miR-Intess™

confident miRBase miRNAs

miRNAknown_cloningHIGH_randfoldOK (17 loci)

cbr-mir-50

Cloning frequencies

absolute	AF16
cbr-mir-50 5arm	223
normalized	AF16
cbr-mir-50 5arm	0.581

block279 (miRBase cbr-mir-50) [miRNAknown_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

miRBase cbr-mir-50

0.001

no

no

0.26/0.36

19/24/0.94

0.0

0.0

138

0

1

0

17

8

5arm

1

nd

0.08

2

223

1

na

na

Families

Member of family miR-50/62/90 (seed GAUAUGU): cel-mir-90, cbr-mir-50, cbr-mir-90, cbr-mir-62

		reads	miRBase family seed
seed	------------------GAUAUGU-------------------------------------------------------------------------------------	222	miR-50/62/90
seed	-------------------AUAUGU-C-----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
cbr-miR-50	-----------------TGATATGT-C----TGATATTCTTGGGTT----------------------------------------------------------------	24	138
	-----------------TGATATGT-C----TGATATTCTTGG-------------------------------------------------------------------	21	27
	-----------------TGATATGT-C----TGATATTCTTGGG------------------------------------------------------------------	22	26
	-----------------TGATATGT-C----TGATATTCTTGGGT-----------------------------------------------------------------	23	18
	-----------------TGATATGT-C----TGATATTCTT---------------------------------------------------------------------	19	13
	------------------GATATGT-C----TGATATTCTTGGGTT----------------------------------------------------------------	23	1
cbriggsae	TTCCACCCACCGGCCGCTGATATGT-C----TGATATTCTTGGGTTATCTGATAATGATTGTTGTAACTCAAG----TATTAGACGTATCGACGGCCGGCTGGGTTGGAA
cremanei	-----------------TGATATGT-C----TGGTATTCTTGGGTTC-GATACTCTGAAAAACG-AACCAAAG----TAGCAGACGTATCG-------------------
celegans	-----------------TGATATGT-C----TGGTATTCTTGGGTTT--GAACTTCCAGCGTTG-AACCCGCA----TATTAGACGTATCG-------------------
cbrenneri	TCTCACCCACCGGCCGCTGATATGT-C----TGGTATTCTTGGGTTC----ATTCCTTACTCTG-AACCAGTT----TATTAGACGTATCGACGGCCGGATCGGGTGAGA
cjaponica	-----------------TGATATGT-TGAAATAGCGAGTTTGGCTTG-CAGCTATAAATAGCTGCAAGCCGAAACTGTTTCATCAATTTCA-------------------
ppacificus	-----------------TGATATGTGT----CATTGAATTTGGCTTT-CTAAGTGCATCCGGAA-AAGTGGAA----TGAATTATATATCG-------------------
	********              **** **                   **          *        * **
	------------------------------ -    ------------------------------------------    --------------------------------------	NM_174569
	------------------------------ -    ------------------------------------------    --------------------------------------	NM_174283
	------------------------------ -    ------------------------------------------    --------------------------------------	NM_002035
	------------------------------ -    ------------------------------------------    --------------------------------------	NM_177366
	++++++++++++++++++++++++++++++ +    ++++++++++++++++++++++++++++++++++++++++++    ++++++++++++++++++++++++++++++++++++++	NM_001107428
	------------------------------ -    ------------------------------------------    --------------------------------------	NM_053878
	++++++++++++++++++++++++++++++ +    ++++++++++++++++++++++++++++++++++++++++++    ++++++++++++++++++++++++++++++++++++++	NM_008665
	++++++++++++++++++++++++++++++ +    ++++++++++++++++++++++++++++++++++++++++++    ++++++++++++++++++++++++++++++++++++++	NM_058481
	------------------------------ -    ------------------------------------------    --------------------------------------	NM_010301
	++++++++++++++++++++++++++++++ +    ++++++++++++++++++++++++++++++++++++++++++    ++++++++++++++++++++++++++++++++++++++	NM_204523
	++++++++++++++++++++++++++++++ +    ++++++++++++++++++++++++++++++++++++++++++    ++++++++++++++++++++++++++++++++++++++	NM_139981
	++++++++++++++++++++++++++++++ +    ++++++++++++++++++++++++++++++++++++++++++    ++++++++++++++++++++++++++++++++++++++	NM_001113428
	++++++++++++++++++++++++++++++ +    ++++++++++++++++++++++++++++++++++++++++++    ++++++++++++++++++++++++++++++++++++++	NM_058485
	++++++++++++++++++++++++++++++ +    ++++++++++++++++++++++++++++++++++++++++++    ++++++++++++++++++++++++++++++++++++++	NM_006289
	++++++++++++++++++++++++++++++ +    ++++++++++++++++++++++++++++++++++++++++++    ++++++++++++++++++++++++++++++++++++++	NM_011602
	++++++++++++++++++++++++++++++ +    ++++++++++++++++++++++++++++++++++++++++++    ++++++++++++++++++++++++++++++++++++++	NM_015059
	++++++++++++++++++++++++++++++ +    ++++++++++++++++++++++++++++++++++++++++++    ++++++++++++++++++++++++++++++++++++++	NM_001081242
	++++++++++++++++++++++++++++++ +    ++++++++++++++++++++++++++++++++++++++++++    ++++++++++++++++++++++++++++++++++++++	NM_001039025
	++++++++++++++++++++++++++++++ +    ++++++++++++++++++++++++++++++++++++++++++    ++++++++++++++++++++++++++++++++++++++	NM_001009560
	++++++++++++++++++++++++++++++ +    ++++++++++++++++++++++++++++++++++++++++++    ++++++++++++++++++++++++++++++++++++++	NM_001123412
cbriggsae	.(((((((((((((((.(((((((( (    (((((..((((((((((..((((.....))))))))))))))    )))))))))))))).))))))).))))).))).	1.000 -57.00
cremanei	.((((((( (    ((.((((....((((( (.............)) ))))..))    )).)))))))))).	1.000 -25.32
celegans	.((((((( (    ((((((...(((((((  .(((.......)))) )))))).)    ))))))))))))).	1.000 -25.40
cbrenneri	((((((((.(((((((.(((((((( (    (((((..((..(((((    (..........)) ))))))..    )))))))))))))).)))))))...))))))))	1.000 -55.00
cjaponica	.((..((. ((((((((....((((((((( ((((((....))))))))))))))).)))))))).))...)).	1.000 -34.60
ppacificus	.((((((((.    ......((((.((((( ((..........)))) ).)).)))    )....)))))))).	0.648 -11.90

cbriggsae	chromosome:chrI:2124810:2124910:1	Opposite_strand|Intronic_non-coding|NM_174569|PABPN1 ## Same_strand|Intronic_non-coding|NM_001107428|Zfp612 ## Opposite_strand|Intronic_coding|NM_053878|Cplx2 ## Same_strand|Intronic_coding|NM_008665|Myt1 ## {Repeats: no} ## {MIR: cbr-mir-50}
cremanei	chromosome:chrUn:17804059:17804199:-1	Same_strand|Intronic_coding|NM_001009560 ## Same_strand|Boundary_coding|NM_058485
celegans	chromosome:chrI:1738575:1738715:1	Same_strand|Intronic_coding|Y71G12B.11a ## {MIR: cel-mir-50}
cbrenneri	chromosome:chrUn:31668280:31668375:-1	Opposite_strand|Intronic_coding|NM_203889 ## Same_strand|Intronic_coding|NM_001113428
cjaponica	chromosome:chrUn:40887817:40887957:1	intergenic
ppacificus	chromosome:chrUn:63058887:63059027:-1	intergenic

cbr-mir-236

Cloning frequencies

absolute	AF16
cbr-mir-236 3arm	225
normalized	AF16
cbr-mir-236 3arm	0.587

block663 (miRBase cbr-mir-236) [miRNAknown_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

miRBase cbr-mir-236

0.001

no

no

0.32/0.50

18/23/0.96

0.0

0.0

140

0

1

0

18

6

3arm

1

nd

0.14

1

225

1

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------AAUACUG----------------------------------------------------	221	miR-236
seed	---------------------------------------------------------------------------------------CUGUCAG------------------------------------------------	2	novel
seed	------------------------------------------------------------------------------------AUACUGU---------------------------------------------------	2	novel
		len	cloning frequencies
			AF16
	----------------------------------------------------------------------------------TAATACTGTCAGGTAATGACGC--------------------------------------	22	140
cbr-miR-236	----------------------------------------------------------------------------------TAATACTGTCAGGTAATGACGCT-------------------------------------	23	39
	----------------------------------------------------------------------------------TAATACTGTCAGGTAATGACG---------------------------------------	21	35
	----------------------------------------------------------------------------------TAATACTGTCAGGTAATG------------------------------------------	18	5
	-----------------------------------------------------------------------------------AATACTGTCAGGTAATGACG---------------------------------------	20	2
	----------------------------------------------------------------------------------TAATACTGTCAGGTAATGA-----------------------------------------	19	1
	----------------------------------------------------------------------------------TAATACTGTCAGGTAATGAC----------------------------------------	20	1
	--------------------------------------------------------------------------------------ACTGTCAGGTAATGACGCT-------------------------------------	19	1
	--------------------------------------------------------------------------------------ACTGTCAGGTAATGACGC--------------------------------------	18	1
cbriggsae	-----------------AAGTGACCAATGTCCA---GCGTCTTACC--TGTTCAATATTTAGACTGACCAAACCCATAGCTCTAATACTGTCAGGTAATGACGCTGGATAGTCTTGTCATTG--------------------
cremanei	----CTGTCCTATTCTTTGGTGACCGATGTCCA---GCGTCTTACC--TGTTCAATATTTAGACTGATTAGCTCATGAGATCTAATACTGTCAGGTAATGACGCTGGATTATCTTGTCATTTATG----ATAAGCAACACAG
celegans	-----------------------------------------TTACC--TGTTCAATATTTAGACTGACTAT-CAAAGAGATCTAATACTGTCAGGTAATGACGC--------------------------------------
cbrenneri	GCTACTGTCCTATTCTGAGGTGACCGATGTCCA---GCGTCTTACC--TGTTCAATATTTAGACTAAC-ACATCAAGAGATCTAATACTGTCAGGTAATGACGCTGGGTAATAGTGTCGCTTATTTGAAATCAACGGTAAGT
cjaponica	-----GTTATTATGTTTCCACGAACGAATTCCACTTATGACGTTCCGATGTTCCGCATTT--TTTTACTGTGGTCTCACAGCGAATACTGCGGAACATCGGAGCATCGCAAGAAAGATTTCCTTC----AGGAACAGTTAAT
	* **  *****   ****    * *          *   * *******      *  *  **
	-----                 ----------------   ----------  --------------------------------------------------------------------------                    -----	NM_004845
	-----                 ----------------   ----------  --------------------------------------------------------------------------                    -----	NM_207682
	-----                 ----------------   ----------  --------------------------------------------------------------------------                    -----	NM_114884
	+++++                 ++++++++++++++++   ++++++++++  ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++                    +++++	NM_001047951
	-----                 ----------------   ----------  --------------------------------------------------------------------------                    -----	NM_001093430
	+++++                 ++++++++++++++++   ++++++++++  ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++                    +++++	NM_000493
cbriggsae	.((((((...((((((   ((((((((((  ((..((.((((.((((((..........))).))))))).)).))))))).))))))))))).....)))))).	1.000 -38.50
cremanei	((((.((..((...((((((.((((((((   ((((((((((  ((..((.((.(((((((.((......)).)).))))))).)).))))))).)))))))))).)))..))))))...)    )..))....))))	0.939 -43.10
celegans	(((((  ((..((.((.(((((((...... .....)).))))))).)).)))))))......	0.998 -11.10
cbrenneri	..((((((....(((..(((((((..((..(((   ((((((((((  ((..((.((.(((((((... ........)).))))))).)).))))))).))))))))...))...)))))))....)))....))))))...	0.995 -42.90
cjaponica	((((...((((((...(((.(((.((..(((.(((.((((((((((((((((...  .((..(((((....)))))..))...)))))))))))))))).))).)))...)).))).)))    .))))))..))))	0.886 -50.90

cbriggsae	chromosome:chrII:5133851:5133950:-1	Opposite_strand|Intronic_non-coding|NM_004845|PCYT1B ## Opposite_strand|Intronic_coding|NM_114884|KICP-02 ## Same_strand|Intronic_coding|NM_001047951|LOC499796 ## Same_strand|Intronic_non-coding|NM_000493|COL10A1 ## {Repeats: no} ## {MIR: cbr-mir-236}
cremanei	chromosome:chrUn:132170869:132170997:1	Opposite_strand|Intronic_coding|NM_205265
celegans	chromosome:chrII:7030055:7030194:-1	Opposite_strand|Boundary_non-coding|C52E12.1.1 ## {MIR: cel-mir-236}
cbrenneri	chromosome:chrUn:68604093:68604228:-1	Same_strand|Intronic_coding|NM_023651
cjaponica	chromosome:chrUn:127532689:127532819:-1	Same_strand|Intronic_coding|NM_067195

cbr-mir-252

Cloning frequencies

absolute	AF16
cbr-mir-252 5arm	73
normalized	AF16
cbr-mir-252 5arm	0.190

block706 (miRBase cbr-mir-252) [miRNAknown_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

miRBase cbr-mir-252

0.002

no

no

0.44/0.48

18/23/0.93

0.0

0.0

68

0

1

0

14

8

5arm

1

nd

0.24

3

73

1

na

na

		reads	miRBase family seed
seed	----------------------------------UAAGUAG----------------------------------------------------------------------------------------------	73	miR-251
seed	-----------------------------------AAGUAGU---------------------------------------------------------------------------------------------	0	miR-252
		len	cloning frequencies
			AF16
	---------------------------------ATAAGTAGTAGTGCCGCAGGT---------------------------------------------------------------------------------	21	68
	---------------------------------ATAAGTAGTAGTGCCGCA------------------------------------------------------------------------------------	18	5
cbr-miR-252	----------------------------------TAAGTAGTAGTGCCGCAGGTAAC------------------------------------------------------------------------------	23	-
cbriggsae	-------------------GGTCTCTCCCAGTTATAAGTAGTAGTGCCGCAGGTAACCGCTTCCAGAAAATTGGTTTACCTACTGCCTTCTGCTTAGAA--TTGGGATTTTGATGACCG----------------
cremanei	----------TATTCTTGAGGTCTCTTTCAGTTATAAGTAGTAGTGCCGCAGGTAACCACTCAAATATA--TGGTTTACCTACTGCCTTCTGCTTAGAA--TTGAAATATCGATGACC-----------------
celegans	---------------CAGGGGTCTCTTTCAGTTATAAGTAGTAGTGCCGCAGGTAACCGCCAGTCTAAA--AGGCTTACCTACTGCCTTCTGCTTAAAA--TTGAAATATTGATGACCATTG-------------
cbrenneri	CTTTCTATATTCCTTTTTTGGTCTCTTTCAGTTATAAGTAGTAGTGCCGCAGGTAACCG---ATTTCAA--TGGTTTACCTACTGCCTCCTGCTTAGAA--TTGAAATTTCGATGACCGTCTTTTGTAATGAAAG
cjaponica	--------------------GTCTCTTCCGATTATAAGTAGTAGTGCCGCAGGTAACTG------GAGA--TTGATTACCTACTGCCTCCTGCTTAAAA--TTGGAA----------------------------
ppacificus	--------GATCACCTATCACTCTGTCCGGGTTCTAAGTAGTAGTGCCGCAGGTAACCAACAATTGAGA---GGTTTACCTATAGCCTTCTGCTTAACACCTTGAAGAGTTGATC--------------------
	*** *     ** ***********************           *    * *******  **** *******  *  ***
	+++++                   ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++                +++++	NM_001031311
	+++++                   ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++                +++++	NM_177732
	+++++                   ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++                +++++	NM_020272
	+++++                   ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++                +++++	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_207243
	+++++                   ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++                +++++	NM_207243
	+++++                   ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++                +++++	NM_207243
	+++++                   ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++                +++++	NM_207243
	+++++                   ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++                +++++	NM_207243
	-----                   --------------------------------------------------------------------------------  ------------------                -----	NM_001129175
cbriggsae	((((((((((((((.(((((((.((.((...(((((((((.((......)).))))).))))...)))).))))))).))  ))))))....)).)))).	1.000 -36.50
cremanei	.........((((((((((((((.(((((((.((.((...(((((((((..........  ))))).))))...)))).))))))).))  ))))))....)).))))	0.995 -30.50
celegans	....((((((((((((((.(((((((.((.((...((((((..(((........  .)))))))))...)))).))))))).))  ))))))....)).))))....	0.999 -33.10
cbrenneri	(((((..(((........(((((((((((((((.(((((((.((.((...(((((((((   .......  ))))).))))...)))).))))))).))  ))))))....)).)))))......)))..)))))	0.971 -34.24
cjaponica	.....((((((((.(((((((.((.((...((((((...      ....  ....))))))...)))).))))))).))  ))))))	0.999 -23.60
ppacificus	(((((......(((((.((.((((..(((((((.((.((...((((((((...........   )))).))))...)))).)))))))..)))).))))))))))))	0.999 -32.30

cbriggsae	chromosome:chrII:7467789:7467886:-1	Same_strand|Intronic_non-coding|NM_001031311|PIK3CB ## Same_strand|Intronic_coding|NM_020272|Pik3cg ## Opposite_strand|Intronic_coding|NM_001129175|W02B12.13 ## {Repeats: no} ## {MIR: cbr-mir-252}
cremanei	chromosome:chrUn:8843495:8843598:1	Opposite_strand|Intronic_coding|NM_001011005 ## Same_strand|Intronic_coding|NM_077846
celegans	chromosome:chrII:11446772:11446874:-1	Opposite_strand|Intronic_coding|W02B12.13 ## {MIR: cel-mir-252}
cbrenneri	chromosome:chrUn:41707048:41707175:1	Opposite_strand|Intronic_coding|NM_001056672 ## Opposite_strand|Boundary_coding|NM_001129175
cjaponica	chromosome:chrUn:63338611:63338687:-1	Opposite_strand|Intronic_coding|NM_001129175
ppacificus	chromosome:chrUn:24531069:24531172:1	Same_strand|Intronic_coding|NM_001114660 ## Opposite_strand|Intronic_coding|NM_174405

cbr-mir-43

Cloning frequencies

absolute	AF16
cbr-mir-43 3arm	46
normalized	AF16
cbr-mir-43 3arm	0.120

block716 (miRBase cbr-mir-43) [miRNAknown_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

miRBase cbr-mir-43

0.001

no

no

0.33/0.43

18/23/0.98

0.0

0.0

33

0

1

0

16

4

3arm

1

nd

0.22

3

46

1

na

na

Clusters

Located in cluster 2: cbr-mir-44, cbr-mir-43, cbr-mir-42

Families

Member of family miR-43 (seed AUCACAG): cbr-mir-43, sblock2_cand

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------------AUCACAG----------------------------------------------------	46	miR-43
		len	cloning frequencies
			AF16
cbr-miR-43	----------------------------------------------------------------------------------------------TATCACAGTT-----TACTTGCTGTCGC--------------------------------	23	33
	----------------------------------------------------------------------------------------------TATCACAGTT-----TACTTGCTGTCG---------------------------------	22	12
	----------------------------------------------------------------------------------------------TATCACAGTT-----TACTTGCT-------------------------------------	18	1
cbriggsae	---------AGGCGATTCT-----------GCCCGTGACATCAAGATGCTTGTGA-TTA----------TGCGAAAAT-------GTTGGGACATATCACAGTT-----TACTTGCTGTCGCAGGCGGATTATTGCTA----------------
cremanei	-------------GATTCT-----------GCCCGTGACAACAAGAAACTTGTGA-TTA----------TGCCTAGAG-AATGAAGAAGGGACATATCACAGTT-----TACTTGCTGTCGCAGGCGGTGTC----------------------
celegans	TCCAAAAAGGGGTAACTATTGGCACTAGTCGCCCGTGACATCAAGAAACTAGTGA-TTA----------TGCCAAACC-------ACAGGGACATATCACAGTT-----TACTTGCTGTCGCGGGCGGTGCTGAGTTTAAGGCCTCTGAAAAGA
cbrenneri	-----------------------------------TGATATCAAGGAACTTGTGATTTA----------TGCCATAACTAACATAACCTCGACATATCACAGTT-----TACTTGCTGTCG---------------------------------
cjaponica	-----GCGGGACCAACTGG-----------TCCCGGGACCGCAAGAAACTCGTGTTATA----------TGCCAAATC-------AGTGGGTCATATCACAGTT-----TACTTGCTGTCCCGGGCGCTTGGTCCTGC----------------
ppacificus	------------------------------------GAAAAGGAGATATCAGAGCTTGATCAGGTCTCTTTCTTAATT----------------TATCACAGTTATTGATATCTTCT-------------------------------------
	**     **      * *    *          * *                      **********     **  * **
	+++++         ++++++++++           +++++++++++++++++++++++++ +++          +++++++++       +++++++++++++++++++     +++++++++++++++++++++++++++++                +++++	NM_001047975
	+++++         ++++++++++           +++++++++++++++++++++++++ +++          +++++++++       +++++++++++++++++++     +++++++++++++++++++++++++++++                +++++	NM_214509
	+++++         ++++++++++           +++++++++++++++++++++++++ +++          +++++++++       +++++++++++++++++++     +++++++++++++++++++++++++++++                +++++	NM_001034039
	+++++         ++++++++++           +++++++++++++++++++++++++ +++          +++++++++       +++++++++++++++++++     +++++++++++++++++++++++++++++                +++++	NM_001033832
	+++++         ++++++++++           +++++++++++++++++++++++++ +++          +++++++++       +++++++++++++++++++     +++++++++++++++++++++++++++++                +++++	NM_214466
	+++++         ++++++++++           +++++++++++++++++++++++++ +++          +++++++++       +++++++++++++++++++     +++++++++++++++++++++++++++++                +++++	NM_080679
	+++++         ++++++++++           +++++++++++++++++++++++++ +++          +++++++++       +++++++++++++++++++     +++++++++++++++++++++++++++++                +++++	NM_080681
	+++++         ++++++++++           +++++++++++++++++++++++++ +++          +++++++++       +++++++++++++++++++     +++++++++++++++++++++++++++++                +++++	NM_080680
	-----         ----------           ------------------------- ---          ---------       -------------------     -----------------------------                -----	NM_133464
cbriggsae	.(((((((((           (((.((((((.((((..(((.(((( (.(          (((......       .....).))))))))))).     ..)))).)))))).))))))..)))))).	1.000 -36.50
cremanei	(((.((           (((.((((((.((((((((.((((( .((          (((((.... .........))).))))))))))))     ).)))).)))))).))))).)))	1.000 -37.32
celegans	.......((((((.....(((((((....(((((((((((.(((((((((.(((( .((          ((((.....       ....)).))))))))))))     ).)))).)))))))))))))))))).......)))))).......	0.997 -55.10
cbrenneri	.((((.((((((((.(((((((((          ((..........))))).........)))))))))     ).)))).)))).	1.000 -15.00
cjaponica	(((((((((...((           (((((((((.((((((((((.(((..(((          ((((.....       ....)).))))))))))))     ).))))).)))))))).))))))))))))	1.000 -54.10
ppacificus	....((((((((((((((((((((.((((..........)))                ))))).)))).))))))))))))	0.928 -16.90

cbriggsae	chromosome:chrII:8049417:8049511:-1	Same_strand|Intronic_coding|NM_001047975|LOC683871 ## Opposite_strand|Intronic_non-coding|NM_133464|ZNF483 ## {Repeats: no} ## {MIR: cbr-mir-43}
cremanei	chromosome:chrUn:8362216:8362306:1	intergenic
celegans	chromosome:chrII:11889810:11889940:1	intergenic ## {MIR: cel-mir-43}
cbrenneri	chromosome:chrUn:172696302:172696436:1	intergenic
cjaponica	chromosome:chrUn:98919151:98919250:-1	intergenic
ppacificus	chromosome:chrUn:65292805:65292869:-1	Same_strand|Intronic_coding|NM_001065794 ## Opposite_strand|Intronic_coding|NM_001087971

cbr-lin-4

Cloning frequencies

absolute	AF16
cbr-lin-4 5arm	1616
normalized	AF16
cbr-lin-4 5arm	4.213

block733 (miRBase cbr-lin-4) [miRNAknown_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

miRBase cbr-lin-4

0.003

no

no

0.52/0.58

18/22/0.96

0.0

0.0

1541

0

1

0

20

5

5arm

1

nd

0.15

1

1616

1

na

na

Families

Member of family lin-4 (seed CCCUGAG): cel-mir-237, cbr-lin-4, sblock71_cand

		reads	miRBase family seed
seed	------------------------------------------CCCUGAG-------------------------------------------------------------------------------------------	1613	lin-4
seed	-------------------------------------------CCUGAGA------------------------------------------------------------------------------------------	2	novel
seed	-----------------------------------------UCCCUGA--------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-----------------------------------------TCCCTGAGACCTCAAGTGTG-------------------------------------------------------------------------------	20	1541
	-----------------------------------------TCCCTGAGACCTCAAGTGT--------------------------------------------------------------------------------	19	66
cbr-lin-4	-----------------------------------------TCCCTGAGACCTCAAGTGTGA------------------------------------------------------------------------------	21	3
	-----------------------------------------TCCCTGAGACCTCAAGTG---------------------------------------------------------------------------------	18	2
	------------------------------------------CCCTGAGACCTCAAGTGTGA------------------------------------------------------------------------------	20	1
	----------------------------------------TTCCCTGAGACCTCAAGTGTG-------------------------------------------------------------------------------	21	1
	------------------------------------------CCCTGAGACCTCAAGTGTG-------------------------------------------------------------------------------	19	1
	-----------------------------------------TCCCTGAGACCTCAAGTGTGAG-----------------------------------------------------------------------------	22	1
cbriggsae	-------------------ATCAGATGCTTTCGGCC--TGTTCCCTGAGACCTCAAGTGTGAGCGTTCTGAACATGCTTCAC-GCCTGGGCTCTCCGGGTAC------CAGGACGGTCTGAG------------------
cremanei	-----------------------------------------TCCCTGAGACCTCAAGTGTGAGCGCACTGTTGATGCTTCAC-GCCTGGGCTCTCTGGGT----------------------------------------
celegans	-----------------------------------------TCCCTGAGACCTCAAGTGTGAGTGTACTATTGATGCTTCAC-ACCTGGGCTCTCCGGGT----------------------------------------
cbrenneri	TGGTTTGGTTGGTTTGATATGATACAGCTCACGGCC--TGCTCCCTGAGACCTCAAGTGTGAGCGTACTGTAGATGCTTCAC-ACCTGGGCTCTCTGGGTAC------CAGGACGGTTCATTCGAGCAACACTTTTTTCA
cjaponica	------------------------TTGCTCACGTCC--TGTTCCCTGAGACCTCAAGTGTGAAAATAT--CTGATATCTCAC-ACCTGGGCTCTCCGGGTAC------CAGGACGGTACTATAGAGCAA-----------
ppacificus	--------------CACACCACGACTGCTAGCAAATGGCGTTCCCTGAGACCTCAATTGTGA-TGAGATACGAGTCAGTCACGGTTTGAGCTCTCATGGCACGCTATGCTTGTCGATGTTGTG-----------------
	*************** *****            *   ****    ** ******  **
	+++++                   +++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++      ++++++++++++++                  +++++	NM_001047975
	+++++                   +++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++      ++++++++++++++                  +++++	NM_001047939
	+++++                   +++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++      ++++++++++++++                  +++++	NM_101724
	-----                   -----------------  -------------------------------------------- -------------------      --------------                  -----	NM_001011629
	+++++                   +++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++      ++++++++++++++                  +++++	NM_001055069
	+++++                   +++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++      ++++++++++++++                  +++++	NM_063457
	+++++                   +++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++      ++++++++++++++                  +++++	NM_067556
	+++++                   +++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++      ++++++++++++++                  +++++	NM_202130
	-----                   -----------------  -------------------------------------------- -------------------      --------------                  -----	NM_014971
	+++++                   +++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++      ++++++++++++++                  +++++	NM_062776
cbriggsae	.((((((.....((.((  ((..(((.((((.((((.((((((((((.......)))).)))) )).)))).)))).)))...      )))).)))))))).	1.000 -40.30
cremanei	.(((.((((.((((.(((((((.(((.......)))))))) )).)))).)))).))).	1.000 -26.50
celegans	.(((.((((.((((.((((((((((.......))))).))) )).)))).)))).))).	1.000 -24.90
cbrenneri	.......(((.((((((.((((.........((.((  ((..(((.((((.((((.((((((((((.......))))).))) )).)))).)))).)))...      )))).))..)))))))))))))..........	0.893 -44.20
cjaponica	.(((((.(((((  ((..(((.((((.((((.((((((......  ........)))) )).)))).)))).)))...      )))))))........))))).	0.980 -40.34
ppacificus	((((.((((((....((((..((((((.((.(((((.((((((((((( (..(((....))).))))))))).))).))))).)).)))))))))).)))).)).))))	1.000 -46.10

cbriggsae	chromosome:chrII:8974959:8975052:-1	Same_strand|Intronic_coding|NM_001047975|LOC683871 ## Same_strand|Intronic_non-coding|NM_101724|AT1G18660 ## Opposite_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## {Repeats: no} ## {MIR: cbr-lin-4}
cremanei	chromosome:chrUn:41494352:41494485:1	Same_strand|Intronic_coding|NM_062776
celegans	chromosome:chrII:5902195:5902328:1	Same_strand|Intronic_coding|F59G1.4 ## {MIR: cel-lin-4}
cbrenneri	chromosome:chrUn:163746733:163746863:1	Same_strand|Intronic_coding|NM_062776
cjaponica	chromosome:chrUn:4235949:4236042:1	Same_strand|Boundary_non-coding|NR_000799 ## Same_strand|Intronic_coding|NM_062776
ppacificus	chromosome:chrUn:16970262:16970369:1	Opposite_strand|Intronic_coding|NM_138747

cbr-mir-35

Cloning frequencies

absolute	AF16
cbr-mir-35 3arm	827
normalized	AF16
cbr-mir-35 3arm	2.156

block973 (miRBase cbr-mir-35) [miRNAknown_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

miRBase cbr-mir-35

0.001

no

no

0.48/0.53

18/23/0.60

0.0

1.2

792

0

1

0

32

6

3arm

1

nd

0.09

1

827

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----------------------------------------------------	810	miR-35/36/38/39/40/41
seed	---------------------------------------------------------------------------------GGGUGAA------------------------------------------------	12	novel
seed	----------------------------------------------------------------------------UCACCGG-----------------------------------------------------	5	novel
		len	cloning frequencies
			AF16
cbr-miR-35	----------------------------------------------------------------------------TCACCGGGTGAAAA------CTTGCAAG--------------------------------	22	486
	----------------------------------------------------------------------------TCACCGGGTGAAAA------CTTGC-----------------------------------	19	306
	----------------------------------------------------------------------------TCACCGGGTGAAAA------CTTG------------------------------------	18	12
	--------------------------------------------------------------------------------CGGGTGAAAA------CTTGCAAG--------------------------------	18	12
	----------------------------------------------------------------------------TCACCGGGTGAAAA------CTTGCAAGT-------------------------------	23	6
	---------------------------------------------------------------------------ATCACCGGGTGAAAA------CTTGCAAG--------------------------------	23	3
	---------------------------------------------------------------------------ATCACCGGGTGAAAA------CTTGC-----------------------------------	20	2
cbriggsae	-----------------TAGTCCAGTTCTGGACATTCGCGGGTTTTTTCCTTCGGTGATATTCGA-AGAATCGCTATCACCGGGTGAAAA------CTTGCAAGTGTCTTGCTTCGACTGGTCATTTTGCTTGTAT
cremanei	-------------------GGTCGGATCGGCCCTCC-ACTGGTTTTCGCC-TCGGTCATATTTCA-AGTATGATTATCACCGGGTGAAAA------TCAGAGCAGGGCCGATTCCACC------------------
celegans	TTCCCAACTATTATTCTCGGATCAGATCGAGCCATT-GCTGGTTTCTTCC-ACAGTGGTACTTTCCATTAGAACTATCACCGGGTGGAAA------CTAGCAGTGGCTCGATCTTTTCC-----------------
cbrenneri	GTTCTCTATTATTCTATTCGGCCGGATCGGACCTAT-GCTGGTTTTCACC-GCGGTTATACTTCTAACAATAATTATCACCGGGTTAAAA------CTTGCAGAGGTCCGGTCCGGCC------------------
cjaponica	----------------------------------CTGGCTGGTATCCGCG-ATGGTGTTACACTACTGTAATG-TATCACCGGGTGGAAA------CTTGCAAG--------------------------------
ppacificus	------TCTGAGTCCCTTCGATCGCCTCTGATCACT---------------ACGATGAAACTGAGATAACGAGTTTTCACCGGGTGAACAGAAGCTGTTGAAGATATCGGA-------------------------
	*   *              * *********  * *         *
	-----                 ------------------------------------------------ ------------------------      ---------------------------------------------	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	..(.((((((..(((((((.((((((((((.((..((((((((..((( ....))).)))))))))).)))))      ))))).)))))))......)))))).).............	1.000 -42.60
cremanei	(((.(((((((((((.. .(((((((((((( .((((.(((..((( ....))).))).))))))))))))      ))))...))))))))))).)))	1.000 -49.80
celegans	..................(((..((((((((((((( (((((((((..(( ...((((((.(((......))).))))))..))..))))      ))))))))))))))))))..)))	0.989 -54.00
cbrenneri	...................(((((((((((((((.( ((.((((((.((( .((((.(((.((........)).))).))))))).))))      )).))).)))))))))))))))	0.989 -52.20
cjaponica	...((.(((.(((((. .(((((.((((.........)) )).))))).))))).)      )).))...	1.000 -21.90
ppacificus	(((((....(((((((.((.((((.(((((               .((.(((((((.........))))).)).))))))).)))).)).)))))))...)))))	1.000 -30.60

cbriggsae	chromosome:chrII:7536620:7536731:1	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} ## {MIR: cbr-mir-35}
cremanei	chromosome:chrUn:26788069:26788158:-1	intergenic ## {SimpF: trf}
celegans	chromosome:chrII:11537510:11537620:1	Opposite_strand|Intronic_coding|Y62F5A.9 ## {MIR: cel-mir-35}
cbrenneri	chromosome:chrUn:47823952:47824061:-1	intergenic
cjaponica	chromosome:chrUn:117591190:117591341:-1	Opposite_strand|Intronic_coding|NM_171042
ppacificus	chromosome:chrUn:171595123:171595212:-1	intergenic ## {Repeats: (GA)n 2 38 -1 class=Simple_repeat} ## {SimpF: trf}

cbr-mir-60

Cloning frequencies

absolute	AF16
cbr-mir-60 3arm	3172.500
normalized	AF16
cbr-mir-60 3arm	8.270

block993 (miRBase cbr-mir-60) [miRNAknown_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

miRBase cbr-mir-60

0.002

no

no

0.22/0.35

18/24/1.00

0.0

0.0

3146

0

1

0

5

6

3arm

1

nd

0.18

2

3175

1

na

na

		reads	miRBase family seed
seed	----------------------------------------------------------AUUAUGC----------------------------------------	3163	miR-60
seed	---------------------------------------------------------UAUUAUG-----------------------------------------	9	novel
seed	-----------------------------------------------------------UUAUGCA---------------------------------------	2	novel
seed	--------------------------------------------------------------UGCACAU------------------------------------	1	novel
		len	cloning frequencies
			AF16
	---------------------------------------------------------TATTATGCACATTTTCTAGTCC--------------------------	22	3146
	---------------------------------------------------------TATTATGCACATTTTCTAGTC---------------------------	21	12
	--------------------------------------------------------ATATTATGCACATTTTCTAGTCC--------------------------	23	6
	---------------------------------------------------------TATTATGCACATTTTCTAGT----------------------------	20	3
	--------------------------------------------------------ATATTATGCACATTTTCTAGTC---------------------------	22	2
	---------------------------------------------------------TATTATGCACATTTTCTA------------------------------	18	2
	----------------------------------------------------------ATTATGCACATTTTCTAGTCCA-------------------------	22	1
	----------------------------------------------------------ATTATGCACATTTTCTAGTC---------------------------	20	1
	-------------------------------------------------------------ATGCACATTTTCTAGTCCAA------------------------	20	1
	--------------------------------------------------------ATATTATGCACATTTTCTAGTCCA-------------------------	24	1
cbr-miR-60	---------------------------------------------------------TATTATGCACATTTTCTAGTCCA-------------------------	23	-
cbriggsae	------------TTCTTGAGCTGGAAAGGTGACATAAAATCATGTCCAAGCACGCGATATTATGCACATTTTCTAGTCCAAGAC---------------------
cremanei	GAAAACCGCTTGTTCTTGAGCTAGAAAGGTGACATAAAATCATGTATAACAACGCGATATTATGCACATTTTCTAGACCAAGACATGA---TTTATCGGTTCATC
celegans	---AACCGCTTGTTCTTGAACTGGAAGAGTGCCATAAAATCATGACAAAGTACGTGATATTATGCACATTTTCTAGTTCAAGACTTGA---GAAATCGGTT----
cbrenneri	GTAAACCGCTTGCTCTTGAGCTGGAAAGGTGACATAAAATCATGTCAGAGAACGCGATATTATGCACATTTTCTAGTCCAAGACTTGA---TTTACCGGTTTAC-
cjaponica	--GAACCGCTTG-TCTTGAGCTGGAAAAGTGCTATAAAATCGAGT---AATTTACGATATTATGCACATTTTCTAGTTCAAGACTTGACGCCCTATTGGTTC---
	****** ** ***  ***  ********  *    *      *********************  ******
	-----            ------------------------------------------------------------------------                     -----	NM_001047975
	-----            ------------------------------------------------------------------------                     -----	NM_001047939
	-----            ------------------------------------------------------------------------                     -----	NM_006389
	+++++            ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++                     +++++	NM_001011629
	-----            ------------------------------------------------------------------------                     -----	NM_001002681
	-----            ------------------------------------------------------------------------                     -----	NM_068373
	-----            ------------------------------------------------------------------------                     -----	NM_075396
cbriggsae	.(((((..(((((((((((.(((((.(((.(((......))).))).)))))))).))))))))..))))).	1.000 -26.30
cremanei	...(((((..((.(((((..(((((((((((.(((((.(((.(((......))).))).)))))))).))))))))..)))))))...   .....)))))....	0.973 -28.70
celegans	(((((((((.((((((((((((((((((.(((((.((((((........)))))).)))))))).)))))))))))))))..)))   )....)))))	0.948 -38.20
cbrenneri	((((((((.....(((((..(((((((((((.(((((.(((.(((......))).))).)))))))).))))))))..))))).....   .....))))))))	0.991 -33.26
cjaponica	(((((((..( (((((((((((((((((((.((((.((((((.   ...)).)))).)))))))).)))))))))))))))).....))......)))))	0.903 -36.80

cbriggsae	chromosome:chrII:8572396:8572467:1	Opposite_strand|Intronic_coding|NM_001047975|LOC683871 ## Opposite_strand|Intronic_non-coding|NM_006389|HYOU1 ## Same_strand|Intronic_coding|NM_001011629|Mblk-1 ## {Repeats: no} ## {MIR: cbr-mir-60}
cremanei	chromosome:chrUn:132859258:132859359:1	intergenic
celegans	chromosome:chrII:6328650:6328744:-1	intergenic ## {MIR: cel-mir-60}
cbrenneri	chromosome:chrUn:156677439:156677539:1	intergenic
cjaponica	chromosome:chrUn:130421852:130421947:1	intergenic

cbr-mir-231

Cloning frequencies

absolute	AF16
cbr-mir-231 3arm	90
normalized	AF16
cbr-mir-231 3arm	0.235

block1779 (miRBase cbr-mir-231) [miRNAknown_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

miRBase cbr-mir-231

0.001

no

no

0.45/0.52

19/25/0.96

0.0

0.0

76

0

1

0

26

6

3arm

1

nd

0.17

3

90

1

na

na

Families

Member of family miR-231/787 (seed AAGCUCG): cbr-mir-231, cbr-mir-787

		reads	miRBase family seed
seed	---------------------------------------------------------------------------AAGCUCG---------------------------------------------------------	89	miR-231/787
seed	--------------------------------------------------------------------------UAAGCUC----------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	--------------------------------------------------------------------------TAAGCTCGTGAACAACAGGCAGG------------------------------------------	23	76
	--------------------------------------------------------------------------TAAGCTCGTGAACAACAGGCA--------------------------------------------	21	3
	--------------------------------------------------------------------------TAAGCTCGTGAACAACAGGCAG-------------------------------------------	22	3
	--------------------------------------------------------------------------TAAGCTCGTGAACAACAGG----------------------------------------------	19	3
	--------------------------------------------------------------------------TAAGCTCGTGAACAACAGGC---------------------------------------------	20	2
cbr-miR-231	--------------------------------------------------------------------------TAAGCTCGTGAACAACAGGCAGGA-----------------------------------------	24	1
	--------------------------------------------------------------------------TAAGCTCGTGAACAACAGGCAGGAC----------------------------------------	25	1
	-------------------------------------------------------------------------ATAAGCTCGTGAACAACAGGCA--------------------------------------------	22	1
cbriggsae	------------CTAGCACCTCAATGTTGTTCTGTCTGTTTCCATAGCTTATATTGT-------AAGGTACTTATAAGCTCGTGAACAACAGGCAGGACAACTGG-AA--GTGGTGTTTTTTTTCA-------------
cremanei	ATTCCCTCTAATCGAGCACCCCGATGTTGTTCTGACTGTTTCCATAGCTTATATTGTCTC----AAAATGCATATAAGCTCGTGAACAACAGGCAGGACAACTGGTCTTTTTGGTGTGCATTTTGATAAAACGGTGAGT
celegans	---------------GCACCAC-AGGTTGTTCTGACTGTTTCAAAAGCTTGTAGTATCTTAATAAATAAACATATAAGCTCGTGATCAACAGGCAGAACAACTCG-GT--TTTGTGTGC--------------------
cbrenneri	-----GCTAAGCCTACCTTTTC-ATGTTGTTCTGACTGTTTCAAAAGCTTATATTGTTCGTTCAAAGTTACTTATAAGCTCGTGATCAACAGGCAGGACAACTAT-CAAAGGGGCGTGC--------------------
cjaponica	------------------CCCC-TTGTGGTTCTGACTGTTTCAGTAGCTTATAGC---------CGTGGGCGTATAAGCTCGTGATCAACAGGCAGGACCAC-------------------------------------
	*   ** ****** *******   ***** **                 * ************* ********** ** **
	-----            ---------------------------------------------       ----------------------------------------- --  ----------------             -----	NM_001022613
	-----            ---------------------------------------------       ----------------------------------------- --  ----------------             -----	NM_009322
	+++++            +++++++++++++++++++++++++++++++++++++++++++++       +++++++++++++++++++++++++++++++++++++++++ ++  ++++++++++++++++             +++++	NM_065267
	-----            ---------------------------------------------       ----------------------------------------- --  ----------------             -----	NM_199029
	+++++            +++++++++++++++++++++++++++++++++++++++++++++       +++++++++++++++++++++++++++++++++++++++++ ++  ++++++++++++++++             +++++	NM_020180
	+++++            +++++++++++++++++++++++++++++++++++++++++++++       +++++++++++++++++++++++++++++++++++++++++ ++  ++++++++++++++++             +++++	NM_204893
	-----            ---------------------------------------------       ----------------------------------------- --  ----------------             -----	NM_199449
	+++++            +++++++++++++++++++++++++++++++++++++++++++++       +++++++++++++++++++++++++++++++++++++++++ ++  ++++++++++++++++             +++++	NM_153693
	-----            ---------------------------------------------       ----------------------------------------- --  ----------------             -----	NM_009517
	+++++            +++++++++++++++++++++++++++++++++++++++++++++       +++++++++++++++++++++++++++++++++++++++++ ++  ++++++++++++++++             +++++	NM_001025087
	+++++            +++++++++++++++++++++++++++++++++++++++++++++       +++++++++++++++++++++++++++++++++++++++++ ++  ++++++++++++++++             +++++	NM_001025088
	+++++            +++++++++++++++++++++++++++++++++++++++++++++       +++++++++++++++++++++++++++++++++++++++++ ++  ++++++++++++++++             +++++	NM_001025089
	-----            ---------------------------------------------       ----------------------------------------- --  ----------------             -----	NM_001128181
	-----            ---------------------------------------------       ----------------------------------------- --  ----------------             -----	NM_027712
cbriggsae	..((((((((...(((((((((((((((..(((((((((((..((       (...))).)))))))).)))...)))))))))))))))..) ).  ..))))))........	1.000 -39.60
cremanei	((((((....(((((((((.((((.(((((((((.(((((..(((((((((((.(((...    .....))))))))))).)))...))))).)))))))))........)))).))))...))))).....)).))))	0.912 -41.60
celegans	(((.((( (((((((((((.((((((((..((((((((.(((........)))....))))))))..)))..))))).)))))))))).. ..  ..)))))))	1.000 -35.10
cbrenneri	((...(((..(((((.. ..(((((((((.((((((((..((((((((..((............)).))))))))..)))..))))).)))))))))... .))))))))..))	0.999 -39.10
cjaponica	.... ..(((((((((.((((((((..((((((((((         (...))).))))))))..)))..))))).)))))))))	1.000 -33.50

cbriggsae	chromosome:chrIII:9825068:9825171:1	Opposite_strand|Intronic_coding|NM_001022613|SPBC215.13 ## Opposite_strand|Intronic_non-coding|NM_009322|Tbr1 ## Same_strand|Intronic_non-coding|NM_065267|R148.2 ## {Repeats: no} ## {MIR: cbr-mir-231}
cremanei	chromosome:chrUn:5285606:5285740:1	intergenic
celegans	chromosome:chrIII:7544978:7545077:-1	intergenic ## {MIR: cel-mir-231}
cbrenneri	chromosome:chrUn:17428280:17428391:1	Same_strand|Intronic_coding|NM_209426
cjaponica	chromosome:chrUn:140689412:140689485:-1	intergenic

cbr-mir-90

Cloning frequencies

absolute	AF16
cbr-mir-90 3arm	377
normalized	AF16
cbr-mir-90 3arm	0.983

block1853 (miRBase cbr-mir-90) [miRNAknown_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

miRBase cbr-mir-90

0.001

no

no

0.28/0.43

18/23/0.97

0.0

0.3

330

0

1

0

18

7

3arm

1

nd

0.14

1

377

1

na

na

Families

Member of family miR-50/62/90 (seed GAUAUGU): cel-mir-90, cbr-mir-50, cbr-mir-90, cbr-mir-62

		reads	miRBase family seed
seed	---------------------------------------------------------------------------GAUAUGU--------------------------------------------------	376	miR-50/62/90
seed	----------------------------------------------------------------------------AUAUGUU-------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
cbr-miR-90	--------------------------------------------------------------------------TGATATGTTGTTTGAATGCCCC------------------------------------	22	227
	--------------------------------------------------------------------------TGATATGTTGTTTGAATGCCC-------------------------------------	21	103
	--------------------------------------------------------------------------TGATATGTTGTTTGAATGCCCCT-----------------------------------	23	23
	--------------------------------------------------------------------------TGATATGTTGTTTGAATG----------------------------------------	18	13
	--------------------------------------------------------------------------TGATATGTTGTTTGAATGCC--------------------------------------	20	10
	---------------------------------------------------------------------------GATATGTTGTTTGAATGCCCC------------------------------------	21	1
cbriggsae	-----------CGCACTCA--TTTCAAGCGGCTTTCAACGACTATATCAACCAAA---TCAAGC-TAGATACGTTGATATGTTGTTTGAATGCCCCTTGAGA------------------TTTTGGAGTGTT
cremanei	TCTCCTTGTTTGGGCCTCA--CTTCGAGCGGTATTCAACGACTATCTCAACCGAT-ATACATAC-CAACCGAGTTGATATGTTGTTTGAATGCCCCTTGAACTCGAGGCCCCTAGTAAACACTCAGA-----
celegans	------AAAACGGGCGCCA--TTTCGAGCGGCTTTCAACGACGATATCAACCGACAACTCACACTTTTGCGTGTTGATATGTTGTTTGAATGCCCCTTGAATTGGATGCCACAGG-----TTTT--------
cbrenneri	-TCCTGGACTTGGGCGCCAAGTTTCGAGCGGCTTTCAACAACGATATCAACCGATTTTCAGTAA-ATTGCGAGTTGATATGTTGTTTGAATGCCCCTTGAGTTGGTTGCCCTTCTTG---TTTTAGGA----
cjaponica	-----------GGACGCCC-GACTCAAGCGGCTTTCAACGGCGCTATCAACCGAA---CTGTGT-GTCGCGTGTTGATATGTTGTTTGAATGCCCCTTGAATCGGCGGTCGCCCCTA---TCCTG-------
	*    *     ** *****  ******  *  * ****** *                  ****************************
	+++++           ++++++++  ++++++++++++++++++++++++++++++++++   ++++++ +++++++++++++++++++++++++++++++++++++                  +++++++++++++++++	NM_001090393
	+++++           ++++++++  ++++++++++++++++++++++++++++++++++   ++++++ +++++++++++++++++++++++++++++++++++++                  +++++++++++++++++	NM_001730
	-----           --------  ----------------------------------   ------ -------------------------------------                  -----------------	NM_070558
cbriggsae	.(((((((  (((((((.(((.(((((((((.((((((((...(   ((.... ..)))..)))))))))))).))))).))).)))))))                  )....)))))).	1.000 -38.30
cremanei	(((...((((((((((((.  .((((((.(((((((((((((.((.(((((((.. ........ ....)).))))).)))))))).))))))).))))))...))))))).....)))))...)))	0.961 -43.94
celegans	(((((.(((((((  .((((((.(((.(((((((((.((((((((((.(((.........))))).)))))))))))))).))).))).)))))).))).))))....)     ))))	1.000 -43.70
cbrenneri	((((((((..(((((((((..((((((.(((.(((((((((.((((((((((((((.....)) ))))...)))))))))))))).))).))).))))))))))).)))).....)   ))).))))	0.999 -48.60
cjaponica	((.((.(( ((.(((((.(((.((((((((((.(((((((((.(   (..... ))..)).)))))))))))))).))).))).))))).))))))....))....   .....	0.984 -40.20

cbriggsae	chromosome:chrIII:13421064:13421160:1	Same_strand|Intronic_non-coding|NM_001090393|Egr1 ## Opposite_strand|Intronic_non-coding|NM_070558|rho-1 ## {Repeats: no} ## {MIR: cbr-mir-90}
cremanei	chromosome:chrUn:78012934:78013056:-1	intergenic
celegans	chromosome:chrIII:8873886:8873996:-1	intergenic ## {MIR: cel-mir-90}
cbrenneri	chromosome:chrUn:17772387:17772509:1	intergenic
cjaponica	chromosome:chrUn:4612015:4612120:-1	Opposite_strand|Intronic_coding|NM_080787 ## Same_strand|Intronic_coding|NM_078517 ## {SimpF: trf}

cbr-mir-124

Cloning frequencies

absolute	AF16
cbr-mir-124 3arm	39
normalized	AF16
cbr-mir-124 3arm	0.102

block2104 (miRBase cbr-mir-124) [miRNAknown_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

miRBase cbr-mir-124

0.001

no

no

0.57/0.60

19/21/0.97

0.0

0.0

38

0

1

0

18

9

3arm

1

nd

0.15

2

39

1

na

na

		reads	miRBase family seed
seed	------------------------------------------------------------------------------------------AAGGCAC---------------------------------------------	39	miR-124
		len	cloning frequencies
			AF16
	-----------------------------------------------------------------------------------------TAAGGCACGCGGTGAATGCC---------------------------------	20	38
	-----------------------------------------------------------------------------------------TAAGGCACGCGGTGAATGC----------------------------------	19	1
cbr-miR-124	-----------------------------------------------------------------------------------------TAAGGCACGCGGTGAATGCCA--------------------------------	21	-
cbriggsae	--------------------------TTCCAGTCGTCATATGGCGTCCACCTGAGTGACTTTAGTG----GACATGTATAGTTTCCAACTAAGGCACGCGGTGAATGCCACGTGGCAATTCTGGGAT---------------
cremanei	CTATTCTTATGTCACTGAT---------CCAGATGTCACTTGGCATACACCTGAGTGACTTTAGTG----GACATCTCAAGTTTCCAACTAAGGCACGCGGTGAATGCCACGTGGCAATTCTGGAGACTTCTCAAAGGTTGG
celegans	-----------------------------------------GGCATGCACCCTAGTGACTTTAGTG----GACATCTAAGTCTTCCAACTAAGGCACGCGGTGAATGCC---------------------------------
cbrenneri	------TTTTGTCATCGATACTAATGCCTCAGTTGTCATCTGGCATACACCTGAGTGACTTTAGTG----GACATCTGAAGTTTCCAACTAAGGCACGCGGTGAATGCCACGTGGCAACT-TGAGGTCTATTGTAAATAAGG
ppacificus	----TGAAGGGTCGTTAAT----------------TCACTTCGCTTTCACC--GGTGACTTTAGTGCTTTGTCACAGAGAG-----AACTAAGGCACGCGGTGAATGCCAAGAGAATAAC---GAATCCATCA---------
cjaponica	-----CTTCGTTAGCCGAT-----TGTCCCTGTTGTCATCTGGCGTCCACCTGAGTGACTTTAGTG----GACAATTTTTGGTTCCAACTAAGGCACGCGGTGAATGCCACGTGGCAACCGGGGACTCGATTCTCGTGG---
	** * ****   ************    * **            ***********************
	-----                          ----------------------------------------    ---------------------------------------------------------               -----	NM_168571
	-----                          ----------------------------------------    ---------------------------------------------------------               -----	NM_208412
	-----                          ----------------------------------------    ---------------------------------------------------------               -----	NM_209040
	+++++                          ++++++++++++++++++++++++++++++++++++++++    +++++++++++++++++++++++++++++++++++++++++++++++++++++++++               +++++	NM_001123230
	-----                          ----------------------------------------    ---------------------------------------------------------               -----	NM_116969
	-----                          ----------------------------------------    ---------------------------------------------------------               -----	NM_001126769
	+++++                          ++++++++++++++++++++++++++++++++++++++++    +++++++++++++++++++++++++++++++++++++++++++++++++++++++++               +++++	NM_069848
cbriggsae	((((((..((((..((((((.((((...(((.((((((((    ((.((.....)).)))).)))))))))..)))).))))))..))))....)))))).	1.000 -43.00
cremanei	(((..(((.((.......(         (((((((((((.((((((.((((...(((.((((((((    ((.((.....)).)))).)))))))))..)))).)))))).))))))..)))))).......)))))..)))	0.975 -49.94
celegans	(((((.((((...(((.((((((((    (((......))))....))))))))))..)))).)))))	1.000 -26.50
cbrenneri	.(((((...(((((.....((((((((((((((.((((((.((((...(((.((((((((    ((.((.....)).)))).)))))))))..)))).)))))).))))))))) .))))).)))))...))))).	0.977 -52.50
ppacificus	.((.((((((((.((                ((.(((.((.((((((  ((((.(((((((.(((((...)))))..     .)))))))))).))))))).)).))).)))))))   )).))).)).	1.000 -44.10
cjaponica	((.((..((.(((.     .((((((((((((((.((((((.((((...(((.((((((((    (((........)).))).)))))))))..)))).)))))).)))))))).))))))))).))..)).))	0.954 -53.70

cbriggsae	chromosome:chrIV:5050234:5050330:-1	Opposite_strand|Intronic_coding|NM_168571|CG32133 ## Same_strand|Intronic_coding|NM_001123230|col4a5 ## Opposite_strand|Intronic_non-coding|NM_116969|GRF1 ## {Repeats: no} ## {MIR: cbr-mir-124}
cremanei	chromosome:chrUn:80236599:80236727:1	Same_strand|Intronic_coding|NM_069848
celegans	chromosome:chrIV:11871689:11871825:1	Same_strand|Intronic_coding|C29E6.2 ## {MIR: cel-mir-124}
cbrenneri	chromosome:chrUn:162403843:162403973:1	Same_strand|Intronic_coding|NM_069848
ppacificus	chromosome:chrUn:138694799:138694901:-1	intergenic ## {SimpF: trf}
cjaponica	chromosome:chrUn:39137220:39137344:1	Same_strand|Intronic_coding|NM_069848 ## Opposite_strand|Intronic_coding|NM_104618

Back to summary page

confident miRBase miRNAs:

Page 1

Previous page

Page 3

Next page

Page 6