miR-Intess: classification

other hairpins

block547729 [novel_lenNOK_gcHIGH]

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	0.509	no	no	0.94/0.94	18/18/0.00	0.0	0.0	2	0	1	0	20	7	5arm	2	nd	0.11	1	2	1	na	na

		reads	miRBase family seed
seed	---------------------CCCGCCC--------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T1S2
	--------------------CCCCGCCCCCTCCGGCCG----------------------------------------------------------	18	2
rat	ttctgcgccactcatttataCCCCGCCCCCTCCGGCCGtaaaggatacctccgaggctgcgcgctgcggagaggtgcgcggtagctgggacagaag
	************************************************************************************************
	----------------------------------------------------------------------------------------------------------	ENSRNOT00000049035 ENSRNOG00000032766
rat	(((((..(((........((((.(((((.(((((((((((..(((....))).....)))).))..))))).)).))).))))..)))..))))).	0.960 -34.40

rat

chromosome:16:73225407:73225502:-1

Opposite_strand|Intronic_coding|ENSRNOT00000049035|ENSRNOG00000032766 ## ENSRNOG00000032766|protein_coding||

block804440 [novel_lenNOK_gcHIGH]

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	0.264	no	no	1.00/1.00	18/18/0.00	0.0	0.0	1	0	1	0	6	4	3arm	2	nd	0.22	2	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------CCCCGCC----------------	1	novel
		len	cloning frequencies
			T4S1
	------------------------------------------------CCCCCGCCCCGCCCCGGG------	18	1
rat	gagtcgcagggaagccgggccaaggggaaaagcaagagtggcgggctaCCCCCGCCCCGCCCCGGGcgcctc
	************************************************************************
	----------------------------------------------------------------------------------	ENSRNOT00000003583 ENSRNOG00000002559 O70369_RAT
	----------------------------------------------------------------------------------	ENSRNOT00000003694 ENSRNOG00000002559 O70369_RAT
rat	(((.(((.(((..((.((((...((((...(((...........))).)))).)))).)))))..))).)))	0.980 -30.40

rat

chromosome:19:25189308:25189379:1

Opposite_strand|Intronic_coding|ENSRNOT00000003694|ENSRNOG00000002559 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000032105|ENSRNOG00000002559 ## ENSRNOG00000002559|protein_coding|O70369_RAT|Class A calcium channel variant riA-II (Fragment). [Source:UniProtKB/TrEMBL;Acc:O70369] ## {Repeats: dust 25189417 25189435 0 class=dust,GC_rich 1 18 1 class=Low_complexity,GC_rich 1 22 1 class=Low_complexity} ## {SimpF: oe = 0.87 0 CpG}

block819370 [novel_lenNOK_gcHIGH]

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	0.498	no	no	1.00/1.00	19/19/0.00	0.0	0.0	1	0	1	0	22	22	5arm	1	nd	0.21	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------------CGCCGCG---------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	----------------------CCGCCGCGCGCGCGGGCGG----------------------------------------------------------------------------	19	1
rat	gtcgccccgctgttatggagacCCGCCGCGCGCGCGGGCGGcgatgatgggcggccatggcccgggcgggcggcggcggcgcagcagctcccgaacgcgcggggggcgcggcgcggc
	*********************************************************************************************************************
	.............................................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000022823 ENSRNOG00000016920 Spire2_predicted
rat	(((((.((((...........(((.(((((((..((((.(((.....((.((.(((...((((....))))...))).)).))...)))))))..))))))).))).)))).)))))	0.770 -68.50

rat

chromosome:19:53658571:53658687:1

intergenic ## {Repeats: GC_rich 1 20 1 class=Low_complexity,dust 53658673 53658687 0 class=dust,GC_rich 1 22 1 class=Low_complexity} ## {SimpF: 1 Eponine}

block1401557 [novel_lenNOK_gcHIGH]

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	0.886	no	no	1.00/1.00	18/18/0.00	0.0	0.0	1	0	1	0	26	11	3arm	1	nd	0.00	0	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------GCGGGCC------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	----------------------------------------------------------------------------GGCGGGCCGGGCCGGGCC--------------------------	18	1
rat	ggcctcctcgggaacatatcggcctctggattcccgcgcctgccgctaggccaaggagtagaaagtgctagggggaGGCGGGCCGGGCCGGGCCgtccgcgttgtccccttaactggttg
	************************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000031510 ENSRNOG00000013479 Stard7
rat	((((.....(((.(((...((((((..((...((((.(((((((.((...((....((((.....)))).)).)).))))))))))))))))))).......))).)))......)))).	0.930 -47.30

rat

chromosome:3:114768440:114768559:-1

block1415495 [novel_lenNOK_gcHIGH]

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	0.438	no	no	1.00/1.00	18/18/0.00	0.0	0.0	1	0	1	0	25	0	5arm	1	nd	0.17	2	1	1	na	na

		reads	miRBase family seed
seed	--------------------------CCGCGCC-----------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	-------------------------GCCGCGCCCCCCCCCCGG-------------------------------------------------------------	18	1
rat	gttgtcaacagtcattagcgcgcggGCCGCGCCCCCCCCCCGGtcccccagtccggggtggggcccgcacctggggcccctgctcgttagcgaacccgggccgc
	********************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000013881 ENSRNOG00000010417 8430427H17Rik
rat	((.(((.....((.((((((.((((((((((..((((((((((.........)))))).))))..)))......)))))..)).)))))).)).....))).))	0.590 -47.50

rat

chromosome:3:143866821:143866924:-1

Same_strand|Intronic_coding|ENSRNOT00000013881|ENSRNOG00000010417 ## ENSRNOG00000010417|protein_coding|8430427H17Rik|RIKEN cDNA 8430427H17 gene Gene [Source:MGI Symbol;Acc:MGI:1918765] ## {Repeats: dust 143866882 143866893 0 class=dust,GC_rich 1 26 -1 class=Low_complexity,GC_rich 1 19 -1 class=Low_complexity} ## {SimpF: 1 Eponine}

block1504853 [novel_lenNOK_gcHIGH]

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	0.848	no	no	1.00/1.00	18/18/0.00	0.0	0.0	1	0	1	0	16	20	5arm	9	nd	0.17	1	1	1	na	na

		reads	miRBase family seed
seed	-----------------GGGCGGG-------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	----------------GGGGCGGGGCGGCGGCGG---------------------------------------------------------------------------	18	1
rat	gcgggccactccgtggGGGGCGGGGCGGCGGCGGgacagcggccctttgtgcgacgcctcgccctgcgcccgccctgcagccgccgccgccgagggtgacaggagcccg
	*************************************************************************************************************
rat	.((((((((((((..((.(((((.((((.((((((...((((........((((....)))).)))).))))))))))..))))).))..)).)))))......)))))	0.930 -60.00

rat

chromosome:3:148945509:148945617:1

intergenic ## {Repeats: GC_rich 2 20 1 class=Low_complexity,dust 148945496 148945514 0 class=dust,GC_rich 1 21 1 class=Low_complexity}

block1545558 [novel_lenNOK_gcHIGH]

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	0.903	no	no	0.95/0.95	19/19/0.00	0.0	0.0	1	0	1	0	16	13	5arm	1	nd	0.16	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------CCCAGCC-------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	----------------GCCCAGCCGCCGCCCCGCC--------------------------------------------------------------------------------	19	1
rat	agcccagcgcccgccaGCCCAGCCGCCGCCCCGCCcgaccccgccgccgctttgggagggctcctgggggagggggcggaggccagcgcggacgggacggggcgggagtcatcgc
	*******************************************************************************************************************
rat	.((...((.((((((..(((..((((.(((((((((..(((((((.((......))..)))....))))....)))))).)))....))))..)))....)))))).))....))	0.840 -61.30

rat

chromosome:4:58658698:58658812:-1

intergenic ## {Repeats: trf 16 35 0 class=trf,GC_rich 16 35 -1 class=Low_complexity,dust 58658778 58658797 0 class=dust,GC_rich 1 44 -1 class=Low_complexity}

block1911891 [novel_lenNOK_gcHIGH]

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	0.318	no	no	0.94/0.94	18/18/0.00	0.0	0.0	1	0	1	0	5	14	3arm	2	nd	0.28	2	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------GCGUCCC---------------	1	novel
		len	cloning frequencies
			T4S2
	-------------------------------------------------------------CGCGTCCCCGGCCGCCCC-----	18	1
rat	cggttgtgccccggcctccccgcggactcgggggcccacgcctggcccgggctccggtcccCGCGTCCCCGGCCGCCCCgctcc
	************************************************************************************
rat	.((..(((....(((....(((.((((.((((((((...(((((...)))))...)))))))).)))).)))..))).))).))	0.820 -41.90

rat

chromosome:6:11619287:11619370:-1

intergenic ## {Repeats: dust 11619292 11619304 0 class=dust}

novel_lenNOK_loopOverlap_randfoldOK_bulgeHIGH (207 loci)

block3306 [novel_lenNOK_loopOverlap_randfoldOK_bulgeHIGH]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
no	0.002	no	no	0.53/0.55	19/20/0.50	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	6 1	-6 0	3arm_loop 3arm	5 5	nd nd	0.45 0.26	5 4	2	2	na	na

		reads	miRBase family seed
seed	-----------------ACCCUGG------------------	1	novel
seed	-----------------------GGACCCU------------	1	novel
		len	cloning frequencies
			T1S1	T4S1
	----------------TACCCTGGGACCCTGAATCA------	20	1	-
	----------------------GGGACCCTGAATCATGATG-	19	-	1
rat	agtatatgatggtcccTACCCTGGGACCCTGAATCATGATGc
	******************************************
	----------------------------------------------------	ENSRNOT00000050277 ENSRNOG00000025496 Usp7
rat	.(((((((((((((((......))))))....)))))).)))	1.000 -16.00

rat

chromosome:10:6912081:6912122:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000046232|ENSRNOG00000025496 ## Opposite_strand|Intronic_coding|ENSRNOT00000050277|ENSRNOG00000025496 ## ENSRNOG00000025496|protein_coding|Usp7|Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.1.2.15) (Ubiquitin thioesterase 7) (Ubiquitin-specific-processing protease 7) (Deubiquitinating enzyme 7) (Herpesvirus-associated ubiquitin-specific protease) (rHAUSP). [Source:UniProtKB/Swiss-Prot;Acc:Q4VSI4]

block14336 [novel_lenNOK_loopOverlap_randfoldOK_bulgeHIGH]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
no	0.003	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	8	-1	3arm	1	nd	0.22	4	1	1	na	na

		reads	miRBase family seed
seed	----------------------------------GGAAUGC------------------	1	novel
		len	cloning frequencies
			T4S2
	---------------------------------TGGAATGCCTTCAAGTGC--------	18	1
rat	gcattttaggtcatttaccactgcattcctttcTGGAATGCCTTCAAGTGCcaatttgc
	***********************************************************
rat	(((..((.((.(((((......(((((((.....)))))))....)))))))))..)))	0.710 -17.40