miR-Intess: classification

other hairpins

block4892 [novel_lenNOK_nonpairedHIGH]

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	0.591	no	no	0.47/0.47	19/19/0.00	0.0	0.0	1	0	1	0	7	32	3arm	1	nd	0.37	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------------GCGUUUG------------------	1	novel
		len	cloning frequencies
			AF16
	----------------------------------------------------------------------------------------------GGCGTTTGTGTGATTTGAC-------	19	1
cbriggsae	tccaagacatctttcgaactcatccgccaattgctccaaaaaagtgcgtctttgtgaagtagtgaagccgtccttgttgacagaacatccatttGGCGTTTGTGTGATTTGACagaggga
	************************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------------------	NM_153821
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_125756
	----------------------------------------------------------------------------------------------------------------------------------	NM_204793
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_079593
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_169386
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_176459
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001016575
	----------------------------------------------------------------------------------------------------------------------------------	NM_001085944
cbriggsae	(((......(((.((((((.((..((((((.((.((.....(((..((.(((((........))))).))..))).......)).)).....))))))..)).))...)))).))).)))	0.420 -24.40

cbriggsae

chromosome:chrX:6644083:6644202:1

Opposite_strand|Intronic_non-coding|NM_153821|Prrx1 ## Same_strand|Intronic_coding|NM_125756|HEN3 ## Same_strand|Intronic_non-coding|NM_079593|pros ## {Repeats: no}

block2867 [novel_lenNOK_nonpairedHIGH]

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	0.085	no	no	0.46/0.46	26/26/0.00	0.0	0.0	1	0	1	0	8	3	3arm	1	nd	0.31	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------CAUUGAU--------------------------	1	novel
		len	cloning frequencies
			AF16
	--------------------------------------------------GCATTGATCAGCCAGTTGAGTGAATG--------	26	1
cbriggsae	cgttccgcttttttgccactacatatggtttgatctgggttacggtagttGCATTGATCAGCCAGTTGAGTGAATGaatggaat
	************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_075117
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_061879
	----------------------------------------------------------------------------------------------	NM_067650
cbriggsae	.((((((.(((.....((((.((..(((.((((((...((.((....)).))...)))))))))..))))))...)))))))))	0.930 -22.70

cbriggsae

chromosome:chrIV_random:166130:166213:-1

Same_strand|Intronic_non-coding|NM_075117|Y59A8B.22 ## Opposite_strand|Intronic_non-coding|NM_067650|Y104H12D.3 ## {Repeats: no}

block2868 [novel_lenNOK_nonpairedHIGH]

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	0.316	no	no	0.48/0.48	25/25/0.00	0.0	0.0	1	0	1	0	5	2	3arm	1	nd	0.32	2	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------UUUGAUC----------------------	1	novel
		len	cloning frequencies
			AF16
	-------------------------------------GTTTGATCTGGGTTACGGTAGTTGC-----	25	1
cbriggsae	cactgaacttcgttccgcttttttgccactacatatgGTTTGATCTGGGTTACGGTAGTTGCattga
	*******************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_075117
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_061879
	-----------------------------------------------------------------------------	NM_067650
cbriggsae	((.((((((((((((((..((...((((.......))))..))..))))..)))).)))).)).)).	1.000 -13.10

cbriggsae

chromosome:chrIV_random:166157:166223:-1

Same_strand|Intronic_non-coding|NM_075117|Y59A8B.22 ## Opposite_strand|Intronic_non-coding|NM_067650|Y104H12D.3 ## {Repeats: no}

novel_shortStem_nonpairedHIGH_bulgeHIGH (24 loci)

block276 [novel_shortStem_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	0.483	no	no	0.45/0.45	22/22/1.00	0.0	0.0	1	0	1	0	0	13	5arm	8	nd	0.45	5	1	1	na	na

		reads	miRBase family seed
seed	-CCAGCUA----------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	TCCAGCTAGTGTGTGGTAGAAT--------------------------------------------	22	1
cbriggsae	TCCAGCTAGTGTGTGGTAGAATgctttactcgtgtagatgacacgtgtggtatctcaaacttgggt
	******************************************************************
	----------------------------------------------------------------------------	NM_174569
	----------------------------------------------------------------------------	NM_002035
	----------------------------------------------------------------------------	NM_177366
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001107428
	----------------------------------------------------------------------------	NM_053878
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_008665
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_067597
cbriggsae	((((...(((.((.((((.......((((.(((((.....))))).)))))))).)).))))))).	0.840 -14.31

cbriggsae

chromosome:chrI:2029064:2029129:1

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}

block292 [novel_shortStem_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	0.702	no	no	0.70/0.70	20/20/1.00	0.0	0.0	1	0	1	0	1	36	5arm	1	58	0.55	4	1	1	na	na

		reads	miRBase family seed
seed	--GACUGCG---------------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-CGACTGCGCACCGACTCCAC---------------------------------------------------------------------------------------------------	20	1
cbriggsae	tCGACTGCGCACCGACTCCACaacaaactactcgcccctccctgagctgagtactcaatctctgagtccggcagaaaataagggtacaaacatggggaagattattttgagtccgattcg
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_060137
	----------------------------------------------------------------------------------------------------------------------------------	NM_001122952
	----------------------------------------------------------------------------------------------------------------------------------	NM_001088550
	----------------------------------------------------------------------------------------------------------------------------------	NM_010905
	----------------------------------------------------------------------------------------------------------------------------------	NM_001122953
	----------------------------------------------------------------------------------------------------------------------------------	NM_011543
	----------------------------------------------------------------------------------------------------------------------------------	NM_001087250
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001025922
	....................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++	NM_058737
cbriggsae	.(((...((....(((((......(((.((.((.((((.((((...(((...(((((.....)))))....)))......)))).........))))..)).)).))))))))))..)))	0.860 -24.10

cbriggsae

chromosome:chrI:3226804:3226923:1

Same_strand|Intronic_coding|NM_060137|F42H11.1 ## Opposite_strand|Intronic_non-coding|NM_001122952|Nfia ## Opposite_strand|Intronic_coding|NM_001088550|FGFR-4c ## Same_strand|Intronic_non-coding|NM_001025922|unc-87 ## {Repeats: no}

block365 [novel_shortStem_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	0.131	no	no	0.45/0.45	20/20/1.00	0.0	0.0	1	0	1	0	4	26	5arm	1	nd	0.40	4	1	1	na	na

		reads	miRBase family seed
seed	-----GCUCUUU--------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	----TGCTCTTTGGCCTTTATTGG--------------------------------------------------------------------------------------	20	1
cbriggsae	ttgaTGCTCTTTGGCCTTTATTGGacactttctaaaatgaactgattctttcttttcaagtttcagtgttgtcatattttagtttcacattcgaatatgctagcatacag
	**************************************************************************************************************
	------------------------------------------------------------------------------------------------------------------------	NM_001103403
	------------------------------------------------------------------------------------------------------------------------	NM_012772
	------------------------------------------------------------------------------------------------------------------------	NM_007723
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_171630
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_008855
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_171940
	------------------------------------------------------------------------------------------------------------------------	NM_007386
	------------------------------------------------------------------------------------------------------------------------	NM_001111130
	------------------------------------------------------------------------------------------------------------------------	NM_060099
	------------------------------------------------------------------------------------------------------------------------	NM_059295
	------------------------------------------------------------------------------------------------------------------------	NM_182309
cbriggsae	.(((((((....(((...((((.((......((((((((.(((((..(((.......)))..))))).......))))))))........)).)))).)))))))).)).	0.920 -19.54

cbriggsae

chromosome:chrI:8402099:8402208:1

Opposite_strand|Intronic_coding|NM_001103403|tlk ## Same_strand|Intronic_non-coding|NM_171630|toca-1 ## Opposite_strand|Intronic_non-coding|NM_007386|Aco1 ## {Repeats: no}

block394 [novel_shortStem_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	0.211	no	no	0.35/0.35	20/20/1.00	0.0	0.0	1	0	1	0	2	3	5arm	1	nd	0.35	4	1	1	na	na

		reads	miRBase family seed
seed	---ACAACAC------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	--AACAACACAAGAGAACACTT------------------------------------------	20	1
cbriggsae	caAACAACACAAGAGAACACTTgccaatgtttatgagaggtaaaacattttctgaaatttgttt
	****************************************************************
	--------------------------------------------------------------------------	NM_001030661
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_067080
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_175441
cbriggsae	.((((((....((((((...(((((.............)))))....)))))).....))))))	0.940 -9.22

cbriggsae

chromosome:chrI:9428668:9428731:1

Opposite_strand|Intronic_non-coding|NM_001030661|SETD1B ## Same_strand|Intronic_coding|NM_067080|Y66D12A.21 ## Same_strand|Intronic_non-coding|NM_175441|Mylk3 ## {Repeats: no}

block539 [novel_shortStem_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	0.025	no	no	0.30/0.30	20/20/1.00	0.0	0.0	1	0	1	0	0	39	3arm	5	nd	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------------AAAGUUU------------	1	novel
		len	cloning frequencies
			AF16
	-------------------------------------------------------------------------------------------GAAAGTTTGGTAAAAGAAAG	20	1
cbriggsae	tttctgaggccgtattcatgaacatttacttttaggtaaatagaacgtgtaaatgatttataaagaggaaaatagagtgattggtattcatGAAAGTTTGGTAAAAGAAAG
	***************************************************************************************************************
	-------------------------------------------------------------------------------------------------------------------------	NM_001027735
	-------------------------------------------------------------------------------------------------------------------------	NM_001027736
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001012569
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001030387
cbriggsae	(((((...((((..((((((((((.(((((((.......(((((.(((....))).)))))............))))))).))...))))))))....))))...))))).	0.650 -21.91

cbriggsae

chromosome:chrI_random:2445151:2445261:1

Opposite_strand|Intronic_non-coding|NM_001027735|feh-1 ## Same_strand|Intronic_non-coding|NM_001012569|AMD1 ## {Repeats: no}

block904 [novel_shortStem_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	0.042	no	no	0.70/0.70	23/23/1.00	0.0	0.0	1	0	1	0	4	10	5arm	1	nd	0.48	4	1	1	na	na

		reads	miRBase family seed
seed	-----GUGAGAG--------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	----GGTGAGAGGCAACAGGCACGCGG-----------------------------------------------------	23	1
cbriggsae	aagaGGTGAGAGGCAACAGGCACGCGGaacgcctcccttgcgggaagtgttctcccgcatatgtcacatccccccctcta
	********************************************************************************
	------------------------------------------------------------------------------------------	NM_006287
	------------------------------------------------------------------------------------------	NM_009829
	------------------------------------------------------------------------------------------	NM_001039276
	------------------------------------------------------------------------------------------	NM_201578
	------------------------------------------------------------------------------------------	NM_001114006
cbriggsae	.(((((.((..((((....((....(((((((.((((....)))).)))))))...))...))))...))....))))).	0.710 -26.60

cbriggsae

chromosome:chrII:4386950:4387029:1

Opposite_strand|Intronic_non-coding|NM_006287|TFPI ## Opposite_strand|Intronic_coding|NM_201578|psmd12 ## {Repeats: no}

block952 [novel_shortStem_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	0.018	no	no	0.36/0.36	22/22/1.00	0.0	0.0	1	0	1	0	3	4	5arm	1	nd	0.41	4	1	1	na	na

		reads	miRBase family seed
seed	----AGUUCUA---------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	---AAGTTCTATGGCACAGTATATC-------------------------------------	22	1
cbriggsae	catAAGTTCTATGGCACAGTATATCagtgaggaacagtgagatgatttgtgagaagttgtga
	**************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_020252
	------------------------------------------------------------------------	NM_063458
	------------------------------------------------------------------------	NM_059843
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_183355
	------------------------------------------------------------------------	NM_073745
	------------------------------------------------------------------------	NM_001080181
	..............................................<<<<<<<<<<<<<<<<<<<<<<<<<<	NM_064115
	..............................................<<<<<<<<<<<<<<<<<<<<<<<<<<	NM_064114
cbriggsae	(((((.((((....(((((....(((.((.....)).)))......))))))))).))))).	1.000 -14.60

cbriggsae

chromosome:chrII:6494209:6494270:1

Same_strand|Intronic_non-coding|NM_020252|Nrxn1 ## Opposite_strand|Intronic_coding|NM_063458|T01B7.8 ## Opposite_strand|Intronic_non-coding|NM_001080181|zgc:158678 ## {Repeats: no}

Page 31

Jump 10 pages forward

Page 70

miR-Intess™

block4892 [novel_lenNOK_nonpairedHIGH]

block2867 [novel_lenNOK_nonpairedHIGH]

block2868 [novel_lenNOK_nonpairedHIGH]

block276 [novel_shortStem_nonpairedHIGH_bulgeHIGH]

block292 [novel_shortStem_nonpairedHIGH_bulgeHIGH]

block365 [novel_shortStem_nonpairedHIGH_bulgeHIGH]

block394 [novel_shortStem_nonpairedHIGH_bulgeHIGH]

block539 [novel_shortStem_nonpairedHIGH_bulgeHIGH]

block904 [novel_shortStem_nonpairedHIGH_bulgeHIGH]

block952 [novel_shortStem_nonpairedHIGH_bulgeHIGH]