miR-Intess™

confident miRBase miRNAs

miRNAknown_cloningHIGH_multiarm_DicerOK_randfoldOK (30 loci)

cel-mir-80

Cloning frequencies

absolute	CE1
cel-mir-80 5arm	4
cel-mir-80 3arm	24868
normalized	CE1
cel-mir-80 5arm	0.003
cel-mir-80 3arm	17.372

sblock28 (miRBase cel-mir-80) [miRNAknown_cloningHIGH_multiarm_DicerOK_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-80

0.005

no

no

0.28/0.50

18/25/0.99

nd 0.0 0.0

nd 0.0 0.0

0 4 23510

0 0 0

0 1 1

0 0 0

18 40 16

5 -15 11

5arm 5arm_loop_3arm 3arm

1 1 1

nd nd nd

0.09 0.50 0.18

1 5 2

24872

1

2

1

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----------------------------------	24430	miR-80/81/82
seed	-------------------------------------------------------------------AGAUCAU---------------------------------	251	novel
seed	----------------------------------------------------------------------UCAUUAG------------------------------	143	novel
seed	-----------------------------------------------------------------UGAGAUC-----------------------------------	26	novel
seed	-----------------------------------------------------------------------CAUUAGU-----------------------------	11	novel
seed	---------------------------------------------------------------------AUCAUUA-------------------------------	7	novel
seed	---------------------------------------------AUCCGCA-------------------------------------------------------	4	novel
seed	----------------------GCUUUCG------------------------------------------------------------------------------	0	novel
		len	cloning frequencies
			CE1
	-----------------------------------------------------------------TGAGATCATTAGTTGAAAGCCG--------------------	22	23510
	-----------------------------------------------------------------TGAGATCATTAGTTGAAAGCC---------------------	21	444
	------------------------------------------------------------------GAGATCATTAGTTGAAAGCCGA-------------------	22	197
	-----------------------------------------------------------------TGAGATCATTAGTTGAAAGCCGAA------------------	24	173
	---------------------------------------------------------------------ATCATTAGTTGAAAGCCGAA------------------	20	140
cel-miR-80	-----------------------------------------------------------------TGAGATCATTAGTTGAAAGCCGA-------------------	23	87
	-----------------------------------------------------------------TGAGATCATTAGTTGAAAGC----------------------	20	77
	-----------------------------------------------------------------TGAGATCATTAGTTGAAAG-----------------------	19	57
	------------------------------------------------------------------GAGATCATTAGTTGAAAGCCG--------------------	21	52
	-----------------------------------------------------------------TGAGATCATTAGTTGAAA------------------------	18	52
	-----------------------------------------------------------------TGAGATCATTAGTTGAAAGCCGAAT-----------------	25	30
	----------------------------------------------------------------TTGAGATCATTAGTTGAAAGCCG--------------------	23	23
	----------------------------------------------------------------------TCATTAGTTGAAAGCCGAA------------------	19	11
	--------------------------------------------------------------------GATCATTAGTTGAAAGCCG--------------------	19	6
	--------------------------------------------AATCCGCA-AGCCCATGTTGT------------------------------------------	20	4
	----------------------------------------------------------------TTGAGATCATTAGTTGAA-------------------------	18	3
	---------------------------------------------------------------------ATCATTAGTTGAAAGCCGA-------------------	19	2
	------------------------------------------------------------------GAGATCATTAGTTGAAAGCC---------------------	20	1
	------------------------------------------------------------------GAGATCATTAGTTGAAAGCCGAA------------------	23	1
	--------------------------------------------------------------------GATCATTAGTTGAAAGCCGAA------------------	21	1
	---------------------------------------------------------------------ATCATTAGTTGAAAGCCG--------------------	18	1
cel-miR-227	------------------A---GCTTTCGA-CATGATTCTGAAC---------------------------------------------------------------	22	-
celegans	ATGGACACTCGTTCGCTCA---GCTTTCGA-CATGATTCTGAACAATCCGCA-AGCCCATGTTGTTGAGATCATTAGTTGAAAGCCGAATGA-TCAGAGATATC---
cbriggsae	TTGGACACTCTTTCGCTCA---GCTTTCGA-CATGATTCTAAACAATACGCTGTCGCAATGTTGTTGAGATCATTAGTTGAAAGCCGAACGA-TTCGAGATATCCAA
cjaponica	--GGTTTCTCTGTCGCTCA---GCTTTCGA-CATGATTCTGAACAATTCCACACATTTATGTTGTTGAGATCATTAGTTGAAAGCCGAATGA-TTCGAGCGAACC--
cbrenneri	--GGACACTCTTTCGCTCA---GCTTTCGA-CATGGTTCTGAACAATACGCATTGCATATGTTGTTGAGATCATTAGTTGAAAGCCGAATGA-TTTGAGATATCC--
ppacificus	---GTCTCTTTATTACTCGTGCTCTTTCTCTCTTCACTCTGATCGGTGA-----------------GAGATCACTAG---------AAATAA-----AGAGAT----
cremanei	--GGACACTCTTTCGCTCA---GCTTTCGA-CATGATTCTAAACAATACGTCGAGACAATGTTGTTGAGATCATTAGTTGAAAGCCGAACGATTTTGAGATATCC--
	*   **   *  ***     *****   * *   *** * *  *                   ******* ***          **  *     **  *
celegans	.......(((..(((.((.   (((((((( ((((((.((.((((((.(... .).....)))))).)))))))..))))))))).)).))) ...))).....	1.000 -30.50
cbriggsae	.((((..(((..(((.((.   (((((((( (((((.(((.(((((((.((....))..))))))).)))))))..))))))))).)).))) ...)))...)))).	1.000 -34.80
cjaponica	((((((((.((((.((.   (((((((( (((((.(((.((((((.............)))))).)))))))..))))))))).)).))) )..))).)))))	0.999 -33.52
cbrenneri	(((..(((..(((.((.   (((((((( (((((.(((.(((((((.((...))...))))))).)))))))..))))))))).)).))) ...)))...)))	1.000 -31.00
ppacificus	(((((((((((.((.(((.((((((.((..((.....))..)).))                 )))).))).))         .)))))     ))))))	1.000 -26.20
cremanei	(((..(((..(((.((.   (((((((( (((((.(((.(((((((.((....))..))))))).)))))))..))))))))).)).)))....)))...)))	1.000 -30.80

celegans	chromosome:III:8865177:8865274:-1	intergenic ## {SimpF: WRM0637aD12 -1 fosmid,WRM0622dD10 -1 fosmid} ## {MIR: cel-mir-80}
cbriggsae	chromosome:chrIII:13406581:13406682:-1	Opposite_strand|Intronic_coding|NM_001026518 ## Same_strand|Intronic_coding|NM_070558 ## {MIR: cbr-mir-80}
cjaponica	chromosome:chrUn:4628117:4628214:1	Same_strand|Intronic_coding|NM_080787 ## Opposite_strand|Intronic_coding|NM_078517
cbrenneri	chromosome:chrUn:17761161:17761258:-1	Same_strand|Intronic_coding|NM_209159
ppacificus	chromosome:chrUn:156165257:156165325:1	intergenic
cremanei	chromosome:chrUn:98380888:98380986:-1	intergenic

cel-mir-235

Cloning frequencies

absolute	CE1
cel-mir-235 5arm	1
cel-mir-235 3arm	82
normalized	CE1
cel-mir-235 5arm	0.001
cel-mir-235 3arm	0.057

sblock3 (miRBase cel-mir-235) [miRNAknown_cloningHIGH_multiarm_DicerOK_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-235

0.003

no

no

0.43/0.62

21/23/1.00

0.0 0.0

0.0 0.0

1 80

0 0

1 1

0 0

18 16

4 10

5arm 3arm

1 1

nd nd

0.30 0.24

2 2

83

1

2

1

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------------AUUGCAC-----------------------------------------------------	80	miR-235
seed	--------------------------------------------------------------------------------------UAUUGCA------------------------------------------------------	1	novel
seed	----------------------------------------------------------------------------------------UUGCACU----------------------------------------------------	1	novel
seed	----------------------------------------GGCCUUG----------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	--------------------------------------------------------------------------------------TATTGCACTCT-CCCCGGCCTG---------------------------------------	21	80
	---------------------------------------------------------------------------------------ATTGCACTCT-CCCCGGCCTGA--------------------------------------	21	1
	-------------------------------------------------------------------------------------ATATTGCACTCT-CCCCGGCCTG---------------------------------------	22	1
	---------------------------------------AGGCCTTGGCTGATTGCA-AAATT------------------------------------------------------------------------------------	23	1
cel-miR-235	--------------------------------------------------------------------------------------TATTGCACTCT-CCCCGGCCTGA--------------------------------------	22	-
celegans	---------------------TCCGAAGATATCAGGATCAGGCCTTGGCTGATTGCA-AAATTGT-TCACCGT---GAAAATTAAATATTGCACTCT-CCCCGGCCTGATCT-----GAGAGTAAGGCG------------------
cbriggsae	TACTATTCCCTATTCTAAAAATCTGAAATCTT--GGATCAGGCTCTGGTCATGTGCATATATTGC-GCTATAT------ATGCTAATATTGCACTTGACCATGGCCTCGTCT----AGAAAGTAAGACAGTTTCAGAAAGGTAAGTA
cjaponica	-----ACGCATAAAAAAGAAAGAAAGAAAGACAAGGATCAGGTCTTGGCCGGTTGCATATATTGCGTCGACA----GAAATGCTAATATTGCACTCG-CCCCGGCCTGATCT-------------GGCACTTTTTTTGCGT------
cbrenneri	---------GAAATCTGAAAATTTCGAAAAAAAAAGATCAGGTCCTGGCTGACTGCATATATTGC-TCAACGTTAAAGAATGCTAATATTGCACTCG-CCCCGGCCTGATCGATAAAGAAATTAGTAAGATTTT-------------
cremanei	--------------------------------------CAGGCCTTGGCCGAATGCATATATTGC-TCAGTT----GAATTGCTAATATTGCACTCG-CCCCGGCCTG---------------------------------------
	****   ***     **** * ****   *                ***********   **  *****
celegans	.((.......((((.((((((((..((..((.(((( (.(((.( ((.....   ))).....))).))))).)). .)).))))))))))     ))......))..	1.000 -31.52
cbriggsae	((((....(((.((((.(((.(((......((  ((((.(((((.((((((.(((((.((((((. ((.....      ..))))))))))))).)))))).))))).))))    ))......)))...))).)))))))..))))	0.962 -44.00
cjaponica	(((((.............(((((((....((((((((((..(((.((.((((.(((((((((.....    ...)))).))))))))))).) ))..))))))))))             ....))))))))))))	1.000 -40.61
cbrenneri	(((((((...((((((..........(((((((((..(((.((.((((.((((((( ...............)).))))))))).))) ))..)))))))))......))))))....)))))))	0.988 -36.35
cremanei	((((((..((.(((.((((.((((((( ......    .....)).))))))))).))) ))..))))))	0.999 -25.00

celegans	chromosome:I:6162293:6162389:-1	intergenic ## {SimpF: WRM0611dF11 -1 fosmid,WRM065bH05 -1 fosmid,WRM0626aC03 -1 fosmid,WRM0621bH03 -1 fosmid} ## {MIR: cel-mir-235}
cbriggsae	chromosome:chrI:8823476:8823609:-1	Same_strand|Intronic_coding|NM_001032899 ## Opposite_strand|Intronic_coding|NM_199320
cjaponica	chromosome:chrUn:154386872:154386989:-1	Same_strand|Intronic_coding|NM_001066065
cbrenneri	chromosome:chrUn:84663076:84663198:1	intergenic
cremanei	chromosome:chrUn:122165177:122165313:1	intergenic

cel-mir-46

Cloning frequencies

absolute	CE1
cel-mir-46 5arm	64
cel-mir-46 3arm	512
normalized	CE1
cel-mir-46 5arm	0.045
cel-mir-46 3arm	0.358

sblock33 (miRBase cel-mir-46) [miRNAknown_cloningHIGH_multiarm_DicerOK_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-46

0.001

no

no

0.45/0.55

18/23/0.99

0.0 0.0

0.0 0.0

59 488

0 0

1 1

0 0

14 16

7 12

5arm 3arm

1 1

nd nd

0.18 0.14

2 3

576

1

2

1

Families

Member of family miR-46/47 (seed GUCAUGG): cel-mir-46, cel-mir-47

		reads	miRBase family seed
seed	----------------------------------------------------------------------------------GUCAUGG-------------------------------------------------	499	miR-46/47
seed	-----------------------------------AGAGAGC------------------------------------------------------------------------------------------------	62	novel
seed	-----------------------------------------------------------------------------------UCAUGGA------------------------------------------------	9	novel
seed	--------------------------------------------------------------------------------------UGGAGUC---------------------------------------------	4	novel
seed	---------------------------------------AGCCGUC--------------------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			CE1
	---------------------------------------------------------------------------------TGTCATGGAGTCGCTCTCTTC------------------------------------	21	488
	----------------------------------AAGAGAGCCGTCTATTGACAGT----------------------------------------------------------------------------------	22	59
	----------------------------------------------------------------------------------GTCATGGAGTCGCTCTCTTCA-----------------------------------	21	7
cel-miR-46	---------------------------------------------------------------------------------TGTCATGGAGTCGCTCTCTTCA-----------------------------------	22	5
	-------------------------------------------------------------------------------------ATGGAGTCGCTCTCTTCA-----------------------------------	18	4
	---------------------------------------------------------------------------------TGTCATGGAGTCGCTCTCTTCAG----------------------------------	23	4
	--------------------------------------GAGCCGTCTATTGACAGTT---------------------------------------------------------------------------------	19	2
	----------------------------------AAGAGAGCCGTCTATTGACAG-----------------------------------------------------------------------------------	21	2
	----------------------------------------------------------------------------------GTCATGGAGTCGCTCTCTTC------------------------------------	20	1
	----------------------------------AAGAGAGCCGTCTATTGAC-------------------------------------------------------------------------------------	19	1
	----------------------------------------------------------------------------------GTCATGGAGTCGCTCTCTTCAG----------------------------------	22	1
	---------------------------------------------------------------------------------TGTCATGGAGTCGCTCTCT--------------------------------------	19	1
	---------------------------------------------------------------------------------TGTCATGGAGTCGCTCTCTT-------------------------------------	20	1
celegans	--------------------CTGAGGTGAAGCTGAAGAGAGCCGTCTATTGACAGTTCAAGACCACGAGTCGTTGTG-TGCTGTCATGGAGTCGCTCTCTTCAGATGATCCGGTCAAT--------------------
cbriggsae	---GGTAAGTTGA--AGAGATACAAGTGAAGCTGAAGAGAGCCGTCTATTGACAGTTC--GCTTGTT-----TCATG-TGCTGTCATGGAGTCGCTCTCTTCAGATGATCTGAATCTAAATGTTATATTTTCC-----
cjaponica	-GCGGTAAGTTGGCCAAAAGACCGGGTGAAGCTGAAGAGAGCCGTCCTTTGACAGTTC--GTCCACGTGGAATATCG-TGCTGTCATGGAGTCGCTCTCTTCAGATGACCACGGTCTTTCTTGGTTTTTTCTTTTTGT
cbrenneri	-------------------------------CTGAAGAGAGCCGTCTATTGACAGTTC--GTCTCTGTTCAGTCAGG-TACTGTCATGGAGTCGCTCTCTTCAGATGATCTCTTGC----------------------
ppacificus	AGACACCAGGACCCCCGGCACCACGCAGAGACCGAAGAGAGCCTTCTGTTGACAGTGC-GGGCCGTTGGTGCTAATGCTATTGTCATGGAGTCGCTCTCTTCAG--GCTTGTGGTCCTCAGGGTACGGTAGCT-----
cremanei	---------------------------------GAAGAGAGCCGTCTATTGACAGTTC--GTTTCTA--TACTTATG-TACTGTCATGGAGTCGCTCTCTTC------------------------------------
	********** **  ******** *  *           *   * *  *********************
celegans	....((.....(((((((((((..(((((.((((((.((((((.....))).))).. .)))))))))))...))))))))))).....)).......	1.000 -39.00
cbriggsae	((.(((((((  ..((((...((.....(((((((((((..((((.(((((((..  ((.....     ....) ))))))))))))...))))))))))).....))..)))).....))).)))).))	0.946 -35.50
cjaponica	((((.(((..((((((((((((((((....(((((((((((..(((..(((((((.(  ((((....)))....)) .))))))).)))...)))))))))))...))).))))))))..)))))....))).))))	0.999 -59.60
cbrenneri	(((((((((((..((((.(((((((..  ...((((......)))) .)))))))))))...)))))))))))............	0.995 -33.10
ppacificus	((..(((...((((..((.(((((...(((.(((((((((((((((...((((((((( .(((.......)))...)).))))))).))))..))))))))).)  )))))))))))...))))..)))..))	0.996 -52.40
cremanei	(((((((((..((((.(((((((.(  ((.....  .....))) .)))))))))))...)))))))))	1.000 -26.70

celegans	chromosome:III:13660395:13660491:1	intergenic ## {SimpF: WRM066cA03 1 fosmid,WRM0629dF02 1 fosmid,WRM0640dG12 1 fosmid,WRM0614aE06 1 fosmid} ## {MIR: cel-mir-46}
cbriggsae	chromosome:chrIII:7878482:7878601:1	Same_strand|Intronic_coding|NM_005249 ## {MIR: cbr-mir-46}
cjaponica	chromosome:chrUn:55670810:55670943:1	Same_strand|Intronic_coding|NM_137355
cbrenneri	chromosome:chrUn:26379439:26379520:-1	Same_strand|Intronic_coding|NM_001043931
ppacificus	chromosome:chrUn:163065258:163065387:1	intergenic
cremanei	chromosome:chrUn:22211359:22211495:-1	Same_strand|Intronic_coding|NM_001104800

cel-mir-232

Cloning frequencies

absolute	CE1
cel-mir-232 5arm	2
cel-mir-232 3arm	37
normalized	CE1
cel-mir-232 5arm	0.001
cel-mir-232 3arm	0.026

sblock38 (miRBase cel-mir-232) [miRNAknown_cloningHIGH_multiarm_DicerOK_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-232

0.001

no

no

0.39/0.41

20/23/1.00

0.0 0.0

1.5 0.0

2 36

0 0

1 1

0 0

18 16

8 7

5arm 3arm

1 1

nd nd

0.17 0.23

2 2

39

1

2

1

		reads	miRBase family seed
seed	----------------------------------------------------------------------------------------AAAUGCA------------------------------------------------	37	miR-232
seed	---------------------------------------------CUGCAGU-------------------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			CE1
	---------------------------------------------------------------------------------------TAAATGCATCTTAACTGCGGTG----------------------------------	22	36
	--------------------------------------------CCTGCAGTTTCGATGATTTTATC----------------------------------------------------------------------------	23	1
cel-miR-232	---------------------------------------------------------------------------------------TAAATGCATCTTAACTGCGGTGA---------------------------------	23	1
	--------------------------------------------CCTGCAGTTTCGATGATTTT-------------------------------------------------------------------------------	20	1
celegans	-----------AAGTTCAATTTT---------------TGGATCCCTGCAGTTTCGATGATTTTATCCTTAATT-CTGAAGATGTGATAAATGCATCTTAACTGCGGTGATCTAGATC--ATGAACA----------------
cbriggsae	-------------TTCAAGATTT---------------CGGATCTCCGTAGTTTTGACCATTTTATCCAAC----CTAATAATGTGATAAATGCATCTTAACTGCGGTGATCTGGATTTTGTGAA------------------
cjaponica	-----------TGGTAAGTTTCTGGGTCCTCACGAGCGTGGATCTCCGTAGTTTCGATCGTTTTATCCAGCGCCACAAACCGTGCGATAAATGCATCTTAACTGCGGTGATCTGCAATTCTGGGACACGCTTTTTTCA-----
cbrenneri	-------------GTCCTTTTTT---------------CGGATCCCCGTAGTTTCGATCATTTTATCCTGCCCAACTCAAAAAGTGATAAATGCATCTTAACTGCGGTGATCTGATTTCAATGGACACGTTTTC---------
cremanei	GAGGTAAGTTGAAGTCTGATTGT---------------CGGATCTCCGTAGTTTCGATCATTTTATCCTATCT--CCAACAAAGCGATAAATGCATCTTAACTGCGGTGATCTGAATTC-TTGGACACTTTTTTCTTTATTTC
	*     * *                ***** * * ***** **   ********       *  *    * ****************************         * *
celegans	..(((((...((               ((((((.((((((((..((((..(((((((.....( (....)).).))))))..))))..)))))))).))))))))..  .))))).	1.000 -35.60
cbriggsae	..(((((.((               ((((((.((((((((..((....((((((((..    .......)).))))))....))..)))))))).)))))))))))))....	1.000 -31.00
cjaponica	.((.((((......((((.((.((..(((((((.((((((((..(((((.((((((..((((........)))))))))))).)))..)))))))).)))))))..)).))))))..))))...)).	0.976 -41.30
cbrenneri	((((.....(               ((((((.((((((((..(((((.((((((((.............)).)))))))).)))..)))))))).))))))).......))))........	1.000 -35.42
cremanei	((((((((..(((((((((...(               ((((((.((((((((..(((((.((((((((....  .......)).)))))))).)))..)))))))).))))))).... ))))))....)))..))))))))	1.000 -37.80

celegans	chromosome:IV:10994139:10994236:-1	intergenic ## {SimpF: WRM0641dF09 -1 fosmid,WRM0637cH04 -1 fosmid} ## {MIR: cel-mir-232}
cbriggsae	chromosome:chrIV:5768761:5768853:1	Same_strand|Intronic_coding|NM_001106790 ## Opposite_strand|Intronic_coding|NM_001128722 ## {MIR: cbr-mir-232-1}
cjaponica	chromosome:chrUn:41745062:41745188:-1	Opposite_strand|Intronic_coding|NM_172827
cbrenneri	chromosome:chrUn:102760956:102761061:1	intergenic
cremanei	chromosome:chrUn:56798774:56798898:-1	Opposite_strand|Intronic_coding|NM_069625

cel-mir-1

Cloning frequencies

absolute	CE1
cel-mir-1 5arm	8
cel-mir-1 3arm	270
normalized	CE1
cel-mir-1 5arm	0.006
cel-mir-1 3arm	0.189

sblock4 (miRBase cel-mir-1) [miRNAknown_cloningHIGH_multiarm_DicerOK_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-1

0.001

no

no

0.28/0.47

18/21/0.85

0.0 0.0

0.8 0.0

8 223

0 0

1 1

0 0

20 16

5 7

5arm 3arm

1 1

nd nd

0.14 0.10

2 1

278

1

1

1

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------------GGAAUGU---------------------------------------------	265	miR-1
seed	---------------------------------AUACUUC-------------------------------------------------------------------------------------------------	8	novel
seed	--------------------------------------------------------------------------------------GAAUGUA--------------------------------------------	4	novel
seed	------------------------------------------------------------------------------------UGGAAUG----------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	------------------------------------------------------------------------------------TGGAATGTAAAGAAGTATGT---------------------------------	20	223
	------------------------------------------------------------------------------------TGGAATGTAAAGAAGTATG----------------------------------	19	36
	--------------------------------CATACTTCCT-TACATGCCCAT-----------------------------------------------------------------------------------	21	5
cel-miR-1	------------------------------------------------------------------------------------TGGAATGTAAAGAAGTATGTA--------------------------------	21	4
	--------------------------------CATACTTCCT-TACATGCCC-------------------------------------------------------------------------------------	19	3
	-------------------------------------------------------------------------------------GGAATGTAAAGAAGTATGTA--------------------------------	20	3
	------------------------------------------------------------------------------------TGGAATGTAAAGAAGTAT-----------------------------------	18	2
	-------------------------------------------------------------------------------------GGAATGTAAAGAAGTATGT---------------------------------	19	1
	-----------------------------------------------------------------------------------ATGGAATGTAAAGAAGTATG----------------------------------	20	1
celegans	AAAGTGACCGTACCG------------AGCTGCATACTTCCT-TACATGCCCATACTATA--------TCA---TAAATGGATATGGAATGTAAAGAAGTATGTAGAACGG---------------GGTGGTAGT--
cbriggsae	-----TGCTGTGCCG------------AGCTGCATACTTCCT-TACATGCCCATACTGTA--------CTG---TGAATGGATATGGAATGTAAAGAAGTATGTAGAACGGAATCT----------AACGGCG----
cjaponica	----TCGCCGTGCCG------------AGCTGCATACTTCCT-TGCATACCCATACTTGATCCCCTGGTCG---GACAGAGATATGGAATGTAAAGAAGTATGTAGAGCGGT-------------------------
cbrenneri	----ATGCCGTGCCG------------AGCTGCATGCTTCTTCTACATGCCCATACTATA--------TCG---TAAATGGATATGGAATGTAAAGAAGTATGTAGAACGGAAAACACGAAACAAAAACGGCAT---
ppacificus	AGAATCTCTCTCTCACTCCTCATTCACCGTTCCGTACTTCTT-TGCAGCCCCATACTTGC--------CCGCATGAAGTGGTTATGGAATGTAAAGAAGTATGT--AATGGTCGAGGCGAGAGCACCACTAGAATCT
cremanei	------GCTGTGCCG------------AGCTGCATACTTCCT-TACATGCCCATACTATA--------TCA---GTAATGGATATGGAATGTAAAGAAGTATGTAGAACGGTTTTG-------AAAAACGGC-----
	*  *  *              * * * * **** * * **  ********                       * **********************  *  **
celegans	......((((..(((            ..(((((((((((.( (((((..(((((((((.        ...   ...)))).))))).)))))).)))))))))))..)))               ..))))...	1.000 -41.40
cbriggsae	.(((((.(((            ..(((((((((((.( (((((..(((((((((.        ...   ...)))).))))).)))))).)))))))))))..))).....          .))))).	1.000 -40.00
cjaponica	.......((((            ..(((((((((((.( (((((..((((((((..(((.......)   ))..))).))))).)))))).)))))))))))..))))	1.000 -39.20
cbrenneri	(((((((.(((            ..(((((((((((((.(((((..(((((((((.        ...   ...)))).))))).))))))))))))))))))..)))................)))))))	0.994 -43.13
ppacificus	(((.(((..(((((...((((....((((((.(((((((((( ((((...(((((.....        ((((.....)))).)))))..)))))))))))))).  )))))).)))).))))).......))).)))	0.988 -44.90
cremanei	(((((((((            ..(((((((((((.( (((((..(((((((((.        ...   ...)))).))))).)))))).)))))))))))..))))....       ....)))))	0.990 -39.30

celegans	chromosome:I:6172664:6172759:-1	intergenic ## {SimpF: WRM0637aE07 -1 fosmid,WRM0638cC08 -1 fosmid,WRM065bH05 -1 fosmid,WRM0626aC03 -1 fosmid} ## {MIR: cel-mir-1}
cbriggsae	chromosome:chrI:7435815:7435908:-1	Opposite_strand|Intronic_coding|NM_001087279 ## Same_strand|Intronic_coding|NM_001075644 ## {MIR: cbr-mir-1}
cjaponica	chromosome:chrUn:124179219:124179310:1	intergenic
cbrenneri	chromosome:chrUn:90239915:90240021:1	Opposite_strand|Intronic_coding|NM_001123230 ## Same_strand|Intronic_coding|NM_009930
ppacificus	chromosome:chrUn:9699697:9699822:-1	intergenic
cremanei	chromosome:chrUn:145319807:145319901:1	intergenic

sblock42 (miRBase cel-mir-789-2) [miRNAknown_cloningHIGH_multiarm_DicerOK_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-789-2

0.001

no

no

0.48/0.59

20/23/1.00

0.3 0.0

1.9 0.3

7 17

0 0

1 1

0 0

16 15

7 8

5arm 3arm

1 2

nd nd

0.04 0.04

1 1

26

1

2

2

Families

Member of family novel5 (seed AUUGAUG): cel-mir-789, cel-mir-789

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------------CCCUGCC------------------------------------------------	17	miR-789a/789b
seed	-------------------------------AUUGAUG------------------------------------------------------------------------------------------------------	6	novel
seed	---------------------------------------------------------------------------------------CUGCCUG----------------------------------------------	2	novel
seed	---------------------------------UGAUGAC----------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
cel-miR-789	------------------------------------------------------------------------------------TCCCTGCCTGGGTCACCAATTGT---------------------------------	23	12
	------------------------------------------------------------------------------------TCCCTGCCTGGGTCACCAATTG----------------------------------	22	5
	--------------------------------------------------------------------------------------CCTGCCTGGGTCACCAATTGT---------------------------------	21	2
	------------------------------AATTGATGACT--------CAGGCAGGG-ACT------------------------------------------------------------------------------	23	2
	------------------------------AATTGATGACT--------CAGGCAGGG-AC-------------------------------------------------------------------------------	22	2
	------------------------------AATTGATGACT--------CAGGCAGGG----------------------------------------------------------------------------------	20	2
	--------------------------------TTGATGACT--------CAGGCAGGG-ACT------------------------------------------------------------------------------	21	1
celegans	------TGTCCTGAAGGCG--------GACAATTGATGACT--------CAGGCAGGG-ACTAATCATGATT--GTCGATTTAGTCCCTGCCTGGGTCACCAATTGTCGGCCCCCGCGGACA------------------
cremanei	-----------------------------CGAATGGTAGCC--------GAGGAAGGGTATCTAGAAAG-----AAGGATTA---CCCTGCCTGGGTCACCATTTG----------------------------------
cbriggsae	-----------------------------CACGTGGTCATC--------CAGGCGGTGCACGTTAAAAGATATAAATG-------CCCTGCCTGGGTCACCATGTG----------------------------------
cbrenneri	------CTGGTTGACGA----------AACGATTGGTCATC--------CAGGCGGAGCATCTCAGAAGGCTTG-----------CCCTGCCTGGGTCACCAATTGTCTCGGAAAACTAGGTTTTTTTTCAATTTCTTCG
cjaponica	GTCAAACGAGGTTAGTGCAACCTTTTCAACAGTTGGTGACC--------CAGGAAGGG-ATTAGAAAAGATTTCACAAGTTCAATCCCTGCCTGGGTCACCAATTGTTGAATTGGTTTCACAAAATGGTCAAGAC-----
ppacificus	------CGGAATTAGAAGGA-------AAGAAAGGGTAATCTCTCTGGGCCAGCGGGGGAATAATGGGGGCCCGGAAGCCTC---CCCTGCCTGATAGATACTCTGTCTCTCT---------------------------
	* *               *  * * *        *                *********    *     **
	-----      -------------        --------------        --------- -------------  ------------------------------------------------                  -----	T28F3.9 T28F3.9 T28F3.9
celegans	.((((((..(((.        ((((((((.(((((        ((((((((( (((((...((...  ..))..))))))))))))))))))).)))))))).)))..)).)))).	1.000 -62.80
cremanei	((((((((..((        .(((.(((((((((......     ..)))).)   )))).))).))..))))))))	1.000 -30.80
cbriggsae	((((((((.(((        (((((((.(((..(((.......))).))       ).)))))))))).))))))))	1.000 -32.10
cbrenneri	((((((..(((          .(((((((((.(((        (((((((.(((..((....))..))           ).)))))))))).))))))))).)))...))))))....................	0.994 -46.50
cjaponica	..............(((.((((..(((((((((((((((((        ((((.(((( (((.(((.............)))))))))).)))))))))))))))))))))..)))).)))..............	0.856 -60.42
ppacificus	...........(((       .(((.(((((.((((.((.(((.(((.(((((.....(((....)))....))))   ).)))))))).))))))))).))).)))	0.999 -34.20

celegans	chromosome:IV:17309262:17309358:-1	Opposite_strand|Intronic_coding|T28F3.9|T28F3.9 ## T28F3.9|protein_coding|T28F3.9|T28F3.9 [Source:RefSeq_peptide;Acc:NP_503076] ## {SimpF: WRM0629dG01 -1 fosmid,WRM0612cD04 -1 fosmid,WRM0629bC01 -1 fosmid,WRM066bG02 -1 fosmid,WRM0619aA04 -1 fosmid,WRM0638bF02 -1 fosmid,WRM0638bF01 -1 fosmid} ## {MIR: cel-mir-789-2}
cremanei	chromosome:chrUn:52159843:52159979:-1	Opposite_strand|Intronic_coding|NM_071305 ## Same_strand|Intronic_coding|NM_071724
cbriggsae	chromosome:chrV:3127567:3127703:-1	Opposite_strand|Intronic_coding|NM_001081076 ## Same_strand|Intronic_coding|NM_074754 ## {MIR: cbr-mir-789b}
cbrenneri	chromosome:chrUn:43323640:43323744:1	intergenic
cjaponica	chromosome:chrUn:75784925:75785050:-1	Same_strand|Intronic_coding|NM_001047261
ppacificus	chromosome:chrUn:140794880:140794976:-1	Same_strand|Intronic_coding|NM_001107675

cel-mir-71

Cloning frequencies

absolute	CE1
cel-mir-71 5arm	1180
cel-mir-71 3arm	38
normalized	CE1
cel-mir-71 5arm	0.824
cel-mir-71 3arm	0.027

sblock5 (miRBase cel-mir-71) [miRNAknown_cloningHIGH_multiarm_DicerOK_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-71

0.004

no

no

0.22/0.53

18/24/0.81

0.0 0.0

1.5 1.2

1051 38

0 0

1 1

0 0

15 20

4 6

5arm 3arm

1 1

nd nd

0.06 0.06

1 1

1218

1

2

2

		reads	miRBase family seed
seed	------------------------------------------GAAAGAC--------------------------------------------------------------------------------------------------	1159	miR-71
seed	--------------------------------------------------------------------------------------AUCACUA------------------------------------------------------	38	novel
seed	-------------------------------------------AAAGACA-------------------------------------------------------------------------------------------------	16	novel
seed	-----------------------------------------UGAAAGA---------------------------------------------------------------------------------------------------	3	novel
seed	----------------------------------------------GACAUG--G--------------------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			CE1
	-----------------------------------------TGAAAGACATG--GGTAGTGAG------------------------------------------------------------------------------------	20	471
	-----------------------------------------TGAAAGACATG--GGTAGTGAGACG---------------------------------------------------------------------------------	23	372
	-----------------------------------------TGAAAGACATG--GGTAGTG--------------------------------------------------------------------------------------	18	208
	-----------------------------------------TGAAAGACATG--GGTAGTGAGAC----------------------------------------------------------------------------------	22	93
	-------------------------------------------------------------------------------------TATCACTATTCTGTTTTTCGCC----------------------------------------	22	27
	-------------------------------------------------------------------------------------TATCACTATTCTGTTTTT--------------------------------------------	18	11
	-----------------------------------------TGAAAGACATG--GGTAGTGAGACGT--------------------------------------------------------------------------------	24	11
	------------------------------------------GAAAGACATG--GGTAGTGAG------------------------------------------------------------------------------------	19	5
	------------------------------------------GAAAGACATG--GGTAGTGAGA-----------------------------------------------------------------------------------	20	5
	------------------------------------------GAAAGACATG--GGTAGTGAGACG---------------------------------------------------------------------------------	22	4
	-------------------------------------A---TGAAAGACATG--GGTAGTGAG------------------------------------------------------------------------------------	21	3
cel-miR-71	-----------------------------------------TGAAAGACATG--GGTAGTGA-------------------------------------------------------------------------------------	19	3
	------------------------------------------GAAAGACATG--GGTAGTGAGAC----------------------------------------------------------------------------------	21	2
	---------------------------------------------AGACATG--GGTAGTGAGACG---------------------------------------------------------------------------------	19	2
	-----------------------------------------TGAAAGACATG--GGTAGTGAGA-----------------------------------------------------------------------------------	21	1
celegans	------------GTCTGC-----------TCTGAACGA---TGAAAGACATG--GGTAGTGAGACGTCGG-----AGCCTCGTCGTATCACTATTCTGTTTTTCGCCG--------------------TCGGGATCGTGACCTGGAA
cbriggsae	-----------------------------GCTGAACGA---TGAAAGACATG--GGTAGTGAGACGTCGG-----AGCCTCGTCGTATCACTATTCTGTTTTTCGCCG-------------------ATCAGT--------------
cjaponica	CTTCGGATGCCAGCATAC------AGTCTGCCCGACGA---TGAAAGACATG--GGTAGTGAGACGTCGG-----AGCCTCGTCGTATCACTATTCTGTTTTTCGCCG---------TCTGGATTGTGACGCAGTTTTGGCCCTAGG
cbrenneri	---GGGATTACTGTAGACTTTGTCGTCGCCGCTACCGT---TGAAAGACATG--GGTAGTGAGACGTCGG-----AGCCTCGTCGTATCACTATTCTGTTTTTCGCCG---------GTACCCAGGCATCGAAATTATGGTAAGCTT
ppacificus	-----GAGTCGTGTCGAC-------GACCGACGAGCGAAGGTGAAAGACCTGTTGGTAGTGAGACGATGAAATTTAATCCTTTCGTATCACTACCCAGGCTTTCGCCC---------------TTGCTTCGGTACAATGGCCTTCTC
cremanei	-----TACCCGTGTCTGTACCACCAAACACTCGAACGA---TGAAAGACATG--GGTAGTGAGACGTCGG-----AGCCTCGTCGTATCACTATTCTGTTTTTCGCCGGTCTTGTGATATACCATGTGTCAGATTTACGAAAGGTA-
	**    ******** **  ************  *      *  *   ***********  * *  *******                      *
	+++++            ++++++           +++++++++   +++++++++++  ++++++++++++++++     +++++++++++++++++++++++++++++++++                    ++++++++++++++++++++++++	F16A11.3c F16A11.3 ppfr-1
	+++++            ++++++           +++++++++   +++++++++++  ++++++++++++++++     +++++++++++++++++++++++++++++++++                    ++++++++++++++++++++++++	F16A11.3d F16A11.3 ppfr-1
	+++++            ++++++           +++++++++   +++++++++++  ++++++++++++++++     +++++++++++++++++++++++++++++++++                    ++++++++++++++++++++++++	F16A11.3a F16A11.3 ppfr-1
	+++++            ++++++           +++++++++   +++++++++++  ++++++++++++++++     +++++++++++++++++++++++++++++++++                    ++++++++++++++++++++++++	F16A11.3b F16A11.3 ppfr-1
celegans	(((((.           (((..(((.   (((((((((.(  ((((((((.(((.(((     ....))).))).)))))))))))))))))).))                    )..))).)).)))......	1.000 -36.30
cbriggsae	(((((.((.   (((((((((.(  ((((((((.(((.(((     ....))).))).)))))))))))))))))).))                   .)))))	1.000 -34.80
cjaponica	(((.((..(((((.((..      .(((..((.((((.   (((((((((.(  ((((((((.(((.(((     ....))).))).)))))))))))))))))).))         )).)).....)))...)).))))))).)))	0.995 -47.10
cbrenneri	.((.(((((((((......(((..(((..(((((.   (((((((((.(  ((((((((.(((.(((     ....))).))).)))))))))))))))))).))         )))....)))..)))..))))))))).)).	0.989 -48.90
ppacificus	(((....((((..       .(((((..(((((.((((((((.((((..((((((((.((((...............)))).)))))))))))))))))))).               ))))))))))....))))...)))	0.870 -51.36
cremanei	(((((((((((((((.......(((..((.((.   (((((((((.(  ((((((((.(((.(((     ....))).))).)))))))))))))))))).)).))..))).........))).)))))..)))...))))	0.824 -42.19

celegans	chromosome:I:9379918:9380011:-1	Same_strand|Intronic_coding|F16A11.3d|F16A11.3 ## F16A11.3|protein_coding|ppfr-1|F16A11.3c [Source:RefSeq_peptide;Acc:NP_001021390] ## {SimpF: WRM0632bF02 -1 fosmid,WRM062bH07 -1 fosmid,CEOP1932 1 Operon,WRM0617dD04 -1 fosmid} ## {MIR: cel-mir-71}
cbriggsae	chromosome:chrI:2252473:2252547:-1	Same_strand|Intronic_coding|NM_002035 ## Opposite_strand|Intronic_coding|NM_001107428 ## {MIR: cbr-mir-71}
cjaponica	chromosome:chrUn:134164445:134164566:1	Same_strand|Intronic_coding|NM_074448
cbrenneri	chromosome:chrUn:140296016:140296140:1	Same_strand|Intronic_coding|NM_001026219
ppacificus	chromosome:chrUn:28889363:28889482:-1	Same_strand|Intronic_coding|NM_001043764 ## Opposite_strand|Intronic_coding|NM_001108615 ## {Repeats: G-rich 1 77 -1 class=Low_complexity,GA-rich 1 57 -1 class=Low_complexity}
cremanei	chromosome:chrUn:83434582:83434712:-1	Same_strand|Intronic_coding|NM_001026219

cel-mir-70

Cloning frequencies

absolute	CE1
cel-mir-70 5arm	10
cel-mir-70 3arm	983
normalized	CE1
cel-mir-70 5arm	0.007
cel-mir-70 3arm	0.687

sblock54 (miRBase cel-mir-70) [miRNAknown_cloningHIGH_multiarm_DicerOK_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-70

0.001

no

no

0.35/0.50

18/24/0.86

0.0 0.0

1.0 0.7

10 828

0 0

1 1

0 0

24 16

4 5

5arm 3arm

1 1

nd nd

0.14 0.17

1 1

993

1

1

2

		reads	miRBase family seed
seed	------------------------------------------------------------------------------AAUACGU----------------------------------------------	969	miR-70
seed	-------------------------GAAA-----UAC----------------------------------------------------------------------------------------------	10	novel
seed	-------------------------------------------------------------------------------AUACGUC---------------------------------------------	8	novel
seed	----------------------------------------------------------------------------------CGUCG---------------UU---------------------------	5	novel
seed	--------------------------------------------------------------------------------UACGUCG--------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	-----------------------------------------------------------------------------TAATACGTCG---------------TTGGTGTTTCC------------------	21	520
cel-miR-70	-----------------------------------------------------------------------------TAATACGTCG---------------TTGGTGTTTCCAT----------------	23	308
	-----------------------------------------------------------------------------TAATACGTCG---------------TTGGTGTTT--------------------	19	135
	------------------------CGAAA-----TACTATCGACGAAT-----------------------------------------------------------------------------------	19	4
	-----------------------------------------------------------------------------TAATACGTCG---------------TTGGTGTTTC-------------------	20	4
	------------------------CGAAA-----TACTATCGACGAATA----------------------------------------------------------------------------------	20	4
	------------------------------------------------------------------------------AATACGTCG---------------TTGGTGTTTCCA-----------------	21	3
	---------------------------------------------------------------------------------ACGTCG---------------TTGGTGTTTCCATA---------------	20	3
	------------------------------------------------------------------------------AATACGTCG---------------TTGGTGTTTCC------------------	20	3
	------------------------CGAAA-----TACTATCGACGAATAAC--------------------------------------------------------------------------------	22	2
	---------------------------------------------------------------------------------ACGTCG---------------TTGGTGTTTCCA-----------------	18	2
	-------------------------------------------------------------------------------ATACGTCG---------------TTGGTGTTTCC------------------	19	1
	------------------------------------------------------------------------------AATACGTCG---------------TTGGTGTTTCCATA---------------	23	1
	-----------------------------------------------------------------------------TAATACGTCG---------------TTGGTGTTTCCATA---------------	24	1
	-----------------------------------------------------------------------------TAATACGTCG---------------TTGGTGTT---------------------	18	1
	------------------------------------------------------------------------------AATACGTCG---------------TTGGTGTTT--------------------	18	1
celegans	TCAAAATAAAACGATGAAAACTATCGAAA-----TACTATCGACGAATAACACTTATG----------AAGAAAT-GTAATACGTCG---------------TTGGTGTTTCCATAGTTTGAATTGTTTAT
cbriggsae	-----------------------TAGGAA-----CAGCCATCATGTAAGACATTTCTAACT-------GAAAGAT-GTAATACGTGA---------------TTGGTGTTCCCA-----------------
cjaponica	--TTCAGTATATGCTCCGAATTGACGAAAACCTCTAATTTTCAACAAAAACTTGGAAAATTTCTTTTTAAATGACAGAAATACGTCCTTTTTTTGGAATTTTTTTTTGTTTTTTTGGTAAATTTTTTGAG-
cbrenneri	------TGGCAGAATTGGAACTTCTGAAC-----CACCACTGACGAATCACATTGAAACTA-------AAGAGAT-GTAATACGTCA--------------TTTGGTGTTTCCGAAGTTTATACTGTCA--
ppacificus	---------------------TCATGAA------CAATCTCAATGTGATTCACTAGGTATT------------AT-GAAATACG------------------TTGTTGTATCATGC---------------
cremanei	-AGATGAACGAGGAGAACAGCTATAGGAA-----TACCGTTGATGCATTACACTAAACATT------TGAAAGAT-GTAATACGTCA--------------TTTGGTGTTCCTATAGTTACCCGTTCAACT
	* *       *      *       *                      *  * ******                  **  ***
	++++++++++++++++++++++++++++++++++     ++++++++++++++++++++++++          +++++++ +++++++++++               ++++++++++++++++++++++++++++++++++	T10H9.5a T10H9.5 pmp-5
	++++++++++++++++++++++++++++++++++     ++++++++++++++++++++++++          +++++++ +++++++++++               ++++++++++++++++++++++++++++++++++	T10H9.5b T10H9.5 pmp-5
	++++++++++++++++++++++++++++++++++     ++++++++++++++++++++++++          +++++++ +++++++++++               ++++++++++++++++++++++++++++++++++	T10H9.5c.1 T10H9.5 pmp-5
	++++++++++++++++++++++++++++++++++     ++++++++++++++++++++++++          +++++++ +++++++++++               ++++++++++++++++++++++++++++++++++	T10H9.5c.2 T10H9.5 pmp-5
celegans	........(((((((..(((((((.((((     (((((.(((((.((.(((.((...          ...)).) )).)).)))))               .))))))))).)))))))..)))))))..	1.000 -32.30
cbriggsae	..((((     ((.((((((((((..(((((((.....       ))..))) ))..)))))))               ).))))))))..	1.000 -23.80
cjaponica	.((((...((...(((((..((((((((.....((..(((..((((((...(((..((((((.((.....)).))))))...)))..)))))))))..))))))))))..)))))...))...)))).	0.904 -23.30
cbrenneri	.(((((.....(((((((.(((.     (((((.(((((.((.(((((.......       ....))) )).)).)))))              ..))))).))).)))))))...))))).	0.998 -32.90
ppacificus	.((((((      (((...(((((((.((((.........            .) ))).))))                  ))))))).))))).	0.999 -13.10
cremanei	...((((((.((.....(((((((((((     (((((.(((((.((((((((.......      ....)).) ))))).)))))              ..)))))))))))))))).))))))))...	1.000 -41.10

celegans	chromosome:V:6665519:6665618:-1	Same_strand|Intronic_coding|T10H9.5c.1|T10H9.5 ## T10H9.5|protein_coding|pmp-5|Peroxisomal Membrane Protein related family member (pmp-5) [Source:RefSeq_peptide;Acc:NP_504689] ## {SimpF: WRM0636bC07 -1 fosmid,WRM0612bA02 -1 fosmid,WRM0624bD04 -1 fosmid,yk387d5 -1 RNAi,WRM0612aG09 -1 fosmid,WRM0634aE04 -1 fosmid,WRM0623cB06 -1 fosmid,WRM0639cC08 -1 fosmid,WRM061bH08 -1 fosmid,T10H9.5 -1 Expression_profile,WRM0615cB04 -1 fosmid,WRM065cH10 -1 fosmid} ## {MIR: cel-mir-70}
cbriggsae	chromosome:chrV:9902597:9902736:-1	Same_strand|Intronic_coding|NM_001011629 ## Opposite_strand|Intronic_coding|NM_001011629 ## Same_strand|Boundary_coding|NM_001028960 ## {MIR: cbr-mir-70}
cjaponica	chromosome:chrUn:80979346:80979473:1	Opposite_strand|Intronic_coding|NM_170793 ## {SimpF: trf}
cbrenneri	chromosome:chrUn:187605846:187605941:-1	Same_strand|Intronic_coding|NM_072288
ppacificus	chromosome:chrUn:157491516:157491655:1	intergenic
cremanei	chromosome:chrUn:142215298:142215401:-1	Same_strand|Intronic_coding|NM_001028960 ## Opposite_strand|Intronic_coding|NM_001101711

cel-mir-358

Cloning frequencies

absolute	CE1
cel-mir-358 5arm	3
cel-mir-358 3arm	22
normalized	CE1
cel-mir-358 5arm	0.002
cel-mir-358 3arm	0.015

sblock55 (miRBase cel-mir-358) [miRNAknown_cloningHIGH_multiarm_DicerOK_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-358

0.007

no

no

0.43/0.58

21/24/1.00

0.0 0.2

0.3 0.0

3 16

0 0

1 1

0 0

16 15

0 3

5arm 3arm

1 1

nd nd

0.17 0.14

1 1

25

1

3

2

Clusters

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

		reads	miRBase family seed
seed	------------------------------------------------------------------------------------AUUGG---------------------UA--------------------------------------	15	novel
seed	-------------------------------------------------------------------------------------UUGG---------------------UAU-------------------------------------	7	novel
seed	-----------------------------CCUGGC--C----------------------------------------------------------------------------------------------------------------	3	novel
		len	cloning frequencies
			CE1
	-----------------------------------------------------------------------------------AATTGG---------------------TATCCCT-GTCAAGGTCT----------------------	23	12
	------------------------------------------------------------------------------------ATTGG---------------------TATCCCT-GTCAAGGTCT----------------------	22	4
	-----------------------------------------------------------------------------------AATTGG---------------------TATCCCT-GTCAAGGTC-----------------------	22	3
cel-miR-358	------------------------------------------------------------------------------------ATTGG---------------------TATCCCT-GTCAAGGTC-----------------------	21	3
	----------------------------ACCTGGC--CAGGC-------ATTCCAACTGTC-----------------------------------------------------------------------------------------	24	2
	----------------------------ACCTGGC--CAGGC-------ATTCCAACTGT------------------------------------------------------------------------------------------	23	1
celegans	CTCGCGACGGCTGG------------CGACCTGGC--CAGGC-------ATTCCAACTGTCAAACTTACAAAGCTTTCTCGACAATTGG---------------------TATCCCT-GTCAAGGTCTCAATCCGTTCAGCGA-------
cbriggsae	TACTCCCCATTCGGA--------TTGATACCCGACTTCCGG--------ATACCAAATGTCATATCCAA---CTCGTTTCGTCAATTGG---------------------TATCCTTAGTCGTGGTCTCAATCTGTACACGGCGAGAGTG
cbrenneri	TTTTCCAGTTTTTGAGCTATATTTTCTGATTCAACCCCACATGATATTTATACCAATCGATAAAGCAAA--ACATTTCCTATCGATTGGTATAAATATCATGCAGGGTTATATCATAAATTATGGCTTAAAAACTGAAAA----------
cremanei	--------------------------CGACCTGGC--CAGGC-------ATTCCAACTGTC-CATCCAAGTACTTTATCGGACAATTGG---------------------TATCCCT-GTCAAGGTCT----------------------
	*     *  *           ** ****  *    *   *              * *****                     ****     *   **  *
	-------------------            ---------  -----       ----------------------------------------                     ------- -------------------------       -----	F25G6.2 F25G6.2 F25G6.2
celegans	.(((((((((.(((            .(((((((.  ((((.       ((.((((.((((...................)))).))))                     .)).))) )))).)))))))..)))))..))))	1.000 -33.11
cbriggsae	..(((((....((((        ((((.((((((((...((        (((((((.((..........   ..........)).))))                     )))))..))))).))).)))))))).....)).)))....	0.994 -40.45
cbrenneri	.....((((((((((((((((.(((.((((..(((((..(((((((((((((((((((((((.......  ........)))))))))))))))))))))))..)))))..)))).))).))))))))))))))))....	1.000 -65.46
cremanei	.(((((((.  ((((.       ((.((((.(((( (................))))).))))                     .)).))) )))).)))).	1.000 -25.49

celegans	chromosome:V:8580842:8580941:-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-358}
cbriggsae	chromosome:chrV:1214362:1214471:-1	Opposite_strand|Intronic_coding|NM_001106714 ## Same_strand|Intronic_coding|NM_001028857 ## {MIR: cbr-mir-358}
cbrenneri	chromosome:chrUn:178230186:178230323:-1	intergenic
cremanei	chromosome:chrUn:25671683:25671822:-1	Opposite_strand|Intronic_coding|NM_199607

cel-mir-250

Cloning frequencies

absolute	CE1
cel-mir-250 5arm	5
cel-mir-250 3arm	397
normalized	CE1
cel-mir-250 5arm	0.003
cel-mir-250 3arm	0.277

sblock56 (miRBase cel-mir-250) [miRNAknown_cloningHIGH_multiarm_DicerOK_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-250

0.001

no

no

0.41/0.59

19/23/1.00

0.0 0.0

0.4 0.0

5 297

0 0

1 1

0 0

16 16

3 6

5arm 3arm

1 1

nd nd

0.23 0.20

2 2

402

1

2

1

Clusters

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

		reads	miRBase family seed
seed	------------------------------------------------------------------------AUCACAG-----------------------------------------------	393	miR-43
seed	------------------------------CUUCAGU-----------------------------------------------------------------------------------------	5	novel
seed	-------------------------------------------------------------------------UCACAGU----------------------------------------------	4	novel
		len	cloning frequencies
			CE1
	-----------------------------------------------------------------------AATCACAGTCAACTGTTGGC-----------------------------------	20	297
	-----------------------------------------------------------------------AATCACAGTCAACTGTTGGCAT---------------------------------	22	88
	-----------------------------------------------------------------------AATCACAGTCAACTGTTGGCATG--------------------------------	23	5
	-----------------------------CCTTCAGTTGCCTCGTGATCCG---------------------------------------------------------------------------	22	3
cel-miR-250	-----------------------------------------------------------------------AATCACAGTCAACTGTTGGCA----------------------------------	21	3
	-----------------------------CCTTCAGTTGCCTCGTGATCC----------------------------------------------------------------------------	21	2
	------------------------------------------------------------------------ATCACAGTCAACTGTTGGCA----------------------------------	20	2
	------------------------------------------------------------------------ATCACAGTCAACTGTTGGC-----------------------------------	19	2
celegans	-------------GGGTCTTCGGACCACGCCTTCAGTTGCCTCGTGATCCGCCAAACACAATAAATGGACGAATCACAGTCAACTGTTGGCATGGTGCTCGTACCCA-------------------
cbriggsae	--CTATTATTCAAGGGTCTTCGGACCACGCCTTCAGTTGCCTCGTGATCCGCCGAATCTG--TAATGGACGAATCACAGTCAACTGTTGGCACGGTCCTTGAAGTTCACCATTTTTGAAGGTTTGG
cjaponica	----------------------------TCCTTCAGTTTTCTCGTGATCCGCCAATCTT---CCATGGACGAATCACAGTCAACTGTTGGC-----------------------------------
cbrenneri	----------------------------GCCGGCAGTTGCCTGTTGATCCGCCGCAATTA--TGATGGACGAATCACAGTCAACTGTTGGC-----------------------------------
cremanei	TGCTGTTATTCGAAGGTCTTCGGACCGCCCCTTCAGTTGACTCGTGATCCGCCGACTTTGATATATGGACGAATCACAGTCACCTGATGGTACGGTCTTTGAATTCCTATATTATTATGGTA----
	**  *****  **  *********           ****************** *** ***
celegans	((((...(((((((.(((..((((((.((.(((((.(((((...........))).)).))))))).))))))..))).))))..))).)))).	0.750 -37.70
cbriggsae	(((...(((((.((((((((((((..(((..((((((.((.(((((.(((((......  ...))).)).))))))).))))))..)))..)))))..))))...)))....)))))....)))	0.898 -40.10
cjaponica	.((..(((((..((.(((((.(((((.....   ...))).)).)))))))..)))))..)).	1.000 -18.60
cbrenneri	(((((((((((.(((.((((.(((((((....  )).))).)).))))))).)))))))))))	1.000 -29.40
cremanei	((((((.......(((..(((((((((..((.((((.(((((.(((((.(((((...........))).)).)))))))))).)))).))..))))))..)))..)))........))))))	0.984 -40.46

celegans	chromosome:V:11769899:11769992:-1	intergenic ## {SimpF: WRM0616dF12 -1 fosmid,WRM0630cB01 -1 fosmid,F55A11.3 -1 Expression_profile,WRM064dC03 -1 fosmid,WRM0611bB04 -1 fosmid,WRM0628cB12 -1 fosmid} ## {MIR: cel-mir-250}
cbriggsae	chromosome:chrV:6755100:6755221:-1	Opposite_strand|Intronic_coding|NM_007734 ## Same_strand|Intronic_coding|NM_000945 ## {MIR: cbr-mir-250}
cjaponica	chromosome:chrUn:133810890:133811023:-1	intergenic
cbrenneri	chromosome:chrUn:84265172:84265305:1	intergenic
cremanei	chromosome:chrUn:126692870:126692991:-1	Opposite_strand|Intronic_coding|NM_073652 ## Same_strand|Intronic_coding|NM_067460

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confident miRBase miRNAs:

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