

0.56/0.58

18/19/0.00

0.0

0.0

90

0

10

0

30

11

3arm

1

nd

0.56

4

154

10

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------AGCCUGA----------------------------------------	121	novel
seed	----------------------------------------------------------------------GAGCCUG-----------------------------------------	32	novel
seed	---------------------------------------------------------------------GGAGCCU------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	----------------------------------------------------------------------GAGCCTGAGAAACGGCTA------------------------------	18	9	4	28	10	4	12	1	3	12	38
	---------------------------------------------------------------------GGAGCCTGAGAAACGGCTA------------------------------	19	1	-	7	1	5	6	2	1	6	3
	--------------------------------------------------------------------AGGAGCCTGAGAAACGGCT-------------------------------	19	-	-	1	-	-	-	-	-	-	-
rat	tcgcccgagcttcggacctgttggtatttctactcgatcaaccctggcctggggccctggcctctgccagGAGCCTGAGAAACGGCTAgagccgcacagactgcggggcgccgcgcga
	**********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000060907 ENSRNOG00000004478 Srrm2_predicted
rat	((((.((.((..((...((((((((...((((..((.(((..((((((..(((((....))))).))))))....)))....))..)))))))).))))....))..))..)).))))	0.410 -49.60

rat

chromosome:10:13063884:13064001:1

Same_strand|Boundary_non-coding|ENSRNOT00000060905|ENSRNOG00000004478 ## Same_strand|Intronic_non-coding|ENSRNOT00000060907|ENSRNOG00000004478 ## ENSRNOG00000004478|protein_coding|Srrm2_predicted| ## {SimpF: oe = 0.84 0 CpG}

block65944 [novel_lenNOK_cloningHIGH_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

0.458

no

no

0.44/0.47

18/19/0.00

0.0

0.0

45

0

9

0

29

13

5arm

1

nd

0.47

4

54

9

na

na

		reads	miRBase family seed
seed	------------------------------GCACUAU-------------------------------------------------------------------------------	53	novel
seed	-------------------------------CACUAUG------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S2	T5S1	T5S2
	-----------------------------GGCACTATGACACTATGAC--------------------------------------------------------------------	19	13	8	5	8	3	7	2	4	3
	------------------------------GCACTATGACACTATGAC--------------------------------------------------------------------	18	1	-	-	-	-	-	-	-	-
rat	gagagcgtgtccatgtgagtacgaggagaGGCACTATGACACTATGACagagggaagatgctaaagttgccctggtctgtcctgccaggtctgctctgcacatctgacgtgtcctc
	********************************************************************************************************************
rat	(((..((((((...(((.(((.(((.(((((((....((((....(((..((((.....((....))..)))).))))))).))))...))).)))))).)))..))))))..)))	0.970 -35.90

rat

chromosome:10:28481301:28481416:1

intergenic

block66939 [novel_lenNOK_cloningHIGH_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

0.134

no

no

0.40/0.47

18/20/0.07

0.5

0.5

175

0

5

0

30

8

3arm

1

nd

0.39

4

235

5

na

na

		reads	miRBase family seed
seed	-------------------------------------------------------------------AACGCCA-----------------------------------------	118	novel
seed	--------------------------------------------------------------------ACGCCAU----------------------------------------	114	novel
seed	------------------------------------------------------------------AAACGCC------------------------------------------	3	novel
		len	cloning frequencies
			T1S2	T2S1	T2S2	T4S2	T5S2
	------------------------------------------------------------------AAACGCCATCATCACAAC-------------------------------	18	2	43	48	1	-
	-------------------------------------------------------------------AACGCCATCATCACAACA------------------------------	18	-	29	55	-	-
	-------------------------------------------------------------------AACGCCATCATCACAACAA-----------------------------	19	-	13	16	-	1
	------------------------------------------------------------------AAACGCCATCATCACAACAA-----------------------------	20	-	3	14	-	-
	------------------------------------------------------------------AAACGCCATCATCACAACA------------------------------	19	-	3	4	-	-
	-----------------------------------------------------------------CAAACGCCATCATCACAA--------------------------------	18	-	2	-	-	-
	-----------------------------------------------------------------CAAACGCCATCATCACAAC-------------------------------	19	-	-	1	-	-
rat	aacagtagcatggtcagtcactagcagttactgaaggtttcctttgggtcaagcatctcttaatccAAACGCCATCATCACAACAagcttgaattgccactgtttcccttctgtt
	*******************************************************************************************************************
rat	(((((.((((((((...(((..(((.(((..(((.(((....(((((((.(((.....))).))))))).))).)))....)))..))))))...)))).))))......)))))	0.570 -24.20

rat

chromosome:10:30845762:30845876:1

intergenic

block98025 [novel_lenNOK_cloningHIGH_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

0.178

no

no

0.39/0.48

18/22/0.10

0.0

0.0

30

0

8

0

13

16

3arm

1

nd

0.42

4

52

8

na

na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------GAUUGGG------------------------	52	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S2	T5S2
	--------------------------------------------------------------------------TGATTGGGATATTTCGTGG-------------	19	2	9	1	4	1	1	21	5
	--------------------------------------------------------------------------TGATTGGGATATTTCGTGGG------------	20	-	-	-	1	-	-	2	-
	--------------------------------------------------------------------------TGATTGGGATATTTCGTG--------------	18	-	1	-	-	-	-	2	-
	--------------------------------------------------------------------------TGATTGGGATATTTCGTGGGGA----------	22	-	-	-	-	-	-	1	-
	--------------------------------------------------------------------------TGATTGGGATATTTCGTGGGG-----------	21	-	-	-	-	-	-	1	-
rat	tcttgccccttactcagtttctatatccccaaggcctttatgattattggttttgttaaagaaaggtgggcaggTGATTGGGATATTTCGTGGggaccgggtagga
	**********************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042984 ENSRNOG00000005133 Mapt
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000045127 ENSRNOG00000005133 Mapt
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000006856 ENSRNOG00000005133 Mapt
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000050070 ENSRNOG00000005133 Mapt
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000043604 ENSRNOG00000005133 Mapt
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000045134 ENSRNOG00000005133 Mapt
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000006947 ENSRNOG00000005133 Mapt
rat	((((((((....((((......(((((((....((((......(((((..((((....))))..)))))..))))....)))))))....))))....))))))))	0.960 -29.30

rat

chromosome:10:93472894:93472999:1

Same_strand|Intronic_coding|ENSRNOT00000006947|ENSRNOG00000005133 ## ENSRNOG00000005133|protein_coding|Mapt|Microtubule-associated protein tau (Neurofibrillary tangle protein) (Paired helical filament-tau) (PHF-tau). [Source:UniProtKB/Swiss-Prot;Acc:P19332]

block111685 [novel_lenNOK_cloningHIGH_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

0.319

no

no

0.35/0.39

18/20/0.02

0.0

0.0

94

0

10

0

5

12

3arm

1

nd

0.37

4

120

10

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------------UUUUGUC----------------	118	novel
seed	------------------------------------------------------------------UUUGUCC---------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	----------------------------------------------------------------ATTTTGTCCTCAGTGTTGT-----	19	19	9	22	9	15	12	-	6	6	8
	----------------------------------------------------------------ATTTTGTCCTCAGTGTTG------	18	3	2	1	-	-	-	-	1	-	3
	----------------------------------------------------------------ATTTTGTCCTCAGTGTTGTT----	20	-	1	-	-	-	-	-	-	-	1
	-----------------------------------------------------------------TTTTGTCCTCAGTGTTGT-----	18	-	-	1	-	-	-	1	-	-	-
rat	cggtggcttttcattgctttcttcaaacatgtaaatgtagtaacatcccaaggtctacacatttATTTTGTCCTCAGTGTTGTtcctg
	****************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000040202 ENSRNOG00000030930 Samsn1
rat	(((..((....(((((.......((((...((((((((.(((((........)).)))))))))))))))....)))))..))..)))	0.960 -14.60

rat

chromosome:11:14643844:14643931:-1

Same_strand|Intronic_coding|ENSRNOT00000040202|ENSRNOG00000030930 ## ENSRNOG00000030930|protein_coding|Samsn1|SAM domain, SH3 domain and nuclear localization signals, 1 [Source:RefSeq_peptide;Acc:NP_570834]

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other hairpins:

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