miR-Intess: classification

other hairpins

novel_lenNOK_cloningOK_shortStem_5varHIGH_loopOverlap_nonpairedHIGH_bulgeHIGH (5 loci)

block2057993 [novel_lenNOK_cloningOK_shortStem_5varHIGH_loopOverlap_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	0.231	no	no	0.39/0.48	19/23/0.33	1.3	2.3	14	0	4	0	0	-11	3arm_loop	1	nd	0.36	4	18	4	na	na

		reads	miRBase family seed
seed	-----------------------CCAACCU----------------------	12	novel
seed	-------------------------AACCUCU--------------------	2	novel
seed	------------------------------CUUGACA---------------	2	novel
seed	---------------------------CCUCUUG------------------	1	novel
seed	---------------------------------GACAGAU------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1	T5S1
	----------------------TCCAACCTCTTGACAGATG-----------	19	2	1	1	5
	----------------------TCCAACCTCTTGACAGATGCA---------	21	-	-	-	3
	------------------------CAACCTCTTGACAGATGCA---------	19	-	-	-	2
	-----------------------------TCTTGACAGATGCATATTCTGTG	23	-	-	-	2
	--------------------------------TGACAGATGCATATTCTGTG	20	1	-	-	-
	--------------------------ACCTCTTGACAGATGCATA-------	19	-	-	-	1
rat	cactttgtgtgtcaccgtccccTCCAACCTCTTGACAGATGCATATTCTGTG
	****************************************************
rat	(((..((((((((...(((..............))).))))))))....)))	0.990 -8.34

rat

chromosome:6:122583946:122583997:1

intergenic

novel_lenNOK_gcHIGH_cloningOK (5 loci)

block140975 [novel_lenNOK_gcHIGH_cloningOK]

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	0.033	no	no	0.94/1.00	18/19/0.00	0.0	0.0	10	0	4	0	19	19	5arm	2	nd	0.22	2	13	4	na	na

		reads	miRBase family seed
seed	--------------------GGGCCGG----------------------------------------------------------------------------------------	11	novel
seed	-----------------------CCGGCGG-------------------------------------------------------------------------------------	1	novel
seed	---------------------GGCCGGC---------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T2S2	T3S1	T5S1
	-------------------GGGGCCGGCGGCGGCGGC------------------------------------------------------------------------------	18	6	2	-	2
	----------------------GCCGGCGGCGGCGGCTCC---------------------------------------------------------------------------	18	-	1	-	-
	--------------------GGGCCGGCGGCGGCGGCTC----------------------------------------------------------------------------	19	-	1	-	-
	-------------------GGGGCCGGCGGCGGCGGCT-----------------------------------------------------------------------------	19	-	-	1	-
rat	actgctcaagctgatcggaGGGGCCGGCGGCGGCGGCtcccggcgcggccttacgctcccgcccaggctgcggcctaggcggccccgttagatctctccgaacgcggcacagcgg
	*******************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000046159 ENSRNOG00000001862 NM_001108847.1
rat	.(((((...((((.(((((((((..(((((.(((.(((...((((((((((...((....))..)))))))).))..))).))))))))...)))))))))...))))..)))))	0.650 -61.10

rat

chromosome:11:85801271:85801385:-1

Opposite_strand|Intronic_coding|ENSRNOT00000046159|ENSRNOG00000001862 ## ENSRNOG00000001862|protein_coding|NM_001108847.1|ubiquitin-conjugating enzyme E2L 3 (predicted) (Ube2l3_predicted), mRNA [Source:RefSeq_dna;Acc:NM_001108847] ## {Repeats: GC_rich 1 31 -1 class=Low_complexity,GC_rich 11 31 -1 class=Low_complexity} ## {SimpF: -1 Eponine}

block896144 [novel_lenNOK_gcHIGH_cloningOK]

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	0.661	no	no	0.89/1.00	18/20/0.05	0.7	0.2	21	0	8	0	11	19	5arm	2	nd	0.11	1	21	8	na	na

		reads	miRBase family seed
seed	----------------GGGCGGG-----------------------------------------------------------------------------------------------	10	novel
seed	---------------CGGGCGG------------------------------------------------------------------------------------------------	9	novel
seed	--------------GCGGGCG-------------------------------------------------------------------------------------------------	1	novel
seed	------------GGGCGGG---------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T4S1	T4S2	T5S2
	---------------CGGGCGGGGCCGGGGGTG-------------------------------------------------------------------------------------	18	3	-	1	3	-	1	-	1
	--------------GCGGGCGGGGCCGGGGGTG-------------------------------------------------------------------------------------	19	-	2	-	1	2	1	2	-
	---------------CGGGCGGGGCCGGGGGTGT------------------------------------------------------------------------------------	19	1	-	-	-	-	-	-	-
	--------------GCGGGCGGGGCCGGGGGT--------------------------------------------------------------------------------------	18	-	-	-	-	-	1	-	-
	-----------GGGGCGGGCGGGGCCGGGG----------------------------------------------------------------------------------------	19	-	-	-	1	-	-	-	-
	-------------GGCGGGCGGGGCCGGGGGTG-------------------------------------------------------------------------------------	20	-	-	1	-	-	-	-	-
rat	gccggggctcgGGGGCGGGCGGGGCCGGGGGTGTccgcgggcgcagaagccgggagcccgcacacgcctccccgcgccgctaccgccgccggctctccgccgctccgcgcgctgcggc
	**********************************************************************************************************************
	...............................................................................................................................>	ENSRNOT00000052377 ENSRNOG00000013123 RGD1563998_predicted
rat	((((.(((.(((((((.(((((((((((.((((...(((((((..((.(((((....))).....)).))..))).))))...)))).))))))..)))))))))).)).))).))))	0.880 -74.00

rat

chromosome:1:167490278:167490395:-1

intergenic ## {Repeats: GC_rich 1 32 -1 class=Low_complexity,dust 167490365 167490385 0 class=dust,GC_rich 1 21 -1 class=Low_complexity} ## {SimpF: 1 Eponine}

block1414550 [novel_lenNOK_gcHIGH_cloningOK]

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	0.892	no	no	0.89/0.94	18/19/0.00	0.0	0.0	23	0	9	0	31	5	5arm	1	nd	0.28	2	28	9	na	na

		reads	miRBase family seed
seed	--------------------------------GGCGCCC------------------------------------------------------------------------------	28	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S2	T4S1	T4S2	T5S1	T5S2
	-------------------------------AGGCGCCCCGCCGCCCCC--------------------------------------------------------------------	18	1	6	1	5	5	1	4	3	1
	-------------------------------AGGCGCCCCGCCGCCCCCT-------------------------------------------------------------------	19	-	-	-	-	-	-	1	-	-
rat	ccacgctgttctagctgcccgctgcccgctgAGGCGCCCCGCCGCCCCCtcgcgatgcgcttaatggacgcgtcgggtcgctgactcagggtgagtttgcaggtcgcggagcagagg
	*********************************************************************************************************************
rat	((...(((((((.((.(((.((.((((.((((((((.((((.(((..((..(((...))).....))..))).)))).)))...)))))))...))..)).))).))))))))).))	0.450 -46.10

rat

chromosome:3:142457140:142457256:-1

intergenic

block1685664 [novel_lenNOK_gcHIGH_cloningOK]

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	0.209	no	no	0.89/0.94	18/19/0.00	0.2	0.4	14	0	5	0	20	8	5arm	1	nd	0.00	0	19	5	na	na

		reads	miRBase family seed
seed	---------------------CCGCCCG---------------------------------------------------------------------------------------	14	novel
seed	----------------------CGCCCGU--------------------------------------------------------------------------------------	5	novel
		len	cloning frequencies
			T1S2	T2S1	T2S2	T3S2	T4S2
	--------------------ACCGCCCGTCCCCGCCCC-----------------------------------------------------------------------------	18	2	1	4	-	3
	---------------------CCGCCCGTCCCCGCCCCC----------------------------------------------------------------------------	18	1	-	3	1	-
	--------------------ACCGCCCGTCCCCGCCCCC----------------------------------------------------------------------------	19	-	2	1	1	-
rat	cccgcccgccgctcagaccgACCGCCCGTCCCCGCCCCCagcgcgcgcttcctgccacgttgcgcaggggcgcggggccagactctgcggcgcggggcctggggggagggccgga
	*******************************************************************************************************************
rat	((.((((.((.(((((.((..((((((((((((((((((.(((((((..........))).)))).)))).)))))).........)))).)))))).))))).)).)))).)).	0.950 -68.80

rat

chromosome:4:148948770:148948884:1

intergenic ## {SimpF: oe = 0.81 1 CpG}

block1899572 [novel_lenNOK_gcHIGH_cloningOK]

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	0.056	no	no	0.94/0.94	18/18/0.00	0.0	0.0	11	0	6	0	26	13	3arm	1	nd	0.22	2	11	6	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------GGGGGGG------------------------------------	11	novel
		len	cloning frequencies
			T1S1	T2S1	T2S2	T3S1	T4S2	T5S1
	----------------------------------------------------------------------------TGGGGGGGGGGGGGGCCC--------------------------	18	2	1	2	2	3	1
rat	agctcagccgcagatctgtagtgatctagccctccctcgcctgggtccaaaactctgcggcaagcagcacaggcagTGGGGGGGGGGGGGGCCCagaaacgtcagtgtctgcccctagcc
	************************************************************************************************************************
rat	.(((.((..(((((((((..((..(((.((((((((((.(((..(((.......((((.....))))....)))....))).))))))))))..))).))..))).))))))..))))).	0.760 -51.30

rat

chromosome:5:166783512:166783631:1

intergenic ## {Repeats: dust 166783589 166783602 0 class=dust}

novel_lenNOK_gcHIGH_shortStem_randfoldOK (5 loci)

block154384 [novel_lenNOK_gcHIGH_shortStem_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
no	0.010	no	no	0.94/0.94	18/18/0.00	0.0	0.0	1	0	1	0	1	20	5arm	1	nd	0.00	0	1	1	na	na

		reads	miRBase family seed
seed	--GCGCCGC--------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	-TGCGCCGCGCGGGGGGCC----------------------------------------------------------------	18	1
rat	gTGCGCCGCGCGGGGGGCCtgcggcatgcgcggggttgtgcgagcgagcgcgcgcgtaaggcccctgctctgtgtgtgtgcac
	***********************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000002286 ENSRNOG00000001682 NP_001101785.1
rat	((((((((((((((((((((...((.((((((...((((....)))).)))))).)).)))))))....))))))).))))))	0.750 -47.00

rat

chromosome:11:34618087:34618169:1

Same_strand|Intronic_non-coding|ENSRNOT00000002286|ENSRNOG00000001682 ## ENSRNOG00000001682|protein_coding|NP_001101785.1|tetratricopeptide repeat domain 3 [Source:RefSeq_peptide;Acc:NP_001101785] ## {Repeats: dust 34618123 34618141 0 class=dust} ## {SimpF: 1 Eponine, -1 Eponine}

block462667 [novel_lenNOK_gcHIGH_shortStem_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
no	0.002	no	no	0.94/0.94	18/18/0.00	0.0	0.0	1	0	1	0	1	8	5arm	1	5	0.17	1	1	1	na	na

		reads	miRBase family seed
seed	--CCGGGGG--------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	-CCCGGGGGCGCAGCGGCC----------------------------------------	18	1
rat	cCCCGGGGGCGCAGCGGCCcggggggcggcggtggcccgggcggcggcggccccggggg
	***********************************************************
	+++++++++++++++++++>>+++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000012828 ENSRNOG00000009669 PO4F1_RAT
rat	((((((((.(((.((.(((((((..((....))..))))))).)).))).)))))))).	1.000 -52.20

rat

chromosome:15:88537982:88538040:-1

Same_strand|Boundary_coding|ENSRNOT00000012828|ENSRNOG00000009669 ## ENSRNOG00000009669|protein_coding|PO4F1_RAT|POU domain, class 4, transcription factor 1 (Brain-specific homeobox/POU domain protein 3A) (Brn-3A) (Fragment). [Source:UniProtKB/Swiss-Prot;Acc:P20266] ## {Repeats: trf 92 97 0 class=trf,dust 88538022 88538037 0 class=dust,trf 92 109 0 class=trf} ## {SimpF: oe = 0.87 0 CpG}

block580428 [novel_lenNOK_gcHIGH_shortStem_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
no	0.003	no	no	1.00/1.00	18/18/0.00	0.0	0.0	1	0	1	0	0	16	5arm	1	nd	0.06	1	1	1	na	na

		reads	miRBase family seed
seed	-CGCGCGG------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	GCGCGCGGGCGGCCGGCC--------------------------------------------------------------	18	1
rat	GCGCGCGGGCGGCCGGCCgcctcggggagctactacacgaaggacgctaccgggaggccctggccgccgcctgcgacgct
	********************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000015142 ENSRNOG00000011349 Lonrf1_predicted
rat	((((((((((((.((((((((((..(((((..((......))...))).))..)))))...)))))))))))))).))).	1.000 -50.90

rat

chromosome:16:59675287:59675366:1

Same_strand|Intronic_non-coding|ENSRNOT00000015142|ENSRNOG00000011349 ## ENSRNOG00000011349|protein_coding|Lonrf1_predicted| ## {Repeats: GC_rich 1 18 1 class=Low_complexity,GC_rich 1 21 1 class=Low_complexity} ## {SimpF: oe = 0.88 0 CpG}

block1890514 [novel_lenNOK_gcHIGH_shortStem_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
no	0.001	no	no	0.94/0.95	18/21/0.50	0.0	1.5	2	0	2	0	1	16	3arm	1	nd	0.11	2	2	2	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------CCCCCCC--------------	2	novel
		len	cloning frequencies
			T1S2	T2S2
	-------------------------------------------------------------------------GCCCCCCCCTCCGGGGGG----	18	-	1
	-------------------------------------------------------------------------GCCCCCCCCTCCGGGGGGGGG-	21	1	-
rat	ccccccccccaaggttgggtaaaagggagcaggcttttatctggcagagacttcttttctttgtttctctgctGCCCCCCCCTCCGGGGGGGGGa
	***********************************************************************************************
rat	(((((((((..(((..(((.....(((((((((.........((((((((.......))))))))..)))))).)))))))))..))))))))).	0.490 -46.80