Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_randfoldOK (7326 loci)

block1889615 [novel_lenNOK_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	0.005	no	no	0.68/0.68	19/22/0.50	0.0	1.5	2	0	1	0	17	13	5arm	1	nd	0.21	3	2	1	na	na

		reads	miRBase family seed
seed	------------------GAGGGAC-------------------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T5S1
	-----------------TGAGGGACCCAGGAGCCTGCAG-----------------------------------------------------------------------------	22	1
	-----------------TGAGGGACCCAGGAGCCTG--------------------------------------------------------------------------------	19	1
rat	gagccttcacatcagccTGAGGGACCCAGGAGCCTGCAGaggaagcctacgacttagaaatcgtaggccaccgtgtggacttctgctcacgtcttcacttttgttagaggaggctc
	********************************************************************************************************************
rat	(((((((((((..((..((((((...((((((.(((((..((..((((((((........))))))))..)).))))).))))))......))))))))..)))....))))))))	0.930 -45.70

rat

chromosome:5:154401566:154401681:1

intergenic

block1890473 [novel_lenNOK_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	0.005	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	18	5	5arm	1	nd	0.21	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------AGCGCAG------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	------------------AAGCGCAGGAATGAAGTGC-------------------------------------------	19	1
rat	gggagccatggcttcccgAAGCGCAGGAATGAAGTGCggtttcgggagccgcttttggcctgcgcttggccaggcgacta
	********************************************************************************
rat	((..(((.(((((.....(((((((((...((((.(((((((...)))))))))))..)))))))))))))))))..)).	0.970 -41.10

rat

chromosome:5:155221484:155221563:1

intergenic ## {SimpF: -1 Eponine,oe = 0.94 1 CpG}

block1891952 [novel_lenNOK_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	0.68/0.68	19/19/0.00	0.0	0.0	2	0	1	0	6	17	5arm	1	nd	0.26	3	2	1	na	na

		reads	miRBase family seed
seed	-------GGGGUGG------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T2S1
	------TGGGGTGGTGGGTGGAGTG-------------------------------------------------------------------	19	2
rat	ctggcaTGGGGTGGTGGGTGGAGTGcagtggtgggggaccttgatagtcagaggtccctgtaacttgggatattctaagacctctctgttag
	********************************************************************************************
rat	((((((.((((.(((...(((((((....(((.(((((((((........)))))))))...))).....)))))))..)))))))))))))	1.000 -34.20

rat

chromosome:5:156992093:156992184:1

intergenic

block1928228 [novel_lenNOK_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	0.005	no	no	0.61/0.61	18/18/0.00	0.0	0.0	1	0	1	0	22	5	5arm	1	nd	0.22	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------CCGCAAU------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------GCCGCAATCCTGTCTCCT--------------------------------------------------------	18	1
rat	ctttggctcctttggcctgttcGCCGCAATCCTGTCTCCTgtctctcggagacgggcgatagctgtggtgttttgacttccgttttacagctggag
	************************************************************************************************
rat	(((..(((....(((...((((((((((...(((((.((((((((...)))))))).))))).)))))))....)))..)))......)))..)))	0.930 -37.60

rat

chromosome:6:41874789:41874884:-1

intergenic

block1928467 [novel_lenNOK_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	0.004	no	no	0.58/0.58	19/19/0.00	0.0	0.0	1	0	1	0	35	1	5arm	1	nd	0.05	1	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------AGAGACA----------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	-----------------------------------CAGAGACAGAGCTCAGACC-----------------------------------------------------------	19	1
rat	ctgcaagcaggcaatacaggaccgagaccaggcccCAGAGACAGAGCTCAGACCtacacgggttttctggaattttgtttctgtagctgtggctgtcctggaattctgctcag
	*****************************************************************************************************************
rat	(((..((((((.....((((((..((.((((((..(((((((((((.((((((((....))))))....)).)))))))))))..))).)))))))))))....)))))))))	1.000 -43.90

rat

chromosome:6:42127059:42127171:-1

intergenic

block2091764 [novel_lenNOK_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	0.37/0.39	18/19/0.00	0.0	0.5	2	0	1	0	7	5	5arm	6	nd	0.11	2	2	1	na	na

		reads	miRBase family seed
seed	--------UGGGGAU----------------------------------------------------------	2	novel
		len	cloning frequencies
			T5S1
	-------CTGGGGATTTAGATTTCAA-----------------------------------------------	19	1
	-------CTGGGGATTTAGATTTCA------------------------------------------------	18	1
rat	attgtatCTGGGGATTTAGATTTCAAtttgccaggagaagtgagttgcaatgtcataggtccctgtgacagta
	*************************************************************************
rat	(((((...(((((((((((((..((((((((........))))))))....))).))))))))))..))))).	0.990 -21.50

rat

chromosome:7:19397537:19397609:-1

intergenic

block2340741 [novel_lenNOK_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	0.009	no	no	0.44/0.44	18/18/0.00	0.0	0.0	2	0	1	0	14	0	3arm	2	nd	0.17	2	2	1	na	na

		reads	miRBase family seed
seed	------------------------------------------UGACAGA------------------------	2	novel
		len	cloning frequencies
			T2S1
	-----------------------------------------CTGACAGACATGTACACA--------------	18	2
rat	cttttctttattgtgtgtatgtgtgtgagagagaggacagaCTGACAGACATGTACACAcatagacacaaaga
	*************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000056818 ENSRNOG00000011348 NP_001101644.1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000015435 ENSRNOG00000011348 NP_001101644.1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000056817 ENSRNOG00000011348 NP_001101644.1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000056816 ENSRNOG00000011348 NP_001101644.1
rat	(((((((....(((((((((((((.((..((..........))..)).))))))))))))).)))...)))).	0.780 -20.70

rat

chromosome:8:93709350:93709422:-1

Same_strand|Intronic_coding|ENSRNOT00000056818|ENSRNOG00000011348 ## ENSRNOG00000011348|protein_coding|NP_001101644.1|sorting nexin 14 [Source:RefSeq_peptide;Acc:NP_001101644]

block2090838 [novel_lenNOK_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	0.37/0.39	18/19/0.00	0.0	0.5	2	0	1	0	22	5	5arm	6	nd	0.11	2	2	1	na	na

		reads	miRBase family seed
seed	-----------------------UGGGGAU---------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T5S1
	----------------------CTGGGGATTTAGATTTCAA----------------------------------------------------------------	19	1
	----------------------CTGGGGATTTAGATTTCA-----------------------------------------------------------------	18	1
rat	actttggggaaaatgtgagtgtCTGGGGATTTAGATTTCAAtttaccaagagaagtgagttgcaatgtcataggtccctgtgacagtatttgtcttttccatggt
	*********************************************************************************************************
rat	(((.(((..((...(((..(((((((((((((((((..((((((((........))))))))....))).)))))))))).)))).))).....))..))).)))	1.000 -31.60

rat

chromosome:7:18802538:18802642:-1

intergenic

novel_lenNOK_bulgeHIGH (5838 loci)

block72 [novel_lenNOK_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	0.148	no	no	0.32/0.32	19/19/0.00	0.0	0.0	1	0	1	0	7	23	3arm	1	nd	0.21	4	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------------------GAUACCC------------------	1	novel
		len	cloning frequencies
			T2S1
	-----------------------------------------------------------------------------TGATACCCAAGCAAATTTT-------	19	1
rat	ggttaagaaaacttggtgtgtcctgggtgttggatttttgacagaccaccacaacatttatccagggtctagtacacTGATACCCAAGCAAATTTTctgaatt
	*******************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------	ENSRNOT00000004346 ENSRNOG00000003198 RGD1305733
rat	.(((.(((((((((((.((((((((((..((((((...((..............))...))))))..)))))......))))))))))....)))))).))).	0.840 -24.04

rat

chromosome:10:139782:139884:-1

Opposite_strand|Intronic_coding|ENSRNOT00000004346|ENSRNOG00000003198 ## ENSRNOG00000003198|protein_coding|RGD1305733|Uncharacterized protein C16orf45 homolog. [Source:UniProtKB/Swiss-Prot;Acc:Q5FVJ5]

block1506 [novel_lenNOK_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	0.136	no	no	0.33/0.33	18/18/0.00	0.0	0.0	1	0	1	0	27	7	3arm	1	nd	0.22	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------GAGGUAG-------------------------------------	1	let-7a/7b/7c/7d/7e/7f/7i/miR-98
		len	cloning frequencies
			T1S1
	----------------------------------------------------------------TGAGGTAGTATGAAACTT---------------------------	18	1
rat	aggattcattttggtgggtcctctctgtcatacctacttatgttcaataagcactcagtgccctTGAGGTAGTATGAAACTTagcagaaatactctaaaagcaagtcct
	*************************************************************************************************************
rat	((((((..((((...((((..(((((((((((.(((((.....((((...((((...))))..))))))))))))))....))).)))...))))..))))..))))))	0.660 -24.50

rat

chromosome:10:3180131:3180239:-1

intergenic

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