miR-Intess™

candidate novel miRNAs

novel_randfoldOK (14 loci)

block366_cand

Cloning frequencies

absolute	AF16
block366_cand 3arm	0.500
normalized	AF16
block366_cand 3arm	0.001

block366 [novel_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

0.38/0.38

21/21/1.00

0.0

0.0

1

0

1

0

9

22

3arm

2

nd

0.19

2

1

1

na

na

Families

Member of family novel5 (seed GCUGUAG): block366_cand, block367_cand

		reads	miRBase family seed
seed	-------------------------------------------------------------------GCUGUAG----------------------	1	novel
		len	cloning frequencies
			AF16
	------------------------------------------------------------------TGCTGTAGGGATTTTATCTAG---------	21	1
cbriggsae	tgcatagctggaaaattttacagtttcagtgaatctacagaatagttagtttactgaacatgataaTGCTGTAGGGATTTTATCTAGactatgtaa
	************************************************************************************************
	----------------------------------------------------------------------------------------------------------	NM_001103403
	----------------------------------------------------------------------------------------------------------	NM_012772
	----------------------------------------------------------------------------------------------------------	NM_007723
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_171630
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_008855
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_171940
	----------------------------------------------------------------------------------------------------------	NM_007386
	----------------------------------------------------------------------------------------------------------	NM_001111130
	----------------------------------------------------------------------------------------------------------	NM_060402
cbriggsae	((((((((((((((((((((((((((((((((((..((......))..)))))))))).........)))))))).))))..))))).))))))).	0.920 -30.80

cbriggsae

chromosome:chrI:8444807:8444902:1

Opposite_strand|Intronic_coding|NM_001103403|tlk ## Same_strand|Intronic_non-coding|NM_171630|toca-1 ## Opposite_strand|Intronic_non-coding|NM_007386|Aco1 ## {Repeats: no}

block367_cand

Cloning frequencies

absolute	AF16
block367_cand 3arm	0.500
normalized	AF16
block367_cand 3arm	0.001

block367 [novel_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

0.38/0.38

21/21/1.00

0.0

0.0

1

0

1

0

9

22

3arm

2

nd

0.19

2

1

1

na

na

Families

Member of family novel5 (seed GCUGUAG): block366_cand, block367_cand

		reads	miRBase family seed
seed	-------------------------------------------------------------------GCUGUAG----------------------	1	novel
		len	cloning frequencies
			AF16
	------------------------------------------------------------------TGCTGTAGGGATTTTATCTAG---------	21	1
cbriggsae	tgcatagctggaaaattttacagtttcagtgaatctacagaatagttagtttactgaacatgataaTGCTGTAGGGATTTTATCTAGactatgtaa
	************************************************************************************************
	----------------------------------------------------------------------------------------------------------	NM_001103403
	----------------------------------------------------------------------------------------------------------	NM_012772
	----------------------------------------------------------------------------------------------------------	NM_007723
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_171630
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_008855
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_171940
	----------------------------------------------------------------------------------------------------------	NM_007386
	----------------------------------------------------------------------------------------------------------	NM_001111130
	----------------------------------------------------------------------------------------------------------	NM_060402
cbriggsae	((((((((((((((((((((((((((((((((((..((......))..)))))))))).........)))))))).))))..))))).))))))).	0.920 -30.80

cbriggsae

chromosome:chrI:8447434:8447529:1

Opposite_strand|Intronic_coding|NM_001103403|tlk ## Same_strand|Intronic_non-coding|NM_171630|toca-1 ## Opposite_strand|Intronic_non-coding|NM_007386|Aco1 ## {Repeats: no}

block433_cand

Cloning frequencies

absolute	AF16
block433_cand 3arm	1
normalized	AF16
block433_cand 3arm	0.003

block433 [novel_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

0.41/0.41

22/22/1.00

0.0

0.0

1

0

1

0

18

5

3arm

1

nd

0.18

2

1

1

na

na

Clusters

Located in cluster 7: block433_cand, block434_cand

		reads	miRBase family seed
seed	---------------------------------------------------------------------------AUCCUAG------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	--------------------------------------------------------------------------TATCCTAGTGCCCAAACTTTGT----------------------------------	22	1
cbriggsae	--------CAGGT---GGTGTGGTCCAAAGTTTCCGC----GATGGGTTATATAGTTATCGTTAAGACTA----TATCCTAGTGCCCAAACTTTGTACTAGATT---------------CTGAACCTGG-
celegans	CTTGGGCTTAGGCTTAGGCTTAGGCTTAGGCTTAGGCTTAAGATTAGGCTTAGATTTAAGCTTAAGGTTAGACTTATCCTAGG--CATAGTCTTGAGCTTAGTTAGGCTTAGGCTTGGGCTGAGTGTGGG
ppacificus	-----------GCCGAGTTATTG--CGAGGATTATCC----TATTGGGCGAGGA--------------------TATCCTAGTGCCAGAATTCCCC----------------------------------
	*    *   * *    * * **   *     **  *      *                    ********   *  *
cbriggsae	(((((   (((.((((.((((((((..((    (.((((..((((((((........)))))    ))))))).)))..)))))))).)))).)))               ....))))).	1.000 -32.20
celegans	((((.(((((.(((((((((((((((((.((.((((((((((((((.((((((...((((((.......)).))))..)))))  ).)))))))))))))))))))))))))))))))))))))).))))	0.997 -60.20
ppacificus	...(((((...(  (.((((.(((((    (........))))                    ))))))...))...)))))...	0.995 -16.20

cbriggsae	chromosome:chrI_random:635737:635831:-1	{Repeats: no}
celegans	chromosome:chrV:19797026:19797153:-1	intergenic ## {Repeats: (GCCTAA)n 4 145 -1 class=Simple_repeat} ## {SimpF: trf,trf}
ppacificus	chromosome:chrUn:76477541:76477675:-1	intergenic

block434_cand

Cloning frequencies

absolute	AF16
block434_cand 5arm	1
normalized	AF16
block434_cand 5arm	0.003

block434 [novel_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

0.43/0.43

21/21/1.00

0.0

0.0

2

0

1

0

18

7

5arm

2

nd

0.19

2

2

1

na

na

Clusters

Located in cluster 7: block433_cand, block434_cand

Families

Member of family novel4 (seed ACCCUAC): block434_cand, block1560_cand

		reads	miRBase family seed
seed	-------------------ACCCUAC--------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			AF16
	------------------TACCCTACGTCT--------GAAGAAAGT-----------------------------------------------------------	21	2
cbriggsae	GAACCTTAAACGGCATGGTACCCTACGTCT--------GAAGAAAGTACAAATGTGTTCTATTGATACTTTCTCAGCCGACGGGTACCGGACCTATATGGGTTC--
cremanei	----------------GATACCCTACAAATTCCGGGAAGGAAAAACTATAAAT---TCCAGGCGTTTTTCTTTCA------------CGGA-TTATGTGGGGTCTC
	* ********   *        * * *** ** ****   * *    * *  * * ***            ****  *** **** **
cbriggsae	((((((.....((..((((((((..((.((        (.((((((((..((((.....))))..))))))))))).))..))))))))..)).....))))))	1.000 -39.00
cremanei	((.((((((((...((((.(((((((((((.......   .......))))))))))).            )))) ...)))))))).))	1.000 -30.64

cbriggsae	chromosome:chrI_random:636788:636883:-1	{Repeats: no}
cremanei	chromosome:chrUn:136399890:136399963:1	Opposite_strand|Intronic_coding|NM_001006894 ## Same_strand|Intronic_coding|NM_171181

block1423_cand

Cloning frequencies

absolute	AF16
block1423_cand 3arm	1
normalized	AF16
block1423_cand 3arm	0.003

block1423 [novel_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

0.008

no

no

0.45/0.45

22/22/1.00

0.0

0.0

1

0

1

0

17

5

3arm

1

nd

0.23

2

1

1

na

na

		reads	miRBase family seed
seed	------------------------------------------------------------------------------UCAAUAU-------------------------------	1	novel
		len	cloning frequencies
			AF16
	-----------------------------------------------------------------------------TTCAATATACAGGATAGCCCCG-----------------	22	1
cbriggsae	TGTATTCAGTCTCTAGTATTC----CCAGTGCTCACTAGGCTTTCCCGTTT-TGTTGAACTAATAGCAAATT-TAAGTTCAATATACAGGATAGCCCCGTGAGTGGAAAGAAAGCA
cremanei	-----------------------------------CCAGACTTTCCGTGTGAAATTGAACC--TACACAGTT-TAGGTTCAATATACCGGATAGTCTGG-----------------
celegans	----TTTTGCCACAACTATTCTATTCTTTATTTCACCAGACTATCTAGGAAATATTGAACTAATA-CAAATT-TTAGTTCAATATACCGGATGGTCTGGTGAAA------------
cbrenneri	---------------GTATCC-------------------CTTTTCAGTTGATGATTGATTGAAGCGTAACT-TCTGATCAATATGATGACAGGGCTCG-----------------
cjaponica	------------------------------GCCGGCAAGAATATTGAATTGATAATAACAAGCTGTTCTATTATCAATTCAATATTC----TTGCCTGGT----------------
	* *           *               * *    *******        * *  *
	++++++++++++++++++++++++++    ++++++++++++++++++++++++++ ++++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++	NM_111381
	--------------------------    -------------------------- -------------------- ------------------------------------------------	NM_139424
	++++++++++++++++++++++++++    ++++++++++++++++++++++++++ ++++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++	NM_180185
	++++++++++++++++++++++++++    ++++++++++++++++++++++++++ ++++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++	NM_023879
	--------------------------    -------------------------- -------------------- ------------------------------------------------	NM_001115091
	--------------------------    -------------------------- -------------------- ------------------------------------------------	NM_001085641
	--------------------------    -------------------------- -------------------- ------------------------------------------------	NM_080500
	--------------------------    -------------------------- -------------------- ------------------------------------------------	NM_080504
	--------------------------    -------------------------- -------------------- ------------------------------------------------	NM_169728
	--------------------------    -------------------------- -------------------- ------------------------------------------------	NM_169729
	--------------------------    -------------------------- -------------------- ------------------------------------------------	NM_169730
	--------------------------    -------------------------- -------------------- ------------------------------------------------	NM_206497
	--------------------------    -------------------------- -------------------- ------------------------------------------------	NM_131119
cbriggsae	.((.(((..(((.........    .....((((((..((((.(((.((.. (((((((((((........) )).)))))))).)).))).))))..)))))))))..))).)).	0.900 -32.33
cremanei	(((((((.((((.(((..((((((((  ((....... )))))))))).))))))).)))))))	1.000 -30.20
celegans	..........................((((((((((((((((.((..((((((((((((.. ...... )))))))))))).))))))))))))))))))	0.963 -38.60
cbrenneri	....((                   ((..(((.......(((((((((((.....)) )).)))))))....))).))))....	0.988 -14.10
cjaponica	(((((((((((((((((((((((((((((.....))..)))))))))))))))))))    ))))).)))	1.000 -35.60

cbriggsae	chromosome:chrIII:7136741:7136850:-1	Same_strand|Intronic_non-coding|NM_111381|AT3G05090 ## Opposite_strand|Intronic_coding|NM_139424|CG11814 ## Same_strand|Intronic_coding|NM_023879|Rpgrip1 ## {Repeats: no}
cremanei	chromosome:chrUn:82777181:82777330:-1	intergenic
celegans	chromosome:chrIII:4571582:4571679:1	Same_strand|Exonic_coding|F35G12.2.1
cbrenneri	chromosome:chrUn:146941660:146941809:1	intergenic
cjaponica	chromosome:chrUn:25898653:25898718:-1	Same_strand|Intronic_coding|NM_001004193

block1560_cand

Cloning frequencies

absolute	AF16
block1560_cand 5arm	1
normalized	AF16
block1560_cand 5arm	0.003

block1560 [novel_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

0.43/0.43

21/21/1.00

0.0

0.0

2

0

1

0

18

7

5arm

2

nd

0.19

2

2

1

na

na

Families

Member of family novel4 (seed ACCCUAC): block434_cand, block1560_cand

		reads	miRBase family seed
seed	-------------------ACCCUAC--------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			AF16
	------------------TACCCTACGTCT--------GAAGAAAGT-----------------------------------------------------------	21	2
cbriggsae	GAACCTTAAACGGCATGGTACCCTACGTCT--------GAAGAAAGTACAAATGTGTTCTATTGATACTTTCTCAGCCGACGGGTACCGGACATATATGGGTTC--
cremanei	----------------GATACCCTACAAATTCCGGGAAGGAAAAACTATAAAT---TCCAGGCGTTTTTCTTTCA------------CGGAT-TATGTGGGGTCTC
	* ********   *        * * *** ** ****   * *    * *  * * ***            ****  *** **** **
	+++++++++++++++++++++++++++++++++++        ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++  +++++	NM_124925
	+++++++++++++++++++++++++++++++++++        ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++  +++++	NM_184109
	-----------------------------------        ------------------------------------------------------------------  -----	NM_013720
	-----------------------------------        ------------------------------------------------------------------  -----	NM_001085471
	+++++++++++++++++++++++++++++++++++        ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++  +++++	NM_031809
	-----------------------------------        ------------------------------------------------------------------  -----	NM_177595
	+++++++++++++++++++++++++++++++++++        ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++  +++++	NM_031808
	-----------------------------------        ------------------------------------------------------------------  -----	NM_204577
	+++++++++++++++++++++++++++++++++++        ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++  +++++	NM_001102968
	+++++++++++++++++++++++++++++++++++        ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++  +++++	NM_061965
	+++++++++++++++++++++++++++++++++++        ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++  +++++	NM_075282
	-----------------------------------        ------------------------------------------------------------------  -----	NM_001122952
	+++++++++++++++++++++++++++++++++++        ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++  +++++	NM_001108816
	-----------------------------------        ------------------------------------------------------------------  -----	NM_005197
	-----------------------------------        ------------------------------------------------------------------  -----	NM_010905
	-----------------------------------        ------------------------------------------------------------------  -----	NM_001122953
	-----------------------------------        ------------------------------------------------------------------  -----	NM_067174
	-----------------------------------        ------------------------------------------------------------------  -----	NM_065676
cbriggsae	((((((.........((((((((..((.((        (.((((((((..((((.....))))..))))))))))).))..)))))))).........))))))	1.000 -36.07
cremanei	((.((((((((...((((.(((((((((((.......   .......))))))))))).            )))). ..)))))))).))	1.000 -30.64

cbriggsae	chromosome:chrIII:12613939:12614034:-1	Same_strand|Intronic_coding|NM_124925|AT5G55430 ## Opposite_strand|Intronic_non-coding|NM_013720|Mga ## Same_strand|Intronic_non-coding|NM_031808|Capn6 ## Opposite_strand|Intronic_coding|NM_065676|C45G9.11 ## {Repeats: no}
cremanei	chromosome:chrUn:136399890:136399963:1	Opposite_strand|Intronic_coding|NM_001006894 ## Same_strand|Intronic_coding|NM_171181

block2703_cand

Cloning frequencies

absolute	AF16
block2703_cand 5arm	0.111
normalized	AF16
block2703_cand 5arm	0.000

block2703 [novel_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

0.002

no

no

0.43/0.43

21/21/1.00

0.0

0.0

1

0

1

0

23

12

5arm

9

nd

0.14

2

1

1

na

na

		reads	miRBase family seed
seed	------------------------CAGAAGA-----------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-----------------------TCAGAAGA-GATTGTGTGATGG---------------------------------------------------------------------------------------	21	1
cbriggsae	GCTCATCTCTGCTTCCTAGGGACTCAGAAGA-GATTGTGTGATGGAAACCCCCGAGG---------------------TAACCTTGGGTATCTATCGCGGGAATTTTCTGAGCTCGGAACGGCCTGTGTTGC
cremanei	-----------------------TCAGAAGATAACTATGATGCGTTAAATATCGAGTAGAACGTACATCTTCTCCATCTTTCTGCGTATGCTCA--------ATTTTC---------------------TGA
cbrenneri	GC-----------------GGAGTCAGAAGA-GGCATTCGGTT-----CTTCAGAGGATACA---------------CTTGCTTCTGATGTTGAGAGTGGAGATTCTG-----------------ATGTTGC
ppacificus	-----------------------GCAGAAGA-GATTGTTGTATGCGAACCACATGG---------------------------TCGGATCGCCGCTAGGATCATTTTC---------------------CGC
	*******      *                 *                                *             *** *                       *
	++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++                     +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001069271
	++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++                     +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_214466
	------------------------------------ -------------------------                     -----------------------------------------------------------	NM_182461
	++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++                     +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_033380
	++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++                     +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_021760
	++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++                     +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_214466
	++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++                     +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_007740
	++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++                     +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_134452
	++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++                     +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001858
	++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++                     +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001011629
	------------------------------------ -------------------------                     -----------------------------------------------------------	NM_001105289
	++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++                     +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001033832
	++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++                     +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_214509
	++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++                     +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001033832
	++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++                     +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001011005
	------------------------------------ -------------------------                     -----------------------------------------------------------	NM_000393
	++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++                     +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_007737
	++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++                     +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_152888
	++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++                     +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_033381
	++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++                     +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_000495
	------------------------------------ -------------------------                     -----------------------------------------------------------	NM_000090
	------------------------------------ -------------------------                     -----------------------------------------------------------	NM_001004090
	++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++                     +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_070204
cbriggsae	((.(((..(((.((((..(((.((((((((( ..((.(((((((((....(((((((                     ...)))))))..))))))))).)).)))))))))))))))))))...)))..))	1.000 -44.30
cremanei	(((((((((.......((((((.(((.((.(((.(((.......))).))).)).)))..)))))).....        ))))))                     )))	0.781 -16.40
cbrenneri	((                 ((.(((((((.. ..(((((....     ..(((((((.....               ....)))))))......)))))....)))))                 )).))))	1.000 -24.50
ppacificus	((.((((( ((((...((..((((.((......                           ..)).)))).))...)))).)))))                     .))	0.989 -15.10

cbriggsae	chromosome:chrIV:9777517:9777626:1	Same_strand|Intronic_coding|NM_001069271|Os09g0271100 ## Opposite_strand|Intronic_coding|NM_182461|set-33 ## Same_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Opposite_strand|Intronic_non-coding|NM_001004090|Tspan5 ## {Repeats: no}
cremanei	chromosome:chrUn:132234171:132234320:-1	Same_strand|Intronic_coding|NM_205265 ## Opposite_strand|Intronic_coding|NM_001026783
cbrenneri	chromosome:chrUn:186126895:186126971:1	Opposite_strand|UTR_coding|NM_001129475
ppacificus	chromosome:chrUn:91694222:91694371:-1	Opposite_strand|Intronic_coding|NM_025287

block2837_cand

Cloning frequencies

absolute	AF16
block2837_cand 5arm	1
normalized	AF16
block2837_cand 5arm	0.003

block2837 [novel_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

0.006

no

no

0.57/0.57

21/21/1.00

0.0

0.0

1

0

1

0

19

19

5arm

1

nd

0.19

2

1

1

na

na

Clusters

Located in cluster 6: block2837_cand, block2838_cand

		reads	miRBase family seed
seed	--------------------UUCUGGG---------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-------------------GTTCTGGGCAAAGCTTGGTCC--------------------------------------------------------------------------------	21	1
cbriggsae	ttggtccatagtttggcctGTTCTGGGCAAAGCTTGGTCCactttttgagccatttaagccattttgattcttctggagtgtcgcagcgtgtccagaactttcagtcgaaattggtccat
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_065289
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_064155
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_065151
	----------------------------------------------------------------------------------------------------------------------------------	NM_061965
	----------------------------------------------------------------------------------------------------------------------------------	NM_072208
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_075402
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_021005
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001026513
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_067834
	----------------------------------------------------------------------------------------------------------------------------------	NM_067080
	----------------------------------------------------------------------------------------------------------------------------------	NM_001027721
	----------------------------------------------------------------------------------------------------------------------------------	NM_067021
	----------------------------------------------------------------------------------------------------------------------------------	NM_001026557
	----------------------------------------------------------------------------------------------------------------------------------	NM_214627
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001094113
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001091618
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001034557
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_028737
	----------------------------------------------------------------------------------------------------------------------------------	NM_174568
	----------------------------------------------------------------------------------------------------------------------------------	NM_011235
	----------------------------------------------------------------------------------------------------------------------------------	NM_001028318
	----------------------------------------------------------------------------------------------------------------------------------	NM_171081
	----------------------------------------------------------------------------------------------------------------------------------	NM_065139
	----------------------------------------------------------------------------------------------------------------------------------	NM_075117
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_061879
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_075282
	----------------------------------------------------------------------------------------------------------------------------------	NM_061817
	----------------------------------------------------------------------------------------------------------------------------------	NM_064619
	----------------------------------------------------------------------------------------------------------------------------------	NM_068079
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_072208
	----------------------------------------------------------------------------------------------------------------------------------	NM_075409
	----------------------------------------------------------------------------------------------------------------------------------	NM_075409
	----------------------------------------------------------------------------------------------------------------------------------	NM_001028390
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_067659
cbriggsae	.(((.(((...((((((..((((((((((..((((((..((((((..(((....(((((....)))))..)))..))))))))).))).)))))))))).....))))))..))).))).	0.470 -39.10

cbriggsae

chromosome:chrIV:14219792:14219911:1

Same_strand|Intronic_non-coding|NM_065289|Y53G8AR.9 ## Opposite_strand|Intronic_non-coding|NM_061965|F08D12.1 ## Opposite_strand|Intronic_coding|NM_072208|K12B6.7 ## Same_strand|Intronic_coding|NM_067834|smf-3 ## {Repeats: no}

block2838_cand

Cloning frequencies

absolute	AF16
block2838_cand 3arm	1
normalized	AF16
block2838_cand 3arm	0.003

block2838 [novel_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

0.004

no

no

0.43/0.43

21/21/1.00

0.0

0.0

1

0

1

0

11

22

3arm

1

nd

0.29

3

1

1

na

na

Clusters

Located in cluster 6: block2837_cand, block2838_cand

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------UCUGAUU------------------------	1	novel
		len	cloning frequencies
			AF16
	-------------------------------------------------------------------------------------GTCTGATTTACTGGGTTTTCG-----------	21	1
cbriggsae	ttcctgttttatcgacctagctggaattggaatttcagaactcttctttggatttggattttgggatctagaaggttccggaggtGTCTGATTTACTGGGTTTTCGgattctggaga
	*********************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_065289
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_064155
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_065151
	-------------------------------------------------------------------------------------------------------------------------------	NM_061965
	-------------------------------------------------------------------------------------------------------------------------------	NM_072208
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_075402
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_021005
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001026513
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_067834
	-------------------------------------------------------------------------------------------------------------------------------	NM_067080
	-------------------------------------------------------------------------------------------------------------------------------	NM_001027721
	-------------------------------------------------------------------------------------------------------------------------------	NM_067021
	-------------------------------------------------------------------------------------------------------------------------------	NM_001026557
	-------------------------------------------------------------------------------------------------------------------------------	NM_214627
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001094113
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001091618
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001034557
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_028737
	-------------------------------------------------------------------------------------------------------------------------------	NM_174568
	-------------------------------------------------------------------------------------------------------------------------------	NM_011235
	-------------------------------------------------------------------------------------------------------------------------------	NM_001028318
	-------------------------------------------------------------------------------------------------------------------------------	NM_171081
	-------------------------------------------------------------------------------------------------------------------------------	NM_065139
	-------------------------------------------------------------------------------------------------------------------------------	NM_075117
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_061879
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_075282
	-------------------------------------------------------------------------------------------------------------------------------	NM_061817
	-------------------------------------------------------------------------------------------------------------------------------	NM_064619
	-------------------------------------------------------------------------------------------------------------------------------	NM_068079
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_072208
	-------------------------------------------------------------------------------------------------------------------------------	NM_075409
	-------------------------------------------------------------------------------------------------------------------------------	NM_075409
	-------------------------------------------------------------------------------------------------------------------------------	NM_001028390
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_067659
cbriggsae	((((.((((....(((((((...((((..((.((((.((((.(((((..((((((........))))))))))))))).))))...))..)))).)))))))...))))...)))).	0.990 -34.50

cbriggsae

chromosome:chrIV:14220147:14220263:1

Same_strand|Intronic_non-coding|NM_065289|Y53G8AR.9 ## Opposite_strand|Intronic_non-coding|NM_061965|F08D12.1 ## Opposite_strand|Intronic_coding|NM_072208|K12B6.7 ## Same_strand|Intronic_coding|NM_067834|smf-3 ## {Repeats: no}

block4517_cand

Cloning frequencies

absolute	AF16
block4517_cand 3arm	0.500
normalized	AF16
block4517_cand 3arm	0.001

block4517 [novel_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

0.43/0.43

23/23/1.00

0.0

0.0

1

0

1

0

13

7

3arm

2

nd

0.17

2

1

1

na

na

Families

Member of family novel1 (seed AACCCAA): block4517_cand, block4979_cand

		reads	miRBase family seed
seed	----------------------------------------------------------------AACCCAA-------------------------------	1	novel
		len	cloning frequencies
			AF16
	---------------------------------------------------------------TAACCCAA-TCACGAAAATGGCTG---------------	23	1
cbriggsae	----------GGAAAGTTCCTTTCAGCCACTTCGGTTGTGGTTATACAAACAGAAGTTGAT-ATAACCCAA-TCACGAAAATGGCTGATGGTGATGTCTG--
cbrenneri	CTGGGCTTGGCGCAGGGTCTTTGCATCT---------------------ACACAAGTTAACAATAACCCAAGTCAC-----------------ATTTCTCAA
	* * * ** ** ** *                      *** ***** *  ********* ****                 ** ***
	+++++          +++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++ ++++++++++++++++++++++++++++  +++++	NM_027552
	+++++          +++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++ ++++++++++++++++++++++++++++  +++++	NM_001019667
	-----          --------------------------------------------------- --------- ----------------------------  -----	NM_011438
cbriggsae	(((.....((..(((((((.((((((((.(((((((..(((....)))..) ))))))))) )..))))..))))))).)).....))).	0.990 -30.10
cbrenneri	.((((..((((...((((..(((...((                     .....))....)))..))))..)))).                 ....)))).	0.627 -12.20

cbriggsae	chromosome:chrX:10971213:10971300:-1	Same_strand|Intronic_non-coding|NM_027552|Kynu ## Same_strand|Intronic_coding|NM_001019667|SPAC17A2.10c ## Opposite_strand|Intronic_non-coding|NM_011438|Sox12 ## {Repeats: no}
cbrenneri	chromosome:chrUn:189575477:189575604:-1	Opposite_strand|Boundary_coding|NM_002264 ## Opposite_strand|Exonic_coding|NM_001014792 ## Opposite_strand|Intronic_coding|NM_001025113

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candidate novel miRNAs:

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