miR-Intess™

noncloned miRBase miRNAs

miRNAknown_randfoldOK (6 loci)

cbr-mir-353

block78 (miRBase cbr-mir-353) [miRNAknown_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

miRBase cbr-mir-353

0.003

no

no

0.38/0.38

21/21/1.00

nd

nd

0

0

0

0

9

11

5arm

1

nd

0.10

1

0

0

na

na

		reads	miRBase family seed
seed	----------AAGUAUC--------------------------------------------------------------------------	0	miR-353
		len	cloning frequencies
cbr-miR-353	---------CAAGTATCATGTGTTGGTATC-------------------------------------------------------------	21
cbriggsae	GCATGGGCACAAGTATCATGTGTTGGTATCATTGTTTCAAGTTATTTGTTGCTATGGTATCGATAAGCATGCTACGTGTGAAGTGCG----
celegans	---------AAAGTATC---TATGGGT----TTTTTAAAGGTT-----TAATTATATTACCTGTAA--AAGCCACTAGTATAGCATACAAC
	*******   * * ***    ** **  * ***     *   ***  ** *  ***  * ** **  **  **
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++    +++++	NM_080376
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++    +++++	NM_166030
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++    +++++	NM_058454
	--------------------------------------------------------------------------------------------    -----	NM_058465
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++    +++++	NM_025451
	--------------------------------------------------------------------------------------------    -----	NM_065146
	--------------------------------------------------------------------------------------------    -----	NM_005235
	--------------------------------------------------------------------------------------------    -----	NM_001042599
	--------------------------------------------------------------------------------------------    -----	NM_170794
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++    +++++	NM_135805
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++    +++++	NM_058998
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++    +++++	NM_173235
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++    +++++	NM_022515
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++    +++++	NM_001126226
cbriggsae	((((...((((.(((.((((((((((((((((.((..((((...))))..)).)))))))))))..))))).))).))))..)))).	1.000 -32.40
celegans	...(((((   (((((((    ((((...((((.     ..........))))..))  ))))).....))))).))))...	0.997 -15.10

cbriggsae	chromosome:chrI:2601063:2601149:-1	Same_strand|Intronic_coding|NM_080376|mam ## Opposite_strand|Intronic_non-coding|NM_058465|src-1 ## Same_strand|Intronic_non-coding|NM_025451|Camk2n1 ## Opposite_strand|Intronic_coding|NM_065146|H14E04.4 ## {Repeats: no} ## {MIR: cbr-mir-353}
celegans	chromosome:chrX:5073209:5073335:-1	Opposite_strand|Boundary_coding|C24H10.1

cbr-mir-356

block1513 (miRBase cbr-mir-356) [miRNAknown_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

miRBase cbr-mir-356

0.001

no

no

0.48/0.48

21/21/1.00

nd

nd

0

0

0

0

19

3

5arm

1

nd

0.29

3

0

0

na

na

		reads	miRBase family seed
seed	-----------------------------UGAGCAA-------------------------------------------------------------------------------------------	0	miR-233/356/87
		len	cloning frequencies
cbr-miR-356	----------------------------ATGAGCAACGCGAACAAATC--------C----------------------------------------------------------------------	21
cbriggsae	---------CCTCATCCAACCAATGTGGATGAGCAACGCGAACAAATC--------CTCTTATAAGAGATTTGCCACGCCGCCGCTCACCACACT-------------GGCTTTCAGAA-GG-----
cremanei	--------CGCTTTTGCCATCGATGTGGTTGAGCAACGCGAACAAATC---ATCGAAAATGACTG-AGATTTGCGCCAACGTGGCTCACCACATC-------------G--AATTGGAG-CG-----
celegans	-GTTAAAGTTTCCTTGAGAACAATGTGGTTGAGCAACGCGAACAAATCATCAATGTAAATTTCAGCGGATTCGTTACGACGTGTCTCACCACATC------GTTAGTAGGATTTCAGAA-C------
cbrenneri	----------------------------ATGAGCAATGT--------------------------CTGATTCAACGTTACGAAGACGAACAGTTA----------------ACTCAGAACCGCTTCC
cjaponica	ACATCGGCTCAAGCTGGCGATGATGTGGATGAGCAATGCGAACAAATCA--ATCGATAATTCAGATGGATTTGTTGCCACGTGGCTCACCTCATCAGATCGAGGAGCAAGCAGTTAGAA-TGT----
ppacificus	----------------------------ATGAGCAATTCCTACATCTT---------CTTCATAGCGGATGCACA--------------------------------------TGGGGA-CGCCAAT
	*******                               ***                                           *  *
	+++++         +++++++++++++++++++++++++++++++++++++++        +++++++++++++++++++++++++++++++++++++++             +++++++++++ ++     +++++	NM_000209
	-----         ---------------------------------------        ---------------------------------------             ----------- --     -----	NM_170975
	-----         ---------------------------------------        ---------------------------------------             ----------- --     -----	NM_007723
	-----         ---------------------------------------        ---------------------------------------             ----------- --     -----	NM_001011571
	+++++         +++++++++++++++++++++++++++++++++++++++        +++++++++++++++++++++++++++++++++++++++             +++++++++++ ++     +++++	NM_075282
	-----         ---------------------------------------        ---------------------------------------             ----------- --     -----	NM_010466
	+++++         +++++++++++++++++++++++++++++++++++++++        +++++++++++++++++++++++++++++++++++++++             +++++++++++ ++     +++++	NM_133381
	+++++         +++++++++++++++++++++++++++++++++++++++        +++++++++++++++++++++++++++++++++++++++             +++++++++++ ++     +++++	NM_075413
	-----         ---------------------------------------        ---------------------------------------             ----------- --     -----	NM_001050895
	-----         ---------------------------------------        ---------------------------------------             ----------- --     -----	NM_001013315
	-----         ---------------------------------------        ---------------------------------------             ----------- --     -----	NM_001105043
	-----         ---------------------------------------        ---------------------------------------             ----------- --     -----	NM_001067238
	-----         ---------------------------------------        ---------------------------------------             ----------- --     -----	NM_001067238
	-----         ---------------------------------------        ---------------------------------------             ----------- --     -----	NM_001067238
	-----         ---------------------------------------        ---------------------------------------             ----------- --     -----	NM_001011405
	-----         ---------------------------------------        ---------------------------------------             ----------- --     -----	NM_203548
	+++++         +++++++++++++++++++++++++++++++++++++++        +++++++++++++++++++++++++++++++++++++++             +++++++++++ ++     +++++	NM_199449
	-----         ---------------------------------------        ---------------------------------------             ----------- --     -----	NM_065202
cbriggsae	((((......(((.(((((.(((((...(((..(((((.        ((((....)))))))))...)))....)))))))))).)             ))......)). ))	0.960 -28.80
cremanei	((((((.....(((((((((.(((((.(((((..((((((   .(((........)) ))))))))))....)).))))))))))))             )  )...)))) ))	0.997 -37.00
celegans	(((......((((....(((.((((((.((((..((((((((.((((.....((.......))...)))).))).)).)))..)))))))))).      )))...))))......)) )	0.992 -29.70
cbrenneri	..((((....(                          ((((...((((((.((....))))).))).                ..)))))...))))..	0.988 -11.20
cjaponica	......(((...(((..((((((((.((.(((((...((.((((((((.  (((((....)).))).))))))))))......))))))).)))))..)))...))).)))........ ...	0.870 -36.40
ppacificus	.((.((..(((((((((((.         ((....)).)))))....                                      )))))) .))))..	0.999 -11.50

cbriggsae	chromosome:chrIII:10353560:10353650:-1	Same_strand|Intronic_non-coding|NM_000209|PDX1 ## Opposite_strand|Intronic_non-coding|NM_170975|C33C12.10 ## Opposite_strand|Intronic_coding|NM_007723|Cnga1 ## {Repeats: no} ## {MIR: cbr-mir-356}
cremanei	chromosome:chrUn:133239914:133240007:-1	Opposite_strand|Intronic_coding|NM_001002694
celegans	chromosome:chrIII:7860071:7860183:1	intergenic ## {MIR: cel-mir-356}
cbrenneri	chromosome:chrUn:182988097:182988227:-1	Opposite_strand|Boundary_coding|NM_001083269
cjaponica	chromosome:chrUn:31081413:31081532:1	intergenic
ppacificus	chromosome:chrUn:165162084:165162214:1	intergenic

cbr-mir-358

block3641 (miRBase cbr-mir-358) [miRNAknown_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

miRBase cbr-mir-358

0.001

no

no

0.45/0.45

22/22/1.00

nd

nd

0

0

0

0

22

0

3arm

1

nd

0.18

2

0

0

na

na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------AAUUGGU------------------------------------	0	miR-358
		len	cloning frequencies
cbr-miR-358	-------------------------------------------------------------------------------CAATTGGTATCCTTAGTCGTGG----------------------	22
cbriggsae	--------------CTCCCCATTCGGATTGATACCCGACTTCCGG-ATACCAAATGTCATATCCA---ACTCGTTTCGTCAATTGGTATCCTTAGTCGTGGTCTCAATCTGTACACGGCGAGA
cremanei	TCTATCATTCAAAATTCACCG--CGGATGGCGACCTGGC--CAGGCATTCCAACTGTC-CATCCAAGTACTTTATCGGACAATTGGTATCCCT-GTCAAGGTCTCAATCC-------------
celegans	---------------TCGCGA--CGGCTGGCGACCTGGC--CAGGCATTCCAACTGTCAAACTTACAAAGCTTTCTCGACAATTGGTATCCCT-GTCAAGGTCTCAATCCGTTCA----GCGA
	** *    *** * *  *** * *  * ** ** **** ****  *   *   *        * ************ * ***  **********
	-----              ------------------------------- -------------------   ------------------------------------------------------------	NM_001106714
	+++++              +++++++++++++++++++++++++++++++ +++++++++++++++++++   ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001028857
	+++++              +++++++++++++++++++++++++++++++ +++++++++++++++++++   ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001028858
	+++++              +++++++++++++++++++++++++++++++ +++++++++++++++++++   ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001062304
	+++++              +++++++++++++++++++++++++++++++ +++++++++++++++++++   ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_029761
	-----              ------------------------------- -------------------   ------------------------------------------------------------	NM_072806
cbriggsae	(((((....((((((((.((((((((...(( (((((((.((.........   ...........)).)))))))))..))))).))).)))))))).....)).))).	0.990 -39.95
cremanei	.....................  .((((...(((((((.  ((((.((.((((.(((( (................))))).)))).)).))) )))).))))...))))	0.936 -29.49
celegans	((((((  (((.(((.(((((((.  ((((.((.((((.((((...................)))).)))).)).))) )))).)))))))..)))))..    ))))	1.000 -33.01

cbriggsae	chromosome:chrV:1214365:1214469:-1	Opposite_strand|Intronic_non-coding|NM_001106714|Slc7a15 ## Same_strand|Intronic_non-coding|NM_001028857|K04F1.14 ## Same_strand|Intronic_coding|NM_001028858|K04F1.14 ## {Repeats: no} ## {MIR: cbr-mir-358}
cremanei	chromosome:chrUn:25671712:25671815:-1	Opposite_strand|Intronic_coding|NM_199607
celegans	chromosome:chrV:8580842:8580940:-1	Opposite_strand|Intronic_coding|F25G6.2 ## {MIR: cel-mir-358}

cbr-mir-789b

block3675 (miRBase cbr-mir-789b) [miRNAknown_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

miRBase cbr-mir-789b

0.002

no

no

0.65/0.65

23/23/1.00

nd

nd

0

0

0

0

16

5

3arm

1

nd

0.09

1

0

0

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------CCCUGCC-------------------------------------------	0	miR-789a/789b
		len	cloning frequencies
cbr-miR-789b	---------------------------------------------------------------------G-------CCCTGCCTGGGTCACCATGTG------------A----------------	23
cbriggsae	------------TTGCCCGACTTCGGATTCACGTGGTCATCCAGGCGGTGCACGTTAAAAGATATAAATG-------CCCTGCCTGGGTCACCATGTG------------AATAGGGAATACGGTCA
cremanei	-----------------------------CGAATGGTAGCCGAGGAAGGGTATCTAGAAAGA------AGGATTA--CCCTGCCTGGGTCACCATTTG-----------------------------
celegans	------------TGTCCTGAAGGCGGA--CAATTGATGACTCAGGCAGGG-ACTAATCATGATTGT--CGATTTAGTCCCTGCCTGGGTCACCAATTGTCGGCCCCCGCGGACAAAGAATATATACT
cbrenneri	----------------CTGGTTGACGAAACGATTGGTCATCCAGGCGGAGCATCTCAGAAGGCTTG-----------CCCTGCCTGGGTCACCAATTGTC--------TCGGAAAACTAG-------
cjaponica	GTCAAACGAGGTTAGTGCAACCTTTTCAACAGTTGGTGACCCAGGAAGGG-ATTAGAAAAGATTTCACAAGTTCAATCCCTGCCTGGGTCACCAATTGTTGAATTGGTTTCACAAAATGGTCAAGAC
	*   ** *     ***  * * *      * *                *****************  **
	-----            ----------------------------------------------------------       ---------------------            ----------------------	NM_001081076
	-----            ----------------------------------------------------------       ---------------------            ----------------------	NM_075157
	+++++            ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++       +++++++++++++++++++++            ++++++++++++++++++++++	NM_074754
	-----            ----------------------------------------------------------       ---------------------            ----------------------	NM_074932
	-----            ----------------------------------------------------------       ---------------------            ----------------------	NM_074581
	+++++            ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++       +++++++++++++++++++++            ++++++++++++++++++++++	NM_074580
	+++++            ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++       +++++++++++++++++++++            ++++++++++++++++++++++	NM_004906
	+++++            ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++       +++++++++++++++++++++            ++++++++++++++++++++++	NM_071419
	-----            ----------------------------------------------------------       ---------------------            ----------------------	NM_131864
	-----            ----------------------------------------------------------       ---------------------            ----------------------	NM_074935
	+++++            ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++       +++++++++++++++++++++            ++++++++++++++++++++++	NM_059170
	+++++            ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++       +++++++++++++++++++++            ++++++++++++++++++++++	NM_001029639
	+++++            ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++       +++++++++++++++++++++            ++++++++++++++++++++++	NM_072577
	-----            ----------------------------------------------------------       ---------------------            ----------------------	NM_074576
	-----            ----------------------------------------------------------       ---------------------            ----------------------	NM_074932
	+++++            ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++       +++++++++++++++++++++            ++++++++++++++++++++++	NM_071744
	+++++            ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++       +++++++++++++++++++++            ++++++++++++++++++++++	NM_074581
	-----            ----------------------------------------------------------       ---------------------            ----------------------	NM_074579
	+++++            ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++       +++++++++++++++++++++            ++++++++++++++++++++++	NM_071647
cbriggsae	.((.(((..(((..(((((((((((.((((((((((.(((..(((.......))).))       ).)))))))))).))))))))            )))..)))...))).))	1.000 -42.70
cremanei	((((((((..((.(((.(((((((((.......      .)))).)  )))).))).))..))))))))	1.000 -30.80
celegans	(((((((..(((.((  ((((((.(((((((((((((( (((((...((.....  ))..))))))))))))))))))).)))))))).)))..)).))))).............	0.990 -63.50
cbrenneri	((((((..(((.(((((((((.((((((((((.(((..((....))..))           ).)))))))))).))))))))).        )))...))))))	1.000 -45.20
cjaponica	..............(((.((((..(((((((((((((((((((((.(((( (((.(((.............)))))))))).)))))))))))))))))))))..)))).)))..............	0.856 -60.42

cbriggsae	chromosome:chrV:3127586:3127681:-1	Opposite_strand|Intronic_coding|NM_001081076|Gucy2g ## Same_strand|Intronic_coding|NM_074754|F26D2.13 ## Same_strand|Intronic_non-coding|NM_004906|WTAP ## {Repeats: no} ## {MIR: cbr-mir-789b}
cremanei	chromosome:chrUn:52159842:52159977:-1	Opposite_strand|Intronic_coding|NM_071305 ## Same_strand|Intronic_coding|NM_071724
celegans	chromosome:chrIV:17309249:17309358:-1	Opposite_strand|Intronic_coding|T28F3.9 ## {MIR: cel-mir-789-2}
cbrenneri	chromosome:chrUn:43323640:43323724:1	intergenic
cjaponica	chromosome:chrUn:75784925:75785050:-1	Same_strand|Intronic_coding|NM_001047261

cbr-mir-785

block4920 (miRBase cbr-mir-785) [miRNAknown_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

miRBase cbr-mir-785

0.001

no

no

0.33/0.33

21/21/1.00

nd

nd

0

0

0

0

16

6

3arm

1

nd

0.00

0

0

0

na

na

		reads	miRBase family seed
seed	------------------------------------------------------------------------------------AAGUGAA--------------------------------------------	0	miR-785/86
		len	cloning frequencies
cbr-miR-785	-----------------------------------------------------------------------------------TAAGTGAA-TACTCTGTGTTGA------------------------------	21
cbriggsae	----------------TTGCTC-TTTCGCAACCGTCAGCACAGAGTGCTTCGACTTACACAGAATTCGTAAAACCAACTGATGTAAGTGAA-TACTCTGTGTTGATGGTGATGATGCTGAA--------------
cremanei	--------------------TC-TTTTTTGTCCGTCAGCGCAGAATTTTTTCGCTTACACGAGTAATG-TAAA-----CGATGTAAGTGAA-TATTCTGTGTCGATGGGTATAAAAAGATAATGATGGTT-----
celegans	TCGGAAAGCTGCCAAAGCTCTT-TTTCTCACCCATCAGCACAGAATTTTTC-GCTAACAGAAACCTC---AAAACA----ATGTAAGTGAATTGTTTTGTGTAGATGGTGGAAATGAGCAGGCAATGTTTTCTGA
cbrenneri	------------------GCTCTTTTCTCTCCCGTTAGCACAAAATATTTT-ACTTACACATAAC-----AAAACATATGATGTAAGTGAA-TACTTTGTGTTAATGGAAAAAGGGC------------------
cjaponica	----------------------------------CTAACCCAGAACAACTC-GCTAACACGAACACTGAGAAA-----TGATGTAAGTGAA-TGTTCTGTGTTGG------------------------------
ppacificus	----------------TCGCAA-GTTTATGTACATTAACATGAAG-----------------GAAATATATAATGAATTAATGAAAGTGAA---ACTTGCTTTGA------------------------------
	* *    *                           **       *** *******      **  *
	+++++                ++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++              +++++	NM_178660
	-----                ------ -------------------------------------------------------------------- -----------------------------              -----	NM_133381
	-----                ------ -------------------------------------------------------------------- -----------------------------              -----	NM_002254
	-----                ------ -------------------------------------------------------------------- -----------------------------              -----	NM_001059519
	-----                ------ -------------------------------------------------------------------- -----------------------------              -----	NM_024598
	-----                ------ -------------------------------------------------------------------- -----------------------------              -----	NM_175804
	-----                ------ -------------------------------------------------------------------- -----------------------------              -----	NM_001089427
	-----                ------ -------------------------------------------------------------------- -----------------------------              -----	NM_001110788
cbriggsae	..((.. ..(((..(((((((((((((((((.(((.((((((((((...............))).)))))))))) )))))))))))))))))..))).))....	1.000 -43.16
cremanei	(( (((((..((((((.(((((((((...((((((((((((....... ....     )).)))))))))) .))))))))).))))))...)))))))...........	0.993 -37.50
celegans	(((((((((((((...((((.. ((((.((.(((((.(((((((((..((( (((.(((........   ......    .))).))))))..))))))))).))))))))))).)))).))))..)))))))))	0.999 -51.76
cbrenneri	((((((((.....(((((((((((((.((.((( (((((((((((..     ......)))).)))))))))) )).))))))))))))).))))))))	1.000 -35.20
cjaponica	(((((.(((((((..(( (((.(((..............     ...))).))))). ))))))).)))))	0.949 -17.83
ppacificus	..(((( ((((((...(((((((((....                 ..........)))..))))))...)))))   .))))).....	0.980 -12.14

cbriggsae	chromosome:chrX:7891064:7891166:1	Same_strand|Intronic_non-coding|NM_178660|Rbms3 ## Opposite_strand|Intronic_non-coding|NM_133381|Crebbp ## Opposite_strand|Intronic_coding|NM_002254|KIF3C ## {Repeats: no} ## {MIR: cbr-mir-785}
cremanei	chromosome:chrUn:4287760:4287861:-1	intergenic
celegans	chromosome:chrX:3004644:3004769:1	intergenic ## {MIR: cel-mir-785}
cbrenneri	chromosome:chrUn:1355192:1355283:1	intergenic
cjaponica	chromosome:chrUn:20283840:20283982:-1	intergenic
ppacificus	chromosome:chrUn:112799539:112799681:-1	Opposite_strand|Intronic_coding|NM_212489 ## Same_strand|Intronic_coding|NM_167334

cbr-mir-392

block5223 (miRBase cbr-mir-392) [miRNAknown_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

miRBase cbr-mir-392

0.001

no

no

0.41/0.41

22/22/1.00

nd

nd

0

0

0

0

15

5

3arm

1

nd

0.14

1

0

0

na

na

		reads	miRBase family seed
seed	----------------------------------------------------------AUCAUCG-----------------------------	0	miR-392
		len	cloning frequencies
cbr-miR-392	---------------------------------------------------------TATCATCGATCATGTGAGCTGT---------------	22
cbriggsae	AAATCCTGCATTTATCTGACATCTCACATTATTGAGGATATAAACTAAATAAAGAAATATCATCGATCATGTGAGCTGTTAGATTATCAGATTT
cremanei	--ATCC-GTGATTATCTGGCGGTTTACATGGTAGAAGATATCAGTATAAAAAATAGATATCATCGATCATGTATGCTGTCAGATTAATGGAT--
celegans	------------------TCAGCATTCGTGGTTGAGGATATCGAACACAAAAAAAGATATCATCGATCACGTGTGATGA---------------
ppacificus	-------------AGCTGATGGAA-GTATGCTATAGAACATCAATATGATAA--TGCTATCATCGTACGTCCATCTGGA---------------
	*  *  *  * **       * **     ********  *         *
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_007734
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_134696
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_203905
	--------------------------------------------------------------------------------------------------------	NM_001065436
cbriggsae	.....(((.((..((((((((.(((((((.(((((.(((((...((......))..))))).))))).))))))).)))))))).)))))....	1.000 -29.20
cremanei	(((( ((....((((((((((.((((((((.((.((((((.((.......)).)))))).)).)))))))).))))))))))..))))))	1.000 -37.60
celegans	(((.(((.(((((((((.((((((.............)))))).))))))))).))).)))	1.000 -22.62
ppacificus	....((((((. (((((..((((...(((.....)))..  ..))))...))))).))))))....	0.974 -16.60

cbriggsae	chromosome:chrX:19202542:19202635:1	Same_strand|Intronic_non-coding|NM_007734|Col4a3 ## Same_strand|Intronic_coding|NM_134696|CG2839 ## Opposite_strand|Intronic_non-coding|NM_001065436|Os07g0150700 ## {Repeats: no} ## {MIR: cbr-mir-392}
cremanei	chromosome:chrUn:96274952:96275040:1	intergenic
celegans	chromosome:chrX:13597142:13597275:1	intergenic ## {MIR: cel-mir-392}
ppacificus	chromosome:chrUn:26983987:26984120:-1	Same_strand|Intronic_coding|NM_136618 ## Same_strand|Boundary_non-coding|NM_070048

miRNAknown (2 loci)

cbr-mir-354

block228 (miRBase cbr-mir-354) [miRNAknown]

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

miRBase cbr-mir-354

0.108

no

no

0.48/0.48

21/21/1.00

nd

nd

0

0

0

0

9

21

3arm

1

nd

0.24

2

0

0

na

na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------CCUUGUU-------------------------------	0	miR-354
		len	cloning frequencies
cbr-miR-354	--------------------------------------------------------------------------------ACCTTGTTTGTTGCTGCTCCT------------------	21
cbriggsae	CCAGAGCCGACTAAGTGCCTTGGTGCGGCTACAGACGGGTATCCGGCTCGATGTTCATACACCGCGAC-TCTTTCCTTTTACCTTGTTTGTTGCTGCTCCTTTTGGTTTT---------
celegans	-------CGACTAAGCACCTTGGTGCGGCTGCAGACGGGTATCCGGCTCGACGTTCATACATCACGACTTCTTTCCTTTTACCTTGTTTGTTGCTGCTCCTATTGGTTTTGATTTGTTG
cjaponica	--------------------TGGTGCGGCTTCGAACGGGTA-ACAGCTCGTCGTTCATAC---------TTCTTCCTTTTACCTTGTTTGTTGCCTCTCCT------------------
	********** *  *******  * *****  ********         *  **********************  *****
	------------------------------------------------------------------------- -----------------------------------------         -----	NM_061066
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++         +++++	NM_067049
	>>>>>>>>>>>>>............................................................ .........................................         .....	NM_017866
	>>>>>>>>>>>>>>>>......................................................... .........................................         .....	NM_001023
	>>>>>>>>>>>>>>>>>>>...................................................... .........................................         .....	NM_079697
	>>>>>>>>>>>>>>>>......................................................... .........................................         .....	NM_001005106
	>>>>>>>>>>>>>>>>......................................................... .........................................         .....	NM_001034438
	>>>>>>>>>>>>>>>>......................................................... .........................................         .....	NM_001085938
	>>>>>>>>>>>>>>>>......................................................... .........................................         .....	NM_001092903
	>>>>>>>>>>>>>>>>......................................................... .........................................         .....	NM_001098339
	>>>>>>>>>>>>>>>>......................................................... .........................................         .....	NM_213204
	>>>>>>>>>>>>>>>>>>>...................................................... .........................................         .....	NM_208340
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         >>>>>	NM_170948
	>>>>>>>>>>>>>>>>>>>...................................................... .........................................         .....	NM_001023427
	>>>>>>>>>>>>>>>>......................................................... .........................................         .....	NM_026147
	>>>>>>>>>>>>>............................................................ .........................................         .....	NM_001040613
	>>>>>>>>>>>>>>>>......................................................... .........................................         .....	NM_001129954
	>>>>>>>>>>>>>>>>......................................................... .........................................         .....	NM_001007603
	>>>>>>>>>>>>>>>>......................................................... .........................................         .....	NM_001124364
cbriggsae	..((((((((...........((.(((((.(((((((((((...((.(((.(((....)))...))). .....))...)))).))))))).))))).))..))))))))	1.000 -30.62
celegans	((((..((.(((..((.(((((.(((((((((((...((...((.(((..........))).))...))...))))).)))))).))))).))....))).)).....))))	0.984 -30.80
cjaponica	.((...(((..(((((((((( (.((......((....))         ......)).)))))).)))))..)))...)).	0.999 -17.60

cbriggsae	chromosome:chrI:10568239:10568347:-1	Opposite_strand|Intronic_non-coding|NM_061066|K03D10.3 ## Same_strand|Intronic_non-coding|NM_067049|Y47D3A.21 ## Same_strand|Exonic_non-coding|NM_170948|rps-20 ## {Repeats: no} ## {MIR: cbr-mir-354}
celegans	chromosome:chrI:14468361:14468472:-1	Same_strand|Exonic_coding|Y105E8A.16.2 ## Same_strand|Boundary_non-coding|Y105E8A.16 ## {MIR: cel-mir-354}
cjaponica	chromosome:chrUn:65822232:65822380:-1	Same_strand|Boundary_non-coding|NM_208340

cbr-mir-792

block558 (miRBase cbr-mir-792) [miRNAknown]

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

miRBase cbr-mir-792

0.028

no

Unknown

0.22/0.22

23/23/1.00

nd

nd

0

0

0

0

8

13

3arm

1

nd

0.17

2

0

0

na

na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------UGAAAUU-------------------------------------	0	miR-792
		len	cloning frequencies
cbr-miR-792	--------------------------------------------------------------------------------TTGAAATTTTTTCTATTTTCGGT----------------------	23
cbriggsae	----------GAAAACATCGAAAAATGAGAAAATTATAATTGTTGGAGGTTGTGACACAAAACTA------TGAAA----TTGAAATTTTTTCTATTTTCGGTCCTTTTTC--------------
celegans	---------------------------GCCAAATTGCCAAAATTGAAGTTTCTGGCAAATCGGCAAATTGCCAGAA----TTGAAATTTCCGGCAAATTGGC-----------------------
cbrenneri	GATTCTAATCGATTTTTTTGGAAAATTAGAACAAAATAAAAATTGGATTTTTTTTGAAAAAAATTTTTTTCTAAAAAATGTTGAAATTTTTTTTGTTCTAATTTTCCAGAAAATCGATAAAAATC
cjaponica	--------------GACGATAAAAGAGAGAAAATTTTCAGATC----ATCTGCATAAAGCAGATAATTTGAT--------TTGAAATTATCTCCAATATCGTTGATGTAC---------------
ppacificus	--------------CCTTTCAATGATGTGAAAATTGTCAAATTCGCTACTATTATGTAGAAGCTACA-------------CTGAAATTTTTTCTATTGAGTG-----------------------
	* *     *                                          *******
	-----          -------------------------------------------------------      -----    -------------------------------              -----	NM_080322
	-----          -------------------------------------------------------      -----    -------------------------------              -----	NM_166960
	-----          -------------------------------------------------------      -----    -------------------------------              -----	NM_166961
	-----          -------------------------------------------------------      -----    -------------------------------              -----	NM_166962
	-----          -------------------------------------------------------      -----    -------------------------------              -----	NM_166963
	-----          -------------------------------------------------------      -----    -------------------------------              -----	NM_166964
	-----          -------------------------------------------------------      -----    -------------------------------              -----	NM_166965
	-----          -------------------------------------------------------      -----    -------------------------------              -----	NM_166966
	-----          -------------------------------------------------------      -----    -------------------------------              -----	NM_166967
	-----          -------------------------------------------------------      -----    -------------------------------              -----	NM_166968
	-----          -------------------------------------------------------      -----    -------------------------------              -----	NM_166969
	-----          -------------------------------------------------------      -----    -------------------------------              -----	NM_166970
	-----          -------------------------------------------------------      -----    -------------------------------              -----	NM_166971
cbriggsae	(((((.((((((((..(((((((((.(((((..(((...(((.....)))..)))      ...))    ))).)))))))))..))))))))...)))))	1.000 -19.00
celegans	(((((.(((((.(((((..((.(((((((((.........)))))))))    ))..)))))..))))).)))))	0.999 -27.60
cbrenneri	((((...(((((.(((((((((((((((((((((((.((((.((.(((.((((((((((((....)))))).)))))).))).)).))))))))))))))))))))))))))))))))...))))	1.000 -41.30
cjaponica	(((((((...((((......(((((((((    ((((((.....))))).....))))        ))))))...))))...))))))).......	1.000 -26.30
ppacificus	...(((((((....(((((((.(((.....(((.((((...)))).)))....             .))))))))))..)))))))..	0.966 -12.10

cbriggsae	chromosome:chrI_random:2916442:2916532:1	Opposite_strand|Intronic_non-coding|NM_080322|dnc ## {Repeats: no} ## {MIR: cbr-mir-792}
celegans	chromosome:chrIII:2845610:2845680:-1	intergenic ## {Repeats: CERP3 -577 788 1 class=Unknown} ## {SimpF: trf,trf,trf,trf}
cbrenneri	chromosome:chrUn:30458692:30458816:-1	Same_strand|Intronic_coding|NM_214690
cjaponica	chromosome:chrUn:72086679:72086762:-1	intergenic
ppacificus	chromosome:chrUn:50536788:50536918:-1	Opposite_strand|Intronic_coding|NM_001045439

miRNAknown_lenNOK_randfoldOK_bulgeHIGH (1 loci)

cbr-mir-268

block3745 (miRBase cbr-mir-268) [miRNAknown_lenNOK_randfoldOK_bulgeHIGH]

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

miRBase cbr-mir-268

0.001

no

no

0.40/0.40

25/25/0.00

nd

nd

0

0

0

0

6

5

5arm

1

nd

0.28

4

0

0

na

na

		reads	miRBase family seed
seed	---------------------GCAAGAA--------------------------------------------------------------------------------	0	miR-268
		len	cloning frequencies
cbr-miR-268	--------------------GGCAAGAATTAGAAGCAGTTTTGGT---------------------------------------------------------------	25
cbriggsae	--------------TGAAGCGGCAAGAATTAGAAGCAGTTTTGGTGTCAGACACACTCACTGACTCACTG---CTTCTTGTTTTTCTTC------------TTCTTCT
cremanei	--------------------AGCAAGAA-AAGAAGCGGTTGAGGTCTC----------TCAGACTCATTGGGACTTTGCGCAATTCAAG------------TTTGACT
celegans	AGAGGAAGTGGCTTTGAAGCGGCAAGAATTAGAAGCAGTTT-GGTGTCAGACACACT-ACTCACTCACTG---CTTCTTGTTTTTTCTGCTTTCTTTGCTTTTCCTCT
cbrenneri	--------------------GGCAAGAATTAGAAGCAGTTTTGGTGTCAG--------ACACACTCACTC---CTTCTTGT--------------------TTTTTCT
	*******  ****** ***  *** **           *  ***** *    ***   *                     **   **
	+++++              ++++++++++++++++++++++++++++++++++++++++++++++++++++++++   ++++++++++++++++            ++++++++++++	NM_125760
	+++++              ++++++++++++++++++++++++++++++++++++++++++++++++++++++++   ++++++++++++++++            ++++++++++++	NM_073462
	+++++              ++++++++++++++++++++++++++++++++++++++++++++++++++++++++   ++++++++++++++++            ++++++++++++	NM_070729
	+++++              ++++++++++++++++++++++++++++++++++++++++++++++++++++++++   ++++++++++++++++            ++++++++++++	NM_007823
	+++++              ++++++++++++++++++++++++++++++++++++++++++++++++++++++++   ++++++++++++++++            ++++++++++++	NM_133969
	+++++              ++++++++++++++++++++++++++++++++++++++++++++++++++++++++   ++++++++++++++++            ++++++++++++	NM_001114375
	-----              --------------------------------------------------------   ----------------            ------------	NM_134696
	+++++              ++++++++++++++++++++++++++++++++++++++++++++++++++++++++   ++++++++++++++++            ++++++++++++	NM_001112929
	+++++              ++++++++++++++++++++++++++++++++++++++++++++++++++++++++   ++++++++++++++++            ++++++++++++	NM_001112929
	+++++              ++++++++++++++++++++++++++++++++++++++++++++++++++++++++   ++++++++++++++++            ++++++++++++	NM_079237
	+++++              ++++++++++++++++++++++++++++++++++++++++++++++++++++++++   ++++++++++++++++            ++++++++++++	NM_079859
	+++++              ++++++++++++++++++++++++++++++++++++++++++++++++++++++++   ++++++++++++++++            ++++++++++++	NM_001039441
	+++++              ++++++++++++++++++++++++++++++++++++++++++++++++++++++++   ++++++++++++++++            ++++++++++++	NM_057559
	+++++              ++++++++++++++++++++++++++++++++++++++++++++++++++++++++   ++++++++++++++++            ++++++++++++	NM_001017348
	-----              --------------------------------------------------------   ----------------            ------------	NM_134696
	-----              --------------------------------------------------------   ----------------            ------------	NM_030763
	-----              --------------------------------------------------------   ----------------            ------------	NM_078262
cbriggsae	.((((.((.((((((.(((((((((....(.(((((.........))))).)))))   ))))).)))))))).)            )))....	1.000 -26.60
cremanei	..((((.. ..((((((...((((((((          ...........)))))))).)))..)))...            ))))...	0.941 -12.60
celegans	((((((((.(((...(((((((.((((((.(((((((((.. ((((..((.....)) ...)))).))))   ))))).)))))).)))))))....)))))))))))	1.000 -41.60
cbrenneri	((.((((((.(((((.(((...(((((...        ..))))).))).   ))))).))                    )))).))	1.000 -13.60

cbriggsae	chromosome:chrV:7334149:7334227:-1	Same_strand|Intronic_coding|NM_125760|SNRK2-5/SNRK2.5/SRK2H ## Opposite_strand|Intronic_coding|NM_134696|CG2839 ## Same_strand|Intronic_non-coding|NM_001112929|LOC100127559 ## Opposite_strand|Intronic_non-coding|NM_078262|let-2 ## {Repeats: no} ## {MIR: cbr-mir-268}
cremanei	chromosome:chrUn:124690097:124690215:-1	intergenic
celegans	chromosome:chrV:11137084:11137186:1	intergenic ## {MIR: cel-mir-268}
cbrenneri	chromosome:chrUn:176677397:176677515:-1	intergenic

miRNAknown_randfoldOK_bulgeHIGH (1 loci)

cbr-mir-791

block4980 (miRBase cbr-mir-791) [miRNAknown_randfoldOK_bulgeHIGH]

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

miRBase cbr-mir-791

0.001

no

no

0.52/0.52

23/23/1.00

nd

nd

0

0

0

0

11

6

3arm

1

nd

0.22

4

0

0

na

na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------------UUGGCAC---------------------------------------------------	0	miR-790/791
		len	cloning frequencies
cbr-miR-791	------------------------------------------------------------------------------------ATTGGCACT--CCGCTGATTT--GGTG--------------------------------	23
cbriggsae	------------------------GAATTCTCGA-------TCACCGTATCACGTGTGGCCAAAGTCAAATCCATTATTG-AACATTGGCACT--CCGCTGATTT--GGTGATCGACT-TTTC--------------------
cremanei	---------------GTTACGTTCGAATTCTCAA-------TCACCTTGTCAGGTTTAGCCAAAGTCAAACATAAACTG--AACTTTGGCACT--CCGCTGATTT--GGTGATAGAGTTTTTTGGC--ATGTTTTC-------
celegans	-------GTCTACTTTGTAGGTTTGAACCTTCGA-------TTACCTTATCCGTTGTAGCCAAAGTTCAACGAAG--CGGCAACTTTGGCACT--CCGCAGATAA--GGCAATCGATTGTTTTTG---ACACTTCAATACCAC
cbrenneri	TTTTTCGATCGACGGGAAGTTGTTGGAGTTTCCA-------TCAC------------AGCCAAGG---AATAGGA------ACGATTGGCACT--CCTGGAATTTCAGATAAT------TTTCAG---AATTTTTCAGAAAAA
cjaponica	----------------AACTTTTTGAAGGTCTTACTGAGAGTAGCCATCGAATTCGGAGCCTGCGCCAAATGAAATATAGTGAATTTGGCACCTGCTTCAAATTC--AATGAC------TATTAGCCAAAAATTTCGCGAGTT
	* *      *       *  *             ***   *   **               *******   *     **        *       * *
	-----                        ----------       --------------------------------------- ------------  ----------  ----------- ----                    -----	NM_027552
	-----                        ----------       --------------------------------------- ------------  ----------  ----------- ----                    -----	NM_001019667
	+++++                        ++++++++++       +++++++++++++++++++++++++++++++++++++++ ++++++++++++  ++++++++++  +++++++++++ ++++                    +++++	NM_011438
cbriggsae	(((...((((       ((((((.((((.(((..(((((..((((........))) )...)))))...  .))))))).)  ))))))))).. .)))	1.000 -31.70
cremanei	...(((((((((..(((.(       (((((..(((((.....((((((((((.........))  ).)))))))...  ...)))))..  )))))).)))...))))).  ))))....	1.000 -34.60
celegans	.......(((.(((((.((((..((((       ((.(((((((((..((.(((((((((...((...  ))..))))))))))).  .))..)))))  )).))))))..))))..)   )).)).)))......	0.807 -37.80
cbrenneri	.(((((((......((((((((((.(((.(((((       ....            .(((((..   .......      ....)))))...  ..))))).))).))))))      ))))..   ......)).))))).	0.806 -23.86
cjaponica	(((((..(((((...........(((((.(((.(((((.(((((....(((((((............)))))))....))))).)))))  .))).)      )))).........))))).)))))	0.806 -27.85

cbriggsae	chromosome:chrX:10981889:10981974:1	Opposite_strand|Intronic_non-coding|NM_027552|Kynu ## Opposite_strand|Intronic_coding|NM_001019667|SPAC17A2.10c ## Same_strand|Intronic_non-coding|NM_011438|Sox12 ## {Repeats: no} ## {MIR: cbr-mir-791}
cremanei	chromosome:chrUn:2002741:2002846:-1	intergenic
celegans	chromosome:chrX:5809292:5809411:1	intergenic ## {MIR: cel-mir-791}
cbrenneri	chromosome:chrUn:93577891:93577994:-1	Opposite_strand|Boundary_coding|NM_067602 ## {SimpF: trf}
cjaponica	chromosome:chrUn:48842583:48842701:1	intergenic

Back to summary page

noncloned miRBase miRNAs:

Page 1

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