miR-Intess™

confident novel miRNAs

novel_cloningOK_randfoldOK (7 loci)

block390_novel

Cloning frequencies

absolute	AF16
block390_novel 5arm	7
normalized	AF16
block390_novel 5arm	0.018

block390 [novel_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

no

0.001

no

no

0.57/0.57

21/23/1.00

0.0

0.0

6

0

1

0

13

13

5arm

1

nd

0.22

2

7

1

na

na

		reads	miRBase family seed
seed	--------------AGCCAAU---------------------------------------------------------------------------------------	7	novel
		len	cloning frequencies
			AF16
	-------------CAGCCAATGCCACGACTGTCATG------------------------------------------------------------------------	23	6
	-------------CAGCCAATGCCACGACTGTCA--------------------------------------------------------------------------	21	1
cbriggsae	TTCATATTTTGAGCAGCCAATGCCACGACTGTCATGGTCTAAAAATCCGATAGCTGGATAATCCGATAGTTCATGACAGTGGTACATTGTCTACTCGAAATTTTTGAA
cremanei	-------------TAGCCAATGTCACTACTGTCATG----------------------TAAATGAAAAGCTCATGACAGTGGTACATTGTCTA---------------
	******** *** *********                      ***    * ** ***********************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_100944
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001059280
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001050497
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001059517
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001082159
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_057483
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_204894
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001106587
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001126434
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_116413
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_116412
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_011530
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_022238
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001114583
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_032056
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_120473
	----------------------------------------------------------------------------------------------------------------------	NM_004098
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_100133
cbriggsae	.(((.((((((((.((.(((((..((.(((((((((..(((...(((((.....))))).......)))..))))))))).)).))))).)).))))))))...))).	1.000 -37.30
cremanei	(((.((((((.((((((((((((                      .............)))))))))))))))))).)))	1.000 -24.72

cbriggsae	chromosome:chrI:9169028:9169135:1	Same_strand|Intronic_coding|NM_100944|PGP10 ## Same_strand|Intronic_non-coding|NM_001106587|Tnpo3 ## Opposite_strand|Intronic_non-coding|NM_004098|EMX2 ## {Repeats: no}
cremanei	chromosome:chrUn:121878067:121878214:1	Opposite_strand|Intronic_coding|NM_010228

block818_novel

Cloning frequencies

absolute	AF16
block818_novel 3arm	2.333
normalized	AF16
block818_novel 3arm	0.006

block818 [novel_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

no

0.001

no

no

0.39/0.43

18/23/0.80

0.0

1.4

5

0

1

0

22

5

3arm

3

nd

0.13

2

5

1

na

na

Families

Member of family novel6 (seed AUCACAA): block818_novel, block1069_novel

		reads	miRBase family seed
seed	----------------------------------------------------------------------------------AU--------------CACAA------------------------------------------	5	novel
		len	cloning frequencies
			AF16
	---------------------------------------------------------------------------------TAT--------------CACAAGAACAGATCC---AGC--------------------------	21	2
	---------------------------------------------------------------------------------TAT--------------CACAAGAACAGATCC---AGCAC------------------------	23	2
	---------------------------------------------------------------------------------TAT--------------CACAAGAACAGATCC--------------------------------	18	1
cbriggsae	CATGAATGGTCAGGTTACCAG-----------TCGACCTGTGCTGCCTCTTTCTTTCGTGATATTTTTCACAGCGTAAAAATAT--------------CACAAGAACAGATCC---AGCACAGGTCGTTTACCTGACATTTAT--
cremanei	GACACTCGGCTAGTCTTCCGG---------------------------------------AACTTTTCGAAAGTATC------------------------------------------ACAAGCTGGCAGAATGAC--------
cbrenneri	CTCGAGCAGCTGAAGCTCCAATGTGGTGGAATTCGATCATTATTCATGTTTGTGATAAGAACATTTTTCAAAGCTTTGAAAAATGTTCTTATCACAAACATGAATAATGATCACCTTGCCAAAGGTGGAAATTTCAAGCCTGGAG
cjaponica	---------CTAGCTTCTCGAT--------------------------------------ACCTTGTCCAA--CTTCAA-----------------------GTGGAAGATCA------CAAGGGCGACGAGCTGA---------
	*                                         *  ** *  *     *                                             * *  *      * *
	--------------------------           ----------------------------------------------------              ---------------   ---------------------------  -----	NM_001030387
cbriggsae	.((((((.(((((((......           .((((((((((((..((((((((..(((((((((((........))))))))              )))))))).)))..)   )))))))))))...)))))))))))))	1.000 -51.60
cremanei	..((.((.(((((.(((...(                                       (((((.....)))).))                                          ..)))))))).)).))..	0.997 -12.70
cbrenneri	(((.((..(((((((.((((...((((((.....(((((((((((((((((((((((((((((((((((((....)))))))))))))))))))))))))))))))))))))...))))))....))))..))))).)))).)))	0.941 -70.30
cjaponica	.((((((.(((..                                      .((((((....  ((((..                       ...))))...)      ))))).))).)))))).	1.000 -21.30

cbriggsae	chromosome:chrII:12876993:12877107:-1	Opposite_strand|Intronic_non-coding|NM_001030387|ARIH1 ## {Repeats: no}
cremanei	chromosome:chrUn:145159924:145160078:1	Opposite_strand|Boundary_coding|NM_059414 ## Opposite_strand|Intronic_coding|NM_007741
cbrenneri	chromosome:chrUn:76323104:76323248:-1	intergenic
cjaponica	chromosome:chrUn:397107:397261:1	Opposite_strand|Intronic_coding|NM_001040096 ## Opposite_strand|Boundary_coding|NM_077467

block1069_novel

Cloning frequencies

absolute	AF16
block1069_novel 3arm	2.333
normalized	AF16
block1069_novel 3arm	0.006

block1069 [novel_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

no

0.001

no

no

0.39/0.43

18/23/0.80

0.0

1.4

5

0

1

0

22

5

3arm

3

nd

0.13

2

5

1

na

na

Families

Member of family novel6 (seed AUCACAA): block818_novel, block1069_novel

		reads	miRBase family seed
seed	----------------------------------------------------------------------------------AU--------------CACAA------------------------------------------	5	novel
		len	cloning frequencies
			AF16
	---------------------------------------------------------------------------------TAT--------------CACAAGAACAGATCC---AGC--------------------------	21	2
	---------------------------------------------------------------------------------TAT--------------CACAAGAACAGATCC---AGCAC------------------------	23	2
	---------------------------------------------------------------------------------TAT--------------CACAAGAACAGATCC--------------------------------	18	1
cbriggsae	CATGAATGGTCAGGTTACCAG-----------TCGACCTGTGCTGCCTCTTTCTTTCGTGATATTTTTCACAGCGTAAAAATAT--------------CACAAGAACAGATCC---AGCACAGGTCGTTTACCTGACATTTAT--
cremanei	GACACTCGGCTAGTCTTCCGG---------------------------------------AACTTTTCGAAAGTATC------------------------------------------ACAAGCTGGCAGAATGAC--------
cbrenneri	CTCGAGCAGCTGAAGCTCCAATGTGGTGGAATTCGATCATTATTCATGTTTGTGATAAGAACATTTTTCAAAGCTTTGAAAAATGTTCTTATCACAAACATGAATAATGATCACCTTGCCAAAGGTGGAAATTTCAAGCCTGGAG
cjaponica	---------CTAGCTTCTCGAT--------------------------------------ACCTTGTCCAA--CTTCAA-----------------------GTGGAAGATCA------CAAGGGCGACGAGCTGA---------
	*                                         *  ** *  *     *                                             * *  *      * *
	++++++++++++++++++++++++++           ++++++++++++++++++++++++++++++++++++++++++++++++++++              +++++++++++++++   +++++++++++++++++++++++++++  +++++	NM_001030387
cbriggsae	.((((((.(((((((......           .((((((((((((..((((((((..(((((((((((........))))))))              )))))))).)))..)   )))))))))))...)))))))))))))	1.000 -51.60
cremanei	..((.((.(((((.(((...(                                       (((((.....)))).))                                          ..)))))))).)).))..	0.997 -12.70
cbrenneri	(((.((..(((((((.((((...((((((.....(((((((((((((((((((((((((((((((((((((....)))))))))))))))))))))))))))))))))))))...))))))....))))..))))).)))).)))	0.941 -70.30
cjaponica	.((((((.(((..                                      .((((((....  ((((..                       ...))))...)      ))))).))).)))))).	1.000 -21.30

cbriggsae	chromosome:chrII:12875615:12875729:1	Same_strand|Intronic_non-coding|NM_001030387|ARIH1 ## {Repeats: no}
cremanei	chromosome:chrUn:145159924:145160078:1	Opposite_strand|Boundary_coding|NM_059414 ## Opposite_strand|Intronic_coding|NM_007741
cbrenneri	chromosome:chrUn:76323104:76323248:-1	intergenic
cjaponica	chromosome:chrUn:397107:397261:1	Opposite_strand|Intronic_coding|NM_001040096 ## Opposite_strand|Boundary_coding|NM_077467

block1267_novel

Cloning frequencies

absolute	AF16
block1267_novel 3arm	14
normalized	AF16
block1267_novel 3arm	0.036

block1267 [novel_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

no

0.009

no

no

0.65/0.67

18/20/0.93

0.0

0.0

13

0

1

0

27

6

3arm

1

nd

0.25

3

14

1

na

na

Clusters

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

		reads	miRBase family seed
seed	-----------------------------------------------------------------------GGACCGC---------------------------------------	14	novel
		len	cloning frequencies
			AF16
	----------------------------------------------------------------------CGGACCGCTGATGTGGCATG---------------------------	20	13
	----------------------------------------------------------------------CGGACCGCTGATGTGGCA-----------------------------	18	1
cbriggsae	tccgttattctttccgaaggccccgccttccatgacacccaagcgtgtctggaatgacagaatggtcctcCGGACCGCTGATGTGGCATGaacggcgggagttggtccctaaaagga
	*********************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001102902
	-------------------------------------------------------------------------------------------------------------------------------	NM_001077612
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_065190
	-------------------------------------------------------------------------------------------------------------------------------	NM_001129219
cbriggsae	(((..........((((....((((((...((((.(((...((((.(((((((..(((......))).)))))))))))...))).))))...))))))..)))).........)))	0.880 -46.81

cbriggsae

chromosome:chrIII:218778:218894:-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}

block1486_novel

Cloning frequencies

absolute	AF16
block1486_novel 5arm	3
normalized	AF16
block1486_novel 5arm	0.008

block1486 [novel_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

no

0.009

no

no

0.57/0.62

21/23/1.00

0.0

0.0

4

0

1

0

8

0

5arm_loop

2

nd

0.24

2

6

1

na

na

Families

Member of family novel2 (seed CUCGGUC): block1486_novel, block1488_cand

		reads	miRBase family seed
seed	---------------------CUCGGUC---------------------------------------------------------------------------------	6	novel
		len	cloning frequencies
			AF16
	--------------------ACTCGGTCCGGAGTCAATGGG--------------------------------------------------------------------	21	4
	--------------------ACTCGGTCCGGAGTCAATGGGTT------------------------------------------------------------------	23	1
	--------------------ACTCGGTCCGGAGTCAATGGGT-------------------------------------------------------------------	22	1
cbriggsae	---TCATTC---------TCACTCGGTCCGGAGTCAATGGGTTATC----ATTC--TCAACCTTCCCATTGGCACCAACTTGCACCGTTGTGTTTTGT-----------
cbrenneri	CTTCCGATTTCATGAAGGTCGCTCGGTCCGGAGTCAATGGGTTACC-ATAATTCACCCCATTCTGCCATTGACACCAACTTG-ACCGTTGCTTTTTGGAGAGATTGTAG
cjaponica	CGACAATTCTT-------TCACTCGGTCCGACGTCGGTGGGTTATCAATGAATC--TGAACCCTCCCATCGGCACCAACTTG-ACCGTTG--TTTTACCTGAATTTTTG
	*          ** *********  ***  ******* *    * **     *   * **** * ********** *******  ****
	-----   ------         ----------------------------    ----  ------------------------------------------           -----	NM_117511
	+++++   ++++++         ++++++++++++++++++++++++++++    ++++  ++++++++++++++++++++++++++++++++++++++++++           +++++	NM_001030661
	+++++   ++++++         ++++++++++++++++++++++++++++    ++++  ++++++++++++++++++++++++++++++++++++++++++           +++++	NM_066606
cbriggsae	.((...         .(((.((((..((.(((((((((.....    ....  ........))))))))).)).......))))..)))...)).	0.950 -20.33
cbrenneri	....(((((((..((((((....(((((.((.((((((((...... ..................)))))))).)).....) ))))..))))))....)))))))...	0.985 -27.66
cjaponica	(((.(((((..       ..((.(((((....(((((((((...(((.......  ))).....)))))))))........) ))))..)  ).......))))).)))	0.833 -22.60

cbriggsae	chromosome:chrIII:8971628:8971707:-1	Opposite_strand|Intronic_non-coding|NM_117511|CKI1 ## Same_strand|Intronic_non-coding|NM_001030661|SETD1B ## Same_strand|Intronic_coding|NM_066606|lin-12 ## {Repeats: no}
cbrenneri	chromosome:chrUn:17628257:17628363:-1	Same_strand|Intronic_coding|NM_209159
cjaponica	chromosome:chrUn:128595930:128596026:1	Same_strand|Intronic_coding|NM_145621

block4618_novel

Cloning frequencies

absolute	AF16
block4618_novel 3arm	6
normalized	AF16
block4618_novel 3arm	0.016

block4618 [novel_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

no

0.004

no

no

0.33/0.33

21/21/1.00

0.0

0.0

6

0

1

0

38

2

3arm

1

nd

0.14

2

6

1

na

na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------UGAGGUA----------------------------------------------------------------	6	novel
		len	cloning frequencies
			AF16
	-------------------------------------------------------------------------------------TTGAGGTAATCTTT--GGTTTTG-------------------------------------------------	21	6
cbriggsae	----------TTTTTTTTTGAGGTTCGAGGCTATC--------------AAGCCCAAATGAATACCTTTCAACTAGAATCCAAAGTTGAGGTAATCTTT--GGTTTTGACAGACGATTCGAGCTGATCATGACCTTCAAAAAGAGA-----------
celegans	AATGCGGAAAACAGGTTGTTCGATCCAAAAATAACGATAATTTTTGTTGAAACGCTTGAAAAGACCTAAAA----TAGTGCCGATTTGAGGTATTTTTCAAGCTTTTCAACAAAAATTAACGTTATTTTTTAGATAGAACAACTTTTTTTCTACGTT
cbrenneri	--------------------------GAAGACTTC--------------AAGCCC--------ACCATT------GAATCC---TTTGAGGTAATCTT-------------GAAGATTTC-------------------------------------
ppacificus	-----------------------------AGCGTC-----------------CCGTCAGAAATATCATCAAG---GTGAGTAATATTGAGGTAGTCTT--------------ACGGTAGCA------------------------------------
	*                 *          * *                   ******** * **              *   *
	-----          -------------------------              --------------------------------------------------  ---------------------------------------------           -----	NM_001026149
cbriggsae	(((((((((((((((((((.((.((              ((..(((((.((.((((..((((((.........)))))))))).)))))  ))..)))).))....))))))))...........)))))))))))	0.710 -35.40
celegans	((((..(((((.(((((((((.(((.((((((((((.(((((((((((((((.((((((((((((((.(((    (.......)))).)))).)))))))))).))))))))))))))).))))))))))..))).))))))))).)))))..))))	0.999 -63.60
cbrenneri	((((.((((              (((...        (((.((      ((....   .)))))))...)))             )))).))))	0.997 -11.40
ppacificus	.((...                 ((((.(((..((((.((((.   ((.....)).)))))))).))).              ))))..)).	0.997 -15.00

cbriggsae	chromosome:chrX:15631738:15631857:-1	Opposite_strand|Intronic_coding|NM_001026149|mes-6 ## {Repeats: no}
celegans	chromosome:chrV:4145125:4145277:-1	Opposite_strand|Intronic_coding|Y45G5AL.1a
cbrenneri	chromosome:chrUn:95608622:95608781:-1	Same_strand|Intronic_coding|NM_010206 ## Opposite_strand|Intronic_coding|NM_063731
ppacificus	chromosome:chrUn:97886086:97886245:1	intergenic

block4666_novel

Cloning frequencies

absolute	AF16
block4666_novel 3arm	20
normalized	AF16
block4666_novel 3arm	0.052

block4666 [novel_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

no

0.001

no

no

0.33/0.36

18/22/0.95

0.0

0.0

18

0

1

0

25

2

3arm

1

nd

0.18

1

20

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---------------------------------------	19	miR-51/52/55
seed	------------------------------------------------------------------------GUAUUUU-----------------------------------	1	novel
		len	cloning frequencies
			AF16
	-------------------------------------------------------------------TACCCGTATTTTTATATCCGAG-------------------------	22	18
	-----------------------------------------------------------------------CGTATTTTTATATCCGAG-------------------------	18	1
	-------------------------------------------------------------------TACCCGTATTTTTATATCCG---------------------------	20	1
cbriggsae	aaagcgctaggtgatccttgactaggatataaaaagaacgtgtgtacatgaatccagtgaatacttgTACCCGTATTTTTATATCCGAGccaaggattgccgttgatcgttttc
	******************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------------	NM_026450
	----------------------------------------------------------------------------------------------------------------------------	NM_001011629
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_064155
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001101467
	----------------------------------------------------------------------------------------------------------------------------	NM_205032
cbriggsae	((((((...((..(((((((.((.(((((((((((..(((...(((((.................))))).))).))))))))))).)).)))))))..))......)))))).	0.980 -39.13

cbriggsae

chromosome:chrX:16837573:16837686:-1

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

novel_cloningHIGH_randfoldOK (5 loci)

block869_novel

Cloning frequencies

absolute	AF16
block869_novel 3arm	30
normalized	AF16
block869_novel 3arm	0.078

block869 [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

0.50/0.52

20/21/1.00

0.0

0.0

27

0

1

0

24

7

3arm

1

nd

0.19

2

30

1

na

na

Families

Member of family miR-34 (seed GGCAGUG): cbr-mir-34, block869_novel

		reads	miRBase family seed
seed	---------------------------------------------------------------------GGCAGU--G----------------------------------------------	30	miR-34
		len	cloning frequencies
			AF16
	--------------------------------------------------------------------TGGCAGT--GTAAGTAGCTGGTG---------------------------------	21	27
	--------------------------------------------------------------------TGGCAGT--GTAAGTAGCTGGT----------------------------------	20	3
cbriggsae	TTCTTCGCCACGTGTCTCCAATGCTCTTCACCTCTATTTCCACT----TCCACCCAAGTAATTTGAAGTGGCAGT--GTAAGTAGCTGGTGAAGAA---------ATTGTTTTGAGACGAAGAG
ppacificus	-----TGTAGCAAGGATACGGTAGT-TGTATCTTTATCTTCACTGCTCTCTTCGCAGTCACTGTGAAGAGGCAGTGAGTGAGT------TGAAGAGACGGATGCCATTATCTCT----------
	*   *  *  * *  *  * *  * ** *** * ****    **  * **   * * ***** ******  ** ***      ******          *** * *
	-------------------------------------------------    ---------------------------  -------------------         ------------------------	NM_075282
	-------------------------------------------------    ---------------------------  -------------------         ------------------------	NM_182230
	-------------------------------------------------    ---------------------------  -------------------         ------------------------	NM_001104235
	-------------------------------------------------    ---------------------------  -------------------         ------------------------	NM_001104236
	-------------------------------------------------    ---------------------------  -------------------         ------------------------	NM_206458
cbriggsae	.(((((.......(((((((((..((((((((.((((((.((((    .((((.((((...))))..)))).)))  ).))))))..)))))))).         ))))....)))))))))).	1.000 -38.31
ppacificus	........(((((.((((.( (((.((((((((((((((((.((((((((((...)))))))))))))))))).))..      )))))).)))).))))..)))))..	0.994 -42.60

cbriggsae	chromosome:chrII:1879118:1879226:1	Opposite_strand|Intronic_non-coding|NM_075282|wrs-1 ## Opposite_strand|Intronic_coding|NM_001104235|CG17816 ## {Repeats: no}
ppacificus	chromosome:chrUn:152202579:152202680:-1	intergenic

block969_novel

Cloning frequencies

absolute	AF16
block969_novel 3arm	202
normalized	AF16
block969_novel 3arm	0.527

block969 [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

0.50/0.58

18/22/0.97

0.0

0.0

182

0

1

0

18

2

3arm

1

nd

0.15

2

202

1

na

na

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--------------------------------	199	miR-35/36/38/39/40/41
seed	---------------------------------------------------------------------------GGGUGAG----------------------------	1	novel
seed	----------------------------------------------------------------------UCACCGG---------------------------------	1	novel
seed	------------------------------------------------------------------------ACCGGGU-------------------------------	1	miR-42
		len	cloning frequencies
			AF16
	----------------------------------------------------------------------TCACCGGGTGAGAATCTTCC--------------------	20	182
	----------------------------------------------------------------------TCACCGGGTGAGAATCTTCCAA------------------	22	13
	----------------------------------------------------------------------TCACCGGGTGAGAATCTTC---------------------	19	3
	---------------------------------------------------------------------ATCACCGGGTGAGAATCTTCC--------------------	21	1
	----------------------------------------------------------------------TCACCGGGTGAGAATCTT----------------------	18	1
	-----------------------------------------------------------------------CACCGGGTGAGAATCTTCC--------------------	19	1
	--------------------------------------------------------------------------CGGGTGAGAATCTTCCAA------------------	18	1
cbriggsae	--------GCGGATCTCTCTGGCCTTGGAGGTTTCTCATCGTAGTGATACAAAACCAAAACCATACGATATCACCGGGTGAGAATCTTCCAAGGTAGGAGGATCCTGC--
cremanei	--------------AGTGCTGA----------TGCCGACCTTGGTAATAGGACTAAACTGTGACAAGCTATCACCGGGTGGGCATTGGTTCT------------------
cbrenneri	TTGCGTAGGGGAACCAAGCTAG----------TTCTTACCGCGGTGCTACAACAAGCATAACAT---CTAACACCGGGTAAAAACTAGCTCGGGTC----CCCCTTGCAA
cjaponica	-----------------GCTGG----------TATCCGCGATGGTGTTACA------CTACTGTAATGTATCACCGGGTGGAAACTTGC---------------------
	**            *          **  **                   ** ********    *
	-----        ----------------------------------------------------------------------------------------------------  -----	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	(((((((.((((.((((((((((.((((((((...((((((...................))))))..)))))))).)))))))))).))))))))).))	0.990 -46.41
cremanei	((.((..(          ((((.(((.((((.((((.................)))).))))))).)))))..)).))	0.988 -25.23
cbrenneri	.((((..(((((.((.((((((          ((.(((((.(((((..................   ....)))))))))).)))))))).)).))    )))..)))).	0.969 -43.35
cjaponica	((.((          (.(((((..(((((.((((      .........)))).))))).))))).))).))	1.000 -20.20

cbriggsae	chromosome:chrII:7536263:7536362:1	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:26788554:26788693:-1	intergenic ## {SimpF: trf}
cbrenneri	chromosome:chrUn:41613587:41613679:-1	Same_strand|Intronic_coding|NM_001056672 ## Opposite_strand|Intronic_coding|NM_171042
cjaponica	chromosome:chrUn:117591206:117591345:-1	Opposite_strand|Intronic_coding|NM_171042

block2886_novel

Cloning frequencies

absolute	AF16
block2886_novel 5arm	509
normalized	AF16
block2886_novel 5arm	1.327

block2886 [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

0.33/0.38

19/27/0.93

0.0

0.0

459

0

1

0

19

21

5arm

1

nd

0.14

1

509

1

na

na

Families

Member of family miR-239a (seed UUGUACU): cel-mir-238, cbr-mir-239a, block2886_novel

		reads	miRBase family seed
seed	--------------------UUGUACU---------------------------------------------------------------------------------------	503	miR-239a
seed	------------------------ACUCAUG-----------------------------------------------------------------------------------	6	novel
		len	cloning frequencies
			AF16
	-------------------TTTGTACTCATGTAAGGTGAC--------------------------------------------------------------------------	21	459
	-------------------TTTGTACTCATGTAAGGTGACAAAG----------------------------------------------------------------------	25	27
	-------------------TTTGTACTCATGTAAGGTGA---------------------------------------------------------------------------	20	6
	-----------------------TACTCATGTAAGGTGACAAA-----------------------------------------------------------------------	20	6
	-------------------TTTGTACTCATGTAAGGTGACAAAGAT--------------------------------------------------------------------	27	6
	-------------------TTTGTACTCATGTAAGGTG----------------------------------------------------------------------------	19	3
	-------------------TTTGTACTCATGTAAGGTGACA-------------------------------------------------------------------------	22	1
	-------------------TTTGTACTCATGTAAGGTGACAAA-----------------------------------------------------------------------	24	1
cbriggsae	tccaatattttcggcaattTTTGTACTCATGTAAGGTGACaaagatagcaaatttgaccgtatccacgtcaattatcatgcatcttcatcagtgcaagaatggccttttttgga
	******************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------------	NM_001028060
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_067672
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_075505
cbriggsae	(((((.......(((.(((((((((((.(((.((((((.((..(((((.....((((.(((....)))))))))))).))))))))))).))))))))))).)))....)))))	1.000 -34.50

cbriggsae

chromosome:chrIV_random:64223:64336:1

Opposite_strand|Intronic_coding|NM_001028060|F56B3.4 ## Same_strand|Intronic_non-coding|NM_067672|nhr-41 ## {Repeats: no}

Back to summary page

confident novel miRNAs:

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