miR-Intess: classification

other hairpins

block4384 [novel_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	0.738	no	no	0.42/0.42	24/24/1.00	0.0	0.0	1	0	1	0	11	14	5arm	1	nd	0.25	4	1	1	na	na

		reads	miRBase family seed
seed	------------UUCAGGC-------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	-----------GTTCAGGCGTAGGAAAATGATAAG---------------------------------------------------------------------------	24	1
celegans	gtaaaatcactGTTCAGGCGTAGGAAAATGATAAGaaataataagaattgccagagtctcgttttcttttttttttcaagctaaatttttttttgaataaacttttttat
	**************************************************************************************************************
	<.......................................................................................................................	C50F7.3 C50F7.3 C50F7.3
celegans	((((((....(((((((((....(((((.((.(((((..((..(((.((....)).)))..))))))).)).)))))..)))...........)))))).....))))))	0.740 -13.80

celegans

chromosome:IV:7732241:7732350:-1

intergenic ## {SimpF: WRM065aD01 -1 fosmid,WRM0640aC10 -1 fosmid,WRM0610cC09 -1 fosmid,WRM0611cE08 -1 fosmid,WRM0631cD04 -1 fosmid,WRM0610aG12 -1 fosmid,WRM0613dH07 -1 fosmid,WRM0636cH09 -1 fosmid,WRM0611aD08 -1 fosmid,WRM0626bG03 -1 fosmid,WRM062cA04 -1 fosmid,WRM067aG11 -1 fosmid,WRM0630cH04 -1 fosmid}

block4693 [novel_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	0.248	no	no	0.21/0.24	19/21/0.75	0.0	0.5	4	0	1	0	10	21	5arm	1	nd	0.24	4	4	1	na	na

		reads	miRBase family seed
seed	-----------AGAUUUG---------------------------------------------------------------------------------------------------	4	novel
		len	cloning frequencies
			CE1
	----------TAGATTTGAATGATATGTTAG--------------------------------------------------------------------------------------	21	3
	----------TAGATTTGAATGATATGTT----------------------------------------------------------------------------------------	19	1
celegans	gtgaaattatTAGATTTGAATGATATGTTAGcatcaaaattgcgtccacatctgcattgatttggattcttttaaacaaatatgagcttaacattttaatattttgaaaatttgcac
	*********************************************************************************************************************
	-------------------------------------------------------------------------------------------------------------------------------	C08F11.8 C08F11.8 ugt-22
celegans	((((((((.(((((.(((((....((((((((.(((...(((.(((((.(((......))).))))).........)))...)))))).))))))))))...))))).))))).)))	0.450 -19.10

celegans

chromosome:IV:13640911:13641027:-1

Opposite_strand|Intronic_coding|C08F11.8|C08F11.8 ## C08F11.8|protein_coding|ugt-22|UDP-GlucuronosylTransferase family member (ugt-22) [Source:RefSeq_peptide;Acc:NP_502633] ## {SimpF: WRM067dG06 -1 fosmid,WRM065aG08 -1 fosmid,WRM065cG01 -1 fosmid,WRM065bD09 -1 fosmid,WRM067bD01 -1 fosmid,WRM0633dA12 -1 fosmid}

novel_lenNOK_loopOverlap_nonpairedHIGH_bulgeHIGH (7 loci)

block8 [novel_lenNOK_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	0.970	no	no	0.68/0.68	19/19/0.00	0.0	0.0	1	0	1	0	21	-2	3arm_loop	1	nd	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------GUGGGAG--------------------------------	1	novel
		len	cloning frequencies
			CE1
	----------------------------------------TGTGGGAGGCCGGTCACCT---------------------	19	1
celegans	gatgtgcgtctcgatctccttgcgggcagcctcgacgttaTGTGGGAGGCCGGTCACCTggaatagaaatagttatattt
	********************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<----------------------------	F53G12.5a.1 F53G12.5 mex-3
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<----------------------------	F53G12.5b F53G12.5 mex-3
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<----------------------------	F53G12.5a.2 F53G12.5 mex-3
celegans	(((((((...((....(((.....(((.(((((..((.....)).)))))..)))....)))...))....)).))))).	0.760 -15.50

celegans

chromosome:I:132080:132159:-1

Opposite_strand|Boundary_coding|F53G12.5a.2|F53G12.5 ## F53G12.5|protein_coding|mex-3|mex-3 encodes two KH domain-containing RNA binding proteins. in the early embryo, maternally provided MEX-3 is required for specifying the identities of the anterior AB blastomere and its descendants, as well as for the identity of the P3 blastomere and proper segregation of the germline P granules. mex-3 mRNA is distributed uniformly in the syncytial core of the adult distal gonad, mature oocytes, and early 1-cell stage embryos, but then becomes more prominent in the AB blastomere and its daughters by the 4-cell stage after which it is rapidly degraded save for the D and P4 blastomeres. MEX-3 protein is also detected uniformly in the cytoplasm of oocytes and 1-cell stage embryos, but like the mRNA, becomes more abundant in AB and its daughters at the 2- and 4-cell stages, respectively, before disappearing. MEX-3 is also detected in association with P granules from the 2-cell stage until the late stages of embryogenesis. [Source: WormBase] ## {SimpF: WRM065cD06 -1 fosmid,WRM0613bH11 -1 fosmid,F53G12.5 -1 Expression_profile,WRM064bF03 -1 fosmid,WRM0638dH05 -1 fosmid}

block1017 [novel_lenNOK_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	0.797	no	no	0.63/0.63	19/19/0.00	0.0	0.0	1	0	1	0	19	-4	3arm_loop	1	nd	0.53	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------GACCAGC------------------------------	1	novel
		len	cloning frequencies
			CE1
	----------------------------------GGACCAGCCAGCGGTAACT-------------------	19	1
celegans	cacattgttctcgcttccaaactgccactgatccGGACCAGCCAGCGGTAACTgaagtttttgattagttgg
	************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<--------------------------	C36B1.5.1 C36B1.5 prp-4
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<--------------------------	C36B1.5.2 C36B1.5 prp-4
celegans	((.((((.((..(((((...(((((..(((........)))...)))))....)))))....)).)))))).	0.990 -12.60

celegans

chromosome:I:8734773:8734844:1

Opposite_strand|Boundary_coding|C36B1.5.2|C36B1.5 ## C36B1.5|protein_coding|prp-4|C36B1.5 [Source:RefSeq_peptide;Acc:NP_492363] ## {SimpF: WRM0614bE10 1 fosmid,WRM0636aB08 1 fosmid,WRM0625cA05 1 fosmid,C36B1.5 1 Expression_profile}

block1168 [novel_lenNOK_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	0.170	no	no	0.30/0.32	23/25/0.33	0.0	0.7	3	0	1	0	8	-2	5arm	2	nd	0.39	4	3	1	na	na

		reads	miRBase family seed
seed	---------AUAUUCA------------------------------------------------------	3	novel
		len	cloning frequencies
			CE1
	--------GATATTCATACTTGACAAAACCAAG-------------------------------------	25	2
	--------GATATTCATACTTGACAAAACCA---------------------------------------	23	1
celegans	atcactttGATATTCATACTTGACAAAACCAAGaactgaattgtcaagcaaaaactgatactgattgtga
	**********************************************************************
	<<<<<<<<<<<<<<<<<<<<<<..........................................................	F35E2.10 F35E2.10 F35E2.10
celegans	.((((.((..((((....((((((((...((.....))..))))))))........))))..))..))))	0.440 -9.80

celegans

chromosome:I:11722910:11722979:1

Opposite_strand|Boundary_non-coding|F35E2.10|F35E2.10 ## F35E2.10|pseudogene|F35E2.10| ## {SimpF: WRM0614aA10 1 fosmid,WRM063dC09 1 fosmid,WRM0635dH04 1 fosmid,WRM0620dC11 1 fosmid,WRM0625aF01 1 fosmid,WRM065bC10 1 fosmid,WRM0640aC01 1 fosmid}

block1968 [novel_lenNOK_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	0.028	no	no	0.31/0.33	24/26/0.67	0.0	0.7	3	0	1	0	5	-5	5arm_loop_3arm	1	nd	0.46	4	3	1	na	na

		reads	miRBase family seed
seed	------AUUUGAU--------------------------------------------	3	novel
		len	cloning frequencies
			CE1
	-----GATTTGATCTTCGACAACTTATTG----------------------------	24	2
	-----GATTTGATCTTCGACAACTTATTGAT--------------------------	26	1
celegans	caatcGATTTGATCTTCGACAACTTATTGATtaagaactgatttcaaaattgattgt
	*********************************************************
celegans	((((((((((((...(((....((((.....))))...)))..))))).))))))).	0.990 -11.30

celegans

chromosome:II:11906427:11906483:-1

intergenic ## {SimpF: WRM061cG08 -1 fosmid,WRM0638cD09 -1 fosmid}

block2334 [novel_lenNOK_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	0.525	no	no	0.38/0.38	26/26/0.00	0.0	0.0	1	0	1	0	31	-1	3arm	1	nd	0.31	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------AAUAGAU-------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	-------------------------------------------------------------GAATAGATTGATGCGAAGATGAAAGC-------------------------------	26	1
celegans	gtcaggggttcgagtcccctaggtggcttgattttttgcagtctgaatattaacttaccccGAATAGATTGATGCGAAGATGAAAGCaactgtcgacaaggaaatatttgaaactgat
	**********************************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>...............................................................................................	F18C5.t1 F18C5.t1 F18C5.t1
celegans	(((((...(((((((..(((.(((.((((...((((((((.((....((((...........))))....))))))))))...)))).))).......)))....))))))).)))))	0.470 -25.20

celegans

chromosome:II:6565242:6565359:1

intergenic ## {SimpF: WRM0631cB07 1 fosmid,WRM0622cA11 1 fosmid,WRM0630dH09 1 fosmid,WRM0636cH03 1 fosmid,F18C5.5 1 Expression_profile,WRM068cB08 1 fosmid}

block5468 [novel_lenNOK_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	0.015	no	no	0.39/0.39	18/18/0.00	0.0	0.0	1	0	1	0	29	-4	5arm_loop	1	nd	0.44	5	1	1	na	na

		reads	miRBase family seed
seed	------------------------------CUACAGC---------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	-----------------------------TCTACAGCCAGTTTTTAC-----------------------------------------------------	18	1
celegans	taaattcatacagttaacgcggatattagTCTACAGCCAGTTTTTACagaccactaaatcgctgcaagacctgaaatctctgcaagctgtgtgcctttaa
	****************************************************************************************************
celegans	((((..(((((((((..((.((((.(((((((.((((..((((............)))).))))..)))).))).)))).))..)))))))))..)))).	0.980 -23.80

celegans

chromosome:IV:5532871:5532970:1

intergenic ## {SimpF: WRM069aH08 1 fosmid,WRM0610cC12 1 fosmid,WRM0619dH04 1 fosmid,WRM0621aB02 1 fosmid,WRM069cB02 1 fosmid,WRM0634cF12 1 fosmid,WRM0625cE08 1 fosmid,WRM0610dA07 1 fosmid}

block7624 [novel_lenNOK_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	0.025	no	no	0.52/0.59	22/25/0.50	0.0	1.5	2	0	1	0	14	-7	5arm_loop	2	nd	0.36	5	2	1	na	na

		reads	miRBase family seed
seed	---------------CAUCACU----------------------------------------------------------------	2	novel
		len	cloning frequencies
			CE1
	--------------GCATCACTCGGACACGGCTTTC--------------------------------------------------	22	1
	--------------GCATCACTCGGACACGGCTTTCAAT-----------------------------------------------	25	1
celegans	tccagcaagcccaaGCATCACTCGGACACGGCTTTCAATactgtaattgtccagttgatccatgtttggcgcaagctttttatgga
	**************************************************************************************
	--------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<---	ZK402.3 ZK402.3 ZK402.3
celegans	((((((..((((((((((((((.(((((..((..........))...)))))))).))....))))))).))..)))......)))	0.500 -23.00

celegans

chromosome:X:1402504:1402589:-1

Opposite_strand|Boundary_coding|ZK402.3|ZK402.3 ## ZK402.3|protein_coding|ZK402.3|ZK402.3 [Source:RefSeq_peptide;Acc:NP_508262] ## {SimpF: WRM0625bG09 -1 fosmid,WRM0633aC09 -1 fosmid,WRM0617aH09 -1 fosmid,WRM064cE08 -1 fosmid,ZK402.3 -1 Expression_profile,WRM0629aD05 -1 fosmid,WRM0635cC09 -1 fosmid,WRM0636bA02 -1 fosmid,WRM063cH01 -1 fosmid,WRM0639aA01 -1 fosmid}

novel_lenNOK_bulgeHIGH (5 loci)

block2149 [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	0.158	no	no	0.36/0.36	25/25/0.00	0.0	0.0	1	0	1	0	13	1	3arm	1	nd	0.24	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------UUAACUU------------------------------	1	novel
		len	cloning frequencies
			CE1
	----------------------------------------------------GTTAACTTGACTCAGGACTCTTTAT-------------	25	1
celegans	ccattgcacaatcatataaagaatttcaatcaagtttattcatcacagcaaaGTTAACTTGACTCAGGACTCTTTATatttaatattggg
	******************************************************************************************
celegans	(((..........(((((((((.(((...(((((((.(((...........))).)))))))....))).))))))))).......))).	0.990 -12.93