miR-Intess: classification

noncloned miRBase miRNAs

cel-mir-254

block7874 (miRBase cel-mir-254) [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-254	0.001	no	no	0.48/0.48	23/23/1.00	nd	nd	0	0	0	0	19	7	3arm	1	nd	0.26	3	0	0	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------GCAAAUC----------------------------------------------	0	miR-254
		len	cloning frequencies

cel-miR-254	--------------------------------------------------------------------------TGCAAATCTTTCGCGACTGTAGG-------------------------------	23
celegans	--------------ACTATGCATATTGCCGCCTACAGAAGCATAGATTTCCACAAACCA--TTCGAGGTGTTTGTGCAAATCTTTCGCGACTGTAGGCGGCGAACATGCAGTTTTT------------
cbriggsae	---AGCACCTCCACTCTATGCGGGTTGCCGTATACAGAAGCATCGATTTTCACACGCCA----TGATGCGCCTGTGCAAATCTTTTGCAACTGTATACGGCGATTTAGCA------------------
cjaponica	----------------------------CGCCTACAGAAGCATAGATTTCCACAAGTTAATTTTTAAGAGCCTGTGCAAATCTGTCGCATCTGTAAGCG-----------------------------
cbrenneri	GCATGATTCACTTAAAAATGCATATTGCCGCCTACAGAAGCATAGATTTTCACATACCGA-TCTGAAGAGTTTGTGCAAATCTGTCGCATCTGTAGGCGGCGATTATGCAGTCATTTGAGCACCTAGC
cremanei	GCATGATGAGCACTAGAATGCATATCGCCGCTTACAGAAGCGTGGATTTTCACATACCAA-TCGGAAGTGTCTGTGCAAATCTATCGCAACTGTACACGGCGATACTGCAGTTATT-GAACACCTTGC
	******* * *** ** * * * *********** * *
	+++++ +++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	ZK455.2 ZK455.2 gcy-9
celegans	....(((((.(((((((((((((..((..((((((.((((((((. ......).))))))).))))))...))..)))))))))))))..)))))......	1.000 -46.90
cbriggsae	...............(((((((((((((((((((..(((..(((((.(((((((.. ....)))..)))).)))))...)))..)))))))))))))))).)))	0.853 -40.60
cjaponica	(((.((((((.((((((((((.((((.(((..........))).)))).)))))))).)).)))))).)))	1.000 -26.60
cbrenneri	..........((((((..((((((((((((((((((((.((((((((((.((((.((... ((....)))).)))).)))))))).)).))))))))))))))).)))))....))))))........	0.974 -53.00
cremanei	(((...((..((.((...((((((((((((..(((((..((((((((((.((((.((... ........)).)))).))))))).)))..)))))..)))))))).))))..)).) )..))...)))	0.971 -43.30

celegans	chromosome:X:11333459:11333558:-1	Same_strand\|Intronic_coding\|ZK455.2\|ZK455.2 ## ZK455.2\|protein_coding\|gcy-9\|gcy-9 encodes a membrane guanylyl cyclase. gcy-9 expression is reportedly weak and variable in non-neuronal tissues. [Source: WormBase] ## {SimpF: WRM067dB12 -1 fosmid,WRM0617bB05 -1 fosmid} ## {MIR: cel-mir-254}
cbriggsae	chromosome:chrX:5320049:5320151:1	Same_strand\|Intronic_coding\|NM_001105250 ## Opposite_strand\|Intronic_coding\|NM_072374 ## {MIR: cbr-mir-254}
cjaponica	chromosome:chrUn:593205:593275:-1	Same_strand\|Intronic_coding\|NM_001109695
cbrenneri	chromosome:chrUn:96346:96472:-1	Same_strand\|Intronic_coding\|NM_001109695
cremanei	chromosome:chrUn:33393203:33393328:-1	Same_strand\|Intronic_coding\|NM_001109695

cel-mir-239b

block7885 (miRBase cel-mir-239b) [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-239b	0.001	no	no	0.32/0.32	22/22/1.00	nd	nd	0	0	0	0	15	6	5arm	1	nd	0.14	2	0	0	na	na

		reads	miRBase family seed
seed	-------------------------------UUGUACU---------------------------------------------------------------------------------------------------	0	miR-239a
		len	cloning frequencies

cel-miR-239b	------------------------------TTTGTACT----------------------ACACAAAAGTACTG---------------------------------------------------------------	22
celegans	GCGAC---------------AGATGCAATTTTTGTACT----------------------ACACAAAAGTACTGGTCATTTAAGTTGAGGCTCAGCACT--TTTGTGGTGTGCAAAAATGGCAAGTTGCTTTTATCT
cbriggsae	------------------------------TTTGTACT----------------------GCACAAAAGTACTGACTATTT---------CTCAGCGCT--TTTGTCCAGTGCAAG---------------------
cjaponica	------------------------------TTTGTACT----------------------ACACATAGGTACTGGTGA----AAACGTGTTTAACCAGTGCCTGGTCTAGTGCAAG---------------------
cbrenneri	GCTGCCATTCCAAACTGACAAGTTGCAGTTTTTGTACT----------------------TCACAAGAGTACTGGCGGTTC-AGGTCCGGCTCAGAACT--TTTGTGGGGTGCAAGAACAGCAAAACTGTCA-----
ppacificus	------------------------------ATTGTACTAATTTATTTATTTATTTATTTAATAAAAAAATAAAAATAA---------------ATAAATAAATAATGTCATACAAG---------------------
cremanei	------------------------------TTTGTACT----------------------GCACAAAAGCTCTGACTGCTC-TGATATGGCTCAGCACT--TTTGTCT-GTGCAAA---------------------
	******* * * * * * * * ***
celegans	((((( ...(((.((((((((((. .(((((((((.((((((.((......))))).))).))) ))))))..)))))))))).))).)))))........	1.000 -37.50
cbriggsae	.((((((( (.(((((((..((((...... .))))..)) ))))).)))))))).	1.000 -24.20
cjaponica	.((((((( (.((.(((((((((((.. (((....))).))))))))))))).)))))))).	1.000 -28.40
cbrenneri	...............(((((..((((.((((((((((. .(((((((((.(((((((... ....)).)).))).))) ))))))..)))))))))).))))...)))))	0.972 -45.90
ppacificus	.(((((.....((((((((((((((((((.............)))))) )))))))))))).....))))).	0.999 -15.32
cremanei	.((((((. ..(((((((..((((..(((. ......)))))))..)) ))))).. )))))).	1.000 -17.90

celegans	chromosome:X:11791226:11791323:-1	intergenic ## {SimpF: WRM064aB01 -1 fosmid,WRM067bC07 -1 fosmid,WRM0624bH08 -1 fosmid,WRM068cE04 -1 fosmid,WRM0610bH05 -1 fosmid,WRM0632aD05 -1 fosmid,WRM0628bH10 -1 fosmid,WRM0621bA09 -1 fosmid,WRM0624aG10 -1 fosmid} ## {MIR: cel-mir-239b}
cbriggsae	chromosome:chrX:15174113:15174250:-1	Opposite_strand\|Intronic_coding\|NM_001099298 ## Same_strand\|Intronic_coding\|NM_077585 ## {MIR: cbr-mir-239b}
cjaponica	chromosome:chrUn:61791059:61791196:-1	intergenic
cbrenneri	chromosome:chrUn:34417669:34417775:1	intergenic
ppacificus	chromosome:chrUn:166913035:166913172:1	Opposite_strand\|Intronic_coding\|NM_145301 ## {Repeats: (TTTA)n 1 21 1 class=Simple_repeat,(TAAA)n 4 35 1 class=Simple_repeat}
cremanei	chromosome:chrUn:26918263:26918400:1	intergenic

cel-mir-247

block8269 (miRBase cel-mir-247) [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-247	0.001	no	no	0.41/0.41	22/22/1.00	nd	nd	0	0	0	0	16	6	3arm	1	nd	0.18	1	0	0	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------------------GACUAGA----------------------------------------------	0	miR-44/45/61
		len	cloning frequencies

cel-miR-247	-----------------------------------------------------------------------------TGACTAGAGC-CTATTCTCTTCT-------------------------------	22
celegans	-----------------ATTACCAGCTATTTTCCAAGTAGAGAAAAGTTTCTAATTACCCATCATGCACAAATGTGGTGACTAGAGC-CTATTCTCTTCTTGG---AAAAGTGGCGACT------------
cbriggsae	TTTCTAGTATTCCTATTCCGAACTTCCTCCCTCCGAGTAGAGTTCAGACCCTGGTGACCTACAGCAGTAGCATGAGGTGACTAGAGTGCTGAGCTCTCCTTGGTTCAGAGGCATCATATTCATGCTATAAA
cjaponica	--------------AGTTTACACTGCTCTTCTCTAACTTG-----------------------GCCGTGACGAGAAGAGACTAGAGA-------------CAGCTGAAAATT-------------------
cremanei	------------------------ATCTTCTTCCGAGCAGAGAATCGCCCCTAGTGACCCACCACAGTAGTGTGAGGTGACTAGAGC-CAATTCTCTTCTTGGTTGCAAGGT-------------------
	** * * * * ******** * *
celegans	.......(((((((((((((.((((((.((.(((((.(((((...(((......))).))))).))))). )).)))))).))))) .))))))))....	1.000 -37.00
cbriggsae	....((((((...(((...((....((((...(((((.(((((((((((.(((((.((((.((((....)).)))))).))))).)).))))))))).)))))....))))..)))))...))))))....	0.814 -45.50
cjaponica	(((((.((((((((((((((..(((( .......)))).)))))..)))). ))).)).)))))	1.000 -16.40
cremanei	(((((...(((((.(((((((.((..(((((.(((((.(((....))))).))).))))).)) ..))))))).)))))....)))))	1.000 -33.20

celegans	chromosome:X:4756941:4757038:1	intergenic ## {SimpF: WRM068cD04 1 fosmid,WRM067dC01 1 fosmid,WRM0618dA09 1 fosmid,WRM0613aH09 1 fosmid,WRM0641aH07 1 fosmid,WRM0632bG03 1 fosmid,WRM0618bG10 1 fosmid} ## {MIR: cel-mir-247}
cbriggsae	chromosome:chrX:9929398:9929528:1	intergenic
cjaponica	chromosome:chrUn:137271405:137271542:-1	Same_strand\|Intronic_coding\|NM_032085
cremanei	chromosome:chrUn:2834964:2835050:-1	Opposite_strand\|Intronic_coding\|NM_057309

cel-mir-360

block8312 (miRBase cel-mir-360) [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-360	0.001	no	no	0.48/0.48	21/21/1.00	nd	nd	0	0	0	0	24	4	3arm	1	nd	0.14	2	0	0	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------GACCGUA-------------------------------------------------	0	miR-360
		len	cloning frequencies

cel-miR-360	----------------------------------------------------------------------------------TGACCGTAATCCCGTTCACAA------------------------------------	21
celegans	--------------------TCTGTTAGGAAGC-ATCAATGTGTTGTGACCGTTGTTACGGTCAATTTGCAAATTGAAAAAATGACCGTAATCCCGTTCACAATACATTGTTCGTTTTCTCCAAAGG------------
cbriggsae	-------------------TTCCATAAAAAAGCGCCTAGGGTTTTGTGACCGTTGTTACGGTCAATTC-ATGTCTGACACAATGACCGTAATCCCGTTCACAACACCTTGTGTGGCTT---------------------
cjaponica	-------------------------------------------TTGTGACCGTTGTTACGGTCAAAAC-ATTCCTG--GAAATGACCGTAGTTTCGTTCACAA------------------------------------
cbrenneri	-------------------------------GC-ATCAAGGTTTTGTGACCGTTGTTACGGTCA-TTT-CAACATG--TAACTGACCGTAATCCCGTTCACAACACATTGTTTGT------------------------
cremanei	CCTTCTAATTTTTCGAGAAATTGTCAAAAAGGCGATCAGGGTTTTGTGACCGTTGTTACGGTCAATTT-CATTCAGAAGCTATGACCGTAATCCCGTTCACAACATCTTGTTTAGCTTGACTCATGAATTGTGTAAAGG
	********************* * ******** * *********
celegans	.((...((((((( ..(((((((((((((.((..((((((((((.(((..........))).))))))))))..)).)))))))))))))...)))))))....)).	1.000 -42.20
cbriggsae	..........((((((.((((((.((((((.((..((((((((((..(( (....))).....))))))))))..)).)))))).)))))).))).)))	0.997 -35.40
cjaponica	.(((((.((..((((((((((...( (....)) ....))))))))))..)).))))).	1.000 -20.00
cbrenneri	(( (.(((.((.((((((.((..(((((((((( .(( ((...)) .)).))))))))))..)).)))))).)).)))..)))	0.999 -26.80
cremanei	((((...((..((((.((....((((....(((...((((((.((((((.((..((((((((((.((( (.....))))...))))))))))..)).)))))).))))))....))))))))).))))..))...))))	0.940 -43.50

celegans	chromosome:X:5919112:5919217:1	intergenic ## {SimpF: WRM062cA07 1 fosmid} ## {MIR: cel-mir-360}
cbriggsae	chromosome:chrX:11095206:11095303:1	Opposite_strand\|Intronic_coding\|NM_014930 ## Same_strand\|Intronic_coding\|NM_011438 ## {MIR: cbr-mir-360}
cjaponica	chromosome:chrUn:44027951:44028096:-1	intergenic
cbrenneri	chromosome:chrUn:38391520:38391598:-1	intergenic
cremanei	chromosome:chrUn:1914811:1914948:-1	Same_strand\|Intronic_coding\|NM_170227

cel-mir-392

block8551 (miRBase cel-mir-392) [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-392	0.001	no	no	0.41/0.41	22/22/1.00	nd	nd	0	0	0	0	14	2	3arm	1	nd	0.14	1	0	0	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------AUCAUCG-------------------------------------------	0	miR-392
		len	cloning frequencies

cel-miR-392	--------------------------------------------------------------------------TATCATCGATCACGTGTGATGA-----------------------------	22
celegans	--------------CTCGCAGAC-GTGTTCAGTCAGCATT---CGTGGTTGAGGATATCGAACACAAAAAAAGATATCATCGATCACGTGTGATGACAGATTTTCTGCG---------------A
cbriggsae	TGATTATTATCTTTTTAAAATCCTGCATTTATCTGACATCTCACATTATTGAGGATATAAACTAAATAAAGAAATATCATCGATCATGTGAGCTGTTAGATTATCAGATTTCTATGGATTCTTCA
cremanei	-------------------ATCC-GTGATTATCTGGCGGTTTACATGGTAGAAGATATCAGTATAAAAAATAGATATCATCGATCATGTATGCTGTCAGATTAATGGAT----------------
	* * * * * * * * * *** * *** * *********** * *** *
celegans	.(((((((. ....((.((((.(((. (((((((((.((((((.............)))))).))))))))).))).)))).))...)))))) )	1.000 -37.02
cbriggsae	.((.....((((.....((((.(((.((..((((((((.(((((((.(((((.(((((...((......))..))))).))))).))))))).)))))))).)))))))))....))))...)).	0.976 -32.10
cremanei	(((( ((....((((((((((.((((((((.((.((((((.((.......)).)))))).)).)))))))).))))))))))..))))))	1.000 -37.60

celegans	chromosome:X:13597163:13597254:1	intergenic ## {SimpF: WRM069aA04 1 fosmid,WRM0617dA01 1 fosmid,WRM0617cH07 1 fosmid,WRM0614bD06 1 fosmid,WRM0610bG08 1 fosmid} ## {MIR: cel-mir-392}
cbriggsae	chromosome:chrX:19202525:19202649:1	Same_strand\|Intronic_coding\|NM_007734 ## Opposite_strand\|Intronic_coding\|NM_001065436 ## {MIR: cbr-mir-392}
cremanei	chromosome:chrUn:96274952:96275040:1	intergenic

cel-mir-1819

block8662 (miRBase cel-mir-1819) [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-1819	0.001	no	no	0.41/0.41	22/22/1.00	nd	nd	0	0	0	0	9	2	3arm	1	nd	0.18	1	0	0	na	na

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

cel-miR-1819	--------------------------------------------------------------TGGAATGATTGAGCTTG-ATGGA-----------------------	22
celegans	--AATCAGTGATCAATCAT------GCTCAA-AA---CATTCGACATAACTTAATTTCTTTGTGGAATGATTGAGCTTG-ATGGATCGATGAAA--------------
cremanei	---------------TCAT------ACGGAATTA---CATTCATCGA-----GAATTTTTGATGGAATGA---ATCTTGTATGT------------------------
cjaponica	GTACTTTGTGGATTTCCTTTTCGTCGCCAAGTTATTTCATTTCACGT---GTAAATTCAACGTGGAATGAAATAATTTGGAGATGAAAATGAAATCCGCGAAGTTGGC
ppacificus	AGAATACGT----TCTCTT------------------CATTTCTCACACTCCCTCATCACAGAGGAATGA--------------AGAGACGGATTCT-----------
	* * **** * * *******
celegans	..(((.(((((.((((. (((((( .. (((((.(((..............))).))))).)))))).)) )).))))).)))..	1.000 -27.84
cremanei	.((( (((..(((. (((((((((( (....))))))).))))) ))..)))))).	1.000 -14.80
cjaponica	..((((((((((((((.((((((((.((((((((((((((((((((( .........))))))))))))))))))))).)))))))).))))))))))))))....	1.000 -58.50
ppacificus	(((((.((. (((((( ((((((((................))))))))) ))))))).)))))	1.000 -23.89

celegans	chromosome:X:16207873:16207953:1	intergenic ## {SimpF: WRM0630aF01 1 fosmid,WRM0612dH12 1 fosmid,WRM0631bF11 1 fosmid} ## {MIR: cel-mir-1819}
cremanei	chromosome:chrUn:21211144:21211264:1	Opposite_strand\|Intronic_coding\|NM_180914 ## Same_strand\|Intronic_coding\|NM_001031159
cjaponica	chromosome:chrUn:52211858:52211962:-1	Same_strand\|Intronic_coding\|NM_001022912
ppacificus	chromosome:chrUn:37356861:37356981:1	intergenic

cel-mir-269

block5205 (miRBase cel-mir-269) [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-269	0.001	no	UNKNOWN	0.50/0.50	20/20/1.00	nd	nd	0	0	0	0	12	12	5arm	1	nd	0.25	3	0	0	na	na

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

cel-miR-269	------------GGCAAGACTCTGGCAAAACT--------------------------------------------------------------	20
celegans	gggcaaaagttgGGCAAGACTCTGGCAAAACTtggatttatgctgcgccaaagtttaacccaagtttgacccaactcttgtcaaatttttgtcc
	**********************************************************************************************
celegans	(((((((((((.(((((((...(((..((((((((.((...(((.......)))..)).))))))))...)))..))))))).)))))))))))	1.000 -35.20

celegans

chromosome:IV:273900:273993:1

intergenic ## {Repeats: trf 4 24 0 class=trf,Ce000066 260 280 -1 class=UNKNOWN} ## {SimpF: WRM0637dH05 1 fosmid,WRM061dB06 1 fosmid,WRM063bB05 1 fosmid,WRM0628dB02 1 fosmid,WRM0626aH07 1 fosmid,WRM0618aB03 1 fosmid} ## {MIR: cel-mir-269}

cel-mir-266

block8246 (miRBase cel-mir-266) [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-266	0.001	no	UNKNOWN	0.50/0.50	20/20/1.00	nd	nd	0	0	0	0	22	3	5arm	1	nd	0.00	0	0	0	na	na

		reads	miRBase family seed
seed	-----------------------GGCAAGA---------------------------------------------------------------------------------------------------------	0	miR-73/74
		len	cloning frequencies

cel-miR-266	----------------------AGGCAAGA----------------CTTTGGCAAAGC-----------------------------------------------------------------------------	20
celegans	TGTCTAAACTTGGGCAAAAGTTAGGCAAGA----------------CTTTGGCAAAGC-------------------------TTGAATCCAAGTTTTGCCAAAGTTTTGCCCAACTTTTGCCCAAATTCAGCCA
cremanei	----------------------AGGCAAGA-----------------------------------------------------CCGAGACACACTCTCCAAGTGGTCGTTTTCCA--------------------
cbriggsae	----------------------TGGCAAGA----------------GTGTGGAAAAGTGTCT---------------------GGAGATCAGACGAATGCTGAAATTCTTGGGC---------------------
cbrenneri	----------------------TGGCAAGATCCATTAGCGCCTTCTGTCGTGCTAGATGGTACTC------------------AGAGATCCAATGCCT-------------------------------------
cjaponica	----------------------AGGCAAGA----------------GACGGGCAGAATAGCA---------------------ATAACTCGCAGTTTTCTCAACTTTTATCGCCA--------------------
ppacificus	----GGAACGATGAGCAGAAGCAGGCAAGA----------------GAGGGCATAGGTAGCACTCTTGCACCCTCTTTGCCTGATAATTCAAAATTATTCCATAAACTTGCACAACTG-----------------
	******* * *
celegans	.(.((.((.(((((((((((((.((((((( (((((((((((( (((....)))))))))))))))))))))).))))))))))))).)).)).).	1.000 -57.30
cremanei	.((.(((( (...(((.((((.....)))))))))))))).	0.993 -10.70
cbriggsae	...((((( ((..((.....((((( (.....))))))....))...)))))))...	1.000 -14.90
cbrenneri	.((((.((((....((..((.((((......)))).))..)). ...))))...)))).	0.889 -16.10
cjaponica	.((((((( (..(((.(((((.((. .......)).))))))))..)))))...))).	0.998 -13.80
ppacificus	((((..((.....(((.(((((.((( (((((..((((.......))))..)))))))))))))....)))...))..)))).................	0.981 -30.30

celegans	chromosome:X:3755135:3755228:1	intergenic ## {Repeats: Ce000066 87 107 1 class=UNKNOWN} ## {SimpF: WRM067bH01 1 fosmid,WRM0613cH07 1 fosmid,WRM0618bD11 1 fosmid,WRM0617bH09 1 fosmid,WRM0633aC01 1 fosmid,WRM0627dF05 1 fosmid,WRM063dB04 1 fosmid} ## {MIR: cel-mir-266}
cremanei	chromosome:chrUn:116109270:116109403:1	intergenic
cbriggsae	chromosome:chrIV:4947211:4947344:1	Same_strand\|Intronic_coding\|NM_168571 ## Opposite_strand\|Intronic_coding\|NM_001123230 ## Same_strand\|Boundary_coding\|NM_133378 ## Same_strand\|Exonic_coding\|NM_069872 ## Same_strand\|Boundary_non-coding\|NM_166790
cbrenneri	chromosome:chrUn:6511836:6511969:1	Opposite_strand\|Boundary_non-coding\|NM_064891
cjaponica	chromosome:chrUn:94347566:94347699:1	Same_strand\|Intronic_coding\|NM_073427
ppacificus	chromosome:chrUn:148505882:148505979:1	intergenic

miRNAknown (7 loci)

cel-mir-354

block630 (miRBase cel-mir-354) [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-354	0.036	no	no	0.48/0.48	21/21/1.00	nd	nd	0	0	0	0	10	15	3arm	1	nd	0.24	2	0	0	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------CCUUGUU-------------------------------	0	miR-354
		len	cloning frequencies

cel-miR-354	-------------------------------------------------------------------------------ACCTTGTTTGTTGCTGCTCCT------------------	21
celegans	CAGAGCCGACTAAGCACCTTGGTGCGGCTGCAGACGGGTATCCGGCTCGACGTTCATACATCACGACTTCTTTCCTTTTACCTTGTTTGTTGCTGCTCCTATTGGTTTTG--------
cbriggsae	------CGACTAAGTGCCTTGGTGCGGCTACAGACGGGTATCCGGCTCGATGTTCATACACCGCGAC-TCTTTCCTTTTACCTTGTTTGTTGCTGCTCCTTTTGGTTTTGATTTGTTG
cjaponica	-------------------TGGTGCGGCTTCGAACGGGTA-ACAGCTCGTCGTTCATAC---------TTCTTCCTTTTACCTTGTTTGTTGCCTCTCCT------------------
	********** * ******* * *** ****** * ******************** ***
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>	Y105E8A.16.1 Y105E8A.16 rps-20
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>	Y105E8A.16.2 Y105E8A.16 rps-20
celegans	(((((((((...........((.(((((.(((((((((((...((...((.(((..........))).))...))...)))).))))))).))))).))..)))))))))	1.000 -33.02
cbriggsae	((((.(((((((..((.(((((.(((((((((((...((.(((.(((....)))...))). .....))...))))).)))))).))))).))....)))....))))))))	0.985 -31.30
cjaponica	.((...(((..(((((((((( (.((......((....)) ......)).)))))).)))))..)))...)).	0.999 -17.60

celegans	chromosome:I:14468369:14468478:-1	Same_strand\|Exonic_non-coding\|Y105E8A.16.1\|Y105E8A.16 ## Y105E8A.16\|protein_coding\|rps-20\|rps-20 encodes a small ribosomal subunit S20 protein. [Source: WormBase] ## {SimpF: CEOP1732 1 Operon} ## {MIR: cel-mir-354}
cbriggsae	chromosome:chrI:10568230:10568340:-1	Opposite_strand\|Intronic_coding\|NM_061066 ## Same_strand\|Intronic_coding\|NM_067049 ## Same_strand\|Boundary_non-coding\|NM_017866 ## Same_strand\|Exonic_coding\|NM_170948 ## {MIR: cbr-mir-354}
cjaponica	chromosome:chrUn:65822231:65822380:-1	Same_strand\|Boundary_non-coding\|NM_208340

cel-mir-260

block2201 (miRBase cel-mir-260) [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-260	0.381	no	no	0.45/0.45	20/20/1.00	nd	nd	0	0	0	0	13	7	3arm	1	nd	0.20	2	0	0	na	na

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

cel-miR-260	-------------------------------------------------------------------GTGATGTCGAACTCTTGTAG-------------	20
celegans	gtacaacaaaattattgcgagagaattttttaacatggcgtttgctttaccaggtcgatagactatcGTGATGTCGAACTCTTGTAGgacaatctggtat
	****************************************************************************************************
	--------------------------------------------------------------------------------------------------------------	F39E9.7 F39E9.7 F39E9.7
celegans	((((..........(((((((((.....((..((((.(((............((((....))))..))).))))..))))))))))).........))))	0.550 -20.65

celegans

chromosome:II:3306231:3306330:1

Opposite_strand|Intronic_coding|F39E9.7|F39E9.7 ## F39E9.7|protein_coding|F39E9.7|F39E9.7 [Source:RefSeq_peptide;Acc:NP_494501] ## {SimpF: F39E9.7 1 Expression_profile,WRM0639dB12 1 fosmid,WRM0622bD02 1 fosmid,WRM0628aD03 1 fosmid} ## {MIR: cel-mir-260}

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noncloned miRBase miRNAs:

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