miR-Intess: classification

other hairpins

novel_lenNOK_nonpairedHIGH_bulgeHIGH (44 loci)

block1738 [novel_lenNOK_nonpairedHIGH_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
no	0.663	no	no	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	24	3	5arm	1	nd	0.50	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------AAUCGAG------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	------------------------GAATCGAGAGCTGTGAAT--------------------------------------------------------	18	1
cbriggsae	ccaaatcgctccgaatatcttcacGAATCGAGAGCTGTGAATggtgataaatttaagaatagccaagatgtgtcgagtattttttacgattagttggc
	**************************************************************************************************
	------------------------------------------------------------------------------------------------------------	NM_021863
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_005249
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_068288
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_059518
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_067241
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001021511
cbriggsae	((((((((....(((((.(((.(((.(((....(((((....(((.....))).....)))))...))).))).))))))))....)))))...))).	0.630 -17.00

cbriggsae

chromosome:chrIII:7854638:7854735:1

Opposite_strand|Intronic_non-coding|NM_021863|Hspa2 ## Same_strand|Intronic_coding|NM_005249|FOXG1 ## Same_strand|Intronic_non-coding|NM_067241|epc-1 ## {Repeats: no}

block1741 [novel_lenNOK_nonpairedHIGH_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
no	0.357	no	no	0.42/0.42	19/19/0.00	0.0	0.0	1	0	1	0	6	8	5arm	1	nd	0.37	4	1	1	na	na

		reads	miRBase family seed
seed	-------AAUACUG------------------------------------------------------------	1	miR-236
		len	cloning frequencies
			AF16
	------GAATACTGGATGTGCTTCT-------------------------------------------------	19	1
cbriggsae	agaggcGAATACTGGATGTGCTTCTcaatttcctacttcctggccctagtccagccatctccattgtcagtttc
	**************************************************************************
	------------------------------------------------------------------------------------	NM_181277
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001088088
	------------------------------------------------------------------------------------	NM_001066926
	------------------------------------------------------------------------------------	NM_001105288
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_007393
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_068288
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_059518
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_122291
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_067241
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001021511
	------------------------------------------------------------------------------------	NM_001130548
	-------------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	NM_067437
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001044899
	-------------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	NM_067438
cbriggsae	.(((((..(((.((((.(((((.........((........)).........))).)).)))).)))..)))))	0.970 -13.47

cbriggsae

chromosome:chrIII:7980384:7980457:1

Opposite_strand|Intronic_coding|NM_181277|Col14a1 ## Same_strand|Intronic_non-coding|NM_001088088|LOC397919 ## Same_strand|Intronic_coding|NM_068288|E03H12.5 ## {Repeats: no}

block1856 [novel_lenNOK_nonpairedHIGH_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
no	0.463	no	no	0.33/0.38	18/21/0.50	0.0	1.5	2	0	1	0	7	3	3arm	1	nd	0.39	5	2	1	na	na

		reads	miRBase family seed
seed	---------------------------------------AUUAUGA--------------------	2	novel
		len	cloning frequencies
			AF16
	--------------------------------------TATTATGAACACTTGAGGAGG-------	21	1
	--------------------------------------TATTATGAACACTTGAGG----------	18	1
cbriggsae	agtgggaggtatggaagttttagtgatgttgtgtgtagTATTATGAACACTTGAGGAGGtttcact
	******************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_070275
cbriggsae	(((((((.......((((.((.(((((((((....))))))))).)).)))).......)))))))	0.880 -8.54

cbriggsae

chromosome:chrIII_random:29581:29646:-1

Same_strand|Intronic_coding|NM_070275|Y37A1A.2 ## {Repeats: no}

block1872 [novel_lenNOK_nonpairedHIGH_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
no	0.522	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	17	3	3arm	1	nd	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------UUUCCCA----------------------------	1	novel
		len	cloning frequencies
			AF16
	--------------------------------------------------------TTTTCCCACGCACGATTGG-----------------	19	1
cbriggsae	tttttttgaatgtttcagctaatcattaaaagtgaagttattttaatccttcttaaTTTTCCCACGCACGATTGGaattgagtttcacaaaa
	********************************************************************************************
cbriggsae	.((((.((((...((((.((((((.......(((((((((.............))))))...)))....))))))...)))).)))).))))	0.580 -10.72

cbriggsae

chromosome:chrIII_random:94506:94597:1

{Repeats: no}

block1899 [novel_lenNOK_nonpairedHIGH_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
no	0.475	no	no	0.32/0.32	19/19/0.00	0.0	0.0	1	0	1	0	26	3	5arm	1	nd	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------UCUUUAA--------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	--------------------------TTCTTTAATGTCCAGTTGT---------------------------------------------------	19	1
cbriggsae	attccagaagctcaattaatctttgcTTCTTTAATGTCCAGTTGTagcagtagtacaaaaaagcccaaaagaggaaaaattttaacggggtcggaa
	************************************************************************************************
	----------------------------------------------------------------------------------------------------------	NM_123965
	----------------------------------------------------------------------------------------------------------	NM_024349
	----------------------------------------------------------------------------------------------------------	NM_008091
	----------------------------------------------------------------------------------------------------------	NM_019034
	----------------------------------------------------------------------------------------------------------	NM_001016369
	----------------------------------------------------------------------------------------------------------	NM_001032772
	----------------------------------------------------------------------------------------------------------	NM_001040602
	----------------------------------------------------------------------------------------------------------	NM_001093711
	----------------------------------------------------------------------------------------------------------	NM_001095157
	----------------------------------------------------------------------------------------------------------	NM_199692
	----------------------------------------------------------------------------------------------------------	NM_001033835
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001047948
	----------------------------------------------------------------------------------------------------------	NM_175092
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_065286
	----------------------------------------------------------------------------------------------------------	NM_001123190
	----------------------------------------------------------------------------------------------------------	NM_001126828
	----------------------------------------------------------------------------------------------------------	NM_001010953
	----------------------------------------------------------------------------------------------------------	NM_001127285
cbriggsae	.((((....((((..((((..(((.(((((((...((....((((.((....))))))....))...)))))))..)))..))))..)))).))))	0.810 -15.70

cbriggsae

chromosome:chrIV:633150:633245:-1

Opposite_strand|Intronic_coding|NM_123965|ARAC2 ## Opposite_strand|Intronic_non-coding|NM_024349|Ak1 ## Same_strand|Intronic_coding|NM_001047948|LOC499584 ## Same_strand|Intronic_non-coding|NM_065286|Y53G8AR.6 ## {Repeats: no}

block1980 [novel_lenNOK_nonpairedHIGH_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
no	0.172	no	no	0.42/0.42	19/19/0.00	0.0	0.0	2	0	1	0	5	9	3arm	1	nd	0.37	4	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------AACUAUU----------------	2	novel
		len	cloning frequencies
			AF16
	----------------------------------------------TAACTATTAAGCCCAGCTG-----	19	2
cbriggsae	tatttcaaaatgtgcttattaatttcaacttgaaaatgagagctatTAACTATTAAGCCCAGCTGagata
	**********************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_070351
	--------------------------------------------------------------------------------	NM_001090906
	--------------------------------------------------------------------------------	NM_182271
	--------------------------------------------------------------------------------	NM_001102902
	--------------------------------------------------------------------------------	NM_070367
cbriggsae	(((((((...((.((((((((((.....(((......)))....)))))....))))).))..)))))))	0.480 -10.40

cbriggsae

chromosome:chrIV:2070542:2070611:-1

Same_strand|Intronic_non-coding|NM_070351|LLC1.2 ## Opposite_strand|Intronic_non-coding|NM_001090906|EEF1D ## Opposite_strand|Intronic_coding|NM_182271|K02E7.4 ## {Repeats: no}

block1984 [novel_lenNOK_nonpairedHIGH_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
no	0.382	no	no	0.47/0.47	19/19/0.00	0.0	0.0	1	0	1	0	33	3	5arm	1	nd	0.37	4	1	1	na	na

		reads	miRBase family seed
seed	----------------------------------GGAAUAG---------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	---------------------------------TGGAATAGGGCTGATTCTC----------------------------------------------------------------	19	1
cbriggsae	gatatcagcattgtgaaacagtaaatatgttaaTGGAATAGGGCTGATTCTCaacggcattagttgaatccaaacggcttatctcatttggttaaatttgtacaaaaaaggtgtca
	********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_070351
	------------------------------------------------------------------------------------------------------------------------------	NM_001090906
	------------------------------------------------------------------------------------------------------------------------------	NM_182271
cbriggsae	((((((....(((((......(((.......((((..(((.(((((....(((((.......))))).......))))))))..))))...)))......)))))....)))))).	0.570 -21.30

cbriggsae

chromosome:chrIV:2100025:2100140:-1

Same_strand|Intronic_non-coding|NM_070351|LLC1.2 ## Opposite_strand|Intronic_non-coding|NM_001090906|EEF1D ## Opposite_strand|Intronic_coding|NM_182271|K02E7.4 ## {Repeats: no}

block2033 [novel_lenNOK_nonpairedHIGH_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
no	0.656	no	no	0.26/0.26	19/19/0.00	0.0	0.0	1	0	1	0	20	10	3arm	1	nd	0.47	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------AUAAUAU-------------------------------	1	novel
		len	cloning frequencies
			AF16
	----------------------------------------------------------------TATAATATCAGTCAGTATC--------------------	19	1
cbriggsae	gaatctcaaaaatatttcctgtttctgaacgttatttttatctaaaaatatatttttttatcagTATAATATCAGTCAGTATCagtatagtagttaacaattc
	*******************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_068260
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_068267
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_068270
	-----------------------------------------------------------------------------------------------------------------	NM_068260
	-----------------------------------------------------------------------------------------------------------------	NM_068270
	-----------------------------------------------------------------------------------------------------------------	NM_068267
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_068262
	-----------------------------------------------------------------------------------------------------------------	NM_071092
	-----------------------------------------------------------------------------------------------------------------	NM_068279
cbriggsae	((((........((((..(((...((((....((((......((((((......)))))).......))))....))))...)))...)))).......))))	0.900 -9.88

cbriggsae

chromosome:chrIV:2977635:2977737:-1

Same_strand|Intronic_coding|NM_068260|str-175 ## Opposite_strand|Intronic_non-coding|NM_068260|str-175 ## Opposite_strand|Intronic_coding|NM_068270|str-159 ## {Repeats: no}

block2057 [novel_lenNOK_nonpairedHIGH_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
no	0.115	no	no	0.37/0.37	19/19/0.00	0.0	0.0	1	0	1	0	11	17	5arm	1	nd	0.42	5	1	1	na	na

		reads	miRBase family seed
seed	------------UUUGUCA------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-----------TTTTGTCAGAGTTAGCCAT-------------------------------------------------------------------	19	1
cbriggsae	ttcatctccgaTTTTGTCAGAGTTAGCCATagtcgtaaaatctctaagaactgattagatttatgtaccattttaatctctgaaatcttcagtgaac
	*************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001105717
	-----------------------------------------------------------------------------------------------------------	NM_112886
	-----------------------------------------------------------------------------------------------------------	NM_079809
	-----------------------------------------------------------------------------------------------------------	NM_020066
cbriggsae	(((((....((((...((((((((((.....((((((((...(((((.......))))))))))).))....)))).))))))))))....))))).	1.000 -17.10

cbriggsae

chromosome:chrIV:3380627:3380723:-1

Same_strand|Intronic_non-coding|NM_001105717|Dpysl2 ## Opposite_strand|Intronic_non-coding|NM_112886|ATATM ## Opposite_strand|Intronic_coding|NM_020066|FMN2 ## {Repeats: no}

block2435 [novel_lenNOK_nonpairedHIGH_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
no	0.092	no	no	0.42/0.42	19/19/0.00	0.0	0.0	1	0	1	0	17	17	5arm	1	nd	0.37	4	1	1	na	na

		reads	miRBase family seed
seed	------------------UGGAUCC------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-----------------TTGGATCCTCAGCAAAATG-------------------------------------------------------------------------	19	1
cbriggsae	tgaataacttcaaatgtTTGGATCCTCAGCAAAATGaatcttgaaaaatatcgagtatcgattcgagtatcaaaataatggcctagagaaccgaaaaatagtttttcag
	*************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------	NM_070351
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001090906
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_182271
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001102902
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_113688
cbriggsae	((((.((((.......(((((.((((..((....(((..(((((.....((((.....)))))))))..)))........))..)).)).)))))....)))).)))).	0.940 -20.00

cbriggsae

chromosome:chrIV:2032546:2032654:1

Opposite_strand|Intronic_non-coding|NM_070351|LLC1.2 ## Same_strand|Intronic_non-coding|NM_001090906|EEF1D ## Same_strand|Intronic_coding|NM_182271|K02E7.4 ## {Repeats: no}

Page 15

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miR-Intess™

block1738 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

block1741 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

block1856 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

block1872 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

block1899 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

block1980 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

block1984 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

block2033 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

block2057 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

block2435 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]