C.elegans small RNAs

miR-Intess™

miR classification

Alignments

noncloned miRBase miRNAs

miRNAknown (7 loci)

cel-mir-356

block3719 (miRBase cel-mir-356) [miRNAknown]

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
miRBase cel-mir-356	0.018	no	no	0.43/0.43	21/21/1.00	nd	nd	0	0	0	0	25	6	5arm	1	nd	0.29	2	0	0	na	na

block3719 hairpin

		reads	miRBase family seed
seed	----------------------------------------------UGAGCAA-------------------------------------------------------------------------------	0	miR-233/356/87
		len	cloning frequencies

cel-miR-356	---------------------------------------------TTGAGCAAC-GCGAACAAATC-A----------------------------------------------------------------	21
celegans	--------------------TAAAGTTTCCTTGAGAACAATGTGGTTGAGCAAC-GCGAACAAATC-ATCAATGTAAATTTCAGCGGATTCGTTACGACGTGTCTCACCACATCGTTAGTAGGATTTCAGAA
cbriggsae	---------------------------------------------ATGAGCAAC-GCGAACAAATCCTCTTAT---AA------GAGATTTGCCACGCCGCCGCTCAC------------------------
cbrenneri	---------------------------------------------TTGAGCAATAGTAGAAATGACCAACAA----AATTTACCCAAATCT----TGTTGTTTTCCAC--------------AATTTCTCAG
cjaponica	---------------------------------------------ATGAGCAAT-GCGAACAAATCAATCGAT---AATTCAGATGGATTTGTTGCCACGTGGCTCAC------------------------
ppacificus	---------------------------------------------TTGAGCAACAGCGTAAGAGAC-ATCGATGGAAA----CGTAGATTACCTTTAATTGTGTTCAT------------------------
cremanei	TAGAGGAAAAGAAATAAAATTAAACCGCTTTTGCCATCGATGTGGTTGAGCAAC-GCGAACAAATC-ATCGA----AAATGACTGAGATTTGCGCCAACGTGGCTCACCACATCG-------AATTGGAGCG
	******* * * * * **
celegans	.......((((....(((.(((((((.(((..(( ((((((.(((( .....((.......))...)))).))).)).)))..)))))))))).)))...))))........	1.000 -29.20
cbriggsae	.(((((... (((..(((((.((((... .) ))))))))...)))....))))).	1.000 -16.00
cbrenneri	.((((.(((.((.((((....(((((( .((((....)))).) ))))).)))).)) .))).)))).	1.000 -13.00
cjaponica	.(((((... ((.((((((((.(((((. ...)).))).))))))))))......))))).	1.000 -18.60
ppacificus	.(((((.((((...(((.... (((.(((.... ))).)))...)))...))))))))).	0.995 -13.00
cremanei	.........................((((((.....(((((((((.(((((.(( (((..(((((( .(((. .......))))))))))))....)).))))))))))))) )...))))))	0.960 -37.30

celegans	chromosome:III:7860073:7860182:1	intergenic ## {SimpF: WRM0615aC07 1 fosmid,ZK652.2 1 Expression_profile,WRM061cC03 1 fosmid,WRM065dF11 1 fosmid,WRM068bA12 1 fosmid,WRM0635aH10 1 fosmid} ## {MIR: cel-mir-356}
cbriggsae	chromosome:chrIII:10353527:10353676:-1	Same_strand\|Intronic_coding\|NM_000209 ## Opposite_strand\|Intronic_coding\|NM_170975 ## {MIR: cbr-mir-356}
cbrenneri	chromosome:chrUn:167667831:167667980:1	intergenic
cjaponica	chromosome:chrUn:31081396:31081545:1	intergenic
ppacificus	chromosome:chrUn:165565819:165565968:1	intergenic
cremanei	chromosome:chrUn:133239914:133240032:-1	Opposite_strand\|Intronic_coding\|NM_001002694

cel-mir-270

block4087 (miRBase cel-mir-270) [miRNAknown]

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
miRBase cel-mir-270	0.017	no	no	0.55/0.55	20/20/1.00	nd	nd	0	0	0	0	12	11	3arm	1	nd	0.15	2	0	0	na	na

block4087 hairpin

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------------GCAUGAU----------------------------------------	0	novel
		len	cloning frequencies

cel-miR-270	-------------------------------------------------------------------------------------------GGCATGATG-TAGCAGTG--GAG-------------------------	20
celegans	------GTCGCTAGCCTCTT---------TACCTGCCTACACACCTT-TCTGCCTACGTGGCACATTGGTAGGCAAGA------------GGGCATGATG-TAGCAGTG--GAGATGGACTGCCAC-------------
cbrenneri	---------------CTTTT---------TCTCTG-----ACACTCT-CATGCACTCACG------TGAGGGATGAAATCCCACACGCACGCGCATGATGATGTCAGTG--AGGAGG----------------------
ppacificus	TACTTGGTGGTAGGGCTGTTAAAATGAAGAACTCGTCTCCCCATTCCACGTGCTCTCTCGTCACTCTGATCGGCGAGA------------GAGCATGATGAATGAAGAGACGGAAGAGACGGTTACAGCCCTACTTGTA
	* * * * ** * * * * ****** * *
celegans	...((.(((((((( (((.(((.(((((((((( ..(((((((...........)))))))..) )))..)).)) )))))))) )))).)).))))...	1.000 -36.10
cbrenneri	((((( ((.((( (((.((( (((((.....(( ((.(((((...))))).)))).....)))))).)))))))).) ))))))	1.000 -35.50
ppacificus	........(((((((((((.....((......(((((((..(((((..((((((((((((((.........))))))) )))))))..)))))..)))))))......))...)))))))))))....	0.994 -58.80

celegans	chromosome:IV:3258451:3258545:-1	intergenic ## {SimpF: WRM0638aG10 -1 fosmid} ## {MIR: cel-mir-270}
cbrenneri	chromosome:chrUn:100735507:100735585:-1	intergenic
ppacificus	chromosome:chrUn:115473103:115473229:1	Opposite_strand\|Intronic_coding\|NM_203861

cel-mir-258

block8115 (miRBase cel-mir-258-2) [miRNAknown]

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
miRBase cel-mir-258-2	0.099	no	no	0.38/0.38	21/21/1.00	nd	nd	0	0	0	0	5	20	5arm	2	nd	0.19	2	0	0	na	na

block8115 hairpin

		reads	miRBase family seed
seed	------GUUUUGA-----------------------------------------------------------------------------------	0	novel
		len	cloning frequencies

cel-miR-258	-----GGTTTTGAGAGGAATCCTTTT----------------------------------------------------------------------	21
celegans	gcaatGGTTTTGAGAGGAATCCTTTTacatatttgttgaagttttcgctcgaatttgtggtcgaatactgtagaaggaagcctgcacgaagttttg
	************************************************************************************************
celegans	.......(((((.((((..((((((((((((((((.....(..(((....)))..).....)))))).))))))))))..))).).))))).....	1.000 -24.60

celegans

chromosome:X:227953:228048:1

intergenic ## {MIR: cel-mir-258-2}

block8116 (miRBase cel-mir-258-1) [miRNAknown]

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
miRBase cel-mir-258-1	0.099	no	no	0.38/0.38	21/21/1.00	nd	nd	0	0	0	0	5	20	5arm	2	nd	0.19	2	0	0	na	na

block8116 hairpin

		reads	miRBase family seed
seed	------GUUUUGA-----------------------------------------------------------------------------------	0	novel
		len	cloning frequencies

cel-miR-258	-----GGTTTTGAGAGGAATCCTTTT----------------------------------------------------------------------	21
celegans	gcaatGGTTTTGAGAGGAATCCTTTTacatatttgttgaagttttcgctcgaatttgtggtcgaatactgtagaaggaagcctgcacgaagttttg
	************************************************************************************************
celegans	.......(((((.((((..((((((((((((((((.....(..(((....)))..).....)))))).))))))))))..))).).))))).....	1.000 -24.60

celegans

chromosome:X:237369:237464:1

intergenic ## {MIR: cel-mir-258-1}

cel-mir-264

block8214 (miRBase cel-mir-264) [miRNAknown]

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
miRBase cel-mir-264	0.278	no	no	0.55/0.55	20/20/1.00	nd	nd	0	0	0	0	14	11	3arm	1	nd	0.25	3	0	0	na	na

block8214 hairpin

		reads	miRBase family seed
seed	------------------------------------------------------------GCGGGUG--------------------------	0	novel
		len	cloning frequencies

cel-miR-264	-----------------------------------------------------------GGCGGGTGGTTGTTGTTATG--------------	20
celegans	tggcggcggtcgacatgtacatatcaccagtctggcttttcccgtttccgcgagcaagcGGCGGGTGGTTGTTGTTATGggataccggagcca
	*********************************************************************************************
celegans	.(((..((((...((((.(((.((((((.(((..(((((((.((....)).))).))))))).))))))...)))))))....))))..))).	1.000 -32.80

celegans

chromosome:X:2819248:2819340:1

intergenic ## {SimpF: WRM0613cD07 1 fosmid,WRM067bH09 1 fosmid,WRM0633aD10 1 fosmid} ## {MIR: cel-mir-264}

miRNAknown_rep_randfoldOK (4 loci)

cel-mir-1818

block606 (miRBase cel-mir-1818) [miRNAknown_rep_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
miRBase cel-mir-1818	0.001	no	DNA	0.39/0.39	23/23/1.00	nd	nd	0	0	0	0	18	4	5arm	1	nd	0.17	1	0	0	na	na

block606 hairpin

		reads	miRBase family seed
seed	-------------------------------GUGGUCU----------------------------------------------------------------------------------------------	0	novel
		len	cloning frequencies

cel-miR-1818	------------------------------TGTGGTCTTCATGCCATGATTTT-------------------------------------------------------------------------------	23
celegans	CTGGAAAGAGTGGCCTTT------------TGTGGTCTTCATGCCATGATTTTAT----CACTCAAACTGATAAAAT---CATAGTTTGG--------AAACCTCGACAGGCTTTTCTTTTCTT--------
cbriggsae	------------------------------TGTGGTCTACA------GTATTTTTTTGAGTATCAATTTCAGAATG------------------------------------------TATCTGTTACCATG
cbrenneri	------------------------------GGTGGTCT-------------------------TAAGGCTAGGGAAC---CAAGGTATTG-------------------GTGTCCTCTTTTTTGAGACCTTT
cjaponica	ATGGAACTGGCGGTGGCTCCCATTCCGAAATGTGGTCTACCCGCCATGGATTTGTTTGACTA-CAATTGCGAACAAC---CTGGATACTACCACATAAAATTGTCCAATGAGGCGTCATGGCTGCTTCCGT-
ppacificus	------------------------------TGTGGTCT---CACACACATTTTCTCGCCCGCTCAAGCTGAGAAAGAGTGTAAAGTATGA--------------------------------AGAGACCGAG
	*****
celegans	..((((((((.(((((.( ((.(((.((((.((.(((((((((( ((.......))))))))) ))).)).))) ).))).))).))))).))))))))..	1.000 -40.40
cbriggsae	.(((((..((( ((((..(((((((.......))))))).) )).)))).))))).	1.000 -14.50
cbrenneri	...((((( (((((..((((((( (((....))) )).))).)).))))))))))...	1.000 -21.10
cjaponica	((((((..(((.(((((.((((((.(((.(((((((.......(((.((..(((((((.... ......)))))))) )))).....)))))))....)))...)))).)).))))).)))..))))))	0.978 -39.50
ppacificus	..(((((( (((((((.(((((((((........)).))))))).))))...)).... .)))))))..	0.982 -20.40

celegans	chromosome:I:13980845:13980941:-1	intergenic ## {SimpF: WRM0637bG05 -1 fosmid,WRM0610cB03 -1 fosmid,WRM0624cC10 -1 fosmid} ## {MIR: cel-mir-1818}
cbriggsae	chromosome:chrX:6785189:6785325:1	Opposite_strand\|Intronic_coding\|NM_153821 ## Same_strand\|Intronic_coding\|NM_125756 ## {Repeats: Mariner7_CB 0 219 -1 class=DNA}
cbrenneri	chromosome:chrUn:97054939:97055075:-1	intergenic
cjaponica	chromosome:chrUn:116767087:116767213:1	Same_strand\|Exonic_coding\|NM_073345
ppacificus	chromosome:chrUn:149498214:149498350:-1	intergenic

cel-mir-1823

block1212 (miRBase cel-mir-1823) [miRNAknown_rep_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
miRBase cel-mir-1823	0.004	no	Satellite	0.36/0.36	22/22/1.00	nd	nd	0	0	0	0	16	3	3arm	1	nd	0.27	2	0	0	na	na

block1212 hairpin

		reads	miRBase family seed
seed	--------------------------------------------------------------------------ACUGGAA---------------------------------------------	0	novel
		len	cloning frequencies

cel-miR-1823	-------------------------------------------------------------------------TACTGGAAGTGTTTAGG--AGTAA-----------------------------	22
celegans	TTTGACCTGAACGT-----CACCCCTAAC--CCTATGCAGTATTTGGAGCTCA---------------TAAAATACTGGAAGTGTTTAGG--AGTAATGCTCAGTTGTCAGAA-------------
cremanei	-----------TGCAGAAGCACTTGCAACAGTTACTGGAATTATTGAT-----------------------GGAACTGGAAGT-TGTGGATCTGCA------------------------------
cbriggsae	CAAAATAACGAAGTTTCTGAAACTCTAAA--TTCCTA-AATTTTTGATATTCAGAAGTTCGGAAATTCTGAAATACTGGAATTAAAAAATTCGGAAATTCGGAAATTTAGAAATTCTGGAATTCTG
cbrenneri	------------------GTTTTTCCAAA-----ATTGAGTTTTTGAT--------------------TAAAAAACTGGAATTTTGAGAG--AAAA------------------------------
ppacificus	------------------GCTCTCCTCAT--TTCCCATTGTCTCTCGT-----CAGTT---AGAGGTAAGTGACACTGGAAAAGAGAGGA--GGAA------------------------------
	* * * ******* *
celegans	((((((((((.((( .((.(((((( .((...((((((((........ ..))))))))..)).))).))) .)).))).))))..)))))).	1.000 -24.70
cremanei	.(((((..(((..((..(((((.(((..........) )))))))...)) .)))..))))).	0.994 -15.60
cbriggsae	((.(((..((.((((((((((..((..(( ((((.( (.((((((((.(((((...(((((.....)))))...))))))))))))).)).)))).))..))..)))))))))).))..))).))	0.980 -30.10
cbrenneri	.(((((((((( (((.(((((((... ..))))))).)).))))).))) ))).	1.000 -13.60
ppacificus	..(((((((.( ((.(((.((((.((..( (.... ...))..)).)))).))).)))..))))) ))..	1.000 -23.10

celegans	chromosome:I:12608609:12608697:1	intergenic ## {SimpF: WRM0635dA11 1 fosmid,WRM066cD10 1 fosmid,WRM0641dE06 1 fosmid,WRM0612aE11 1 fosmid,WRM0638dG06 1 fosmid} ## {MIR: cel-mir-1823}
cremanei	chromosome:chrUn:75746237:75746365:1	Same_strand\|Exonic_coding\|NM_069609 ## Same_strand\|Boundary_non-coding\|NM_207113 ## Same_strand\|Boundary_coding\|NM_001088723
cbriggsae	chromosome:chrII:4263615:4263737:-1	Opposite_strand\|Intronic_coding\|NM_140813 ## Same_strand\|Intronic_coding\|NM_006287 ## {Repeats: MINISAT4_CB 99 468 -1 class=Satellite}
cbrenneri	chromosome:chrUn:129274557:129274685:-1	Opposite_strand\|Intronic_coding\|NM_065052
ppacificus	chromosome:chrUn:25976493:25976621:-1	intergenic

cel-mir-792

block6401 (miRBase cel-mir-792) [miRNAknown_rep_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
miRBase cel-mir-792	0.001	no	DNA,RC,Satellite	0.30/0.30	23/23/1.00	nd	nd	0	0	0	0	13	6	3arm	1	nd	0.13	1	0	0	na	na

block6401 hairpin

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------UGAAAUC-------------------------------------------------------	0	novel
		len	cloning frequencies

cel-miR-792	------------------------------------------------------------------------------TTGAAATCTCTTCAACTTTCAGA----------------------------------------	23
celegans	---AAGTTGGTCAACGTTTGAGAGTTCAAAAGATTTAGC---AATTTTATACGAGTG------------------AAATTGAAATCTCTTCAACTTTCAGACGTTTTCTGATTT---------------------------
cremanei	------------GGAATTTA----TTCGAAAAAT--------GATGTCATATCGAGAAGTTTTG-----------ATTATGAAATCTTCT---------AGTGATCTCC--------------------------------
cbriggsae	TTTGAAGTGTCCAGATTTTCAAATTTTGAAAATATTAG----AATTTCAAAATTTCAGAACTCCAAAATTACAGAATTTTGAAATCTCAG-AATTT---GAAATTCTCAAAGTTTGAAATTCCTGGAACTCGGA-------
cbrenneri	---------------------GTTTCTGCAATTCGCAT----GATTTCAAA----------CTGCGCTGAAGAACAATTTGAAATCT-----ATCTGACAGAAAT------------------------------------
cjaponica	---------CGCTGAACTCAACGCTATGCGATTTTCATTTTGGTCTCCAAATTATTTCATTTCACGTATAAATTCAACATGAAATCAAAT-AATTT---GGAGA---CCAAAATGGAAATCGAATAGCGTTGAGTTCAGCG
ppacificus	--------------------------TATAAAGTGAAGACCTGATTGAA------------TTCCTCTGTATCGCGAACTGAAATCTCTTCACTCTTGTA-----------------------------------------
	* * *******
celegans	((((..(..((((((((((((((.((.(((((...( ((((((((....))) )))))).))))).)).))))))))))))))..)..))))	1.000 -32.20
cremanei	(((..((( ((.(((.... (((.((((((((((....)))) )).)))).)))))). )))))..)))	0.993 -13.00
cbriggsae	((((.(((.(((((..(((((((((((((........( (((((((((.(((.(((....(((((((....)))))))...))).)) ).))) ))))))))))))))))))))...))))))))))))	0.997 -35.40
cbrenneri	(((((((....(((.(( ((((((((( .((..........)).))))))))). )).))))))))))	0.978 -13.30
cjaponica	((((((((((((((((((.(((((((((((((((((((((((((((((.((((((.((.........)).)))))).)))) ))))) ))))) ))))))))))))))).))))))))))))))))))	1.000 -79.60
ppacificus	(((((((((((((...((((... (((...........)))....)))))))))))).)))))	0.892 -10.70

celegans	chromosome:V:3042091:3042180:-1	intergenic ## {SimpF: WRM0623bG08 -1 fosmid,WRM0614aB12 -1 fosmid,WRM0624bG01 -1 fosmid,WRM0638aC03 -1 fosmid,WRM0622cA02 -1 fosmid,WRM0615aE03 -1 fosmid} ## {MIR: cel-mir-792}
cremanei	chromosome:chrUn:67954661:67954790:1	Same_strand\|Intronic_coding\|NM_001087437
cbriggsae	chromosome:chrII:3428513:3428638:-1	Opposite_strand\|Intronic_coding\|NM_012623 ## {Repeats: DNA8-12_CB 327 419 -1 class=DNA,MINISAT4_CB -2 553 1 class=Satellite,HELITRON7_CB -577 804 1 class=RC} ## {SimpF: trf}
cbrenneri	chromosome:chrUn:173017142:173017271:-1	intergenic
cjaponica	chromosome:chrUn:137584682:137584806:1	intergenic
ppacificus	chromosome:chrUn:27677621:27677750:-1	Same_strand\|Intronic_coding\|NM_015802

cel-mir-271

block8238 (miRBase cel-mir-271) [miRNAknown_rep_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
miRBase cel-mir-271	0.005	no	DNA	0.60/0.60	20/20/1.00	nd	nd	0	0	0	0	23	1	5arm	1	nd	0.10	1	0	0	na	na

block8238 hairpin

		reads	miRBase family seed
seed	-----------------------------------------CGCCGGG---------------------------------------------------------------------------------	0	novel
		len	cloning frequencies

cel-miR-271	----------------------------------------TCGCCGGGTGGGA--AAGCATT-------------------------------------------------------------------	20
celegans	-----------------AATAGAAAACGGGGCCCGCCGGCTCGCCGGGTGGGA--AAGCATTCGACAGCAAGACGTGTTTTTCA--------ATCTGCGACTCGGCGATTCCC-ATCATCACT------
cremanei	----------------------------------------CCGCCGGGAAATTCTAGG------------AGAGTC------------------------CGCGACGATTCTCTAGAAGTCCGGTGG--
cbriggsae	-----------------------------GGTGACCCGGCCCGCCGGGCCGGGCCGGG---TCGAAAAAAAAATCT------------------------TCCGGCCCGGCCCGGTCGGCCCGGGTACC
cjaponica	TTGCCAGGCAGAGAGTGTGTAAGCGATGCCGCGCTGCGCCGCGCCGGGTGGCGACGAGGCGCAGACTGCGAGAGTGCGTTGTCATTCGACGCAACCGCGGCGCGGCGCGTCGACATCGG--CGGCAA--
	******* * * * ** * * *
celegans	..........((((..(((((..((((.((((.((( ((((((((........)).))))))))). ))))))))..)))))..)))) .........	1.000 -36.70
cremanei	((((((((...(((((.( (((((( ......)))))))))))).))))))))	1.000 -27.60
cbriggsae	(((.((((((.(((((((((((((((((( ..((........)). ))))))))))))))).))).)))))))))	1.000 -58.90
cjaponica	.((((..((...((...(((..(((.((((((((((((..(((.((((((((((((...(((.....)))......)))))))))))).)))...)))))))))))))))..))))).) ))))).	0.836 -65.80

celegans	chromosome:X:3411992:3412086:1	intergenic ## {SimpF: WRM0620aA11 1 fosmid,WRM0618dH04 1 fosmid,WRM0627bE05 1 fosmid,WRM0631aG02 1 fosmid,WRM0624cH01 1 fosmid,WRM0615dE08 1 fosmid,WRM0637dG11 1 fosmid,WRM0631cF07 1 fosmid,WRM0624dD03 1 fosmid,WRM0638aH11 1 fosmid,WRM069aE06 1 fosmid} ## {MIR: cel-mir-271}
cremanei	chromosome:chrUn:102249215:102249349:1	Same_strand\|Intronic_coding\|NM_071374
cbriggsae	chromosome:chrX:11365346:11365418:-1	Opposite_strand\|Intronic_coding\|NM_004906 ## Same_strand\|Intronic_coding\|NM_001122952 ## {Repeats: MuDR-14_CB 1 375 -1 class=DNA} ## {SimpF: trf}
cjaponica	chromosome:chrUn:30767042:30767166:-1	Opposite_strand\|Boundary_non-coding\|NM_172084 ## Same_strand\|Intronic_coding\|NM_001006872 ## Opposite_strand\|Intronic_coding\|NM_001028132

miRNAknown_rep_shortStem_randfoldOK (2 loci)

cel-mir-1828

block1117 (miRBase cel-mir-1828) [miRNAknown_rep_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
miRBase cel-mir-1828	0.002	no	DNA	0.35/0.35	23/23/1.00	nd	nd	0	0	0	0	0	5	3arm	1	nd	0.27	3	0	0	na	na

block1117 hairpin

		reads	miRBase family seed
seed	---------------------------------------------------------------------CUGGAAG-----------------------------------	0	novel
		len	cloning frequencies

cel-miR-1828	--------------------------------------------------------------------ACTGGAAGCATTTAAGTGATAGT--------------------	23
celegans	-----------------------GATCACTTTTATCGGTTCCGGTCCCTCTGCAAAAAAG-----TGGACTGGAAGCATTTAAGTGATAGT--------------------
cremanei	CGGGGACGACGTGCGGGTCTCGTGGCGGCTTTCTACCGTAC---TTCACTCATAAAAA--------GTTCTGGAAGTACAGTAGTCGCAACGAGACCCGCCCACGTCTCCG
cbriggsae	-----------------------GATCAAT---CATCGTGCCGATTGACCTGAAGCCAAAACTTTTGGACTGGAAGA--TGAAGCTTGGTC--------------------
cjaponica	--GAACCCGAGAGCTTTCTGGCCGGCTACTTTTCATGCTTCCTGTCCACCGTTTATCA--------GAACTGGAAGCATTGAAGTGGCGGCGCCTGAATGTTTATTGGTTT
	* * * * * * * *****
	+++++ +++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++++ +++++	T22A3.5 T22A3.5 pash-1
celegans	.(((((((..((.(.(((((((((..((.......)) .))))))))).)))..)))))))...	1.000 -25.10
cremanei	((((((((....(((((((((((.((((((....((.(((( ((((((.......) ))....))))))).)))))))).)))))))))))...))))))))	1.000 -53.30
cbriggsae	((((((( ((((...(((.....((.((((......)))).))..)))..)) )))...))))))	0.964 -14.50
cjaponica	(((((...((((.(((.(((..((((((((..((((((((..((............ ))...)))))))).))))))))...))).))).))))...)))))	1.000 -35.70

celegans	chromosome:I:10600452:10600514:1	Same_strand\|Intronic_coding\|T22A3.5\|T22A3.5 ## T22A3.5\|protein_coding\|pash-1\|pash-1 encodes an RNA-binding protein that is orthologous to Drosophila Pasha and mammalian DGCR8. pash-1 activity is required for processing of primary miRNA transripts (pri-miRNAs), such as that of let-7, to generate pre-miRNAs that will then be processed by DCR-1 to generate mature miRNAs. accordingly, pash-1 mutants show defects in let-7-mediated developmental processes, namely the transition from late larval to adult cell fates. [Source: WormBase] ## {SimpF: WRM0621aA07 1 fosmid,WRM0630aE12 1 fosmid} ## {MIR: cel-mir-1828}
cremanei	chromosome:chrUn:23148206:23148305:1	intergenic
cbriggsae	chromosome:chrV_random:248632:248734:-1	Same_strand\|Intronic_coding\|NM_072444 ## Opposite_strand\|Intronic_coding\|NM_062190 ## {Repeats: Mariner21_CB -32 418 1 class=DNA}
cjaponica	chromosome:chrUn:74907003:74907103:-1	Opposite_strand\|Intronic_coding\|NM_001017254

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noncloned miRBase miRNAs:

Page 3

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