miR-Intess: classification

other hairpins

novel_shortStem_loopOverlap_nonpairedHIGH_bulgeHIGH (2 loci)

block8223 [novel_shortStem_loopOverlap_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	0.356	no	no	0.57/0.57	23/23/1.00	0.0	0.0	1	0	1	0	2	-3	5arm_loop	2	nd	0.48	4	1	1	na	na

		reads	miRBase family seed
seed	---AACAGCU---------------------------------------	1	novel
		len	cloning frequencies
			CE1
	--GAACAGCTCCAGACTGAGGTTGG------------------------	23	1
celegans	agGAACAGCTCCAGACTGAGGTTGGcaaccttcttccattcgtagttct
	*************************************************
	-----------------------------------------------------------	M02F4.1 M02F4.1 M02F4.1
celegans	.(((((.((....((..(((((.....)))))..)).....)).)))))	0.960 -9.70

celegans

chromosome:X:3027598:3027646:1

Opposite_strand|Intronic_coding|M02F4.1|M02F4.1 ## M02F4.1|protein_coding|M02F4.1|M02F4.1 [Source:RefSeq_peptide;Acc:NP_508516] ## {SimpF: WRM0622dA11 1 fosmid,WRM0638aF07 1 fosmid,WRM0636dE03 1 fosmid,WRM0640dE08 1 fosmid,WRM0617aC02 1 fosmid,WRM0621bG09 1 fosmid}

novel_5varHIGH_bulgeHIGH (1 loci)

block4838 [novel_5varHIGH_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	0.546	no	no	0.50/0.52	21/24/1.00	2.8	3.8	4	0	1	0	7	17	5arm	2	nd	0.29	4	4	1	na	na

		reads	miRBase family seed
seed	--------UGAUGUG---------------------------------------------------------------------------------------------------------	2	novel
seed	----------------AUGAUGG-------------------------------------------------------------------------------------------------	1	novel
seed	-----------UGUGGAU------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	-------ATGATGTGGATGATGGCGTGGAAG-----------------------------------------------------------------------------------------	24	1
	-------ATGATGTGGATGATGGCGTGG--------------------------------------------------------------------------------------------	21	1
	----------ATGTGGATGATGGCGTGGAAG-----------------------------------------------------------------------------------------	21	1
	---------------GATGATGGCGTGGAAGAAGTTG-----------------------------------------------------------------------------------	22	1
celegans	ggcgaggATGATGTGGATGATGGCGTGGAAGAAGTTGatgaagaggcagggtccggttgggagaatatctttttgttttggggtaggtttccacggcggccgacaatttccgagtttcgc
	************************************************************************************************************************
celegans	.(((((((...(((((....((.((((((((.....((..((((((.....(((.....))).....))))))..))..........)))))))).)).)).)))...))).....))))	0.450 -31.16

celegans

chromosome:IV:14780738:14780857:-1

intergenic ## {Repeats: trf 5 35 0 class=trf} ## {SimpF: oe = 1.21 0 CpG}

novel_Multihit_nonpairedHIGH (1 loci)

block8299 [novel_Multihit_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	0.430	no	no	0.43/0.43	23/23/1.00	0.0	0.0	1	0	1	0	18	3	5arm	25	nd	0.39	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------AAAUAUA----------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	------------------CAAATATAGTGACTCTGGCCGTT-------------------------------------------------------	23	1
celegans	gtgactctggccgttcacCAAATATAGTGACTCTGGCCGTTcaccaagattagtgactctgaccgttcaccataaatagtgactctggccgttcgc
	************************************************************************************************
celegans	((((...((((((.((((....(((.((((...(((.((.((((........))))...)).))).)))).)))....))))...)))))).))))	0.870 -22.20

celegans

chromosome:X:5542308:5542403:1

intergenic ## {Repeats: trf 59 82 0 class=trf} ## {SimpF: WRM0625aF10 1 fosmid,WRM0633dC07 1 fosmid,WRM0624aC10 1 fosmid}

novel_Multihit_randfoldOK_nonpairedHIGH (1 loci)

block4241 [novel_Multihit_randfoldOK_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	0.002	no	no	0.48/0.48	21/21/1.00	0.0	0.0	1	0	1	0	9	1	3arm	14	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------CACACAC----------------------	1	novel
		len	cloning frequencies
			CE1
	--------------------------------------------ACACACACACACACACACAAC---------	21	1
celegans	actgaagaaaatgtgtgtgagtatatgtgtgaagagccgccaacACACACACACACACACACAACtaactagtg
	**************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	F41H10.6c F41H10.6 F41H10.6
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	F41H10.6a F41H10.6 F41H10.6
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	F41H10.6b F41H10.6 F41H10.6
celegans	((((.......((((((((.((...((((((............))))))...)).))))))))......)))).	0.900 -19.32

celegans

chromosome:IV:5360178:5360251:-1

Same_strand|Intronic_coding|F41H10.6a|F41H10.6 ## F41H10.6|protein_coding|F41H10.6|Histone deacetylase 6 (EC 3.5.1.98). [Source:UniProtKB/Swiss-Prot;Acc:Q20296] ## {Repeats: trf 1 20 0 class=trf,dust 52229 52248 0 class=dust} ## {SimpF: WRM0612cF05 -1 fosmid,WRM061aH06 -1 fosmid}

novel_Multihit_shortStem (1 loci)

block6448 [novel_Multihit_shortStem]

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	0.071	no	no	0.43/0.43	23/23/1.00	0.0	0.0	1	0	1	0	4	29	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	tcacCAAATATAGTGACTCTGGCCGTTcaccaaaattagtgactctggctgttcaccagatatagtgactcggaccgttcaccaaaattagtgactctggccattcaccaagtatagtga
	************************************************************************************************************************
celegans	((((...((((.((((...((((((.((((........((((...((((((.((((........))))..))).))).))))........))))...)))))).))))...)))).))))	0.920 -29.29

celegans

chromosome:V:5284671:5284790:-1

intergenic ## {Repeats: trf 1490 1513 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}

novel_Multihit_shortStem_nonpairedHIGH (1 loci)

block2784 [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	0.254	no	no	0.43/0.43	23/23/1.00	0.0	0.0	1	0	1	0	3	6	3arm	25	nd	0.35	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------AAAUAUA------------------	1	novel
		len	cloning frequencies
			CE1
	--------------------------------------------CAAATATAGTGACTCTGGCCGTT---	23	1
celegans	gtgactctggccgttcaccataagaagtgactctggccgttcacCAAATATAGTGACTCTGGCCGTTcac
	**********************************************************************
celegans	((((...((((((.((((.(((....(((((.......)).)))....))).))))...)))))).))))	0.590 -16.90

celegans

chromosome:III:931119:931188:-1

intergenic ## {Repeats: trf 25 48 0 class=trf} ## {SimpF: WRM0637dB11 1 fosmid,WRM0640cE06 -1 fosmid,WRM0636bH03 1 fosmid,WRM065aC03 -1 fosmid}

novel_cloningHIGH_nonpairedHIGH_bulgeHIGH (1 loci)

block2823 [novel_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	0.349	no	no	0.57/0.72	18/23/0.74	0.0	0.8	30	0	1	0	10	21	5arm	1	nd	0.38	4	34	1	na	na

		reads	miRBase family seed
seed	-----------CGUGCCC----------------------------------------------------------------------------------------------------	31	novel
seed	-----------------CUGCCUG----------------------------------------------------------------------------------------------	2	novel
seed	---------------CCCUGCC------------------------------------------------------------------------------------------------	1	miR-789a/789b
		len	cloning frequencies
			CE1
	----------TCGTGCCCTGCCTGGGTCACC---------------------------------------------------------------------------------------	21	22
	----------TCGTGCCCTGCCTGGGTC------------------------------------------------------------------------------------------	18	8
	----------------CCTGCCTGGGTCACCAATTGT---------------------------------------------------------------------------------	21	2
	--------------GCCCTGCCTGGGTCACCAA-------------------------------------------------------------------------------------	19	1
	----------TCGTGCCCTGCCTGGGTCACCAA-------------------------------------------------------------------------------------	23	1
celegans	gattgcaggtTCGTGCCCTGCCTGGGTCACCaattgtcgaattgatctcgtcgacagatgtagattgtgaagtttcgttgttgtagtatctcaaacttgggtaattaaaccttttatc
	**********************************************************************************************************************
celegans	(((...(((((..(((((....((((..((((((...((((.((((((((((....)))).))))))......))))..))))..))..)))).....)))))....)))))...)))	0.930 -28.00

celegans

chromosome:III:2430989:2431106:-1

intergenic ## {SimpF: WRM0638bF12 -1 fosmid,WRM0633dB01 -1 fosmid,WRM0632dH11 -1 fosmid}

novel_cloningOK_multiarm_DicerNOK_Multihit_5varHIGH (1 loci)

sblock35 [novel_cloningOK_multiarm_DicerNOK_Multihit_5varHIGH]

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	0.021	no	no	0.50/0.61	21/23/1.00	0.0 1.7	1.0 2.3	2 3	0 0	1 1	0 0	28 11	8 19	5arm 3arm	31 31	nd nd	0.26 0.27	3 4	5	1	11	8

		reads	miRBase family seed
seed	-----------------------------GUUGAGU------------------------------------------------------------------------------------	2	novel
seed	-----------------------------------------------------------------------------------UUCCAAG------------------------------	2	novel
seed	----------------------------------------------------------------------------------------AGGAGAC-------------------------	1	novel
		len	cloning frequencies
			CE1
	----------------------------------------------------------------------------------GTTCCAAGGAGACGGTATGGT-----------------	21	1
	----------------------------TGTTGAGTGGACCAACACCCC-----------------------------------------------------------------------	21	1
	---------------------------------------------------------------------------------------AAGGAGACGGTATGGTTCGTCG-----------	22	1
	----------------------------------------------------------------------------------GTTCCAAGGAGACGGTATGGTT----------------	22	1
	----------------------------TGTTGAGTGGACCAACACCCCGG---------------------------------------------------------------------	23	1
celegans	aggaggatacaaacaacgaccgtatcacTGTTGAGTGGACCAACACCCCGGatggagctgccaagcaattccgccgtgaatgGTTCCAAGGAGACGGTATGGTTCGTCGtaagaacctcc
	************************************************************************************************************************
celegans	.(((((......((.((((((((...((((((...(((((((.(((..((((....(((....)))...))))..)))..)))).)))....))))))))))).))).)).....)))))	0.860 -41.30

celegans

chromosome:IV:5457310:5457429:-1

intergenic ## {SimpF: WRM0641cA07 -1 fosmid,Y4C6A.C -1 Expression_profile,WRM0620aH12 -1 fosmid,WRM0627dA08 -1 fosmid}

novel_lenNOK_cloningOK_5varHIGH_loopOverlap (1 loci)

block925 [novel_lenNOK_cloningOK_5varHIGH_loopOverlap]

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	0.348	no	no	0.35/0.38	21/26/0.60	3.8	1.4	5	0	1	0	13	-7	5arm_loop_3arm	2	nd	0.16	3	5	1	na	na

		reads	miRBase family seed
seed	----------------------UUUGAUG------------------------------------------------------	2	novel
seed	---------------UUGAUUG-------------------------------------------------------------	1	novel
seed	--------------GUUGAUU--------------------------------------------------------------	1	novel
seed	------------------AUUGUUU----------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	---------------------GTTTGATGGTCTATCTAGTAG-----------------------------------------	21	2
	-------------GGTTGATTGTTTGATGGTCTATCT----------------------------------------------	24	1
	-----------------GATTGTTTGATGGTCTATCTAGTAG-----------------------------------------	25	1
	--------------GTTGATTGTTTGATGGTCTATCTAGT-------------------------------------------	26	1
celegans	cttcggcatttccGGTTGATTGTTTGATGGTCTATCTAGTAGacaagacgagaattaaactgatttttatggaaaatcttaag
	***********************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<..................................................	C10G11.9 C10G11.9 C10G11.9
celegans	(((.((..((((((...(((((((((((.((((((...)))))).........))))))).))))....))))))..)).)))	0.740 -15.40

celegans

chromosome:I:6275233:6275315:1

Opposite_strand|Boundary_non-coding|C10G11.9|C10G11.9 ## C10G11.9|protein_coding|C10G11.9|C10G11.9 [Source:RefSeq_peptide;Acc:NP_491812] ## {SimpF: oe = 1.42 0 CpG,yk549h6 1 RNAi,C10G11.9 1 Expression_profile,WRM063bD01 1 fosmid,WRM0641dD07 1 fosmid,WRM0630cE04 1 fosmid,WRM0614aA05 1 fosmid,WRM0636aC01 1 fosmid,WRM0639bG02 1 fosmid}

novel_lenNOK_cloningOK_5varHIGH_nonpairedHIGH_bulgeHIGH (1 loci)

block261 [novel_lenNOK_cloningOK_5varHIGH_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	0.340	no	no	0.35/0.38	21/26/0.43	2.7	2.4	7	0	1	0	6	14	5arm	2	nd	0.38	5	7	1	na	na

		reads	miRBase family seed
seed	---------------UUUGAUG----------------------------------------------------------------------------------------	4	novel
seed	--------UUGAUUG-----------------------------------------------------------------------------------------------	1	novel
seed	-----------AUUGUUU--------------------------------------------------------------------------------------------	1	novel
seed	-------GUUGAUU------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	--------------GTTTGATGGTCTATCTAGTAG---------------------------------------------------------------------------	21	2
	--------------GTTTGATGGTCTATCTAGTAGAGAAG----------------------------------------------------------------------	26	2
	-------GTTGATTGTTTGATGGTCTATCTAGT-----------------------------------------------------------------------------	26	1
	----------GATTGTTTGATGGTCTATCTAGTAG---------------------------------------------------------------------------	25	1
	------GGTTGATTGTTTGATGGTCTATCT--------------------------------------------------------------------------------	24	1
celegans	atttccGGTTGATTGTTTGATGGTCTATCTAGTAGAGAAGacgagggttagactgatttttaaggaaaatcttcagcttttatagtgagcattgatgaccttttgagata
	**************************************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<..................................................................................	T27A3.4 T27A3.4 T27A3.4
celegans	(((((.(((((.....((((((.((...(((....(((((..(((((((...((........))...)))))))..))))).))).)).)))))))))))....))))).	0.810 -21.90

celegans

chromosome:I:6098902:6099011:-1

Opposite_strand|Boundary_non-coding|T27A3.4|T27A3.4 ## T27A3.4|protein_coding|T27A3.4|T27A3.4 [Source:RefSeq_peptide;Acc:NP_491760] ## {SimpF: oe = 1.34 0 CpG,T27A3.4 -1 Expression_profile,WRM0617cA08 -1 fosmid,WRM0632dE08 -1 fosmid,WRM0640cD10 -1 fosmid,WRM0623cH06 -1 fosmid}

Page 42

miR-Intess™

block8223 [novel_shortStem_loopOverlap_nonpairedHIGH_bulgeHIGH]

block4838 [novel_5varHIGH_bulgeHIGH]

block8299 [novel_Multihit_nonpairedHIGH]

block4241 [novel_Multihit_randfoldOK_nonpairedHIGH]

block6448 [novel_Multihit_shortStem]

block2784 [novel_Multihit_shortStem_nonpairedHIGH]

block2823 [novel_cloningHIGH_nonpairedHIGH_bulgeHIGH]

sblock35 [novel_cloningOK_multiarm_DicerNOK_Multihit_5varHIGH]

block925 [novel_lenNOK_cloningOK_5varHIGH_loopOverlap]

block261 [novel_lenNOK_cloningOK_5varHIGH_nonpairedHIGH_bulgeHIGH]