miR-Intess™

cel-mir-35

Cloning frequencies

absolute	AF16
cel-mir-35 5arm	10
cel-mir-35 3arm	740.567
normalized	AF16
cel-mir-35 5arm	0.026
cel-mir-35 3arm	1.930

block5112 (miRBaseHomolog cel-mir-35) [miRBaseHomolog_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

miRBaseHomolog cel-mir-35

0.001

no

no

0.47/0.48

19/21/0.94

0.0

0.0

16

0

1

0

26

5

3arm

2

nd

0.19

2

17

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-----------------------------------------------------------	17	miR-35/36/38/39/40/41
		len	cloning frequencies
			AF16
	-------------------------------------------------------------------------------------------TCACCGGGTGAAAATTGGTAC----------------------------------------------	21	16
	-------------------------------------------------------------------------------------------TCACCGGGTGAAAATTGGT------------------------------------------------	19	1
cbriggsae	---------------GAAGTTGATAGTCTGGA-----TCGGACCTGCGTCAGTTT-TTATCACTGTGATATTCCAAG--CATAACGG-TTATCACCGGGTGAAAATTGGTACAGGTCCGATCCATTCGAACG------------------ACTTCA--
cremanei	-------------------------GGTCGGA-----TCGGCCCTCCACTGGTTT-TCGCCTCGGTCATATTTCAAG--TATGA----TTATCACCGGGTGAAAATCAGAGCAGGG----CCGATTCCACC---------------------------
celegans	------TTCCCAACTATTATTCTCGGATCAGA-----TCGAGCCATTGCTGGTTT-CTTCCACAGTGGTACTTTCCA----TTAGAA-CTATCACCGGGTGGAAACTAGCAGTGGC---------TCGATCT------------------TTTCC---
cbrenneri	--------------------TTCAGGGGTGGA-----TCGGGCCTGTGCTGATTT-TTGCCGCTGTGATATTTCTAAGCCATGA----TTATCACCGGGCGAAAATTTGGCACAGG----CCTCGTCCGCCC------------------TTCCTGAG
cjaponica	GGTGAACACTTGCAGTGGTCCCTCGGGGCAGAAGAGCCAGGACCTACATCAGTTTCTTTCCGCGGTAATAAATAATA--CATTA----TTATCACCGGGAGAAAAACTGGAGTAGGACCTGCGACTCGACTCGACCTTTATTCCGCTGTATTTTTGCT
ppacificus	---------------------------TCTGA-------GTCCCTTCGATCGCCTCTGATCACTACGATGAAACTGA--GATAACGAGTTTTCACCGGGTGAACAGAAGCTGTTGA----AGATATCGGA----------------------------
	**       *  **          *     * *     *            * *     * ******** * * *   *     *          **
cbriggsae	(((((((......((((     (((((((((..((((((( (((((...((((((..((...  ......)) .))))))..))))))))))))..)))))))))))))......))                  ))))).	1.000 -56.00
cremanei	(((.(((     ((((((((...((((((( (((((.((((.(((..(((..  ..)))    .))).))))))))))))))))...))))    ))))))).)))	1.000 -49.80
celegans	..................(((..(((     (((((((((((((((((( (..((...((((((.(((...    ...))) .))))))..))..)))))))))))))))         )))))))                  ..)))	0.989 -54.00
cbrenneri	.(((((((((((     (.(((((((((((((((( (((((...((((((..((........))    .))))))..)))))))))).))))))))    ))).))))))))                  ...)))).	1.000 -59.20
cjaponica	((..((....((((((((......((((..((.(((.((((.(((((..((((((.(((((.((((.((.(((((..  ..)))    )))).))))))))).))))))..))))).))))...)))...))..))))....))))))))..))..))	0.958 -55.70
ppacificus	(((((       ....(((((((.((.((((.(((((.((.(((((((..  .......))))).)).))))))).)))).)).)))))    ))...)))))	1.000 -30.60

cbriggsae	chromosome:chrX:15333569:15333682:1	{Repeats: no}
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:47821549:47821654:-1	intergenic ## {SimpF: trf}
cjaponica	chromosome:chrUn:117591693:117591844:-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}

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

		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}

block5115 (miRBaseHomolog cel-mir-35) [miRBaseHomolog_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

miRBaseHomolog cel-mir-35

0.005

no

no

0.50/0.52

21/22/1.00

0.0

0.0

19

0

1

0

28

5

3arm

1

nd

0.19

2

20

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--------------------------------------------	19	miR-35/36/38/39/40/41
seed	-----------------------------------------------------------------------------------UCACCGG---------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-----------------------------------------------------------------------------------TCACCGGGTGACAATTAGGAC-------------------------------	21	19
	----------------------------------------------------------------------------------ATCACCGGGTGACAATTAGGAC-------------------------------	22	1
cbriggsae	--------TAATCTTTGAGGTCCGAGTCGGACCTGCCCTGATTCTTGCTGCAGTGATATTTCGAACGGCTA-------GATTATCACCGGGTGACAATTAGGACAGGTC--CGACCCC-TAGTGACCCGGATTGC
cremanei	-----------------TCGGTCGGATCGGACCTACACTGGTTTTCGCTGCGGTGATAC----------TTCGAGAATGATTATCACCGGGTGAAAATCAGGGCAGGTC--CGATTCCACCGA------------
celegans	TTCCCAACTATTATTCTCGGATCAGATCGAGCCATTGCTGGTTTCTTCCACAGTGGTACT---------TTCCATTAGAACTATCACCGGGTGGAAACTAGCAGTGGCT--CGATCTTTTCC-------------
cbrenneri	-------GTGAGTTTAGCAGGTCTTGT--GACCTCGGTGGTTTCTTGCCGCGGTGATATGCACATTCACTTCCATAATTGATATCACCGGGTGAAAAATCACCAAGGTCGACGATTCTGTTCTATTTTTTCTCGC
cjaponica	---------------------------------ACAGTTATTTTTTGCTACAGTTCTATTCCGAAGTTTTTTCG----AAATAGCACCGGGCCGACAATATCTAA------------------------------
	**    *  * **  **           *           ** *******     *
cbriggsae	((((((....((((...((((((((((.(((((((.(((((...((((((..((.........       )).))))))..))))).))))))).))))))  ))))... ....)))).)))))).	0.920 -44.10
cremanei	(((((.(((((((((((...((((((((((((.((((((((.          .((......)).))))))))))))))))))))...)))))  )))))).)))))	1.000 -55.10
celegans	..................(((..((((((((((((((((((((((..((...((((((.(         ((......))).))))))..))..))))))))))))))))  ))))))..)))	0.989 -54.00
cbrenneri	(((((...((((((..((((  (((((.((((((((.(((((.(((((((((.((................)))))))))))))))).)))))))).))))).)))).)))))).........)))))	0.999 -47.09
cjaponica	..((.((((.((.(((...((.(((((.(((((...)))))    .))))).))..))).)).)))).))..	0.999 -12.50

cbriggsae	chromosome:chrX:15334006:15334122:1	{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:41613114:41613239:-1	Same_strand|Intronic_coding|NM_001056672 ## Opposite_strand|Intronic_coding|NM_171042
cjaponica	chromosome:chrUn:110443635:110443791:1	Opposite_strand|Boundary_coding|NM_058329

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

		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

		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

		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

		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

		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

		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

		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

		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

		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}

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}

sblock23 (miRBaseHomolog cel-mir-35) [miRBaseHomolog_cloningHIGH_multiarm_DicerOK_randfoldOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

miRBaseHomolog cel-mir-35

0.001

no

no

0.43/0.56

18/23/0.62

0.0 0.0

0.8 1.1

8 673

0 0

1 1

0 0

16 14

5 5

5arm 3arm

1 1

nd nd

0.14 0.14

2 2

716

1

1

2

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--------------------------------	695	miR-35/36/38/39/40/41
seed	-------------------GCAGGUU--------------------------------------------------------------------------	10	novel
seed	-----------------------------------------------------------------GGGUGAA----------------------------	7	novel
seed	--------------------------------------------------------------ACCGGGU-------------------------------	3	miR-42
seed	------------------------------------------------------------UCACCGG---------------------------------	1	novel
		len	cloning frequencies
			AF16
	------------------------------------------------------------TCACCGGGTGAAAATTTGCAAG------------------	22	416
	------------------------------------------------------------TCACCGGGTGAAAATTTGC---------------------	19	257
	------------------------------------------------------------TCACCGGGTGAAAATTTGCAAGT-----------------	23	12
	------------------------------------------------------------TCACCGGGTGAAAATTTG----------------------	18	8
	----------------------------------------------------------------CGGGTGAAAATTTGCAAG------------------	18	7
	------------------CGCAGGTTTTTGCTTCGGTGAT------------------------------------------------------------	22	5
	------------------CGCAGGTTTTTGCTTCGGTG--------------------------------------------------------------	20	3
	------------------------------------------------------------TCACCGGGTGAAAATTTGCAA-------------------	21	2
	-------------------------------------------------------------CACCGGGTGAAAATTTGCAAG------------------	21	2
	------------------CGCAGGTTTTTGCTTCGGTGA-------------------------------------------------------------	21	1
	------------------CGCAGGTTTTTGCTTCGG----------------------------------------------------------------	18	1
	-------------------------------------------------------------CACCGGGTGAAAATTTGCA--------------------	19	1
	-----------------------------------------------------------ATCACCGGGTGAAAATTTGC---------------------	20	1
cbriggsae	--CCCAGTTCCGGACACTCGCAGGTTTTTGCTTCGGTGATATTCGAAGAGCC---GT-TATCACCGGGTGAAAATTTGCAAGTGTCCGGT--AACTGG--
cremanei	TCGGTCGGATCGGACCTACACTGGTTTTCGCTGCGGTGATACTTCGAGA---ATGAT-TATCACCGGGTGAAAATCAGGGCAGGTCCGATTCCACCGA--
celegans	-GGATCAGATCGAGCCATTGCTGGTTTCTTCCACAGTGGTACTTTC--CATTAGAAC-TATCACCGGGTGGAAACTAGCAGTGGCTCGATCTTTTCC---
cbrenneri	-----------------GTGCTGATTTTTGCCGCTGTGATATTTCTA-AGCCATGAT-TATCACCGGGCGAAAATTTGGCAC------------------
cjaponica	-GTCCAGAATTAGACACTGGCTGGTATCCGCGATGGTGTTAC----ACTACTGTAATGTATCACCGGGTGGAAACTTGCAAGTGTC---TCCAACTGGAT
ppacificus	--TCTGAGTCCCTTCGATCGCCTCTGATCACTACGATGAAACTGAGATAACGA--GT-TTTCACCGGGTGAACA---GAAGCTGTTGAAGATATCGGA--
	*   *     *     **  *                 * ******** * * *   *
	-----  --------------------------------------------------   -- --------------------------------  ------  -----	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 -54.10
cremanei	(((((.(((((((((((...((((((((((((.((((((((..((....   ..)). ))))))))))))))))))))...))))))))))).)))))	1.000 -55.10
celegans	(((..((((((((((((((((((((((..((...((((((.(((.  .....))). ))))))..))..))))))))))))))))))))))..)))	0.992 -53.70
cbrenneri	(((((((((((((((...((((((..((.. ......)). ))))))..)))))))))).)))))	1.000 -23.10
cjaponica	((((((....(((((((.((.(((.(((((..(((((.(((    (.........)))).))))).))))).))).)).))))))   )....))))))	1.000 -40.00
ppacificus	(((((....(((((((.((.((((.(((((.((.(((((((.........)  )) )).)).))))))).))   )).)).)))))))...)))))	1.000 -30.60

cbriggsae	chromosome:chrII:7536385:7536474:1	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}
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:47821538:47821667:-1	intergenic ## {SimpF: trf}
cjaponica	chromosome:chrUn:117591227:117591318:-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}