miR-Intess: classification

candidate miRBase miRNAs

miRNAknown_cloningHIGH_multiarm_DicerNOK_randfoldOK (11 loci)

cel-mir-73

Cloning frequencies
absolute	CE1
cel-mir-73 5arm	1
cel-mir-73 3arm	814
normalized	CE1
cel-mir-73 5arm	0.001
cel-mir-73 3arm	0.569

sblock71 (miRBase cel-mir-73) [miRNAknown_cloningHIGH_multiarm_DicerNOK_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-73	0.006	no	no	0.40/0.54	19/24/0.99	0.0 0.0	0.0 0.0	1 737	0 0	1 1	0 0	22 15	0 2	5arm 3arm	1 1	nd nd	0.25 0.17	2 2	815	1	4	2

Clusters
Located in cluster 8: cel-mir-73, cel-mir-74

Families
Member of family miR-73/74 (seed GGCAAGA): cel-mir-74, cel-mir-72, cel-mir-73

		reads	miRBase family seed
seed	------------------------------------------------------------------------GGCAAGA-----------------------------------------------	795	miR-73/74
seed	-------------------------------------------------------------------------GCAAGAU----------------------------------------------	10	novel
seed	----------------------------------------------------------------------------AGAUGUA-------------------------------------------	9	novel
seed	------------------------GGACUUC-----------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
cel-miR-73	-----------------------------------------------------------------------TGGCAAGATGTAGGCAGTTCAGT--------------------------------	23	737
	-----------------------------------------------------------------------TGGCAAGATGTAGGCAGTTC-----------------------------------	20	24
	-----------------------------------------------------------------------TGGCAAGATGTAGGCAGTTCAG---------------------------------	22	23
	-----------------------------------------------------------------------TGGCAAGATGTAGGCAGTTCAGTT-------------------------------	24	8
	---------------------------------------------------------------------------AAGATGTAGGCAGTTCAGT--------------------------------	19	8
	------------------------------------------------------------------------GGCAAGATGTAGGCAGTTCAGT--------------------------------	22	8
	-----------------------------------------------------------------------TGGCAAGATGTAGGCAGTT------------------------------------	19	3
	------------------------------------------------------------------------GGCAAGATGTAGGCAGTTCAGTT-------------------------------	23	2
	---------------------------------------------------------------------------AAGATGTAGGCAGTTCAGTT-------------------------------	20	1
	-----------------------TGGACTTCCATATCGAGCCACAGC-------------------------------------------------------------------------------	24	1
celegans	CAGTGAG-AGTCCCACACACGACTGGACTTCCATATCGAGCCACAGCT------ATC---AACGAATTTGCTGGCAAGATGTAGGCAGTTCAGTTGTGCGTTTATGGAG-----------------
cbriggsae	--------GGTCCCTCAAACAACCGAGCTTCCCCGTCAAGCCACAGCT------ATC---TCTGACATTGCTGGCAAGATGTTGGCAGTTCAGTTGTATG---ACGGAGACC--------------
cjaponica	GTGTGAGCGGTCCATCGAGCGACCGAACTTCCATATCGAGCC-CAGCCCACTCGACC---AAATAAGACGCTGGCAAGATGTTGGCAGTTCAGTCGCAAG---ATTGTGACCAATACTTGCTCCAC
cbrenneri	--------GGTCCTTAATACGACTGAGCTTCCACATCAGACCACAGCT------ATTCACAAAAAAAATGCTGGCAAGATGTAGGCAGTTCAGTTGTATG----CGGTGACC--------------
cremanei	CAGCGAGAGGTCCCTCAAACGACTGAGCTTCCACGTCAAGCCTCAGCT------ATCGAATGAAAAATTGCTGGCAAGATGTAGGCAGTTCAGTTGTATG----CGGAGACCAATTTCCTG-----
	**** * ** * *** ** * * *********** ********* * * * *
celegans	....... ..(((.((.((((((((((((.(((((((..((((..((. ... .........))))))..))))).)).)))))))))))).))....))).	1.000 -35.52
cbriggsae	(((((((((.(((((.(((((.((.((((..(((..(((. ... .........))))))..))))..)).))))).))))).)) ).)).))))	0.916 -34.42
cjaponica	(((.((((((((((((..(((((.(((((.(((((((..((. ((((....((.... ......)).))))))..))))).)).))))).)))))..) ).)).)))).......)))))))	0.997 -44.31
cbrenneri	((((((..(((((((((((((.(((((((......((((. ...............))))....))))).)).))))))))))))). .)).))))	1.000 -36.59
cremanei	(((.((((((((((.((.(((((((((((.(((((((..(((..(((. ...............))))))..))))).)).))))))))))).)) .)).))))..)))))))	0.999 -45.19

celegans	chromosome:X:2368759:2368857:1	intergenic ## {SimpF: WRM0640dB08 1 fosmid,WRM0614bE04 1 fosmid,WRM0611cC07 1 fosmid,WRM0624bG04 1 fosmid,WRM066bF02 1 fosmid,WRM0639bG12 1 fosmid,WRM067cD10 1 fosmid,WRM0612dD05 1 fosmid,WRM0620aG05 1 fosmid,WRM0612dG02 1 fosmid,WRM064dH03 1 fosmid,WRM0617aH11 1 fosmid} ## {MIR: cel-mir-73}
cbriggsae	chromosome:chrX:4493864:4493955:-1	Opposite_strand\|Intronic_coding\|NM_001087279 ## Same_strand\|Intronic_coding\|NM_001109816 ## {MIR: cbr-mir-73}
cjaponica	chromosome:chrUn:6831545:6831663:1	intergenic
cbrenneri	chromosome:chrUn:1030699:1030792:-1	intergenic
cremanei	chromosome:chrUn:103837693:103837803:-1	intergenic

miRNAknown_randfoldOK (7 loci)

cel-mir-794

Cloning frequencies
absolute	CE1
cel-mir-794 5arm	1
normalized	CE1
cel-mir-794 5arm	0.001

block1210 (miRBase cel-mir-794) [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-794	0.007	no	no	0.41/0.41	22/22/1.00	0.0	0.0	1	0	1	0	14	5	5arm	1	nd	0.23	2	1	1	na	na

		reads	miRBase family seed
seed	---------------GAGGUAA---------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
cel-miR-794	--------------TGAGGTAATCATCGTTGTCACT-------------------------------------------------------	22	1
celegans	CTGAGCGTGTCTCTTGAGGTAATCATCGTTGTCACTTCGCAAAGTTGGAA------TTGAAAACGTTGTCTATCTCGAAAGGCTTATCAG-
cremanei	--------------TGAGGTAAT-------------------GGCTGGAAATATCGACGACGAAACGGATTTTTTCGCCATTTTTTTCTCT
cbrenneri	-------------AGGAGGTAAT----------TCTCCGTTTGGCTGTGG------CCGAATGCTCGGGCAAGAGCGGTGAACGTCTTCCT
ppacificus	--------------AGAGGTAACGCTTTTTGATTCTT------GGTGGAA------GCAAGCAAGCAAGTTAGTTCG--------------
	******* * ** * **
celegans	((((....((((.((((((((..((.((((.(((.(((.((....))))) .))).)))).))..)))))))).))))...))))	1.000 -27.10
cremanei	.((((.((( (((.(((((.(((..((......))))).)))))))))))....)))).	0.999 -15.20
cbrenneri	((((((...( ((.((((((.....((. ((((....)))).)).)))))).)))...))))))	0.929 -25.70
ppacificus	.(((.((((((((((((.((((. ...)))) .)))).))))..)))).))).	1.000 -13.90

celegans	chromosome:I:12595679:12595762:1	intergenic ## {SimpF: WRM0624dH02 1 fosmid,WRM0612aE11 1 fosmid,WRM0638dG06 1 fosmid} ## {MIR: cel-mir-794}
cremanei	chromosome:chrUn:83560617:83560740:1	intergenic
cbrenneri	chromosome:chrUn:105462742:105462803:-1	Same_strand\|Intronic_coding\|NM_073857 ## Opposite_strand\|Intronic_coding\|NM_071200
ppacificus	chromosome:chrUn:158296156:158296279:-1	Same_strand\|Intronic_coding\|NM_063800

cel-mir-38

Cloning frequencies
absolute	CE1
cel-mir-38 3arm	1
normalized	CE1
cel-mir-38 3arm	0.001

block2590 (miRBase cel-mir-38) [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-38	0.001	no	no	0.50/0.50	22/22/1.00	0.0	0.0	1	0	1	0	16	7	3arm	1	nd	0.14	2	1	1	na	na

Clusters
Located in cluster 1: cel-mir-35, cel-mir-36, cel-mir-37, cel-mir-38, cel-mir-39, cel-mir-40, cel-mir-41

Families
Member of family miR-35/36/38/39/40/41 (seed CACCGGG): cel-mir-40, cel-mir-35, cel-mir-36, cel-mir-37, cel-mir-39, cel-mir-41, cel-mir-38

		reads	miRBase family seed
seed	----------------------------------------------------------------------------------------CACCGGG--------------------------------------------------	1	miR-35/36/38/39/40/41
		len	cloning frequencies
			CE1
cel-miR-38	---------------------------------------------------------------------------------------TCACCGGGAGAAAAACTGGAGT------------------------------------	22	1
celegans	-------TCTGT--------------GAGCCAGGTCCTGTTCCGGTTTTT-TCCGTG-GTGATAACGCATCCAAAA----GTCTCTATCACCGGGAGAAAAACTGGAGTAGGACCTGTGACTCAT--------------------
cbriggsae	------GTCCGATGGGTATTCATGTGGAGCCTGGACCTGTACCGGGTTCTCTTTGTG-GTGATATGACAACTCATAACCATTCCTTATCACCGGGAGACAACCTGGTATAGGTCCAGCGACTCTGCTGGATGGTCCCGTTGCCC-
cjaponica	GCAGTGGTCCCTCGGGGCAGAA----GAGCCAGGACCTACATCAGTTTCTTTCCGCG-GTAATAAATAATACATTA--------TTATCACCGGGAGAAAAACTGGAGTAGGACCTGCGACTCGACTCGACCTTTATTCCGCTGT
cbrenneri	-----GGTCTATTTCGTTTCCA----GAGCCAGGACCTGTTCCAGTTTTTTTCCGCG-GTAATAACGCGAGCAAGT-------CCTATCACCGGGAGAAAAACTGGAGTAGGTCCTGCGACTCTACAAGGATGTTCAGTAGTCT-
ppacificus	----------GTACCGTACCCA-------CCCCGTCCTGCATCGCGTATCGCCCGTGTGTGCTCGCATAAGAAGTA----------CTCACCGGGAGAAATGC-GATGTAGG-CCCGTGGCCTACCGTAC---------------
cremanei	--------------------------------------ATACCGGTTTAACTTCGTG-GTGATATGACACATATTA--CATTCTTTATCACCGGGAGTAAAACTGGTAT------------------------------------
	* * * * ** * ********** * * * *
	----- ----- ------------------------ ------ ------------------ --------------------------------------------- -----	Y62F5A.9 Y62F5A.9 Y62F5A.9
celegans	...(( (((((((((((((((((((((((( ..(.(( ((((((..((........ ))...)))))))).)..)))))))))))))))))))).).)))))	1.000 -50.10
cbriggsae	...(((((((((((((.((((((.((((((((((((((((((((((..((( (((((((((....)))))........)))))))..)))))..)))))))))))))))))...))))))))))))..)))))))...	0.997 -66.80
cjaponica	(((((((......((((..((. (((.((((.(((((..((((((.(((((.(( ((.((.(((((....))) )))).))))))))).))))))..))))).))))...)))...))..))))....)))))))	0.964 -51.50
cbrenneri	((.(((((.....(((( (((.((((((((((((((((((((((((.(( ((.(((..((......)) ..))).))))))))))))))))))))))))))))...))))....))).....))))).))	0.997 -55.90
ppacificus	((((.(((.((( (.....((((((((((((.((.((((((.((((((......)).))) ).))).))).)).)))) )))))))) ...))))..))).))))	1.000 -46.70
cremanei	((((((((((.(((((.(( ((((((............ .......))))))))))))).))))))))))	1.000 -26.31

celegans	chromosome:II:11537846:11537943:1	Opposite_strand\|Intronic_coding\|Y62F5A.9\|Y62F5A.9 ## Y62F5A.9\|protein_coding\|Y62F5A.9\|Y62F5A.9 [Source:RefSeq_peptide;Acc:NP_741048] ## {MIR: cel-mir-38}
cbriggsae	chromosome:chrII:7535848:7535984:1	Opposite_strand\|Intronic_coding\|NM_177732 ## Same_strand\|Intronic_coding\|NM_001101718 ## {MIR: cbr-mir-38}
cjaponica	chromosome:chrUn:117591702:117591833:-1	Opposite_strand\|Intronic_coding\|NM_171042
cbrenneri	chromosome:chrUn:41613392:41613518:-1	Same_strand\|Intronic_coding\|NM_001056672 ## Opposite_strand\|Intronic_coding\|NM_171042
ppacificus	chromosome:chrUn:118860534:118860634:1	Same_strand\|Intronic_coding\|NM_133957 ## {Repeats: (CCCTA)n 5 80 1 class=Simple_repeat}
cremanei	chromosome:chrUn:8778778:8778845:-1	Same_strand\|Intronic_coding\|NM_001011005 ## Opposite_strand\|Intronic_coding\|NM_171042

cel-mir-255

Cloning frequencies
absolute	CE1
cel-mir-255 3arm	2
normalized	CE1
cel-mir-255 3arm	0.001

block7127 (miRBase cel-mir-255) [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-255	0.006	no	no	0.27/0.27	22/22/1.00	0.0	0.0	2	0	1	0	27	6	3arm	1	nd	0.18	3	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------AACUGAA--------------------------------------------------	2	miR-255
		len	cloning frequencies
			CE1
cel-miR-255	----------------------------------------------------------------------------------AAACTGAAGAG--------ATTTTTTACAG----------------------------	22	2
celegans	CAGTGGTTCGACTAAATTTTGGA---GGTAAGAAATC---TTTGTAGT-------TCTCCG------TATTGTGAC--GTGAAAACTGAAGAG--------ATTTTTTACAGACT-TCACAAATTTGAAATATATTCCTG
cbriggsae	--------GATGTCTCTTCATTATCAGGTAAGAAATC---TTTGTAGT-------TTTCCG------CGAGTCAAC--GTGAAAACTGAAGAG--------ATTTTTTACAGATTCCGGAGGAGCATC------------
cbrenneri	-------------------------AGGTAAGAAATC---TTTGTGGT-------TTTCCG------TTATGAGAC--GAGAAAACTGAAGAG--------ATTTTTTACAG----------------------------
cjaponica	------CTCACGCAAATCCTGGA---------------------CAGT-------TTACGG------AGATTGAACCGGCGAAAACTGAATGT--------TTGTATTGAA-----------------------------
ppacificus	GGATATTAGTTGTGGATTCCGAAAAGAGTGCGCAATCAGAGTCACGGTCTCTTCATTACCGAGCTATTGAGAGAGT--GTGCGAACTGAAGAGACGGTGACACGTATTGCGCATTCTCTCGGTTCAGTTGTGTAGTATCT
cremanei	-------------------------AGGTAAGAAATC---TTTGTGGT-------TTTCCG------TGTTTAAAC--GCGAAAACTGAAGAG--------ATTTTTTACAG----------------------------
	** * * * * * ******* * **
celegans	(((..((.....((((((((((( ((((((((((( (((.(((( (.(((( (......)) ).)).))))).)))) )))))))))...)) ))).)))))))......))..)))	1.000 -29.40
cbriggsae	((((.((((((...(((..(((((((((( (((.(((( (((.(( ((......) )))))))))).)))) ))))))))).)))....))))))))))	1.000 -37.60
cbrenneri	..(((((((((( (((.(((( (((((( ((....))) ).)))))))).)))) )))))))))..	1.000 -25.00
cjaponica	.(((.((((((...... (((( ((.((( ........)))....))))))...)) ))))..))).	0.875 -10.90
ppacificus	((((((((......((..((((..((((((((((((....(((((.(((((((((....((.((..((....)).. )).))...))))))))).)))))....)))))))))))).)))).)).......))))))))	0.991 -54.92
cremanei	..(((((((((( (((.(((( (((((( (......)) ).)))))))).)))) )))))))))..	1.000 -24.80

celegans	chromosome:V:5440623:5440732:1	intergenic ## {SimpF: WRM064dG03 1 fosmid,WRM0628aF03 1 fosmid,WRM0615bE04 1 fosmid,WRM0629cD12 1 fosmid,WRM0634bA01 1 fosmid,WRM0612bH07 1 fosmid,WRM0619cH11 1 fosmid} ## {MIR: cel-mir-255}
cbriggsae	chromosome:chrV:8908222:8908315:1	Opposite_strand\|Intronic_coding\|NM_001011629 ## {MIR: cbr-mir-255}
cbrenneri	chromosome:chrUn:186086568:186086717:1	intergenic
cjaponica	chromosome:chrUn:104537755:104537904:-1	Same_strand\|Intronic_coding\|NM_066158
ppacificus	chromosome:chrUn:118664607:118664744:1	Opposite_strand\|Intronic_coding\|NM_102771
cremanei	chromosome:chrUn:141254722:141254871:1	Opposite_strand\|Intronic_coding\|NM_072673

cel-mir-257

Cloning frequencies
absolute	CE1
cel-mir-257 5arm	1
normalized	CE1
cel-mir-257 5arm	0.001

block7504 (miRBase cel-mir-257) [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-257	0.004	no	no	0.50/0.57	21/22/1.00	nd 0.0	nd 0.0	0 1	0 0	0 1	0 0	15 24	15 7	5arm 5arm	1 1	nd nd	0.18 0.29	1 2	1	1	na	na

		reads	miRBase family seed
seed	-------------------------AGUACC----C----------------------------------------------------------------------	1	novel
seed	----------------AGUAUCA-----------------------------------------------------------------------------------	0	novel
		len	cloning frequencies
			CE1
	------------------------GAGTACC----CAGTGATCGCCTTC---------------------------------------------------------	21	1
cel-miR-257	---------------GAGTATCAGGAGTACC----CAGTGA-----------------------------------------------------------------	22	-
celegans	ATAATATTTCCCGCTGAGTATCAGGAGTACC----CAGTGATCGCCTTCACATATTGGGAAGAAGTATGTGATTGCGTCCTGCAGTTCTTCCATGATGTACTCAGG
cbriggsae	---------------GAGTATCAGGAGAATCAGAGAAATGATATTTTGAATTTTCTAAAAGAAATTCAAATATTGAAGACTGA----TTTTCATGA-ATACCC---
	************ * * * **** * * * * * ** * ** * * * *
celegans	.............((((((((((((((.((. (((.((.(((..(((((((((.......)))))))))..))))))))..))..)))).)))..))))))).	1.000 -33.80
cbriggsae	..((((((.(((((((((......((((.((((((((((......)))))))))))))).....)))) ))))).))) .)))..	0.999 -21.50

celegans	chromosome:V:17140637:17140738:1	intergenic ## {SimpF: WRM0640aH01 1 fosmid,WRM0634cB09 1 fosmid,WRM0636cC05 1 fosmid,WRM0627bC04 1 fosmid,WRM0614cF07 1 fosmid,WRM0622dB08 1 fosmid,WRM0641aD01 1 fosmid,WRM0611aG03 1 fosmid,WRM0638aE05 1 fosmid,WRM0639bG06 1 fosmid,WRM066bB01 1 fosmid,WRM066dE06 1 fosmid,WRM0622dH05 1 fosmid,WRM0619dB07 1 fosmid,WRM0625bF02 1 fosmid} ## {MIR: cel-mir-257}
cbriggsae	chromosome:chrII:4706533:4706674:1	Opposite_strand\|Intronic_coding\|NM_061909 ## Same_strand\|Intronic_coding\|NM_001047951

cel-mir-249

Cloning frequencies
absolute	CE1
cel-mir-249 3arm	2
normalized	CE1
cel-mir-249 3arm	0.001

block7671 (miRBase cel-mir-249) [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-249	0.001	no	no	0.52/0.52	23/23/1.00	0.0	0.0	2	0	1	0	14	7	3arm	1	nd	0.13	1	2	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------CACAGGA----------------------------------------------------	2	miR-249
		len	cloning frequencies
			CE1
cel-miR-249	--------------------------------------------------------------------------------TCACAGGACTTTTGAGCGTTGCC-------------------------------------	23	2
celegans	-----------------ATACTCT-TGAACGACTAGCAACGCACAAACGTCTTCTGTGCGACAA--CATCTGAATGTTTGTCACAGGACTTTTGAGCGTTGCCAGTC---GAAAGAGGAA--------------------
cbriggsae	GCTATTTGTTATTTTGTGCGCCCTCAATGCTACTAGCAACGCTCAAAAAT-CACTGTACGACAAATGACT--ATATTTTGTCACAGGATTTTTGAGTGTTGCTAGTC---GGAGAAGGGCCGTCTTGAAATAATTCAGGT
cjaponica	-----TTTTAAATTGTTTTCCTCTCCCTGT--CTAGCGGCGC-CAAAAGATTACTGTGAGGCAAAGAAATGGTGAGCTTGTCACAGGACTTTTGAGCGTTGCTAGTTATAGAGGATGGAATTGTAAGTTTTTGA------
cbrenneri	-CTAACTTTTATTTTTTTGTCTCTCTGAGCTACTAGCAACGC-TAGAAGTCTACTGTTAGACAGAGTACA-GAAATTTTGTCACAGGACTTTTGAGCGTTGCTGGTTAATGAGAGCCTATT--TTAGTAATTAGTAAG--
cremanei	TCTCATTACT-TCTATTTTGTTTTCTACGTGACTAGCAACGCACAAAAGT-TTCTGTGCGACAA---ATATGAAATTTTGTCACAGGACTTTTGAGCGTTGCTAGTT---GAAAGAAGATTCACTATGATCAGATCAGG-
	* *** * * * **** * ** * ********* *** * *
celegans	...(((( (...(((((.(((((((.((((.(((..((((((((..( (((....))))))).)))))))).)))).))))))).)))) ).)))))...	1.000 -40.60
cbriggsae	(((....(((((((((.(((((((.....((((((((((((((((((((( (.((((..((((((..... ....)))))))))))))))))))))))))))))). ))...))))).))..)))))))))...)))	0.968 -54.70
cjaponica	....(((((...((((..((((((( (((((((((( ((((((....(((((((((.............)))..))))))..)))))).))))))))))..)))).))).)))).....)))))....	0.993 -42.12
cbrenneri	...(((.(((((.......(((((......((((((((((( ((((((((..((((..((((((((... ...))))))))))))))))))).))))))))))))....)))))...... ..)))))..)))...	0.987 -45.96
cremanei	.((.(((... ((......(((((((...(((((((((((((.((((((. ((((((..((((( (........)))))))))))))))))).)))))))))))) )..))))))).......))...))).)).	0.826 -45.32

celegans	chromosome:X:3006432:3006528:-1	intergenic ## {SimpF: yk384d7 -1 RNAi} ## {MIR: cel-mir-249}
cbriggsae	chromosome:chrX:7892480:7892613:-1	Opposite_strand\|Intronic_coding\|NM_178660 ## Same_strand\|Intronic_coding\|NM_133381 ## {MIR: cbr-mir-249}
cjaponica	chromosome:chrUn:20281422:20281547:1	intergenic
cbrenneri	chromosome:chrUn:1355930:1356062:-1	intergenic
cremanei	chromosome:chrUn:4287059:4287189:1	intergenic

cel-mir-359

Cloning frequencies
absolute	CE1
cel-mir-359 3arm	1
normalized	CE1
cel-mir-359 3arm	0.001

block8220 (miRBase cel-mir-359) [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-359	0.001	no	no	0.45/0.50	20/22/1.00	0.0	0.0	1	0	1	0	27	5	3arm	1	nd	0.18	1	1	1	na	na

Clusters
Located in cluster 9: cel-mir-359, cel-mir-785

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------------------CACUGGU---------------------------------------------------------	1	miR-359
		len	cloning frequencies
			CE1
	--------------------------------------------------------------------------------------------TCACTGGTCTTTCTCTGACG---------------------------------------------	20	1
cel-miR-359	--------------------------------------------------------------------------------------------TCACTGGTCTTTCTCTGACGAA-------------------------------------------	22	-
celegans	---------AA--TGCTCCTTGAAA-----TT--------TCAATCGTTAGAGTAACACAC-------AGTTACACGACCTCATCAATCGTGTCACTGGTCTTTCTCTGACGAATTGAAGTTCTGGAGACAATTTTGGT--TG--------------
cbriggsae	----AAGATAAGTTACAAATCTAGACAAATCT--------TCATCCGTCAGAGCATATCTC-------AGTTACACAACTTCCTAAATAGTGTCACTGGTTATCCTCTGTCGAAATGAAGATGTCAAAAGTAGCTGTTTT-----------------
cjaponica	------------TTGCGCTG----------CC--------TCAATCATTGGAAAAATTCAC-------AGTAACAAGAGATTCCCAACT-TGCCACTGGTGTTTTTCTGATGAATTGAAGTCAGTGGCAA---------------------------
cbrenneri	---------CATTTGTATTCTGAAAAAAAACTCAAATCGTTCGATTGTCAGAGCAATCCTC-------AGTAACACGTACTCATTATTTGTGTCACTGGTTTTCTTCTGACGAATCGAAATGCTCGAGTTCTGGTTTGTTTTGCGAGAAAATGAATG
ppacificus	--------------------------------------------ATGTGAGAGTAGTGCACCACTTTGAATGATGGAAATGTATCA----TGACACTGGTTACCT--CGACAA--------------------------------------------
cremanei	GCAAAAGACTAATGGCCTCGATAAA-----CT--------TCATTGGTCAGAGCAACACGC-------AGTCACATAAGTTTCTGAAATGTGTCACTGGTTTTCCTCTGACTAATTGAAGATATCGAGTAAATTTTTTTGT----------------
	* ** * * * * * * * ***** * *
celegans	.. ((((((..(((. (( (((((((((((((.((.((.( (((.((((((.........)))))).)))))).)).)))))))).)))))))))).)))).))........ ..	1.000 -39.40
cbriggsae	(((((.((((((.......((((..((( ((((.((.(((((.(((..(( (((.((((.............)))).))))).))).))))).))..)))))))))))....)))))))))))	0.999 -33.62
cjaponica	.((((((( .( ((((((((..(((((((...( (((..((((..........)) ))..))))..)))))))..)))).))).)).))))).)).	1.000 -30.40
cbrenneri	(((((((.(((((((((.(((((....(((((((((((((((((.((...(( (((.(((((...........))))).)))))..)).))))))).))))))).....))).....))))).)))).)).))).)))))))	0.810 -35.60
ppacificus	.((((((.(((....((((......((((((......))))) ).....))))))))) ).))).	0.995 -12.90
cremanei	((((((((...((...(((((((.. (( (((((((((((((.((.((.( (((.(((((...........))))).)))))).)).))))))))))).)))).)))))))...))))))))))	0.997 -39.50

celegans	chromosome:X:3004283:3004392:1	intergenic ## {MIR: cel-mir-359}
cbriggsae	chromosome:chrX:7890588:7890708:1	Same_strand\|Intronic_coding\|NM_178660 ## Opposite_strand\|Intronic_coding\|NM_133381 ## {MIR: cbr-mir-359}
cjaponica	chromosome:chrUn:20284297:20284388:-1	intergenic
cbrenneri	chromosome:chrUn:1354700:1354840:1	intergenic
ppacificus	chromosome:chrUn:37820070:37820219:1	intergenic
cremanei	chromosome:chrUn:4288224:4288344:-1	intergenic

cel-mir-785

Cloning frequencies
absolute	CE1
cel-mir-785 3arm	4
normalized	CE1
cel-mir-785 3arm	0.003

block8221 (miRBase cel-mir-785) [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-785	0.001	no	no	0.26/0.29	19/22/0.80	0.0	0.5	4	0	1	0	14	2	3arm	1	nd	0.18	2	4	1	na	na

Clusters
Located in cluster 9: cel-mir-359, cel-mir-785

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

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------AAGUGAA----------------------------------------------	4	miR-785/86
		len	cloning frequencies
			CE1
	------------------------------------------------------------------------------TAAGTGAATTGTTTTGTGTAG---------------------------------	21	3
	------------------------------------------------------------------------------TAAGTGAATTGTTTTGTGT-----------------------------------	19	1
cel-miR-785	------------------------------------------------------------------------------TAAGTGAATTGTTTTGTGTAGA--------------------------------	22	-
celegans	------------GCTCTTTTTCTCACCCATCAGCACAGAATTTTTCG-CTAACAGAAACCTC---AAAACA----ATGTAAGTGAATTGTTTTGTGTAGATGGTGGAAATG----AGC--------------
cbriggsae	TTGAAATGCGTTGCTC--TTTCGCAACCGTCAGCACAGAGTGCTTCGACTTACACAGAATTCGTAAAACCAACTGATGTAAGTGAA-TACTCTGTGTTGATGGTGATGATGCTGAAACGTAATGTATTCTAG
cjaponica	------------GCTCTCTTTT-----CACTAACCCAGAACAACTCG-CTAACACGAACACTGAGAAA-----TGATGTAAGTGAA-TGTTCTGTGTTGGTGGAGATGATG----AGT--------------
cbrenneri	------------GCTC-TTTTCTCTCCCGTTAGCACAAAATATTTTA-CTTACACATAAC-----AAAACATATGATGTAAGTGAA-TACTTTGTGTTAATGGAAAAAGGGC--------------------
ppacificus	ACTGTTGGAAGTGCTC-----------AATAAACTGAAAC--------CTGGCATGAAC------AATTCA--------AAGTGAATCGCTTCCAGCAGA--------------------------------
cremanei	-------AAACCGCTC--TTTTTTGTCCGTCAGCGCAGAATTTTTTCGCTTACACGAGT------AATGTAAACGATGTAAGTGAA-TATTCTGTGTCGATGGGTATAAAAAGATAATGATGGTTT------
	**** * * * * ***** * *
celegans	((((..((((.((((.(((.(((((((((..(((( ((.(((........ ...... .))).))))))..))))))))).))))))))))).) )))	1.000 -36.26
cbriggsae	....((((((((((.. ((((((((((((((((((((((((.(((.((((((((((...............))).)))))))))) ))))))))))))))))).....))).)))).))))))))))....	1.000 -52.06
cjaponica	(((((((((( (((((((.(((((((..((( ((.(((.............. ...))).))))). ))))))).))))))))))).)).) )))	0.949 -32.33
cbrenneri	(((( ((((.....(((((((((((((.((.(((( ((((((((((.. ......)))).)))))))))) )).))))))))))))).))))))))	1.000 -35.20
ppacificus	.((((((((((((.(( (......((((.. .((.......) ).)))) ...)))..)))))))))))).	0.543 -20.80
cremanei	((((((.(( (((((..((((((.(((((((((...((((((((((((... ........)).)))))))))) .))))))))).))))))...)))))))......))))))	0.999 -39.50

celegans	chromosome:X:3004660:3004753:1	intergenic ## {MIR: cel-mir-785}
cbriggsae	chromosome:chrX:7891054:7891182:1	Same_strand\|Intronic_coding\|NM_178660 ## Opposite_strand\|Intronic_coding\|NM_133381 ## {MIR: cbr-mir-785}
cjaponica	chromosome:chrUn:20283862:20283951:-1	intergenic
cbrenneri	chromosome:chrUn:1355192:1355283:1	intergenic
ppacificus	chromosome:chrUn:73925300:73925433:1	intergenic ## {Repeats: AT_rich 1 47 1 class=Low_complexity}
cremanei	chromosome:chrUn:4287759:4287868:-1	intergenic

miRNAknown_cloningOK (2 loci)

cel-mir-78

Cloning frequencies
absolute	CE1
cel-mir-78 3arm	6
normalized	CE1
cel-mir-78 3arm	0.004

block6032 (miRBase cel-mir-78) [miRNAknown_cloningOK]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
miRBase cel-mir-78	0.593	no	no	0.55/0.57	20/21/1.00	0.0	0.0	5	0	1	0	15	5	3arm	1	nd	0.24	2	6	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------GGAGGCC----------------------------	6	novel
		len	cloning frequencies
			CE1
cel-miR-78	------------------------------------------------------------TGGAGGCCTGGTTGTTTGTGC---------------	21	5
	------------------------------------------------------------TGGAGGCCTGGTTGTTTGTG----------------	20	1
celegans	aataaaatatattgtttcatagtgtccgtaaaataactagatttattttgtaaaaactatTGGAGGCCTGGTTGTTTGTGCtggaatgtttcgaga
	************************************************************************************************
celegans	..............((((..((..((((((((((((((((.(((.....((....)).....)))..)))))))))).))).)).)..))..))))	1.000 -15.00

celegans

chromosome:IV:15165608:15165703:1

intergenic ## {SimpF: WRM063cD05 1 fosmid} ## {MIR: cel-mir-78}

cel-mir-248

Cloning frequencies
absolute	CE1
cel-mir-248 3arm	8
normalized	CE1
cel-mir-248 3arm	0.006

block7654 (miRBase cel-mir-248) [miRNAknown_cloningOK]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
miRBase cel-mir-248	0.016	no	no	0.50/0.55	22/24/1.00	0.3	0.0	7	0	1	0	16	4	3arm	1	nd	0.23	2	8	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------ACACGUG---------------------------------------------------	5	miR-248
seed	-------------------------------------------------------------------------------UACACGU----------------------------------------------------	3	novel
		len	cloning frequencies
			CE1
	-------------------------------------------------------------------------------TACACGTGCACGGATAACGCTC-------------------------------------	22	5
	------------------------------------------------------------------------------ATACACGTGCACGGATAACGCTC-------------------------------------	23	2
	------------------------------------------------------------------------------ATACACGTGCACGGATAACGCT--------------------------------------	22	1
cel-miR-248	------------------------------------------------------------------------------ATACACGTGCACGGATAACGCTCA------------------------------------	24	-
celegans	-----------TTTCCCGGCT-----GCAACTACGGTAAGCGGTA--TCCAGCCGATGTTTTCAATACTGCAT-TTGAATACACGTGCACGGATAACGCTCATTGTTTTTCGCATGC---------------------
cbriggsae	-----------TTTTATTGCAAACTGATATTCACGATAAGCGCTA--TCCTTCCGTTGTATTCAAGCTTGGTTGTCGAGTACACGTGCTCGGATAACGCTCATCGAGTCTGATCGGTTATGTTGGTAAAG--------
cjaponica	------------------GCT-----TCCATTACGATTAGCGCTA--TCCAGCCGAAGTATTCTAGAAAAGAT-TCGAGTACACGTGCACGGATAGTGCTCATTGTTTTTGGAGAGC-----------ACGAAATTCA
cbrenneri	CTTCTGGTATTTTTCTTGGCA-----GTTATCACGATCAGCGCTA--TCCAGCCGTTGTAATCAAGAACGGAGGTTGACTACACGTGCACGGATAACGCTCATTGTCATAGGTTGCC---ATTTTTAAAGTTAAGAAG
ppacificus	-------------------GA-----TCGTTCTCGATGAGTGATACTTCCCACAGT-----------------------TACACGTGCACCGACAGCGGTC-------------------------------------
cremanei	ATTTGCTAGTATTTTTTGGCA-----GAGATTACGATTAGCGATA--TCCAGCCGTTGTATTCAATAGCGCAT-TTGAGTACACGTGCACGGATA-CGCTCATCGTTTTTGTATTGCCACTTCGATTGAGTAAGT---
	** * ** * * * * ********* * ** * * **
celegans	.......((( ((((..(((((.((((.(( (((.((((.(((.(((((........ ))))).))))).))..))))).)))).)))))..)).))).))	1.000 -29.60
cbriggsae	.((((((((((((((((.....((((.((((.(( (((...((.(((((((..((......)).))))))))).....))))).)))).))))......))))))).))).)))))).	0.942 -33.10
cjaponica	((( ((((..(((((.((((((( (((.((((..((((((..(((....) )))))))).)).))..)))))))))).)))))...)))).))) ..........	0.944 -37.60
cbrenneri	(((((...(((((...((((( ..(((.(((((.((((.(( (((.((((.((((.((((.........)))).)))))).))..))))).)))).))))).)))...)))) ).....)))))..)))))	0.995 -37.80
ppacificus	(( (((((.(((.((.(((..(((......))) ..)))...)).))).)))))))	0.994 -15.40
cremanei	(((((((.........((((( (.((..(((((.((((.(( (((.((((.(((((((((........ ))))))))))).))..))))) )))).)))))..))...)))))).........)))))))	0.999 -44.37

celegans	chromosome:X:2262367:2262464:-1	intergenic ## {SimpF: WRM0638dD08 -1 fosmid,WRM0641cB06 -1 fosmid,WRM0631cG01 -1 fosmid,WRM0617dB01 -1 fosmid,WRM0625bA05 -1 fosmid,WRM0620aC04 -1 fosmid} ## {MIR: cel-mir-248}
cbriggsae	chromosome:chrX:4610288:4610404:1	Same_strand\|Intronic_coding\|NM_001087279 ## Opposite_strand\|Intronic_coding\|NM_001046332 ## {MIR: cbr-mir-248}
cjaponica	chromosome:chrUn:6737767:6737867:-1	intergenic
cbrenneri	chromosome:chrUn:1122535:1122662:1	Opposite_strand\|Intronic_coding\|NM_001107657
ppacificus	chromosome:chrUn:145903676:145903813:1	Same_strand\|Intronic_coding\|NM_001110778 ## Opposite_strand\|Intronic_coding\|NM_001085507
cremanei	chromosome:chrUn:103926403:103926528:1	intergenic