miR-Intess™

candidate novel miRNAs

novel_randfoldOK (8 loci)

block659_cand

Cloning frequencies

absolute	CE1
block659_cand 5arm	0.500
normalized	CE1
block659_cand 5arm	0.000

block659 [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

0.009

no

no

0.65/0.65

20/20/1.00

0.0

0.0

1

0

1

0

9

20

5arm

2

nd

0.20

2

1

1

na

na

		reads	miRBase family seed
seed	----------UCCAGUA---------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	---------GTCCAGTAGCGGCAGCTTGC---------------------------------------------------------------------------	20	1
celegans	ctttaacttGTCCAGTAGCGGCAGCTTGCttacgagcagcattttcccgaatcgccttcacctctgcctcctcagcatcctgttgctccttgacaatcgtaagt
	********************************************************************************************************
	------------------------------------------------------------------------------------------------------------------	Y74C9A.4a Y74C9A.4 Y74C9A.4
	------------------------------------------------------------------------------------------------------------------	Y74C9A.4b Y74C9A.4 Y74C9A.4
celegans	(((....(((((.((.((((((((..((((...((((((........((...)).........)))).))...))))..)))))))).)).)))))....))).	1.000 -27.73

celegans

chromosome:I:23262:23365:1

Opposite_strand|Intronic_coding|Y74C9A.4b|Y74C9A.4 ## Y74C9A.4|protein_coding|Y74C9A.4|Y74C9A.4b [Source:RefSeq_peptide;Acc:NP_490662] ## {SimpF: yk383e12 1 RNAi}

block1572_cand

Cloning frequencies

absolute	CE1
block1572_cand 5arm	1
normalized	CE1
block1572_cand 5arm	0.001

block1572 [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

0.43/0.43

21/21/1.00

0.0

0.0

1

0

1

0

16

20

5arm

1

nd

0.24

2

1

1

na

na

		reads	miRBase family seed
seed	-----------------------------UCUGAAA------------------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	----------------------------CTCTGAAAATAGGCAGTCTAC-----------------------------------------------------------------------------------------------------	21	1
celegans	--TGGAAG----------CTGGAAATTTCTCTGAAAATAGGCAGTCTACCGGAC---------ATCTCAGGTCTTACATAGGTAGTTTGTAATTGGAATCCGGAGATTGCAATTT--AATTTTCAATTTCCGTTTTTCAT----------
cremanei	----------------------------ATCTGAAAATAGGATTTTT----------------GTCTCAAAAATT------GGATTTTTTGTC------TCAAAAATCGGAATTTTGGACTAAAAATCTGCAATTTTCAGCCCAAAACTT
cbriggsae	GATGGAGGTCTCCTAATTTTATTGATTTTTCTGAAAATTGTGAGTTTTTTGGGATTTTTTTGAATTTCGAAATTTTTTCAAAAAATTTTTTTCAAGTTTTCAAATTTTTGGATTTTTAAATGAGAGT-----ATTTTCATC---------
	********* *    * *                 * **     **        * *** *          *  *  *    ****   * *   * *      ******
celegans	((((((          .(((((((.....(((((((..(((((((.(((((.         .((.(((...(((((.........)))))))))).)))))))))))).....  .)))))))))))))).)))))).	0.990 -34.20
cremanei	..((((((((.((((((((                (((.(((((.((      .(((((((....      ..))))))).)).)))))))).))))))))...))))))))..........	1.000 -26.70
cbriggsae	((((((((((((.....((((..(((((...((((((((..(((((((((((((...(((((.....)))))...)))))))))))))......)))))))).......)))))..))))...))).     )))))))))	0.934 -29.50

celegans	chromosome:II:3246178:3246294:-1	intergenic ## {SimpF: WRM0630dD06 -1 fosmid}
cremanei	chromosome:chrUn:144178829:144178985:-1	intergenic ## {SimpF: trf}
cbriggsae	chromosome:chrUn:6796066:6796201:-1	Same_strand|Intronic_coding|NM_061817

block2960_cand

Cloning frequencies

absolute	CE1
block2960_cand 5arm	1
normalized	CE1
block2960_cand 5arm	0.001

block2960 [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

0.67/0.67

24/24/1.00

0.0

0.0

2

0

1

0

16

9

5arm

2

nd

0.25

2

2

1

na

na

Families

Member of family novel4 (seed GCCAAGC): block2960_cand, block3587_cand

		reads	miRBase family seed
seed	-----------------GCCAAGC-------------------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			CE1
	----------------TGCCAAGCGCTACG-TCACCAGGGG--------------------------------------------------------------------------	24	2
celegans	GTCGACCGAGCGTCCGTGCCAAGCGCTACG-TCACCAGGGGATAACTGTCGGAAGGCGGTTAGTCCCGGGTGCATAAGGAGTCGTGGATGGTTCAGGACCGAAAGGTAGCAGACA
cbriggsae	----------------TGCCAAGCGCTACG-TCGCCAGGGGTTGTCTGTCGGAGGACGGACGGTCCCGGGCGCATAAGGAGTGGTCTA---------------------------
cbrenneri	---------GCGTCCGTGCCAAGCGCTACG-TCGCTAGGGGTCATCAGACGGAAGTTTGAAGGTCCCGGGCGCATAAGGAGTGGTGTATGGTTCAGG------------------
cjaponica	---------------GTGCCAAGCGCTGCG-TCGCCAGGGGTCATCCGGCGGAGGCTGGGCGGTCCCGGGCGCTTAAGGAGTGGTGTATGGCTC---------------------
cremanei	----------------TGCCAAGCGCTGCGTTCACTAGGGGTCATCCTTCGGAAGAGGGGCGGTCCCGGGTGCATAAGGAGCGGTGGATGGTT----------------------
	*********** ** ** * *****    *   **** *   *   ******** ** *******  **  *
	----------------------------------- -----------------------------------------------------------------------------------------	R144.1 R144.1 klp-6
celegans	(((.(((...(((((..((((.(((((..( (((((.(((..((((((((....))))))))..))).)))).))....)).)))...))))...))).))...)))....))).	0.920 -49.10
cbriggsae	.((((....((..( (((((.(((..((((((((....))))))))..))).)))).))..))..))))...	0.985 -33.00
cbrenneri	....((..((((.(((((((. .((((.((((((.((((((....)))))).)))))).))))........))))))).))))...))	0.999 -37.90
cjaponica	..((((.(((((((. .((((.((((((..(((((....)))))..)))))).))))........))))))).))))..	0.876 -38.40
cremanei	.((((..((((((...((((.((((((..(((((....)))))..)))))).))))........))))))..)))).	1.000 -34.90

celegans	chromosome:III:5031463:5031576:-1	Opposite_strand|Intronic_coding|R144.1|R144.1 ## R144.1|protein_coding|klp-6|klp-6 encodes a predicted monomeric kinesin and member of the UNC-104 family. [Source: WormBase] ## {SimpF: WRM065dA04 -1 fosmid,WRM0617cE05 -1 fosmid,WRM0623aF05 -1 fosmid,WRM068bC01 -1 fosmid,WRM0610cB11 -1 fosmid,WRM0624cG01 -1 fosmid}
cbriggsae	chromosome:chrX:20313769:20313922:-1	Opposite_strand|Exonic_coding|NM_065481
cbrenneri	chromosome:chrUn:106785266:106785352:1	intergenic
cjaponica	chromosome:chrUn:12702827:12702904:-1	intergenic
cremanei	chromosome:chrUn:133256206:133256359:1	Opposite_strand|Exonic_coding|NM_065481 ## Same_strand|Intronic_coding|NM_001002694

block3587_cand

Cloning frequencies

absolute	CE1
block3587_cand 5arm	1
normalized	CE1
block3587_cand 5arm	0.001

block3587 [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

0.67/0.67

24/24/1.00

0.0

0.0

2

0

1

0

16

9

5arm

2

nd

0.25

2

2

1

na

na

Families

Member of family novel4 (seed GCCAAGC): block2960_cand, block3587_cand

		reads	miRBase family seed
seed	-----------------GCCAAGC--------------------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			CE1
	----------------TGCCAAGCGCTACG-TCACCAGGGG---------------------------------------------------------------------------	24	2
celegans	GTCGACCGAGCGTCCGTGCCAAGCGCTACG-TCACCAGGGGATAACTGTCGGAAGGC-GGTTAGTCCCGGGTGCATAAGGAGTCGTGGATGGTTCAGGACCGAAAGGTAGCAGACA
cremanei	----------------TGCCAAGCGCTGCGTTCACTAGGGGTCATCCTTCGGAAGAG-GGGCGGTCCCGGGTGCATAAGGAGCGGTGGATGGTT----------------------
cbriggsae	----------------TGCCAAGCGCTACG-TCGCCAGGGGTTGTCTGTCGGAGGAC-GGACGGTCCCGGGCGCATAAGGAGTGGTCTA---------------------------
cbrenneri	---------GCGTCCGTGCCAAGCGCTACG-TCGCTAGGGGTCATCAGACGGAAGTT-TGAAGGTCCCGGGCGCATAAGGAGTGGTGTATGGTTCAGG------------------
cjaponica	----------------TGCCAAGCGCCGCG-TCGCCAGGGGCAGTCTGTCGGAAGGCTGGGCTGTCCCGGGTGCATAAGGAGCGGTGTA---------------------------
	**********  ** ** * *****    *   **** *    *   ******** **********  **  *
celegans	(((.(((...(((((..((((.(((((..( (((((.(((..((((((((....))) )))))..))).)))).))....)).)))...))))...))).))...)))....))).	0.920 -49.10
cremanei	.((((..((((((...((((.((((((..(((((....))) ))..)))))).))))........))))))..)))).	1.000 -34.90
cbriggsae	.((((....((..( (((((.(((..((((((((....))) )))))..))).)))).))..))..))))...	0.985 -33.00
cbrenneri	....((..((((.(((((((. .((((.((((((.((((((....))) ))).)))))).))))........))))))).))))...))	0.999 -37.90
cjaponica	......(((((((. .((((.(((((((((((((....))).)))))))))).))))........))))))).	1.000 -40.50

celegans	chromosome:III:5211275:5211388:1	intergenic ## {SimpF: WRM0613bD07 1 fosmid,WRM067cB03 1 fosmid,WRM0621cH09 1 fosmid,WRM0641dA10 1 fosmid}
cremanei	chromosome:chrUn:133256206:133256359:1	Opposite_strand|Exonic_coding|NM_065481 ## Same_strand|Intronic_coding|NM_001002694
cbriggsae	chromosome:chrX:20313769:20313922:-1	Opposite_strand|Exonic_coding|NM_065481
cbrenneri	chromosome:chrUn:171087346:171087432:1	intergenic
cjaponica	chromosome:chrUn:142157721:142157874:1	Opposite_strand|Exonic_coding|NM_065481 ## Same_strand|Intronic_coding|NM_073733

block4332_cand

Cloning frequencies

absolute	CE1
block4332_cand 3arm	2
normalized	CE1
block4332_cand 3arm	0.001

block4332 [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

0.45/0.45

20/20/1.00

0.0

0.0

2

0

1

0

30

6

3arm

1

nd

0.05

1

2

1

na

na

Families

Member of family miR-80/81/82 (seed GAGAUCA): cel-mir-82, cel-mir-81, cel-mir-80, block4332_cand

		reads	miRBase family seed
seed	-----------------------------------------------------------GAGAUCA------------------------------------------	2	miR-80/81/82
		len	cloning frequencies
			CE1
	----------------------------------------------------------AGAGATCAGGCAATAGGTTC------------------------------	20	2
celegans	GTGACGATATTCAATTGCAACCTGTTGGTTGATCTCCTAC----CAAATAATGGA-TAAGAGATCAGGCAATAGGTTCAAAAGTGAATAATATTGATTTTTGAGTGAC
cbriggsae	----------------GAAACTTTGATGTTGTCATCTCA------AAATCAGTGA-GATCAGCTCA------AGGCTC------------------------------
cjaponica	------------------GGCATTCAACTTGATCTCCTACACCTCAATTCGAGGAGTAAGAGATCAAGGGTTTGACCC------------------------------
ppacificus	-----------------CTATATTTTCTCTGATCTCTCGCTC--TGCCTGACCGG-CAAGAGATCACGGAAAATGTGA------------------------------
cremanei	-----------------TGGCTTATTGATTGGTCTCCTAC----CACTTTTTGGA-TATGAGATCATTCGATGAGCCC------------------------------
	*      **   **            *    *   *  ** ***
celegans	.......((((((.(((.(((((((((.((((((((.(((    ((.....))). )).)))))))).))))))))))))...))))))...................	0.690 -33.70
cbriggsae	....((((((.((((..((((((      .......))) ))))))))))      )))...	1.000 -13.70
cjaponica	((((.....(((((((((.(((.((((.....)))).))).)))))))))....)).)).	0.983 -25.20
ppacificus	.((((((((((.((((((((.....  ((((.....)) )))))))))).)))))))))).	1.000 -24.60
cremanei	.((((((((((.(((((((.(((    ((.....))). )).))))))).)))))))))).	1.000 -27.40

celegans	chromosome:IV:6660600:6660702:-1	intergenic ## {SimpF: WRM068bB04 -1 fosmid,WRM067cF04 -1 fosmid}
cbriggsae	chromosome:chrX:13344079:13344221:-1	Opposite_strand|Intronic_coding|NM_001108848 ## Same_strand|Intronic_coding|NM_001086847
cjaponica	chromosome:chrUn:22177437:22177579:-1	intergenic
ppacificus	chromosome:chrUn:45735264:45735406:-1	Same_strand|Intronic_coding|NM_063191
cremanei	chromosome:chrUn:120634238:120634380:1	intergenic

block4864_cand

Cloning frequencies

absolute	CE1
block4864_cand 3arm	1
normalized	CE1
block4864_cand 3arm	0.001

block4864 [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

0.007

no

no

0.21/0.21

24/24/1.00

0.0

0.0

1

0

1

0

14

9

3arm

1

nd

0.21

3

1

1

na

na

		reads	miRBase family seed
seed	------------------------------------------------------------------UUAAUAG------------------------------	1	novel
		len	cloning frequencies
			CE1
	-----------------------------------------------------------------GTTAATAGTGATTGATAATATTAG--------------	24	1
celegans	aattagcattttcaggaatagtttattgagcacagtaactgtccaatgttgtacctgcattggttGTTAATAGTGATTGATAATATTAGaatatatgttgatt
	*******************************************************************************************************
celegans	(((((((((.(((...((((..(((((((.(((..((((...(((((((.......)))))))..))))...))).))))))))))).)))...)))))))))	0.970 -25.20

celegans

chromosome:IV:14937718:14937820:-1

intergenic ## {SimpF: WRM0637dE03 -1 fosmid,WRM0637cB12 -1 fosmid,WRM0641aG05 -1 fosmid,WRM0612aC11 -1 fosmid}

block5234_cand

Cloning frequencies

absolute	CE1
block5234_cand 3arm	1
normalized	CE1
block5234_cand 3arm	0.001

block5234 [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

0.48/0.48

21/21/1.00

0.0

0.0

1

0

1

0

19

5

3arm

1

nd

0.19

3

1

1

na

na

Clusters

Located in cluster 4: sblock43_cand, block5234_cand

		reads	miRBase family seed
seed	----------------------------------------------------------------------AAGACCA----------------------------------	1	novel
		len	cloning frequencies
			CE1
	---------------------------------------------------------------------AAAGACCA--CCGGTTACACTAC-------------------	21	1
celegans	CGGAAAAACCATGCCTCCCAATGGTGAGTGTAACCGCACGTCTTGTTTCAAAACTCAATATATGGA--AAAAGACCA--CCGGTTACACTACATTATTGGTTGGAGTCTGA
cremanei	--GTATAAAAATCTCTGAGATTTGTCCAAAACTGACTGAGTTCTGATAAAAAAATGTAT---TGGCAGAAAAGACCA-----CTTGGACCA-------------AATCTCA
cbrenneri	CGG------------TCCAATTTGT---------------TCTTGTCCGGATGATCATTATCTGGC--TAAAGACCATGCAACTTGTACTA--------------------
	*            *   * * **               *  **     *   *   *   ***    ********      **  ** *
celegans	((((.........((..(((((((((((((((((((...(((((.(((((............))))  ).)))))..  .)))))))))).)))))))))..))..)))).	0.830 -39.10
cremanei	.............((((((((((((((......((...(((((...((........)   )..))))).))....     .)))))).)             )))))))	0.950 -19.40
cbrenneri	.((            (.(((.((((               ((((..((((((((...)))))))).  ..))))....)))).))).))).	0.998 -15.80

celegans	chromosome:IV:1027193:1027299:1	intergenic
cremanei	chromosome:chrUn:93036443:93036530:1	intergenic ## {SimpF: trf}
cbrenneri	chromosome:chrUn:191779505:191779651:1	Same_strand|Boundary_coding|NM_058870

block5734_cand

Cloning frequencies

absolute	CE1
block5734_cand 5arm	2
normalized	CE1
block5734_cand 5arm	0.001

block5734 [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

0.30/0.30

20/20/1.00

0.0

0.0

2

0

1

0

28

8

5arm

1

nd

0.25

3

2

1

na

na

		reads	miRBase family seed
seed	-----------------------------GGCAGAU------------------------------------------------------------------------------------------------	2	miR-72
		len	cloning frequencies
			CE1
	----------------------------AGGCAGAT------------CAATCAATTTTT------------------------------------------------------------------------	20	2
celegans	TGTATATTGTTTAGTCCATTCAGTTTGTAGGCAGAT------------CAATCAATTTTTAGGTTTATATAAATAATCCTAAAGTCGATTGCTCTACCCACAAAAAGTAATGTTGACTTGAAGTTATGTATA
cremanei	----------------------------AGGCAGAT------------CGG--AGATCGTAGATATTCAGAAGCCAAT-----GTCACTT-CTCCATC---------------------------ACCT---
cbrenneri	TGCCGGCA--------------------AGGCAGATGCCGGTAAATGCCGGTAAAATCGCAAATTT-TACCGGTAAACTT---ACCGGTT-TTTTACC---------------------------GTCGGTA
	********            *    *  *   *  * *  *      *         *  **  *  * *
celegans	(((((((..((.((((((((...(((((.((.(((.            (((((...(((((((.((((....)))).)))))))..))))).))).)).)))))....))))..)))).))....)))))))	1.000 -29.80
cremanei	(((..(((            .((  (((..((.((((((........)))     ))))).) )))))))                           .)))	1.000 -14.10
cbrenneri	(((((((.                    .((.(((.((((((((.((((((((((((.....)))) ))))))))...))   )))))). .))).))                           )))))))	0.999 -37.50

celegans	chromosome:IV:10914560:10914679:1	intergenic ## {SimpF: WRM0618aB12 1 fosmid,WRM063cG12 1 fosmid,WRM0639cD01 1 fosmid}
cremanei	chromosome:chrUn:135048028:135048187:1	Same_strand|Boundary_non-coding|NM_070423
cbrenneri	chromosome:chrUn:177580941:177581020:1	intergenic

novel_cloningHIGH_multiarm_DicerNOK_randfoldOK (2 loci)

sblock65_cand

Cloning frequencies

absolute	CE1
sblock65_cand 5arm	0.833
sblock65_cand 3arm	22.500
normalized	CE1
sblock65_cand 5arm	0.001
sblock65_cand 3arm	0.016

sblock65 [novel_cloningHIGH_multiarm_DicerNOK_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

0.43/0.59

18/23/0.96

1.0 1.0

1.0 0.7

2 25

0 0

1 1

0 0

19 16

9 7

5arm 3arm

3 3

nd nd

0.00 0.00

0 0

49

1

-1

1

Families

Member of family novel3 (seed CCGGCCC): sblock65_cand, sblock79_cand

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------GUAUUAA----------------------------------------------------	23	novel
seed	---------------------------------------------------------------------------------AUGUAUU------------------------------------------------------	7	novel
seed	-------------------------------------------------------------------------------------AUUAAAC--------------------------------------------------	7	novel
seed	---------------------------------------------------------------------------------------UAAACGG------------------------------------------------	5	novel
seed	------------------------------------------------------------------------------------UAUUAAA---------------------------------------------------	4	novel
seed	---------------------CCGGCCC------------------------------------------------------------------------------------------------------------------	1	novel
seed	-----------------------GGCCCU----------------U------------------------------------------------------------------------------------------------	1	novel
seed	--------------------------------------------------------------------------------------UUAAACG-------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	----------------------------------------------------------------------------------TGTATTAAACGGTA------------------AGGGCCGGC-------------------	23	11
	----------------------------------------------------------------------------------TGTATTAAACGGTA------------------AGGGCCGG--------------------	22	6
	------------------------------------------------------------------------------------TATTAAACGGTA------------------AGGGCCGGCT------------------	22	4
	--------------------------------------------------------------------------------------TTAAACGGTA------------------AGGGCCGGCTG-----------------	21	4
	----------------------------------------------------------------------------------TGTATTAAACGGTA------------------AGGGCCG---------------------	21	3
	----------------------------------------------------------------------------------TGTATTAAACGGTA------------------AGGGCC----------------------	20	3
	--------------------------------------------------------------------------------CATGTATTAAACGGTA------------------AGGGC-----------------------	21	3
	-----------------------------------------------------------------------------------GTATTAAACGGTA------------------AGGGCCGGC-------------------	22	3
	------------------------------------------------------------------------------------TATTAAACGGTA------------------AGGGCCGGCTG-----------------	23	2
	--------------------------------------------------------------------------------CATGTATTAAACGGTA------------------AGGGCC----------------------	22	2
	--------------------------------------------------------------------------------CATGTATTAAACGGTA------------------AGGGCCG---------------------	23	2
	----------------------CGGCCCT----------------TACCGTTTAAT--------------------------------------------------------------------------------------	18	1
	-----------------------------------------------------------------------------------GTATTAAACGGTA------------------AGGGCCGGCT------------------	23	1
	--------------------------------------------------------------------------------------TTAAACGGTA------------------AGGGCCGGCTGG----------------	22	1
	-------------------------------------------------------------------------------------ATTAAACGGTA------------------AGGGCCGGCTGG----------------	23	1
	------------------------------------------------------------------------------------TATTAAACGGTA------------------AGGGCC----------------------	18	1
	--------------------GCCGGCCCT----------------TACCGTTTAATAC------------------------------------------------------------------------------------	22	1
celegans	-AAATGAATGTAAAGCCCCAGCCGGCCCT----------------TACCGTTTAATACATGTTCC---CGGTCGATGCACCATGTATTAAACGGTA------------------AGGGCCGGCTGGGGCTTTACAACATTT-
cremanei	ACAGAGAACGC---GTTATATTAGGTTGTTCAGGTCATGTAAAGGTGTAATTAAATACACCGTTCGTGAATAAGGTGAAATATGTATTAAAATGCATTTTTACATGACCTGAATAAGCTCATCACTAGCTTTTTATTACTGT
cbriggsae	---------------CATTTGTTGGCGTTGGCGGT----------TGCGGTTGAAA---------------TAGTTCAAAACTGTATTAAACTCCA-------------------AGCCCAAGTG-----------------
cjaponica	---------------TGGAAACCGGTTTTTTTGT-----------AACCGGTGGAAACCGGTTTC---TACCGGTTTTCACCGGTATTAAAAAACA-----------------------------CCGGTTTTTA-------
	**   *                      *  *                  * *       ********    *
	----- ----------------------------                --------------------   ----------------------------                  --------------------------- -----	F55F3.1.1 F55F3.1 aakb-1
celegans	(((((..(((((((((((((((((((((                ((((((((((((((((....   ((.....))...))))))))))))))))                  ))))))))))))))))))))).)))))	1.000 -73.00
cremanei	((((((((.((   ........((.((((((((((((((((((((((((.((.((((((...((((.........))))...)))))).)).)))))))))))))))))))))))).))........)).))))....))))	0.989 -46.29
cbriggsae	((((((..(((.((((.(((          ((((((((((.               ...))))..))))))....))))))                   ))))))))))	1.000 -18.50
cjaponica	((((((((((((((((((.           .((((((((((((((((...   .))))))))))))))))..))))))).)                             ))))))))))	1.000 -46.10

celegans	chromosome:X:13759150:13759252:-1	Opposite_strand|Boundary_non-coding|F55F3.1.2|F55F3.1 ## Opposite_strand|Intronic_non-coding|F55F3.1.1|F55F3.1 ## F55F3.1|protein_coding|aakb-1|AMP-Activated Kinase Beta subunit family member (aakb-1) [Source:RefSeq_peptide;Acc:NP_510298] ## {SimpF: WRM0635dA09 -1 fosmid,WRM0620cB06 -1 fosmid,WRM0641dG10 -1 fosmid,WRM0622bA08 -1 fosmid}
cremanei	chromosome:chrUn:93758642:93758780:-1	intergenic
cbriggsae	chromosome:chrX:7209357:7209499:-1	Opposite_strand|Intronic_coding|NM_178660
cjaponica	chromosome:chrUn:80799570:80799712:-1	intergenic ## {SimpF: trf,trf}

sblock79_cand

Cloning frequencies

absolute	CE1
sblock79_cand 5arm	0.833
sblock79_cand 3arm	22.500
normalized	CE1
sblock79_cand 5arm	0.001
sblock79_cand 3arm	0.016

sblock79 [novel_cloningHIGH_multiarm_DicerNOK_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

0.43/0.59

18/23/0.96

1.0 1.0

1.0 0.7

2 25

0 0

1 1

0 0

25 27

10 7

5arm 3arm

3 3

nd nd

0.00 0.00

0 0

49

1

-1

1

Families

Member of family novel3 (seed CCGGCCC): sblock65_cand, sblock79_cand

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------------------------------GUAUUAA---------------------------------------------------------------	23	novel
seed	-----------------------------------------------------------------------------------------------------AUGUAUU-----------------------------------------------------------------	7	novel
seed	---------------------------------------------------------------------------------------------------------AUUAAAC-------------------------------------------------------------	7	novel
seed	-----------------------------------------------------------------------------------------------------------UAAACGG-----------------------------------------------------------	5	novel
seed	--------------------------------------------------------------------------------------------------------UAUUAAA--------------------------------------------------------------	4	novel
seed	----------------------------------------------------------------------------------------------------------UUAAACG------------------------------------------------------------	1	novel
seed	-----------------------------------CCGGCCC-----------------------------------------------------------------------------------------------------------------------------------	1	novel
seed	-------------------------------------GGCCCUU---------------------------------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	------------------------------------------------------------------------------------------------------TGTATTAAACGGTAAG-------GGCCGGC-----------------------------------------	23	11
	------------------------------------------------------------------------------------------------------TGTATTAAACGGTAAG-------GGCCGG------------------------------------------	22	6
	--------------------------------------------------------------------------------------------------------TATTAAACGGTAAG-------GGCCGGCT----------------------------------------	22	4
	----------------------------------------------------------------------------------------------------------TTAAACGGTAAG-------GGCCGGCTG---------------------------------------	21	4
	------------------------------------------------------------------------------------------------------TGTATTAAACGGTAAG-------GGCCG-------------------------------------------	21	3
	-------------------------------------------------------------------------------------------------------GTATTAAACGGTAAG-------GGCCGGC-----------------------------------------	22	3
	------------------------------------------------------------------------------------------------------TGTATTAAACGGTAAG-------GGCC--------------------------------------------	20	3
	----------------------------------------------------------------------------------------------------CATGTATTAAACGGTAAG-------GGC---------------------------------------------	21	3
	----------------------------------------------------------------------------------------------------CATGTATTAAACGGTAAG-------GGCC--------------------------------------------	22	2
	----------------------------------------------------------------------------------------------------CATGTATTAAACGGTAAG-------GGCCG-------------------------------------------	23	2
	--------------------------------------------------------------------------------------------------------TATTAAACGGTAAG-------GGCCGGCTG---------------------------------------	23	2
	---------------------------------------------------------------------------------------------------------ATTAAACGGTAAG-------GGCCGGCTGG--------------------------------------	23	1
	------------------------------------CGGCCCTT------ACCGT----------------TTAAT-------------------------------------------------------------------------------------------------	18	1
	--------------------------------------------------------------------------------------------------------TATTAAACGGTAAG-------GGCC--------------------------------------------	18	1
	-------------------------------------------------------------------------------------------------------GTATTAAACGGTAAG-------GGCCGGCT----------------------------------------	23	1
	----------------------------------------------------------------------------------------------------------TTAAACGGTAAG-------GGCCGGCTGG--------------------------------------	22	1
	----------------------------------GCCGGCCCTT------ACCGT----------------TTAATAC-----------------------------------------------------------------------------------------------	22	1
celegans	---------ATTTAGGAAATGTTGTAAAGCCCCAGCCGGCCCTT------ACCGT----------------TTAATACATGGTGCATCGACCGGG---AACATGTATTAAACGGTAAG-------GGCCGGCTGGGGCTTTACATTCATTTATTGTTAGAA------------
cremanei	TTGAGTCTTACAGAGAACGCGTTAT--------ATTAGGTTGTT------CAGGTCATGTAAAGGTGTAATTAAATACACCGTTCGTGAATAAGGTGAAATATGTATTAAAATGCATTTTTACATGACCTGAATAAGCTCATCACTAGCTTTTTATTACTGTTTTAGACTTAA
cbriggsae	---------------CATTTGTTGG--------CGTTGGCGGTT------GCGGT-------------------------------TGAAATAGTTCAAAACTGTATTAAACTCCAAGCCCAAGTG-----------------------------------------------
cjaponica	----------------ACCGGTGGA--------AACCGGTTTTTTTGTAACCGGT-------------------GGAAACCGGTT-TCTACCGGTTTTCACCGGTATTAAAAAACA-----------------------------CCGGTTTTTATCGGT-------------
	*   **               **   **         **                               *  *   *     *   ********    *
	+++++         +++++++++++++++++++++++++++++++++++      +++++                ++++++++++++++++++++++++   ++++++++++++++++++++       ++++++++++++++++++++++++++++++++++++            +++++	F55F3.1.1 F55F3.1 aakb-1
celegans	.(((((.(((((.((((((((((((((((((((((      (((((                ((((((((((.....((....)).   ..))))))))))))))))))       )))))))))))))))))))..)))))....))))).	1.000 -77.60
cremanei	.(((((((.((((((((.((.....        ...((.(((((      (((((((((((((((((((.((.((((((...((((.........))))...)))))).)).)))))))))))))))))))))))).))........)).))))....))))...))))))).	0.989 -55.69
cbriggsae	((((((..((        (.((((.((((      (((((                               ((((....))))..))))))....))))))))))))))))	1.000 -18.50
cjaponica	(((((((((        ((((((((((((((..((((((                   ((((((((((. ...))))))))))))))))..))))))).)                             )))))))))))))))	1.000 -56.90

celegans	chromosome:X:13759143:13759262:1	Same_strand|Intronic_non-coding|F55F3.1.1|F55F3.1 ## Same_strand|Boundary_non-coding|F55F3.1.2|F55F3.1 ## F55F3.1|protein_coding|aakb-1|AMP-Activated Kinase Beta subunit family member (aakb-1) [Source:RefSeq_peptide;Acc:NP_510298] ## {SimpF: WRM0622bA08 1 fosmid,WRM0635dA09 1 fosmid,WRM0620cB06 1 fosmid,WRM0641dG10 1 fosmid}
cremanei	chromosome:chrUn:93758631:93758789:-1	intergenic
cbriggsae	chromosome:chrX:7209346:7209505:-1	Opposite_strand|Intronic_coding|NM_178660
cjaponica	chromosome:chrUn:121223588:121223674:1	intergenic ## {SimpF: trf,trf}

Back to summary page

candidate novel miRNAs:

Page 1

Page 2