miR-Intess™

other hairpins

novel_lenNOK_cloningOK_multiarm_DicerNOK_randfoldOK (23 loci)

sblock723 [novel_lenNOK_cloningOK_multiarm_DicerNOK_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

0.002

no

no

0.43/0.53

19/23/0.46

0.0 0.0 0.0 0.4

0.8 0.0 0.0 0.0

10 2 1 11

0 0 0 0

5 1 1 1

0 0 0 0

16 36 18 12

0 -18 19 24

5arm 5arm_loop_3arm 3arm 3arm

1 1 1 1

nd nd nd nd

0.26 0.48 0.68 0.47

3 5 7 6

24

5

11

3

		reads	miRBase family seed
seed	-----------------GUCCUGG--------------------------------------------------------------------------	10	novel
seed	-------------------------------------------------------------------UCACCAG------------------------	7	novel
seed	--------------------------------------------------------------------CACCAGU-----------------------	4	novel
seed	-------------------------------------CUGCCAG------------------------------------------------------	2	novel
seed	--------------------------------------------------------------CCUCUUC-----------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S1	T3S2	T5S1	T5S2
	----------------TGTCCTGGTTCTGTTAGGA---------------------------------------------------------------	19	2	1	1	3	1
	------------------------------------------------------------------TTCACCAGTCTCCTACAGTG------------	20	-	-	-	7	-
	-------------------------------------------------------------------TCACCAGTCTCCTACAGTG------------	19	-	-	-	4	-
	------------------------------------TCTGCCAGCTTCCTAACCACT-----------------------------------------	21	-	-	-	2	-
	----------------TGTCCTGGTTCTGTTAGGATTCT-----------------------------------------------------------	23	-	-	-	2	-
	-------------------------------------------------------------TCCTCTTCACCAGTCTCCT------------------	19	1	-	-	-	-
rat	gggctcaccctcctgcTGTCCTGGTTCTGTTAGGAttctgccagcttcctaaccactatcttcctcTTCACCAGTCTCCTACAGTGggaaccagtcct
	**************************************************************************************************
rat	(((((.....(((..((((.(((((...(((((((..((...))..)))))))................)))))......))))..)))...))))).	0.900 -27.11

rat

chromosome:1:129002843:129002940:-1

intergenic

sblock7694 [novel_lenNOK_cloningOK_multiarm_DicerNOK_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

0.002

no

no

0.50/0.59

18/24/0.58

1.0 0.0

3.9 1.2

8 4

0 0

4 3

0 0

14 14

8 10

5arm 3arm

1 2

nd nd

0.10 0.11

1 1

12

6

4

3

		reads	miRBase family seed
seed	---------------CUCCCAG---------------------------------------------------------------------------	5	novel
seed	--------------------------------------------------------------UUGUGGU----------------------------	4	novel
seed	-----------------CCCAGCU-------------------------------------------------------------------------	2	novel
seed	-------------------CAGCUGU-----------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S2	T3S1	T3S2	T4S1
	----------------TCCCAGCTGTGACTGACAAG-------------------------------------------------------------	20	-	-	-	-	1	1
	-------------------------------------------------------------TTTGTGGTTTCAGCTGGG------------------	18	-	-	1	-	1	-
	--------------TCTCCCAGCTGTGACTGACAAG-------------------------------------------------------------	22	1	-	-	1	-	-
	-------------------------------------------------------------TTTGTGGTTTCAGCTGGGCCTT--------------	22	-	1	-	-	-	-
	--------------TCTCCCAGCTGTGACTGAC----------------------------------------------------------------	19	1	-	-	-	-	-
	--------------TCTCCCAGCTGTGACTGA-----------------------------------------------------------------	18	-	-	-	1	-	-
	-------------------------------------------------------------TTTGTGGTTTCAGCTGGGC-----------------	19	-	-	-	-	1	-
	--------------TCTCCCAGCTGTGACTGACAAGCC-----------------------------------------------------------	24	1	-	-	-	-	-
	------------------CCAGCTGTGACTGACAAGCCCT---------------------------------------------------------	22	1	-	-	-	-	-
rat	cgggtggctgggcaTCTCCCAGCTGTGACTGACAAGCCCTgcaggtgcttggtacagcgggTTTGTGGTTTCAGCTGGGCCTTttgagctacaccga
	*************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000009627 ENSRNOG00000007102 LOC682152
rat	(((((((((.((.....((((((((.((((.((((((((.((..((((...)))).)))))))))))))).))))))))....)).)))))).))).	1.000 -49.80

rat

chromosome:3:141306404:141306500:-1

Same_strand|Intronic_coding|ENSRNOT00000009627|ENSRNOG00000007102 ## Same_strand|Boundary_non-coding|ENSRNOT00000009723|ENSRNOG00000007102 ## ENSRNOG00000007102|protein_coding|LOC682152|acyl-CoA synthetase short-chain family member 1 [Source:RefSeq_peptide;Acc:NP_001099994]

sblock796 [novel_lenNOK_cloningOK_multiarm_DicerNOK_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

0.003

no

no

0.50/0.60

19/21/0.60

0.0 0.0

0.5 0.8

4 12

0 0

2 6

0 0

23 30

5 2

5arm 3arm

1 1

nd nd

0.20 0.10

2 1

25

6

-2

2

		reads	miRBase family seed
seed	--------------------------------------------------------------CAGAAGG-------------------------------------------	21	novel
seed	------------------------GUUGGUU---------------------------------------------------------------------------------	4	novel
		len	cloning frequencies
			T1S1	T1S2	T2S2	T3S1	T3S2	T4S1
	-------------------------------------------------------------ACAGAAGGATCCTGCCACCGT------------------------------	21	1	-	-	1	6	1
	-------------------------------------------------------------ACAGAAGGATCCTGCCACC--------------------------------	19	-	1	1	4	1	1
	-------------------------------------------------------------ACAGAAGGATCCTGCCACCG-------------------------------	20	1	-	-	1	2	-
	-----------------------AGTTGGTTCAGGATCCGTC----------------------------------------------------------------------	19	-	-	-	1	1	-
	-----------------------AGTTGGTTCAGGATCCGTCT---------------------------------------------------------------------	20	-	-	-	-	2	-
rat	tcagcacgcaagggtctgcttgcAGTTGGTTCAGGATCCGTCTgatggtaataccaagtccACAGAAGGATCCTGCCACCGTgagcgggatcttctacctttttggatctga
	****************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000015065 ENSRNOG00000011213 NP_001100996.1
rat	((((..((.((((((((((((((.((.((..((((((((.((((.(((...........))))))).)))))))))))).))))))))........)))))).))...))))	0.440 -42.50

rat

chromosome:1:136294714:136294825:-1

Same_strand|Intronic_coding|ENSRNOT00000015065|ENSRNOG00000011213 ## ENSRNOG00000011213|protein_coding|NP_001100996.1|Bloom syndrome homolog [Source:RefSeq_peptide;Acc:NP_001100996]

sblock8893 [novel_lenNOK_cloningOK_multiarm_DicerNOK_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

0.59/0.68

18/23/0.50

1.0 1.0

2.5 1.3

2 25

0 0

2 3

0 0

2 7

-1 2

5arm_loop 3arm

2 2

nd nd

0.20 0.37

3 5

34

4

4

-4

		reads	miRBase family seed
seed	--------------------------------------GCUCUCA-------------------	16	novel
seed	-----------------------------------GCUGCUC----------------------	5	novel
seed	------------------------------------CUGCUCU---------------------	5	novel
seed	-------------------------------------UGCUCUC--------------------	4	novel
seed	-----AGCAGGG----------------------------------------------------	1	novel
seed	---------------------------------------CUCUCAG------------------	1	novel
seed	---AGAGCAG------------------------------------------------------	1	novel
seed	------------------------------GUGCUGC---------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T3S2	T4S2
	-------------------------------------TGCTCTCAGACCTGCCCT---------	18	6	-	-	-
	-------------------------------------TGCTCTCAGACCTGCCCTGC-------	20	3	1	-	1
	-------------------------------------TGCTCTCAGACCTGCCCTG--------	19	4	1	-	-
	----------------------------------TGCTGCTCTCAGACCTGCC-----------	19	4	-	-	-
	------------------------------------CTGCTCTCAGACCTGCCCTGC-------	21	4	-	-	-
	-----------------------------------GCTGCTCTCAGACCTGCCCTG--------	21	2	1	-	-
	-----------------------------------GCTGCTCTCAGACCTGCCCTGC-------	22	2	-	-	-
	----------------------------------TGCTGCTCTCAGACCTGC------------	18	1	-	-	-
	-----------------------------TGTGCTGCTGCTCTCAGACCTG-------------	22	1	-	-	-
	--TAGAGCAGGGCTGAGGACTG------------------------------------------	20	1	-	-	-
	--------------------------------------GCTCTCAGACCTGCCCTGC-------	19	-	1	-	-
	----GAGCAGGGCTGAGGACTGCAGTG-------------------------------------	23	-	-	1	-
rat	gctagagcagggctgaggactgcagtgtctgtgcTGCTGCTCTCAGACCTGCCCTGCgctagct
	****************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000060641 ENSRNOG00000007474 ST7
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000010219 ENSRNOG00000007474 ST7
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042575 ENSRNOG00000007474 ST7
rat	(((((.((((((((((((...(((((......)))))...))))).....))))))).))))).	1.000 -34.80

rat

chromosome:4:43408637:43408700:1

Same_strand|Intronic_coding|ENSRNOT00000010219|ENSRNOG00000007474 ## ENSRNOG00000007474|protein_coding|ST7|suppression of tumorigenicity 7 isoform a [Source:RefSeq_peptide;Acc:NP_001004102]

sblock9410 [novel_lenNOK_cloningOK_multiarm_DicerNOK_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

0.004

no

no

0.32/0.41

18/22/0.23

0.0 0.0

0.0 1.5

7 2

0 0

2 2

0 0

13 8

4 11

5arm 3arm

1 1

nd nd

0.32 0.23

4 3

13

3

5

5

		reads	miRBase family seed
seed	--------------CAGAUGA---------------------------------------------------------------	8	novel
seed	------------CUCAGAU-----------------------------------------------------------------	3	novel
seed	-------------------------------------------------------GACUUUU----------------------	2	novel
		len	cloning frequencies
			T2S2	T4S1	T5S1
	-------------TCAGATGAAAGTCCATTTG----------------------------------------------------	19	-	1	7
	-----------TCTCAGATGAAAGTCCATTTGC---------------------------------------------------	22	-	-	2
	------------------------------------------------------TGACTTTTAGACTTTCAGA-----------	19	1	-	-
	-----------TCTCAGATGAAAGTCCAT-------------------------------------------------------	18	-	-	1
	------------------------------------------------------TGACTTTTAGACTTTCAGACTC--------	22	-	-	1
rat	cttctggggagtcTCAGATGAAAGTCCATTTGcgcctgaagttggtgtatttcttgacttttagactttcagactcccagttgg
	************************************************************************************
rat	......((((((((.((.((((((((....((((((.......))))))......))))))))..))...))))))))......	1.000 -29.80

rat

chromosome:5:114551002:114551085:-1

intergenic

sblock9496 [novel_lenNOK_cloningOK_multiarm_DicerNOK_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

0.48/0.67

18/25/0.53

0.0 0.0

1.2 2.4

8 9

0 0

5 4

0 0

25 35

2 4

5arm 3arm

1 1

nd nd

0.15 0.11

1 1

17

6

2

0

		reads	miRBase family seed
seed	-------------------------------------------------------------AGACCUC--------------------------------------------------	9	novel
seed	--------------------------CAGUUGC-------------------------------------------------------------------------------------	8	novel
		len	cloning frequencies
			T1S2	T2S1	T3S1	T3S2	T4S2	T5S1
	-------------------------ACAGTTGCTTGGGACAGGA--------------------------------------------------------------------------	19	1	2	1	-	-	-
	------------------------------------------------------------CAGACCTCTCCCGGCAAC----------------------------------------	18	2	1	-	-	-	-
	------------------------------------------------------------CAGACCTCTCCCGGCAACTCCTC-----------------------------------	23	-	-	-	2	-	-
	------------------------------------------------------------CAGACCTCTCCCGGCAACTCC-------------------------------------	21	-	-	-	2	-	-
	-------------------------ACAGTTGCTTGGGACAGGAT-------------------------------------------------------------------------	20	2	-	-	-	-	-
	-------------------------ACAGTTGCTTGGGACAGGATT------------------------------------------------------------------------	21	-	-	-	-	-	1
	------------------------------------------------------------CAGACCTCTCCCGGCAACTC--------------------------------------	20	-	-	1	-	-	-
	------------------------------------------------------------CAGACCTCTCCCGGCAACTCCT------------------------------------	22	-	-	-	1	-	-
	-------------------------ACAGTTGCTTGGGACAGGATTAGCT--------------------------------------------------------------------	25	-	-	-	-	1	-
rat	tctaagagcctgacagggcatctccACAGTTGCTTGGGACAGGATTAGCTtcagaagaagCAGACCTCTCCCGGCAACTCCTCacaggtggttctgtcctggccctggcaaacttggg
	**********************************************************************************************************************
rat	.(((((.(((...(((((((...((((((((((.(((((.(((.((.(((((....))))).))))).)))))))))))........))))...))))))).....)))...))))).	0.870 -50.40

rat

chromosome:5:135468592:135468709:-1

intergenic

sblock9858 [novel_lenNOK_cloningOK_multiarm_DicerNOK_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

0.004

no

no

0.70/0.72

18/24/0.60

0.0 0.0

1.9 0.0

9 1

0 0

2 1

0 0

13 18

2 5

5arm 3arm

1 2

nd nd

0.29 0.28

3 2

10

2

3

-2

		reads	miRBase family seed
seed	--------------ACAGCGG--------------------------------------------------------------------	9	novel
seed	------------------------------------------------------CACCCCU----------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2
	-------------CACAGCGGAGCTGGGCACTG--------------------------------------------------------	20	2	2
	-------------CACAGCGGAGCTGGGCAC----------------------------------------------------------	18	2	1
	-----------------------------------------------------CCACCCCTGGCTCTGCTG------------------	18	1	-
	-------------CACAGCGGAGCTGGGCACTGGCGT----------------------------------------------------	24	1	-
	-------------CACAGCGGAGCTGGGCACTGG-------------------------------------------------------	21	-	1
rat	gcccatcctgaccCACAGCGGAGCTGGGCACTGGCGTcacgcagtccttgttgCCACCCCTGGCTCTGCTGgatctcagggctggtgcc
	*****************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000046802 ENSRNOG00000013825 Q5EB70_RAT
rat	(((((((((((....(((((((((..((...(((((.((.........)).)))))..))..)))))))))....)))))).))).)).	1.000 -44.70

rat

chromosome:5:156425081:156425169:1

Same_strand|Intronic_coding|ENSRNOT00000046802|ENSRNOG00000013825 ## Same_strand|Boundary_non-coding|ENSRNOT00000018544|ENSRNOG00000013825 ## ENSRNOG00000013825|protein_coding|Q5EB70_RAT|Rap1ga1 protein (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q5EB70]

novel_lenNOK_cloningOK_randfoldOK_bulgeHIGH (23 loci)

block65026 [novel_lenNOK_cloningOK_randfoldOK_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

18/20/0.06

0.0

0.4

16

0

7

0

10

25

5arm

2

nd

0.22

4

16

7

na

na

		reads	miRBase family seed
seed	-----------UCCAGUU------------------------------------------------------------------------------------------------------	16	miR-145
		len	cloning frequencies
			T1S2	T2S1	T2S2	T3S2	T4S2	T5S1	T5S2
	----------GTCCAGTTTTCCCAAGGT--------------------------------------------------------------------------------------------	18	1	1	2	2	2	3	-
	----------GTCCAGTTTTCCCAAGGTT-------------------------------------------------------------------------------------------	19	1	-	-	-	2	-	1
	----------GTCCAGTTTTCCCAAGGTTC------------------------------------------------------------------------------------------	20	-	-	-	1	-	-	-
rat	cttgaagaagGTCCAGTTTTCCCAAGGTTCatttgtgttcttgcccacttgccaattaccagctttggcatctggtgggtaaactgaggcaggcagccattggggataggagcttagagc
	************************************************************************************************************************
rat	(((....(((.(((....(((((((((((..(((((.((.(((((((((((((((.........))))))...)))))))))...)).))))).)))).)))))))..))).))).))).	0.990 -44.40

rat

chromosome:10:25708993:25709112:1

intergenic

block345441 [novel_lenNOK_cloningOK_randfoldOK_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

0.006

no

no

0.33/0.37

18/19/0.00

0.0

0.3

11

0

7

0

8

2

5arm

1

nd

0.21

4

11

7

na

na

		reads	miRBase family seed
seed	---------UUAAACA--------------------------------------------------------------	11	novel
		len	cloning frequencies
			T1S1	T2S1	T2S2	T4S1	T4S2	T5S1	T5S2
	--------TTTAAACATCCTTGACTC----------------------------------------------------	18	1	-	1	1	1	2	2
	--------TTTAAACATCCTTGACTCC---------------------------------------------------	19	1	1	-	1	-	-	-
rat	tcaagtgtTTTAAACATCCTTGACTCCctacagatttagaaagggtaaagggatgtaccaagtgttaaaatattatga
	******************************************************************************
rat	(((((((((((((((((((((....((((............))))...))))))))........)))))))))).)))	0.970 -19.40

rat

chromosome:14:31054626:31054703:-1

intergenic

block345867 [novel_lenNOK_cloningOK_randfoldOK_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

0.005

no

no

0.33/0.33

18/18/0.00

0.0

0.0

14

0

2

0

12

8

3arm

1

nd

0.22

4

14

2

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------GGAAUGU----------------------	14	miR-1/206
		len	cloning frequencies
			T4S1	T4S2
	----------------------------------------------------TGGAATGTTTTCTTTGTG------------	18	5	9
rat	ggaccactatggctacatgagagaaagaacctctagagagaaaactctctaaTGGAATGTTTTCTTTGTGgaacccacatcc
	**********************************************************************************
rat	(((.........(((((.(((((((....((..(((((((....)))))))..))....))))))))))))........)))	0.460 -23.63

rat

chromosome:14:32588523:32588604:-1

intergenic

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other hairpins:

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