Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_shortStem_nonpairedHIGH (12839 loci)

block1883201 [novel_lenNOK_shortStem_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	0.063	no	no	0.56/0.56	18/18/0.00	0.0	0.0	2	0	1	0	1	32	3arm	1	nd	0.39	3	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------CCAUGCU-----------	2	novel
		len	cloning frequencies
			T3S2
	----------------------------------------------------------------------------------------GCCATGCTGGTCAGTCTA-	18	2
rat	ctggaagggggaggggcaggggaggggcgacgcgacgcgactgtggtcttctgggtagaaggaagggttgttcaggaagccctacgctGCCATGCTGGTCAGTCTAg
	***********************************************************************************************************
	................................................................................................>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000038888 ENSRNOG00000028083 OTTMUSG00000009332
rat	(((((..((..((.(((((....(((((.....((.((((((....((((((....))))))...)))))))).....)))))...)))))...))..))..)))))	0.910 -35.90

rat

chromosome:5:146568612:146568718:1

Same_strand|Boundary_non-coding|ENSRNOT00000038888|ENSRNOG00000028083 ## ENSRNOG00000028083|protein_coding|OTTMUSG00000009332|predicted gene, OTTMUSG00000009332 Gene [Source:MGI Symbol;Acc:MGI:3758095]

block1888064 [novel_lenNOK_shortStem_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	0.533	no	no	0.58/0.58	19/19/0.00	0.0	0.0	2	0	1	0	0	6	5arm	2	nd	0.37	3	2	1	na	na

		reads	miRBase family seed
seed	-CACCAGG----------------------------------------------	2	novel
		len	cloning frequencies
			T2S2
	GCACCAGGGAAGGAAGATC-----------------------------------	19	2
rat	GCACCAGGGAAGGAAGATCatgggcctgtgtgtagcttggctttcctgcggggc
	******************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000039571 ENSRNOG00000023423 Aim1l_predicted
rat	((.((.(((((((..((...((.((....)).))..))..)))))))...))))	0.510 -14.50

rat

chromosome:5:152828329:152828382:1

Same_strand|Boundary_non-coding|ENSRNOT00000056157|ENSRNOG00000023423 ## Same_strand|Intronic_coding|ENSRNOT00000039571|ENSRNOG00000023423 ## ENSRNOG00000023423|protein_coding|Aim1l_predicted|

block1888066 [novel_lenNOK_shortStem_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	0.533	no	no	0.58/0.58	19/19/0.00	0.0	0.0	2	0	1	0	0	6	5arm	2	nd	0.37	3	2	1	na	na

		reads	miRBase family seed
seed	-CACCAGG----------------------------------------------	2	novel
		len	cloning frequencies
			T2S2
	GCACCAGGGAAGGAAGATC-----------------------------------	19	2
rat	GCACCAGGGAAGGAAGATCatgggcctgtgtgtagcttggctttcctgcggggc
	******************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000039571 ENSRNOG00000023423 Aim1l_predicted
rat	((.((.(((((((..((...((.((....)).))..))..)))))))...))))	0.510 -14.50

rat

chromosome:5:152829081:152829134:1

Same_strand|Boundary_non-coding|ENSRNOT00000056157|ENSRNOG00000023423 ## Same_strand|Intronic_coding|ENSRNOT00000039571|ENSRNOG00000023423 ## ENSRNOG00000023423|protein_coding|Aim1l_predicted|

block1911792 [novel_lenNOK_shortStem_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	0.436	no	no	0.63/0.63	19/19/0.00	0.0	0.0	1	0	1	0	2	24	5arm	1	nd	0.32	3	1	1	na	na

		reads	miRBase family seed
seed	---GGCCUGC----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	--GGGCCTGCGGAAAGCAGTT-----------------------------------------------------------------------	19	1
rat	ttGGGCCTGCGGAAAGCAGTTgagatccgggtggctaccctgacaagtctgcaggtagaagacggaagtggctagcgcggtcgctggaacgg
	********************************************************************************************
rat	.((..((.((((...(((((((...((((.....(((.((((.((....)))))))))....))))..))))).))....)))).))..)).	0.550 -30.00

rat

chromosome:6:11524958:11525049:-1

intergenic

block1941502 [novel_lenNOK_shortStem_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	0.849	no	no	0.37/0.37	19/19/0.00	0.0	0.0	1	0	1	0	4	8	5arm	2	nd	0.32	3	1	1	na	na

		reads	miRBase family seed
seed	-----AAGUUAC--------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	----TAAGTTACATTTAGCCCTG---------------------------------------------------------	19	1
rat	cactTAAGTTACATTTAGCCCTGccaaccacagcccagtacttagtcagtgttttgcctgttatttgttgttatttagta
	********************************************************************************
rat	.((.(((((.(((..((((...((.((.(((.................))).)).))..))))..)))....))))))).	0.850 -8.53

rat

chromosome:6:69320431:69320510:-1

intergenic

block136324 [novel_lenNOK_shortStem_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	0.094	no	no	0.26/0.26	19/19/0.00	0.0	0.0	1	0	1	0	2	14	5arm	3	nd	0.32	3	1	1	na	na

		reads	miRBase family seed
seed	---UGACUGA----------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	--CTGACTGACTTTTTTTTTT-----------------------------------------------------	19	1
rat	taCTGACTGACTTTTTTTTTTttggtcacaatgctgtatagctcagaatcctggaatacaggagtcgtccgtac
	**************************************************************************
rat	(((.(((.(((((((...(((..((.......(((....))).......))..)))...)))))))))).))).	0.450 -16.64

rat

chromosome:11:78979801:78979874:-1

intergenic ## {Repeats: dust 78979854 78979863 0 class=dust}

novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH (12710 loci)

block35 [novel_lenNOK_shortStem_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	0.246	no	no	0.58/0.58	19/19/0.00	0.0	0.0	1	0	1	0	2	24	5arm	2	nd	0.37	4	1	1	na	na

		reads	miRBase family seed
seed	---CAGUAGC-------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	--TCAGTAGCCAGGCCCTGAA--------------------------------------------------------------------------------------	19	1
rat	caTCAGTAGCCAGGCCCTGAAgcagagaggtgtggggaaatgtggggagggtaattatggtgattcccacaagaaacatggcttctggccagaatactcagtggatg
	***********************************************************************************************************
rat	(((.((((....((((..(((((.......((((((((..(((((.........)))))....)))))))).........))))).))))....))))..)))....	0.530 -29.39

rat

chromosome:10:67529:67635:-1

intergenic

block101 [novel_lenNOK_shortStem_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	0.103	no	no	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	2	4	3arm	3	nd	0.50	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------UCUGUUG------------	1	novel
		len	cloning frequencies
			T1S1
	------------------------------------ATCTGTTGGGCAAAAAGG--	18	1
rat	cgctgttggagagacctgacatttacaatggattgtATCTGTTGGGCAAAAAGGgc
	********************************************************
rat	.(((.((.......((..(((..(((((....)))))..)))..))....)).)))	0.990 -14.30

rat

chromosome:10:197928:197983:-1

intergenic

block698 [novel_lenNOK_shortStem_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	0.295	no	no	0.39/0.39	18/18/0.00	0.0	0.0	1	0	1	0	4	19	5arm	3	nd	0.50	4	1	1	na	na

		reads	miRBase family seed
seed	-----GGUGACA--------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	----GGGTGACATAAAACACAA----------------------------------------------------------	18	1
rat	ttagGGGTGACATAAAACACAAatgatgatctttagaagaggcggctcagaaaggttttctgtaggtgtgacaagctaga
	********************************************************************************
rat	((((..((.((((...(((.....((.(((((((....(((....)))..))))))).)))))..)))).))...)))).	0.980 -15.10

rat

chromosome:10:1235862:1235941:-1

intergenic

block717 [novel_lenNOK_shortStem_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	0.159	no	no	0.33/0.37	18/19/0.00	0.0	0.0	4	0	2	0	2	8	5arm	2	nd	0.33	4	7	2	na	na

		reads	miRBase family seed
seed	---AAAAUGU-----------------------------------------------------------------	7	novel
		len	cloning frequencies
			T1S1	T1S2
	--TAAAATGTGGTTGCTTAC-------------------------------------------------------	18	4	1
	--TAAAATGTGGTTGCTTACC------------------------------------------------------	19	1	1
rat	gtTAAAATGTGGTTGCTTACctgaaatttctttacttttaattttatgataccccctagcacccatattctatgc
	***************************************************************************
rat	..((.(((((((.((((....(((((((...........)))))))...........)))).))))))).))...	0.880 -9.86

rat

chromosome:10:1264444:1264518:-1

intergenic

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