Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_shortStem (3551 loci)

block914091 [novel_shortStem]

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	0.652	no	no	0.25/0.25	20/20/1.00	0.0	0.0	1	0	1	0	1	35	3arm	1	nd	0.30	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------------AGGUAAA-------------	1	novel
		len	cloning frequencies
			T2S1
	----------------------------------------------------------------------------------------------TAGGTAAATGTTTTTGTTCA-	20	1
rat	atgagtaatacaggctgagtgttgaggaaatggctctgcagctttaagtaacacgtgtttgtgattgaagccaagtccctttgctgtgctgcttTAGGTAAATGTTTTTGTTCAt
	*******************************************************************************************************************
rat	((((((((.(((.(((((((((..((.(((.((..((...(((((((....((((....)))).)))))))..))..))))).))..)).))))..)))...)))..))))))))	0.670 -24.90

rat

chromosome:1:208425353:208425467:-1

intergenic

block1848495 [novel_shortStem]

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	0.029	no	no	0.65/0.65	23/23/1.00	0.0	0.0	1	0	1	0	0	12	5arm	1	nd	0.30	2	1	1	na	na

		reads	miRBase family seed
seed	-GGACACC------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	TGGACACCAGGCACAGGGAGAGC---------------------------------------------------	23	1
rat	TGGACACCAGGCACAGGGAGAGCtgaggcctgaaggatactgtggagtcagttgtgccctaggcaggatggcca
	**************************************************************************
rat	.((.((((..((..((((..((((((..((...((....))..))..))))))...))))..)).)).)).)).	0.990 -26.70

rat

chromosome:5:79246054:79246127:1

intergenic

block1891239 [novel_shortStem]

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	0.161	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	0	16	3arm	1	nd	0.21	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------CAUGCAU------------	1	novel
		len	cloning frequencies
			T4S1
	--------------------------------------------------------------------------------CCATGCATGGGTGGGTTCTT	20	1
rat	aggaaacagcagtcgtatgttatggtcacagcagaatgacgtgtttatctgatcacaactcacacagataagcacttgctCCATGCATGGGTGGGTTCTT
	****************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000055950 ENSRNOG00000021437 O08591_RAT
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000055948 ENSRNOG00000021437 O08591_RAT
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000039341 ENSRNOG00000021437 O08591_RAT
rat	(((((...((.....((((.(((((....(((((......(((((((((((.............))))))))))))))))))))))))).))...)))))	0.510 -24.42

rat

chromosome:5:156264869:156264968:1

Same_strand|Intronic_coding|ENSRNOT00000055950|ENSRNOG00000021437 ## ENSRNOG00000021437|protein_coding|O08591_RAT|Perlecan (Fragment). [Source:UniProtKB/TrEMBL;Acc:O08591]

block914226 [novel_shortStem]

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	0.118	no	no	0.50/0.50	20/20/1.00	0.0	0.0	1	0	1	0	0	38	3arm	1	nd	0.21	1	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------------------GGCCAUC------------	1	novel
		len	cloning frequencies
			T3S2
	-------------------------------------------------------------------------------------------------AGGCCATCGTTTAAGTCAGC	20	1
rat	gctgcctaagttgatgtctgcacagtgaattccagaggcttaggaagctctgcgctgccgcgtgtccaggcctttctcaggaatccctgtgtgtcgaAGGCCATCGTTTAAGTCAGC
	*********************************************************************************************************************
rat	((((.((.((.((((((((((((((.((.((((((((((((.(((......((((....)))).)))))))))))....)))))).)))))).....)))).)))).)).)).))))	0.990 -40.00

rat

chromosome:1:208478593:208478709:-1

intergenic

block1918873 [novel_shortStem]

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	0.729	no	no	0.75/0.75	20/20/1.00	0.0	0.0	1	0	1	0	0	32	3arm	1	nd	0.26	1	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------------AGCAAUG------------	1	novel
		len	cloning frequencies
			T3S1
	--------------------------------------------------------------------------------------CAGCAATGGCGGCCGGTGGC	20	1
rat	cctccgccccacttcctccctccaggccccgccccatgccggtgcgcctgcgcccgggcgaacacgtggctgccgcggagctagagCAGCAATGGCGGCCGGTGGC
	**********************************************************************************************************
	................................................................................................>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000035320 ENSRNOG00000026316 LOC362703
rat	((.((((((((.((.((..(((..(((.((((..((.(((((((((((((....))))))..))).))))))..)))).))).))).)).))))).))).)).)).	0.980 -44.00

rat

chromosome:6:23990221:23990326:-1

Same_strand|Boundary_non-coding|ENSRNOT00000035320|ENSRNOG00000026316 ## ENSRNOG00000026316|protein_coding|LOC362703|LOC362703 protein. [Source:UniProtKB/TrEMBL;Acc:Q4KLJ6]

block1022287 [novel_shortStem]

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	0.570	no	no	0.60/0.60	20/20/1.00	0.0	0.0	2	0	1	0	0	11	5arm	10	nd	0.30	3	2	1	na	na

		reads	miRBase family seed
seed	-GGCAGAG-------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T5S1
	CGGCAGAGAAACGGTGTCAG-------------------------------------------------------	20	2
rat	CGGCAGAGAAACGGTGTCAGgcccagccacttcagcagaggctctaagagtatggcccgccgggtcctccaggcc
	***************************************************************************
rat	.(((.((((..(((((...((((.((((.((.....)).))))..........)))))))))..)).))...)))	0.700 -24.70

rat

chromosome:1:187722715:187722789:1

intergenic

block2624194 [novel_shortStem]

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	0.190	no	no	0.35/0.38	20/21/1.00	0.0	0.5	2	0	1	0	0	13	5arm	2	nd	0.29	3	2	1	na	na

		reads	miRBase family seed
seed	-ACAAGCA------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T5S1
	AACAAGCAAACTGTTTCACA------------------------------------------------------------	20	1
	AACAAGCAAACTGTTTCACAG-----------------------------------------------------------	21	1
rat	AACAAGCAAACTGTTTCACAGtctggttactcctttcacacaggcaaagctagaatctctgtgagtgaggccagccctgt
	********************************************************************************
rat	.(((.((...((..((((((((((((((...(((.......)))...)))))))....)))))))..))....))..)))	0.510 -18.50

rat

chromosome:9:81370807:81370886:1

intergenic

block2951445 [novel_shortStem]

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	0.274	no	no	0.60/0.60	20/20/1.00	0.0	0.0	2	0	1	0	0	13	5arm	10	nd	0.30	3	2	1	na	na

		reads	miRBase family seed
seed	-GGCAGAG------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T5S1
	CGGCAGAGAAACGGTGTCAG------------------------------------------------------------	20	2
rat	CGGCAGAGAAACGGTGTCAGgcccagccacttcagcagaggctggctctaagagtgtggcccgccgggtcctccaagccc
	********************************************************************************
rat	.(((.((((..(((((...((((((((((((((....)))).))))........)).)))))))))..)).))...))).	0.650 -30.30

rat

chromosome:X:26627956:26628035:1

intergenic

block2651933 [novel_shortStem]

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	0.093	no	no	0.45/0.45	20/20/1.00	0.0	0.0	1	0	1	0	1	34	3arm	2	nd	0.30	2	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------------UGGAUUC-------------	1	novel
		len	cloning frequencies
			T2S1
	-------------------------------------------------------------------------------------------TTGGATTCTCTGAGGCATGT-	20	1
rat	aggcgggcttttccgggttcctaggtgtaggatttgtttagtagttaagtagtcttaactggtcctggctgctgtgctctctgttctgcctTTGGATTCTCTGAGGCATGTt
	****************************************************************************************************************
rat	.((((.(((((...((..(((.(((.(((((((..((.(((((((((..((((....))))....))))))))).)).....)))))))))).)))..))..))))).))))	0.800 -32.10

rat

chromosome:9:112830503:112830614:1

intergenic

novel_loopOverlap_nonpairedHIGH_bulgeHIGH (2749 loci)

block282 [novel_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	0.233	no	no	0.50/0.53	19/24/0.75	0.2	1.5	4	0	1	0	21	-3	5arm_loop	3	nd	0.45	4	4	1	na	na

		reads	miRBase family seed
seed	----------------------UAGGACA---------------------------------------------------------------	3	novel
seed	-----------------------AGGACAA--------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	---------------------CTAGGACAAAGCATTCGCCAAC-------------------------------------------------	22	2
	----------------------TAGGACAAAGCATTCGCCAACTCC----------------------------------------------	24	1
	---------------------CTAGGACAAAGCATTCGCC----------------------------------------------------	19	1
rat	gatgactctctttgaatggcaCTAGGACAAAGCATTCGCCAACTCCgtgatgtaggtagctattctctgctcgtcaaacttggagagttttt
	********************************************************************************************
rat	...((((((((((((..((((..((((...(((....(((.((........)).))).))).)))).))))..))))....))))))))...	0.810 -22.50

rat

chromosome:10:450263:450354:-1

intergenic

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