miR-Intess: classification

other hairpins

block3508 [novel_lenNOK_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	0.032	no	no	0.24/0.24	25/25/0.00	0.0	0.0	2	0	1	0	8	7	5arm	1	nd	0.28	4	2	1	na	na

		reads	miRBase family seed
seed	---------AUCAAGA------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			CE1
	--------GATCAAGATTTTATTTAGAAAAACG-------------------------------------------------------------	25	2
celegans	cgggcattGATCAAGATTTTATTTAGAAAAACGacaaatgacaggtttatttccattagttgctcttctaaattcttgaattatccacgctcgc
	**********************************************************************************************
celegans	(((((..(((((((((....((((((((...((((.((((.............)))).))))...)))))))))))))).))).....))))).	1.000 -20.52

celegans

chromosome:III:4059607:4059700:1

intergenic ## {SimpF: WRM0625cH11 1 fosmid,WRM0627aC06 1 fosmid,WRM0641dG03 1 fosmid,WRM0633aE06 1 fosmid,E03A3.4 1 Expression_profile}

block4215 [novel_lenNOK_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	0.015	no	no	0.58/0.58	26/26/0.00	0.0	0.0	1	0	1	0	8	16	5arm	2	nd	0.23	4	1	1	na	na

		reads	miRBase family seed
seed	---------CAGAAUG------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	--------GCAGAATGGGCCATGGCGACTTGTTG------------------------------------------------------------------------------------	26	1
celegans	cagattggGCAGAATGGGCCATGGCGACTTGTTGaaggagttatgagaactcgcagtgaagattatgacaaaaccttctcaatttatagtagccttcttatctctgtcctagatctga
	**********************************************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<.....................................................................................................	Y59E9AR.1 Y59E9AR.1 Y59E9AR.1
celegans	((((((((((((((((((....(((.(((.((((((((.(((((((..((.....)).....)))))))....)))..)))))....))).)))..))))).)))))))..)))))).	0.960 -35.20

celegans

chromosome:IV:5249321:5249438:-1

block5412 [novel_lenNOK_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	0.015	no	no	0.58/0.58	26/26/0.00	0.0	0.0	1	0	1	0	8	16	5arm	2	nd	0.23	4	1	1	na	na

		reads	miRBase family seed
seed	---------CAGAAUG------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	--------GCAGAATGGGCCATGGCGACTTGTTG------------------------------------------------------------------------------------	26	1
celegans	cagattggGCAGAATGGGCCATGGCGACTTGTTGaaggagttatgagaactcgcagtgaagattatgacaaaaccttctcaatttatagtagccttcttatctctgtcctagatctga
	**********************************************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<.....................................................................................................	Y59E9AR.7 Y59E9AR.7 Y59E9AR.7
celegans	((((((((((((((((((....(((.(((.((((((((.(((((((..((.....)).....)))))))....)))..)))))....))).)))..))))).)))))))..)))))).	0.960 -35.20

celegans

chromosome:IV:5241762:5241879:1

block6026 [novel_lenNOK_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	0.28/0.28	18/18/0.00	0.0	0.0	3	0	1	0	35	1	5arm	1	nd	0.28	4	3	1	na	na

		reads	miRBase family seed
seed	------------------------------------UUAACGU-------------------------------------------------------------------------	3	novel
		len	cloning frequencies
			CE1
	-----------------------------------TTTAACGTTAATGAAGTC---------------------------------------------------------------	18	3
celegans	ttggaaataagtataaacttgattgaaatgattacTTTAACGTTAATGAAGTCtaggtgaaagaagaaattaaactatatgttatgtgaactcaacaagttcatatgtatttttaa
	********************************************************************************************************************
celegans	.((((((((.((((.((((((.((((.....((((..((((((((((....(((.......)))....))))......)))))).))))..)))))))))).)))).)))))))).	0.440 -20.00

celegans

chromosome:IV:15098385:15098500:1

intergenic

novel_lenNOK_shortStem_randfoldOK (5 loci)

block4178 [novel_lenNOK_shortStem_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	0.68/0.68	19/19/0.00	0.0	0.0	1	0	1	0	1	10	5arm	1	nd	0.16	1	1	1	na	na

		reads	miRBase family seed
seed	--CCCCUGC--------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	-TCCCCTGCCTGGGTCACCA---------------------------------------------------	19	1
celegans	gTCCCCTGCCTGGGTCACCAaatgttggcacggttgccaacagttttcgtatccaagtagtccaagggaca
	***********************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	C09B9.3 C09B9.3 C09B9.3
celegans	(((((((((.(((((.((.(((((((((((....))))))))..))).))))))).)))).....))))).	1.000 -29.00

celegans

chromosome:IV:5022917:5022987:-1

Same_strand|Intronic_coding|C09B9.3|C09B9.3 ## C09B9.3|protein_coding|C09B9.3|Uncharacterized protein C09B9.3. [Source:UniProtKB/Swiss-Prot;Acc:Q17851] ## {SimpF: WRM0637cB03 -1 fosmid,WRM064cG05 -1 fosmid,WRM069dH02 -1 fosmid,yk220e2 -1 RNAi,WRM0633bA08 -1 fosmid}

block4190 [novel_lenNOK_shortStem_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	0.46/0.46	26/26/0.00	0.0	0.0	3	0	1	0	4	6	5arm	2	nd	0.23	3	3	1	na	na

		reads	miRBase family seed
seed	-----UUUGCAA------------------------------------------------------------------------	3	novel
		len	cloning frequencies
			CE1
	----GTTTGCAACGTTCATCGCTTCAGTTG------------------------------------------------------	26	3
celegans	tattGTTTGCAACGTTCATCGCTTCAGTTGattagcttgctaaacaattgctgcttgattgagaactgatgatttgtgaacaat
	************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<......................................................................	C02B10.6 C02B10.6 C02B10.6
celegans	.((((((..(((...((((((.(((((((((.((((.............)))).)))))))))...)))))).)))..))))))	0.990 -25.12

celegans

chromosome:IV:5070856:5070939:-1

Opposite_strand|Boundary_non-coding|C02B10.6|C02B10.6 ## C02B10.6|protein_coding|C02B10.6|C02B10.6 [Source:RefSeq_peptide;Acc:NP_500718] ## {SimpF: WRM0613bC11 -1 fosmid,WRM0617bD02 -1 fosmid,WRM0619bD05 -1 fosmid,WRM068bA09 -1 fosmid,WRM0639aG02 -1 fosmid,WRM0639aC05 -1 fosmid,WRM0612bE11 -1 fosmid,WRM061bH04 -1 fosmid,WRM0613bB12 -1 fosmid}

block5016 [novel_lenNOK_shortStem_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	0.22/0.22	18/18/0.00	0.0	0.0	1	0	1	0	4	4	3arm	1	nd	0.11	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------UUAAACU--------------	1	novel
		len	cloning frequencies
			CE1
	--------------------------------------------------TTTAAACTTTATTGAGAC----	18	1
celegans	ttctgtttcacaaagttttcataatatttaaactaatgccccaaatttggTTTAAACTTTATTGAGACagaa
	************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	Y105C5B.16 Y105C5B.16 lgc-19
celegans	.(((((((((..........((((..((((((((((..........))))))))))..))))))))))))).	0.940 -17.40

celegans

chromosome:IV:15957338:15957409:-1

Same_strand|Intronic_coding|Y105C5B.16|Y105C5B.16 ## Y105C5B.16|protein_coding|lgc-19|Putative uncharacterized protein lgc-19. [Source:UniProtKB/TrEMBL;Acc:Q9NAM5] ## {SimpF: WRM065bD04 -1 fosmid,WRM0615dA03 -1 fosmid,WRM0611aH08 -1 fosmid}

block5421 [novel_lenNOK_shortStem_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	0.46/0.46	26/26/0.00	0.0	0.0	3	0	1	0	4	6	5arm	2	nd	0.23	3	3	1	na	na

		reads	miRBase family seed
seed	-----UUUGCAA------------------------------------------------------------------------	3	novel
		len	cloning frequencies
			CE1
	----GTTTGCAACGTTCATCGCTTCAGTTG------------------------------------------------------	26	3
celegans	tattGTTTGCAACGTTCATCGCTTCAGTTGattagcttgctaaacaattgctgcttgattgagaactgatgatttgtgaacaat
	************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<......................................................................	F36H12.10 F36H12.10 F36H12.10
celegans	.((((((..(((...((((((.(((((((((.((((.............)))).)))))))))...)))))).)))..))))))	0.990 -25.12

celegans

chromosome:IV:5254711:5254794:1

Opposite_strand|Boundary_non-coding|F36H12.10|F36H12.10 ## F36H12.10|protein_coding|F36H12.10|F36H12.10 [Source:RefSeq_peptide;Acc:NP_500756] ## {SimpF: WRM0613dD04 1 fosmid}

block6670 [novel_lenNOK_shortStem_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	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	4	4	3arm	1	nd	0.28	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------UAGUUAG--------------	1	novel
		len	cloning frequencies
			CE1
	------------------------------GTAGTTAGGGCATTCGCT----	18	1
celegans	ttcagtcagtgcaacttcgatcagacgattGTAGTTAGGGCATTCGCTgaaa
	****************************************************
	.................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<-----------	C29A12.3b C29A12.3 lig-1
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<-----------	C29A12.3a C29A12.3 lig-1
celegans	((((((.(((((((((.(((((....))))).))))...))))).)))))).	1.000 -18.60

celegans

chromosome:V:10814906:10814957:-1

Opposite_strand|Boundary_non-coding|C29A12.3b|C29A12.3 ## Opposite_strand|Boundary_coding|C29A12.3a|C29A12.3 ## C29A12.3|protein_coding|lig-1|lig-1 is orthologous to the human gene LIM HOMEOBOX PROTEIN 3 ISOFORM B (LIG1. OMIM:600577), which when mutated leads to disease. [Source: WormBase] ## {SimpF: WRM0638cB12 -1 fosmid,C29A12.3 -1 Expression_profile,WRM067cC08 -1 fosmid,WRM0618aF08 -1 fosmid,WRM062aC01 -1 fosmid,WRM066cE03 -1 fosmid,WRM063dD05 -1 fosmid,WRM0621aD04 -1 fosmid}

novel_shortStem_bulgeHIGH (5 loci)

block1696 [novel_shortStem_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	0.653	no	no	0.45/0.45	22/22/1.00	0.0	0.0	1	0	1	0	4	19	3arm	1	nd	0.23	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------AUUUGAG------------------	1	novel
		len	cloning frequencies
			CE1
	--------------------------------------------------------------------------GATTTGAGAGTGAAGCGCTTCT----	22	1
celegans	tcaaggaagacgagttctggaaattgaatatcaacttttgcgaaataggaaataacttacaacgaggccaaagtGATTTGAGAGTGAAGCGCTTCTtaga
	****************************************************************************************************
celegans	((.((((((.((..(((......((((((....(((((.((....((((......)))).......)).))))).))))))....))).)))))))).))	0.660 -15.30

celegans

chromosome:II:5639509:5639608:-1

intergenic ## {SimpF: WRM063aB04 -1 fosmid,WRM0630dF09 -1 fosmid,WRM0622cF10 -1 fosmid,WRM0622cD10 -1 fosmid,WRM0629bD10 -1 fosmid,WRM0610dH02 -1 fosmid,WRM0627bF08 -1 fosmid,WRM0631cG08 -1 fosmid,WRM0618cF02 -1 fosmid,F59E12.3 -1 Expression_profile,WRM0610bD09 -1 fosmid,WRM0611bA01 -1 fosmid,WRM068cE02 -1 fosmid}

Page 37

miR-Intess™

block3508 [novel_lenNOK_bulgeHIGH]

block4215 [novel_lenNOK_bulgeHIGH]

block5412 [novel_lenNOK_bulgeHIGH]

block6026 [novel_lenNOK_bulgeHIGH]

block4178 [novel_lenNOK_shortStem_randfoldOK]

block4190 [novel_lenNOK_shortStem_randfoldOK]

block5016 [novel_lenNOK_shortStem_randfoldOK]

block5421 [novel_lenNOK_shortStem_randfoldOK]

block6670 [novel_lenNOK_shortStem_randfoldOK]

block1696 [novel_shortStem_bulgeHIGH]