C.elegans small RNAs

miR-Intess™

miR classification

Alignments

noncloned miRBase miRNAs

miRNAknown_randfoldOK (18 loci)

cel-mir-1824

block1240 (miRBase cel-mir-1824) [miRNAknown_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-1824	0.004	no	no	0.52/0.52	23/23/1.00	nd	nd	0	0	0	0	12	4	5arm	1	nd	0.13	2	0	0	na	na

block1240 hairpin

		reads	miRBase family seed
seed	-------------GGCAGUG-------------------------------------------------------------------------	0	miR-34
		len	cloning frequencies

cel-miR-1824	------------TGGCAGTGTTTCTCCCCCAACTT----------------------------------------------------------	23
celegans	gttcaccagagtTGGCAGTGTTTCTCCCCCAACTTttgttacagaattgcaaaaatgttggccgtggtgaacacttccgcctctggtttgaag
	*********************************************************************************************
	-------------------------------------------------------------------------------------------------------	Y87G2A.18 Y87G2A.18 Y87G2A.18
celegans	.((((((((((.(((.(((((((..((((((((((((((.........))))))..)))))..).)).))))))).))).)))))))..))).	1.000 -32.80

celegans

chromosome:I:13513943:13514035:1

Opposite_strand|Intronic_coding|Y87G2A.18|Y87G2A.18 ## Y87G2A.18|protein_coding|Y87G2A.18|Y87G2A.18 [Source:RefSeq_peptide;Acc:NP_001021834] ## {SimpF: Y87G2A.D 1 Expression_profile} ## {MIR: cel-mir-1824}

cel-mir-267

block1995 (miRBase cel-mir-267) [miRNAknown_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-267	0.001	no	no	0.60/0.60	20/20/1.00	nd	nd	0	0	0	0	10	9	5arm	1	nd	0.20	1	0	0	na	na

block1995 hairpin

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

cel-miR-267	----------------------CCCGTGAA-----------GTGTCTGCTGCA---------------------------------------------------------------	20
celegans	----GTTTCAAAAC--------CCCGTGAA-----------GTGTCTGCTGCAAT---------CTAAATTTTTAGATATAGATGCAGTCGACTCTTCATTGGGTTTTCAGGAACC
cremanei	----ATTTTCAAAAAAATTTAGTCCGTGAAATTGGCTAAAAATCTGTTTTTCGACTGGTTTCGGCTG--------------------------TTTTTACTGGAT-----------
cbriggsae	----------------------GCCGTGAA-----------GCGTATTTTCAGAA---------TCAGGTGTAAATACACACCGATTCTATATTTTTCATTTG-------------
cbrenneri	GGGAATTTCTGGCAAAAT---GCCCGTGAATTTGG------GCGCCTTGCCCGCGTGAGTTCGGCAAGGCGCCCAAATTCACGGGCACTTCGCCCATTTTC---------------
cjaponica	----------------------CCCGTGAAAAT--------ACGCATTTTCCA----------------TTTAAAAGTGCAAAAATGCTATA-TTTTCATGGT-------------
	******* * *
	----- ---------- -------- -------------- ---------------------------------------------------------	Y38E10A.18 Y38E10A.18 nhr-234
celegans	(((((((((( ((.((((( (.(((.(((((.(( (((.(((....))).)))))))))).))).)))))).)))))))..))))).	1.000 -37.50
cremanei	.................((((((((((..((((..(((((.(((....))).))))).)))). .)))))).))))	0.857 -16.00
cbriggsae	...((((( (.((((....(((( ((.(((((......))))))))))))))).))))))...	0.997 -17.00
cbrenneri	((((((....(((.((.( (((((((((((((( ((((((((((.((....))..))))))))))))))))))))))))).)).))).))))))	0.954 -63.50
cjaponica	.(((((((((( (.(((((((.(( ((....))))..)))))))..)) ))))))))).	1.000 -18.40

celegans	chromosome:II:12638050:12638133:-1	Opposite_strand\|Intronic_coding\|Y38E10A.18\|Y38E10A.18 ## Y38E10A.18\|protein_coding\|nhr-234\|Nuclear Hormone Receptor family member (nhr-234) [Source:RefSeq_peptide;Acc:NP_496701] ## {SimpF: WRM0637aC04 -1 fosmid,WRM0626aG08 -1 fosmid,Y38E10A.R -1 Expression_profile,WRM0623aD06 -1 fosmid,WRM065aC11 -1 fosmid,WRM0625cD02 -1 fosmid,WRM0636bC01 -1 fosmid} ## {MIR: cel-mir-267}
cremanei	chromosome:chrUn:94429321:94429395:1	intergenic
cbriggsae	chromosome:chrII:9192538:9192661:-1	Same_strand\|Intronic_coding\|NM_001047939 ## Opposite_strand\|Intronic_coding\|NM_001090075
cbrenneri	chromosome:chrUn:105679745:105679836:-1	Same_strand\|Intronic_coding\|NM_064105
cjaponica	chromosome:chrUn:124277413:124277536:-1	intergenic

cel-mir-1822

block2318 (miRBase cel-mir-1822) [miRNAknown_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-1822	0.001	no	no	0.50/0.50	22/22/1.00	nd	nd	0	0	0	0	14	5	3arm	1	nd	0.23	2	0	0	na	na

block2318 hairpin

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

cel-miR-1822	--------------------------------------------------------------GAGCTGCCCTCA----GAAAAACTCT----------------------------	22
celegans	TTCTTGAAAACT-CCAATAGTTTCTCTGGGAAAGCTATCGGCCAAA--TTTAACT---GTCCGAGCTGCCCTCA----GAAAAACTCTTGGC---------TCATCGAGAA-----
cbriggsae	-TCTAGAAAGGT-CCGAGAGCCTATCCCGGAACGCTATCGGTTGCACTTTTCAAA--AAACCGAGCTGCCCGGG----GATAGACTCTTGGC------------TTCAGA------
cjaponica	ACGTCAAAGAGC-CCGAGAGCATATCCAGGAAAGCTATCGGAAGAAT-TTCCAATTTTATCCGAGCTGCCCTAG----GATACGCCCTCTGT--------CTTGTTTGGACGT---
cbrenneri	GTCTCGAACACCACCAAGAGTTTATCCAGGAAAGCTATCGGACTGACATTTAGTA-----CCGAGCTGCCCTGG----GATAGACTCTTGGT---------AATTTTAGAGAC---
ppacificus	-----------------------GCCCCAGCAAG-----GGAGAAGCACTTCGCGTACTTCGAAGCTGCCCTTGCCAAGGTATCTTCCACGT---------CTCTTTATTG-----
cremanei	-----------G-CCGAGAGTTTATCCAGGAAAGCTATCGGCCGAGTACTTAGAA-----CCGAGCTGCCCTCG----GATAGACTCTTGGCGAAAATCAACCATTCACAAACAGG
	* * * * ** * * ******** * * * * *
	+++++++++++++++++ +++++++++++++++++++++++++++++++++ +++++++ ++++++++++++++++ ++++++++++++++ ++++++++++ +++++	ZK84.2 ZK84.2 ZK84.2
celegans	.((((((..... ((((.(((((.((((((..(((..((((.((.. ......) ).)))))))..)).)) )).))))).)))). ...)))))).	1.000 -31.00
cbriggsae	(((.((..((. (((((((.(((((((((...((..((((((............ .))))))...))))))) .)))).)))))))) ))))))	0.998 -35.02
cjaponica	(((((...(((. ..(((.((.((((((((..(((..(((((.(((. .......))).))))))))..))).) )))).)).)))... ))).....)))))	0.998 -34.50
cbrenneri	(((((.......((((((((((((((((((..(((..(((((((((...))))). )))))))..))))) .))))))))))))) .......)))))	1.000 -46.14
ppacificus	(((...((((( ((...(((..((((.......))))))).)))))))...)))........... ..........	0.925 -20.40
cremanei	( (((((((((((((((((..(((..((((.............. )))))))..))).) ))))))))))))))........................	0.867 -37.34

celegans	chromosome:II:6015495:6015586:1	Same_strand\|Intronic_coding\|ZK84.2\|ZK84.2 ## ZK84.2\|protein_coding\|ZK84.2\|ZK84.2 [Source:RefSeq_peptide;Acc:NP_495200] ## {SimpF: WRM0624aF03 1 fosmid,ZK84.2 1 Expression_profile,WRM0632dB05 1 fosmid,WRM068cG09 1 fosmid,WRM061cD12 1 fosmid,WRM066bB08 1 fosmid} ## {MIR: cel-mir-1822}
cbriggsae	chromosome:chrII:8862553:8862642:-1	Same_strand\|Intronic_coding\|NM_001047975 ## Opposite_strand\|Intronic_coding\|NM_001011629
cjaponica	chromosome:chrUn:5014614:5014712:1	Same_strand\|Intronic_coding\|NM_062799
cbrenneri	chromosome:chrUn:49225410:49225504:1	Same_strand\|Intronic_coding\|NM_062799
ppacificus	chromosome:chrUn:84123368:84123441:-1	intergenic
cremanei	chromosome:chrUn:133094413:133094507:-1	Same_strand\|Intronic_coding\|NM_062799

cel-mir-273

block2745 (miRBase cel-mir-273) [miRNAknown_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-273	0.001	no	no	0.65/0.65	20/20/1.00	nd	nd	0	0	0	0	16	3	3arm	1	nd	0.10	2	0	0	na	na

block2745 hairpin

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

cel-miR-273	-----------------------------------------------------------------TGCCCGTACTGTGTCGGCTG-----------------	20
celegans	ACCTC---GTTTTGGGAGCAGC--CGGCATTTT--ACGGGCTACACTTTTTTTAAAATTGATGTGTGCCCGTACTGTGTCGGCTGCTTTGAAAATTTCGGT-
cjaponica	TTGTCAAAGTTCTATTCGCCACGGAGACATTCTCGATGGGC----------TTAAAC---ATGCCCGCCCGTAC--TGTCGTCTTC-------ACGTCGGCG
	* * ** * * **** * * ** * * ****** * * * ****
	++++++++++ ++++++++++++++ +++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	E01F3.1b E01F3.1 pde-3
celegans	(((.. (((((.(((((((( ((((((..( ((((((.((((................)))))))))))..)))))))))))))).)))))...)))	1.000 -48.69
cjaponica	................((((((((((((((...((.((((( ...... ..)))))..))... .)).))).)) .))).))))	0.977 -22.30

celegans	chromosome:II:14946941:14947034:1	Same_strand\|Intronic_coding\|E01F3.1b\|E01F3.1 ## Same_strand\|Boundary_non-coding\|E01F3.1a\|E01F3.1 ## E01F3.1\|protein_coding\|pde-3\|Probable 3',5'-cyclic phosphodiesterase pde-3 (EC 3.1.4.17). [Source:UniProtKB/Swiss-Prot;Acc:Q8I0P7] ## {SimpF: WRM0623dE11 1 fosmid,WRM0640dF03 1 fosmid} ## {MIR: cel-mir-273}
cjaponica	chromosome:chrUn:104330552:104330631:1	Same_strand\|Exonic_coding\|NM_069356 ## Same_strand\|Intronic_coding\|NM_210683 ## Opposite_strand\|Intronic_coding\|NM_011212

cel-mir-265

block4664 (miRBase cel-mir-265) [miRNAknown_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-265	0.001	no	no	0.55/0.55	20/20/1.00	nd	nd	0	0	0	0	7	15	3arm	1	nd	0.20	1	0	0	na	na

block4664 hairpin

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

cel-miR-265	-----------------------------------------------------------TGAGGGAGGAAGGGTGGTAT-------------------------	20
celegans	GGTTTGACTTACCCCCTCCTTCCGCTGGCCGCCGTTTTTATTATGAACTTGATGTGGTTTGAGGGAGGAAGGGTGGTATTTGAACC------------------
ppacificus	--------TTCTCCCCTCTGTTCACT-----CCTTCTTCGATCTAAA-TAGAGTAAGTGAGAGGGAGGAAGGGGGGGG--GGAATCTCTCCCTCTATCACGTGT
	**** * * * ** * * ** * *********** *** *
celegans	((((..(..((((((((((((((.(..(((((.((((.......)))).....)))))..).)))))).)))).)))).)..))))	1.000 -36.50
ppacificus	(((((((((((.(((.(( (((((((...(((... .)))......)))))))))))).))))))) ))))....................	0.990 -37.30

celegans	chromosome:IV:12740413:12740498:-1	intergenic ## {SimpF: WRM069bD03 -1 fosmid,WRM0639bE02 -1 fosmid,WRM061aB09 -1 fosmid,WRM0635bD10 -1 fosmid,WRM0630bD03 -1 fosmid,WRM0620dB12 -1 fosmid,WRM067bF06 -1 fosmid,WRM0627aC07 -1 fosmid} ## {MIR: cel-mir-265}
ppacificus	chromosome:chrUn:123644390:123644477:1	Opposite_strand\|Intronic_coding\|NM_060423 ## Same_strand\|Intronic_coding\|NM_028821

cel-mir-243

block5344 (miRBase cel-mir-243) [miRNAknown_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-243	0.001	no	no	0.65/0.65	23/23/1.00	nd	nd	0	0	0	0	15	5	3arm	1	nd	0.04	1	0	0	na	na

block5344 hairpin

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

cel-miR-243	---------------------------------------------------------------------------CGGTACGATCGCG--GCGGGATATC---------------	23
celegans	TGTTCACGCATAAGCCTGATATCTCGGTGCGATCGTACCGTATCGCT--------------CACACT-TAGATTACGGTACGATCGCG--GCGGGATATCAGGTACGTGATTGGA
cbriggsae	-------------GCCAGAAT-----CCGCGTTGGCACGTCGTCGAG----------ATTCTACAATAAGGGTCTCGGTACGATCGGAAGGCGCGGCG----------AATGGAC
cbrenneri	--------------------------AGGCGATGGGTCCTAGTCGCCTTGTCAGTCGATCCATCGAT-TGGCTTGAGGTACGACTGGA--GCTTCACC----------A------
ppacificus	--------------CTCCGTA-----ATCCGATCGTACCCAGCCGCG-------------CCCTGGT-CGGCT--GGGTACGATCGGA--TTACGGTA----------G------
	** * * * ** * * * ******* *
	++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++ ++++++++++++++++++++ ++++++++++++++++++++++++++++++	R08C7.12.1 R08C7.12 R08C7.12
celegans	...(((((.....(((((((((((((.(((((((((((((((((... ...... ..)).))))))))))))))) .))))))))))))).))))).....	1.000 -55.70
cbriggsae	.(((.... (((((((....(((((((((( (((((......)))))))))..)))).))...))))))).. ..)))..	1.000 -32.50
cbrenneri	.((.((.((.(((.((((((((((((((((((....))))) ))))..))))..)))))))) .)))).)) .	1.000 -31.60
ppacificus	..((((( (((((((((((((((((((.( (....)) ))))) ))))))))))))) )))))).. .	1.000 -51.40

celegans	chromosome:IV:4450772:4450869:1	Same_strand\|Intronic_non-coding\|R08C7.12.1\|R08C7.12 ## Same_strand\|Boundary_non-coding\|R08C7.12.2\|R08C7.12 ## R08C7.12\|protein_coding\|R08C7.12\|Uncharacterized protein R08C7.12. [Source:UniProtKB/Swiss-Prot;Acc:Q9GQ60] ## {SimpF: WRM0639cG05 1 fosmid,WRM0637aA04 1 fosmid} ## {MIR: cel-mir-243}
cbriggsae	chromosome:chrI:10235666:10235742:1	Opposite_strand\|Intronic_coding\|NM_212577 ## Same_strand\|Intronic_coding\|NM_067049 ## Same_strand\|Boundary_coding\|NM_060599
cbrenneri	chromosome:chrUn:179683520:179683657:-1	intergenic
ppacificus	chromosome:chrUn:174279691:174279828:-1	intergenic

cel-mir-1821

block6402 (miRBase cel-mir-1821) [miRNAknown_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-1821	0.004	no	no	0.38/0.38	21/21/1.00	nd	nd	0	0	0	0	23	5	3arm	1	nd	0.19	3	0	0	na	na

block6402 hairpin

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

cel-miR-1821	------------------------------------------------------------TGAGGTCTTATAGTTAGGTAG-----------------------	21
celegans	ATATGTAGTTGGTACAAGTTTGCCCAACTTGCAGACTTTTCAATTTTCGGCAAGTGGAATTGAGGTCTTATAGTTAGGTAGACATTTACTACAACTAATATATA
cremanei	----------------------CTTTTTTCTTAGACCCCCC--TTCTCATCGGGGG-----GAGGTCTTATAG-GAGATAG-----------------------
	* * **** * * * * ********** ***
celegans	((((((((((((((...(((((((.((((...(((((..((((((((........)))))))))))))...)))).)))))))...)))..)))))).))))).	1.000 -29.80
cremanei	((.((((((.((((((((( ((......))))) ).)))))...)) )))).))	1.000 -21.40

celegans	chromosome:V:3042529:3042632:-1	intergenic ## {SimpF: WRM0623bG08 -1 fosmid,WRM0614aB12 -1 fosmid,WRM0624bG01 -1 fosmid,WRM0638aC03 -1 fosmid,WRM0622cA02 -1 fosmid,WRM0615aE03 -1 fosmid} ## {MIR: cel-mir-1821}
cremanei	chromosome:chrUn:108725394:108725537:-1	intergenic ## {SimpF: trf}

cel-mir-268

block7292 (miRBase cel-mir-268) [miRNAknown_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-268	0.002	no	no	0.42/0.42	24/24/1.00	nd	nd	0	0	0	0	17	5	5arm	1	nd	0.17	2	0	0	na	na

block7292 hairpin

		reads	miRBase family seed
seed	------------------------GCAAGAA-----------------------------------------------------------------------------------	0	miR-268
		len	cloning frequencies

cel-miR-268	-----------------------GGCAAGAATTAGAAGCAGT-TTGGT------------------------------------------------------------------	24
celegans	------GGAAGTGGCTTTGAAGCGGCAAGAATTAGAAGCAGT-TTGGTGTCAGACACACT-ACTCACTCACTGCTTCTTGTTTTTTCTGCTTTCTTTGCTTTT-----------
cbriggsae	GGGAAAGGAAGTGTCTTTGAAGCGGCAAGAATTAGAAGCAGTTTTGGTGTCAGACACACTCACTGACTCACTGCTTCTTGTTTTTCTTCTTCTTCTTCTTCTGCTTCTTCTTCC
cbrenneri	-----------------------GGCAAGAATTAGAAGCAGTTTTGGTGTCAGACAC--------ACTCACTCCTTCTTGTTTTTTCT--------------------------
cremanei	-----------------------GGCAAGAATTAGACGGGGT-----GGCTCGACAC-----------CACCA-GTCTTGTTTTTTTC--------------------------
	************* * ** * *** * **********
celegans	.((((..(....(((((((.((((((.((((((((( ..((((..((.....)) ...)))).))))))))).)))))).)))))))..)..)))).	1.000 -32.60
cbriggsae	((((.(((((((......((((.((.(((((..(((((((((...((.(((((.........)))))))))))))))).....))))))).)))).......))))))).))))	0.999 -36.22
cbrenneri	((.((((((.(((((.(((...(((((.....)) ))).))).))))).)))))).))	1.000 -13.60
cremanei	...((((((.((((((((( (......))) ).)). )))).))))))...	1.000 -16.00

celegans	chromosome:V:11137087:11137181:1	intergenic ## {SimpF: WRM0635dB04 1 fosmid,WRM0630cC08 1 fosmid,WRM0634bB08 1 fosmid} ## {MIR: cel-mir-268}
cbriggsae	chromosome:chrV:7334131:7334244:-1	Same_strand\|Intronic_coding\|NM_125760 ## Opposite_strand\|Intronic_coding\|NM_134696 ## {Repeats: (GAA)n 3 46 -1 class=Simple_repeat} ## {SimpF: trf} ## {MIR: cbr-mir-268}
cbrenneri	chromosome:chrUn:67478937:67479071:1	Same_strand\|Intronic_coding\|NM_001114364
cremanei	chromosome:chrUn:20043304:20043438:-1	intergenic

cel-mir-796

block7651 (miRBase cel-mir-796) [miRNAknown_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-796	0.001	no	no	0.35/0.35	23/23/1.00	nd	nd	0	0	0	0	15	3	5arm	1	nd	0.17	2	0	0	na	na

block7651 hairpin

		reads	miRBase family seed
seed	-------------------------------------GGAAUGU------------------------------------------------------------------------------------------------------------	0	miR-1
		len	cloning frequencies

cel-miR-796	------------------------------------TGGAATGTAGTTGAGG---TTAGTAA------------------------------------------------------------------------------------------	23
celegans	---------------------ACTCTAATGACAAGCTGGAATGTAGTTGAGG---TTAGTAAAAGCACTATACTTGTTACAAAC-CTTGCCACGTTCC-------------GACTTGTCAAAAGAGT-------------------------
cremanei	TCGTCTTGA-ACTTCCTCGTCTCCTTCGGTTGCCTTTGGAATGTCGGTGAGAGCGTTGGTGAGTACCTCATCCT-----CAACC---------TTTCC-------------GAGTTCGAGAAGCGCCTTTCCGTAGAGGAAGTTGACCTCGA
cbriggsae	-------GCTACACCATCTTCAC------------CTGGAATGT------GC---CTAGTTTGTAGACTATCCTGT---CGAAC-----TCACTTCCA-------------CTTTGGTGGAGCTTCGTGTACAGC-----------------
cbrenneri	----------AGTTTTTGGTGAATTGCCAGCCAAAACGGAATGTTGCT-CGC---TTAGAAAAATCACGATTTG-----CAAGCACCAGCCACTTTCC-------------GTTTTCTTGCCGCAGTCATTCAGCAAACAACT---------
cjaponica	-------GCAATGGAAAAGTGACAATAAGGACAAACTGGAATGTGT---GGAATCTACGTACAAATAC-GTCTG-----GGACTGTTTTGCACTTCCA-------------CTTTTGTTC--------------------------------
ppacificus	TAATTGAGAAAGATAATTATGAT------ATCGCAGTGGAATGTAGTTTGAA----ATGTAAAGGGATGAGCCT-----TCATCAGTTGGCCCTTCCCATGCTACTCTGCTGCGTTGTGATAGTCGTTTTCCGTTG----------------
	******* * * * * *
celegans	(((((..(((((((.((((((((.(..(((( ((.(((((((.......))).)))).))) )))..)))))))) ).)))))))..)))))	1.000 -35.50
cremanei	..(((...( ((((((((.........((.(((.(((.((((.((((...(((.(((((((((...)))))... ))))) )).)) )))))).))).)))))........)))))))))))).....	0.955 -38.03
cbriggsae	(((((((...(((((( ((((((.(( (. ..(((((((((......))). ))))) ))))))))) ....)))))))....))))..)))	1.000 -27.30
cbrenneri	((((((((.((((((((..((.(((((((((.((.((( .(( ((....((((....)))). .))))...))).)).)))) )))))...)).)))))...))).)))).))))	0.999 -29.90
cjaponica	.....................(((((((.(((((.(((. .(((((((((((....))) ))... )))...)))..)))))))) ..)))))))	0.829 -21.50
ppacificus	((((.(((((.(((.(((((((. ..(((((..((..(((((..... (((..(((((.(((.... ...))).....)))))..))))))))))..)))))))))))).))).))))).))))	0.941 -36.20

celegans	chromosome:X:1798924:1799012:-1	intergenic ## {SimpF: WRM0634aB01 -1 fosmid,WRM065dB05 -1 fosmid,WRM068aC12 -1 fosmid,WRM0639cA04 -1 fosmid,WRM0619dF11 -1 fosmid,WRM0618dG07 -1 fosmid} ## {MIR: cel-mir-796}
cremanei	chromosome:chrUn:116332607:116332730:-1	Same_strand\|Intronic_coding\|NM_071930
cbriggsae	chromosome:chrV_random:1354380:1354465:1	Same_strand\|Intronic_coding\|NM_062003 ## Same_strand\|Boundary_non-coding\|NM_069221
cbrenneri	chromosome:chrUn:169086564:169086674:-1	intergenic
cjaponica	chromosome:chrUn:15517346:15517436:1	Same_strand\|Exonic_coding\|NM_074729
ppacificus	chromosome:chrUn:98819157:98819277:1	Same_strand\|Intronic_coding\|NM_058427

cel-mir-784

block7748 (miRBase cel-mir-784) [miRNAknown_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-784	0.005	no	no	0.50/0.50	22/22/1.00	nd	nd	0	0	0	0	13	5	5arm	1	nd	0.23	2	0	0	na	na

block7748 hairpin

		reads	miRBase family seed
seed	-----------------------------GGCACAA---------------------------------------------------------------------------------------	0	miR-784
		len	cloning frequencies

cel-miR-784	----------------------------TGGCACAATCTGCGTACGTAGA-------------------------------------------------------------------------	22
celegans	---------------TTCGACGTCCACGTGGCACAATCTGCGTACGTAGAAAGATCAAAAAGTCACTTCTATGTA---CAAA--TGTTGCGCTGCCTGGCACAGTGAA---------------
cremanei	----------------------------TGGCACAATCTC---------AAAGTTTGGCGTTTTCAACTGAAAAAGGCAAAACTTATTATACTTTTGAGCGG---------------------
cbriggsae	--------------TTTGTACTACCAAGTGGCACAATACCTGTATGTAGATAGTGAAGTAATATTGTTCTACATA---CACC--TATTGAGCCACCTGGTGGATTCGCAAAACTCTTTGATG-
cjaponica	GCTATGTTCTGATCTTCCCTCTGCCAGAAGGCACAATTTGTGTACGTAGAAAATATTGCTATTACGGTTTCTCTACGCCATA--TTTTGTGCCATCTGGCTTTGTGGAAATGTTCATTTTTGC
	******** * * * * * ** * *
celegans	.(((..(((((.(..((.((((.(..((((((((((.(((......)))..))))))))) )..) .)))).))..).))).))..))).	1.000 -28.70
cremanei	..((.(((.... .((((((.((.(((((....)))))..)).)))))).........))).))..	0.960 -11.14
cbriggsae	(((((.((((((.(((((.(((((..(((((((((((((((......)))))).))))))) )).. ))))).))))).))))))....)))))...........	0.828 -38.90
cjaponica	.........(((..((((....((((((.(((((((..((((..((((((....((((......))))...)))))).)))) ..))))))).)))))).....))))....))).......	0.938 -39.00

celegans	chromosome:X:8074864:8074951:-1	intergenic ## {SimpF: WRM0615dD08 -1 fosmid,WRM0635cH06 -1 fosmid,WRM061cG12 -1 fosmid,WRM0629dB04 -1 fosmid,WRM065bG01 -1 fosmid,WRM0620aB08 -1 fosmid} ## {MIR: cel-mir-784}
cremanei	chromosome:chrUn:111585136:111585263:-1	intergenic
cbriggsae	chromosome:chrX:13820017:13820119:-1	Same_strand\|Intronic_coding\|NM_003107 ## {MIR: cbr-mir-784}
cjaponica	chromosome:chrUn:16681627:16681747:1	intergenic

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noncloned miRBase miRNAs:

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