miR-Intess: classification

other hairpins

novel_lenNOK_shortStem_randfoldOK (2599 loci)

block1504824 [novel_lenNOK_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	0.50/0.50	18/20/0.60	0.0	1.2	5	0	4	0	0	35	3arm	3	nd	0.11	2	5	4	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------------------GGUCUGG------------	5	novel
		len	cloning frequencies
			T1S1	T1S2	T4S1	T4S2
	-------------------------------------------------------------------------------------------------TGGTCTGGTTCACACTTGTG	20	-	1	1	1
	-------------------------------------------------------------------------------------------------TGGTCTGGTTCACACTTG--	18	2	-	-	-
rat	acacttgtgctggaccctggacctgtggtctggttcacgcttgtgctgggtcctggatctgtgatctggttcacacttgtgctggaccctggacctgTGGTCTGGTTCACACTTGTG
	*********************************************************************************************************************
rat	.(((..(((.((((((..(((((...((((((((((((((..(((.((((.((.(((((...))))))))))))))..))).))))))..)))))...))))))))))))))..)))	1.000 -52.90

rat

chromosome:3:148873670:148873786:1

intergenic ## {Repeats: trf 191 211 0 class=trf}

block1572787 [novel_lenNOK_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	0.61/0.61	18/18/0.00	0.0	0.0	1	0	1	0	0	26	5arm	1	nd	0.28	2	1	1	na	na

		reads	miRBase family seed
seed	-GGGAGCA------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	TGGGAGCACTCCTGATCC--------------------------------------------------------------------------	18	1
rat	TGGGAGCACTCCTGATCCaaatgtaatgtgtggagagtcatttcatggagatttgatgcctacacatgtgagtaggcaggtcctatgctccc
	********************************************************************************************
rat	.(((((((..((((..((.......((((((((...((((..((.....))..))))..)))))))).......)))))).....)))))))	0.830 -32.94

rat

chromosome:4:116140210:116140301:-1

intergenic

block1590437 [novel_lenNOK_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	0.008	no	no	0.33/0.33	18/18/0.00	0.0	0.0	1	0	1	0	2	26	3arm	1	nd	0.11	2	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------AAUUAAC------------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------------------------------------------------------------------GAATTAACTTAGTCCCTA--	18	1
rat	ctggaggactgactctgtggtttcttcgcgcatgcgttcttggtctttcggatgttcttgcatctcccagagtagagcgagtgcaGAATTAACTTAGTCCCTAga
	*********************************************************************************************************
rat	((((.((((((.......((((..(((..((((.(((((.((.(((...((((((....))))))...))).))))))).)))).)))..)))))))))))))).	0.930 -37.41

rat

chromosome:4:149330645:149330749:-1

intergenic

block1804808 [novel_lenNOK_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	0.56/0.56	18/18/0.00	0.0	0.0	1	0	1	0	2	11	5arm	2	nd	0.22	3	1	1	na	na

		reads	miRBase family seed
seed	---UCUGUGC---------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	--CTCTGTGCACTGCAGAGT-----------------------------------------------------	18	1
rat	gcCTCTGTGCACTGCAGAGTgcagctgtacatggcctctgtgcactgcagaatgcggctgtgcacagctggca
	*************************************************************************
	-----------------------------------------------------------------------------------	ENSRNOT00000011960 ENSRNOG00000008802 NP_001102164.1
rat	(((.((((((((((((...(((((.((((((.......)))))))))))...))))...))))))))..))).	0.910 -36.40

rat

chromosome:5:169171711:169171783:-1

Opposite_strand|Intronic_coding|ENSRNOT00000011960|ENSRNOG00000008802 ## ENSRNOG00000008802|protein_coding|NP_001102164.1|DnaJ (Hsp40) homolog, subfamily C, member 11 [Source:RefSeq_peptide;Acc:NP_001102164] ## {Repeats: trf 78 96 0 class=trf}

block913823 [novel_lenNOK_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	0.61/0.61	18/18/0.00	0.0	0.0	1	0	1	0	4	30	5arm	1	nd	0.22	2	1	1	na	na

		reads	miRBase family seed
seed	-----CCUCGUU-------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	----GCCTCGTTCACTGCCTAC---------------------------------------------------------------------------------------------	18	1
rat	cgctGCCTCGTTCACTGCCTACggtcctcggagccagacccgggccggagcctgagcggcaaccggcccgaggaggggcttcagagccgcggccgtgggcgggcgatgctgcagc
	*******************************************************************************************************************
rat	.(((((..((((..(((((((((((((((((((((...((((((((((.(((.....)))..)))))))).))...)))))).)))....))))))))))))..))))..)))))	1.000 -72.70

rat

chromosome:1:208100570:208100684:-1

intergenic

block1825198 [novel_lenNOK_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	0.47/0.47	19/19/0.00	0.0	0.0	1	0	1	0	4	28	5arm	1	nd	0.21	3	1	1	na	na

		reads	miRBase family seed
seed	-----GUGAACA------------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	----CGTGAACATGCACACTTGA-------------------------------------------------------------------------------------------------	19	1
rat	gtttCGTGAACATGCACACTTGAactgccacctagacagaacggagtccgtaaaactaattcctcttctgtctaggtggcagttcaagtgtagggtaattttaatggatgggaatgaagg
	************************************************************************************************************************
rat	.((((((...(((.(((((((((((((((((((((((((((.(((((..((...))..)))))..)))))))))))))))))))))))))..............)).)))...)))))).	0.610 -57.63

rat

chromosome:5:34637676:34637795:1

intergenic

block1874124 [novel_lenNOK_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	0.008	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	2	23	3arm	2	25	0.17	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------UCCUUCU------------	1	novel
		len	cloning frequencies
			T2S1
	--------------------------------------------------------------------------------CTCCTTCTTTGCAAAGGC--	18	1
rat	ggggtcttccaatgtctctctgagggaggttcacaaacagggtttcagcctttaagctagagtttgtaactgctgttgacCTCCTTCTTTGCAAAGGCcc
	****************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000050749 ENSRNOG00000032988
rat	.(((((((....(((......((((((((((....(((((((((.((..(((((...)))))..)).)))).)))))))))))))))...))))))))))	0.960 -34.60

rat

chromosome:5:134205929:134206028:1

Same_strand|Intronic_coding|ENSRNOT00000050749|ENSRNOG00000032988 ## ENSRNOG00000032988|protein_coding||

novel_lenNOK_randfoldOK_nonpairedHIGH_bulgeHIGH (2552 loci)

block640 [novel_lenNOK_randfoldOK_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	0.001	no	no	0.37/0.37	19/19/0.00	0.0	0.0	1	0	1	0	11	14	3arm	1	nd	0.32	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------UGUAAGU----------------------	1	novel
		len	cloning frequencies
			T1S1
	------------------------------------------------------------------TTGTAAGTGGTTTTGAGAC-----------	19	1
rat	gtaggggttacaacaaaacacacaagcagggtatgtgaagcacacaattttttgttacacaatactTTGTAAGTGGTTTTGAGACtaatatctaca
	************************************************************************************************
	----------------------------------------------------------------------------------------------------------	ENSRNOT00000003115 ENSRNOG00000002286 Mkl2
rat	((((..((((...((((((.(((..((((((((((((.((((..........)))).)))).))))))))..)))))))))....))))..)))).	1.000 -29.00

rat

chromosome:10:1120662:1120757:-1

block769 [novel_lenNOK_randfoldOK_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	0.005	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	26	13	5arm	2	nd	0.33	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------CCCUAGU----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	--------------------------TCCCTAGTTTTTGGAGGG------------------------------------------------------------------------	18	1
rat	ccaggcgtgcccaccactgaggtccaTCCCTAGTTTTTGGAGGGatgatttgaatggtttgcccttccttcttccttccctcattagacagggtctcactgtgtagccctgtctgg
	********************************************************************************************************************
	------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000061706 ENSRNOG00000022305 LOC688708
rat	(((((((.((..((((.((((..((....(((((....(((((((.((...(((.((....)).)))..)).)))))))...)))))...))..)))).)).)).))..)))))))	0.940 -41.40

rat

chromosome:10:1432778:1432893:-1

block892 [novel_lenNOK_randfoldOK_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	0.006	no	no	0.28/0.28	18/18/0.00	0.0	0.0	2	0	2	0	22	7	5arm	1	nd	0.44	4	2	2	na	na

		reads	miRBase family seed
seed	-----------------------GUAAACA--------------------------------------------------------------	2	miR-30a/30b/30c/30d/30e/384
		len	cloning frequencies
			T1S1	T4S2
	----------------------TGTAAACATTTCACCATA----------------------------------------------------	18	1	1
rat	cctatctcaataatactagtgaTGTAAACATTTCACCATAtacaagctatatgtctgtagaggttgagtgtatttggggggtagaggtagga
	********************************************************************************************
rat	((((((((.((....((...(((....((((((.(((...((((.((.....)).))))..))).)))))))))...)).)).)))))))).	0.440 -24.30