miR-Intess™

confident novel miRNAs

novel_cloningHIGH_randfoldOK (5 loci)

block4662_novel

Cloning frequencies

absolute	AF16
block4662_novel 3arm	206
normalized	AF16
block4662_novel 3arm	0.537

block4662 [novel_cloningHIGH_randfoldOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

no

0.001

no

no

0.42/0.50

18/24/0.96

0.0

0.0

133

0

1

0

27

6

3arm

1

nd

0.22

3

206

1

na

na

Clusters

Located in cluster 10: cel-mir-56, cbr-mir-55, block4662_novel, cel-mir-54, block4665_novel, block4666_novel

		reads	miRBase family seed
seed	---------------------------------------------------------------ACCCGUG------------------------------------------	199	novel
seed	-------------------------------------------------------------------GUGAUUC--------------------------------------	5	novel
seed	----------------------------------------------------------------CCCGUGA-----------------------------------------	2	novel
		len	cloning frequencies
			AF16
	--------------------------------------------------------------TACCCGTGATTCCATGTATCGAG---------------------------	23	133
	--------------------------------------------------------------TACCCGTGATTCCATGTATCG-----------------------------	21	31
	--------------------------------------------------------------TACCCGTGATTCCATGTATCGAGT--------------------------	24	30
	------------------------------------------------------------------CGTGATTCCATGTATCGAG---------------------------	19	3
	--------------------------------------------------------------TACCCGTGATTCCATGTAT-------------------------------	19	3
	------------------------------------------------------------------CGTGATTCCATGTATCGA----------------------------	18	2
	---------------------------------------------------------------ACCCGTGATTCCATGTATCGAGT--------------------------	23	1
	--------------------------------------------------------------TACCCGTGATTCCATGTATCGA----------------------------	22	1
	---------------------------------------------------------------ACCCGTGATTCCATGTATCGAG---------------------------	22	1
	--------------------------------------------------------------TACCCGTGATTCCATGTA--------------------------------	18	1
cbriggsae	gagcacgagctgatctttgactcgaacctggacatcgttttgtacacgaagtcaagctgctgTACCCGTGATTCCATGTATCGAGtcaacgatcgcctttaaaaatgtgctt
	****************************************************************************************************************
	--------------------------------------------------------------------------------------------------------------------------	NM_026450
	--------------------------------------------------------------------------------------------------------------------------	NM_001011629
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_064155
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001101467
	--------------------------------------------------------------------------------------------------------------------------	NM_205032
cbriggsae	(((((((((.(((((.(((((((((((.((((.((((....(((((...((.....))..)))))...)))))))).)).))))))))).))))).))).......))))))	0.980 -39.41

cbriggsae

chromosome:chrX:16837100:16837211:-1

Opposite_strand|Intronic_non-coding|NM_026450|Zfp169 ## Same_strand|Intronic_non-coding|NM_064155|Y17G7B.3 ## {Repeats: no}

block4665_novel

Cloning frequencies

absolute	AF16
block4665_novel 3arm	370
normalized	AF16
block4665_novel 3arm	0.965

block4665 [novel_cloningHIGH_randfoldOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

no

0.003

no

no

0.44/0.50

18/20/0.98

0.0

0.0

363

0

1

0

18

3

3arm

1

nd

0.25

2

370

1

na

na

Clusters

Located in cluster 10: cel-mir-56, cbr-mir-55, block4662_novel, cel-mir-54, block4665_novel, block4666_novel

Families

Member of family miR-51/52/55 (seed ACCCGUA): cel-mir-56, cel-mir-54, cbr-mir-55, cbr-mir-52, cbr-mir-51, block4665_novel, block4666_novel

		reads	miRBase family seed
seed	------------------------------------------------------------------------------ACCCGUA--------------------------------------------------	370	miR-51/52/55
		len	cloning frequencies
			AF16
	-----------------------------------------------------------------------------TACCCGTA--CTTCCAACTTCC------------------------------------	20	363
	-----------------------------------------------------------------------------TACCCGTA--CTTCCAACTTC-------------------------------------	19	6
	-----------------------------------------------------------------------------TACCCGTA--CTTCCAACTT--------------------------------------	18	1
cbriggsae	---CGTGA-----GCCGA--------TCCTTGACTGGAACTTGGATATCGTTCG---TATACAGCAAAATAGTCCTGTACCCGTA--CTTCCAACTTCCAAAT--------CAAGGATCGTCGTG----------
cremanei	AATTGTAGATCTCACCGAGTTTTATGTATCTGATCTGAAATGGAATAGC-TTCGAACTGCGGAGCAAAGACACTCTG-ACCCGTAAGCTGCTCAATTTCAGATTAGATACATAGAAATCGGTAAGATATACAATT
	**        ****        *   ***   *** * * *** * ****   *    ******      *** *******  ** *  * ** ** **         *   ****    *
	-----   -----     -----        ----------------------------   ----------------------------  ----------------        --------------          -----	NM_026450
	-----   -----     -----        ----------------------------   ----------------------------  ----------------        --------------          -----	NM_001011629
	+++++   +++++     +++++        ++++++++++++++++++++++++++++   ++++++++++++++++++++++++++++  ++++++++++++++++        ++++++++++++++          +++++	NM_064155
	+++++   +++++     +++++        ++++++++++++++++++++++++++++   ++++++++++++++++++++++++++++  ++++++++++++++++        ++++++++++++++          +++++	NM_001101467
	-----   -----     -----        ----------------------------   ----------------------------  ----------------        --------------          -----	NM_205032
cbriggsae	.....     ..(((        (((((((.(((((.(((((....((.((   ..(((((..........)))))..)).)  ).))))).)))))..)        ))))))))).....	1.000 -33.40
cremanei	(((((((.((((.(((((.((((((((((((((((((((((.((.(((( ((((.....(((((........))))) ...)).)))))).)).)))))))))))))))))))))).))))).)))).)))))))	1.000 -61.90

cbriggsae	chromosome:chrX:16837432:16837527:-1	Opposite_strand|Intronic_non-coding|NM_026450|Zfp169 ## Same_strand|Intronic_non-coding|NM_064155|Y17G7B.3 ## {Repeats: no}
cremanei	chromosome:chrUn:118806979:118807111:-1	Opposite_strand|Intronic_coding|NM_064591

novel_cloningHIGH_multiarm_DicerOK_randfoldOK (3 loci)

sblock19_novel

Cloning frequencies

absolute	AF16
sblock19_novel 5arm	2
sblock19_novel 3arm	26
normalized	AF16
sblock19_novel 5arm	0.005
sblock19_novel 3arm	0.068

sblock19 [novel_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

no

0.001

no

no

0.57/0.63

19/23/0.96

0.0 0.0

0.0 0.0

2 22

0 0

1 1

0 0

16 18

4 6

5arm 3arm

1 1

nd nd

0.19 0.19

2 2

28

1

1

2

Families

Member of family miR-788 (seed CCGCUUC): cbr-mir-788, sblock19_novel

		reads	miRBase family seed
seed	---------------------------------------------------------------GGCAAGA--------------------------------	26	miR-73/74
seed	-----------------CCGCUUC------------------------------------------------------------------------------	2	miR-788
		len	cloning frequencies
			AF16
	--------------------------------------------------------------TGGCAAGACAGGCA-GCGGTAG------------------	21	22
	----------------ACCGCTTCCTTCCTTGCGCAC-----------------------------------------------------------------	21	2
	--------------------------------------------------------------TGGCAAGACAGGCA-GCGGTA-------------------	20	2
	--------------------------------------------------------------TGGCAAGACAGGCA-GCGGTAGAT----------------	23	1
	--------------------------------------------------------------TGGCAAGACAGGCA-GCGGT--------------------	19	1
cbriggsae	AGTCCCTCTCTTTGTCACCGCTTCCTTCCTTGCGCACACCTAATTCCAGTAGTAAAG-GATGTGGCAAGACAGGCA-GCGGTAGATAAGGGAGATTGAGACA
cremanei	--------CCAGTGAGCCGGAATCCTTCTGTGCAC---TCTGCATTCATTATACAAG---------AGGGCAAGAA-GCC--------TGGAATCTGG----
celegans	---------------CACTTTTTCCTTCGC--------CTTTCCCCAAAAGTTCAAGCAAACTTGAAGGGCAAGACTGCG--------GAAAAACTG-----
ppacificus	---------GATCTACCCTCTTCCCTTCT---------TGTGATGTCATCGCAAAAGTGTGGCGACATGGCAAGAA-GGG--------AAGAGGATGC----
	*     *****            *      *      ***         * * ** *   *             *   **
	-------------------------------------------------------------- ------------------ ------------------------------	NM_075282
	-------------------------------------------------------------- ------------------ ------------------------------	NM_182230
	-------------------------------------------------------------- ------------------ ------------------------------	NM_001104235
	-------------------------------------------------------------- ------------------ ------------------------------	NM_001104236
	-------------------------------------------------------------- ------------------ ------------------------------	NM_206458
cbriggsae	.(((.(((.(((((((((((((.(((..(((((.(((((((..............)) ).)))))))))..))).) ))))).)))))))))).....))).	1.000 -40.94
cremanei	((((....((((....(((((.(((.(   (((..............))         )).))))))) ).)        )))...))))	0.994 -20.94
celegans	((.(((((((.....        (((.(((...(((((......)))))...))).))).....)        )))))).))	0.998 -15.00
ppacificus	.......(((((((((((((         (((.(((((..((((....))))..))))).))))))) )))        ))))))....	1.000 -43.70

cbriggsae	chromosome:chrII:1875303:1875402:1	Opposite_strand|Intronic_non-coding|NM_075282|wrs-1 ## Opposite_strand|Intronic_coding|NM_001104235|CG17816 ## {Repeats: no}
cremanei	chromosome:chrUn:117888273:117888412:1	intergenic
celegans	chromosome:chrX:16024050:16024189:-1	intergenic
ppacificus	chromosome:chrUn:108173577:108173716:-1	intergenic

sblock28_novel

Cloning frequencies

absolute	AF16
sblock28_novel 5arm	462
sblock28_novel 3arm	6
normalized	AF16
sblock28_novel 5arm	1.204
sblock28_novel 3arm	0.016

sblock28 [novel_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

no

0.001

no

no

0.39/0.50

19/24/0.99

0.0 0.0

0.0 0.0

422 6

0 0

1 1

0 0

16 17

3 4

5arm 3arm

1 1

nd nd

0.25 0.23

2 1

468

1

1

2

Clusters

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

Families

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

		reads	miRBase family seed
seed	-----------------AUGACAC----------------------------------------------------------------------------------	454	miR-64
seed	-------------------------------------------------------------UUACGGU--------------------------------------	6	novel
seed	---------------------CACAGAA------------------------------------------------------------------------------	4	novel
seed	------------------UGACACA---------------------------------------------------------------------------------	3	novel
seed	--------------------ACACAGA-------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	----------------AATGACACAGAAGAACTGGCAATG------------------------------------------------------------------	24	422
	----------------AATGACACAGAAGAACTGGCAAT-------------------------------------------------------------------	23	12
	----------------AATGACACAGAAGAACTGGC----------------------------------------------------------------------	20	7
	------------------------------------------------------------ATTACGGTCTG-------TGTGCCATAGC-----------------	22	6
	----------------AATGACACAGAAGAACTGG-----------------------------------------------------------------------	19	6
	----------------AATGACACAGAAGAACTGGCAA--------------------------------------------------------------------	22	5
	--------------------ACACAGAAGAACTGGCAATGAAA---------------------------------------------------------------	23	4
	----------------AATGACACAGAAGAACTGGCA---------------------------------------------------------------------	21	2
	-----------------ATGACACAGAAGAACTGGCAATG------------------------------------------------------------------	23	2
	-------------------GACACAGAAGAACTGGCAA--------------------------------------------------------------------	19	1
	-----------------ATGACACAGAAGAACTGGCAAT-------------------------------------------------------------------	22	1
cbriggsae	GGCTAGACATGCCTGCAATGACACAGAAGAACTGGCAATGAAACCAATACTACTTATTTCATTACGGTCTG-------TGTGCCATAGCTGGCGTGTCTCTAGCCA
cjaponica	TGTTTGCCA-------AATGACACAGAA-AGTGAGACATGAGACCAAAACGCACTTTTCCATGTTTGTCTTGATTTCCTGTGCCGCCGC------------AATCA
	* * * **       ************ *    *  **** ***** **    * ** ***    ****        ******   **            *  **
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++       +++++++++++++++++++++++++++++++++	NM_001102902
	----------------------------------------------------------------------------       ---------------------------------	NM_001077612
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++       +++++++++++++++++++++++++++++++++	NM_065190
	----------------------------------------------------------------------------       ---------------------------------	NM_001129219
cbriggsae	(((((((((((((.((.(((.((((..((.((((..(((((((.............))))))).)))))).       )))).))).)).)))))))))..)))).	1.000 -40.42
cjaponica	((.((((..       ..((.(((((.( (((((((((.......((((.....)))).......)))))).)))).))))).))..))            )).))	0.939 -15.64

cbriggsae	chromosome:chrIII:219144:219242:-1	Same_strand|Intronic_non-coding|NM_001102902|LOC100124966 ## Opposite_strand|Intronic_coding|NM_001077612|zgc:153009 ## Opposite_strand|Intronic_non-coding|NM_001129219|nhr-121 ## {Repeats: no}
cjaponica	chromosome:chrUn:83684483:83684568:1	intergenic

sblock69_novel

Cloning frequencies

absolute	AF16
sblock69_novel 5arm	5
sblock69_novel 3arm	330
normalized	AF16
sblock69_novel 5arm	0.013
sblock69_novel 3arm	0.860

sblock69 [novel_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

no

0.001

no

no

0.52/0.59

19/23/0.84

0.0 0.0

0.0 0.0

5 275

0 0

1 1

0 0

28 29

3 5

5arm 3arm

1 1

nd nd

0.30 0.29

4 3

335

1

2

1

Clusters

Located in cluster 9: cbr-mir-74, sblock69_novel, cbr-mir-73

Families

Member of family miR-73/74 (seed GGCAAGA): cel-mir-73, cbr-mir-74, cbr-mir-73, sblock19_novel, sblock69_novel

		reads	miRBase family seed
seed	------------------------------------------------------------------------------GGCAAGA-------------------------------------------	329	miR-73/74
seed	-------------------------------------GGACUUC------------------------------------------------------------------------------------	5	novel
seed	-----------------------------------------------------------------------------UGGCAAG--------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-----------------------------------------------------------------------------TGGCAAGACTA-GGCAGTCCAG-----------------------------	21	275
	-----------------------------------------------------------------------------TGGCAAGACTA-GGCAGTCC-------------------------------	19	53
	------------------------------------TGGACTTCCTTCTCGTTCCCAGC---------------------------------------------------------------------	23	5
	----------------------------------------------------------------------------CTGGCAAGACTA-GGCAGTCCAG-----------------------------	22	1
	-----------------------------------------------------------------------------TGGCAAGACTA-GGCAGTCCAGAT---------------------------	23	1
cbriggsae	GCTACTATTCAAGCCCCTG--------CCACACTTTTGGACTTCCTTCTCGTTCCCAGC--AAAATGCACAGTTTGCTGGCAAGACTA-GGCAGTCCAGATGTGTGGCAGCGGCAGTTTTTGGTGAGT
cremanei	---GTGACCGAAGACGCTGGAAAAGGTCGACACGTTTGGACTTCCGTCTCTTTCCCAGCTGATATTGGATAGCATGCTGGCAAGAA-ATGGCAGTCCAGATGTGTACACCTTCAAGCTCTTGTCAT--
cbrenneri	-----------------------------------TTGGGCTTCCAAGTC-TACCCAGC---ACTTAAAAAAGTGGCTGGCAAGACTATGGCAGTCCAC-----------------------------
cjaponica	---------AAGGCCACTG-----------CACGTTTGGGCTTCCTTCTCCTTCCCAGC---AACCCTCAATTTTGCTGGCAAGACTA-GGCAGTCTACACGTGCAGTGGTCTT--------------
	**** *****   ** * ******           *    **********  * ******* *
	------------------------        --------------------------------  --------------------------- --------------------------------------------	NM_001087279
	------------------------        --------------------------------  --------------------------- --------------------------------------------	NM_072843
	++++++++++++++++++++++++        ++++++++++++++++++++++++++++++++  +++++++++++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++	NM_001109816
	------------------------        --------------------------------  --------------------------- --------------------------------------------	NM_065440
	++++++++++++++++++++++++        ++++++++++++++++++++++++++++++++  +++++++++++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++	NM_020367
cbriggsae	(((((((.....(((.(((        ((((((.((((((((.(((..((....(((((  (((........))))))))...))..) )).)))))))).))))))))).)))......)))).)))	1.000 -55.40
cremanei	(((((..((((.(((....(((((..(((((((((((((.((((.((((..(((((((.(((...))).)).))))).)))). )))).)))))))))))))..)))))..))))))))))))	1.000 -51.70
cbrenneri	.((((((.((((((( (..(((((   ((((....))))).))))..))))).))).)))))).	1.000 -28.70
cjaponica	((((((((((           (((((.((((((.(((....(((.(((((   ((.........))))))).)))...) )).)))))).)))))))))))))))	1.000 -49.30

cbriggsae	chromosome:chrX:4493687:4493803:-1	Opposite_strand|Intronic_non-coding|NM_001087279|fbxl5 ## Same_strand|Intronic_coding|NM_001109816|MHC ## Same_strand|Intronic_non-coding|NM_020367|PARP11 ## {Repeats: no}
cremanei	chromosome:chrUn:103837391:103837512:-1	intergenic
cbrenneri	chromosome:chrUn:1030240:1030397:-1	intergenic
cjaponica	chromosome:chrUn:6831718:6831807:1	intergenic

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confident novel miRNAs:

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