miR-Intess: classification

other hairpins

novel_cloningOK_nonpairedHIGH_bulgeHIGH (3 loci)

block4202 [novel_cloningOK_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	0.357	no	no	0.62/0.68	19/21/0.80	0.0	0.0	4	0	1	0	2	14	5arm	3	nd	0.29	2	5	1	na	na

		reads	miRBase family seed
seed	---GAUGGCG--------------------------------------------------------------------------	5	novel
		len	cloning frequencies
			CE1
	--CGATGGCGGACAAGTCGGCTT-------------------------------------------------------------	21	4
	--CGATGGCGGACAAGTCGGC---------------------------------------------------------------	19	1
celegans	aaCGATGGCGGACAAGTCGGCTTacatgggcgctggtggctatggatcgggctacatgggatccaatgcttcttcgtcaggtta
	************************************************************************************
	.........>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	C24D10.8 C24D10.8 nspd-6
celegans	(((..(((((((.((((.((.((.(((((((.(((((........)))))))).)))).)).))...)))).))))))).))).	0.850 -25.30

celegans

chromosome:IV:5165637:5165720:-1

Same_strand|Boundary_non-coding|C24D10.8|C24D10.8 ## C24D10.8|protein_coding|nspd-6|Nematode Specific Peptide family, group D family member (nspd-6) [Source:RefSeq_peptide;Acc:NP_001076664] ## {SimpF: WRM0633dC11 -1 fosmid,C24D10.8 -1 Expression_profile}

block5518 [novel_cloningOK_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	0.168	no	no	0.38/0.48	21/21/1.00	0.9	0.9	7	0	1	0	4	1	3arm	1	nd	0.29	3	7	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------GGAGUUG-----------------	5	novel
seed	----------------------------------------------------------AUUGGAG--------------------	2	novel
		len	cloning frequencies
			CE1
	------------------------------------------------------------TGGAGTTGTTTCAGTCAGGTC----	21	5
	---------------------------------------------------------TATTGGAGTTGTTTCAGTCAG-------	21	2
celegans	gacacttttacccactgttttacgtattctattttcctcaactctattgaaatcaatTATTGGAGTTGTTTCAGTCAGGTCgtcc
	*************************************************************************************
	-----------------------------------------------------------------------------------------------	Y73B6BL.35 Y73B6BL.35 Y73B6BL.35
celegans	(((......(((.((((.....................((((((((.(((......))).))))))))...))))..))).))).	0.470 -12.65

celegans

chromosome:IV:6413188:6413272:1

Opposite_strand|Intronic_coding|Y73B6BL.35|Y73B6BL.35 ## Y73B6BL.35|protein_coding|Y73B6BL.35|Y73B6BL.35 [Source:RefSeq_peptide;Acc:NP_741424] ## {SimpF: WRM0631aB07 1 fosmid,WRM0614aD01 1 fosmid}

block6169 [novel_cloningOK_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	0.312	no	no	0.29/0.30	20/21/1.00	0.0	0.0	7	0	1	0	1	7	3arm	1	nd	0.24	3	8	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------UAUAUUU--------------	8	novel
		len	cloning frequencies
			CE1
	------------------------------------------------TTATATTTTCAGTCAAGTCGT-	21	7
	------------------------------------------------TTATATTTTCAGTCAAGTCG--	20	1
celegans	ccactgcttcattcaactgttatgtgttttaacgatttacagtttcaaTTATATTTTCAGTCAAGTCGTg
	**********************************************************************
celegans	.(((.((((......((((..(((((....(((........))).....)))))...)))).)))).)))	0.870 -9.00

celegans

chromosome:IV:16163494:16163563:1

intergenic ## {SimpF: WRM0610aE06 1 fosmid,WRM0621bE04 1 fosmid}

novel_lenNOK_cloningOK (3 loci)

block3499 [novel_lenNOK_cloningOK]

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	0.876	no	no	0.42/0.47	19/26/0.00	0.0	0.0	5	0	1	0	6	1	5arm	1	nd	0.19	3	6	1	na	na

		reads	miRBase family seed
seed	-------UUGAGAA------------------------------------------------------------	6	novel
		len	cloning frequencies
			CE1
	------GTTGAGAAAGTGGCTTGCTAAGTGTT------------------------------------------	26	5
	------GTTGAGAAAGTGGCTTGCT-------------------------------------------------	19	1
celegans	cgtattGTTGAGAAAGTGGCTTGCTAAGTGTTgaattcaatcaatagacgatgctgtctgtatctgaaaatcgc
	**************************************************************************
celegans	((.....((.(((.((((((((((((...((((....))))...))).))).)))).))...))).))...)).	0.420 -10.90

celegans

chromosome:III:3830844:3830917:1

intergenic ## {SimpF: WRM065cE05 1 fosmid,C36A4.10 1 Expression_profile,WRM0624bD07 1 fosmid,WRM0640dH02 1 fosmid,WRM063dB07 1 fosmid,WRM0626aB12 1 fosmid,WRM062aH09 1 fosmid,WRM0634bH05 1 fosmid,WRM0613aC06 1 fosmid}

block4267 [novel_lenNOK_cloningOK]

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	0.084	no	no	0.33/0.33	18/18/0.00	0.0	0.0	6	0	1	0	12	9	3arm	1	nd	0.00	0	6	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------AAUGUGA----------------------	6	novel
		len	cloning frequencies
			CE1
	----------------------------------------------------------TAATGTGATTTTGGGTTG------------	18	6
celegans	aaaaataattaactgtttcaaagttacattagatataatttgtgttcgagcattgcgaTAATGTGATTTTGGGTTGaaaaatgttttt
	****************************************************************************************
celegans	(((((((.((((((....(((((((((((((..........((((....)))).....)))))))))))))))))))....)))))))	0.860 -15.96

celegans

chromosome:IV:5580568:5580655:-1

intergenic ## {SimpF: WRM0630cD06 -1 fosmid,WRM063bD03 -1 fosmid,WRM0615dA02 -1 fosmid}

block6385 [novel_lenNOK_cloningOK]

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	0.639	no	no	0.39/0.39	18/23/0.20	0.0 0.0	0.0 0.0	1 4	0 0	1 1	0 0	21 17	-5 4	3arm_loop 3arm	1 1	nd nd	0.35 0.22	4 1	5	1	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------AAUUGGC---------------------------	4	novel
seed	-------------------------------------------------AUCGGUU------------------------------------	1	novel
		len	cloning frequencies
			CE1
	---------------------------------------------------------GAATTGGCATGTTTCTCT-----------------	18	4
	------------------------------------------------GATCGGTTTGAATTGGCATGTTT---------------------	23	1
celegans	ggtactcgtcgaagttttccgaggaaacgaagttccactttccaacaagatcggtttGAATTGGCATGTTTCTCTgaaaaaaagattatatt
	********************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<------------------------	Y40B10A.1a Y40B10A.1 lbp-9
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<........................	Y40B10A.1b Y40B10A.1 lbp-9
celegans	.......(((....(((((.((((((.....((.(((..(((.(((.......))).))).))).)).)))))).)))))...)))......	0.910 -15.90

celegans

chromosome:V:2068545:2068636:-1

Opposite_strand|Boundary_coding|Y40B10A.1a|Y40B10A.1 ## Opposite_strand|Boundary_non-coding|Y40B10A.1b|Y40B10A.1 ## Y40B10A.1|protein_coding|lbp-9|Fatty acid-binding protein homolog 9. [Source:UniProtKB/Swiss-Prot;Acc:Q965W1] ## {SimpF: Y40B10A.H -1 Expression_profile}

novel_loopOverlap_randfoldOK_nonpairedHIGH_bulgeHIGH (3 loci)

block1376 [novel_loopOverlap_randfoldOK_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	0.003	no	no	0.45/0.45	22/22/1.00	0.0	0.0	1	0	1	0	20	-3	5arm_loop	1	nd	0.32	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------CACAAGU------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	--------------------TCACAAGTCAAGACAGAGCTTC----------------------------------------------	22	1
celegans	cttgtcctagtccagaagcaTCACAAGTCAAGACAGAGCTTCaccgttctgtcttgtaatgtgacgcgctactcttatatcggaggag
	****************************************************************************************
celegans	(((.(((......(((.((.(((((...(((((((((((......)))))))))))...))))).)).....)))......))).)))	0.930 -31.50

celegans

chromosome:I:15064529:15064616:1

intergenic ## {SimpF: WRM066aE11 1 fosmid,WRM068cA11 1 fosmid,WRM067aB07 1 fosmid,WRM0628aC12 1 fosmid,WRM0625cG10 1 fosmid,WRM0619bG03 1 fosmid,WRM0629dE08 1 fosmid,WRM0637dE09 1 fosmid,WRM0623dH11 1 fosmid,WRM0631aD12 1 fosmid,WRM0640bG08 1 fosmid,WRM0626cH01 1 fosmid,WRM0615cH09 1 fosmid}

block5259 [novel_loopOverlap_randfoldOK_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	0.004	no	no	0.41/0.41	22/22/1.00	0.0	0.0	1	0	1	0	31	-2	5arm_loop	1	nd	0.36	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------CUAGCCG----------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	-------------------------------GCTAGCCGAGAAGAAAATAACA--------------------------------------------------------	22	1
celegans	agaaatcagattttatcctcgccgtctttccGCTAGCCGAGAAGAAAATAACAataaatttattttctcacaggttgtcggttttttttttttgaaaaatttgaattct
	*************************************************************************************************************
celegans	((((.(((((((((.((............(((.(((((....(((((((((........)))))))))....))))).)))............))))))))))).))))	0.980 -25.35

celegans

chromosome:IV:1972920:1973028:1

intergenic

block7331 [novel_loopOverlap_randfoldOK_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	0.001	no	no	0.35/0.35	23/23/1.00	0.0	0.0	1	0	1	0	31	-3	3arm_loop	1	nd	0.43	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------UCGAAUA----------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	--------------------------------------------------------TTCGAATATTTTTTGGGTGTGGT-------------------------------	23	1
celegans	tcttcgttgattatcacaccttaaaaacatttagcttaacgagcgcccgaagttcgTTCGAATATTTTTTGGGTGTGGTcattgtaggcaaggtgtggtgataacgatga
	**************************************************************************************************************
celegans	((.(((((.(((((((((((((...........((((.(((((((((((((((((....))))....))))))))).....)))))))))))))))))))))))))).))	0.690 -38.50

celegans

chromosome:V:12548212:12548321:1

intergenic ## {SimpF: WRM0631aC03 1 fosmid,WRM0630cG01 1 fosmid,WRM0628cD03 1 fosmid,WRM067dA01 1 fosmid,WRM0636dC04 1 fosmid,WRM0610dC02 1 fosmid,WRM0629cA07 1 fosmid,WRM062bC01 1 fosmid,WRM0614dA08 1 fosmid,WRM0630cB10 1 fosmid,WRM0619cH03 1 fosmid,WRM0626aD09 1 fosmid,WRM0612bB10 1 fosmid,WRM0617cE03 1 fosmid,WRM0640cD02 1 fosmid}

novel_cloningOK_loopOverlap_nonpairedHIGH_bulgeHIGH (2 loci)

block6340 [novel_cloningOK_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	0.43/0.50	20/24/1.00	0.0	0.0	7	0	1	0	29	-3	5arm_loop_3arm	1	nd	0.43	4	11	1	na	na

		reads	miRBase family seed
seed	------------------------------UUUGAAG---------------------------------------------------------------	7	novel
seed	---------------------------------GAAGAAG------------------------------------------------------------	2	novel
seed	--------------------------------UGAAGAA-------------------------------------------------------------	1	novel
seed	-----------------------------AUUUGAA----------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	-----------------------------ATTTGAAGAAGGTGGTAGCCTTG------------------------------------------------	23	7
	--------------------------------TGAAGAAGGTGGTAGCCTTG------------------------------------------------	20	2
	----------------------------GATTTGAAGAAGGTGGTAGCCTTG------------------------------------------------	24	1
	-------------------------------TTGAAGAAGGTGGTAGCCTTGAGG---------------------------------------------	24	1
celegans	ttctagcttagcaagtttggtcgaagaagATTTGAAGAAGGTGGTAGCCTTGaggacactttcacaaataggtttttcaatagttactttgggcctaggg
	****************************************************************************************************
celegans	.(((((((((..((((...((.((((((.(((((..(((((((....((....)).))))))).)))))...)))))).))....))))))))).)))).	0.990 -24.50