miR-Intess: classification

other hairpins

novel_lenNOK_loopOverlap_nonpairedHIGH (8 loci)

block310 [novel_lenNOK_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
no	0.759	no	no	0.46/0.48	25/26/0.00	0.0	0.3	3	0	1	0	33	-1	3arm	1	nd	0.32	3	3	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------UUUCAAG---------------------------------------------------	3	novel
		len	cloning frequencies
			CE1
	-----------------------------------------------------------GTTTCAAGTGACATCATCCGACTCC----------------------------------	25	2
	-----------------------------------------------------------GTTTCAAGTGACATCATCCGACTCCT---------------------------------	26	1
celegans	ccttgcaaaataccagtgctgccgagaaaatcgtgagctgaatgaccatatgaagaatcGTTTCAAGTGACATCATCCGACTCCTttttgatcacagtaaccttgtgtagaatgaggt
	**********************************************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<..................................................	C17F3.3 C17F3.3 C17F3.3
celegans	((((.....((((.(((((((..((..(((....(((.((.((((.(((.(((((.....))))).)))...)))).)).)))...)))..)).)))))..)).)))).....)))).	0.740 -21.10

celegans

chromosome:I:6682324:6682441:-1

Opposite_strand|Boundary_non-coding|C17F3.3|C17F3.3 ## C17F3.3|protein_coding|C17F3.3|C17F3.3 [Source:RefSeq_peptide;Acc:NP_491917] ## {SimpF: WRM0612cD09 -1 fosmid,WRM0613cE07 -1 fosmid,WRM0636aD02 -1 fosmid,C17F3.3 -1 Expression_profile,WRM0626dH04 -1 fosmid}

block1145 [novel_lenNOK_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
no	0.666	no	no	0.28/0.38	18/26/0.00	0.0	5.0	3	0	1	0	18	-10	5arm_loop_3arm	2	nd	0.39	3	3	1	na	na

		reads	miRBase family seed
seed	-------------------AUAAAUA----------------------------------------------------	3	novel
		len	cloning frequencies
			CE1
	------------------GATAAATAGTGAATCGATACACTCC-----------------------------------	25	1
	------------------GATAAATAGTGAATCGATACACTCCG----------------------------------	26	1
	------------------GATAAATAGTGAATCGAT------------------------------------------	18	1
celegans	cattatgaatatgttgtaGATAAATAGTGAATCGATACACTCCGccatcagttgatttgtttaataagcaggtagtgt
	******************************************************************************
	<<<<<<<<................................................................................	F46A8.6 F46A8.6 F46A8.6
celegans	((((((.....((((.(((((((((..(((..((........))...)))....)))))))))...)))).)))))).	0.600 -11.40

celegans

chromosome:I:11244993:11245070:1

intergenic ## {SimpF: F46A8.6 1 Expression_profile,WRM0637aG08 1 fosmid}

block2326 [novel_lenNOK_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
no	0.576	no	no	0.16/0.16	25/25/0.00	0.0	0.0	1	0	1	0	34	-3	3arm_loop	1	nd	0.32	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------AUUAUUA---------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	--------------------------------------------------------GATTATTATTTCTTGATTTTATTTG----------------------------------	25	1
celegans	cgtttatcgaattgtttgtaaaaatgaaacagatctcaatcaaaaatcaatatttcGATTATTATTTCTTGATTTTATTTGcttcttcagccagtgtgaaccattgaagcaacga
	*******************************************************************************************************************
	..................................................................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	C29F5.3 C29F5.3 C29F5.3
celegans	((((..((((...(((..((....((((.(((((...((((((.((..((((.......))))..)).))))))..)))))....)))).....))..)))..))))...)))).	0.640 -15.70

celegans

chromosome:II:6290543:6290657:1

Opposite_strand|Boundary_non-coding|C29F5.3|C29F5.3 ## C29F5.3|protein_coding|C29F5.3|C29F5.3 [Source:RefSeq_peptide;Acc:NP_495262] ## {SimpF: WRM0635dH06 1 fosmid,WRM0613aG12 1 fosmid,WRM0638cF02 1 fosmid,C29F5.3 1 Expression_profile,WRM0626bD10 1 fosmid,WRM065aE09 1 fosmid,WRM064aE02 1 fosmid}

block4148 [novel_lenNOK_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
no	0.159	no	no	0.36/0.44	22/25/0.50	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	21 11	-4 9	3arm_loop 3arm	1 1	nd nd	0.36 0.32	3 3	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------CAAUUCC--------------------------------------	1	novel
seed	------------------------------------------------------------UAAUCAG-------------------------	1	novel
		len	cloning frequencies
			CE1
	----------------------------------------------GCAATTCCGTAGTGTAATCAGCCAT---------------------	25	1
	-----------------------------------------------------------GTAATCAGCCATATTTGTATGC-----------	22	1
celegans	ggttcgtctgttgctgtactctttgtagttgactcactaccatcaaGCAATTCCGTAGTGTAATCAGCCATATTTGTATGCacaaatttgct
	********************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<..........................	F29B9.7 F29B9.7 F29B9.7
celegans	(((..((.((.(((.((((....(((.(((((..((((((....((....))..))))))...))))).)))...))))))))).))..)))	0.990 -19.10

celegans

chromosome:IV:4649843:4649934:-1

Opposite_strand|Boundary_non-coding|F29B9.7|F29B9.7 ## F29B9.7|protein_coding|F29B9.7|F29B9.7 [Source:RefSeq_peptide;Acc:NP_500603] ## {SimpF: WRM0637aB09 -1 fosmid,WRM0629aB05 -1 fosmid,WRM0639aG12 -1 fosmid,WRM0615bH02 -1 fosmid,F29B9.7 -1 Expression_profile,WRM068dB06 -1 fosmid,WRM0616dA11 -1 fosmid,WRM0618aF09 -1 fosmid}

block4768 [novel_lenNOK_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
no	0.033	no	no	0.32/0.32	19/19/0.00	0.0	0.0	1	0	1	0	31	-2	5arm_loop	1	nd	0.37	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------GGAUGAU------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	-------------------------------GGGATGATTGAAGTTATTT-------------------------------------------------------	19	1
celegans	gtttatatttgtgtcgaaaaatattatttatGGGATGATTGAAGTTATTTattgttgtttcaaaaaaattttatgttttaatattttttaatgtttctgatgagc
	*********************************************************************************************************
	-------------------------------------------------------------------------------------------------------------------	Y64G10A.7 Y64G10A.7 Y64G10A.7
celegans	((((((......((..((((((((((..((((((((..((((((..((.....))..))))))....))))))))...))))))))))..)).......))))))	0.980 -17.22

celegans

chromosome:IV:14309623:14309727:-1

Opposite_strand|Intronic_coding|Y64G10A.7|Y64G10A.7 ## Y64G10A.7|protein_coding|Y64G10A.7|The Y64G10A.7 gene encodes a homolog of the human gene FIBRILLIN-1, which when mutated leads to Marfan syndrome (OMIM:154700). [Source: WormBase] ## {SimpF: WRM0610dE08 -1 fosmid}

block4827 [novel_lenNOK_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
no	0.190	no	no	0.33/0.33	18/18/0.00	0.0	0.0	1	0	1	0	35	-4	3arm_loop	1	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------CAUCUCA---------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	-----------------------------------------------TCATCTCAAAATTGAAGC-----------------------------------	18	1
celegans	ggtttcagaatatttttatcagagttcgagattttcaatttttttagTCATCTCAAAATTGAAGCaggtaaacatcgatctgaaaattgtactcgaatcc
	****************************************************************************************************
	--------------------------------------------------------------------------------------------------------------	Y57G11C.2 Y57G11C.2 lgc-7
celegans	((.(((.((.(((..((.(((((..((((.((((((((((((...((....)).))))))))))...)).....))))))))).))..))).))))).))	0.880 -17.00

celegans

chromosome:IV:14712508:14712607:-1

Opposite_strand|Intronic_coding|Y57G11C.2|Y57G11C.2 ## Y57G11C.2|protein_coding|lgc-7|Y57G11C.2 [Source:RefSeq_peptide;Acc:NP_502777] ## {Repeats: Ce000433 917 923 -1 class=___LONGPAL3_DNA/MuDR___AT_rich_Low_complexity} ## {SimpF: Y57G11C.2 -1 Expression_profile,WRM0620bA12 -1 fosmid}

block7626 [novel_lenNOK_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
no	0.542	no	no	0.47/0.47	19/19/0.00	0.0	0.0	1	0	1	0	19	-1	5arm_loop	3	nd	0.32	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------AAUGGUG--------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	-------------------GAATGGTGACTTGAATGGC---------------------------------------	19	1
celegans	accagacacggtggcacttGAATGGTGACTTGAATGGCaaggagaccagaagcatttattctgtcctgtaaacggta
	*****************************************************************************
	............................................................<<<<<<<<<<-----------------	ZK402.3 ZK402.3 ZK402.3
celegans	(((....((((.((((...((((((((.(((...(((........))).))))))).))))))))))))....))).	0.780 -16.40

celegans

chromosome:X:1402835:1402911:-1

intergenic ## {SimpF: WRM0625bG09 -1 fosmid,WRM0633aC09 -1 fosmid,WRM0617aH09 -1 fosmid,WRM064cE08 -1 fosmid,WRM0626cF12 -1 fosmid,WRM0629aD05 -1 fosmid,WRM0635cC09 -1 fosmid,WRM0636bA02 -1 fosmid,WRM063cH01 -1 fosmid,WRM0639aA01 -1 fosmid}

block8084 [novel_lenNOK_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
no	0.362	no	no	0.42/0.42	19/19/0.00	0.0	0.0	1	0	1	0	6	-2	5arm_loop	1	nd	0.37	3	1	1	na	na

		reads	miRBase family seed
seed	-------CACAAUG---------------------------------------	1	novel
		len	cloning frequencies
			CE1
	------TCACAATGATATTGCCGAG----------------------------	19	1
celegans	ccgagcTCACAATGATATTGCCGAGaagctggaaaattacgaagtgggattgg
	*****************************************************
celegans	((((.(((((..((((.((.(((......))))).))))....))))).))))	1.000 -10.10

celegans

chromosome:X:16952200:16952252:-1

intergenic ## {SimpF: WRM068bE11 -1 fosmid,WRM069cH11 -1 fosmid}

novel_Multihit (7 loci)

block6449 [novel_Multihit]

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	0.068	no	no	0.43/0.43	23/23/1.00	0.0	0.0	1	0	1	0	8	3	5arm	25	nd	0.30	3	1	1	na	na

		reads	miRBase family seed
seed	---------AAAUAUA--------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	--------CAAATATAGTGACTCTGGCCGTT-----------------------------------------------	23	1
celegans	ccgttcacCAAATATAGTGACTCTGGCCGTTcaccaaaattagtgactctggctgttcaccagatatagtgactcgga
	******************************************************************************
celegans	(((.((((...((((.((((...((((((.((((........))))...)))))).))))...)))).))))..))).	1.000 -19.70

celegans

chromosome:V:5284717:5284794:-1

intergenic ## {Repeats: trf 21 44 0 class=trf,trf 1542 1565 0 class=trf} ## {SimpF: WRM0611cF03 -1 fosmid,WRM0631aH03 -1 fosmid,WRM0640dH06 -1 fosmid,WRM0636dH04 -1 fosmid,WRM0621bA04 -1 fosmid,WRM0637dF09 -1 fosmid,WRM0630dG02 -1 fosmid,WRM068dH05 -1 fosmid,WRM066dC01 -1 fosmid}

block6450 [novel_Multihit]

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	0.329	no	no	0.43/0.43	23/23/1.00	0.0	0.0	1	0	1	0	18	3	5arm	25	nd	0.30	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------AAAUAUA----------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	------------------CAAATATAGTGACTCTGGCCGTT-------------------------------------------------------	23	1
celegans	gtgactctgaccgttcacCAAATATAGTGACTCTGGCCGTTcaccaaaaatagtgactctggccgttcaccaagtatagtgactctggccgttcac
	************************************************************************************************
celegans	((((...((.(((.((((...((((.((((...((((((.((((........))))...)))))).))))...)))).))))...))).)).))))	0.760 -21.30

celegans

chromosome:V:5284935:5285030:-1

intergenic ## {Repeats: trf 65 87 0 class=trf,trf 1638 1661 0 class=trf,trf 117 140 0 class=trf,trf 23 46 0 class=trf} ## {SimpF: WRM0611cF03 -1 fosmid,WRM0631aH03 -1 fosmid,WRM0640dH06 -1 fosmid,WRM0636dH04 -1 fosmid,WRM0637dF09 -1 fosmid,WRM0630dG02 -1 fosmid,WRM068dH05 -1 fosmid,WRM066dC01 -1 fosmid}

Page 34

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Page 45

miR-Intess™

block310 [novel_lenNOK_loopOverlap_nonpairedHIGH]

block1145 [novel_lenNOK_loopOverlap_nonpairedHIGH]

block2326 [novel_lenNOK_loopOverlap_nonpairedHIGH]

block4148 [novel_lenNOK_loopOverlap_nonpairedHIGH]

block4768 [novel_lenNOK_loopOverlap_nonpairedHIGH]

block4827 [novel_lenNOK_loopOverlap_nonpairedHIGH]

block7626 [novel_lenNOK_loopOverlap_nonpairedHIGH]

block8084 [novel_lenNOK_loopOverlap_nonpairedHIGH]

block6449 [novel_Multihit]

block6450 [novel_Multihit]