miR-Intess™

confident miRBase miRNAs

miRNAknown_cloningHIGH_multiarm_DicerOK_randfoldOK (30 loci)

miRNAknown_cloningHIGH_randfoldOK (23 loci)

cel-mir-2

Cloning frequencies

absolute	CE1
cel-mir-2 3arm	17893
normalized	CE1
cel-mir-2 3arm	12.500

block411 (miRBase cel-mir-2) [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-2

0.001

no

no

0.42/0.56

18/24/0.98

0.0

0.0

16893

0

1

0

15

9

3arm

1

nd

0.17

2

17893

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-------------------------------------------------------------	17486	miR-43
seed	---------------------------------------------------------------------------------------UCACAGC------------------------------------------------------------	215	novel
seed	------------------------------------------------------------------------------------------CAGCCAG---------------------------------------------------------	171	novel
seed	----------------------------------------------------------------------------------------CACAGCC-----------------------------------------------------------	9	novel
seed	-------------------------------------------------------------------------------------------AGCCAGC--------------------------------------------------------	7	novel
seed	-------------------------------------------------------------------------------------UAUCACA--------------------------------------------------------------	5	novel
		len	cloning frequencies
			CE1
cel-miR-2	-------------------------------------------------------------------------------------TATCACAGCCAGCTT--TGAT---------GTGC-----------------------------------	23	16893
	-------------------------------------------------------------------------------------TATCACAGCCAGCTT--TGAT---------GTG------------------------------------	22	258
	--------------------------------------------------------------------------------------ATCACAGCCAGCTT--TGAT---------GTGC-----------------------------------	22	207
	-----------------------------------------------------------------------------------------ACAGCCAGCTT--TGAT---------GTGC-----------------------------------	19	165
	-------------------------------------------------------------------------------------TATCACAGCCAGCTT--TGA-------------------------------------------------	18	159
	-------------------------------------------------------------------------------------TATCACAGCCAGCTT--TGAT---------GTGCT----------------------------------	24	68
	-------------------------------------------------------------------------------------TATCACAGCCAGCTT--TGAT---------G--------------------------------------	20	54
	-------------------------------------------------------------------------------------TATCACAGCCAGCTT--TGAT---------GT-------------------------------------	21	45
	-------------------------------------------------------------------------------------TATCACAGCCAGCTT--TGAT------------------------------------------------	19	9
	------------------------------------------------------------------------------------------CAGCCAGCTT--TGAT---------GTGC-----------------------------------	18	7
	---------------------------------------------------------------------------------------TCACAGCCAGCTT--TGAT---------GTGC-----------------------------------	21	5
	-----------------------------------------------------------------------------------------ACAGCCAGCTT--TGAT---------GTG------------------------------------	18	5
	--------------------------------------------------------------------------------------ATCACAGCCAGCTT--TGAT---------GTG------------------------------------	21	3
	---------------------------------------------------------------------------------------TCACAGCCAGCTT--TGAT---------GTGCT----------------------------------	22	3
	------------------------------------------------------------------------------------ATATCACAGCCAGCTT--TGAT---------GTGC-----------------------------------	24	3
	------------------------------------------------------------------------------------ATATCACAGCCAGCTT--TGAT---------GTG------------------------------------	23	2
	--------------------------------------------------------------------------------------ATCACAGCCAGCTT--TGAT---------GTGCT----------------------------------	23	2
	--------------------------------------------------------------------------------------ATCACAGCCAGCTT--TGAT------------------------------------------------	18	1
	---------------------------------------------------------------------------------------TCACAGCCAGCTT--TGAT---------GTG------------------------------------	20	1
	-----------------------------------------------------------------------------------------ACAGCCAGCTT--TGAT---------GTGCT----------------------------------	20	1
	--------------------------------------------------------------------------------------ATCACAGCCAGCTT--TGAT---------GT-------------------------------------	20	1
	--------------------------------------------------------------------------------------ATCACAGCCAGCTT--TGAT---------G--------------------------------------	19	1
celegans	----------TAAACAGTATA---------CAGAAAGC----CATCAAAGCGGTGGTTGATGTGTTG--CAAATTATGACTTTCATATCACAGCCAGCTT--TGAT---------GTGCTGCCTGTTGCACTGT--------------------
cjaponica	AAATAA---CTGAAACGCATTG-----------GTAGCT---CGTCGAA-CTGCAGCTGATCTGCCG----CTCTAAAATGGACATATCACAGCCAGCTT--TGAT---------GTGCTACCTTTTCAGCTGTTT------------------
cbrenneri	--CTGA---TTCCCATGTACAGTGAACCTCCAGAAAGCA---CGTCAAAGTGGCGCGTGTTATGTCGGAAATATGAAAAGGATCATATCACAGCCAGCTT--TGAT---------GTGCTT-------GACTGTGTTCAGCTAGGAAATGTCGG
ppacificus	GGAAAGATATGAACGAGTATAG------ATCACGTAGCTGACCGGCAGTTCTGCGCGTGATGCGTGG--TAGTTATAAGCATCCGTATCACAGCCGGACTGCTGATCTGCCGATCTTGCTTCTTCTCATAGTATACTCC---------------
cremanei	GGATGAATATTCCATACCATAGTA----TACGGAAAGCC---CGTCAAAGTGGCTCGTGTTATGTTG--AATCTTGAAGTAATCATATCACAGCCAGCTT--TGAT---------GTGCTTCCTGAAGTACTATCCTTTGTCACTTGTCATTC-
	*                ***    *  *      *    ** *  *  *                * ********** *  *  ****          ****           * *
	+++++          +++++++++++         ++++++++    +++++++++++++++++++++++++  +++++++++++++++++++++++++++++++  ++++         +++++++++++++++++++                    +++++	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 -38.40
cjaponica	(((((.   ((((((......(           (((((.   ((((((( (((..((((((.(((((    ........))).)).))))..))))).))  ))))         ).)))))).)))))).)))))	0.999 -32.40
cbrenneri	((((   ((((...((....(((((...(((.(((((   ((((((((((((..(((.((((((..............)).)))).))).)))).)))  ))))         ))))))       ..))).)))))))..)))...)))))	0.986 -44.24
ppacificus	(((....(((((..(((((.((      (((.....((.((.(((((((((.((..((((((((.((  (.((.....))))))))))))).)).))))))))).)).)).))))))))))....)))))......)))	0.992 -47.10
cremanei	((((((......((....((((((    (.(((.((((.   (((((((((((((.(((.((((...  ..............)))).)))))))).)))  ))))         ).)))).)))..)))))))....)).......))))))	0.958 -40.15

celegans	chromosome:I:9372759:9372856:-1	Same_strand|Intronic_coding|F16A11.3b|F16A11.3 ## F16A11.3|protein_coding|ppfr-1|F16A11.3c [Source:RefSeq_peptide;Acc:NP_001021390] ## {SimpF: WRM0612aC09 -1 fosmid,CEOP1932 1 Operon,WRM0632bF02 -1 fosmid,WRM062bH07 -1 fosmid} ## {MIR: cel-mir-2}
cjaponica	chromosome:chrUn:94987973:94988075:1	Same_strand|Intronic_coding|NM_007674
cbrenneri	chromosome:chrUn:140304597:140304724:1	Same_strand|Intronic_coding|NM_001026219
ppacificus	chromosome:chrUn:160261320:160261450:1	Same_strand|Intronic_coding|NM_001109726
cremanei	chromosome:chrUn:83423063:83423195:-1	Same_strand|Intronic_coding|NM_001026219

cel-mir-1817

Cloning frequencies

absolute	CE1
cel-mir-1817 5arm	213
normalized	CE1
cel-mir-1817 5arm	0.149

block492 (miRBase cel-mir-1817) [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-1817

0.002

no

no

0.36/0.41

18/23/0.96

0.0

1.3

197

0

1

0

20

5

5arm

1

nd

0.15

1

213

1

na

na

		reads	miRBase family seed
seed	---------------------AGCCAAU--------------------------------------------------------------------------------------	209	novel
seed	-------------------------AAUGUCU----------------------------------------------------------------------------------	3	novel
seed	----------------------GCCAAUG-------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	--------------------TAGCCAATGTCTTCTCTATC--------------------------------------------------------------------------	20	110
cel-miR-1817	--------------------TAGCCAATGTCTTCTCTATCATG-----------------------------------------------------------------------	23	87
	--------------------TAGCCAATGTCTTCTCTA----------------------------------------------------------------------------	18	4
	--------------------TAGCCAATGTCTTCTCTATCAT------------------------------------------------------------------------	22	4
	------------------------CAATGTCTTCTCTATCATG-----------------------------------------------------------------------	19	3
	--------------------TAGCCAATGTCTTCTCTAT---------------------------------------------------------------------------	19	2
	--------------------TAGCCAATGTCTTCTCTATCA-------------------------------------------------------------------------	21	2
	---------------------AGCCAATGTCTTCTCTATCATG-----------------------------------------------------------------------	22	1
celegans	TGTACATTTCAATTTTCGAGTAGCCAATGTCTTCTCTATCATGCATTTTACAAATAATGAGTACATGATAG--TGAAA--TATTTGCTTCCTGAATTTC-----AGAGATGTTT
cbriggsae	--------------------AAGCCAATTTTT-------------CGTTGCTTCATCGGAGTACATGACTA-----------ACGCCGTCATGGAGAAC---GTAAAAGTGCAG
cbrenneri	--------------------TAGCCAATCGTT--------------------------GAGATTGTGATGAATTCGAAGAAAATTACTTCATAAA---------ACGATTGCTT
cjaponica	--------------------TAGCCAATTTGT------------------------CGAAATTTTTTGTCG---------AATTTTTGTCGACAAAATTTCGACAAATTTGTCA
ppacificus	--------------------TAGCCAATTGTT-----------------------AAGAAGGAAAAACTAG--CAAAAGTGATTTTTTTTCTGAGCAA------AATTGTGTTT
	*******   *                           *                            *               *    **
celegans	...(((((((....((((.(.(((.(((((.(((.((((((((.((((..........)))).))))))))  .))))  )))).))).).))))....     .)))))))..	1.000 -27.30
cbriggsae	..((..((((((             ((((.(((((((((.((.........           )).)))..)))))))))   ).))))))))..	0.853 -16.30
cbrenneri	.((.((((((((                          ....((((((..((((.......))))...)))))))         ))))))))).	0.953 -12.00
cjaponica	..((.(((((((                        ((((((..(((((((         (.......))))))))))))))))))))).))..	1.000 -23.40
ppacificus	.(((((((((((                       .(((((((((((((..  ....)))..)))))))))).)))).      .)))).))).	1.000 -12.30

celegans	chromosome:I:10869363:10869467:-1	intergenic ## {SimpF: WRM0638bB08 -1 fosmid,WRM068aG01 -1 fosmid,WRM0629cD02 -1 fosmid} ## {MIR: cel-mir-1817}
cbriggsae	chromosome:chrX:7135776:7135920:1	Same_strand|Intronic_coding|NM_178660 ## Opposite_strand|Intronic_coding|NM_153821 ## {SimpF: trf}
cbrenneri	chromosome:chrUn:41649762:41649906:-1	Same_strand|Intronic_coding|NM_001056672 ## Opposite_strand|Exonic_coding|NM_001026725
cjaponica	chromosome:chrUn:88872449:88872593:1	intergenic ## {SimpF: trf}
ppacificus	chromosome:chrUn:155434944:155435088:-1	Same_strand|Intronic_coding|NM_001041377 ## Opposite_strand|Intronic_coding|NM_001077648

cel-mir-50

Cloning frequencies

absolute	CE1
cel-mir-50 5arm	858
normalized	CE1
cel-mir-50 5arm	0.599

block706 (miRBase cel-mir-50) [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-50

0.001

no

no

0.33/0.44

18/25/0.95

0.0

1.4

794

0

1

0

15

5

5arm

1

nd

0.12

3

858

1

na

na

Families

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

		reads	miRBase family seed
seed	------------------------------GAUAUGU---------------------------------------------------------------------------------------	844	miR-50/62/90
seed	----------------------------------UGU-CUGG----------------------------------------------------------------------------------	8	novel
seed	-------------------------------AUAUGU-C-------------------------------------------------------------------------------------	6	novel
		len	cloning frequencies
			CE1
	-----------------------------TGATATGT-CTGGTA----TTCTTGGGTT------------------------------------------------------------------	24	295
cel-miR-50	-----------------------------TGATATGT-CTGGTA----TTCTTGGG--------------------------------------------------------------------	22	209
	-----------------------------TGATATGT-CTGGTA----TTCTTGG---------------------------------------------------------------------	21	186
	-----------------------------TGATATGT-CTGGTA----TTCTTGGGT-------------------------------------------------------------------	23	104
	-----------------------------TGATATGT-CTGGTA----TTCTTGGGTTT-----------------------------------------------------------------	25	32
	-----------------------------TGATATGT-CTGGTA----TTCTTG----------------------------------------------------------------------	20	16
	------------------------------GATATGT-CTGGTA----TTCTTGGGTT------------------------------------------------------------------	23	6
	---------------------------------ATGT-CTGGTA----TTCTTGGG--------------------------------------------------------------------	18	5
	-----------------------------TGATATGT-CTGGTA----TTCT------------------------------------------------------------------------	18	2
	---------------------------------ATGT-CTGGTA----TTCTTGGGTT------------------------------------------------------------------	20	2
	---------------------------------ATGT-CTGGTA----TTCTTGGGTTT-----------------------------------------------------------------	21	1
celegans	--------------CTGCCCGCCGGCCGCTGATATGT-CTGGTA----TTCTTGGGTTTG-----AACTTCCAGCGTTG-AACCCGCATATTAGACGTATCGACGGCCGGCGGGGCAGGTAATG
cbriggsae	-------------TCCACCCACCGGCCGCTGATATGT-CTGATA----TTCTTGGGTTAT---CTGATAATGATTGTTGTAACTCAAGTATTAGACGTATCGACGGCCGGCTGGGTTGGA----
cjaponica	CACTATATTCCCGCTCGCCCACCGGACCTTGATATGT-CTAGTA----TTCTAGGTTTCG-CCCTTTTATTGGCATGCG-AACCAGTTTATTAGATATATCGACGTCCGGTTTGGGCGGCG---
cbrenneri	------------TCTCACCCACCGGCCGCTGATATGT-CTGGTA----TTCTTGGGTTCATTCCTTACTCTG--------AACCAGTTTATTAGACGTATCGACGGCCGGATCGGGTGAGA---
ppacificus	------------------------------GATATGTGCTGGTAAGTCCTCTAAGTTCAA------GGTCTAGGAGGTGATTTCCAATTAAC-----TATC-----------------------
cremanei	-----------------------------TGATATGT-CTGGTA----TTCTTGGGTTCG----ATACTCTGAAAAACG-AACCAAAGTAGCAGACGTATCG----------------------
	******* **  **     ***  * *                               **       ****
	+++++              +++++++++++++++++++++++ ++++++    ++++++++++++     ++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++	Y71G12B.11a Y71G12B.11 Y71G12B.11
celegans	((((((((((((((.(((((((( ((((((    (...(((((((.     (((.......)))) )))))).))))))))))))))).)))))))).))))))......	1.000 -59.60
cbriggsae	(((((((((((((((.(((((((( ((((((    ..((((((((((   ..((((.....)))))))))))))))))))))))))))).))))))).))))).)))	1.000 -56.00
cjaponica	...........(((.((((((((((((.((((((((( ((((((    ..((.((.(((( (((.......))...))) ))))))..))))))))))))))).)))))))..))))))))	1.000 -56.90
cbrenneri	((((((((.(((((((.(((((((( ((((((    ..((..((((((..........))        ))))))..)))))))))))))).)))))))...))))))))	1.000 -55.00
ppacificus	((((.((..(((.((..(((((.((.....      ...)).)))))...)).)))....))     ))))	0.999 -12.20
cremanei	.((((((( (((.((    ((....((((((    .............)) ))))..)))).)))))))))).	1.000 -25.32

celegans	chromosome:I:1738636:1738734:1	Same_strand|Intronic_coding|Y71G12B.11a|Y71G12B.11 ## Same_strand|Boundary_non-coding|Y71G12B.11b|Y71G12B.11 ## Y71G12B.11|protein_coding|Y71G12B.11|Y71G12B.11a [Source:RefSeq_peptide;Acc:NP_490886] ## {MIR: cel-mir-50}
cbriggsae	chromosome:chrI:2124811:2124909:1	Opposite_strand|Intronic_coding|NM_174569 ## Same_strand|Intronic_coding|NM_001107428 ## {MIR: cbr-mir-50}
cjaponica	chromosome:chrUn:44675841:44675954:-1	Same_strand|Intronic_coding|NM_143141
cbrenneri	chromosome:chrUn:31668280:31668375:-1	Opposite_strand|Intronic_coding|NM_203889 ## Same_strand|Intronic_coding|NM_001113428
ppacificus	chromosome:chrUn:5001520:5001658:-1	intergenic
cremanei	chromosome:chrUn:17804059:17804197:-1	Same_strand|Intronic_coding|NM_001009560 ## Same_strand|Boundary_coding|NM_058485

cel-mir-236

Cloning frequencies

absolute	CE1
cel-mir-236 3arm	175
normalized	CE1
cel-mir-236 3arm	0.122

block1752 (miRBase cel-mir-236) [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-236

0.001

no

no

0.32/0.50

18/24/0.95

0.0

0.0

146

0

1

0

15

5

3arm

1

nd

0.13

1

175

1

na

na

		reads	miRBase family seed
seed	----------------------------------------------------------------------------------------------AAUACUG-------------------------------------------------	172	miR-236
seed	--------------------------------------------------------------------------------------------------CUGUCAG---------------------------------------------	2	novel
seed	-----------------------------------------------------------------------------------------------AUACUGU------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
cel-miR-236	---------------------------------------------------------------------------------------------TAATACTGTCAGGTAATGACGCT----------------------------------	23	146
	---------------------------------------------------------------------------------------------TAATACTGTCAGGTAATGACGC-----------------------------------	22	17
	---------------------------------------------------------------------------------------------TAATACTGTCAGGTAATG---------------------------------------	18	6
	----------------------------------------------------------------------------------------------AATACTGTCAGGTAATGACGCT----------------------------------	22	1
	---------------------------------------------------------------------------------------------TAATACTGTCAGGTAATGACG------------------------------------	21	1
	---------------------------------------------------------------------------------------------TAATACTGTCAGGTAATGACGCTG---------------------------------	24	1
	-------------------------------------------------------------------------------------------------ACTGTCAGGTAATGACGCT----------------------------------	19	1
	---------------------------------------------------------------------------------------------TAATACTGTCAGGTAATGA--------------------------------------	19	1
	-------------------------------------------------------------------------------------------------ACTGTCAGGTAATGACGC-----------------------------------	18	1
celegans	--------------TCGGTGACCGAT----------GTCCAGCGTCTTACC--------TGTTCAATATTTAGACTGACTAT-CAAAGAGATCTAATACTGTCAGGTAATGACGCTGGATTGTCATGTCAT-------------------
cbriggsae	----------------------------------------AGCGTCTTACC--------TGTTCAATATTTAGACTGACCAAACCCATAGCTCTAATACTGTCAGGTAATGACGCT----------------------------------
cjaponica	--------------TTGATTAATAAT---------------------------------TGAAGAATTTTC------ACTACATAAGAAGTGAAAATACTGACA-------------------ATTATAGTTTT----------------
cbrenneri	TACTGTCCTATTCTGAGGTGACCGAT----------GTCCAGCGTCTTACC--------TGTTCAATATTTAGACTAAC-ACATCAAGAGATCTAATACTGTCAGGTAATGACGCTGGGTAATAGTGTCGCTTATTTGAAATCAACGGTA
ppacificus	-----------------GTGAAGAATCAACAAGAGGGACAGGCATGATACCGTTAACTGGGAACGATATTTTATAATATTTTATCATAATATACAATACTGGCACCCATTTACGTTTGATGAAATTGTACTTTTTTGGAATTTGGGC---
cremanei	--CTGTCCTATTCTTTGGTGACCGAT----------GTCCAGCGTCTTACC--------TGTTCAATATTTAGACTGATTAGCTCATGAGATCTAATACTGTCAGGTAATGACGCTGGATTATCTTGTCATTTATGATAAGCAACACAG-
	*    ** **       *          *     ******* **
celegans	...(((((.(((          (((((((((((((((        ((..((.((((.(((((...... .....)).))))))).)).))))))).))))))))).))))..)))))	1.000 -36.50
cbriggsae	(((((((((((        ((..((.((.((((((((..........))).))))))).)).))))))).))))))	1.000 -21.50
cjaponica	..((((.(((((                                 ((.((.((((((      (((........))))))))).))..))                   )))))))))..	1.000 -14.70
cbrenneri	((((((....(((..(((((((..((          ..(((((((((((((        ((..((.((.(((((((... ........)).))))))).)).))))))).))))))))...))...)))))))....)))....))))))	0.995 -42.00
ppacificus	.....((((...((((((((((((.(((.....((.(((.((((..((.((((.((((.(((......))).)))).)))).))...)))).)))))....)))...)))).))))))))..))))....	0.847 -21.10
cremanei	((((.((..((...((((((.(((          (((((((((((((((        ((..((.((.(((((((.((......)).)).))))))).)).))))))).)))))))))).)))..))))))...))..))....))))	0.939 -43.10

celegans	chromosome:II:7030119:7030216:-1	intergenic ## {SimpF: WRM0622cH07 -1 fosmid,WRM068aG05 -1 fosmid,WRM0619aC05 -1 fosmid} ## {MIR: cel-mir-236}
cbriggsae	chromosome:chrII:5133868:5133935:-1	Opposite_strand|Intronic_coding|NM_004845 ## Same_strand|Intronic_coding|NM_001047951 ## {MIR: cbr-mir-236}
cjaponica	chromosome:chrUn:86501543:86501680:-1	Opposite_strand|Intronic_coding|NM_024331 ## Same_strand|Intronic_coding|NM_000215
cbrenneri	chromosome:chrUn:68604096:68604226:-1	Same_strand|Intronic_coding|NM_023651
ppacificus	chromosome:chrUn:139137016:139137145:1	Same_strand|Intronic_coding|NM_171584 ## {Repeats: AT_rich 1 28 1 class=Low_complexity}
cremanei	chromosome:chrUn:132170869:132170997:1	Opposite_strand|Intronic_coding|NM_205265

cel-mir-252

Cloning frequencies

absolute	CE1
cel-mir-252 5arm	1141
normalized	CE1
cel-mir-252 5arm	0.797

block1927 (miRBase cel-mir-252) [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-252

0.009

no

no

0.43/0.53

18/24/0.99

0.0

0.0

1079

0

1

0

20

7

5arm

1

nd

0.19

1

1141

1

na

na

		reads	miRBase family seed
seed	----------------------------------UAAGUAG----------------------------------------------------------------------------------------------	1118	miR-251
seed	-----------------------------------AAGUAGU---------------------------------------------------------------------------------------------	16	miR-252
seed	--------------------------------------UAGUAGU------------------------------------------------------------------------------------------	7	novel
		len	cloning frequencies
			CE1
	---------------------------------ATAAGTAGTAGTGCCGCAGGT---------------------------------------------------------------------------------	21	1079
	---------------------------------ATAAGTAGTAGTGCCGCAGG----------------------------------------------------------------------------------	20	15
cel-miR-252	---------------------------------ATAAGTAGTAGTGCCGCAGGTAA-------------------------------------------------------------------------------	23	15
	----------------------------------TAAGTAGTAGTGCCGCAGGTA--------------------------------------------------------------------------------	21	8
	----------------------------------TAAGTAGTAGTGCCGCAGGT---------------------------------------------------------------------------------	20	8
	-------------------------------------GTAGTAGTGCCGCAGGTAA-------------------------------------------------------------------------------	19	7
	---------------------------------ATAAGTAGTAGTGCCGCAGGTA--------------------------------------------------------------------------------	22	5
	---------------------------------ATAAGTAGTAGTGCCGCA------------------------------------------------------------------------------------	18	3
	---------------------------------ATAAGTAGTAGTGCCGCAGGTAAC------------------------------------------------------------------------------	24	1
celegans	-------------TCCAGGGGTCTCTTTCAGTTATAAGTAGTAGTGCCGCAGGTAACCGCCAGTCTAAA--AGGCTTACCTACTGCCTTCTGCTTAAAA--TTGAAATATTGATG--------------------
cbriggsae	-----------------GAGGTCTCTCCCAGTTATAAGTAGTAGTGCCGCAGGTAACCGCTTCCAGAAAATTGGTTTACCTACTGCCTTCTGCTTAGAA--TTGGGATTTTGATGACCGTC--------------
cjaponica	-------------------------TTCCGATTATAAGTAGTAGTGCCGCAGGTAACTG------GAGA--TTGATTACCTACTGCCTCCTGCTTAAAA--TTGGAA----------------------------
cbrenneri	CTTTCTATATTCCTTTTTTGGTCTCTTTCAGTTATAAGTAGTAGTGCCGCAGGTAACCG---ATTTCAA--TGGTTTACCTACTGCCTCCTGCTTAGAA--TTGAAATTTCGATGACCGTCTTTTGTAATGAAAG
ppacificus	--------GATCACCTATCACTCTGTCCGGGTTCTAAGTAGTAGTGCCGCAGGTAACCAACAATTGAGA---GGTTTACCTATAGCCTTCTGCTTAACACCTTGAAGAGTTGATC--------------------
cremanei	-------------------GGTCTCTTTCAGTTATAAGTAGTAGTGCCGCAGGTAACCACTCAAATATA--TGGTTTACCTACTGCCTTCTGCTTAGAA--TTGAAATATCGATGACC-----------------
	*     ** ***********************           *    * *******  **** *******  *  ***
	-----             --------------------------------------------------------  ----------------------------  --------------                    -----	W02B12.13 W02B12.13 W02B12.13
celegans	.......(((..((((((((.(((((((.((.((.(.((((((..(((........  .))))))))).).)))).))))))).))  ))))))....))).	1.000 -29.50
cbriggsae	..((((((((((((((.(((((((.((.((...(((((((((.((......)).))))).))))...)))).))))))).))  ))))))....)).))))...	1.000 -36.70
cjaponica	.(((((((.(((((((.((.((...((((((...      ....  ....))))))...)))).))))))).))  ))))).	0.999 -23.60
cbrenneri	(((((..(((........(((((((((((((((.(((((((.((.((...(((((((((   .......  ))))).))))...)))).))))))).))  ))))))....)).)))))......)))..)))))	0.971 -34.24
ppacificus	(((((......(((((.((.((((..(((((((.((.((...((((((((...........   )))).))))...)))).)))))))..)))).))))))))))))	0.999 -32.30
cremanei	((((((((((((((.(((((((.((.((...(((((((((..........  ))))).))))...)))).))))))).))  ))))))....)).))))	1.000 -30.30

celegans	chromosome:II:11446779:11446876:-1	Opposite_strand|Intronic_coding|W02B12.13|W02B12.13 ## W02B12.13|protein_coding|W02B12.13|Putative uncharacterized protein. [Source:UniProtKB/TrEMBL;Acc:A3FPK4] ## {MIR: cel-mir-252}
cbriggsae	chromosome:chrII:7467787:7467888:-1	Same_strand|Intronic_coding|NM_001031311 ## Opposite_strand|Intronic_coding|NM_001129175 ## {MIR: cbr-mir-252}
cjaponica	chromosome:chrUn:63338611:63338682:-1	Opposite_strand|Intronic_coding|NM_001129175
cbrenneri	chromosome:chrUn:41707048:41707175:1	Opposite_strand|Intronic_coding|NM_001056672 ## Opposite_strand|Boundary_coding|NM_001129175
ppacificus	chromosome:chrUn:24531069:24531172:1	Same_strand|Intronic_coding|NM_001114660 ## Opposite_strand|Intronic_coding|NM_174405
cremanei	chromosome:chrUn:8843504:8843598:1	Opposite_strand|Intronic_coding|NM_001011005 ## Same_strand|Intronic_coding|NM_077846

cel-mir-234

Cloning frequencies

absolute	CE1
cel-mir-234 3arm	25
normalized	CE1
cel-mir-234 3arm	0.017

block2076 (miRBase cel-mir-234) [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-234

0.003

no

no

0.38/0.40

20/21/1.00

0.0

0.0

23

0

1

0

15

9

3arm

1

nd

0.14

2

25

1

na

na

		reads	miRBase family seed
seed	------------------------------------------------------------------------------UAUUGCU---------------------------------------------	25	miR-234
		len	cloning frequencies
			CE1
cel-miR-234	-----------------------------------------------------------------------------TTATTGCTCGAGAATACCCTT--------------------------------	21	23
	-----------------------------------------------------------------------------TTATTGCTCGAGAATACCCT---------------------------------	20	2
celegans	----------------CAAAAAATGATCAAACGGTATTCCAGAGTTGATAATAAAAATG-CGTCAGTCCGCAATCTATTATTGCTCGAGAATACCCTTTGAC------TACTATGTGTA-----------
cbriggsae	-----------------------------AACGGTATTCCTGAGTGAATAATAAAAATG-------AGTCCATTCTATTATTGCTCGAGAATACCCTT--------------------------------
cjaponica	-----------AAAAACACACCACGTTCGATAGGTGTTCCAGAGTTGATAATAATCGTGCCAT--GTGCACATT-TATTATTGCTTGAGAATACCCCTCGGCAGATTGTGTTCTGTTTTT----------
cbrenneri	------GAATTCATGCAACAATCAGCTCAAACGGTATTCTTTGGTTAATAATAAGGATGGCATCACGACTCATTATATTATTGCTCAAGAATACCCTTTGACAAATGTCGCGTGACATC-----------
cremanei	GATGAATGGTAAGTGGTGAACCAAGCTCAAACGGTATTCGACGGTGAATAATAAAAATGACATTGCGACTCATTCTATTATTGCTCGAGAATACCCTTTGACACGGTTCACCTTTTTTTTGGTATTTGTC
	*  *** ***    **  *******   **           ** * **********  ********* *
celegans	..........(((((.(((((((..((((.(((((((....(( ((......))))...)))))))))))..))))))).))))).      ...........	1.000 -25.80
cbriggsae	...(((((((.(((((.(((((((..((((       ....)))).)))))))))))).)))))))...	1.000 -19.60
cjaponica	(((((((...((((.((((..(((((((..(((.(((((((((..((((...  ..))))..) )))))))))))..)))))))..)))).....))))...)))))))	0.980 -32.00
cbrenneri	....((((((.(((......(((((.(((((((((.((.((((((((..(((((.........))))).)))))))))).))))))))).)))))....))).))))))....	0.999 -32.00
cremanei	((..((((.((((.((((((((....(((((.(((((((..((((.(((((((..(((((.........))))).))))))))).)).))))))).)))))...)))))))).....)))).))))..))	1.000 -40.40

celegans	chromosome:II:14466166:14466261:-1	intergenic ## {SimpF: WRM0610dF04 -1 fosmid,WRM0628cE10 -1 fosmid,WRM0621aF07 -1 fosmid} ## {MIR: cel-mir-234}
cbriggsae	chromosome:chrII:319362:319497:1	Same_strand|Intronic_coding|NM_001111076 ## Opposite_strand|Intronic_coding|NM_012560 ## {MIR: cbr-mir-234}
cjaponica	chromosome:chrUn:86889440:86889545:-1	intergenic
cbrenneri	chromosome:chrUn:129395905:129396017:1	intergenic
cremanei	chromosome:chrUn:46416256:46416385:1	intergenic

cel-lin-4

Cloning frequencies

absolute	CE1
cel-lin-4 5arm	1022
normalized	CE1
cel-lin-4 5arm	0.714

block2315 (miRBase cel-lin-4) [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-lin-4

0.001

no

no

0.52/0.58

18/22/0.99

0.0

0.0

989

0

1

0

15

7

5arm

1

nd

0.15

1

1022

1

na

na

Families

Member of family lin-4 (seed CCCUGAG): cel-lin-4, cel-mir-237

		reads	miRBase family seed
seed	-----------------------------------CCCUGAG---------------------------------------------------------------------------	1011	lin-4
seed	------------------------------------CCUGAGA--------------------------------------------------------------------------	10	novel
seed	---------------------------------UUCCCUG-----------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	----------------------------------TCCCTGAGACCTCAAGTGTG---------------------------------------------------------------	20	989
	-----------------------------------CCCTGAGACCTCAAGTGTGA--------------------------------------------------------------	20	9
	----------------------------------TCCCTGAGACCTCAAGTGT----------------------------------------------------------------	19	9
	----------------------------------TCCCTGAGACCTCAAGTGTGAG-------------------------------------------------------------	22	8
cel-lin-4	----------------------------------TCCCTGAGACCTCAAGTGTGA--------------------------------------------------------------	21	3
	----------------------------------TCCCTGAGACCTCAAGTG-----------------------------------------------------------------	18	2
	--------------------------------GTTCCCTGAGACCTCAAGTGTG---------------------------------------------------------------	22	1
	-----------------------------------CCCTGAGACCTCAAGTGTG---------------------------------------------------------------	19	1
celegans	-----------------ATGCTTCCGGCC--TGTTCCCTGAGACCTCAAGTGTGAGTGTACTATTGATGCTTCAC-ACCTGGGCTCTCCGGGTACCAGGACGGTTTGAGCAGAT---
cbriggsae	----------------------------------TCCCTGAGACCTCAAGTGTGAGCGTTCTGAACATGCTTCAC-GCCTGGGCTCTCCGGGT------------------------
cjaponica	----------TTCAGAATTGCTCACGTCC--TGTTCCCTGAGACCTCAAGTGTGAAAATAT--CTGATATCTCAC-ACCTGGGCTCTCCGGGTACCAGGACG---------------
cbrenneri	GTTGGTTTGATATGATACAGCTCACGGCC--TGCTCCCTGAGACCTCAAGTGTGAGCGTACTGTAGATGCTTCAC-ACCTGGGCTCTCTGGGTACCAGGACGGTTCATTCGAGCAAC
ppacificus	-------CACACCACGACTGCTAGCAAATGGCGTTCCCTGAGACCTCAATTGTGA-TGAGATACGAGTCAGTCACGGTTTGAGCTCTCATGGCA-CGCTATGCTTGTCGATGTTGTG
cremanei	----------------------------------TCCCTGAGACCTCAAGTGTGAGCGCACTGTTGATGCTTCAC-GCCTGGGCTCTCTGGGT------------------------
	*************** *****            *   ****    ** ******  **
	+++++                 ++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++   +++++	F59G1.4 F59G1.4 F59G1.4
celegans	.((((((((.((  ((..(((.((((.((((.(((((((.((((....).)))))))) )).)))).)))).)))...)))).)))...)))))...	1.000 -41.80
cbriggsae	.(((.((((.((((.((((((((((.......))))).))) )).)))).)))).))).	1.000 -26.60
cjaponica	..............(((((  ((..(((.((((.((((.((((((......  ........)))) )).)))).)))).)))...)))))))	0.847 -34.64
cbrenneri	....((((((.((((.........((.((  ((..(((.((((.((((.((((((((((.......))))).))) )).)))).)))).)))...)))).))..))))))))))...	0.936 -42.80
ppacificus	((((.((((((....((((..((((((.((.(((((.((((((((((( (..(((....))).))))))))).))).))))).)).) ))))))))).)))).)).))))	1.000 -46.10
cremanei	.(((.((((.((((.(((((((.(((.......)))))))) )).)))).)))).))).	1.000 -26.50

celegans	chromosome:II:5902220:5902313:1	Same_strand|Intronic_coding|F59G1.4|F59G1.4 ## F59G1.4|protein_coding|F59G1.4|Putative uncharacterized protein (F59G1.4). [Source:UniProtKB/TrEMBL;Acc:Q21051] ## {SimpF: WRM0616dA09 1 fosmid,WRM0638dH01 1 fosmid,CEOP2232 1 Operon,WRM0625aG09 1 fosmid,WRM0624cA08 1 fosmid,WRM0616bH08 1 fosmid,WRM0616bF09 1 fosmid,WRM0610dE11 1 fosmid,WRM0627dG02 1 fosmid,WRM0634bE09 1 fosmid,WRM0613aD08 1 fosmid,WRM063aG02 1 fosmid,WRM0625bH02 1 fosmid} ## {MIR: cel-lin-4}
cbriggsae	chromosome:chrII:8974934:8975067:-1	Same_strand|Intronic_coding|NM_001047975 ## Opposite_strand|Intronic_coding|NM_001011629 ## {MIR: cbr-lin-4}
cjaponica	chromosome:chrUn:4235942:4236028:1	Same_strand|Exonic_coding|NR_000799 ## Same_strand|Intronic_coding|NM_062776
cbrenneri	chromosome:chrUn:49019393:49019506:1	Same_strand|Intronic_coding|NM_062776
ppacificus	chromosome:chrUn:16970262:16970369:1	Opposite_strand|Intronic_coding|NM_138747
cremanei	chromosome:chrUn:41494357:41494490:1	Same_strand|Intronic_coding|NM_062776

cel-mir-40

Cloning frequencies

absolute	CE1
cel-mir-40 3arm	5310
normalized	CE1
cel-mir-40 3arm	3.709

block2593 (miRBase cel-mir-40) [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-40

0.001

no

no

0.50/0.61

18/24/0.90

0.0

0.0

4638

0

1

0

17

6

3arm

1

nd

0.15

1

5310

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------------------------------------------------	5232	miR-35/36/38/39/40/41
seed	----------------------------------------------------------------------------ACCGGGU-----------------------------------------------	43	miR-42
seed	-------------------------------------------------------------------------------GGGUGUA--------------------------------------------	32	novel
seed	------------------------------------------------------------------------UAUCACC---------------------------------------------------	2	novel
seed	-------------------------------------------------------------------------AUCACCG--------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	--------------------------------------------------------------------------TCACCGGGTGTACATCAGCT------------------------------------	20	4638
	--------------------------------------------------------------------------TCACCGGGTGTACATCAGC-------------------------------------	19	473
cel-miR-40	--------------------------------------------------------------------------TCACCGGGTGTACATCAGCTAA----------------------------------	22	64
	---------------------------------------------------------------------------CACCGGGTGTACATCAGCTA-----------------------------------	20	33
	------------------------------------------------------------------------------CGGGTGTACATCAGCTAA----------------------------------	18	32
	--------------------------------------------------------------------------TCACCGGGTGTACATCAGCTAAG---------------------------------	23	25
	--------------------------------------------------------------------------TCACCGGGTGTACATCAGCTA-----------------------------------	21	25
	--------------------------------------------------------------------------TCACCGGGTGTACATCAG--------------------------------------	18	6
	---------------------------------------------------------------------------CACCGGGTGTACATCAGCT------------------------------------	19	5
	---------------------------------------------------------------------------CACCGGGTGTACATCAGC-------------------------------------	18	4
	-----------------------------------------------------------------------CTATCACCGGGTGTACATCAGC-------------------------------------	22	2
	---------------------------------------------------------------------------CACCGGGTGTACATCAGCTAAG---------------------------------	22	1
	--------------------------------------------------------------------------TCACCGGGTGTACATCAGCTAAGG--------------------------------	24	1
	------------------------------------------------------------------------TATCACCGGGTGTACATCAGCT------------------------------------	22	1
celegans	-----------TCCTGT--CCGCACCTCAGTGGATGTATGCCATGATGATAAGATA---TCAGAAA---TCCTATCACCGGGTGTACATCAGCTAAGGTGCGGGTACAGGT-------------------
cbriggsae	ATCTCTGTATCCCCTGC--CCTCACCCCAGCGGGTTTTCATCGCAGTGATATGACGCATTCAAACCATTTCTTATCACCGGGTGTCAATCAGCTAGGGTGTGGGCGCGGGT-----ATCCACAGAGGT--
cbrenneri	CTCCCT-----TCCTGAGGCGGGAACCGAGCTGATTTCTCCACTGGTGATAATTC----CAAGAATAGTGTTTATCACCGGGAGTAAATCTGCTCTGGTCCCGTCTCGGGACATTCAAACAAGGTGAG--
cjaponica	-----------GCCCGC--CAGCACCCCAGCTGATGTTTTCCGTGGTGATACGATAC--ATATTTAGTCCACTATCACCGGGTTTACATCTGCTTGGGTGTATGGCTGGGT-------------------
ppacificus	------------TCTGAGTCCCTTCGATCGCCTCTGATCACTACGATGAAAC-------TGAGATAACGAGTTTTCACCGGGTGAACAGAAGCT--GTTGAAGATATCGGA-------------------
cremanei	-TATCTTCAAACCCTGC--CCGTAACCTAGTTGATGTTCATCGCAGTGATATGACGCA-TCAGTACATTCCTTATCACCGGGTGTACATCAGCTAGGGTGCGGGTTCAGGTTCTTTATCATTGAAAGGTA
	* *   *         *    *           *** *          *          * ********     *   ***  * *         **
	-----           ------  -------------------------------------   -------   ------------------------------------------                   -----	Y62F5A.9 Y62F5A.9 Y62F5A.9
celegans	.(((((  ((((((((.(((.((((((((((.((.(((((.(((.   ......)   )).))))).)))))))))))).))).))))))))..))))).	1.000 -46.20
cbriggsae	((((((((..(((.(((  ((.(((((.(((.((((..((((...((((((.((...............)).))))))..))))..)))).))).))))).))))).))).     ....))))))))	0.997 -50.76
cbrenneri	((((((     ((((((((((((.(((((((.(((((((((...((((((((...    ............)))))))).)))).))))).)))).)))))))))))))))..........))).)))	0.994 -57.96
cjaponica	((((((  ((((((((.(((.(((((...((.((((((((.(((..  .......)))...))))))))))...))))).))).)))))).)))).))))	0.999 -46.60
ppacificus	(((((....(((((((.((.((((.(((((.((.((((((       (.........))))).)).))))))).)))).)).  )))))))...)))))	1.000 -30.60
cremanei	((((((((((((..((  (((((.((((((((((((.((((...((((((((((... ...)).)).....))))))..)))).)))))))))))).)))))))...)))).........)))).))))	0.923 -46.80

celegans	chromosome:II:11538100:11538191:1	Opposite_strand|Intronic_coding|Y62F5A.9|Y62F5A.9 ## Y62F5A.9|protein_coding|Y62F5A.9|Y62F5A.9 [Source:RefSeq_peptide;Acc:NP_741048] ## {SimpF: Y62F5A.D 1 Expression_profile} ## {MIR: cel-mir-40}
cbriggsae	chromosome:chrII:7536133:7536253:1	Opposite_strand|Intronic_coding|NM_177732 ## Same_strand|Intronic_coding|NM_001101718 ## {MIR: cbr-mir-40}
cbrenneri	chromosome:chrUn:47822131:47822249:-1	intergenic
cjaponica	chromosome:chrUn:117591457:117591552:-1	Opposite_strand|Intronic_coding|NM_171042
ppacificus	chromosome:chrUn:171595123:171595212:-1	intergenic ## {Repeats: (GA)n 2 38 -1 class=Simple_repeat} ## {SimpF: trf}
cremanei	chromosome:chrUn:8778471:8778596:-1	Same_strand|Intronic_coding|NM_001011005 ## Opposite_strand|Intronic_coding|NM_171042

cel-mir-67

Cloning frequencies

absolute	CE1
cel-mir-67 3arm	82
normalized	CE1
cel-mir-67 3arm	0.057

block3016 (miRBase cel-mir-67) [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-67

0.001

no

no

0.41/0.45

18/24/0.98

0.0

0.8

75

0

1

0

16

4

3arm

1

nd

0.30

3

82

1

na

na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------CACAACC----------------------------------------------	80	miR-67
seed	--------------------------------------------------------------------------UCACAAC-----------------------------------------------	1	novel
seed	--------------------------------------------------------------------------------CCUCCUA-----------------------------------------	1	novel
		len	cloning frequencies
			CE1
	--------------------------------------------------------------------------TCACAACCTCCTAGAAAGAGTAG-------------------------------	23	45
	--------------------------------------------------------------------------TCACAACCTCCTAGAAAGAGT---------------------------------	21	30
	--------------------------------------------------------------------------TCACAACCTCCTAGAAAGAG----------------------------------	20	2
cel-miR-67	--------------------------------------------------------------------------TCACAACCTCCTAGAAAGAGTAGA------------------------------	24	2
	-------------------------------------------------------------------------ATCACAACCTCCTAGAAAGAGT---------------------------------	22	1
	--------------------------------------------------------------------------TCACAACCTCCTAGAAAG------------------------------------	18	1
	-------------------------------------------------------------------------------ACCTCCTAGAAAGAGTAG-------------------------------	18	1
celegans	---------GATCAAAGAT--TCGTCGATCCGCTCATTCTGCCGGTTGTTATGCTATTATCAGA---TTAAGCATCACAACCTCCTAGAAAGAGTAGATCGATTTTAAAACTT---------------
cbriggsae	------TAAAATTCTAGAT--ATTTCGATCAACTCATTCTGCTGGTTGTTATGCTGACAATTGATGATTAAGCATCACAACCTCCTAGAAAGAGTAGACCGATTCTATCTTATCTTTTTA--------
cjaponica	GAATACGTCGGTCCGAGATAACCGTCGATCCGCTCGTTCTGATGGTTGTTATGCCGATCCGAGA-GAAGAAGCATCACAACCTCCAAGAAAGAGTAGATCGACACCGTATCTCAATTCAAGGTTCTTC
cbrenneri	------------------------------AACTCATTCTGCTGGTTGTTATGCCAAACATTGAAATTTAAGCATCACAACCTCCTAGAAAGAGTG--------------------------------
ppacificus	---TACCGTAGTCCACGGT--TCACC--TCAACGCCCTCTGTGGGTTGTCTGACTCACAGTGAG---ATCAGTCACACAACCTCCTAGAGTGTGTCGA--GGTTCGTGATCTACCGTA----------
cremanei	---------------AGAT--TATTCGATCAACTCGTTCTGCTGGTTGTTATGCTGAAACAGAA---AGAAGCATCACAACCTCCTAGAAAGAGTAGATCGATTCAATCT------------------
	* *  ****  ******    *                **   ********** ***  * **
	+++++         ++++++++++  +++++++++++++++++++++++++++++++++++++++++++   ++++++++++++++++++++++++++++++++++++++++++++++               +++++	EGAP1.3 EGAP1.3 zmp-1
celegans	..........  ..(((((((..(((.(((((..((((((.(((((.........   ...))))).))))))...))))).)))..)))))))..........	1.000 -32.20
cbriggsae	(((((....((((  (..(((.((.((((.(((((..((((((.(((((...............))))).))))))...))))).)))).)).)))...))))).....)))))	0.999 -31.36
cjaponica	((((.....((...((((((...(((((((..(((.((((...((((((.((((...((..... ...)).)))).))))))....)))).)))..)))))))....))))))...))...))))...	0.899 -41.50
cbrenneri	.((((.(((((..((((((.((((.................)))).))))))...))))).)))).	1.000 -19.73
ppacificus	(((.((((..(((((.  ..(((  ((.((((.(((((.((((((((((((((.....)))   .))))....)))))))..))))).)))).))  ))))))))..)))).)))	1.000 -44.80
cremanei	((((  (..((((((.((((.(((((..((((((.(((((.........   ...))))).))))))...))))).)))).))))))...)))))	1.000 -34.70

celegans	chromosome:III:5931300:5931398:-1	Same_strand|Intronic_coding|EGAP1.3|EGAP1.3 ## EGAP1.3|protein_coding|zmp-1|zmp-1 encodes a zinc matrix metalloproteinase that enables anchor cell (AC) invasion during postembryonic vulval development. ZMP-1's proteinase activity has been confirmed in vitro. N-terminus to C-terminus, ZMP-1 is predicted to have a signal sequence, peptidoglycan-binding domain, a central matrix protease domain, a coiled-coil domain, and four hemopexin domains. ZMP-1 is expressed in AC during larval development, vulD and vulE in larvae and adults, and vulA in young adults onward. ZMP-1 is expressed in AC at the time it invades the basement membrane (L3 larval stage), and is localized to puncta often concentrated at the invasive basolateral membrane. ZMP-1::GFP diffuses from AC to utse cytoplasm upon fusion of these cells. ZMP-1 expression in AC requires EGL-43 (perhaps directly), and FOS-1A (indirectly). transcription of zmp-1 in AC, vulA, and vulE is driven by physically distinct sites in the zmp-1 5' flanking sequence. other regulators of ZMP-1 expression in other cell types include COG-1, EGL-38, LIN-11, LIN-29, and NHR-67. zmp-1(cg115) and zmp-1(RNAi) animals have no grossly obvious phenotypes, but null zmp-1(cg115) mutations enhance a subtle defect of AC invasion seen with null cdh-3(pk87) or him-4(rh319) mutations. [Source: WormBase] ## {SimpF: WRM0639dE02 -1 fosmid,WRM0633cF08 -1 fosmid,WRM067aB08 -1 fosmid,WRM0624bE02 -1 fosmid,WRM064bH05 -1 fosmid,WRM062aE09 -1 fosmid} ## {MIR: cel-mir-67}
cbriggsae	chromosome:chrIII:2802674:2802785:1	Same_strand|Intronic_coding|NM_001011629 ## Opposite_strand|Intronic_coding|NM_007496 ## {MIR: cbr-mir-67}
cjaponica	chromosome:chrUn:137728626:137728752:1	Same_strand|Intronic_coding|NM_171138
cbrenneri	chromosome:chrUn:27481488:27481626:-1	Opposite_strand|Intronic_coding|NM_171138
ppacificus	chromosome:chrUn:118105751:118105856:1	Opposite_strand|Intronic_coding|NM_080760
cremanei	chromosome:chrUn:20982884:20982973:1	Same_strand|Intronic_coding|NM_001051693

cel-mir-238

Cloning frequencies

absolute	CE1
cel-mir-238 3arm	1131
normalized	CE1
cel-mir-238 3arm	0.790

block3156 (miRBase cel-mir-238) [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-238

0.001

no

no

0.42/0.50

18/23/0.98

0.0

0.8

1086

0

1

0

16

8

3arm

1

nd

0.18

3

1131

1

na

na

Families

Member of family miR-239a (seed UUGUACU): cel-mir-238, cel-mir-239a

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------UUGUACU-----------------------------------------	1099	miR-239a
seed	---------------------------------------------------------------------------------------UGUACUC----------------------------------------	23	novel
seed	-------------------------------------------------------------------------------------UUUGUAC------------------------------------------	7	novel
seed	------------------------------------------------------------------------------------------ACUCCGA-------------------------------------	1	novel
seed	----------------------------------------------------------------------------------------GUACUCC---------------------------------------	1	novel
		len	cloning frequencies
			CE1
	-------------------------------------------------------------------------------------TTTGTACTCCGATGCCATTC-----------------------------	20	669
	-------------------------------------------------------------------------------------TTTGTACTCCGATGCCATTCAG---------------------------	22	417
	--------------------------------------------------------------------------------------TTGTACTCCGATGCCATTC-----------------------------	19	13
	-------------------------------------------------------------------------------------TTTGTACTCCGATGCCATT------------------------------	19	7
	--------------------------------------------------------------------------------------TTGTACTCCGATGCCATTCAG---------------------------	21	7
cel-miR-238	-------------------------------------------------------------------------------------TTTGTACTCCGATGCCATTCAGA--------------------------	23	5
	------------------------------------------------------------------------------------CTTTGTACTCCGATGCCATTCAG---------------------------	23	4
	------------------------------------------------------------------------------------CTTTGTACTCCGATGCCATTC-----------------------------	21	3
	--------------------------------------------------------------------------------------TTGTACTCCGATGCCATTCAGA--------------------------	22	2
	-------------------------------------------------------------------------------------TTTGTACTCCGATGCCAT-------------------------------	18	1
	---------------------------------------------------------------------------------------TGTACTCCGATGCCATTC-----------------------------	18	1
	--------------------------------------------------------------------------------------TTGTACTCCGATGCCATTCAGAT-------------------------	23	1
	-----------------------------------------------------------------------------------------TACTCCGATGCCATTCAGA--------------------------	19	1
celegans	----------------TCTCCATTG-----ACTGTTTGGATGTTCTCGGACGTTCAAAGCTACATCC--AACAAATT--GGTAGCTTTGTACTCCGATGCCATTCAGATAGTTATGAGCCATG-----------
cbriggsae	CCAAAACTTCTTCTTATCCTCATGAATATGACTGTTTGGGTGTCCTTGGATGTAAAAAGCTATAAATCTGTTAA-----GATTGCTTTGTACTCCGATGCCATCCACATGGTCTGACGACAAGAAGATATGG--
cjaponica	-----------------CCTCA--------ACCGTTTGGACGTGATTGGATGTTCAAAGCCAGCGCCATATCGAAATATGGCAGCTTTGTACTCCGATGCCGTTCAGAGGGT----------------------
cbrenneri	--------GACCAGGTTCCAGG--------ACCGTCTGGATGTGATCGGGTGTAAAAAGCTATCCACGAAG--------AATCGCTTTGTACTCCGATGCCATTCAGAGGGTTTTCCAA---------ATGGTC
cremanei	TCAAAGTCAACGTGGACCACTGTGA----TACCATTTGGGTGGACACGGACGTAAAAAGCTATGCCCGTGGTTAGGTA-TTTAGCTTTGTACTCCGATGCCATTCAAATGGTTGTGTGGTTTTGGATTGTGG--
	*            **  * ***  *     **  **  ***** *                     ****************** * ** *  **
celegans	.(((...((     ((((((((((((...(((((.((.((((((((...((  ((....))  )))))))))).)))))))...)))))))))))))).))).....	1.000 -38.40
cbriggsae	(((.....(((((((.((.(((.......((((((.((((((...(((((.(((.(((((....(((((....)     ))))))))).))))))))...)))))).))))))))).)).)))))))..)))	0.997 -38.61
cjaponica	.....        (((.((((((((..((((((.((.((((((....(((((((....))))))).)))))).))))))))..)))))))).)))	1.000 -38.80
cbrenneri	(((((......(((        (((.((((((((..((((((.(((.(((((..((......)        )...))))).)))))))))..)))))))).))))))....         .)))))	0.998 -40.40
cremanei	.((.((((.....(((((((.....    .(((((((((((((.((((((.(((.(((((((((((........)))) ..))))))).))))))).)))))))))))))))...)))))))..)))).)).	1.000 -50.80

celegans	chromosome:III:8867235:8867332:-1	intergenic ## {SimpF: WRM0637aD12 -1 fosmid,WRM0622dD10 -1 fosmid} ## {MIR: cel-mir-238}
cbriggsae	chromosome:chrIII:13410775:13410901:-1	Opposite_strand|Intronic_coding|NM_001026518 ## Same_strand|Intronic_coding|NM_070558
cjaponica	chromosome:chrUn:4625393:4625479:1	Same_strand|Intronic_coding|NM_080787 ## Opposite_strand|Intronic_coding|NM_078517
cbrenneri	chromosome:chrUn:17763342:17763442:-1	Same_strand|Intronic_coding|NM_209159
cremanei	chromosome:chrUn:98387127:98387253:-1	intergenic

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confident miRBase miRNAs:

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