C.briggsae small RNAs

miR-Intess™

miR classification

Alignments

candidate homolog loci of miRBase miRNAs

miRBaseHomolog_cloningOK_Multihit_randfoldOK (13 loci)

block5114 (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	6	3arm	15	nd	0.26	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

block5114 hairpin

		reads	miRBase family seed
seed	------------------------------------------------------------------------------------CACCGGG-----------------------------------------	7	miR-35/36/38/39/40/41
		len	cloning frequencies
			AF16
	-----------------------------------------------------------------------------------TCACCGGGTGAAAACTGGTAG----------------------------	21	5
	-----------------------------------------------------------------------------------TCACCGGGTGAAAACTGGTAGAG--------------------------	23	2
cbriggsae	------------------TTGGATCGGACCTCTGCTGGTTTCTGCCGCAGTGAT---ATTCCAACGTAGTGGTTA--------TCACCGGGTGAAAACTGGTAGAGGTCCGA--------------TCCAGA
cremanei	----------------GGTCGGATCGGCCCTCCACTGGTTTTCGCCTCGGTCAT---ATTTCAAG--TATGATTA--------TCACCGGGTGAAAATCAGAGCAGGGCCGA-------------TTCCACC
celegans	---------------GGATCAGATCGAGCCATTGCTGGTTTCTTCCACAGTGGT--ACTTTCCAT--TAGAACTA--------TCACCGGGTGGAAACTAGCAGTGGCTCGA---------TCTTTTCC---
cbrenneri	-------------------------------GTGCTGATTTTTGCCGCTGTGAT---ATTTCTAAGCCATGATTA--------TCACCGGGCGAAAATTTGGCAC---------------------------
cjaponica	GATATTCTTGCTCTTTCTCCAGCTCGGACCTCCGCTGGTTTCT-TTTCGTTGATACGATTTTAAT--CATG-TTA--------TCACCGGGTTGAAACTGGTAGAGGTCCGACGCTGGAGGCCTCTCATATC
ppacificus	--------CATAGTGCATTCAGTGCAGCCCGCAGTGGGTGTCTGCCTCGGTC-TGAAGTGTGAGATGCATGATCCTCCGTTCTTCACCGGGTGAACATCCATTGCGGGCGCA-----------TGCACCCTG
	* * * * * * * ******** * *
cbriggsae	(((((((((((((((((..((((..(((...((((( (..(((......))).)) ))))..)))..))))..)))))))))))) ))))).	1.000 -54.20
cremanei	(((.(((((((((((...((((((((((((.((((.(( (..(((.. ..))).)) ).))))))))))))))))...)))))))) ))).)))	1.000 -49.80
celegans	(((..((((((((((((((((((((((..((...((((( (.(((.... ..))).)) ))))..))..))))))))))))))))))) )))..)))	0.992 -53.70
cbrenneri	(((((((((((((((...((((( (..((........)).)) ))))..)))))))))).)))))	1.000 -23.10
cjaponica	...............(((((((((((((((((..((((((((. .((((.(((((.(((....)) )... .)) ))).))))..))))))))..))))))))).))))))))...........	0.974 -52.40
ppacificus	....(((((.....(((.(((((((((((((((..(((.((((. .((((...(((..........)))....)))))))))))..)))))))))))))))))) )))))....	0.999 -54.40

cbriggsae	chromosome:chrX:15333880:15333968:1	{Repeats: no}
cremanei	chromosome:chrUn:26788069:26788158:-1	intergenic ## {SimpF: trf}
celegans	chromosome:chrII:11537528:11537620:1	Opposite_strand\|Intronic_coding\|Y62F5A.9 ## {MIR: cel-mir-35}
cbrenneri	chromosome:chrUn:47821539:47821667:-1	intergenic ## {SimpF: trf}
cjaponica	chromosome:chrUn:117592041:117592160:-1	Opposite_strand\|Intronic_coding\|NM_171042
ppacificus	chromosome:chrUn:21366661:21366772:-1	Opposite_strand\|Intronic_coding\|NM_001032504 ## Same_strand\|Intronic_coding\|NM_066966 ## {Repeats: G-rich 6 78 -1 class=Low_complexity}

block5116 (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	0.002	no	no	0.52/0.52	21/23/1.00	0.0	0.6	7	0	1	0	16	6	3arm	15	nd	0.22	3	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

block5116 hairpin

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------CACCGGG---------------------------------------	7	miR-35/36/38/39/40/41
		len	cloning frequencies
			AF16
	----------------------------------------------------------------------------------TCACCGGGTGAAAACTGGTAG--------------------------	21	5
	----------------------------------------------------------------------------------TCACCGGGTGAAAACTGGTAGAG------------------------	23	2
cbriggsae	--------------TCTGATAGTCTG---GATCGAATCTTTGCTGGTTTC-CTCTGCGGTGATATTCCAAATGAAGTGCTTATCACCGGGTGAAAACTGGTAGAGATCCG--------ATCCCGTCGGA
cremanei	---------------------TCCCTAATGACGGGAACCGTGCTGGTTTCGAACT-CGGTAATAGACCAGAAGAAAG--CTATCACCGGGTGGAAACTGGTACGGGTCCCCGAGTCGTGCTATTCTGGA
celegans	CCCAACTATTATTCTCGGATCA-------GATCGAGCCATTGCTGGTTTC-TTCCACAGTGGTACTTTCCATTAGAA--CTATCACCGGGTGGAAACTAGCAGTGGCTCG--------ATCTTTTCC--
cbrenneri	-----------------------TCCTGAGACGGGAACCGAGCTGATTTCACTTT-CGGTGATATGTCC-ATGATGCGCCTATCACCGGGTGTAAATTGGCTCGGGTCCC----------GTCTCGGGA
cjaponica	-----------------------CTG---GCTGGTATCCGCGATGGTGTTACACTACTGTAATG----------------TATCACCGGGTGGAAACTTGCAAG-------------------------
ppacificus	----CATAGTGCATTCAGTGCAGCCCGCAGTGGGTGTCTGCCTCGGTCTGAAGT----GTGAGATGCATGATCCTCCGTTCTTCACCGGGTGAACATCCATTGCGGGCGC--------ATGCACCCTG-
	* * * * * * ******** * *
cbriggsae	((((((.....( (((((.((((((((..((((. ..((.((((((((...((.......))..))))))))))...))))..)))))))).)) )))).))))))	1.000 -41.00
cremanei	......(((((((((.((((((..(((((..((( ((((.((((............ )))).))))))).)))))..)))))).))))...)))))...........	0.928 -44.10
celegans	................(((..( ((((((((((((((((((((( ..((...((((((.(((......))) .))))))..))..)))))))))))))))))) ))))..)))	0.990 -54.00
cbrenneri	(((((((((((((.((((((..((((((((.. ((((((((.((.( (...)).)).)))))))))))).))))..)))))).)))) )))))))))	1.000 -60.80
cjaponica	... ((.(((.(((((..(((((.((((.........)) )).))))).))))).))).))...	1.000 -21.90
ppacificus	....(((((.....(((.(((((((((((((((..(((.((((..((((. ..(((..........)))....)))))))))))..))))))))))))))))) ))))))....	0.999 -54.40

cbriggsae	chromosome:chrX:15334766:15334868:1	{Repeats: no}
cremanei	chromosome:chrUn:26788204:26788308:-1	intergenic ## {SimpF: trf}
celegans	chromosome:chrII:11537512:11537620:1	Opposite_strand\|Intronic_coding\|Y62F5A.9 ## {MIR: cel-mir-35}
cbrenneri	chromosome:chrUn:47818899:47818992:-1	intergenic
cjaponica	chromosome:chrUn:117591205:117591347:-1	Opposite_strand\|Intronic_coding\|NM_171042
ppacificus	chromosome:chrUn:21366661:21366772:-1	Opposite_strand\|Intronic_coding\|NM_001032504 ## Same_strand\|Intronic_coding\|NM_066966 ## {Repeats: G-rich 6 78 -1 class=Low_complexity}

block5117 (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	19	9	3arm	15	nd	0.13	1	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

block5117 hairpin

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------CACCGGG------------------------------------------	7	miR-35/36/38/39/40/41
		len	cloning frequencies
			AF16
	------------------------------------------------------------------------------TCACCGGGTGAAAACTGGTAG-----------------------------	21	5
	------------------------------------------------------------------------------TCACCGGGTGAAAACTGGTAGAG---------------------------	23	2
cbriggsae	-----------------TGGTCTGGATCGGACCTCCACCGATTTTTTCTGCGGTGATAC---TCCAATGGGACGATTATCACCGGGTGAAAACTGGTAGAGGTCCGAT--------CCAGTCAGACCA
cremanei	------------------TGGTCGGATCGGCCATTCACTGGTTCTCGCCGCGGTCATAT---TTCAAATAT--GATTATCACCGGGTGAAAATCAGAGCAGGGCCGAT-------------CCCACCG
celegans	TTCCCAACTATTATTCTCGGATCAGATCGAGCCATTGCTGGTTTCTTCCACAGTGGTAC--TTTCCATTAG--AACTATCACCGGGTGGAAACTAGCAGTGGCTCGAT-------------CTTTTCC
cbrenneri	--------------------CTGAGACGGGAACCGAGCTGGTTTCTTCTTCGGTGATAA---TTCCATTGAGTGTCTATCACCGGG-AGTAATTGGCTCGGGTCCCGT-----------CTTGGGCC-
cjaponica	---GATATTCTTGCTCTTTCTCCAGCTCGGACCTCCGCTGGTTTCTTTT-CGTTGATACGATTTTAATCAT---GTTATCACCGGGTTGAAACTGGTAGAGGTCCGACGCTGGAGGCCTCTCATATC-
ppacificus	----------------------GGGAT---------GCATATTCTAACC-CGGTGA------CTCAATAAACAATGAGTCACCGGGTTAGAATATGT----------------------------CCA
	* * ** * * * ****** * *
cbriggsae	.(((((((((((((((((.((((.(((((.((.((((((((. (((....)))....)))))))))).))))).)))).)))))))))) )))....)))).	1.000 -53.30
cremanei	.(((.(((((((((.....((((((.(((((.((((.(((. .(((....) )).))).))))))))).)))))).....))))))) )).))).	1.000 -46.80
celegans	..................(((..((((((((((((((((((((((..((...((((((. (((......) )).))))))..))..)))))))))))))))))))) ))..)))	0.989 -54.00
cbrenneri	(((((((((((.((((((..(((.((((..((((((((( (((....))))...)))))))))) )).)))..)))))).)))))) )))))...	1.000 -52.00
cjaponica	...............(((((((((((((((((..((((((((..(( ((.(((((.(((....))).. ..))))).))))..))))))))..))))))))).))))))))...........	0.974 -52.40
ppacificus	.((.. ((((((((((((( (((((( ((((........))))))))))))))))))))))) )).	1.000 -42.10

cbriggsae	chromosome:chrX:15334941:15335040:1	{Repeats: no}
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:47818616:47818707:-1	intergenic
cjaponica	chromosome:chrUn:117592041:117592160:-1	Opposite_strand\|Intronic_coding\|NM_171042
ppacificus	chromosome:chrUn:47519699:47519838:1	Same_strand\|Intronic_coding\|NM_001003336

block5118 (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	21	5	3arm	15	nd	0.09	1	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

block5118 hairpin

		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	-----------------ATGGTCT-------------GGGTCGGACCTTTGCCAATTT-TCTCCGCGGTGATACTCCAATGCGACGATTATCACCGGGTG-AAAACTGGTAGAGGTC---CGAGCCAGTCAGACCATC-----------
cremanei	-----------------TCGGTC--------------GGATCGGACCTACACTGGTTT-TCGCTGCGGTGATACTTCGA-G-AATGATTATCACCGGGTG-AAAATCAGGGCAGGTC---CGATTCCACCGA-----------------
celegans	TTCCCAACTATTATTCTCGGATC--------------AGATCGAGCCATTGCTGGTTT-CTTCCACAGTGGTACTTTCC-ATTAGAACTATCACCGGGTG-GAAACTAGCAGTGGCT---CGATCTTTTCC------------------
cbrenneri	-------------------GGCC--------------GGATCGGACCTATGCTGGTTT-TCACCGCGGTTATACTTCTA-ACAATAATTATCACCGGGTT-AAAACTTGCAGAGGTC---CGGTCCGGCC-------------------
cjaponica	-------------TGCAGTGGTCCCTCGGGGCAGAAGAGCCAGGACCTACATCAGTTTCTTTCCGCGGTAATAAAT-AATAC-ATTATTATCACCGGGAGAAAAACTGGAGTAGGACCTGCGACTCGACTCGACCTTTATTCCGCTGTA
ppacificus	-----------------------------------------GGGATGCATATT------CTAACCCGGTGACTCAATAA-ACAATGA--GTCACCGGGTT-------AGAATATGTC---CA---------------------------
	* * ** * * ******** * * *
cbriggsae	((((((( (((((((((((((((((.((( ((.((.((((((((.((.........)).)))))))))).) )))).))))))))))) ))).))...)))))))).	1.000 -58.80
cremanei	(((((. (((((((((((...((((((( (((((.((((((((..((.. . ...)).)))))))))))) ))))))))...))))) )))))).)))))	1.000 -55.10
celegans	..................(((.. ((((((((((((((((((((( (..((...((((((.(((.. ....))).))))))..)).. )))))))))))))))) ))))))..)))	0.989 -54.00
cbrenneri	(((( (((((((((((.(((.((((( (.(((.((((.(((.((... .....)).))).))))))). )))))).))).))))) ))))))))))	1.000 -51.90
cjaponica	((((((((......((((..((.(((.((((.(((((..((((((.(((((.((((.((.((( ((... .))))))).))))))))).))))))..))))).))))...)))...))..))))....))))))))	0.964 -52.50
ppacificus	.((..((((((( ((((((((((((((((.... ....))) ))))))))))) )))))))))) ).	1.000 -42.10

cbriggsae	chromosome:chrX:15335080:15335182:1	{Repeats: no}
cremanei	chromosome:chrUn:26787656:26787749:-1	intergenic
celegans	chromosome:chrII:11537510:11537620:1	Opposite_strand\|Intronic_coding\|Y62F5A.9 ## {MIR: cel-mir-35}
cbrenneri	chromosome:chrUn:47823952:47824042:-1	intergenic
cjaponica	chromosome:chrUn:117591701:117591834:-1	Opposite_strand\|Intronic_coding\|NM_171042
ppacificus	chromosome:chrUn:47519698:47519840:1	Same_strand\|Intronic_coding\|NM_001003336

block5119 (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	27	6	3arm	15	nd	0.17	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

block5119 hairpin

		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	------------------ATGAAGCGTAGTTTG--GGTC-GGACCTCCGCTGGCTTT-TTCCACGGTGATACTCCAAAGCAAGTGGTTATCACCGGGTGAAAA-CTGGTAGAGG--------TCCGATCCACTCGGACCACCATCATT---------
cremanei	----------------------------GGTCG--GATC-GGCCCTCCACTGGTTTT-CGCCTCGGTCATATTTCAAGT---ATGATTATCACCGGGTGAAAA-TCAGAGCAGG--------GCCGATTCCACC-----------------------
celegans	---------TTCCCAACTATTATTCTCGGATCA--GATC-GAGCCATTGCTGGTTTC-TTCCACAGTGGTACTTTCCATT--AGAACTATCACCGGGTGGAAA-CTAGCAGTGG--------CTCGATCTTTTCC----------------------
cbrenneri	--------------------------AGGGGTG--GATC-GGGCCTGTGCTGATTTT-TGCCGCTGTGATATTTCTAAGCC-ATGATTATCACCGGGCGAAAATTTGGCACAGG--------CCTCGTCCGCCCTT---------------------
cjaponica	GGGTGAACACTTGCAGTGGTCCCTCGGGGCAGAAGAGCCAGGACCTACATCAGTTTCTTTCCGCGGTAATAAATAATAC---ATTATTATCACCGGGAGAAAAACTGGAGTAGGACCTGCGACTCGACTCGACCTTTATTCCGCTGTATTTTTGCTT
ppacificus	------------------ATTTTGCTGGAGATAAG-----GGATGCATATT-----C-TAACCCGGTGACTCAATAAACA--ATGA--GTCACCGGG-------TTAGAATATG--------TCCAATTTTTGCGAAAT------------------
	* * * ****** * * *
cbriggsae	((((...((.((((( (((( (((((((..((((.((( (.((.((((((((..(((.......))).)))))))))).)))). ))))..)))) )))))))))....))).))..)))).	0.640 -53.00
cremanei	(((.( (((( ((((((...(((((((( ((((.((((.(((..(((... .))).))).)))))))))))) ))))...))) )))))))).)))	1.000 -49.80
celegans	..................(((..( (((( ((((((((((((((((( ..((...((((((.(((..... .))).))))))..))..)))) )))))))))) ))))))))..)))	0.989 -54.00
cbrenneri	((((((( (((. ((((((((((((((((( ((((...((((((..((...... ..)).))))))..)))))))))).)))))))) ))).))))))))))	1.000 -57.50
cjaponica	.((..((....((((((((......((((..((.(((.((((.(((((..((((((.(((((.((((.((.(((((... .))))))).))))))))).))))))..))))).))))...)))...))..))))....))))))))..))..)).	0.961 -56.20
ppacificus	(((((((.((((((... ((..((((((( ( (((((((((((((((....... .))) ))))))))) )))))))))) ))).)))))))))))))	1.000 -49.00

cbriggsae	chromosome:chrX:15335266:15335382:1	{SimpF: trf}
cremanei	chromosome:chrUn:26788069:26788158:-1	intergenic ## {SimpF: trf}
celegans	chromosome:chrII:11537510:11537620:1	Opposite_strand\|Intronic_coding\|Y62F5A.9 ## {MIR: cel-mir-35}
cbrenneri	chromosome:chrUn:47821555:47821651:-1	intergenic ## {SimpF: trf}
cjaponica	chromosome:chrUn:117591692:117591845:-1	Opposite_strand\|Intronic_coding\|NM_171042
ppacificus	chromosome:chrUn:47519721:47519811:1	Same_strand\|Intronic_coding\|NM_001003336

block5120 (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	13	6	3arm	15	nd	0.17	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

block5120 hairpin

		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	---------------------GACTGGATCGGACCTCCGCTGGTTTTTCCCGCGG---------TGATAT--TCCGAAGCAAGTGGTTATCACCGGGTGAAAA-CTGGTAGAGGTCCGATCCAGTC----------------
cremanei	-------------------TCGGTCGGATCGGACCTACACTGGTTTTCGCTGCGG---------TGATAC--TTCGAGA---ATGATTATCACCGGGTGAAAA-TCAGGGCAGGTCCGATTCCACCGA--------------
celegans	--------------------GGATCAGATCGAGCCATTGCTGGTTTCTTCCACAG---------TGGTAC--TTTCCAT--TAGAACTATCACCGGGTGGAAA-CTAGCAGTGGCTCGATCTTTTCC---------------
cbrenneri	GTTCATATTTTTCATATTCAGGGGTGGATCGGGCCTGTGCTGATTTTTGCCGCTG---------TGATAT--TTCTAAGCC-ATGATTATCACCGGGCGAAAATTTGGCACAGGCCTCGTCCGCCCTTCCTGAGACGGGAAC
cjaponica	-----GATATTCTTGCTCTTTCTCCAGCTCGGACCTCCGCTGGTTTCT-TTTCGT---------TGATACGATTTTAATCAT---GTTATCACCGGGTTGAAA-CTGGTAGAGGTCCGACGCTGGAGGCCTCTCATATC---
ppacificus	-------------CATAGTGCATTCAGTGCAGCCCGCAGTGGGTGTCTGCCTCGGTCTGAAGTGTGAGAT--GCATGATCCTCCGTTCTTCACCGGGTGAACATCCATTGCGGGCGC-ATGCACCCTG--------------
	* * ** * * * * ** * ******** * * **
cbriggsae	((((((((((((((((..((((((((..((.((( (((((. .(((.......))).))))))))))..)))) ))))..))))))))))))))))	1.000 -62.40
cremanei	(((((.(((((((((((...((((((((((((.((( (((((. .((.... ..)).)))))))))))))))) ))))...))))))))))).)))))	1.000 -55.10
celegans	(((..((((((((((((((((((((((..((...( (((((. (((.... ..))).))))))..))..)))) ))))))))))))))))))..)))	0.992 -53.70
cbrenneri	((((.....(((((.....((((((((((.(((((((((((((((((((((...( (((((. .((...... ..)).))))))..)))))))))).))))))))))).))))))))))..)))))...))))	0.852 -61.90
cjaponica	...............(((((((((((((((((..((((((((. .((((. (((((.(((....))).. ..))))).))))..)))) ))))..))))))))).))))))))...........	0.974 -52.40
ppacificus	....(((((.....(((.(((((((((((((((..(((.((((..((((...(((.. ........)))....)))))))))))..))))))))))))))))) ))))))....	0.999 -54.40

cbriggsae	chromosome:chrX:15335427:15335519:1	{SimpF: trf}
cremanei	chromosome:chrUn:26787656:26787749:-1	intergenic
celegans	chromosome:chrII:11537528:11537620:1	Opposite_strand\|Intronic_coding\|Y62F5A.9 ## {MIR: cel-mir-35}
cbrenneri	chromosome:chrUn:47821541:47821670:-1	intergenic ## {SimpF: trf}
cjaponica	chromosome:chrUn:117592041:117592160:-1	Opposite_strand\|Intronic_coding\|NM_171042
ppacificus	chromosome:chrUn:21366661:21366772:-1	Opposite_strand\|Intronic_coding\|NM_001032504 ## Same_strand\|Intronic_coding\|NM_066966 ## {Repeats: G-rich 6 78 -1 class=Low_complexity}

block5121 (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	19	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

block5121 hairpin

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------CACCGGG-----------------------------------------	7	miR-35/36/38/39/40/41
		len	cloning frequencies
			AF16
	----------------------------------------------------------------------------------TCACCGGGTGAAAACTGGTAG----------------------------	21	5
	----------------------------------------------------------------------------------TCACCGGGTGAAAACTGGTAGAG--------------------------	23	2
cbriggsae	---------------------GGTCTGGGTCGGACCTCCGCTGTTTTTCTCCGCGGTGATAC---TCCAAAGAAAGTCGTTATCACCGGGTGAAAACTGGTAGAGGTCCGATTCAGTCGGACCA-------
cremanei	TCCAATCCTGCCCTTTTACTCCCTAATGACGGGAACCGTGCTGGTTTCGAACTCGGTAATAGA--CCAGAAGAAAG---CTATCACCGGGTGGAAACTGGTACGGGTCC--CCGAGTCGTGCTATTCTGGA
celegans	---TTCCCAACTATTATTCTCGGATCAGATCGAGCCATTGCTGGTTTCTTCCACAGTGGTACT--TTCCATTAGAA---CTATCACCGGGTGGAAACTAGCAGTGGCTCGATCTTTTCC------------
cbrenneri	----------------------CCTGAGACGGGAACCGAGCTGGTTTCTCTACTGGTGATATA--TCCAATCATAGTGTTTATCACCGGGAGTAAATTGGCTCGGGTCCCGTCTCGGG-------------
cjaponica	------GATATTCTTGCTCTTTCTCCAGCTCGGACCTCCGCTGGTTTCTTT-TCGTTGATACGATTTTAATCATG----TTATCACCGGGTTGAAACTGGTAGAGGTCCGACGCTGGAGGCCTCTCATATC
ppacificus	------------------------------GGGATGCATA-----TTCTAACCCGGTGACTCA--ATAAACAATGA-----GTCACCGGGTTAGAATATGTCCA---------------------------
	* ** * * * ****** *
cbriggsae	(((((((((((((((((..((..(((((.((.((((((((. ...............)))))))))).)))))..))..))))))))))....))))))).	1.000 -50.19
cremanei	((((.....((..............(((((((((.((((((..(((((..(((((((.((((. ........... )))).))))))).)))))..)))))).))) )...))))))).....))))	0.873 -46.03
celegans	..................(((..((((((((((((((((((((((..((...((((((.( ((......))) .))))))..))..))))))))))))))))))))))..)))	0.989 -54.00
cbrenneri	((((((((((((.((((((..(((((((..(((((((((.. ...............)))))))))))).))))..)))))).))))))))))))	1.000 -56.73
cjaponica	...............(((((((((((((((((..((((((((..( (((.(((((.(((....)))... .))))).))))..))))))))..))))))))).))))))))...........	0.974 -52.40
ppacificus	.((..((((( (((((((((((((((((( ........))) )))))))))))))))))))))).	1.000 -42.10

cbriggsae	chromosome:chrX:15335590:15335689:1	{SimpF: trf}
cremanei	chromosome:chrUn:26788204:26788327:-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:117592041:117592160:-1	Opposite_strand\|Intronic_coding\|NM_171042
ppacificus	chromosome:chrUn:47519699:47519838:1	Same_strand\|Intronic_coding\|NM_001003336

block5122 (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	0.17	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

block5122 hairpin

		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	----------------CGAAGGTCTGGA----TCGGACCTCCGCTGGTTT-TTCCCGCG---------GTGATATTCCGAAGCAAGTGGTTATCACCGGGTGAAAA-CTGGTAGAGG--------TCCGATCCAGTCGTACCATCG-----
cremanei	------------------TCGGTCGGA-----TCGGACCTACACTGGTTT-TCGCTGCG---------GTGATACTTCGAG---AATGATTATCACCGGGTGAAAA-TCAGGGCAGG--------TCCGATTCCACCGA------------
celegans	-TTCCCAACTATTATTCTCGGATCAGA-----TCGAGCCATTGCTGGTTT-CTTCCACA---------GTGGTACTTTCCATTAGA--ACTATCACCGGGTGGAAA-CTAGCAGTGG--------CTCGATCTTTTCC-------------
cbrenneri	GTTCATATTTTTCATATTCAGGGGTGGA----TCGGGCCTGTGCTGATTT-TTGCCGCT---------GTGATATTTCTAAGC-CATGATTATCACCGGGCGAAAATTTGGCACAGG--------CCTCGTCCGCCCT-------------
cjaponica	-----TGCAGTGGTCCCTCGGGGCAGAAGAGCCAGGACCTACATCAGTTTCTTTCCGCG---------GTAATAAAT---AATACATTATTATCACCGGGAGAAAAACTGGAGTAGGACCTGCGACTCGACTCGACCTTTATTCCGCTGTA
ppacificus	-------CATAGTGCATTCAG-----------TGCAGCCCGCAGTGGGTGTCTGCCTCGGTCTGAAGTGTGAGATGCATGATCCTCCGTTCTTCACCGGGTGAACATCCATTGCGGG---------CGCATGCACCCTG------------
	* ** * * * ** * ******** * * * ** *
cbriggsae	(((.(((((((( (((((((((..((((((( (..((.(( ((((((..(((.......))).))))))))))..)))) ))))..)))) ))))))))))....))).)))	1.000 -62.90
cremanei	(((((.((( ((((((((...((((((( (((((.(( ((((((..((... ...)).)))))))))))))))) ))))...))) )))))))).)))))	1.000 -55.10
celegans	..................(((..((( (((((((((((((((((( (..((... ((((((.(((......)) ).))))))..))..)))) )))))))))) ))))))))..)))	0.989 -54.00
cbrenneri	....................(((((((( (.(((((((((((((((( (((((... ((((((..((..... ...)).))))))..)))))))))).)))))))) ))).)))))))))	0.944 -57.20
cjaponica	((((((((......((((..((.(((.((((.(((((..((((((.(((((.(( ((.((.((( ((....))))))).))))))))).))))))..))))).))))...)))...))..))))....))))))))	0.964 -52.50
ppacificus	....(((((..... (((.(((((((((((((((..(((.((((..((((...(((..........)))....)))))))))))..)))))))))))))) )))))))))....	0.999 -54.40

cbriggsae	chromosome:chrX:15335737:15335843:1	{SimpF: trf}
cremanei	chromosome:chrUn:26787656:26787749:-1	intergenic
celegans	chromosome:chrII:11537510:11537620:1	Opposite_strand\|Intronic_coding\|Y62F5A.9 ## {MIR: cel-mir-35}
cbrenneri	chromosome:chrUn:47821556:47821670:-1	intergenic ## {SimpF: trf}
cjaponica	chromosome:chrUn:117591701:117591834:-1	Opposite_strand\|Intronic_coding\|NM_171042
ppacificus	chromosome:chrUn:21366661:21366772:-1	Opposite_strand\|Intronic_coding\|NM_001032504 ## Same_strand\|Intronic_coding\|NM_066966 ## {Repeats: G-rich 6 78 -1 class=Low_complexity}

block5123 (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	19	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

block5123 hairpin

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------CACCGGG-----------------------------------------	7	miR-35/36/38/39/40/41
		len	cloning frequencies
			AF16
	----------------------------------------------------------------------------------TCACCGGGTGAAAACTGGTAG----------------------------	21	5
	----------------------------------------------------------------------------------TCACCGGGTGAAAACTGGTAGAG--------------------------	23	2
cbriggsae	---------------------GGTCTGGGTCGGACCTCCGCTGTTTTTCTCCGCGGTGATAC---TCCAAAGAAAGTCGTTATCACCGGGTGAAAACTGGTAGAGGTCCGATTCAGTCGGACCA-------
cremanei	TCCAATCCTGCCCTTTTACTCCCTAATGACGGGAACCGTGCTGGTTTCGAACTCGGTAATAGA--CCAGAAGAAAG---CTATCACCGGGTGGAAACTGGTACGGGTCC--CCGAGTCGTGCTATTCTGGA
celegans	---TTCCCAACTATTATTCTCGGATCAGATCGAGCCATTGCTGGTTTCTTCCACAGTGGTACT--TTCCATTAGAA---CTATCACCGGGTGGAAACTAGCAGTGGCTCGATCTTTTCC------------
cbrenneri	----------------------CCTGAGACGGGAACCGAGCTGGTTTCTCTACTGGTGATATA--TCCAATCATAGTGTTTATCACCGGGAGTAAATTGGCTCGGGTCCCGTCTCGGG-------------
cjaponica	------GATATTCTTGCTCTTTCTCCAGCTCGGACCTCCGCTGGTTTCTTT-TCGTTGATACGATTTTAATCATG----TTATCACCGGGTTGAAACTGGTAGAGGTCCGACGCTGGAGGCCTCTCATATC
ppacificus	------------------------------GGGATGCATA-----TTCTAACCCGGTGACTCA--ATAAACAATGA-----GTCACCGGGTTAGAATATGTCCA---------------------------
	* ** * * * ****** *
cbriggsae	(((((((((((((((((..((..(((((.((.((((((((. ...............)))))))))).)))))..))..))))))))))....))))))).	1.000 -50.19
cremanei	((((.....((..............(((((((((.((((((..(((((..(((((((.((((. ........... )))).))))))).)))))..)))))).))) )...))))))).....))))	0.873 -46.03
celegans	..................(((..((((((((((((((((((((((..((...((((((.( ((......))) .))))))..))..))))))))))))))))))))))..)))	0.989 -54.00
cbrenneri	((((((((((((.((((((..(((((((..(((((((((.. ...............)))))))))))).))))..)))))).))))))))))))	1.000 -56.73
cjaponica	...............(((((((((((((((((..((((((((..( (((.(((((.(((....)))... .))))).))))..))))))))..))))))))).))))))))...........	0.974 -52.40
ppacificus	.((..((((( (((((((((((((((((( ........))) )))))))))))))))))))))).	1.000 -42.10

cbriggsae	chromosome:chrX:15335905:15336004:1	{SimpF: trf}
cremanei	chromosome:chrUn:26788204:26788327:-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:117592041:117592160:-1	Opposite_strand\|Intronic_coding\|NM_171042
ppacificus	chromosome:chrUn:47519699:47519838:1	Same_strand\|Intronic_coding\|NM_001003336

block5124 (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	0.17	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

block5124 hairpin

		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	----------------CGAAGGTCTGGA----TCGGACCTCCGCTGGTTT-TTCCCGCG---------GTGATATTCCGAAGCAAGTGGTTATCACCGGGTGAAAA-CTGGTAGAGG-------------TCCGATCCAGTCACATCATCG
cremanei	------------------TCGGTCGGA-----TCGGACCTACACTGGTTT-TCGCTGCG---------GTGATACTTCGAG---AATGATTATCACCGGGTGAAAA-TCAGGGCAGG-------------TCCGATTCCACCGA-------
celegans	-TTCCCAACTATTATTCTCGGATCAGA-----TCGAGCCATTGCTGGTTT-CTTCCACA---------GTGGTACTTTCCATTAGA--ACTATCACCGGGTGGAAA-CTAGCAGTGG-------------CTCGATCTTTTCC--------
cbrenneri	GTTCATATTTTTCATATTCAGGGGTGGA----TCGGGCCTGTGCTGATTT-TTGCCGCT---------GTGATATTTCTAAGC-CATGATTATCACCGGGCGAAAATTTGGCACAGG-------------CCTCGTCCGCCCT--------
cjaponica	-----TGCAGTGGTCCCTCGGGGCAGAAGAGCCAGGACCTACATCAGTTTCTTTCCGCG---------GTAATAAAT---AATACATTATTATCACCGGGAGAAAAACTGGAGTAGGACCTGCGACTCGACTCGACCTTTATTCCGCTGTA
ppacificus	-------CATAGTGCATTCAG-----------TGCAGCCCGCAGTGGGTGTCTGCCTCGGTCTGAAGTGTGAGATGCATGATCCTCCGTTCTTCACCGGGTGAACATCCATTGCGGG-------------CGCATGCACCCTG--------
	* ** * * * ** * ******** * * * **
cbriggsae	(((.(((((((( (((((((((..((((((( (..((.(( ((((((..(((.......))).))))))))))..)))) ))))..)))) ))))))))))....))).)))	1.000 -60.30
cremanei	(((((.((( ((((((((...((((((( (((((.(( ((((((..((... ...)).)))))))))))))))) ))))...))) )))))))).)))))	1.000 -55.10
celegans	..................(((..((( (((((((((((((((((( (..((... ((((((.(((......)) ).))))))..))..)))) )))))))))) ))))))))..)))	0.989 -54.00
cbrenneri	....................(((((((( (.(((((((((((((((( (((((... ((((((..((..... ...)).))))))..)))))))))).)))))))) ))).)))))))))	0.944 -57.20
cjaponica	((((((((......((((..((.(((.((((.(((((..((((((.(((((.(( ((.((.((( ((....))))))).))))))))).))))))..))))).))))...)))...))..))))....))))))))	0.964 -52.50
ppacificus	....(((((..... (((.(((((((((((((((..(((.((((..((((...(((..........)))....)))))))))))..)))))))))))))) )))))))))....	0.999 -54.40

cbriggsae	chromosome:chrX:15336052:15336158:1	{SimpF: trf}
cremanei	chromosome:chrUn:26787656:26787749:-1	intergenic
celegans	chromosome:chrII:11537510:11537620:1	Opposite_strand\|Intronic_coding\|Y62F5A.9 ## {MIR: cel-mir-35}
cbrenneri	chromosome:chrUn:47821556:47821670:-1	intergenic ## {SimpF: trf}
cjaponica	chromosome:chrUn:117591701:117591834:-1	Opposite_strand\|Intronic_coding\|NM_171042
ppacificus	chromosome:chrUn:21366661:21366772:-1	Opposite_strand\|Intronic_coding\|NM_001032504 ## Same_strand\|Intronic_coding\|NM_066966 ## {Repeats: G-rich 6 78 -1 class=Low_complexity}

Back to summary page

candidate homolog loci of miRBase miRNAs:

Page 1

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