miR-Intess: classification

confident miRBase miRNAs

miRNAknown_cloningOK_multiarm_DicerOK_randfoldOK (7 loci)

cbr-mir-253

Cloning frequencies
absolute	AF16
cbr-mir-253 5arm	3
cbr-mir-253 3arm	4
normalized	AF16
cbr-mir-253 5arm	0.008
cbr-mir-253 3arm	0.010

sblock60 (miRBase cbr-mir-253) [miRNAknown_cloningOK_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 cbr-mir-253	0.001	no	no	0.43/0.55	18/22/0.62	0.0 nd 0.0	1.0 nd 1.0	3 0 4	0 0 0	1 0 1	0 0 0	21 28 24	4 -3 6	5arm 5arm_loop 3arm	1 1 1	nd nd nd	0.10 0.29 0.09	1 4 1	7	1	1	2

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------------------------UAGUAGG------------------------------------------------------	4	novel
seed	-------------------------------------------UUCUCAC------------------------------------------------------------------------------------------------------------	3	novel
seed	--------------------------------------------------ACAC-CUC----------------------------------------------------------------------------------------------------	0	miR-253
		len	cloning frequencies
			AF16
	------------------------------------------CTTCTCACACAC-CTCACT-------------------------------------------------------------------------------------------------	18	2
	------------------------------------------------------------------------------------------------TTAGTAGGCGTTGTGGGAAGGG----------------------------------------	22	2
	------------------------------------------------------------------------------------------------TTAGTAGGCGTTGTGGGAAGG-----------------------------------------	21	1
	------------------------------------------------------------------------------------------------TTAGTAGGCGTTGTGGGAA-------------------------------------------	19	1
	------------------------------------------CTTCTCACACAC-CTCACTAAC----------------------------------------------------------------------------------------------	21	1
cbr-miR-253	-------------------------------------------------CACAC-CTCACTAACAC----------TAACT-----------------------------------------------------------------------------	21	-
cbriggsae	---------------------AACATTTTTCGAGTTTCAGTCCTTCTCACACAC-CTCACTAACAC----------TAACTACAGATTTCTAGATGTTAGTAGGCGTTGTGGGAAGGGCGGAGATGACGAATACTTTGTGCA----------------
celegans	-------------ATTTATTTAGAATTGTTCCGATCGCCGCTCTTTTCACACAC-CTCACTAACAC----------TGACCACCGATGCATAGATGTTAGTAGGCGTTGTGGGAAGGGCGGCGACAGTGAACGTCGTTTCTC-------ATTATAAAT
cbrenneri	--TTTCCTATTTGCATCCTGAATACTCATTCGATGTTCCACCCTTTTCACACAC-CTGACTAACACAA---------AACCGCAGATGTATTGATGTTAGTAGGCGTTGTGGGAAGGGTGGCGATGATGAGCATATTTTCATGAAAAATCCTAGAAA-
cjaponica	GGTAATCGGATTGTTTTTTGTTGAATATTTCGAGTTGCAGCCATTCTCACACAC-CTCACTATCAC-----------AGACGCGATCGTCTAGATGTTAGTAGGCGTTGTGGGAAGGGCGGCGATGGCGAAAAGTTTG----GAAACATGTGATAACT
ppacificus	---------------------TCCCTCTTTCG---------TCTTCTCACACACTCTAATTTCCATAATTGTTTATTAATTCCAGA---ATGGAAGATGCGGGATGTAGTGGGAAG------------------------------------------
	* * ****** * * ** * * ** * * * ******
	+++++ +++++++++++++++++++++++++++++++++ +++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	NM_001011629
	+++++ +++++++++++++++++++++++++++++++++ +++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	NM_214466
	+++++ +++++++++++++++++++++++++++++++++ +++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	NM_071851
	+++++ +++++++++++++++++++++++++++++++++ +++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	NM_001003090
	----- --------------------------------- ----------- ------------------------------------------------------------------ -----	NM_062593
	+++++ +++++++++++++++++++++++++++++++++ +++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	NM_152229
	+++++ +++++++++++++++++++++++++++++++++ +++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	NM_070565
	+++++ +++++++++++++++++++++++++++++++++ +++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	NM_214509
	----- --------------------------------- ----------- ------------------------------------------------------------------ -----	NM_005334
	+++++ +++++++++++++++++++++++++++++++++ +++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	NM_070407
	+++++ +++++++++++++++++++++++++++++++++ +++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	NM_001031045
	+++++ +++++++++++++++++++++++++++++++++ +++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	NM_001122918
	+++++ +++++++++++++++++++++++++++++++++ +++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	NM_072114
	+++++ +++++++++++++++++++++++++++++++++ +++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	NM_182377
cbriggsae	.(((...((((.(((((.(((((((((((((.( ((.(((((((( ((............))).)))))))))).).)))))))))))).)))))..)))).....)))...	1.000 -41.50
celegans	((((((..((((.(((((...(((((((((((..(((((.( ((.(((((((( ((..((....))..))).)))))))))).)).)))..)))))))))))....)))))....)))). ...))))))	0.998 -48.60
cbrenneri	.............((.((((..((((((....(((((((((((..(((((.( ((.(((((((((( .((.......)).))).)))))))))).)).)))..)))))))).)))))))))......)))).)).............	0.921 -44.20
cjaponica	(((.((((.((.((((((....((((.(((((.(((((.(((.(((((((((.( ((.((((.((. (((((....)))))...)).))))))).)).))))))).))).)))))..))))).))))) ))))))).)))).)))	0.997 -49.60
ppacificus	........... .((((((((((((((((.((((((((((((.....)))))..... ))))))).)).))).))).))))))))	0.970 -20.40

cbriggsae	chromosome:chrV:9138936:9139045:-1	Same_strand\|Intronic_non-coding\|NM_001011629\|Mblk-1 ## Same_strand\|Intronic_coding\|NM_214466\|COLP3alpha ## Opposite_strand\|Intronic_coding\|NM_062593\|ZK622.1 ## Opposite_strand\|Intronic_non-coding\|NM_005334\|HCFC1 ## {Repeats: no} ## {MIR: cbr-mir-253}
celegans	chromosome:chrV:5780482:5780608:-1	Same_strand\|Intronic_coding\|F44E7.5b ## {MIR: cel-mir-253}
cbrenneri	chromosome:chrUn:46020854:46020998:-1	Same_strand\|Intronic_coding\|NM_072114
cjaponica	chromosome:chrUn:55160314:55160455:1	intergenic
ppacificus	chromosome:chrUn:132611440:132611522:1	Same_strand\|Intronic_coding\|NM_001356 ## Opposite_strand\|Intronic_coding\|NM_001047975

cbr-mir-49

Cloning frequencies
absolute	AF16
cbr-mir-49 5arm	3
cbr-mir-49 3arm	13
normalized	AF16
cbr-mir-49 5arm	0.008
cbr-mir-49 3arm	0.034

sblock66 (miRBase cbr-mir-49) [miRNAknown_cloningOK_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 cbr-mir-49	0.001	no	no	0.48/0.58	19/24/0.94	0.0 0.0	0.3 0.0	3 11	0 0	1 1	0 0	19 15	4 7	5arm 3arm	1 1	nd nd	0.13 0.05	1 1	16	1	2	1

Families
Member of family miR-49/83 (seed AGCACCA): cbr-mir-83, cbr-mir-49

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------AGCACCA-------------------------------------------------	13	miR-49/83
seed	-------------------------------------GCAG-UUU------------------------------------------------------------------------------------------	3	novel
		len	cloning frequencies
			AF16
	------------------------------------------------------------------------------AAGCACCACGAGAAGCTGCAG------------------------------------	21	11
	------------------------------------CGCAG-TTTTTTGTAGTGTGCTCCG--------------------------------------------------------------------------	24	2
cbr-miR-49	------------------------------------------------------------------------------AAGCACCACGAGAAGCTGCAGA-----------------------------------	22	1
	------------------------------------CGCAG-TTTTTTGTAGTGTGCTCC---------------------------------------------------------------------------	23	1
	------------------------------------------------------------------------------AAGCACCACGAGAAGCTGC--------------------------------------	19	1
cbriggsae	---------------ACCGAAACCAT--TTGCCATCCGCAG-TTTTTTGTAGTGTGCTCCGCGCCATCTTAGTGCCCGAAGCACCACGAGAAGCTGCAGATGGAA-----------------GTTTTGGTT----
cremanei	-----------------------------------CCGCAG-TTTCTTATGATGTGCTCCGAGCCAAC-ATGTGTTCGAAGCACCACGAGAAGCTGCAG------------------------------------
celegans	---------------------------ACCACCGTCCGCAG-TTTGTTGTGATGTGCTCCAAGCAATC-ATGAGTCTGAAGCACCACGAGAAGCTGCAGATGGAG-----------------GT-----------
cbrenneri	----------TGAGTTTAGAAACAGT--TGGCCGTCCGCGGTTTTTTTGTGTAGTGCTCCGCACCATC-GAGTGTTCGAAGCACCACGAGAAGCTGCAGATGGAG-----------AAGCTTGTTTCCGTTCTTA
cjaponica	GCAAGGTAAGTTTGCTCCGAAGCCGTCACTTCCATCCGCAGTTTTTTTGTGCTGTGCTCCGAACC--C-GAGTGGTCGAAGCACCACGAGAAGCTGCAGATGGGATGAGAGCGGCGATTTGTGTTTTGTTTTGT-
	**** * * * ******* * * * * **********************
	+++++ +++++++++++ +++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++ +++++	NM_001027419
	+++++ +++++++++++ +++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++ +++++	NM_175605
	----- ----------- ------------- --------------------------------------------------------------- --------- -----	NM_181874
	+++++ +++++++++++ +++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++ +++++	NM_006531
	----- ----------- ------------- --------------------------------------------------------------- --------- -----	NM_001052861
	+++++ +++++++++++ +++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++ +++++	NM_001110786
	----- ----------- ------------- --------------------------------------------------------------- --------- -----	NM_000844
	+++++ +++++++++++ +++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++ +++++	NM_001122952
	+++++ +++++++++++ +++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++ +++++	NM_001122953
	+++++ +++++++++++ +++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++ +++++	NM_010905
cbriggsae	((((((((... ...(((((.(((( ((((((((.(.(((((.((.(((......).)).)).)))))))))))))))))).))))).. )))))))).	1.000 -42.90
cremanei	..(((( (((((..((..(((((.(((((((.. .)).))))).)))))))..)))))))))..	1.000 -29.70
celegans	(((.(((((.(((( (((.(((((..(((((.((.((.... ....)).)).)))))))))).))))))).))))).) ))	0.999 -36.40
cbrenneri	((((....(((((((( (..(((((.((((.(((((((((..(((((.(((((.... ..)))..)).)))))))))))))))))).))))).. .)))).)))))....))))	0.998 -40.90
cjaponica	((((..((((..(((......(((((((.(((((((.((((.(((((((((..(((((.((.((( . ....))))).)))))))))))))))))).)))))))))...))))).....))).))))..))))	0.966 -49.70

cbriggsae	chromosome:chrX:3590186:3590281:-1	Same_strand\|Intronic_non-coding\|NM_001027419\|F45G2.2 ## Same_strand\|Intronic_coding\|NM_175605\|IFT88 ## Opposite_strand\|Intronic_coding\|NM_181874\|GRM7 ## Opposite_strand\|Intronic_non-coding\|NM_001052861\|Os02g0222100 ## {Repeats: no} ## {MIR: cbr-mir-49}
cremanei	chromosome:chrUn:14818085:14818220:-1	intergenic
celegans	chromosome:chrX:9989227:9989304:1	intergenic ## {MIR: cel-mir-49}
cbrenneri	chromosome:chrUn:21067423:21067533:-1	intergenic
cjaponica	chromosome:chrUn:761222:761352:1	intergenic

cbr-mir-75

Cloning frequencies
absolute	AF16
cbr-mir-75 5arm	1
cbr-mir-75 3arm	7
normalized	AF16
cbr-mir-75 5arm	0.003
cbr-mir-75 3arm	0.018

sblock68 (miRBase cbr-mir-75) [miRNAknown_cloningOK_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 cbr-mir-75	0.004	no	no	0.45/0.48	20/22/1.00	0.0 0.0	0.0 0.3	1 7	0 0	1 1	0 0	15 15	6 10	5arm 3arm	1 1	nd nd	0.19 0.24	2 2	8	1	1	1

Families
Member of family miR-75/79 (seed UAAAGCU): cbr-mir-75, cbr-mir-79

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------------UAAAGCU------------------------------------------------	7	miR-75/79
seed	---------------------------------------AGUCGGU----------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	------------------------------------------------------------------------------------TTAAAGCTACCAACCGCCTTC-----------------------------------	21	5
	------------------------------------------------------------------------------------TTAAAGCTACCAACCGCCTT------------------------------------	20	2
	--------------------------------------CAGTCGGTTGCAAGCTTCAAT---------------------------------------------------------------------------------	21	1
cbr-miR-75	------------------------------------------------------------------------------------TTAAAGCTACCAACCGCCTTCA----------------------------------	22	-
cbriggsae	-----------------------TGCGAGACCGAATTGCAGTCGGTTGCAAGCTTCAATACA-----GACAATGGTTCTTGATATTAAAGCTACCAACCGCCTTCAAATCGTGCATCGCG--------------------
cremanei	---CTTATTTTTGACCACA----TGCATTGATGAGTTGAAGTCGGTTATAAGCTTAAATACA-----GAACATACCCGTTGTTATTAAAGCTACCAACCGACTTCAGATCATACTTTGCATACTTTTACAAAGGTAAG--
celegans	GGTTTTTTTTTCTACTTTCTTGTTGCTTTGAAGAATTGCAGTCGGTTGCAAGCTTAAATACAAATCCGAA--------TTGTTATTAAAGCTACCAACCGGCTTCAAGTCTGAAAGAGCA--GTTGAAAAAAGGTAAGCC
cbrenneri	--CTCTGCTATTTTTGTTAATCCTGCCTCGACGAGTTGAGGTCGGTTGCAAGCTTCAATACATTTATGAAA-------TTGATATTAAAGCTACCAACCGGCTTCAAATCGAAAAGTGCGTGTTTGTTCAAAGAAGTGAG
cjaponica	------ATTTTGAAACATAAAAGTAGCTGATGGTCTTGCAGTCGGTTGCAAGCTTAAATACA-----GACAA------TAGTTATTAAAGCTACCAACCGGCTCCAAGACTGA--TTGCCTCATTGTCTCACGAT-----
	* * * *** ** ** * * **************** ** * **
	----- --------------------------------------- ----------------------------------------------------- -----	NM_001087279
	----- --------------------------------------- ----------------------------------------------------- -----	NM_072843
	----- --------------------------------------- ----------------------------------------------------- -----	NM_178655
	----- --------------------------------------- ----------------------------------------------------- -----	NM_001034168
	+++++ +++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	NM_001109816
	----- --------------------------------------- ----------------------------------------------------- -----	NM_065440
	+++++ +++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	NM_020367
cbriggsae	.((((...(((.(((.((.((((((..(((((.(((((( (((....)))..)).)))).)))))..)))))).)).))).)))....)))).	1.000 -28.80
cremanei	((((((((((.....( ((((...((((.((((((((((((...(((((.((((.. .(((......)))..)))).)))))...)))))))))))).))))....))))).......))))))))))	0.998 -40.30
celegans	(((((.....(((..((((...(((((((..(((.(((.(((((((((..(((((.(((((((....... )))).))).)))))..))))))))).))).)))...)))))) )..))))..))).)))))	0.942 -39.90
cbrenneri	(((.(((.((((((.(((...(((((...(((.(((((((((((((..(((((.((((((.((....)) .)).)))).)))))..))))))))))))).)))...)).)))...)))..))))))))))))	0.999 -39.30
cjaponica	....(((.(((....((..((...((((((((.(((((((((..(((((.(((((. ..... ..)).))).)))))..))))))))).)))))))). ..))))...))).)))....	0.971 -33.90

cbriggsae	chromosome:chrX:4486715:4486806:-1	Opposite_strand\|Intronic_non-coding\|NM_001087279\|fbxl5 ## Same_strand\|Intronic_coding\|NM_001109816\|MHC ## Same_strand\|Intronic_non-coding\|NM_020367\|PARP11 ## {Repeats: no} ## {MIR: cbr-mir-75}
cremanei	chromosome:chrUn:103833694:103833819:-1	intergenic
celegans	chromosome:chrX:2372432:2372561:1	intergenic ## {MIR: cel-mir-75}
cbrenneri	chromosome:chrUn:1025856:1025986:-1	intergenic
cjaponica	chromosome:chrUn:6839248:6839363:1	intergenic

miRNAknown_cloningOK_randfoldOK (7 loci)

cbr-mir-355

Cloning frequencies
absolute	AF16
cbr-mir-355 5arm	11
normalized	AF16
cbr-mir-355 5arm	0.029

block693 (miRBase cbr-mir-355) [miRNAknown_cloningOK_randfoldOK]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
miRBase cbr-mir-355	0.001	no	no	0.38/0.38	21/21/1.00	0.0	0.0	11	0	1	0	32	3	5arm	1	nd	0.14	2	11	1	na	na

		reads	miRBase family seed
seed	------------------------------------------UUGUUUU-----------------------------------------------------------------------------------------------	11	miR-355
		len	cloning frequencies
			AF16
cbr-miR-355	-----------------------------------------TTTGTTTTAGCCTGAGCTATG----------------------------------------------------------------------------------	21	11
cbriggsae	--CTACTGATTATGATTA-----GTCAGCAATCGGATGG--TTTGTTTTAGCCTGAGCTATGTGTTATT-GCATATTCATAGCTACTTG---CTAAAACA-------TACCAATCGAG-TTGACTGACAT--------------
cremanei	------------------------------------TGG--TTTGTTTTAGCCTGAGCTATGTGTTATT-GCACATACATAGCTTCTTG---TTAAAACA-------TACCA--------------------------------
celegans	-----CTGTTTGAGATTAATAATGTCAAGAATTGAATGG--TTTGTTTTAGCCTGAGCTATGAGTCATCGGAATATGCATAGCTTCTTG---CTAAAACA-------TGCCAATCAATCTTAATTGACGAAGTTTTTGAAACAG
cbrenneri	-----CTTATTCTTCTTCGAAGTCATCAGAAGGGAATGG--TTTGTTTTAGCCTGAGCTATGTGTTATT-GCACATACATAGCTACTTG---TTAAAACA-------TACCAATCCAA-TGAACTGACTGCTATTTGGTAAG--
cjaponica	---------------------AGCCCATCCATTGAATGG--TTTGTTTTAGCCTGAGCTATGGAAAATT-ATAGCCGCATAGCTTCTTG---CTAAAACA-------AACCAGTCGAT--------------------------
ppacificus	GGACAAGAATCGCACTAACGAAGAGAAACAACCACCTGGAATTTGTTTTTGCCGGCATCATTTTTGAAA-TAGCGTAGATGTCGACTTGAGCTTGAGACAGCACCAGAGCCATTTCTTTTTCGTTCAAACGGATGTTC------
	* **** * * ** * ** * **** * * * *
	----- ---------------- ---------------- ---------------------------- ------------------- -------- ----------- ----------- -----	NM_020252
	+++++ ++++++++++++++++ ++++++++++++++++ ++++++++++++++++++++++++++++ +++++++++++++++++++ ++++++++ +++++++++++ +++++++++++ +++++	NM_063458
	+++++ ++++++++++++++++ ++++++++++++++++ ++++++++++++++++++++++++++++ +++++++++++++++++++ ++++++++ +++++++++++ +++++++++++ +++++	NM_059843
	----- ---------------- ---------------- ---------------------------- ------------------- -------- ----------- ----------- -----	NM_183355
	+++++ ++++++++++++++++ ++++++++++++++++ ++++++++++++++++++++++++++++ +++++++++++++++++++ ++++++++ +++++++++++ +++++++++++ +++++	NM_073745
cbriggsae	.........(((.((( ((((((..((((.((( (.(((((((((..(((((((((((.... )))....))))))).)..) )))))))) .)))).))))) )))))))))))	1.000 -42.60
cremanei	.(( (.(((((((((..(((((((((((.... ....)))))))))))...) )))))))) .))).	1.000 -26.60
celegans	((((((.(((..(((..((((((..(((((.((( (.(((((((((..((((((((..((....)).....))))))))...) )))))))) .)))).))))).....))))))..)))))).))))))	0.999 -42.40
cbrenneri	((((((.........((((((((....(((.((( (.(((((((((...((((((((((.... ....))))))))))....) )))))))) .)))).))).. )))..))))).......))))))	0.953 -40.29
cjaponica	.........(((((.((( (((((((((((..((((((((....... .......))))))))...) )))))))) ))))).)))))	0.999 -32.44
ppacificus	(((((....(((....((((((((((((.......((((...(((((((.(((((((((.......... .......)))))))......))..)))))))..)))).....)))))))).))))....))).)))))	0.912 -28.13

cbriggsae	chromosome:chrII:6505548:6505656:-1	Opposite_strand\|Intronic_non-coding\|NM_020252\|Nrxn1 ## Same_strand\|Intronic_coding\|NM_063458\|T01B7.8 ## {Repeats: no} ## {MIR: cbr-mir-355}
cremanei	chromosome:chrUn:9664785:9664847:1	Opposite_strand\|Intronic_coding\|NM_066413 ## Same_strand\|Intronic_coding\|NM_062542
celegans	chromosome:chrII:11833447:11833573:-1	intergenic ## {MIR: cel-mir-355}
cbrenneri	chromosome:chrUn:154072129:154072251:-1	intergenic
cjaponica	chromosome:chrUn:90387998:90388081:-1	intergenic
ppacificus	chromosome:chrUn:46891746:46891882:1	intergenic

cbr-mir-39

Cloning frequencies
absolute	AF16
cbr-mir-39 3arm	17
normalized	AF16
cbr-mir-39 3arm	0.044

block966 (miRBase cbr-mir-39) [miRNAknown_cloningOK_randfoldOK]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
miRBase cbr-mir-39	0.001	no	no	0.50/0.50	18/22/0.94	0.0	0.0	16	0	1	0	19	6	3arm	1	nd	0.23	2	17	1	na	na

Clusters
Located in cluster 3: cbr-mir-36, cbr-mir-38, cbr-mir-39, cbr-mir-40, block969_novel, cel-mir-35, cbr-mir-41, cbr-mir-35

Families
Member of family miR-35/36/38/39/40/41 (seed CACCGGG): cel-mir-35, cel-mir-35, cel-mir-36, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cbr-mir-39, cbr-mir-35, cbr-mir-36, cbr-mir-40, cbr-mir-41, cbr-mir-38, block969_novel, block5129_cand

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------CACCGGG---------------------------------------------------	16	miR-35/36/38/39/40/41
seed	---------------------------------------------------------------------------------------------GGGUGAA-----------------------------------------------	1	novel
		len	cloning frequencies
			AF16
cbr-miR-39	----------------------------------------------------------------------------------------TCACCGGGTGAAAAACGG--TTAG-----------------------------------	22	16
	--------------------------------------------------------------------------------------------CGGGTGAAAAACGG--TTAG-----------------------------------	18	1
cbriggsae	------------------CAGAGATGC-----AGGGAGCCCAACTGGTTC-TCACTGCAGTGAT------AAGCTATGTTACAGTCTATCACCGGGTGAAAAACGG--TTAGGCTCTTTA---------------AGCATCTCTGT-
cremanei	-------------TCGGTCGGA----------TCGGACCTACACTGGTTT-TCGCTGCGGTGATACTTCGAGA--ATGA------TTATCACCGGGTGAAAATCAGG-GCAGGTCC-------------------GATTCCACCGA-
celegans	CTACTGATTATTGAATTCCTGATATAC-----CGAGAGCCCAGCTGATT--TCGTCTTGGTAATA-----AGCTCGTCATTGAGATTATCACCGGGTGTAAATCAG--CTTGGCTCT------------------GGTGTCTCCGAA
cbrenneri	GTTCATATTTTTCATATTCAGGGGTGGA----TCGGGCCTGTGCTGATTT-TTGCCGCTGTGATATTTCTAAGCCATGA------TTATCACCGGGCGAAAATTTGGCACAGGCC--------------------TCGTCCGCCCT-
cjaponica	-----TGCAGTGGTCCCTCGGGGCAGAAGAGCCAGGACCTACATCAGTTTCTTTCCGCGGTAATAAA--TAATACATTA------TTATCACCGGGAGAAAAACTGGAGTAGGACCTGCGACTCGACTCGACCTTTATTCCGCTGTA
ppacificus	-----------------TCTGAGTCCC-----TTCGATCGCCTCTGA----TCACTACGATGAAACT--GAGATAACGA-----GTTTTCACCGGGTGAACAGAAGCTGTTG-----------------------AAGATATCGGA-
	* * * * * * * * * ******** * * * * * *
	----- --------- ------------------ ------------- ------------------------------------ ------------ ----------- -----	NM_177732
	----- --------- ------------------ ------------- ------------------------------------ ------------ ----------- -----	NM_214509
	----- --------- ------------------ ------------- ------------------------------------ ------------ ----------- -----	NM_207243
	----- --------- ------------------ ------------- ------------------------------------ ------------ ----------- -----	NM_207243
	----- --------- ------------------ ------------- ------------------------------------ ------------ ----------- -----	NM_207243
	----- --------- ------------------ ------------- ------------------------------------ ------------ ----------- -----	NM_207243
	----- --------- ------------------ ------------- ------------------------------------ ------------ ----------- -----	NM_207243
	----- --------- ------------------ ------------- ------------------------------------ ------------ ----------- -----	NM_207243
	----- --------- ------------------ ------------- ------------------------------------ ------------ ----------- -----	NM_207243
	----- --------- ------------------ ------------- ------------------------------------ ------------ ----------- -----	NM_207243
	----- --------- ------------------ ------------- ------------------------------------ ------------ ----------- -----	NM_207243
	----- --------- ------------------ ------------- ------------------------------------ ------------ ----------- -----	NM_207243
	----- --------- ------------------ ------------- ------------------------------------ ------------ ----------- -----	NM_207243
	----- --------- ------------------ ------------- ------------------------------------ ------------ ----------- -----	NM_001030843
	+++++ +++++++++ ++++++++++++++++++ +++++++++++++ ++++++++++++++++++++++++++++++++++++ ++++++++++++ +++++++++++ +++++	NM_001101718
	+++++ +++++++++ ++++++++++++++++++ +++++++++++++ ++++++++++++++++++++++++++++++++++++ ++++++++++++ +++++++++++ +++++	NM_001011629
	----- --------- ------------------ ------------- ------------------------------------ ------------ ----------- -----	NM_207243
	----- --------- ------------------ ------------- ------------------------------------ ------------ ----------- -----	NM_207243
	----- --------- ------------------ ------------- ------------------------------------ ------------ ----------- -----	NM_207243
	----- --------- ------------------ ------------- ------------------------------------ ------------ ----------- -----	NM_207243
	----- --------- ------------------ ------------- ------------------------------------ ------------ ----------- -----	NM_207243
	----- --------- ------------------ ------------- ------------------------------------ ------------ ----------- -----	NM_171042
cbriggsae	((((((((( ((((((((.(((((.((. (((((...((((( (..((.......))..))))))..))))).)).))) )).)))))))). .))))))))).	1.000 -45.60
cremanei	(((((.((( ((((((((...((((((( (((((.((((((((..((.... ..)) .)))))))))))))))))))). ..)))))) ))))).)))))	1.000 -55.10
celegans	...............(((..((.(((( (.((((((.(((((((( (((.((((((.((( (.((((....)))).)))).)))))))).))))))) )).)))))) ))))).)).)))	0.957 -45.10
cbrenneri	....................(((((((( (.(((((((((((((((( (((((...((((((..((........)) .))))))..)))))))))).)))))))))) ).)))))))))	0.944 -57.20
cjaponica	((((((((......((((..((.(((.((((.(((((..((((((.(((((.((((.((.(( (((....))) )))).))))))))).))))))..))))).))))...)))...))..))))....))))))))	0.964 -52.50
ppacificus	(((((....( ((((((.((.((((. (((((.((.((((((( .........) )))).)).))))))).)))).)).)))) )))...)))))	1.000 -30.60

cbriggsae	chromosome:chrII:7536042:7536140:1	Opposite_strand\|Intronic_non-coding\|NM_177732\|Slc35d1 ## Opposite_strand\|Intronic_coding\|NM_214509\|COLP1alpha ## Same_strand\|Intronic_coding\|NM_001101718\|LOC100009540 ## Same_strand\|Intronic_non-coding\|NM_001011629\|Mblk-1 ## {Repeats: no} ## {MIR: cbr-mir-39}
cremanei	chromosome:chrUn:26787656:26787749:-1	intergenic
celegans	chromosome:chrII:11537983:11538097:1	Opposite_strand\|Intronic_coding\|Y62F5A.9 ## {MIR: cel-mir-39}
cbrenneri	chromosome:chrUn:47821556:47821670:-1	intergenic ## {SimpF: trf}
cjaponica	chromosome:chrUn:117591701:117591834:-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}

cbr-mir-67

Cloning frequencies
absolute	AF16
cbr-mir-67 3arm	18
normalized	AF16
cbr-mir-67 3arm	0.047

block1647 (miRBase cbr-mir-67) [miRNAknown_cloningOK_randfoldOK]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
miRBase cbr-mir-67	0.002	no	no	0.42/0.45	20/24/1.00	0.0	0.0	16	0	1	0	14	4	3arm	1	nd	0.26	3	18	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------CACAACC----------------------------------------------	16	miR-67
seed	--------------------------------------------------------------------------UCACAAC-----------------------------------------------	1	novel
seed	------------------------------------------------------------------------------AACCUCC-------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	--------------------------------------------------------------------------TCACAACCTCCTAGAAAGAGTAG-------------------------------	23	16
	-----------------------------------------------------------------------------CAACCTCCTAGAAAGAGTAG-------------------------------	20	1
	-------------------------------------------------------------------------ATCACAACCTCCTAGAAAGAGTAG-------------------------------	24	1
cbr-miR-67	--------------------------------------------------------------------------TCACAACCTCCTAGAAAGAGTAGA------------------------------	24	-
cbriggsae	--------------TAGAT--ATTTCGATCAACTCATTCTGCTGGTTGTTATGCTGACAATTGATGATTAAGCATCACAACCTCCTAGAAAGAGTAGACCGAT------TCTATCTT-----------
cremanei	----------------GAT--TATTCGATCAACTCGTTCTGCTGGTTGTTATGCTGAAACAGAA---AGAAGCATCACAACCTCCTAGAAAGAGTAGATCGATTC-----------------------
celegans	--------CGATCAAAGAT--TCGTCGATCCGCTCATTCTGCCGGTTGTTATGCTATTATCAGA---TTAAGCATCACAACCTCCTAGAAAGAGTAGATCGAT------TTTAAAACTTTGAATTTCG
cbrenneri	------------------------------AACTCATTCTGCTGGTTGTTATGCCAAACATTGAAATTTAAGCATCACAACCTCCTAGAAAGAGTG--------------------------------
cjaponica	GAATACGTCGGTCCGAGATAACCGTCGATCCGCTCGTTCTGATGGTTGTTATGCCGATCCGAGA-GAAGAAGCATCACAACCTCCAAGAAAGAGTAGATCGACACCGTATCTCAATTCAAGGTTCTTC
ppacificus	---TACCGTAGTCCACGGT--TCACC--TCAACGCCCTCTGTGGGTTGTCTGACTCACAGTGAG---ATCAGTCACACAACCTCCTAGAGTGTGTCGA--GGTTCGTGATCTACCGTA----------
	* * ** **** * ****** * * **
	+++++ +++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++ +++++	NM_001011629
	+++++ +++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++ +++++	NM_001022613
	----- ----- ---------------------------------------------------------------------------------- -------- -----	NM_007496
	----- ----- ---------------------------------------------------------------------------------- -------- -----	NM_013743
	----- ----- ---------------------------------------------------------------------------------- -------- -----	NM_065840
	+++++ +++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++ +++++	NM_080331
	----- ----- ---------------------------------------------------------------------------------- -------- -----	NM_009573
	+++++ +++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++ +++++	NM_171138
cbriggsae	.(((( (..(((.((.((((.(((((..((((((.(((((...............))))).))))))...))))).)))).)).))). ..))))).	1.000 -30.56
cremanei	... ...((((((.((((.(((((..((((((.(((((......... ...))))).))))))...))))).)))).))))))...	1.000 -32.00
celegans	...((((((.. ..(((((((..(((.(((((..((((((.(((((......... ...))))).))))))...))))).)))..))))))) .......))))))......	0.999 -36.50
cbrenneri	.((((.(((((..((((((.((((.................)))).))))))...))))).)))).	1.000 -19.73
cjaponica	((((.....((...((((((...(((((((..(((.((((...((((((.((((...((..... ...)).)))).))))))....)))).)))..)))))))....))))))...))...))))...	0.899 -41.50
ppacificus	(((.((((..(((((. ..((( ((.((((.(((((.((((((((((((((.....))) .))))....)))))))..))))).)))).)) ))))))))..)))).)))	1.000 -44.80

cbriggsae	chromosome:chrIII:2802682:2802776:1	Same_strand\|Intronic_non-coding\|NM_001011629\|Mblk-1 ## Same_strand\|Intronic_coding\|NM_001022613\|SPBC215.13 ## Opposite_strand\|Intronic_non-coding\|NM_007496\|Zfhx3 ## Opposite_strand\|Intronic_coding\|NM_065840\|SR-famA ## {Repeats: no} ## {MIR: cbr-mir-67}
cremanei	chromosome:chrUn:20982885:20982968:1	Same_strand\|Intronic_coding\|NM_001051693
celegans	chromosome:chrIII:5931291:5931399:-1	Same_strand\|Intronic_coding\|EGAP1.3 ## {MIR: cel-mir-67}
cbrenneri	chromosome:chrUn:27481490:27481624:-1	Opposite_strand\|Intronic_coding\|NM_171138
cjaponica	chromosome:chrUn:137728626:137728752:1	Same_strand\|Intronic_coding\|NM_171138
ppacificus	chromosome:chrUn:118105751:118105856:1	Opposite_strand\|Intronic_coding\|NM_080760

cbr-mir-790

Cloning frequencies
absolute	AF16
cbr-mir-790 5arm	6
normalized	AF16
cbr-mir-790 5arm	0.016

block2187 (miRBase cbr-mir-790-1) [miRNAknown_cloningOK_randfoldOK]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
miRBase cbr-mir-790-1	0.002	no	no	0.65/0.68	20/22/1.00	0.0	0.8	5	0	1	0	16	3	5arm	2	nd	0.14	1	6	1	na	na

Clusters
Located in cluster 5: cbr-mir-790, cbr-mir-790

Families
Member of family miR-790/791 (seed UUGGCAC): cbr-mir-790, cbr-mir-790

		reads	miRBase family seed
seed	-----------------UUGGCA---C----------------------------------------------------------------------------	6	miR-790/791
		len	cloning frequencies
			AF16
cbr-miR-790	----------------CTTGGCA---CTCGCGAACACCGCG--------------------------------------------------------------	22	3
	----------------CTTGGCA---CTCGCGAACACCG----------------------------------------------------------------	20	2
	----------------CTTGGCA---CTCGCGAACACCGC---------------------------------------------------------------	21	1
cbriggsae	AAGTCCCTTCCGATTGCTTGGCA---CTCGCGAACACCGCGATCACTTCCAATATCGATCCGCGGAGTTAGCCA-GTGTCAACCAAATGGATGTTTGAGACTT
cremanei	----------------CTTGGCA---CTCGCGAACACCGCGATCTTATCAGATA---AATCGCGGAGTTAGCCG-GTGGCAAC--------------------
celegans	--GTCCCTTCAGCCGGCTTGGCA---CTCGCGAACACCGCGATTTC----ACTTATAACTCGCGGCGTTAGCTCTGTGTCAAACCGGC---------------
cbrenneri	----------------CTTGGCA---CTCGCGAACACCGCGATCTAACTGTATA---AATCGCGGCGTTAGCTC-GTGGCAAA--------------------
cjaponica	----------------CTTGGCA---CTCGCGAACACCGCGCTTCACAACTAAAAGATGTCGCGGCGTTGGCTTGGTGCCAAA--------------------
ppacificus	----------------CTTGGCACAGCTAAAAAATACCG-ATTCTCTGAAAATTTGAAATCTGGGGTTCTTAAGGGTGCTGATG-------------------
	***** ** * * ** * *** *
	++++++++++++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++	NM_066961
cbriggsae	(((((.(.((((.(((.(((((( ((.((.(((.((((((((............))).))))).))).)).) ))))))).))).)))).....).)))))	1.000 -36.50
cremanei	.(((.(( ((.((.(((.(((((((.((((...))) )))))))).))).)).) ))).))).	1.000 -24.70
celegans	.........(((((.(((((( (..((.(((.((((((.... .........)))))).))).))...))))))).)))))	1.000 -34.42
cbrenneri	.(((.(( (..((.(((.(((((((.((......)) .))))))).))).)).. ))).))).	1.000 -23.70
cjaponica	.(((((( ((.((.(((.(((((..((..........))...))))).))).))..)))))))).	1.000 -28.00
ppacificus	.(((((((..((.((.((..((( (((.((.........)))))).))..)).)).)).)))))))..	0.999 -12.60

cbriggsae	chromosome:chrIV:8548022:8548120:-1	Same_strand\|Intronic_non-coding\|NM_066961\|W09D10.4 ## {Repeats: no} ## {MIR: cbr-mir-790-1}
cremanei	chromosome:chrUn:101798598:101798736:1	intergenic
celegans	chromosome:chrIV:5566400:5566478:1	intergenic ## {MIR: cel-mir-790}
cbrenneri	chromosome:chrUn:156782538:156782676:1	intergenic
cjaponica	chromosome:chrUn:34737964:34738102:1	intergenic
ppacificus	chromosome:chrUn:159875557:159875695:1	Same_strand\|Intronic_coding\|NM_066967

block2188 (miRBase cbr-mir-790-2) [miRNAknown_cloningOK_randfoldOK]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
miRBase cbr-mir-790-2	0.007	no	no	0.65/0.68	20/22/1.00	0.0	0.8	5	0	1	0	5	2	5arm	2	nd	0.14	1	6	1	na	na

Clusters
Located in cluster 5: cbr-mir-790, cbr-mir-790

Families
Member of family miR-790/791 (seed UUGGCAC): cbr-mir-790, cbr-mir-790

		reads	miRBase family seed
seed	-------------------UUGGCAC-------------------------------------------------------------------------------	6	miR-790/791
		len	cloning frequencies
			AF16
cbr-miR-790	------------------CTTGGCACTCGCGAACACCG---CG--------------------------------------------------------------	22	3
	------------------CTTGGCACTCGCGAACACCG-------------------------------------------------------------------	20	2
	------------------CTTGGCACTCGCGAACACCG---C---------------------------------------------------------------	21	1
cbriggsae	-------------GACTGCTTGGCACTCGCGAACACCG---CGGTCGAA----GTTAC---TCGCGGAGTTAGCCA-GTGTCAACCAGATG--------------
cremanei	------------------CTTGGCACTCGCGAACACCG---CGATCTTATCAGATAAA---TCGCGGAGTTAGCCG-GTGGCAACCAGG----------------
celegans	-------------GCCGGCTTGGCACTCGCGAACACCG---CGATTTCACT-TATAAC---TCGCGGCGTTAGCTCTGTGTCAAACCGGC---------------
cbrenneri	AAGGTCCCGTTCTACCTGCTTGGCACTCGCGAACACCG---CGATCTAACTGTATAAA---TCGCGGCGTTAGCTC-GTGGCAAACAGGTGATGCTGAAGACTTT
cjaponica	TCCAGTCCCTCCAAACTGCTTGGCACTCGCGAACACCG---CGCTTCACAACTAAAAGATGTCGCGGCGTTGGCTTGGTGCCAAACAGGATGAGAGTTTGAGA--
ppacificus	------------------CTTGGCACAGCTCAAAATCGATTCTCTGAAGCTATGTGAA---TCGGGGTTCTCGAGG-GTGCTGAT--------------------
	****** * ** * * * * * * *** *
	+++++ +++++++++++++++++++++++++ ++++++++ +++++ +++++++++++++++ ++++++++++++++ +++++	NM_066961
cbriggsae	..(((.((((((((.((.(((.((( ((((.... ...)) .))))).))).)).) ))))))).)))...	1.000 -29.30
cremanei	.(((.((((.((.(((.((( ((((.((((...))))) )))))).))).)).) ))).))).....	1.000 -24.70
celegans	(((((.(((((((..((.(((.((( (((....... ...... )))))).))).))...))))))).)))))	1.000 -34.22
cbrenneri	((((((..((..((((((.(((.(((..((.(((.((( ((((.((......)).) )))))).))).)).. ))).))).))))))..))....))))))	1.000 -38.30
cjaponica	..(((...(((((..(((.((((((((.((.(((.((( ((..((..........))...))))).))).))..)))))))).)))..)).))).)))...	1.000 -38.10
ppacificus	.(((((((..(((((..(((((((.............))) ))))..))...))). ))))))).	0.994 -17.52

cbriggsae	chromosome:chrIV:8548664:8548730:-1	Same_strand\|Intronic_non-coding\|NM_066961\|W09D10.4 ## {Repeats: no} ## {MIR: cbr-mir-790-2}
cremanei	chromosome:chrUn:101798609:101798715:1	intergenic
celegans	chromosome:chrIV:5566409:5566478:1	intergenic ## {MIR: cel-mir-790}
cbrenneri	chromosome:chrUn:156782556:156782653:1	intergenic
cjaponica	chromosome:chrUn:34737982:34738081:1	intergenic
ppacificus	chromosome:chrUn:90815662:90815768:-1	Opposite_strand\|Intronic_coding\|NM_062686

cbr-mir-233

Cloning frequencies
absolute	AF16
cbr-mir-233 3arm	16
normalized	AF16
cbr-mir-233 3arm	0.042

block4811 (miRBase cbr-mir-233) [miRNAknown_cloningOK_randfoldOK]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
miRBase cbr-mir-233	0.001	no	no	0.53/0.59	19/23/0.65	0.0	1.1	15	0	1	0	16	5	3arm	1	nd	0.14	1	16	1	na	na

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

		reads	miRBase family seed
seed	------------------------------------------------------------UGAGCAA--------------------------------	16	miR-233/356/87
		len	cloning frequencies
			AF16
	-----------------------------------------------------------TTGAGCAATGCGCATGTGC---------------------	19	6
	-----------------------------------------------------------TTGAGCAATGCGCATGTGCG--------------------	20	5
	-----------------------------------------------------------TTGAGCAATGCGCATGTGCGGG------------------	22	4
	-----------------------------------------------------------TTGAGCAATGCGCATGTGCGG-------------------	21	1
cbr-miR-233	-----------------------------------------------------------TTGAGCAATGCGCATGTGCGGGA-----------------	23	-
cbriggsae	AAGCATTTTTCTGTCCCGCGCATCCCTTTGTTCCAATATTCAAACCAGTAGAAAGATTATTGAGCAATGCGCATGTGCGGGACAGATTGAATAGCTG--
cremanei	--------------CCCGCTCATCCTGTTGTTCCAATATTCCAACAGCCC-AGTGATTATTGAGCAATGCGCATGTGCGGG------------------
celegans	---CATCTTTCTGTCTCGCCCATCCCGTTGCTCCAATATTCTAACAA-CA-AGTGATTATTGAGCAATGCGCATGTGCGGGATAGACTG-ATG------
cbrenneri	--GCGTCTTTCTGTCTCGCCCATCCCGTTGTTCCAATATTCCAACAA-CA-AGTGATTATTGAGCAATGCGCATGTGCGGGACAGACTG-ATGTCTGCT
cjaponica	CAGCGACCTTCCGTCTCGCCCATCCCTTTGCTCCA------TATCGA-TT-CATGATTATTGAGCAATGCGCATGTGCGGGACGGATTG-AGCGCTG--
	* * * * **** * * ***************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	NM_001011629
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	NM_018658
	------------------------------------------------------------------------------------------------------ -----	NM_009152
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	NM_134696
	------------------------------------------------------------------------------------------------------ -----	NM_178014
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	NM_170742
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	NM_170741
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	NM_077618
cbriggsae	.(((((((.((((((((((((((.((.((((((.((((.((.............)).)))))))))).).).))))))))))))))..)))).))).	1.000 -38.92
cremanei	(((((.(((..(((((((.(((((.((..((..... .)))).))))))))))))...))).)))))	0.994 -19.60
celegans	((((..((((((((((.(((..(((((((.(((((.((...... .. ...)).))))))))))))...))).))))))))))..) )))	1.000 -35.00
cbrenneri	(((((..((((((((((.(((..(((((((.(((((.((..((.. .. .)))).))))))))))))...))).))))))))))..) )))).....	1.000 -35.60
cjaponica	(((((....((((((((((.(((....((((((.( (((((. .. ..)))).)).)))))).....))).))))))))))... ..)))))	1.000 -36.90

cbriggsae	chromosome:chrX:1703782:1703878:1	Same_strand\|Intronic_non-coding\|NM_001011629\|Mblk-1 ## Opposite_strand\|Intronic_non-coding\|NM_009152\|Sema3a ## Same_strand\|Intronic_coding\|NM_134696\|CG2839 ## {Repeats: no} ## {MIR: cbr-mir-233}
cremanei	chromosome:chrUn:72771485:72771621:1	Same_strand\|Intronic_coding\|NM_077618 ## Opposite_strand\|Intronic_coding\|NM_009930
celegans	chromosome:chrX:12078515:12078601:-1	Same_strand\|Intronic_coding\|W03G11.4.2 ## {MIR: cel-mir-233}
cbrenneri	chromosome:chrUn:19160377:19160470:1	Same_strand\|Intronic_coding\|NM_001030940 ## Opposite_strand\|Intronic_coding\|NM_007735
cjaponica	chromosome:chrUn:7867828:7867915:1	Same_strand\|Intronic_coding\|NM_001071380 ## Opposite_strand\|Intronic_coding\|NM_001093204

cbr-mir-786

Cloning frequencies
absolute	AF16
cbr-mir-786 3arm	21
normalized	AF16
cbr-mir-786 3arm	0.055

block5032 (miRBase cbr-mir-786) [miRNAknown_cloningOK_randfoldOK]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
miRBase cbr-mir-786	0.001	no	no	0.43/0.45	22/23/1.00	0.0	0.0	19	0	1	0	14	5	3arm	1	nd	0.13	2	21	1	na	na

Clusters
Located in cluster 11: cbr-mir-240, cbr-mir-786

		reads	miRBase family seed
seed	------------------------------------------------------------------AAUGCCC---------------------------------------	21	miR-786
		len	cloning frequencies
			AF16
cbr-miR-786	-----------------------------------------------------------------TAATGCCCTGTACGAGATTTGGT------------------------	23	19
	-----------------------------------------------------------------TAATGCCCTGTACGAGATTTGG-------------------------	22	2
cbriggsae	----------GGGACCCTTCCCAACAAAATCTCAAATAGTGGCATTTACACAAGCAATGGTA-TGTAATGCCCTGTACGAGATTTGGTTGGTGAGAAGTCTC----------
cremanei	-------------------------AGAGTCTCGGACAG-GGCATTTACATACAAGATAAATTTGTAATGCCCTTGCTGAGATTCC--------------------------
celegans	AGTAAGTAAAGGGATAGTTCCCGATCGAATATCAGTTGG-GGTATTTACA-AAAAGACAAAATTGTAATGCCCTGAATGATGTTCAATCGGTGATGAATCTCATTTTTTATT
	* * ** * ***** * * ********* **
	----- ---------------------------------------------------- --------------------------------------- -----	NM_003107
	+++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++ +++++	NM_177736
	+++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++ +++++	NM_133381
	+++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++ +++++	NM_001110160
cbriggsae	(((((.((..(((((.(((((((..((((.((((((...(((.((....)). )))))))))))))..))))))).)))))..))..)))))	1.000 -35.20
cremanei	.(((((((((..(( ((((.(((((.............)))))))))))..))))))))).	1.000 -26.42
celegans	((((((.((.(((((.((..(((((.((((((((.(((( ((((.((((( (..........)))))))))))))).)))))))).)))))..))..))))).)).))))))	1.000 -38.70

cbriggsae	chromosome:chrX:13573558:13573648:1	Opposite_strand\|Intronic_non-coding\|NM_003107\|SOX4 ## Same_strand\|Intronic_non-coding\|NM_177736\|Lrrc61 ## {Repeats: no} ## {MIR: cbr-mir-786}
cremanei	chromosome:chrUn:181380:181510:-1	intergenic
celegans	chromosome:chrX:7882686:7882795:1	intergenic ## {MIR: cel-mir-786}