miR-Intess: classification

other hairpins

novel_lenNOK_gcHIGH_loopOverlap (17 loci)

block928393 [novel_lenNOK_gcHIGH_loopOverlap]

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	0.708	no	no	0.94/0.95	18/19/0.00	0.0	0.5	2	0	2	0	34	-2	3arm_loop	1	nd	0.11	1	2	2	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------CGCCGCC---------------------------------------------	2	novel
		len	cloning frequencies
			T3S1	T4S2
	-------------------------------------------------------------------CCGCCGCCCCCCTCCCGCC----------------------------------	19	-	1
	-------------------------------------------------------------------CCGCCGCCCCCCTCCCGC-----------------------------------	18	1	-
rat	ggcggcaaggctgacggaggggccccgcgtgcgttcaggcggtgagtcagggagggttatgcaagctCCGCCGCCCCCCTCCCGCCcgcccccggcacctccccgcggtctttcaccccg
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000021055 ENSRNOG00000015518 Rbp4
rat	((.((.(((((((.(((.((((..(((...(((....(((((.((....(((.((((...((.......)).)))))))))))))))))...)))..)))).))))))))))...)))).	0.850 -52.70

rat

chromosome:1:242451084:242451203:-1

Same_strand|Intronic_non-coding|ENSRNOT00000021055|ENSRNOG00000015518 ## ENSRNOG00000015518|protein_coding|Rbp4|Plasma retinol-binding protein precursor (PRBP) (RBP). [Source:UniProtKB/Swiss-Prot;Acc:P04916] ## {Repeats: dust 242451118 242451136 0 class=dust,GC_rich 1 29 -1 class=Low_complexity,GC_rich 11 29 -1 class=Low_complexity}

block1064154 [novel_lenNOK_gcHIGH_loopOverlap]

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	0.066	no	no	1.00/1.00	18/19/0.00	0.7	1.3	3	0	2	0	41	-4	5arm_loop	3	nd	0.28	3	3	2	na	na

		reads	miRBase family seed
seed	-------------------------------------------CGCCCCG---------------------------------------------------------------	2	novel
seed	------------------------------------------CCGCCCC----------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2
	------------------------------------------CCGCCCCGCCCGCCCGCGG----------------------------------------------------	19	1	1
	-----------------------------------------GCCGCCCCGCCCGCCCGC------------------------------------------------------	18	1	-
rat	ctgatccctgccgggctgcggggggaggagctggcgtggggGCCGCCCCGCCCGCCCGCGGgagggatcgggcggggtccctggcctcttccgcctgggtttcaggaggtcgg
	*****************************************************************************************************************
rat	((((((((((..(((((.((((.(((((((.....((.((((..(((((((((((((......)))..)))))))))))))).))))))))).))))))))))))).))))))	0.990 -69.30

rat

chromosome:20:9225729:9225841:-1

intergenic ## {Repeats: GC_rich 2 22 -1 class=Low_complexity,GC_rich 1 25 -1 class=Low_complexity}

block1108024 [novel_lenNOK_gcHIGH_loopOverlap]

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	0.649	no	no	1.00/1.00	18/18/0.00	0.0	0.0	3	0	2	0	34	-1	5arm_loop	2	nd	0.28	2	3	2	na	na

		reads	miRBase family seed
seed	-----------------------------------GGCGCCG---------------------------------------------------------------------	3	novel
		len	cloning frequencies
			T2S2	T3S2
	----------------------------------GGGCGCCGGGGGCGGGGG-----------------------------------------------------------	18	2	1
rat	gcggggcggggcgcgcggctcgggcggggggcgcGGGCGCCGGGGGCGGGGGcgggcctggcgagccacggcgtgcggcccggatcggaagtgccacgcggagcccgcgca
	***************************************************************************************************************
rat	(((((((....((((.(((.....(((.((((.((.((((((((.((.(((.....))).))...)).)))))).))))))...))).....))).))))..)))).))).	0.790 -62.80

rat

chromosome:20:28632040:28632150:1

intergenic ## {Repeats: G-rich 70 88 1 class=Low_complexity,dust 28632016 28632034 0 class=dust,G-rich 4 94 1 class=Low_complexity,trf 5 23 0 class=trf}

block2030928 [novel_lenNOK_gcHIGH_loopOverlap]

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	0.616	no	no	0.94/0.95	18/19/0.00	0.5	0.0	2	0	2	0	29	-4	3arm_loop	1	nd	0.28	2	2	2	na	na

		reads	miRBase family seed
seed	----------------------------------------------------UGCGGGG---------------------------------------	1	novel
seed	---------------------------------------------------CUGCGGG----------------------------------------	1	novel
		len	cloning frequencies
			T3S2	T5S1
	--------------------------------------------------GCTGCGGGGCGCCGCGGGC-----------------------------	19	1	-
	---------------------------------------------------CTGCGGGGCGCCGCGGGC-----------------------------	18	-	1
rat	gcggggagatggggaaggggcggggactggcttggcctctggcacccggaGCTGCGGGGCGCCGCGGGCtccagctcccggtcccgggaaggctgagc
	**************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000010948 ENSRNOG00000008249 Brms1l
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000059441 ENSRNOG00000008249 Brms1l
rat	((..((..........(((((.((((((((...(((((.((((.((((......))))..)))).))))))))).)))).))))).......))..))	0.440 -47.63

rat

chromosome:6:76177951:76178048:1

block2083775 [novel_lenNOK_gcHIGH_loopOverlap]

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	0.062	no	no	0.94/0.94	18/18/0.00	0.0	0.0	2	0	1	0	38	-1	3arm	1	nd	0.17	1	2	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------CGCGGGC------------------------------------------------	2	novel
		len	cloning frequencies
			T3S2
	-----------------------------------------------------------CCGCGGGCGCGCAGCCCC--------------------------------------	18	2
rat	cgcctccccttcccttccggcgggggcgggaggcggagcctgagctcccgcgccccctcCCGCGGGCGCGCAGCCCCgcccccctcacccctgcgcgactcagcctacctggtgc
	*******************************************************************************************************************
rat	((((.............(((((((((.(((.(((((.((.((.((.((((((........)))))).)).)))).))))).)))...))))))).)).............)))).	0.600 -56.37

rat

chromosome:7:11078748:11078862:-1

intergenic ## {Repeats: GC_rich 1 38 -1 class=Low_complexity,GC_rich 8 26 -1 class=Low_complexity,dust 11078786 11078804 0 class=dust}

block2170826 [novel_lenNOK_gcHIGH_loopOverlap]

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	0.260	no	no	1.00/1.00	18/18/0.00	0.0	0.0	1	0	1	0	37	-1	5arm_loop	1	nd	0.22	2	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------GGGGGCC---------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------------------GGGGGGCCCCCGGCCCGG-----------------------------------------------------------------	18	1
rat	cgagtgtctgcgagggtgtctctgggccggtgtgcgcGGGGGGCCCCCGGCCCGGgagcggaaccgagggctccccccgctggctcgcctcctcccgccgctctcagcagagctgcctcg
	************************************************************************************************************************
rat	((((.(((((((((((((....((((..((((.((((((((((.((((((.(((....)))..))).)))..))))))))..)).))))....)))).))))))).)))).))...))))	0.990 -65.00

rat

chromosome:7:138413925:138414044:-1

intergenic ## {Repeats: GC_rich 2 20 -1 class=Low_complexity,GC_rich 1 23 -1 class=Low_complexity}

block2529097 [novel_lenNOK_gcHIGH_loopOverlap]

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	0.380	no	no	0.94/0.94	18/18/0.00	0.0	0.0	1	0	1	0	20	-1	5arm_loop	1	nd	0.28	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------CCGCCGG----------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	--------------------GCCGCCGGTGGCGGGGCG------------------------------------------	18	1
rat	gcctcccctcccccacggccGCCGCCGGTGGCGGGGCGcgagccttcccggcaacggggcggcgcggggccggcgcggct
	********************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000021528 ENSRNOG00000015633 NP_001100393.1
rat	(((...((..((((.((.(((((.(((.((.((((((....)))...))).)).)))))))))).))))..))...))).	0.800 -49.30

rat

chromosome:9:79653211:79653290:-1

block2536453 [novel_lenNOK_gcHIGH_loopOverlap]

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	0.518	no	no	1.00/1.00	18/18/0.00	0.0	0.0	7	0	5	0	17	-1	3arm	1	nd	0.28	2	7	5	na	na

		reads	miRBase family seed
seed	--------------------------------------CGCGGGC---------------------------	7	novel
		len	cloning frequencies
			T1S2	T2S1	T2S2	T3S1	T4S1
	-------------------------------------GCGCGGGCGGGGCCGGGG-----------------	18	1	1	1	1	3
rat	cgggcgcagaggtggtctgggccggggcggggcgcgaGCGCGGGCGGGGCCGGGGcgcaaacagcgggctcg
	************************************************************************
rat	(((((((....(((.(((((.((...((...(((....)))..)).)).))))).))).....))..)))))	0.480 -27.80

rat

chromosome:9:88165628:88165699:-1

intergenic ## {Repeats: dust 88165645 88165663 0 class=dust,C-rich 99 117 -1 class=Low_complexity,C-rich 5 155 -1 class=Low_complexity,trf 3 21 0 class=trf} ## {SimpF: oe = 0.77 -1 CpG}

block2588766 [novel_lenNOK_gcHIGH_loopOverlap]

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	0.426	no	no	0.94/0.94	18/18/0.00	0.0	0.0	2	0	2	0	8	-1	3arm	1	nd	0.17	1	2	2	na	na

		reads	miRBase family seed
seed	------------------------------------CCGCGGG------------------	2	novel
		len	cloning frequencies
			T1S1	T3S1
	-----------------------------------GCCGCGGGCGCGCGACGG--------	18	1	1
rat	cttgcgacgccggcggcgggactcgcggaggcaggGCCGCGGGCGCGCGACGGagcgcggg
	*************************************************************
	-----------------------------------------------------------------------	ENSRNOT00000025243 ENSRNOG00000018623 NP_001101683.1
rat	((((((...(((.(((((...(((((((........)))))))))).)).)))..))))))	0.950 -30.30

rat

chromosome:9:37067802:37067862:1

Opposite_strand|Intronic_non-coding|ENSRNOT00000025243|ENSRNOG00000018623 ## ENSRNOG00000018623|protein_coding|NP_001101683.1|REV1-like [Source:RefSeq_peptide;Acc:NP_001101683] ## {SimpF: oe = 0.91 0 CpG}

novel_lenNOK_multiarm_Multihit_loopOverlap_nonpairedHIGH (17 loci)

block847622 [novel_lenNOK_multiarm_Multihit_loopOverlap_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	0.040	no	no	0.40/0.60	20/25/0.67	0.0 0.0	2.5 0.0	2 1	0 0	1 1	0 0	15 9	-20 -2	5arm_loop_3arm 3arm_loop	52 52	nd nd	0.55 0.50	8 3	3	2	na	na

		reads	miRBase family seed
seed	----------------GCAGGAC--------------------------------	2	novel
seed	---------------------------ACUGGCA---------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2
	---------------TGCAGGACCTCTACTGGCACAAAAA---------------	25	-	1
	--------------------------TACTGGCACAAAAATTCCAC---------	20	1	-
	---------------TGCAGGACCTCTACTGGCAC--------------------	20	-	1
rat	tcagcagctagaagtTGCAGGACCTCTACTGGCACAAAAATTCCACagttgctgg
	*******************************************************
	-----------------------------------------------------------------	ENSRNOT00000041486 ENSRNOG00000033456 LOC308198
rat	.((((((((.(((.((((((........)))...)))...)))...)))))))).	0.960 -15.10