miR-Intess: classification

confident miRBase miRNAs

miRNAknown_cloningHIGH_randfoldOK (23 loci)

cel-mir-74

Cloning frequencies
absolute	CE1
cel-mir-74 3arm	940
normalized	CE1
cel-mir-74 3arm	0.657

block8198 (miRBase cel-mir-74) [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-74	0.001	no	no	0.39/0.53	18/22/0.73	0.0	0.5	907	0	1	0	16	5	3arm	1	nd	0.21	1	940	1	na	na

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--------------------------------------------	930	miR-73/74
seed	---------------------------------------------------------------------------------------GCAAGAA-------------------------------------------	6	miR-268
seed	------------------------------------------------------------------------------------------AGAAAUG----------------------------------------	2	novel
seed	-------------------------------------------------------------------------------------UGGCAAG---------------------------------------------	2	novel
		len	cloning frequencies
			CE1
	-------------------------------------------------------------------------------------TGGCAAGAAATGGCAGTCTAC-------------------------------	21	664
	-------------------------------------------------------------------------------------TGGCAAGAAATGGCAGTCT---------------------------------	19	243
cel-miR-74	-------------------------------------------------------------------------------------TGGCAAGAAATGGCAGTCTACA------------------------------	22	17
	--------------------------------------------------------------------------------------GGCAAGAAATGGCAGTCTACA------------------------------	21	4
	-------------------------------------------------------------------------------------TGGCAAGAAATGGCAGTCTA--------------------------------	20	4
	-------------------------------------------------------------------------------------TGGCAAGAAATGGCAGTC----------------------------------	18	2
	-----------------------------------------------------------------------------------------AAGAAATGGCAGTCTACA------------------------------	18	2
	--------------------------------------------------------------------------------------GGCAAGAAATGGCAGTCT---------------------------------	18	2
	-----------------------------------------------------------------------------------C-TGGCAAGAAATGGCAGTCTAC-------------------------------	22	1
	-----------------------------------------------------------------------------------C-TGGCAAGAAATGGCAGTC----------------------------------	19	1
celegans	-----------------AAATGGTTCAAAAAACGTTCGGGCTTCCATC-TCTTTCCCAGCCTAC--ATC--TCAACCTGG--GC-TGGCAAGAAATGGCAGTCTACACGT--------------TTTTCAACCAAA-
cbriggsae	-----CGAGACTAAGAAAAAAGGTCC---GCACTTTTGGGCTTCCATA-TCTTTCCCAGCTCCT--CTCATTTACTATGGATGC-TGGCAAGAAATGGCAGTCTAGATGTGCAAAATCCTGCAACTCTCTCTCTCG-
cjaponica	CTGTGAAGCGGTGAAGTGAATGGCGACACGCGCGATTGGGCTTCCATA-TCTTTCCCAGCTGAAACATCTTTTAAC------GC-TGGCAAGAAATGGCAGTCTACTCGCGCATGCCT-----GCTCCCGCTCTCAG
cbrenneri	------TGACTCGGAGCGAAAGGATA---GCACGTTTGGGCTTCCATTATCTTTCCCAGCAGGTTCA----CGAACGTAT--GC-TGGCAAGAAATGGCAGTCCACATGTGTAAATCCTCGAAGCTCTCGTCA----
ppacificus	---------------ATGAAGAG---------------------CATTTCCTTTCTCAGGTCATTGATCTTCTAGCCTTG--GCTTGGCAAGAAATGG---------------------------TCTCTTCAT---
cremanei	GTGACCGAAGACGCTGGAAAAGGTCG---ACACGTTTGGACTTCCGTC-TCTTTCCCAGCTGAT--ATTGGATAGCAT----GC-TGGCAAGAAATGGCAGTCCAGATGTGTACACCTTC-AAGCTCTTGTCAT---
	** * * * *** * * *********** *
celegans	...(((((..((((((((..(((((.((((. ((((..((((((((. ... ......))) )) ))).)))).)))).)))))..)))) )))).)))))..	1.000 -38.60
cbriggsae	(((((...(((....(((... ((((.((((((((.((((. ((((..((((((((. ............))).)) ))).)))).)))).)))))))).)))).....))).....)))...)))))	1.000 -44.22
cjaponica	(((.((.((((.((.((....((((....((((((.((((((.((((. ((((..((((((((((....))))).. )) ))).)))).)))).)))))).)))))).)))). )))))))))).)))	0.981 -52.00
cbrenneri	.(((..(((((...(((((. ((((((.((((((.(((((.((((..((((((.(((.. ..)))...) )) ))).))))))))).)))))).))))))..)))))....))))).))).	1.000 -51.20
ppacificus	(((((((( ((((((.....((((((((...............)) ))))))...)))))). .))))))))	0.640 -19.76
cremanei	(((((..((((.(((....(((((.. (((((((((((((.((((. ((((..(((((((.( ((...))).)). )) ))).)))).)))).)))))))))))))..))))). .))))))))))))	1.000 -51.70

celegans	chromosome:X:2369037:2369133:1	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-74}
cbriggsae	chromosome:chrX:4493555:4493678:-1	Opposite_strand\|Intronic_coding\|NM_001087279 ## Opposite_strand\|Boundary_non-coding\|NM_178655 ## Same_strand\|Intronic_coding\|NM_001109816 ## {MIR: cbr-mir-74}
cjaponica	chromosome:chrUn:6831841:6831964:1	intergenic
cbrenneri	chromosome:chrUn:1030413:1030529:-1	intergenic
ppacificus	chromosome:chrUn:17469661:17469797:-1	intergenic
cremanei	chromosome:chrUn:103837391:103837512:-1	intergenic

cel-mir-81

Cloning frequencies
absolute	CE1
cel-mir-81 3arm	9157.500
normalized	CE1
cel-mir-81 3arm	6.397

block8205 (miRBase cel-mir-81) [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-81	0.001	no	no	0.37/0.45	18/23/0.97	0.0	0.0	8025	0	1	0	20	8	3arm	1	nd	0.18	2	9184	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-----------------------------------------------------	9046	miR-80/81/82
seed	-----------------------------------------------------------------------------------AGAUCAU----------------------------------------------------	66	novel
seed	--------------------------------------------------------------------------------------UCAUCGU-------------------------------------------------	63	novel
seed	-------------------------------------------------------------------------------------AUCAUCG--------------------------------------------------	8	miR-392
seed	------------------------------------------------------------------------------------GAUCAUC---------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
cel-miR-81	---------------------------------------------------------------------------------TGAGATCATCGTGAAAGCTAGT---------------------------------------	22	8025
	---------------------------------------------------------------------------------TGAGATCATCGTGAAAGCTAG----------------------------------------	21	437
	---------------------------------------------------------------------------------TGAGATCATCGTGAAAGCTAGTT--------------------------------------	23	339
	---------------------------------------------------------------------------------TGAGATCATCGTGAAAGCT------------------------------------------	19	178
	----------------------------------------------------------------------------------GAGATCATCGTGAAAGCTAGT---------------------------------------	21	61
	-------------------------------------------------------------------------------------ATCATCGTGAAAGCTAGT---------------------------------------	18	60
	---------------------------------------------------------------------------------TGAGATCATCGTGAAAGC-------------------------------------------	18	53
	---------------------------------------------------------------------------------TGAGATCATCGTGAAAGCTA-----------------------------------------	20	14
	------------------------------------------------------------------------------------GATCATCGTGAAAGCTAGT---------------------------------------	19	8
	-------------------------------------------------------------------------------------ATCATCGTGAAAGCTAGTT--------------------------------------	19	3
	----------------------------------------------------------------------------------GAGATCATCGTGAAAGCTAG----------------------------------------	20	3
	----------------------------------------------------------------------------------GAGATCATCGTGAAAGCT------------------------------------------	18	2
	-----------------------------------------------------------------------------------AGATCATCGTGAAAGCTAGT---------------------------------------	20	1
celegans	--------------ATCAGTGCCATCGTGCCCAACAGTCGGTTTTCACCGTGATCTGAGAGCAAT-CCAAAAATGCTTTTCTGAGATCATCGTGAAAGCTAGTTGTTGGTCTACGGGCTTTTG-------------------
cbriggsae	------------------------------------GTCGGTTTTCACCTTGATCTGAGAGCAATAACCAGAATGCTTATCTGAGATCATCGTGAAAGCTAGT---------------------------------------
cjaponica	------------------------------------GTCGGTTTTCCCATTGATCTGAGAGCTAA---CTGTACGC-TATCTGAGATCATCGTGAAAGCTAGT---------------------------------------
cbrenneri	------------------------------------GTCGGTTTTCACCTTGATCTGAGAGCTAT---CTGAATGC-TATCTGAGATCATCGTGAAAGCTAGT---------------------------------------
ppacificus	------------------------TCACTCCCGGCATGCGGTTTTCACGTTGATCTGAGAGCTAA--TCGATATG--TTTCTGAGATCATAGTGAAAGCTACTTGCCGAAGTGA----------------------------
cremanei	TTGACTATTCTAAAACCACTGCCCTCGTGGCCAGCAGTCGGTTTTCACCTTGATCTGAGAGCTAA--ACATAATGCTTATCTGAGATCATCGTGAAAGCTAGTTGCAGGTACACAGGCTCTTTGACATTAATGAATAATCGA
	******** * ************ * * * * ********* ******** *
	----- --------------------------------------------------- --------------------------------------------------------- -----	T07D1.2.2 T07D1.2 T07D1.2
	----- --------------------------------------------------- --------------------------------------------------------- -----	T07D1.2.1 T07D1.2 T07D1.2
	----- --------------------------------------------------- --------------------------------------------------------- -----	T07D1.2.3 T07D1.2 T07D1.2
celegans	......(((..((((.(((((((..(((((((((.(((((((.((((((.. .......)))...))).))))))).)))))))))..)))))))..))))))).....	1.000 -43.60
cbriggsae	...(((((((((..((((((.((((((..........)))...))).))))))..)))))))))...	1.000 -23.70
cjaponica	...(((((((....((((((.(((((... ......)) ..))).))))))....)))))))...	1.000 -17.70
cbrenneri	...(((((((((..((((((.(((((... ......)) ..))).))))))..)))))))))...	1.000 -23.80
ppacificus	(((((..(((((...(((((((((..((((((.(((((... .......) )).)).))))))..)))))))))...))))).)))))	1.000 -36.00
cremanei	((((.(((((..........(((...((((((.((((..(((((((((..((((((.(((((... .......))...))).))))))..)))))))))..)))).))).))).)))..............))))).))))	0.918 -43.85

celegans	chromosome:X:2431067:2431174:1	Opposite_strand\|Intronic_coding\|T07D1.2.2\|T07D1.2 ## T07D1.2\|protein_coding\|T07D1.2\|T07D1.2 [Source:RefSeq_peptide;Acc:NP_508444] ## {SimpF: WRM069cB10 1 fosmid,WRM062aG12 1 fosmid,WRM0618aC04 1 fosmid,WRM0630cF03 1 fosmid,WRM0631bE05 1 fosmid,WRM0636aE07 1 fosmid} ## {MIR: cel-mir-81}
cbriggsae	chromosome:chrX:4426639:4426786:-1	Opposite_strand\|Intronic_coding\|NM_001087279 ## Same_strand\|Intronic_coding\|NM_001109816 ## {MIR: cbr-mir-81}
cjaponica	chromosome:chrUn:6896845:6896992:1	intergenic
cbrenneri	chromosome:chrUn:978926:979073:-1	Opposite_strand\|Intronic_coding\|NM_076043 ## {SimpF: trf}
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}
cremanei	chromosome:chrUn:34151995:34152134:-1	Opposite_strand\|Intronic_coding\|NM_076043

cel-mir-786

Cloning frequencies
absolute	CE1
cel-mir-786 3arm	32
normalized	CE1
cel-mir-786 3arm	0.022

block8366 (miRBase cel-mir-786) [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-786	0.001	no	no	0.35/0.42	19/23/0.88	0.4	1.2	30	0	1	0	14	3	3arm	1	nd	0.17	2	32	1	na	na

Clusters
Located in cluster 10: cel-mir-240, cel-mir-786

		reads	miRBase family seed
seed	--------------------------------------------------------------------------AAUGCCC-----------------------------------------------	20	miR-786
seed	---------------------------------------------------------------------------AUGCCCU----------------------------------------------	12	novel
		len	cloning frequencies
			CE1
cel-miR-786	-------------------------------------------------------------------------TAATGCCCTGAATGATGTTCAAT--------------------------------	23	11
	-------------------------------------------------------------------------TAATGCCCTGAATGATGTTC-----------------------------------	20	8
	--------------------------------------------------------------------------AATGCCCTGAATGATGTTCAAT--------------------------------	22	7
	--------------------------------------------------------------------------AATGCCCTGAATGATGTTC-----------------------------------	19	4
	-------------------------------------------------------------------------TAATGCCCTGAATGATGTTCA----------------------------------	21	1
	--------------------------------------------------------------------------AATGCCCTGAATGATGTTCA----------------------------------	20	1
celegans	-----------------GGGATAGTTCCCGATCGAATATCAGTTGG-GGTATTTACAAA--AAGACAAAATTGTAATGCCCTGAATGATGTTCAATCGGTGATGAATCTC------------------
cbriggsae	-GGTGAGAGTAAGTTTAGGGACCCTTCCCAACAAAATCTCAAATAGTGGCATTTACACA--AGCAATGGTATGTAATGCCCTGTACGAGATTTGGTTGGTGAGAAGTCTCTACAATAGGTATCATT--
cjaponica	TTCTTCTGTATTATCTGGGGACATTTCCCATTAGAAACTCAGCTTG--GTAGTTACATGTAATGGAAAATCTGTAATGCCCTGCATGAGGTTCTATTGGGAAGAAATTCCTTTTTTTCACTGACTGGA
cremanei	------------------------------ATAGAGTCTCGGACAG-GGCATTTACATAC-AAGATAAATTTGTAATGCCCTTGCTGAGATTCCAT--------------------------------
	* ** * * * ***** * ********* ** *
celegans	(((((.((..(((((.((((((((.(..( ((((((.((((. .........)))))))))))..).)))))))).)))))..))..)))))	1.000 -36.70
cbriggsae	.((((.........(((((((..((((((((.(((((((..((((.((((((...((( .((....)).)))))))))))))..))))))).))))).)))..))))))).........)))).	0.998 -41.07
cjaponica	.(((((.((.......(((((..(((((((.(((((.((((((..( (((.(((((.((........)).)))))))))..)).)))).))))).)))))))...))))).......)).))..)))	0.893 -35.54
cremanei	...(((((((((..(( ((((.(((((... ..........)))))))))))..)))))))))...	1.000 -26.42

celegans	chromosome:X:7882696:7882785:1	intergenic ## {SimpF: WRM064aB09 1 fosmid,WRM0621bE08 1 fosmid,WRM0633bB07 1 fosmid,WRM065dC03 1 fosmid,WRM0619cA11 1 fosmid,WRM0633cC10 1 fosmid,WRM0611bE01 1 fosmid,WRM0618bB10 1 fosmid} ## {MIR: cel-mir-786}
cbriggsae	chromosome:chrX:13573542:13573664:1	Opposite_strand\|Intronic_coding\|NM_003107 ## Same_strand\|Intronic_coding\|NM_177736 ## {MIR: cbr-mir-786}
cjaponica	chromosome:chrUn:156278193:156278318:-1	intergenic
cremanei	chromosome:chrUn:181380:181509:-1	intergenic

miRNAknown_cloningOK_randfoldOK (8 loci)

cel-mir-795

Cloning frequencies
absolute	CE1
cel-mir-795 5arm	15
normalized	CE1
cel-mir-795 5arm	0.010

block1209 (miRBase cel-mir-795) [miRNAknown_cloningOK_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-795	0.001	no	no	0.46/0.48	19/24/0.94	0.0	0.0	13	0	1	0	14	2	5arm	1	nd	0.17	2	15	1	na	na

Families
Member of family miR-241/48/let-7/84 (seed GAGGUAG): cel-mir-795, cel-mir-48, cel-mir-241, cel-let-7, cel-mir-84

		reads	miRBase family seed
seed	------------------------GAGGUAG----------------------------------------------------------------------------------	15	miR-241/48/let-7/84
		len	cloning frequencies
			CE1
cel-miR-795	-----------------------TGAGGTAGAT-----TGATCAGCGAGCTT-------------------------------------------------------------	24	13
	-----------------------TGAGGTAGAT-----TGATCAGCG------------------------------------------------------------------	19	1
	-----------------------TGAGGTAGAT-----TGATCAGCGAGCT--------------------------------------------------------------	23	1
celegans	---------GAAACGTTACCTGCTGAGGTAGAT-----TGATCAGCGAGCTTGATACCCCGTTCAAAATCGTGATCAGTATACTTCGTCAGGCAGCTTGTTTT----------
cremanei	-----------------------TGAGGTAGACAC--AGTGGCTACGAATCTA-----CCAACCAGGGTTCGAGTCCACATACCTCA--------------------------
cbriggsae	-----------------------CGAGGTAGAT-----TGAGAATTGAGATTG--------------ATTGAAATCAACTCGGCTCACTTTCAGTATCCTG------------
cjaponica	GTGTGATTGGGGCGCGTTTGCACTGAGGTAGGTGCCAGCATGCCGTGATACTTCCATTTCAACATATTTCTGCTCCACCACGTCTCAGTTTTCACGCGTTTCCATTTTCAAAC
ppacificus	-----------------------CGAGGTAGAAATGCATTCG-TATGAGTTTGAGTGGATGATCGAAATC-AAGTGACCGTTTCTAACTGCG---------------------
	***** * * *
celegans	((((((((.((((.(((((((.(( ((((((.(((..((((........))))..))))))))))).))))))).)))).)))..)))))	1.000 -33.50
cremanei	.((((((..... .((((((.(((((((. .......))))))))).)))).)))))).	1.000 -22.20
cbriggsae	..(((...(( (((((..((((.((( ((((....))).)))))))).)))))))..))).	1.000 -15.90
cjaponica	...(((.((((((((((....(((((((..((((..((((.....(((..........))).........)))).))))...)))))))....))))))).)))...)))...	0.996 -30.34
ppacificus	((((.((((((((...((( ..(((.(((((........))))).)) )..))).)))))))).)).))	0.960 -15.80

celegans	chromosome:I:12594558:12594646:1	intergenic ## {SimpF: WRM0624dH02 1 fosmid,WRM0612aE11 1 fosmid,WRM0638dG06 1 fosmid} ## {MIR: cel-mir-795}
cremanei	chromosome:chrUn:129581540:129581668:-1	intergenic
cbriggsae	chromosome:chrI:3896350:3896478:1	Same_strand\|Intronic_coding\|NM_026450 ## Opposite_strand\|Intronic_coding\|NM_001024290
cjaponica	chromosome:chrUn:141216652:141216764:1	intergenic
ppacificus	chromosome:chrUn:27273809:27273937:-1	intergenic

cel-mir-242

Cloning frequencies
absolute	CE1
cel-mir-242 5arm	13
normalized	CE1
cel-mir-242 5arm	0.009

block5338 (miRBase cel-mir-242) [miRNAknown_cloningOK_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-242	0.005	no	no	0.52/0.55	20/22/1.00	0.0	0.0	12	0	1	0	15	6	5arm	1	nd	0.25	3	13	1	na	na

		reads	miRBase family seed
seed	-----------------------------------UGCGUAG--------------------------------------------------------------------------------------------------------------	13	miR-242
		len	cloning frequencies
			CE1
	----------------------------------TTGCGTAGGCCTTTGCTTCG--------------------------------------------------------------------------------------------------	20	12
	----------------------------------TTGCGTAGGCCTTTGCTTCGAG------------------------------------------------------------------------------------------------	22	1
cel-miR-242	----------------------------------TTGCGTAGGCCTTTGCTTCGA-------------------------------------------------------------------------------------------------	21	-
celegans	-------------------TGGCTCGCGAGAGTATTGCGTAGGCCTTTGCTTCGAGAGAGAAGCTTCAGTT---------CGCAGCAATATCCTCCGCA---------------AAACTTTCCCCGGCTATGCAAAAAA-------------
cremanei	TATTCGGTATCGAGTACCAACCACGTTAAGAATATTGCGTAGGCCTTTGCTTCGAAAGAAACACTT-TACTGTT------CGCAGCAATCTCCTCCGCA---------------ATATTTTTTGATGAATTTGGTTAAAATTGAGGTGAGTG
cbrenneri	-----------------TCAAACTAGAAAAAATATTGCGTAGGCCTTTGCTTCGAAAGCCACTTGTCCCACATT------CGTAGCAATATCCTACGCA---------------ATATTTTTAC----------------------------
cjaponica	----------------------------------TTGCGTAGGCCTTTGCTTCGAAAGAAATTCTCAAAATGTT------CGCAGCAATTTCCTCCGCA---------------A-------------------------------------
ppacificus	-GAAAAAGGTTAGTCAGCTGGGACGGTCCGTGGTTTGCGTAGGCCTTCGATTGGCGATATTTCTGCACATGAATGCATCGCGCATCGACGATCTGCGCATGCCATGAACGTTCCATACCTTTTTT---------------------------
	************* * ** * * ** * * * ** *
celegans	(((((.(.((((((.(((((.(((...(((((.((((.(((....)))..)) )).)))))...))).)))) ).)))))).).))))).........	1.000 -33.40
cremanei	((((((...((((..(((((...((((((((((((((((.(((...(((((.((((((........ ..)).)) )).)))))...))).)))) )))))))).))))...))))).....))))..))))))	0.955 -37.80
cbrenneri	..........((((((((((((((((...(((((.((((................)) )).)))))...)))))))) ))))))))..	0.967 -29.69
cjaponica	.((((.(((...(((((.((((....(((.....))).)) )).)))))...))).)))) .	0.994 -17.90
ppacificus	(((((((((........(((((((...((((((.((((((((...((((.(((((((..(((.......)))...))))).))))))...)))))))).))))))..))))))).)))))))))	0.805 -49.90

celegans	chromosome:IV:4274240:4274335:1	intergenic ## {SimpF: WRM063cA10 1 fosmid,WRM0612bD07 1 fosmid} ## {MIR: cel-mir-242}
cremanei	chromosome:chrUn:129720662:129720791:-1	intergenic
cbrenneri	chromosome:chrUn:53580716:53580801:1	intergenic
cjaponica	chromosome:chrUn:34617459:34617594:-1	intergenic
ppacificus	chromosome:chrUn:148942988:148943111:-1	Same_strand\|Intronic_coding\|NM_001103783 ## Opposite_strand\|Intronic_coding\|NM_133295

cel-mir-357

Cloning frequencies
absolute	CE1
cel-mir-357 3arm	16
normalized	CE1
cel-mir-357 3arm	0.011

block6587 (miRBase cel-mir-357) [miRNAknown_cloningOK_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-357	0.001	no	no	0.48/0.55	19/23/0.94	0.4	0.0	14	0	1	0	22	3	3arm	1	nd	0.22	2	16	1	na	na

Clusters
Located in cluster 5: cel-mir-357, cel-mir-358

		reads	miRBase family seed
seed	---------------------------------------------------------------------------AAAUGCC-------------------------------------	9	miR-357
seed	----------------------------------------------------------------------------AAUGCCA------------------------------------	6	novel
seed	------------------------------------------------------------------------------UGCCAGU----------------------------------	1	novel
		len	cloning frequencies
			CE1
cel-miR-357	--------------------------------------------------------------------------TAAATGCCAGTCGTTGCAGGAGT----------------------	23	9
	---------------------------------------------------------------------------AAATGCCAGTCGTTGCAGGAGT----------------------	22	5
	---------------------------------------------------------------------------AAATGCCAGTCGTTGCAGG-------------------------	19	1
	-----------------------------------------------------------------------------ATGCCAGTCGTTGCAGGAGT----------------------	20	1
celegans	----ACGCTGTACTACTCACCAGCGGATCCCTACAA-CGCTGCGCATATGCATGAAC-----ACAATGAAAATGTAAATGCCAGTCGTTGCAGGAGTTCGCATACAGTAGTAAAATGCG
cbriggsae	AGAGA---------------CAGCGAATCCCGGCAATCACCGTGCATTTTCAT---CTACCAGAGGCACTAATGAAAATGCCAGTCATTGACGGAATTCGTTGAATCT-----------
cjaponica	GAAAACGAGAAATT------TGGCGAATTGTTGTAACTTTTGTGCATCTGCTTGGAAAATTTTAAGTGA----GCAAATGCCAATTGTTGCAAAAATTCGCTGAA--------------
cbrenneri	----------------------GCGAATCCCTGTAA-TACTGTGCATATACATGTCATACA------ACTAATGTAAATGCCAGTCGTTGCAGGAATTCGCTAAAAGTCAGCT------
ppacificus	--------------------------AGCATTGTAGATATGAGGTATCCTTGCAACATTTC------GATAACAAAAATGCCTATATTTTCAGGACT----------------------
cremanei	-TCAACGATGTGCTGCCTAACAGCGGATTCCAGTAA-CTCTGAGCATATACATGAAGTTTCAA----AACAATGTAAATGCCAGTCGTTGCTGGAATTCGATAAGCACTCGTGA-----
	* * * ***** * ** * *
	----- -------------------------------- -------------------- --------------------------------------------------------------	F25G6.2 F25G6.2 F25G6.2
celegans	.(((..(((((((.....(((((..(((.((( (((((.((((.(((((.... .........))))).))))))).))))).)))..)))))....)))))))....)))	1.000 -42.62
cbriggsae	(((.. ((((((((.(((.((((.((...(((((((((( ...((...)).....))))))))))..)).)))).))).))))))))..)))	1.000 -30.10
cjaponica	............(( ..(((((((.(((((((..(((.((((.(((((..............)) ))).)))))))..))))))).)))))))..))	0.994 -33.24
cbrenneri	((((((.((((((( (((((.((((.(((((........ ....))))).)))))))).)))))))).))))))............	0.919 -33.00
ppacificus	((..(((.((((((.((((((..(((......... .....)))..)))))))))))).)))..))	0.994 -10.54
cremanei	...((((.(((((.........((((((((((((( (.(((.((((.(((((...(((.... ))).))))).)))))))..))))))))))))))...)))))))))..	0.948 -44.20

celegans	chromosome:V:8580520:8580628:-1	Opposite_strand\|Intronic_coding\|F25G6.2\|F25G6.2 ## F25G6.2\|protein_coding\|F25G6.2\|F25G6.2 [Source:RefSeq_peptide;Acc:NP_505210] ## {SimpF: CEOP5204 -1 Operon,WRM0626aA01 -1 fosmid,WRM0619bH10 -1 fosmid} ## {MIR: cel-mir-357}
cbriggsae	chromosome:chrV:1213917:1214006:-1	Opposite_strand\|Intronic_coding\|NM_001106714 ## Same_strand\|Intronic_coding\|NM_001028857 ## {MIR: cbr-mir-357-1}
cjaponica	chromosome:chrUn:73154317:73154411:1	Opposite_strand\|Intronic_coding\|NM_165217
cbrenneri	chromosome:chrUn:96165556:96165639:1	Opposite_strand\|Intronic_coding\|NM_125384
ppacificus	chromosome:chrUn:14492983:14493131:-1	Same_strand\|Intronic_coding\|NM_001045869 ## Same_strand\|Boundary_coding\|NM_063816
cremanei	chromosome:chrUn:25671347:25671454:-1	Opposite_strand\|Intronic_coding\|NM_199607

cel-mir-61

Cloning frequencies
absolute	CE1
cel-mir-61 3arm	16
normalized	CE1
cel-mir-61 3arm	0.011

block6710 (miRBase cel-mir-61) [miRNAknown_cloningOK_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-61	0.001	no	no	0.41/0.44	18/22/0.76	0.0	0.9	14	0	1	0	16	5	3arm	1	nd	0.14	2	16	1	na	na

Clusters
Located in cluster 6: cel-mir-250, cel-mir-61

Families
Member of family miR-44/45/61 (seed GACUAGA): cel-mir-61, cel-mir-44, cel-mir-45

		reads	miRBase family seed
seed	---------------------------------------------------------------------------GACUAGA-----------------------------------------	16	miR-44/45/61
		len	cloning frequencies
			CE1
cel-miR-61	--------------------------------------------------------------------------TGACTAGAACCGTTACTCATC----------------------------	21	10
	--------------------------------------------------------------------------TGACTAGAACCGTTACTC-------------------------------	18	4
	--------------------------------------------------------------------------TGACTAGAACCGTTACTCATCT---------------------------	22	2
celegans	--------------TATCGCTGAACCTCGAGATGGGT-TACGGGGCTTAGTCCTTCCTCCGT-----ATGGCAATGACTAGAACCGTTACTCATCTCGAGGTTTCGG-----------TGAT-
cbriggsae	----------------TCG--GTGTCTCGAGCCGAGT-TAAGGCTAATAGTCCTTCCGGTGT-----ATGGTAATGACTAGAACCTTGACTCTGCTCGAGTTACTGA-----GCTCTTTGA--
cjaponica	--------GTCAAATTTACGCGATTCGCGAGTTGGGCGCACGGCGTTTAGTCCTTTCAACACGTGAAATGGTAATGACTAGAACCGTCGCTCATCCCGCGTCTATGC-----GGCTATTTGTC
cbrenneri	CCAGTCTCGTAAAACAT-GTTGAACTTCGAGTTGGGT-CACGGTGCTTAGTCCTTCCAACAG-----TCGGTAATGACTAGAACCGTGACTCAGCTCGAGGAAGCGACAGTTTTTCACTGG--
cremanei	--------GCGTAATATCG--GTCTTCCGAGTTGGGT-CACGGCGCTTAGTCCTTCCGACAT-----ATGGCAATGACTAGAACCTTGGCTCAGCTCGGGACTCCGA-----------TGAGC
	* * **** * * * ****** * *********** * *** * ** * * *
celegans	.(((((((((((((((((((((( .((((..((.((((.((((..... ..)).)).))))))..)))).))))))))))))))).))) ))))	1.000 -50.50
cbriggsae	((( (((.(((((((.(((( (((((....(((((.(((((.... .))).)).)))))...))))))))).))))))).)))))) .........	0.998 -42.10
cjaponica	..(((((...((((...((((...((((((.((((..(((((((((((((.....))))).)).....)))))).))))))))))...))))....))) )...)))))..	0.994 -36.70
cbrenneri	(((((.....(((((.( ((((..((((((((((((( ((((((..((((((.((((..... ..)).)).)))))).)))))))))))))))))))...))))))))))..)))))	1.000 -55.70
cremanei	......((((( (..((((((((((((( ((.((..((.((((.(((((.... .))).)).))))))..)).)))))))))))))))..)))) ))...	1.000 -43.80

celegans	chromosome:V:11770038:11770128:-1	intergenic ## {SimpF: WRM0616dF12 -1 fosmid,WRM0630cB01 -1 fosmid,WRM064dC03 -1 fosmid,WRM0611bB04 -1 fosmid,WRM0628cB12 -1 fosmid} ## {MIR: cel-mir-61}
cbriggsae	chromosome:chrV:6755266:6755357:-1	Opposite_strand\|Intronic_coding\|NM_007734 ## Same_strand\|Intronic_coding\|NM_000945 ## {MIR: cbr-mir-61}
cjaponica	chromosome:chrUn:133811034:133811143:-1	intergenic
cbrenneri	chromosome:chrUn:84265051:84265164:1	intergenic
cremanei	chromosome:chrUn:126693023:126693118:-1	Opposite_strand\|Intronic_coding\|NM_073652 ## Same_strand\|Intronic_coding\|NM_067460

cel-mir-788

Cloning frequencies
absolute	CE1
cel-mir-788 5arm	10
normalized	CE1
cel-mir-788 5arm	0.007

block7767 (miRBase cel-mir-788) [miRNAknown_cloningOK_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-788	0.001	no	no	0.45/0.48	21/24/1.00	0.3	0.4	9	0	1	0	9	1	5arm	1	nd	0.12	2	10	1	na	na

		reads	miRBase family seed
seed	-------------------------CCGCU---UC--------------------------------------------------------------------------------------	6	miR-788
seed	--------------------------CGCU---UCU-------------------------------------------------------------------------------------	4	novel
		len	cloning frequencies
			CE1
cel-miR-788	------------------------TCCGCT---TCTAACT--TCCATTTGCAG--------------------------------------------------------------------	24	4
	-------------------------CCGCT---TCTAACT--TCCATTTGCAG--------------------------------------------------------------------	23	3
	------------------------TCCGCT---TCTAACT--TCCATTTGC----------------------------------------------------------------------	22	2
	-------------------------CCGCT---TCTAACT--TCCATTTGC----------------------------------------------------------------------	21	1
celegans	---------------GCTCACTTTTCCGCT---TCTAACT--TCCATTTGCAGAGTTCA----AGTAATCTG-GAAAT-GGATTAGAATCGTGGAAAAGTTAGT-----------------
cbriggsae	TTCGATTAGCCTGAAACTAACTTTTCCGCT---TCTCAATGCTCCATTTGCAAAATCAAATTGATTTTCTTG-CAAATGGGATGAGAACCG--GAAACGTTTGATTGACGGAAACTTTGAA
cjaponica	--------TCCACAACCCTACTTTTCCGCT---TCTAGCT--TCCATTTGCAAAGCAGT----AAGTCTCTG-AAAAT-GGACTAGAAACGTGAAAAAGTTGGTGGA--------------
cbrenneri	------------------CACTTTACCGCT---TCTATAC--TCCATGCGCAGTGTTTG----AAAACTCTG-AGCAT-GGAATAGAGGAG--GAAAAGTG--------------------
ppacificus	------------------GACCGCTTCGATTGATCTATCCG-TCTTTCTGATAGGCTAA----AGATCATTGCGAAAT---------------GAGAGGTTTGTTCGT-------------
cremanei	-------GGCCTGAAACTTACGTCTCCGCT---TCTAACT--TCCATTTGCAGAGTTCA--TCAATTCTCTG-GAAAT-GGATTAGAACCGT-GAAATGTTAGTATGATGGTC--------
	* * * * * * * **
celegans	(((.((((((((((( (((((.. (((((((.((((..... .....)))) .)))) )))))))))..)))))))))).)))	1.000 -32.40
cbriggsae	.((((....((.......(((.((((((.( (((((....(((((((((((((((.....)))))...)) )))))))).)))))).)) )))).)))........)).....)))).	0.943 -34.36
cjaponica	(((((......((((((.(((( (((((.. (((((((......(((. ......))) .)))) )))))))))..))).))))))..)))))	0.999 -25.60
cbrenneri	((((((.((.(( (((((.. (((((((.(((.(((.. ..))).))) .)))) )))))))))).) ).))))))	1.000 -33.10
ppacificus	((((.(((((..((((((....( (((.......))))... ))))))...)))... .)).)))).......	0.973 -15.30
cremanei	((((....(((.((((.((((.( (((((.. (((((((.(((((.... ......))))) .)))) ))))))))).)). )).)))).))).....))))	1.000 -32.60

celegans	chromosome:X:8485234:8485311:-1	intergenic ## {SimpF: WRM0618bE11 -1 fosmid,WRM0634aF10 -1 fosmid,WRM0639bF01 -1 fosmid,WRM0611cG03 -1 fosmid,WRM0631aC01 -1 fosmid} ## {MIR: cel-mir-788}
cbriggsae	chromosome:chrX:16579511:16579625:-1	Opposite_strand\|Intronic_coding\|NM_004119 ## Same_strand\|Intronic_coding\|NM_064155 ## {MIR: cbr-mir-788}
cjaponica	chromosome:chrUn:39355856:39355943:1	intergenic
cbrenneri	chromosome:chrUn:95872853:95872922:1	intergenic
ppacificus	chromosome:chrUn:164896637:164896706:-1	intergenic
cremanei	chromosome:chrUn:100052245:100052340:-1	Same_strand\|Intronic_coding\|NM_170227

cel-mir-799

Cloning frequencies
absolute	CE1
cel-mir-799 3arm	6
normalized	CE1
cel-mir-799 3arm	0.004

block7768 (miRBase cel-mir-799) [miRNAknown_cloningOK_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-799	0.001	no	no	0.45/0.45	22/22/1.00	0.0	0.0	6	0	1	0	14	6	3arm	1	nd	0.18	2	6	1	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------GAACCCU----------------------------	6	novel
		len	cloning frequencies
			CE1
cel-miR-799	---------------------------------------------------------TGAACCCTGATAAAGCTAGTGG--------------	22	6
celegans	gtttttcaatttttttcaccggttttaaaaagtggtttcacattcaataaagacatgTGAACCCTGATAAAGCTAGTGGaaatatcggaaaac
	*********************************************************************************************
	-------------------------------------------------------------------------------------------------------	F18E9.1 F18E9.1 F18E9.1
celegans	(((((((.((..(((((((..((((((...((.((((.(((((((......)).)))))))))))..))))))..))))))).)).)))))))	1.000 -28.70

celegans

chromosome:X:8600584:8600676:-1

Opposite_strand|Intronic_coding|F18E9.1|F18E9.1 ## F18E9.1|protein_coding|F18E9.1|F18E9.1 [Source:RefSeq_peptide;Acc:NP_509458] ## {SimpF: WRM0612dA07 -1 fosmid,WRM0620aH04 -1 fosmid,WRM0610aE12 -1 fosmid,F18E9.1 -1 Expression_profile,WRM069dB12 -1 fosmid,WRM0611dD01 -1 fosmid} ## {MIR: cel-mir-799}

cel-mir-797

Cloning frequencies
absolute	CE1
cel-mir-797 5arm	24
normalized	CE1
cel-mir-797 5arm	0.017

block8270 (miRBase cel-mir-797) [miRNAknown_cloningOK_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-797	0.001	no	no	0.35/0.38	19/25/0.84	0.0	0.8	18	0	1	0	14	4	5arm	1	nd	0.21	3	24	1	na	na

Families
Member of family miR-43 (seed AUCACAG): cel-mir-2, cel-mir-797, cel-mir-43

		reads	miRBase family seed
seed	--------------------AUCACAG-----------------------------------------------------------------------------------------------	24	miR-43
		len	cloning frequencies
			CE1
	-------------------TATCACAGCAATCACAATGA--------GAAG-----------------------------------------------------------------------	24	13
	-------------------TATCACAGCAATCACAATGA--------G--------------------------------------------------------------------------	21	5
	-------------------TATCACAGCAATCACAATG------------------------------------------------------------------------------------	19	3
	-------------------TATCACAGCAATCACAATGA-----------------------------------------------------------------------------------	20	2
	-------------------TATCACAGCAATCACAATGA--------GA-------------------------------------------------------------------------	22	1
cel-miR-797	-------------------TATCACAGCAATCACAATGA--------GAAGA----------------------------------------------------------------------	25	-
celegans	-----CGTCCAATGGACGATATCACAGCAATCACAATGA--------GAAGAATACATCTAGATACTCTTTTCATTGGTTTCTGTGAAATCGTATTTGAATG--------------------
cremanei	TCTGAAAGTTTGCTCATTTTATCACAGAAATCACAGTT-GCCTTTTCGAACCCGATATTCCTCCCGAATTGGCACTCGTTTTTTCTGGGATGGAAAGTGAGCAAAAAATCCAACTTTTCGGG
cbriggsae	-------------------TATCACAG-ATCGAGAGTGAGTACAATAGGAAGGCTACTGTAGATT---------TTCGCATGTTTGGAGTA-------------------------------
cbrenneri	-------------------AATCACAG-AAAAATTCTGAGAAAATCCGGAAAATTCACGGAAA-------AATCTCGGAAAATTCTGGAAA-------------------------------
ppacificus	------------CGTACCTTATCACAG-AAC-----TCAGTGCACTTGAGCTGCTCATTCAGCTTCGAGTAGCACAGGGCAATGTTGAGGAAGGCCGCG-----------------------
	******* * * * * *
celegans	(((.(((...(((((.((((((.((...(((((( (((((.((........)).)))))))))))..)))))))).)))))..))).)))	1.000 -28.40
cremanei	.((((((((((((((((((((((.((((((..((((.( (((..((((................))))..)))))).))..)))))).))))))..))))))))).........))))))).	0.985 -37.89
cbriggsae	..((.((( (((((((((...((((.(((.....))).)))).))) ))))...)))))))...	0.999 -11.90
cbrenneri	..((.((( ((...((((((((...((((((....)).)))).. ..))))))))..)))))))..	0.999 -20.60
ppacificus	(((.((((.(((((. ..( ((.((((((((((((((......))))).))))).)))).)))...))).))..))))..)))	1.000 -29.10

celegans	chromosome:X:4757079:4757167:1	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-797}
cremanei	chromosome:chrUn:102111838:102111958:-1	Opposite_strand\|Intronic_coding\|NM_001122918
cbriggsae	chromosome:chrV:10617288:10617416:1	Same_strand\|Intronic_coding\|NM_075092 ## Opposite_strand\|Intronic_coding\|NM_001011629 ## Opposite_strand\|Exonic_coding\|NM_182420
cbrenneri	chromosome:chrUn:160848361:160848489:-1	Same_strand\|Intronic_coding\|NM_063434 ## {SimpF: trf,trf,trf,trf,trf}
ppacificus	chromosome:chrUn:168847191:168847271:1	Same_strand\|Intronic_coding\|NM_011564 ## Opposite_strand\|Intronic_coding\|NM_119701