miR-Intess: classification

confident miRBase miRNAs

miRNAknown_cloningHIGH_randfoldOK (23 loci)

cel-mir-90

Cloning frequencies
absolute	CE1
cel-mir-90 3arm	1111
normalized	CE1
cel-mir-90 3arm	0.776

block3157 (miRBase cel-mir-90) [miRNAknown_cloningHIGH_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-90	0.001	no	no	0.28/0.44	18/24/0.99	0.0	0.5	977	0	1	0	14	8	3arm	1	nd	0.13	1	1111	1	na	na

Families
Member of family miR-50/62/90 (seed GAUAUGU): cel-mir-50, cel-mir-90, cel-mir-62

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------GAUAUGU------------------------------------------------	1087	miR-50/62/90
seed	---------------------------------------------------------------------------------------AUAUGUU-----------------------------------------------	11	novel
seed	------------------------------------------------------------------------------------------UGUUG-UU-------------------------------------------	10	novel
seed	----------------------------------------------------------------------------------------UAUGUUG----------------------------------------------	3	novel
		len	cloning frequencies
			CE1
	-------------------------------------------------------------------------------------TGATATGTTG-TTTGAATGCCCC---------------------------------	22	524
cel-miR-90	-------------------------------------------------------------------------------------TGATATGTTG-TTTGAATGCCCCT--------------------------------	23	453
	-------------------------------------------------------------------------------------TGATATGTTG-TTTGAATGCCC----------------------------------	21	77
	-------------------------------------------------------------------------------------TGATATGTTG-TTTGAATGCC-----------------------------------	20	19
	-------------------------------------------------------------------------------------TGATATGTTG-TTTGAATGCCCCTT-------------------------------	24	10
	--------------------------------------------------------------------------------------GATATGTTG-TTTGAATGCCCC---------------------------------	21	7
	-----------------------------------------------------------------------------------------ATGTTG-TTTGAATGCCCCT--------------------------------	19	5
	-----------------------------------------------------------------------------------------ATGTTG-TTTGAATGCCCC---------------------------------	18	5
	--------------------------------------------------------------------------------------GATATGTTG-TTTGAATGCCCCT--------------------------------	22	3
	-------------------------------------------------------------------------------------TGATATGTTG-TTTGAATG-------------------------------------	18	3
	---------------------------------------------------------------------------------------ATATGTTG-TTTGAATGCCC----------------------------------	19	1
	---------------------------------------------------------------------------------------ATATGTTG-TTTGAATGCCCCT--------------------------------	21	1
	-------------------------------------------------------------------------------------TGATATGTTG-TTTGAATGC------------------------------------	19	1
	---------------------------------------------------------------------------------------ATATGTTG-TTTGAATGCCCCTT-------------------------------	22	1
	--------------------------------------------------------------------------------------GATATGTTG-TTTGAATGCCC----------------------------------	20	1
celegans	---------------------GGGCGCCA--TTTCGAGCGGCTTTCAACGACGATATCAACCGACAAC-TCACACTTTTGCGTGTTGATATGTTG-TTTGAATGCCCCTTGAATTGGATGCCA------------------
cbriggsae	TCTGGATTACTGTAGATCCTGCAGCACCA--TTTCAAGCGGCCTTCAACGACTATATCAACCGA-----ATCCAAATTCGCGAGTTGATATGTTGTTTTGAATGTCACTTGAGGTTTTTGCTTTTTCGGATTTTATCCTGG
cjaponica	-------------------------------------GCGGCTTTCAACGGCGCTATCAACCGA-----ACTGTGTGTCGCGTGTTGATATGTTG-TTTGAATGCCCC---------------------------------
cbrenneri	-----------TCCTGGACTTGGGCGCCAAGTTTCGAGCGGCTTTCAACAACGATATCAACCGATTT--TCAGTAAATTGCGAGTTGATATGTTG-TTTGAATGCCCCTTGAGTTGGTTGCCCTTCTTGTT----TTAGGA
cremanei	----------TCTCCTTGTTTGGGCCTCA--CTTCGAGCGGTATTCAACGACTATCTCAACCGATATACATACCAAC---CGAGTTGATATGTTG-TTTGAATGCCCCTTGAACTCGAGGCCC--CTAGTAAACACTCAGA
	** **** * * ****** ********** ****** * *
celegans	.((((((( .((((((.(((.(((((((((.((((((((((.(((. ........))))).)))))))))))) .))))).))).)))))).))).)))).	1.000 -43.20
cbriggsae	...((((......((((((...((((..( (((((((.(((.(((((((((.((((((((((( ((....)))))...)))))))))))))..)))).))).))))))))...)))).....)))))).))))...	0.804 -41.50
cjaponica	..(((.((((((((((.(((((((((. ((.....))..)).)))))))))))) )).))).)))..	1.000 -22.90
cbrenneri	((((((((..(((((((((..((((((.(((.(((((((((.(((((((((((((( .....))))))...)))))))))))) )).))).))).))))))))))).)))).....))) ).))))	0.999 -48.60
cremanei	(((...((((((((((((. .((((((.(((((((((((((.((.(((((((.............. )).))))).)))))) )).))))))).))))))...))))))) .....)))))...)))	0.961 -43.94

celegans	chromosome:III:8873894:8873991:-1	intergenic ## {SimpF: WRM0637aD12 -1 fosmid,WRM0622dD10 -1 fosmid} ## {MIR: cel-mir-90}
cbriggsae	chromosome:chrIII:13422670:13422803:-1	Opposite_strand\|Intronic_coding\|NM_001090393 ## Same_strand\|Intronic_coding\|NM_070558
cjaponica	chromosome:chrUn:4612006:4612143:-1	Opposite_strand\|Intronic_coding\|NM_080787 ## Same_strand\|Intronic_coding\|NM_078517 ## {SimpF: trf}
cbrenneri	chromosome:chrUn:17772387:17772509:1	intergenic
cremanei	chromosome:chrUn:78012934:78013056:-1	intergenic

cel-mir-86

Cloning frequencies
absolute	CE1
cel-mir-86 5arm	3802
normalized	CE1
cel-mir-86 5arm	2.656

block3302 (miRBase cel-mir-86) [miRNAknown_cloningHIGH_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-86	0.001	no	no	0.40/0.47	19/25/0.97	0.0	0.0	3157	0	1	0	15	6	5arm	1	nd	0.22	2	3802	1	na	na

Families
Member of family miR-785/86 (seed AAGUGAA): cel-mir-86, cel-mir-785

		reads	miRBase family seed
seed	------------------------------------AAGUGAA----------------------------------------------------------------------------------------------------	3759	miR-785/86
seed	----------------------------------------GAAUGCU------------------------------------------------------------------------------------------------	25	novel
seed	-------------------------------------AGUGAAU---------------------------------------------------------------------------------------------------	18	novel
		len	cloning frequencies
			CE1
cel-miR-86	-----------------------------------TAAGTGAATGCTTTGCCACAGTC-------------------------------------------------------------------------------------	23	3157
	-----------------------------------TAAGTGAATGCTTTGCCACAGTCT------------------------------------------------------------------------------------	24	306
	-----------------------------------TAAGTGAATGCTTTGCCACAGT--------------------------------------------------------------------------------------	22	168
	-----------------------------------TAAGTGAATGCTTTGCCAC-----------------------------------------------------------------------------------------	19	90
	---------------------------------------TGAATGCTTTGCCACAGTC-------------------------------------------------------------------------------------	19	22
	-----------------------------------TAAGTGAATGCTTTGCCACAGTCTT-----------------------------------------------------------------------------------	25	20
	------------------------------------AAGTGAATGCTTTGCCACAGTC-------------------------------------------------------------------------------------	22	17
	-----------------------------------TAAGTGAATGCTTTGCCACAG---------------------------------------------------------------------------------------	21	14
	-----------------------------------TAAGTGAATGCTTTGCCACA----------------------------------------------------------------------------------------	20	4
	---------------------------------------TGAATGCTTTGCCACAGTCT------------------------------------------------------------------------------------	20	3
	------------------------------------AAGTGAATGCTTTGCCACAGTCT------------------------------------------------------------------------------------	23	1
celegans	--------------------CGTGTCCACGCCGTCTAAGTGAATGCTTTGCCACAGTCTT-CGATGTT-CTGAAA--TGAAGCCTGGGCTCAGATTCGCTT-AGGCCGGAGTTTGACACGGCA--------------------
cbriggsae	-CCCTTCCTCTTCAACAAACCGAGTCAATGCCGTTTAAGTGAATGCTTTGCCACAGTCTT-CGATCAT-GTCACA--TGAAGCCTGGGCTTAGATTCACTT-AGGCCGGCGTTCCTTGACTCAGCCTTTTTTTCTTCTTGGG-
cjaponica	-----------------------------------TAAGTGAATGCTTTGCCACAGTCTTCCGATCTCTGTCGAATGTGAAGCCTGGGTCGAGATTCGCTT-A----------------------------------------
cbrenneri	-CCCCTTTTTAAAAATACAACGAGTCGGCGCCGTCTAAGTGAATGCTTTGCCACAGTCTT-CGACCAT-GTCAAA--GGAAGCCTGGGCTCAGATTCGCTT-AGGCCGGCGTTCGACACGTTTCTTTGTGGGCTGCTTTGGGG
ppacificus	-----CATGCCTCGATATTAGAATTCGGTCCCAAGCAAGTGAATGTCCGCACAGCGCATC-CACTAGTAGTCACA---GTGGCATCGCCGTCCATTCCTTTCACTCCTCCGTTTC----------------------------
cremanei	TCCCATACTTTTCAA----ACGAGTCGGCGCCGTCTAAGTGAATGCTTTGCCACAGTCTT-CGACCAT-GTCAAA--TGAAGCCTGGGCTAAGATTCGCTT-AGGCCGGCGTTTTTCGACACGGATCTTCAACTTTGGTGA--
	******* * * * * * * ** * * ** *
	+++++ ++++++++++++++++++++++++++++++++++++++++ +++++++ ++++++ ++++++++++++++++++++++++ +++++++++++++++++++++ +++++	Y56A3A.7b Y56A3A.7 Y56A3A.7
	+++++ ++++++++++++++++++++++++++++++++++++++++ +++++++ ++++++ ++++++++++++++++++++++++ +++++++++++++++++++++ +++++	Y56A3A.7a Y56A3A.7 Y56A3A.7
celegans	((((((.((.((((((((((((((.((..(((.(((.((( ((.(... ....). ))))).))))))..)))))))))) ))).))).))..))))))...	1.000 -42.60
cbriggsae	(((.................(((((((((((((((((((((((.((..(((.(((.((( ((..... ...... ))))).))))))..)))))))))) )))).)))))....)))))).................)))	0.842 -45.18
cjaponica	(((((((((.(((.(((.(((.((((((.((......)).)).)))).)))))).))))))))))) )	1.000 -24.50
cbrenneri	((((..........(((((((.(((((((((((((((((((((.((..(((.(((.((( ((((... )))... .)))).))))))..)))))))))) )))).))))).)))).))).....)))).........))))	0.824 -55.61
ppacificus	...............(((..(((........(((.(((((..((....(((.((( ((((.((....))) )))).)))))))..))))))))........))).)))	0.903 -21.99
cremanei	(((((.......... .((.(((((((((((((((((((((.(((.(((.(((.((( ((((... )))... .)))).)))))).))))))))))) )))).)))))....)))).))............))).))	0.908 -49.00

celegans	chromosome:III:11936518:11936615:-1	Same_strand\|Intronic_coding\|Y56A3A.7a\|Y56A3A.7 ## Y56A3A.7\|protein_coding\|Y56A3A.7\|Y56A3A.7 [Source:RefSeq_peptide;Acc:NP_499557] ## {SimpF: CEOP3841 1 Operon,WRM0624cH06 -1 fosmid} ## {MIR: cel-mir-86}
cbriggsae	chromosome:chrIII:4132883:4133018:-1	Same_strand\|Intronic_coding\|NM_177732 ## Opposite_strand\|Intronic_coding\|NM_001043354 ## {MIR: cbr-mir-86}
cjaponica	chromosome:chrUn:58779718:58779855:1	intergenic
cbrenneri	chromosome:chrUn:102433287:102433423:1	Same_strand\|Intronic_coding\|NM_211666
ppacificus	chromosome:chrUn:50014221:50014326:1	Opposite_strand\|Intronic_coding\|NM_001086814
cremanei	chromosome:chrUn:4696101:4696232:1	intergenic

cel-mir-64

Cloning frequencies
absolute	CE1
cel-mir-64 5arm	3270
normalized	CE1
cel-mir-64 5arm	2.284

block3452 (miRBase cel-mir-64) [miRNAknown_cloningHIGH_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-64	0.007	no	no	0.37/0.50	18/26/0.98	0.0	0.0	2959	0	1	0	16	5	5arm	1	nd	0.14	2	3270	1	na	na

Clusters
Located in cluster 3: cel-mir-229, cel-mir-64, cel-mir-65, cel-mir-66

Families
Member of family miR-64 (seed AUGACAC): cel-mir-64, cel-mir-229, cel-mir-65, cel-mir-66, cel-mir-63

		reads	miRBase family seed
seed	-------------------------------------AUGACAC-------------------------------------------------------------------------------------------------	3213	miR-64
seed	-----------------------------------------CACUGAA---------------------------------------------------------------------------------------------	23	novel
seed	--------------------------------------UGACACU------------------------------------------------------------------------------------------------	23	novel
seed	------------------------------------UAUGACA--------------------------------------------------------------------------------------------------	7	novel
seed	-----------------------------------AUAUGAC---------------------------------------------------------------------------------------------------	3	novel
seed	------------------------------------------ACUGAAG--------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	------------------------------------TATGACACTGAAGCGTT-ACCG-----------------------------------------------------------------------------------	21	2959
cel-miR-64	------------------------------------TATGACACTGAAGCGTT-ACCGAA---------------------------------------------------------------------------------	23	146
	------------------------------------TATGACACTGAAGCGTT-ACCGA----------------------------------------------------------------------------------	22	47
	------------------------------------TATGACACTGAAGCGTT-A--------------------------------------------------------------------------------------	18	23
	------------------------------------TATGACACTGAAGCGTT-ACC------------------------------------------------------------------------------------	20	23
	----------------------------------------ACACTGAAGCGTT-ACCGAA---------------------------------------------------------------------------------	19	23
	-------------------------------------ATGACACTGAAGCGTT-ACCGA----------------------------------------------------------------------------------	21	18
	------------------------------------TATGACACTGAAGCGTT-AC-------------------------------------------------------------------------------------	19	7
	-----------------------------------ATATGACACTGAAGCGTT----------------------------------------------------------------------------------------	18	5
	------------------------------------TATGACACTGAAGCGTT-ACCGAACC-------------------------------------------------------------------------------	25	4
	-------------------------------------ATGACACTGAAGCGTT-ACCGAA---------------------------------------------------------------------------------	22	3
	------------------------------------TATGACACTGAAGCGTT-ACCGAACCG------------------------------------------------------------------------------	26	3
	-----------------------------------ATATGACACTGAAGCGTT-ACCG-----------------------------------------------------------------------------------	22	2
	----------------------------------AATATGACACTGAAGCGTT-ACCG-----------------------------------------------------------------------------------	23	2
	-------------------------------------ATGACACTGAAGCGTT-ACCG-----------------------------------------------------------------------------------	20	1
	-------------------------------------ATGACACTGAAGCGTT-ACC------------------------------------------------------------------------------------	19	1
	----------------------------------AATATGACACTGAAGCGTT----------------------------------------------------------------------------------------	19	1
	------------------------------------TATGACACTGAAGCGTT-ACCGAAC--------------------------------------------------------------------------------	24	1
	-----------------------------------------CACTGAAGCGTT-ACCGAA---------------------------------------------------------------------------------	18	1
celegans	----------CGCT----------GACCTCGCCGAATATGACACTGAAGCGTT-ACCGAACCGTTTTCCCACAC--CTGGATTCGGTGCAACGATCAGTGGCATGCTCGGCTAGCGCCAGT--------------------
cremanei	------------------------------------CATGACACTCAAGCATACCATGGACTGACTTTCAG-----CAGAATCCA------------------TGTATGGTTAGTGTTATC--------------------
cbriggsae	---CAAGAATCCTC----------GGCCTCGCCGACCATGACACTGAAGCGTG-TACGGATGGAAAGTTGAAGCCTTCCGTTCCGCTAGTGTGCCATGCAA------CGGCGAGTGCCTTGGCACTTTG------------
cbrenneri	GTCCGATATTCTTTCCCCTCTTCGGGCCTCGCCGATTATGACACTTATGCATA-GGTGGACCA---TTCAAGACCATAGGATCCA--GCTACGCTAAGTGGAATAGTCGGCGAGTGCCTGAAGTATTTTCTAGTATTCTGC
	******** * ** * * * * * *
celegans	.((( (..((.(((((.((((.((((((..(((( (((((((((........... .))).)))))))..))).)))))).)))).))))).))...))))	1.000 -37.00
cremanei	.((((((((.((.((((.(((((((((........ )))..)))) )))))).)))))))))).	1.000 -21.80
cbriggsae	((((...((.. ((((((((((..((((.(((...((((.. .(((((.((..........)).)))))..))))...))).))))... ))))))).)))..))...))))	0.997 -43.70
cbrenneri	((..((((((.........((((((((((((((((((((..((((((.((.(( (.((((((. ............)).)))) .))).))))))))..)))))))))))).))))))))........))))))..))	0.980 -58.75

celegans	chromosome:III:2172841:2172938:1	intergenic ## {MIR: cel-mir-64}
cremanei	chromosome:chrUn:10328890:10329027:1	intergenic
cbriggsae	chromosome:chrIII:218903:219011:-1	Same_strand\|Intronic_coding\|NM_001102902 ## Opposite_strand\|Intronic_coding\|NM_001077612 ## {MIR: cbr-mir-64}
cbrenneri	chromosome:chrUn:131006152:131006286:-1	intergenic ## {SimpF: trf}

cel-mir-76

Cloning frequencies
absolute	CE1
cel-mir-76 3arm	316
normalized	CE1
cel-mir-76 3arm	0.221

block3475 (miRBase cel-mir-76) [miRNAknown_cloningHIGH_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-76	0.001	no	no	0.39/0.43	18/23/0.99	0.0	0.0	309	0	1	0	16	10	3arm	1	nd	0.10	1	316	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------------------------UCGUUGU-----------------------------------------------------------	313	novel
seed	----------------------------------------------------------------------------------------UGUUGAU-------------------------------------------------------	3	novel
		len	cloning frequencies
			CE1
	-----------------------------------------------------------------------------------TTCGTTGTTGATGAA----------GCCTTG------------------------------------	21	309
	---------------------------------------------------------------------------------------TTGTTGATGAA----------GCCTTGA-----------------------------------	18	3
	-----------------------------------------------------------------------------------TTCGTTGTTGATGAA----------GCCTT-------------------------------------	20	2
	-----------------------------------------------------------------------------------TTCGTTGTTGATGAA----------GCCTTGAT----------------------------------	23	2
cel-miR-76	-----------------------------------------------------------------------------------TTCGTTGTTGATGAA----------GCCTTGA-----------------------------------	22	-
celegans	ATTTCAGCT--------------CCTGTCTGGGCTTCACAATAGTCGAATACCTTAAATTTCAAA---------ATTTGGATATTCGTTGTTGATGAA----------GCCTTGATGGGGGTGAGAAAGA--------------------
cbriggsae	-----------ATCCCTCATTCGCCAATTAGGACTTCACAACATGCGAATACCACCACTTCTATG--------------GATATTCGTTGTTGATGAA----------GTCTTAATGGACGTCTGCGGGGTCCAGG--------------
cjaponica	GTTTTAAATTC------------CTAAATTAAATTTAAAAATTTCCAAAAATCGAAAAGTTCAAAAAAAATTTTAGCGAAATTTTCGTTGTTTTTCGATTTTCTGCTTGTTTTTACAGTTATTTTTGAAGTAGAAC--------------
cbrenneri	-------------GCCCTATCCATCTGTCAGGACTTCACAATAGTCGAATACCGAT------------------AGCAGGATATTCGTTGTTGATGAA----------GTCTTAATGGGTGTTTTGATGGGGT-----------------
ppacificus	-----------------CGTAGAATGATTGGATCTTAACGACTTTCGTAT----------TTAGA---------CGTGAGATACTCGTTGTCTAATCA----------TTCTATA-----------------------------------
cremanei	AGTTTGATCTACTCGCCCGTCCACCTTTTAGGACTTCACGACAATCGAATACC-----TTCCACA---------CACTGGATATTCGTTGTTGATGAA----------GTCTTAATGGGTGTCTTGAATCGGGGACCGTTTTTTTAAACT
	** * * * * ***** * * *
celegans	.((((.((( ((((((.((((((((((((((.((((((((..(((((....) )))))).)))))))))))).)))) )))).)))))))))..))))..	1.000 -41.30
cbriggsae	(((((.((..((((.(((((((((((((((((.((((((((((.........)) ).)))))))))))).)))) )))))))))).))..)).))))).....	1.000 -42.70
cjaponica	((((((..((( ..(((.(((...(((((((...(((((((((((((...(((..((((((((...))))))))..))).))))))))))).))...)))))))...))).))).))).))))))	0.948 -21.90
cbrenneri	(((((((((((((((.(((((((((((((((.((((((((... ....)).)))))))))))).)))) ))))).)))))))....))))))))	1.000 -42.10
ppacificus	.(((((((((((((((...((((((((.(((.. ....) )).)))....)))))))))))))) )))))).	0.997 -24.80
cremanei	(((((((...((((.(((((((((((.(((((((((((((((((.((((((.. .((((.. ...)))))))))))))))).)))) ))))))).)))))....))..))))))..))....)))))))	0.994 -46.50

celegans	chromosome:III:3142035:3142131:1	intergenic ## {MIR: cel-mir-76}
cbriggsae	chromosome:chrIII_random:852345:852445:1	intergenic
cjaponica	chromosome:chrUn:125242034:125242157:1	intergenic
cbrenneri	chromosome:chrUn:44284723:44284814:-1	intergenic
ppacificus	chromosome:chrUn:173841405:173841541:1	Same_strand\|Intronic_coding\|NM_001107673 ## Opposite_strand\|Intronic_coding\|NM_001106714
cremanei	chromosome:chrUn:119622817:119622942:-1	intergenic

cel-mir-53

Cloning frequencies
absolute	CE1
cel-mir-53 5arm	125
normalized	CE1
cel-mir-53 5arm	0.087

block4539 (miRBase cel-mir-53) [miRNAknown_cloningHIGH_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-53	0.002	no	no	0.47/0.52	19/25/0.97	0.0	0.0	109	0	1	0	15	5	5arm	1	nd	0.25	3	125	1	na	na

Families
Member of family miR-51/52/55 (seed ACCCGUA): cel-mir-53, cel-mir-51, cel-mir-55, cel-mir-54, cel-mir-56, cel-mir-52

		reads	miRBase family seed
seed	----------------------------------ACCCGUA---------------------------------------------------------------------------------------------	123	miR-51/52/55
seed	--------------------------------------GUACAUU-----------------------------------------------------------------------------------------	1	novel
seed	------------------------------------CCGUACA-------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
cel-miR-53	---------------------------------CACCCGTACATTTGTTTCCGTGCT-----------------------------------------------------------------------------	24	109
	---------------------------------CACCCGTACATTTGTTTCCGTGC------------------------------------------------------------------------------	23	9
	---------------------------------CACCCGTACATTTGTTTCCGTGCTT----------------------------------------------------------------------------	25	3
	---------------------------------CACCCGTACATTTGTTTCCGTG-------------------------------------------------------------------------------	22	1
	---------------------------------CACCCGTACATTTGTTTCCG---------------------------------------------------------------------------------	20	1
	-------------------------------------CGTACATTTGTTTCCGTGC------------------------------------------------------------------------------	19	1
	-----------------------------------CCCGTACATTTGTTTCCGTGCT-----------------------------------------------------------------------------	22	1
celegans	------------------CCGATTCTGACAGTCCACCCGTACATTTGTTTCCGTGCTTGACTTCAAAGCTCAATCACGGC-ACAATATATGGGTCGCCAGTCATTGTAGTCGGA--------------------
cbriggsae	----------------TTCCCGCTCTGACAGTCCACCCGTACATATGTTTCCGTGCTTGACA-TAGAGCTCAATCACGAT-ACAATGAGCGGGTAGCCGGTCATCG-AGTCGGAA-------------------
cjaponica	TATT------TCGACGCTCCTCCAACGACAGACCACCCGTACATATGTTTCCGTGCTTGACTCTACGCCTCAATCACGTTAACAATTTATGGTTCGCCGGTCACG--AGTTGAGCTTTTGCGTTTGATG-----
cbrenneri	TATTGGCTAGTATTCTTTTCGGCTCTGACAGTCCACCCGTACATATGTTTCCGTGCTTGACAAT-GAGTTCAATCACGTC-ACAATTTATGGGTCGCCGGTCATTG-AGTTGAACATTTGAACCAGATCTAATA
cremanei	-----------------ACCCTCTACTACCGTCCACCCGTACATATGTTTCCGTGCTTGACATT-GTGCTCAATCACGTT-ACAATATATGGGTCGCCGGTCTT---AGGCGGT--------------------
	* ** * ********** ************ ***** * * * * ** *
celegans	((((((.((((.....(((((((...((((..(((((.((((((....)).)))).))))). ))))..))))))).....))))....)))))).	1.000 -31.60
cbriggsae	.(((.((((((((.....((((((.(((.(((...((((.((((.. ......)))).)))).. )))))).)))))).....))))..) ))).))).	1.000 -33.90
cjaponica	.... (((((((..((.((((....((((...((..((((((((..((((.((((.........)))).))))..))))...))))...))..))))... .)))))).....))))).))..	0.979 -29.10
cbrenneri	((((((......(((..((((((((((((.....(((((((.((.(((...((((.((((.... ....)))).)))).. ))))).))))))).....))))..) ))))))).....)))......))))))	0.838 -31.90
cremanei	(((.((((..((((...(((((((.((.(((...((((.((((.... ....)))).)))).. ))))).)))))))...))))..) ))).)))	1.000 -28.80

celegans	chromosome:IV:11027567:11027661:-1	intergenic ## {SimpF: WRM0616dB12 -1 fosmid,WRM063bC05 -1 fosmid,WRM064bF06 -1 fosmid} ## {MIR: cel-mir-53}
cbriggsae	chromosome:chrIV:5731131:5731226:1	Same_strand\|Intronic_coding\|NM_001106790 ## Opposite_strand\|Intronic_coding\|NM_001128722 ## {MIR: cbr-mir-52}
cjaponica	chromosome:chrUn:11282764:11282884:1	intergenic
cbrenneri	chromosome:chrUn:102731927:102732057:1	intergenic
cremanei	chromosome:chrUn:56827927:56828018:-1	Opposite_strand\|Intronic_coding\|NM_069625

cel-mir-59

Cloning frequencies
absolute	CE1
cel-mir-59 3arm	27
normalized	CE1
cel-mir-59 3arm	0.019

block4579 (miRBase cel-mir-59) [miRNAknown_cloningHIGH_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-59	0.001	no	no	0.36/0.40	20/23/1.00	0.0	1.4	26	0	1	0	15	6	3arm	1	nd	0.13	2	27	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------CGAAUCG-------------------------------------------------	27	novel
		len	cloning frequencies
			CE1
	----------------------------------------------------------------------------------------TCGAATCGTTTATCAGGATG-------------------------------------	20	14
cel-miR-59	----------------------------------------------------------------------------------------TCGAATCGTTTATCAGGATGATG----------------------------------	23	12
	----------------------------------------------------------------------------------------TCGAATCGTTTATCAGGATGAT-----------------------------------	22	1
celegans	--------------------AGTTGATCTAGATATGACATCGTCCTGAAAACGAAACGGAACAAA---AGTTCAAGATATTGAT---TTCGAATCGTTTATCAGGATGATGTGATTAAAATCAACT-------------------
cbriggsae	-----CGTGTGTT------CGAATATTCGAATTTTGA----ATTCCAGAGGCGTGGTGGA----------------------------TCGAATCGGTAATCAACATATG-----------------------------------
cjaponica	-------TAGGTT------CGGTTCATCCGATAATGAC---GTTCTGAAATCGACGCGAAATTGG--AATTGAAAATTTGAGAT---TTCGAATCGTTTATCAGGATGTCATCATTCATTGAGCCCCTG----------------
cbrenneri	-GATTCTTCTGTTATTTTTTTTTTGAATCAAATATGACAACGTCCTGAAAACGAAACGAAACTGATTCATTGTAAAG---AGAT---TTCGAATCGTTTATCAGGATGTTGCCATTGGATTCAAATGAAAAGGTGAGACTGATC-
ppacificus	CGGTCATTACGGT------GGTCAGCGCCGAC--TTACTGCGTTTAGCAAACAAATAGCGCC-----CCTGTCAAAATTTCGACAGACTCGAATCGCTTGCTAA-ATACAGAAAGTTCGTGCGAGCCGCTCCCATCTTATGAGCG
cremanei	--GTTATTCTGTT------CCCTTGATTCATAGATGACATCGTCCTGAAAACGAAGCGAAACTAA--CATCAGAAGATA-AGAT---TTCGAATCGTTTATCAGGATGATGTCATTATTGAAACATTCATTTTTGGTAAT-----
	* * * * * * ******** * * **
celegans	(((((((......((.((((((((((((((((((..(((((.... ...((((....))))) ))))..)))))).)))))))))))).))....)))))))	1.000 -35.71
cbriggsae	(((((((( .((.((.((((..((((( ..((((.........)))) ))))))))))).))))))))))	0.972 -14.60
cjaponica	((((.. .((((((...(((.((((( (((((((...(((..(((((((.( (((.....))))..))) ))))..)))....)))))))))))).)))...))))))))))	0.999 -37.90
cbrenneri	((((..(((..(((((((((((((((((....(((.(((((((((((((((((..(((((((.............. )).) ))))..)))))).))))))))))).)))..)))))))).))))))))))))..))))	0.990 -44.24
ppacificus	((.((((...((( (((..((((.((( ((.(((..((((((((........((.. .(((((........)))))...))......))))))) )..))).))))).))))..))))))........)))).))	0.973 -43.94
cremanei	((((((..... ....((.((((..((((((((((((((((((((((..(((((((.. .(((....))). )).) ))))..)))))).))))))))))))))))..)))).)).........))))))	0.919 -42.27

celegans	chromosome:IV:11309125:11309224:-1	intergenic ## {SimpF: WRM0637aE10 -1 fosmid,WRM0640dE06 -1 fosmid,WRM0616dC03 -1 fosmid,WRM065bG03 -1 fosmid,WRM068cC11 -1 fosmid} ## {MIR: cel-mir-59}
cbriggsae	chromosome:chrV:600964:601103:1	Opposite_strand\|Intronic_coding\|NM_001847 ## Same_strand\|Intronic_coding\|NM_001028815 ## Opposite_strand\|Boundary_coding\|NM_060528
cjaponica	chromosome:chrUn:22230736:22230843:-1	intergenic
cbrenneri	chromosome:chrUn:148292271:148292407:-1	intergenic
ppacificus	chromosome:chrUn:108228994:108229124:1	intergenic
cremanei	chromosome:chrUn:57015039:57015164:-1	Opposite_strand\|Intronic_coding\|NM_069625

cel-mir-259

Cloning frequencies
absolute	CE1
cel-mir-259 5arm	34
normalized	CE1
cel-mir-259 5arm	0.024

block6662 (miRBase cel-mir-259) [miRNAknown_cloningHIGH_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-259	0.001	no	no	0.33/0.43	21/25/0.97	0.0	0.0	30	0	1	0	18	1	5arm_loop	1	nd	0.13	1	34	1	na	na

		reads	miRBase family seed
seed	---------------------------------------AAUCUCA-------------------------------------------------------------------------------------------------	31	miR-259
seed	------------------------------------------CUCAUCC----------------------------------------------------------------------------------------------	2	novel
seed	--------------------------------------AAAUCUC--------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	--------------------------------------AAATCTCATCCTAATCTGGTAG---C-------------------------------------------------------------------------------	23	30
	-----------------------------------------TCTCATCCTAATCTGGTAG---CA------------------------------------------------------------------------------	21	2
	-------------------------------------TAAATCTCATCCTAATCTGGT-------------------------------------------------------------------------------------	21	1
	--------------------------------------AAATCTCATCCTAATCTGGTAG---CAT-----------------------------------------------------------------------------	25	1
cel-miR-259	--------------------------------------AAATCTCATCCTAATCTGGTAG---CA------------------------------------------------------------------------------	24	-
celegans	--------------------TCAGTCATTGAAACGAGTAAATCTCATCCTAATCTGGTAG---CATCTTTCGAACCT----TGCCACCGATTTGGC-ATGGGATTGACT--TGTTAAATAGTGACTTTTTT------------
cbriggsae	---------TCAGGTTGGTGATAGTCATCGAAACGAGTAAATCTCATCCTAATCTGGTTG---CATTTTCAATACTTTT--TGCTACCGATTTGGT-TTGGGATTGGCT--TGTCTAGTATTGACATTTTATTGATATACTGA
cjaponica	--------GGTAAGCTCTGTTTTGTCAGCAATACGAGTAAATCTCATCCTAATCTGGTCGCAAAATTATCAAAATGGACAATGCTACCGGTTCGGCTTTGGGATTGACTCGTGTTTAGAACTGACACTTTCTTCC--------
cbrenneri	CGAATCAAAAAAGGTAAGTGATTGTCAGTGAAACGAGTTAATCTCATCCTAATCTGGTCG---CATCACAAAACTTACC--TGCTACCGATTTGGC-TTGGGATTGACT--CGTTGAATTTTGACTATTGTCCTAGTTTTCG-
cremanei	--------------------------------------AAATCTCATCCTAATCTGGTTGACACAACACAAGGAAG-----TGCTACCGATTTGGC-TTGGGATTG-------------------------------------
	******************* * * * ******
celegans	..((((((((.(((((((.((((((((((.((((.(((.( ((............ ))).))))))).)). )))))))).))) ))))...)))))))).....	1.000 -35.30
cbriggsae	((((((..((((..((((.....((((((.(((((((..((((..((((.( ((.............. ))).))))..)))). .))))))).))) ))).......))))...))))..))...))))	0.936 -36.54
cjaponica	..............((((((.(((((((((.(((((((.((.((.(((((.(((...((.((......)).))))).))))))).))...))))))).))))))))).....)))))).........	0.879 -35.00
cbrenneri	(((...(((..(((....((((.(((((...(((((((((((((((..((((..((((.( ((.............. ))).))))..)))). .))))))))))) )))).....))))).)))).)))..))))))	0.983 -39.44
cremanei	.(((((((..((((..((((...(((...........) ))..))))..)))). .))))))).	0.987 -16.10

celegans	chromosome:V:10538996:10539096:-1	intergenic ## {SimpF: WRM0616dG08 -1 fosmid,WRM061dC04 -1 fosmid,WRM063dB11 -1 fosmid,WRM0613bH10 -1 fosmid,WRM061dD06 -1 fosmid} ## {MIR: cel-mir-259}
cbriggsae	chromosome:chrV:7917229:7917354:1	Opposite_strand\|Intronic_coding\|NM_080814 ## Same_strand\|Intronic_coding\|NM_070877 ## {MIR: cbr-mir-259}
cjaponica	chromosome:chrUn:47919156:47919282:-1	Same_strand\|Intronic_coding\|NM_021343
cbrenneri	chromosome:chrUn:67725522:67725655:1	intergenic
cremanei	chromosome:chrUn:57576526:57576666:-1	Opposite_strand\|Intronic_coding\|NM_001114256 ## Same_strand\|Intronic_coding\|NM_067581

cel-mir-82

Cloning frequencies
absolute	CE1
cel-mir-82 3arm	19854.500
normalized	CE1
cel-mir-82 3arm	13.870

block7661 (miRBase cel-mir-82) [miRNAknown_cloningHIGH_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-82	0.002	no	no	0.42/0.50	18/24/0.97	0.0	0.0	16772	0	1	0	15	5	3arm	1	nd	0.14	1	19881	1	na	na

Families
Member of family miR-80/81/82 (seed GAGAUCA): cel-mir-82, cel-mir-81, cel-mir-80, block4332_cand

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------------GAGAUCA-------------------------------------------------	19547	miR-80/81/82
seed	--------------------------------------------------------------------------------------AGAUCAU------------------------------------------------	182	novel
seed	-----------------------------------------------------------------------------------------UCAUCGU---------------------------------------------	145	novel
seed	----------------------------------------------------------------------------------------AUCAUCG----------------------------------------------	7	miR-392
		len	cloning frequencies
			CE1
cel-miR-82	------------------------------------------------------------------------------------TGAGATCATCGTGAAAGCCAGT-----------------------------------	22	16772
	------------------------------------------------------------------------------------TGAGATCATCGTGAAAGCCAG------------------------------------	21	1944
	------------------------------------------------------------------------------------TGAGATCATCGTGAAAGCC--------------------------------------	19	438
	------------------------------------------------------------------------------------TGAGATCATCGTGAAAGCCAGTT----------------------------------	23	315
	-------------------------------------------------------------------------------------GAGATCATCGTGAAAGCCAGT-----------------------------------	21	149
	----------------------------------------------------------------------------------------ATCATCGTGAAAGCCAGT-----------------------------------	18	139
	------------------------------------------------------------------------------------TGAGATCATCGTGAAAGC---------------------------------------	18	53
	-------------------------------------------------------------------------------------GAGATCATCGTGAAAGCCAG------------------------------------	20	23
	------------------------------------------------------------------------------------TGAGATCATCGTGAAAGCCA-------------------------------------	20	22
	-------------------------------------------------------------------------------------GAGATCATCGTGAAAGCC--------------------------------------	18	6
	----------------------------------------------------------------------------------------ATCATCGTGAAAGCCAGTT----------------------------------	19	5
	-------------------------------------------------------------------------------------GAGATCATCGTGAAAGCCAGTT----------------------------------	22	4
	---------------------------------------------------------------------------------------GATCATCGTGAAAGCCAGT-----------------------------------	19	4
	---------------------------------------------------------------------------------------GATCATCGTGAAAGCCAG------------------------------------	18	3
	------------------------------------------------------------------------------------TGAGATCATCGTGAAAGCCAGTTG---------------------------------	24	3
	----------------------------------------------------------------------------------------ATCATCGTGAAAGCCAGTTG---------------------------------	20	1
celegans	--------------------GAAATAGGTTCTTTTAGCAACCGGTTTTCTCTGTGATCTACAGAAT----GACAGCTAATCGTCTGAGATCATCGTGAAAGCCAGTTGTTTTTATGAACTC--------------------
cbriggsae	-----TTCGATATTAAAACTATAAAAAGTTCTTCTAGCGACAGGTTTTCGCCGTGATCTGCAGAGTTCCATGAAGAAA-ACATCTGAGATCATCGTGAAAGCCAGTTGCTTAAGAGGACTCATTGTGAAAAACTAGAGAA-
ppacificus	---------------------------TCACTCCCGGCATGCGGTTTTCACGTTGATCTG-AGAGC---TAATCGATATGTTTCTGAGATCATAGTGAAAGCTACTTGCCGAAGTGA------------------------
cjaponica	--------------------------TATTCTTCTAGCGACCGGTTTTCTCCGTGATCTGCAGAGC----TTTTGCAT-ACTTCTGAGATCATCGTGAAAGCCAGTTGCTTAAAAGAATAGTTTATC--------------
cbrenneri	TGGAAGTATTAAAGTGAAATAAAATATGTTCTCCTAGCAACAGGTTCTCACTGTGATCTGCAGAGT---ATAAAGCCT-ACATCTGAGATCATCGTGAAAGCCAGTTGCTT--ACGAACTAAATTCATAAAAAGTAGTCTA
cremanei	--------------------------AGTTCTTCTAGCGACAGGTTTTCCCTGTGATCTGCAGAGT---ACAAAGAAATACATCTGAGATCATCGTGAAAGCCAGTTGTTTCCAAGAACT---------------------
	** * **** * * ********* ****** * *** *
	+++++ ++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	T07D1.2.2 T07D1.2 T07D1.2
	+++++ ++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	T07D1.2.1 T07D1.2 T07D1.2
	+++++ ++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	T07D1.2.3 T07D1.2 T07D1.2
celegans	......(((((....((((((.(((((((.(.(((((((.((((.( ((.......)))))))))))))).).))))))).)))))).....))))).	1.000 -35.30
cbriggsae	..............(((((..(((((((..((((((.(((((((((.(((((((.((((.(((......))). ...))))))))))).))))))))).))))))...)))))))..))))).............	0.945 -45.70
ppacificus	(((((..(((((...(((((((((..((((((. ((((( ..........))).)).))))))..)))))))))...))))).)))))	1.000 -36.00
cjaponica	(((((((..((((((.(((((((...(((((((.(((((( ....)).. ...)))))))))))...))))))).))))))...))))))).......	1.000 -36.60
cbrenneri	((((..((((...(((((.........((((....((((((.((((.((((.(((((((.(((((( (.......) )).))))))))))).)))).)))).)))))). ..))))....)))))....)))).))))	0.925 -39.02
cremanei	(((((((..((((((.(((((((...(((((((.(((((( (........))).)))))))))))...))))))).))))))...)))))))	1.000 -34.90

celegans	chromosome:X:2435253:2435349:-1	Same_strand\|Intronic_coding\|T07D1.2.1\|T07D1.2 ## T07D1.2\|protein_coding\|T07D1.2\|T07D1.2 [Source:RefSeq_peptide;Acc:NP_508444] ## {SimpF: WRM069cB10 -1 fosmid,WRM0630cF03 -1 fosmid,WRM062aG12 -1 fosmid,WRM0618aC04 -1 fosmid,WRM0636aE07 -1 fosmid,WRM0631bE05 -1 fosmid} ## {MIR: cel-mir-82}
cbriggsae	chromosome:chrX:4423722:4423855:1	Same_strand\|Intronic_coding\|NM_001087279 ## Opposite_strand\|Intronic_coding\|NM_001109816 ## {MIR: cbr-mir-82}
ppacificus	chromosome:chrUn:128697181:128697266:-1	Same_strand\|Intronic_coding\|NM_022416 ## Opposite_strand\|Intronic_coding\|NM_001028815 ## {Repeats: GA-rich 1 89 -1 class=Low_complexity}
cjaponica	chromosome:chrUn:6900594:6900689:-1	intergenic
cbrenneri	chromosome:chrUn:976012:976146:1	intergenic
cremanei	chromosome:chrUn:34149150:34149240:1	intergenic

cel-mir-1022

Cloning frequencies
absolute	CE1
cel-mir-1022 5arm	27
normalized	CE1
cel-mir-1022 5arm	0.019

block7725 (miRBase cel-mir-1022) [miRNAknown_cloningHIGH_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-1022	0.001	no	no	0.41/0.45	20/24/1.00	0.0	1.4	25	0	1	0	14	1	5arm	1	nd	0.25	2	27	1	na	na

		reads	miRBase family seed
seed	---------------AGAUCAU--------------------------------------------------------------------------------	27	novel
		len	cloning frequencies
			CE1
	--------------AAGATCAT--------TGTTAGGACGCCATCT--------------------------------------------------------	24	10
cel-miR-1022	--------------AAGATCAT--------TGTTAGGACGCCATC---------------------------------------------------------	23	8
	--------------AAGATCAT--------TGTTAGGACGCC------------------------------------------------------------	20	7
	--------------AAGATCAT--------TGTTAGGACGCCAT----------------------------------------------------------	22	2
celegans	GGTCCAAAATCGGCAAGATCAT--------TGTTAGGACGCCATCTTGAAGCAA-----TATAAAGATGATAGTCCA-ATGATGATCCAGCTGTTCAAGGCT
cremanei	--------------AAGATCAT--------TGTTGCGATAT-----------------TGATAGAGATGAATATCGATATGATGATTAT-------------
cbriggsae	--------------AAGATCAT--------TGTTGTTCTCTAGTCATCGATTGAATGCTGCCAGAATTGGAGTTTCAACGTACGATCCA-------------
cbrenneri	--------------AAGATCATGTGAGTGATGACTTCATTTAATTTTGGGG--------ATCACTGCTCATTGTTCA-----TGATTCA-------------
cjaponica	--------------AAGATCAT--------TGAT---------TGGTGGATTGA----CTGTAATCGTGCCGATTGA---AATGGTCCA-------------
ppacificus	--------------AAGATCAT--------AGTT---------TATTGAGGTTT----CATTAAAATTGAATATTCATAGATTGGTCCC-------------
	******** * * * * * * *
celegans	((((......((((..(((((( ..((.((((..((((((....... ....))))))...))))) )..))))))..)))).....))))	1.000 -29.80
cremanei	..(((((( (((..(((((( (.((....)).)))))))..)))))))))..	1.000 -14.90
cbriggsae	..((((.. (((((..(((((((..((...............)))))))))...)))))...))))..	0.916 -13.76
cbrenneri	..((((((((((((..((((((((........))))) .)))..))))).....)) )))))..	1.000 -18.20
cjaponica	..(((((( (((( ((((((((((. ...))))).)))))))).. )))))))..	1.000 -15.60
ppacificus	..(((((. .((( ((.((((..(( ((.......))))..))))))))))))))..	1.000 -10.00

celegans	chromosome:X:6435382:6435469:-1	intergenic ## {SimpF: WRM061bC10 -1 fosmid,WRM0618aG06 -1 fosmid,WRM0632bC06 -1 fosmid,WRM0616bF06 -1 fosmid,WRM0612aH08 -1 fosmid,WRM0635bC02 -1 fosmid,WRM0624cB01 -1 fosmid} ## {MIR: cel-mir-1022}
cremanei	chromosome:chrUn:127506019:127506146:1	Opposite_strand\|Intronic_coding\|NM_005692
cbriggsae	chromosome:chrI_random:1455667:1455794:-1	Same_strand\|Intronic_coding\|NM_001105378 ## Opposite_strand\|Intronic_coding\|NM_069533 ## Same_strand\|Boundary_coding\|NM_058815
cbrenneri	chromosome:chrUn:20993626:20993753:1	Same_strand\|Boundary_coding\|NM_077289
cjaponica	chromosome:chrUn:68667524:68667651:-1	Same_strand\|Intronic_coding\|NM_065404
ppacificus	chromosome:chrUn:147901201:147901328:1	Opposite_strand\|Intronic_coding\|NM_001088036 ## {SimpF: trf}

cel-mir-233

Cloning frequencies
absolute	CE1
cel-mir-233 3arm	25
normalized	CE1
cel-mir-233 3arm	0.017

block7892 (miRBase cel-mir-233) [miRNAknown_cloningHIGH_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-233	0.001	no	no	0.55/0.59	20/22/1.00	0.0	0.3	24	0	1	0	16	5	3arm	1	nd	0.14	1	25	1	na	na

Families
Member of family miR-233/356/87 (seed UGAGCAA): cel-mir-233, cel-mir-87

		reads	miRBase family seed
seed	---------------------------------------------------------------UGAGCAA-------------------------------	25	miR-233/356/87
		len	cloning frequencies
			CE1
	--------------------------------------------------------------TTGAGCAATGCGCATGTGCGGG-----------------	22	17
cel-miR-233	--------------------------------------------------------------TTGAGCAATGCGCATGTGCGG------------------	21	7
	--------------------------------------------------------------TTGAGCAATGCGCATGTGCG-------------------	20	1
celegans	ATATAGCATCTTTCTGTCTCGCCCATCCCGTTGCTCCAATATTCTAAC--AACAAGTGATTATTGAGCAATGCGCATGTGCGGGATAGACTGATGGCTGC-
cbriggsae	-----------------CCCGCGCATCCCTTTGTTCCAATATTCAAACCAGTAGAAAGATTATTGAGCAATGCGCATGTGCGGG-----------------
cjaponica	---CAGCGACCTTCCGTCTCGCCCATCCCTTTGCTCC-ATATC-------GATTCATGATTATTGAGCAATGCGCATGTGCGGGACGGATTGAGCGCTG--
cbrenneri	-----GCGTCTTTCTGTCTCGCCCATCCCGTTGTTCCAATATTCCAAC--AACAAGTGATTATTGAGCAATGCGCATGTGCGGGACAGACTGATGTCTGCT
cremanei	-----------------CCCGCTCATCCTGTTGTTCCAATATTCCAAC-AGCCCAGTGATTATTGAGCAATGCGCATGTGCGGG-----------------
	* * * * * *************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	W03G11.4.2 W03G11.4 W03G11.4
	+++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	W03G11.4.1 W03G11.4 W03G11.4
celegans	...(((((((..((((((((((.(((.(((((((((.((((.((.... .......)).)))))))))))).).))).))))))))))..))).)))).	1.000 -39.40
cbriggsae	(((((((((....(((((.(((((.((.............)).)))))))))).....)))))))))	0.999 -21.92
cjaponica	(((((....((((((((((.(((....((((((. ((((( (.....)))).)).)))))).....))).)))))))))).....)))))	1.000 -36.90
cbrenneri	(((((..((((((((((.(((..(((((((.(((((.((..(( .....)))).))))))))))))...))).))))))))))..))))).....	1.000 -35.60
cremanei	(((((.(((..(((((((.(((((.((..(( ......)))).))))))))))))...))).)))))	0.994 -19.60

celegans	chromosome:X:12078510:12078607:-1	Same_strand\|Intronic_coding\|W03G11.4.1\|W03G11.4 ## W03G11.4\|protein_coding\|W03G11.4\|W03G11.4 [Source:RefSeq_peptide;Acc:NP_510019] ## {SimpF: WRM066dD06 -1 fosmid,WRM0618aH01 -1 fosmid,WRM0626dA10 -1 fosmid,WRM0637aC08 -1 fosmid,WRM0638bC07 -1 fosmid,WRM069aG02 -1 fosmid,WRM0631cH03 -1 fosmid,WRM0635cH03 -1 fosmid,WRM068bB09 -1 fosmid} ## {MIR: cel-mir-233}
cbriggsae	chromosome:chrX:1703761:1703898:1	Same_strand\|Intronic_coding\|NM_001011629 ## Opposite_strand\|Intronic_coding\|NM_009152 ## {MIR: cbr-mir-233}
cjaponica	chromosome:chrUn:7867828:7867915:1	Same_strand\|Intronic_coding\|NM_001071380 ## Opposite_strand\|Intronic_coding\|NM_001093204
cbrenneri	chromosome:chrUn:19160377:19160470:1	Same_strand\|Intronic_coding\|NM_001030940 ## Opposite_strand\|Intronic_coding\|NM_007735
cremanei	chromosome:chrUn:72771484:72771621:1	Same_strand\|Intronic_coding\|NM_077618 ## Opposite_strand\|Intronic_coding\|NM_009930