miR-Intess: classification

candidate homolog loci of miRBase miRNAs

miRBaseHomolog_cloningOK_Multihit_randfoldOK (13 loci)

block5125 (miRBaseHomolog cel-mir-35) [miRBaseHomolog_cloningOK_Multihit_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
miRBaseHomolog cel-mir-35	0.001	no	no	0.52/0.52	21/23/1.00	0.0	0.6	7	0	1	0	22	6	3arm	15	nd	0.09	2	7	1	na	na

Clusters
Located in cluster 13: cel-mir-35, block5113_cand, 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

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---------------------------------------------------	7	miR-35/36/38/39/40/41
		len	cloning frequencies
			AF16
	----------------------------------------------------------------------------------TCACCGGGTGAAAA-CTGGTAG-------------------------------------	21	5
	----------------------------------------------------------------------------------TCACCGGGTGAAAA-CTGGTAGAG-----------------------------------	23	2
cbriggsae	-------------CCGAAGGTCTGGG-----TCGAGCCTCCGCTGGTTTTTTACCGCGGTGATATTCCAAATAAAATGGTTATCACCGGGTGAAAA-CTGGTAGAGG--------TCCGATCCAGTCGTACCATCG-----
cremanei	------------------TGGTCGGA-----TCGGCCATTCACTGG-TTCTCGCCGCGGTCATATTTCAAAT---ATGATTATCACCGGGTGAAAA-TCAGAGCAGG--------GCCGATCCCACCG-------------
celegans	TTCCCAACTATTATTCTCGGATCAGA-----TCGAGCCATTGCTGG-TTTCTTCCACAGTGGTACTTTCCAT--TAGAACTATCACCGGGTGGAAA-CTAGCAGTGG--------CTCGATCTTTTCC-------------
cbrenneri	--------------TTCAGGGGTGGA-----TCGGGCCTGTGCTGA-TTTTTGCCGCTGTGATATTTCTAAG-CCATGATTATCACCGGGCGAAAATTTGGCACAGG--------CCTCGTCCGCCCTTCCTGAG------
cjaponica	----TGCAGTGGTCCCTCGGGGCAGAAGAGCCAGGACCTACATCAGTTTCTTTCCGCGGTAATAAATAATAC---ATTATTATCACCGGGAGAAAAACTGGAGTAGGACCTGCGACTCGACTCGACCTTTATTCCGCTGTA
ppacificus	------------------GGGATGCA--------------------TATTCTAACCCGGTGACTCAATAAAC--AATGA--GTCACCGGG-------TTAGAATATG--------TCCA----------------------
	* * * * ** * * ******** * *
cbriggsae	.(((.(((((((( (((..((((..((((.((((((((.((((((((..(((.......))).)))))))))))))))) ))))..)))) ..))))))))....))).)))	1.000 -57.20
cremanei	.(((.((( ((((((.....(((( ((.(((((.((((.(((..(((... .))).))).))))))))).)) )))).....) )))))))).))).	1.000 -46.80
celegans	..................(((..((( ((((((((((((((( ((((..((...((((((.(((.... ..))).))))))..))..)))) )))))))))) ))))))))..)))	0.989 -54.00
cbrenneri	.((((((((((( (.((((((((((((( ((((((((...((((((..((.... ....)).))))))..)))))))))).)))))))) ))).))))))))...)))).	1.000 -59.20
cjaponica	((((((((......((((..((.(((.((((.(((((..((((((.(((((.((((.((.(((((... .))))))).))))))))).))))))..))))).))))...)))...))..))))....))))))))	0.964 -52.50
ppacificus	.((..((( ((((((((((((((((((((...... ..))) ))))))))) )))))))))) ))).	1.000 -42.10

cbriggsae	chromosome:chrX:15336203:15336311:1	{SimpF: trf}
cremanei	chromosome:chrUn:26788903:26788994:-1	intergenic
celegans	chromosome:chrII:11537510:11537620:1	Opposite_strand\|Intronic_coding\|Y62F5A.9 ## {MIR: cel-mir-35}
cbrenneri	chromosome:chrUn:47821549:47821654:-1	intergenic ## {SimpF: trf}
cjaponica	chromosome:chrUn:117591701:117591834:-1	Opposite_strand\|Intronic_coding\|NM_171042
ppacificus	chromosome:chrUn:47519693:47519841:1	Same_strand\|Intronic_coding\|NM_001003336

block5126 (miRBaseHomolog cel-mir-35) [miRBaseHomolog_cloningOK_Multihit_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
miRBaseHomolog cel-mir-35	0.001	no	no	0.52/0.52	21/23/1.00	0.0	0.6	7	0	1	0	20	2	3arm	15	nd	0.22	2	7	1	na	na

Clusters
Located in cluster 13: cel-mir-35, block5113_cand, 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

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---------------------------------------------------	7	miR-35/36/38/39/40/41
		len	cloning frequencies
			AF16
	-------------------------------------------------------------------------------TCACCGGGTG-AAAACTGGTAG-------------------------------------	21	5
	-------------------------------------------------------------------------------TCACCGGGTG-AAAACTGGTAGAG-----------------------------------	23	2
cbriggsae	----------------AATGGTCTGGGTCGGACCTCCGCTGTTTTTCTCCG-CGGTGATACTCCAAA-GAAAGTCGTTATCACCGGGTG-AAAACTGGTAGAGGTCCG---ATTCAGTCGGACCAT------------
cremanei	-TCCCTAAT----------------GACGGGAACCGTGCTGGTTTCGAACT-CGGTAATAGACCAGAAGAAAG---CTATCACCGGGTG-GAAACTGGTACGGGTCCCCGAGTCGTGCTATTCTGGA-----------
celegans	-TTCCCAACTATTATTCTCGGATCAGATCGAGCCATTGCTGGTTTCTTCCA-CAGTGGTACTTTCCATTAGAA---CTATCACCGGGTG-GAAACTAGCAGTGGCTCG-------ATCTTTTCC--------------
cbrenneri	---CCTGA-----------------GACGGGAACCGAGCTGGTTTCTCTAC-TGGTGATATATCCAATCATAGTGTTTATCACCGGGAG-TAAATTGGCTCGGGTCCC-----------GTCTCGGG-----------
cjaponica	TGCAGTGGTCCCTCGGGGCAGAAGAGCCAGGACCTACATCAGTTTCTTTCCGCGGTAATAAATAATA-CATTA---TTATCACCGGGAGAAAAACTGGAGTAGGACCTGCGACTCGACTCGACCTTTATTCCGCTGTA
ppacificus	----------------------------GGGATGCATA-----TTCTAACC-CGGTGACTCAATAAACAATGA-----GTCACCGGGT-------TAGAATATGTCCA------------------------------
	* * * ******** * * * *
cbriggsae	.(((((((((((((((((((..((..(((((.((. ((((((((....... .........)))))))))).) ))))..))..)))))))) ))....)))))))))	1.000 -51.49
cremanei	......(( (((((((.((((((..(((((..((( ((((.((((............ )))).))))))). )))))..)))))).))))...)))))...........	0.928 -44.10
celegans	..................(((..((((((((((((((((((((((..((. ..((((((.(((......))) .))))))..)).. )))))))))))))))))) ))))..)))	0.989 -54.00
cbrenneri	((((( (((((((.((((((..(((((((..( ((((((((.................)))))))))))) .))))..)))))).)))) ))))))))	1.000 -56.73
cjaponica	((((((((......((((..((.(((.((((.(((((..((((((.(((((.((((.((.(((((.. ..))) )))).))))))))).))))))..))))).))))...)))...))..))))....))))))))	0.964 -52.50
ppacificus	.((..((((( (((((((( ((((((((((........))) )))))))))) )))))))))))).	1.000 -42.10

cbriggsae	chromosome:chrX:15336370:15336473:1	{Repeats: no}
cremanei	chromosome:chrUn:26788204:26788308:-1	intergenic ## {SimpF: trf}
celegans	chromosome:chrII:11537510:11537620:1	Opposite_strand\|Intronic_coding\|Y62F5A.9 ## {MIR: cel-mir-35}
cbrenneri	chromosome:chrUn:47817083:47817176:-1	intergenic
cjaponica	chromosome:chrUn:117591701:117591834:-1	Opposite_strand\|Intronic_coding\|NM_171042
ppacificus	chromosome:chrUn:47519696:47519839:1	Same_strand\|Intronic_coding\|NM_001003336

block5127 (miRBaseHomolog cel-mir-35) [miRBaseHomolog_cloningOK_Multihit_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
miRBaseHomolog cel-mir-35	0.001	no	no	0.52/0.52	21/23/1.00	0.0	0.6	7	0	1	0	12	8	3arm	15	nd	0.22	2	7	1	na	na

Clusters
Located in cluster 13: cel-mir-35, block5113_cand, 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

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---------------------------------------------	7	miR-35/36/38/39/40/41
		len	cloning frequencies
			AF16
	--------------------------------------------------------------------------TCACCGGGTG----AAAACTGGTAG----------------------------	21	5
	--------------------------------------------------------------------------TCACCGGGTG----AAAACTGGTAGAG--------------------------	23	2
cbriggsae	------------------CTG--GGTCGGACCTCTGCTGGTATTCTCTGCGATGATAT-TTTGAAAAAAGCTTATCACCGGGTG----AAAACTGGTAGAGGTCCGATCCAGT--------------
cremanei	---------------TCCCTAATGACGGGAACCGTGCTGGTTTCGAACTCGGTAATAG-ACCAGAAGAAAGCTATCACCGGGTG----GAAACTGGTACGGGTCC--CCGAGTCGTGCTATTCTGGA
celegans	---------------GGATCA--GATCGAGCCATTGCTGGTTTCTTCCACAGTGGTAC-TTTCCATTAGAACTATCACCGGGTG----GAAACTAGCAGTGGCTCGATCTTTTCC------------
cbrenneri	----------------GGCCG--GATCGGACCTATGCTGGTTTTCACCGCGGTTATAC-TTCTAACAATAATTATCACCGGGTT----AAAACTTGCAGAGGTCCGGTCCGGCC-------------
cjaponica	GATATTCTTGCTCTTTCTCCA--GCTCGGACCTCCGCTGGTTT-CTTTTCGTTGATACGATTTTAATCATGTTATCACCGGGTT----GAAACTGGTAGAGGTCCGACGCTGGAGGCCTCTCATATC
ppacificus	--------TCTGAGTCCCTTC--GATCG--CCTCTGAT------CACTACGATGAAAC-TGAGATAACGAGTTTTCACCGGGTGAACAGAAGCTGTTGAAGAT---ATCGGA---------------
	* * * * * * * * * ******* ** *
cbriggsae	((( ((((((((((((((..((.(((.((.((.(((((( (((....))))..))))).)))).) )).))..))))))))))))))))).	1.000 -49.30
cremanei	......(((((((((.((((((..(((((..(((((((.(((( ............)))).))))))). )))))..)))))).))) )...)))))...........	0.928 -44.10
celegans	(((..( (((((((((((((((((((((..((...((((((. (((......))).))))))..)).. ))))))))))))))))))))))..)))	0.992 -53.70
cbrenneri	((((( ((((((((((.(((.((((((.(((.((((.(((. ((........)).))).))))))). )))))).))).)))))))))))))))	1.000 -51.90
cjaponica	...............(((((( (((((((((((..((((((( (..((((.(((((.(((....)))....))))).)))).. ))))))))..))))))))).))))))))...........	0.974 -52.40
ppacificus	(((((....(((( (((.( (.((((.( ((((.((.(((((( (.........))))).)).))))))).)))).)).))))))).. .)))))	1.000 -30.60

cbriggsae	chromosome:chrX:15336518:15336605:1	{Repeats: no}
cremanei	chromosome:chrUn:26788204:26788308:-1	intergenic ## {SimpF: trf}
celegans	chromosome:chrII:11537528:11537620:1	Opposite_strand\|Intronic_coding\|Y62F5A.9 ## {MIR: cel-mir-35}
cbrenneri	chromosome:chrUn:47823952:47824042:-1	intergenic
cjaponica	chromosome:chrUn:117592041:117592160:-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}

miRBaseHomolog_randfoldOK (2 loci)

cel-mir-1822

Cloning frequencies
absolute	AF16
cel-mir-1822 3arm	3
normalized	AF16
cel-mir-1822 3arm	0.008

block731 (miRBaseHomolog cel-mir-1822) [miRBaseHomolog_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
miRBaseHomolog cel-mir-1822	0.002	no	no	0.64/0.65	22/23/1.00	0.3	0.0	3	0	1	0	15	3	3arm	1	nd	0.22	3	3	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------AGCUGCC------------------------------	2	novel
seed	------------------------------------------------------------GAGCUGC-------------------------------	1	novel
		len	cloning frequencies
			AF16
	------------------------------------------------------------GAGCTGCCCGGGGATAGACTCT----------------	22	2
	-----------------------------------------------------------CGAGCTGCCCGGGGATAGACTCT----------------	23	1
cbriggsae	GTCTAGAAAGGT-CCGAGAGCCTATCCCGGAACGCTATCGGTTGCACTTTTCAAAAAACCGAGCTGCCCGGGGATAGACTCTTGGC-TTCAGAAAGAC
cremanei	----------------AGAGTTTATCCAGGAAAGCTATCGGCCGAGTACTT---AGAACCGAGCTGCCCTCGGATAGACTCT----------------
celegans	TTCTTGAAAACT-CCAATAGTTTCTCTGGGAAAGCTATCGGCCAAA---TTTAACTGTCCGAGCTGCCCTCAGAAAAACTCTTGGC--TCATCGAGAA
cbrenneri	GTCTCGAACACCACCAAGAGTTTATCCAGGAAAGCTATCGGACTGACATTT---AGTACCGAGCTGCCCTGGGATAGACTCTTGGTAATTTTAGAGAC
	* ** * **** ********* * *****
	+++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++	NM_001047975
	+++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++	NM_001047939
	+++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++	NM_101724
	----------------- ------------------------------------------------------------------------- ----------------	NM_001011629
	+++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++	NM_001058128
	+++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++	NM_063457
	+++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++	NM_068373
	+++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++	NM_067556
	+++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++	NM_202130
	----------------- ------------------------------------------------------------------------- ----------------	NM_014971
	+++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++	NM_062799
cbriggsae	((((....(((. (((((((.(((((((((...((..((((((.............))))))...))))))).)))).)))))))) )).....))))	1.000 -37.12
cremanei	((((((((((((((..(((..((((.......... ....)))))))..))).)))))))))))	1.000 -25.74
celegans	.((((((..... ((((.(((((.((((((..(((..((((.((.. ......)).)))))))..)).)))).))))).)))). ...)))))).	1.000 -31.00
cbrenneri	(((((.......((((((((((((((((((..(((..(((((((((...)) ))).)))))))..))))).))))))))))))).......)))))	1.000 -46.14

cbriggsae	chromosome:chrII:8862548:8862643:-1	Same_strand\|Intronic_coding\|NM_001047975\|LOC683871 ## Same_strand\|Intronic_non-coding\|NM_101724\|AT1G18660 ## Opposite_strand\|Intronic_non-coding\|NM_001011629\|Mblk-1 ## {Repeats: no}
cremanei	chromosome:chrUn:133094406:133094541:-1	Same_strand\|Intronic_coding\|NM_062799
celegans	chromosome:chrII:6015495:6015586:1	Same_strand\|Intronic_coding\|ZK84.2 ## {MIR: cel-mir-1822}
cbrenneri	chromosome:chrUn:49225410:49225504:1	Same_strand\|Intronic_coding\|NM_062799

cel-mir-82

Cloning frequencies
absolute	AF16
cel-mir-82 3arm	1
normalized	AF16
cel-mir-82 3arm	0.003

block2351 (miRBaseHomolog cel-mir-82) [miRBaseHomolog_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
miRBaseHomolog cel-mir-82	0.002	no	no	0.45/0.45	20/20/1.00	0.0	0.0	1	0	1	0	18	6	3arm	1	nd	0.20	2	1	1	na	na

Families
Member of family miR-80/81/82 (seed GAGAUCA): cel-mir-82, cbr-mir-81, cbr-mir-80, cbr-mir-82

		reads	miRBase family seed
seed	----------------------------------------------------------------------GAGAUCA------------------------------------------------	1	miR-80/81/82
		len	cloning frequencies
			AF16
	---------------------------------------------------------------------TGAGATCA------------------TTCAAGAAGCCC------------------	20	1
cbriggsae	-------------TGAAATTTTCAATACGTTGGCTTTTTGGCTGGTCTCATACCGTTTAGTACTGGATATGAGATCA------------------TTCAAGAAGCCCAAAAAAGAGTTCATTTCA
cremanei	-----------CTTAGGTCATGTCTTTCACTCACTTTTTG----------------------------ATGAGATCA------------------TTCATGCACCTGCC----------------
celegans	TGAACTCATGAAATAGGTTCTTTTAGCAACCGGTTTTCTCTGTGATCTACAGAATGACAGCTAATCGTCTGAGATCATCGTGAAAGCCAGTTGTTTTTATGAACTCTTATCAAGAA---AATTCA
cbrenneri	-----CCGGGTTGTAGAATTCTTCAGTAATTAGTATCTTGTACA-------------------TAACTGTGAGATCA------------------TTCAACAGCCTTC-----------------
ppacificus	-----------------CTCTCAATTTCGCCTGCTCTCTCGTCA------------TCTCTGATCGATGAGAGATCA------------------TTCGAAA-------TGAAGAG---------
	* *****
	+++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++	NM_071218
	+++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++	NM_067556
	+++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++	NM_001083250
	----- ---------------------------------------------------------------- -----------------------------------	NM_001085890
	+++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++	NM_070819
	+++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++	NM_002710
cbriggsae	.(((((.(((........(((((((((..(((((((((((((........))).)))))))))) ..))))))))).......)))...))))).	0.980 -31.86
cremanei	..(((((((((..(((((.(((.....)) ))))))... ..)))).)))))..	1.000 -11.80
celegans	.(((.((.(((...((((((....((((((.(((((((...(((((((.(((.((((.......))))))))))))))...))))))).)))))).....)))).))..))).)). ..))).	0.989 -37.40
cbrenneri	..(((((((.((((((((((((.((..((((...))))) ).)))).))))..) ))).)))))))..	1.000 -16.90
ppacificus	((((..((((((..((.(((((((((( ((...))).))))))))).)) ..))))) )..))))	1.000 -25.10

cbriggsae	chromosome:chrIV:149566:149659:1	Same_strand\|Intronic_coding\|NM_071218\|str-253 ## Same_strand\|Intronic_non-coding\|NM_001083250\|rom-4 ## Opposite_strand\|Intronic_non-coding\|NM_001085890\|MGC52856 ## {Repeats: no}
cremanei	chromosome:chrUn:131347292:131347425:-1	intergenic
celegans	chromosome:chrX:2435237:2435358:-1	Same_strand\|Intronic_coding\|T07D1.2.1 ## {MIR: cel-mir-82}
cbrenneri	chromosome:chrUn:117808779:117808912:1	intergenic
ppacificus	chromosome:chrUn:120702368:120702501:-1	Same_strand\|Intronic_coding\|NM_008447

miRBaseHomolog_cloningHIGH_multiarm_DicerOK_randfoldOK_bulgeHIGH (1 loci)

cel-mir-65

Cloning frequencies
absolute	AF16
cel-mir-65 5arm	332
cel-mir-65 3arm	135
normalized	AF16
cel-mir-65 5arm	0.865
cel-mir-65 3arm	0.352

sblock25 (miRBaseHomolog cel-mir-65) [miRBaseHomolog_cloningHIGH_multiarm_DicerOK_randfoldOK_bulgeHIGH]

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
miRBaseHomolog cel-mir-65	0.001	no	no	0.50/0.55	19/24/0.98	0.0 0.0	0.0 0.0	310 114	0 0	1 1	0 0	14 17	9 9	5arm 3arm	1 1	nd nd	0.23 0.26	4 2	467	1	0	2

Clusters
Located in cluster 4: cel-mir-65, sblock26_cand, block1267_novel, cbr-mir-64, sblock28_novel

Families
Member of family miR-64 (seed AUGACAC): cel-mir-65, cbr-mir-64, sblock28_novel, sblock26_cand

		reads	miRBase family seed
seed	--------------------------------AUGACA------C--------------------------------------------------------------------------------------------------	332	miR-64
seed	---------------------------------------------------------------------------------CUACCGG-------------------------------------------------------	121	novel
seed	-------------------------------------------------------------------------------------CGGGUUC---------------------------------------------------	8	novel
seed	----------------------------------------------------------------------------------UACCGGG------------------------------------------------------	6	novel
		len	cloning frequencies
			AF16
	-------------------------------CATGACA------CTGAAGCGGGAATGG------------------------------------------------------------------------------------	22	310
	--------------------------------------------------------------------------------CCTACCGGGTTCAGTGTCATACT----------------------------------------	23	114
	-------------------------------CATGACA------CTGAAGCGGGAATG-------------------------------------------------------------------------------------	21	9
	-------------------------------CATGACA------CTGAAGCGGGAAT--------------------------------------------------------------------------------------	20	9
	------------------------------------------------------------------------------------CCGGGTTCAGTGTCATACT----------------------------------------	19	7
	---------------------------------------------------------------------------------CTACCGGGTTCAGTGTCATACT----------------------------------------	22	6
	--------------------------------------------------------------------------------CCTACCGGGTTCAGTGTCATACTT---------------------------------------	24	4
	-------------------------------CATGACA------CTGAAGCGGGAA---------------------------------------------------------------------------------------	19	3
	--------------------------------------------------------------------------------CCTACCGGGTTCAGTGTCAT-------------------------------------------	20	2
	-------------------------------CATGACA------CTGAAGCGGGAATGGAA----------------------------------------------------------------------------------	24	1
	--------------------------------------------------------------------------------CCTACCGGGTTCAGTGTCATAC-----------------------------------------	22	1
	------------------------------------------------------------------------------------CCGGGTTCAGTGTCATACTT---------------------------------------	20	1
cbriggsae	-----------------AGACCCTCACCAATCATGACA------CTGAAGCGGGAATGGAAGCGTAGTCAGATTGCAATTCCTACCGGGTTCAGTGTCATACTTGGTGCG---------------GATGAGTCTG--------
cremanei	-------------------------------CATGACA------CCGATCTCGCGATGG---------------TCGTTTTCCAAAGCGATCGATAAGGCGGTAG--------------------AGTTGTCCTG--------
celegans	GTGCTCTTGGAGCCATGGAGCCTTCGCCGATTATGACA------CTGAAGCGTAACCGAACACCATAT----TTTGAGATTCTGCTACGCGCAGTGCCATGCTCGGCGCGTTGGCTCCATTAAAAAACGGCCACAAAAATGCC
cbrenneri	-------------------------------AATGACA------CTGAAGTGGG--------------------CCAAGTTTTGAGTTTTTTTTTGGAACTTTG---------------------AGTGCTCATA--------
cjaponica	-------------------------------CATGACA------CTGACAATAAGGAGG-------------TTGGGAGCTCTACGTACCTAAACTATATT------------------------AAAGTGCATA--------
ppacificus	-------------------------------CATGACACATCGCCTGAGAATCAATCGAA--------------TTAAGTTTCATTTCGCTAATTGAATCTCAATT-------------------GAGTTTCATA--------
	****** * **
	+++++ +++++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++ +++++	NM_001102902
	----- --------------------- ------------------------------------------------------------------ ---------- -----	NM_001077612
	+++++ +++++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++ +++++	NM_065190
	----- --------------------- ------------------------------------------------------------------ ---------- -----	NM_001129219
cbriggsae	((((((.((((((..(((((( (((((.(((....((((..(((((...)))))..))))..)))..)))))))))))..)))))).) )....)))).	1.000 -40.60
cremanei	((.(((( ....((((((.(((( ((((((....)))))))).))...)))..)) )..)))).))	0.964 -14.90
celegans	..((..(((..(((((((((((..((((((.((((.(( (((..(((((...(((...((... ..))...)))...))))).))))).)))).))))))....))))))))........)))..)))....)).	0.957 -49.40
cbrenneri	.(((((( (((((((... (((((.............))))).))))). )))).)))).	0.997 -14.62
cjaponica	.(((.(( ((...((((.((... (((((.((.....)).))))).)).)))) ..))))))).	1.000 -13.00
ppacificus	.((((.((.(((..(((((.((((((((( ...........))))...))))).)))))..) )))).)))).	0.999 -16.70

cbriggsae	chromosome:chrIII:218506:218602:-1	Same_strand\|Intronic_non-coding\|NM_001102902\|LOC100124966 ## Opposite_strand\|Intronic_coding\|NM_001077612\|zgc:153009 ## Opposite_strand\|Intronic_non-coding\|NM_001129219\|nhr-121 ## {Repeats: no}
cremanei	chromosome:chrUn:30737923:30738059:1	Opposite_strand\|Boundary_non-coding\|NM_181404 ## Opposite_strand\|Boundary_coding\|NM_061875 ## Same_strand\|Intronic_coding\|NM_182266
celegans	chromosome:chrIII:2172976:2173108:1	intergenic ## {MIR: cel-mir-65}
cbrenneri	chromosome:chrUn:96785595:96785731:-1	intergenic
cjaponica	chromosome:chrUn:125505645:125505781:-1	Same_strand\|Intronic_coding\|NM_067721
ppacificus	chromosome:chrUn:116309862:116309998:-1	Opposite_strand\|Intronic_coding\|NM_031126 ## Opposite_strand\|Boundary_coding\|NM_001029437 ## Same_strand\|Intronic_coding\|NM_198493

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candidate homolog loci of miRBase miRNAs:

Page 1

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miR-Intess™

block5125 (miRBaseHomolog cel-mir-35) [miRBaseHomolog_cloningOK_Multihit_randfoldOK]

block5126 (miRBaseHomolog cel-mir-35) [miRBaseHomolog_cloningOK_Multihit_randfoldOK]

block5127 (miRBaseHomolog cel-mir-35) [miRBaseHomolog_cloningOK_Multihit_randfoldOK]

cel-mir-1822

block731 (miRBaseHomolog cel-mir-1822) [miRBaseHomolog_randfoldOK]

cel-mir-82

block2351 (miRBaseHomolog cel-mir-82) [miRBaseHomolog_randfoldOK]

cel-mir-65

sblock25 (miRBaseHomolog cel-mir-65) [miRBaseHomolog_cloningHIGH_multiarm_DicerOK_randfoldOK_bulgeHIGH]