miR-Intess: classification

other hairpins

novel_lenNOK_nonpairedHIGH_bulgeHIGH (22 loci)

block5995 [novel_lenNOK_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	0.401	no	no	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	10	14	3arm	1	nd	0.39	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------UCGAAUA--------------------	1	novel
		len	cloning frequencies
			CE1
	------------------------------------------------------------TTCGAATAGCCCCTTTAC----------	18	1
celegans	gtttttttaaaatattgtttcaacattgccatttttaaaatgtaatttttgaaaatatgaTTCGAATAGCCCCTTTACaaaaaaaacg
	****************************************************************************************
celegans	(((((((((((...((((((.(((((....((((((((((......))))))))))))).)).))))))....))))...))))))).	0.470 -9.10

celegans

chromosome:IV:14861854:14861941:1

intergenic ## {SimpF: WRM0618dC06 1 fosmid,WRM0628aH09 1 fosmid,WRM0617bF06 1 fosmid,WRM0619cE05 1 fosmid}

block6183 [novel_lenNOK_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	0.392	no	no	0.33/0.33	18/18/0.00	0.0	0.0	1	0	1	0	20	8	3arm	1	nd	0.39	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------AAUAGCA------------------------------	1	novel
		len	cloning frequencies
			CE1
	----------------------------------------------------------------TAATAGCAGAGATAGAGT--------------------	18	1
celegans	atattcaaaattttaaagctgtttcaatattctgacaaattatttagattttattcaaatgtatTAATAGCAGAGATAGAGTaaacggacaattattgaata
	******************************************************************************************************
celegans	.(((((((((((......((((((...(((((((....((((..((.((((.....)))).)).))))..))))).))....))))))..)))).)))))))	0.640 -12.30

celegans

chromosome:IV:16374045:16374146:1

intergenic ## {SimpF: WRM062dA08 1 fosmid,WRM0621bE04 1 fosmid}

block6315 [novel_lenNOK_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	0.104	no	no	0.36/0.36	28/28/0.00	0.0	0.0	1	0	1	0	19	11	3arm	1	nd	0.43	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------UUGCUAU---------------------------------------	1	novel
		len	cloning frequencies
			CE1
	------------------------------------------------------------------ATTGCTATAGAAGGTTTAAGAGGTTACC-------------------	28	1
celegans	ctatacgaattatttatttttacactattttctgtgttatttatttcttttgcttgaggtaaggatATTGCTATAGAAGGTTTAAGAGGTTACCataattttttcgttataga
	*****************************************************************************************************************
celegans	(((((((((....((((....((.(((((((((((((..((((((((........))))))))......)).)))))))))...))..))....))))....))))).)))).	0.510 -19.30

celegans

chromosome:MtDNA:5783:5895:1

intergenic

block6818 [novel_lenNOK_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	0.316	no	no	0.40/0.40	25/25/0.00	0.0	0.0	1	0	1	0	10	14	5arm	2	nd	0.40	4	1	1	na	na

		reads	miRBase family seed
seed	-----------UUUUAUU------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	----------GTTTTATTCAATACGAGGATGTCCG-------------------------------------------------------	25	1
celegans	gcatacaaaaGTTTTATTCAATACGAGGATGTCCGatacactttgatgggtaccacttcagaacatatcctcgttggcggcttcaatgct
	******************************************************************************************
	..............................................................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	H12D21.13 H12D21.13 nspa-4
celegans	((((....(((((....(((..((((((((((.........((((((((...)))..)))))..))))))))))))).)))))..)))).	0.690 -18.10

celegans

chromosome:V:14884766:14884855:-1

intergenic ## {SimpF: WRM0639cE11 -1 fosmid,WRM0625cE01 -1 fosmid,WRM0628aA08 -1 fosmid,WRM0613bG05 -1 fosmid,WRM0623dF08 -1 fosmid}

block6886 [novel_lenNOK_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	0.068	no	no	0.42/0.42	26/26/0.00	0.0	0.0	1	0	1	0	8	7	3arm	1	nd	0.46	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------UAUUAGU--------------------------	1	miR-230
		len	cloning frequencies
			CE1
	----------------------------------------------------GTATTAGTGTTGGTGGGAGTGGTTTT--------	26	1
celegans	acttgtcgtacagatccacaacgcacgtgctttgttccggacagagagcgcaGTATTAGTGTTGGTGGGAGTGGTTTTtcgaggag
	**************************************************************************************
celegans	.(((.(((.((...(((.((((((..(((((.(((((........))))).)))))..))))))...)))...))....))).)))	1.000 -27.50

celegans

chromosome:V:17069122:17069207:-1

intergenic ## {SimpF: WRM0612aF04 -1 fosmid,WRM0635dG10 -1 fosmid,WRM0629cH07 -1 fosmid,WRM0619bF01 -1 fosmid,WRM067aD09 -1 fosmid,WRM0641cE12 -1 fosmid,WRM0636dH06 -1 fosmid,WRM0615aG02 -1 fosmid,WRM0629bB03 -1 fosmid,WRM0614cA06 -1 fosmid,WRM0621aD01 -1 fosmid}

block7023 [novel_lenNOK_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	0.743	no	no	0.47/0.47	19/19/0.00	0.0	0.0	1	0	1	0	28	12	3arm	1	nd	0.37	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------AGAAGAC---------------------------------------	1	novel
		len	cloning frequencies
			CE1
	-------------------------------------------------------------------GAGAAGACGGTCGAAATCT----------------------------	19	1
celegans	ctttcctcgggttggctggcagaggacggtgttgcatccaacgcagacgacgacggtggtggcgtgcGAGAAGACGGTCGAAATCTgaaaaaaaaaccgaattagtatgggaaa
	******************************************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<-----------------------------------	F56E10.4.1 F56E10.4 rps-27
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<-----------------------------------	F56E10.4.2 F56E10.4 rps-27
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<-----------------------------------	F56E10.4.4 F56E10.4 rps-27
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<-----------------------------------	F56E10.4.3 F56E10.4 rps-27
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<-----------------------------------	F56E10.4.5 F56E10.4 rps-27
celegans	.(((((((((.........((((.(((.((.((...((..((((..((.((....)).)).))))..)).)).)).)))....)))).........))))........))))).	0.960 -27.57

celegans

chromosome:V:103512:103625:1

Opposite_strand|Boundary_coding|F56E10.4.4|F56E10.4 ## F56E10.4|protein_coding|rps-27|rps-27 encodes a small ribosomal subunit S27 protein. [Source: WormBase] ## {SimpF: WRM0629cC03 1 fosmid,F56E10.4 1 Expression_profile}

block7078 [novel_lenNOK_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	0.078	no	no	0.16/0.16	19/19/0.00	0.0	0.0	2	0	1	0	19	18	5arm	1	nd	0.42	4	2	1	na	na

		reads	miRBase family seed
seed	--------------------UUAGUUC------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			CE1
	-------------------TTTAGTTCATTTTTTTTTC-------------------------------------------------------------------	19	2
celegans	cggggcctctggaaacattTTTAGTTCATTTTTTTTTCagatttacacgtggtgctgccaggcattacggtttgatctacaaaaaatgcgggaatttttcatcct
	*********************************************************************************************************
	<<<<<<<<<<<<<------------------------------------------------------------------------------------------------------	Y45G12B.3 Y45G12B.3 Y45G12B.3
celegans	.((((....((((((.((((((....((((((((....(((((.((.(((((((((....)))))))))))..)))))..)))))))).))))))))))))))))	0.450 -25.70

celegans

chromosome:V:2688798:2688902:1

Opposite_strand|Intronic_coding|Y45G12B.3|Y45G12B.3 ## Y45G12B.3|protein_coding|Y45G12B.3|L-2-hydroxyglutarate dehydrogenase, mitochondrial precursor (EC 1.1.99.2). [Source:UniProtKB/Swiss-Prot;Acc:Q9N4Z0] ## {Repeats: dust 64491 64499 0 class=dust}

block7707 [novel_lenNOK_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	0.086	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	19	6	5arm	1	nd	0.39	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------ACUGGCC------------------------------------------------------------------------------------------	1	miR-240
		len	cloning frequencies
			CE1
	-------------------TACTGGCCCCCAAAATCT--------------------------------------------------------------------------------	18	1
celegans	tcaatgaaacagcaacaacTACTGGCCCCCAAAATCTgctcacacatctgcctctctccaatcatttcaccaaaacagtgagcagctgggtgtcgactgttccccgcgcacatttga
	*********************************************************************************************************************
celegans	((((.......((...(((...((((.((((....((((((((..................................)))))))).)))).))))...)))....))......))))	0.850 -23.50

celegans

chromosome:X:5124515:5124631:-1

intergenic ## {SimpF: WRM0619cF05 -1 fosmid,WRM0617cD05 -1 fosmid,WRM069aH02 -1 fosmid,WRM069bC12 -1 fosmid,WRM0632bA11 -1 fosmid,WRM068bC11 -1 fosmid,WRM0611cD12 -1 fosmid,WRM0629dC11 -1 fosmid}

block8144 [novel_lenNOK_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	0.371	no	no	0.61/0.61	18/18/0.00	0.0	0.0	1	0	1	0	27	4	3arm	1	nd	0.33	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------GACACGU-------------------------------------	1	novel
		len	cloning frequencies
			CE1
	----------------------------------------------------------------------CGACACGTTCTACGAGGG---------------------------	18	1
celegans	ttggactttttcgctggtttggtggagctggacgatggattctttggagcaaccgcatcagatgacgaagCGACACGTTCTACGAGGGaattgactagtttcatcatcttatcca
	*******************************************************************************************************************
celegans	.((((.........(((..((((((((((((.((((...(((((((((((...(((.((.......)).)))....)))))).))))).)))).))))))))))))..)))))))	0.620 -30.80

celegans

chromosome:X:1012093:1012207:1

intergenic ## {SimpF: WRM0636dA04 -1 fosmid,WRM0625cH06 1 fosmid,WRM0621dF04 -1 fosmid,WRM0621bD10 -1 fosmid,WRM0631cA02 -1 fosmid,WRM0625aB08 -1 fosmid,WRM0627dH08 -1 fosmid,WRM0631bF01 -1 fosmid,WRM0625aG07 1 fosmid}

block8461 [novel_lenNOK_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	0.077	no	no	0.28/0.28	18/18/0.00	0.0	0.0	1	0	1	0	11	26	3arm	1	nd	0.39	4	1	1	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------------------------------------UUAUAAU---------------------	1	novel
		len	cloning frequencies
			CE1
	---------------------------------------------------------------------------------------ATTATAATAACGGTCGAA-----------	18	1
celegans	ctcttctttctttgattacttttatcctgtttatgcctccttttgccactttttgccacttcatacctcttctaatttcaggttcccATTATAATAACGGTCGAAataaggagaga
	********************************************************************************************************************
celegans	((((((((..(((((((....((((..((.....((((...............((......))................))))...))..))))....)))))))..)))))))).	0.470 -16.68

celegans

chromosome:X:9884133:9884248:1

intergenic ## {SimpF: WRM069aD01 1 fosmid,WRM0632cB05 1 fosmid,WRM0637dH10 1 fosmid,WRM0631dF04 1 fosmid,WRM0617dA08 1 fosmid,WRM0625cF08 1 fosmid,WRM0612cH11 1 fosmid,WRM063aH11 1 fosmid,WRM0619bB09 1 fosmid}

Page 19

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miR-Intess™

block5995 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

block6183 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

block6315 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

block6818 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

block6886 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

block7023 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

block7078 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

block7707 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

block8144 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

block8461 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]