Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_multiarm_DicerNOK_Multihit_randfoldOK_nonpairedHIGH_bulgeHIGH (14 loci)

sblock246 [novel_multiarm_DicerNOK_Multihit_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	0.004	no	no	0.43/0.45	20/22/1.00	0.0 0.0 0.0	0.0 0.0 0.0	1 1 1	0 0 0	1 1 1	0 0 0	23 31 25	12 3 1	5arm 5arm 3arm	18 18 25	nd nd nd	0.45 0.33 0.36	6 4 6	3	1	-2	-2

		reads	miRBase family seed
seed	------------------------GCAAAGC---------------------------------------------------------------------------	1	novel
seed	--------------------------------GACAACA-------------------------------------------------------------------	1	novel
seed	------------------------------------------------------------CCUCUAG---------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------------AGACAACAGAGATTGGATGAG------------------------------------------------------	21	1
	-----------------------TGCAAAGCAGACAACAGAGA---------------------------------------------------------------	20	1
	-----------------------------------------------------------TCCTCTAGGAAAGTCTCAGTGT-------------------------	22	1
rat	tgagctaacaaaaaactacaaccTGCAAAGCAGACAACAGAGATTGGATGAGgataaaaTCCTCTAGGAAAGTCTCAGTGTctcacaggatgttcctgttctctca
	**********************************************************************************************************
	--------------------------------------------------------------------------------------------------------------------	ENSRNOT00000049496 ENSRNOG00000031160 LOC685793
	--------------------------------------------------------------------------------------------------------------------	ENSRNOT00000042408 ENSRNOG00000031160 LOC685793
	--------------------------------------------------------------------------------------------------------------------	ENSRNOT00000050327 ENSRNOG00000031160 LOC685793
	--------------------------------------------------------------------------------------------------------------------	ENSRNOT00000040838 ENSRNOG00000031160 LOC685793
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000059958 ENSRNOG00000030545 LOC685793
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000049483 ENSRNOG00000030545 LOC685793
rat	.(((..((((.......(((.((((......(((((...((((((....((((((...))))))......))))))..)))))..)))).)))...))))..))).	0.890 -28.80

rat

chromosome:1:50127730:50127835:-1

Same_strand|Intronic_non-coding|ENSRNOT00000049483|ENSRNOG00000030545 ## Same_strand|Intronic_coding|ENSRNOT00000059958|ENSRNOG00000030545 ## Same_strand|Boundary_non-coding|ENSRNOT00000039913|ENSRNOG00000030545 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000041575|ENSRNOG00000031160 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000042408|ENSRNOG00000031160 ## ENSRNOG00000030545|protein_coding|LOC685793| ## ENSRNOG00000031160|protein_coding|LOC685793|

sblock305 [novel_multiarm_DicerNOK_Multihit_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	0.43/0.45	20/22/1.00	0.0 0.0 0.0	0.0 0.0 0.0	1 1 1	0 0 0	1 1 1	0 0 0	2 10 8	12 3 1	5arm 5arm 3arm	18 18 25	nd nd nd	0.45 0.33 0.36	6 4 6	3	1	-2	-2

		reads	miRBase family seed
seed	-----------GACAACA--------------------------------------------------	1	novel
seed	---------------------------------------CCUCUAG----------------------	1	novel
seed	---GCAAAGC----------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	--TGCAAAGCAGACAACAGAGA----------------------------------------------	20	1
	--------------------------------------TCCTCTAGGAAAGTCTCAGTGT--------	22	1
	----------AGACAACAGAGATTGGATGAG-------------------------------------	21	1
rat	ccTGCAAAGCAGACAACAGAGATTGGATGAGgataaaaTCCTCTAGGAAAGTCTCAGTGTctcacagg
	********************************************************************
rat	((((......(((((...((((((....((((((...))))))......))))))..)))))..))))	0.980 -21.00

rat

chromosome:1:50345007:50345074:-1

intergenic

sblock454 [novel_multiarm_DicerNOK_Multihit_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	0.43/0.45	20/22/1.00	0.0 0.0 0.0	0.0 0.0 0.0	1 1 1	0 0 0	1 1 1	0 0 0	2 10 8	12 3 1	5arm 5arm 3arm	18 18 25	nd nd nd	0.45 0.33 0.36	6 4 6	3	1	-2	-2

		reads	miRBase family seed
seed	-----------GACAACA--------------------------------------------------	1	novel
seed	---------------------------------------CCUCUAG----------------------	1	novel
seed	---GCAAAGC----------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	--TGCAAAGCAGACAACAGAGA----------------------------------------------	20	1
	--------------------------------------TCCTCTAGGAAAGTCTCAGTGT--------	22	1
	----------AGACAACAGAGATTGGATGAG-------------------------------------	21	1
rat	ccTGCAAAGCAGACAACAGAGATTGGATGAGgataaaaTCCTCTAGGAAAGTCTCAGTGTctcacagg
	********************************************************************
rat	((((......(((((...((((((....((((((...))))))......))))))..)))))..))))	0.980 -21.00

rat

chromosome:1:52375244:52375311:-1

intergenic

novel_Multihit_loopOverlap_bulgeHIGH (13 loci)

block473176 [novel_Multihit_loopOverlap_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	0.168	no	no	0.48/0.48	23/23/1.00	0.0	0.0	1	0	1	0	27	-1	3arm	17	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------AGCCUCA------------------------------------------	1	novel
		len	cloning frequencies
			T4S1
	----------------------------------------------------------------------CAGCCTCAGTAACAGGACTTTGA---------------------------	23	1
rat	gcctctatctagcttccatgtgttctgcttttggttagattcatatgtgcaagcttaatgagggctcggaCAGCCTCAGTAACAGGACTTTGAtctggccagtggctggagcagaaggcc
	************************************************************************************************************************
rat	((((...(((.((.((((........(((.(((((((((.(((...((......(((.(((.((((.....))))))).)))....))..)))))))))))).)))))))))))))))).	0.430 -34.90

rat

chromosome:15:5387301:5387420:1

intergenic

block843621 [novel_Multihit_loopOverlap_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	0.241	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	5	-3	5arm_loop	15	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	------AGCAGGU--------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-----TAGCAGGTGTGCTTCCTGAC--------------------------	20	1
rat	gttttTAGCAGGTGTGCTTCCTGACcagagaagacagatgactgcatgagc
	***************************************************
rat	((((...((((((.((((((((....)).)))).)).))..))))..))))	1.000 -12.50

rat

chromosome:1:49877127:49877177:-1

intergenic

block846661 [novel_Multihit_loopOverlap_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	0.020	no	no	0.42/0.52	19/25/0.71	0.5 0.0	1.0 0.0	4 3	0 0	1 1	0 0	9 22	7 -2	5arm 5arm_loop	25 25	nd nd	0.28 0.43	4 4	7	1	na	na

		reads	miRBase family seed
seed	-----------------------AGAACUG-------------------------------------------------------	3	novel
seed	----------CUCCAAA--------------------------------------------------------------------	3	novel
seed	------------CCAAAGU------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------AAGAACTGCACCGTATGAGAG------------------------------------------	21	3
	---------CCTCCAAAGTTGGAAGAACTG-------------------------------------------------------	21	2
	---------CCTCCAAAGTTGGAAGAACTGCACC---------------------------------------------------	25	1
	-----------TCCAAAGTTGGAAGAACTG-------------------------------------------------------	19	1
rat	gttgcatgaCCTCCAAAGTTGGAAGAACTGCACCGTATGAGAGcctcaactgttgcaggacctccaatgttgtaggaacacaata
	*************************************************************************************
rat	((((.....(((.(((.((((((....((((((.((.((((...)))))).)).))))....)))))).))).)))....)))).	1.000 -23.40

rat

chromosome:1:51402543:51402627:-1

intergenic

block961893 [novel_Multihit_loopOverlap_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	0.243	no	no	0.45/0.50	20/24/1.00	0.7 0.5	0.7 1.5	3 2	0 0	1 2	0 0	9 0	-7 2	3arm_loop 3arm	16 16	nd nd	0.30 0.26	4 4	5	2	na	na

		reads	miRBase family seed
seed	-------------------------------------CCCUAAA-------------------------	2	novel
seed	-----------------------------------------------CCACUGU---------------	1	novel
seed	----------------------------------------------UCCACUG----------------	1	novel
seed	---------------------------------------CUAAACU-----------------------	1	novel
		len	cloning frequencies
			T4S1	T5S1
	------------------------------------TCCCTAAACTTCCACTGTTGGAGT---------	24	-	2
	--------------------------------------CCTAAACTTCCACTGTTGGA-----------	20	-	1
	----------------------------------------------TCCACTGTTGGAGTACCTCA---	20	-	1
	---------------------------------------------TTCCACTGTTGGAGTACCTCAACT	24	1	-
rat	aagttgcaagacctttacgggcactggaagtcactgTCCCTAAACTTCCACTGTTGGAGTACCTCAACT
	*********************************************************************
rat	.(((((....((((..((((....(((((((............))))))))))).)).))....)))))	0.510 -14.40

rat

chromosome:1:51065424:51065492:1

intergenic

block962341 [novel_Multihit_loopOverlap_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	0.087	no	no	0.43/0.45	20/22/1.00	0.3	0.3	3	0	2	0	40	-4	5arm_loop	36	nd	0.30	4	3	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------GGGAAGG----------------------------------------------------------------------	2	novel
seed	------------------------------------------GGAAGGA---------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	-----------------------------------------GGGAAGGACAAAGTACAAAG---------------------------------------------------------	20	1	-
	----------------------------------------TGGGAAGGACAAAGTACAAAG---------------------------------------------------------	21	-	1
	----------------------------------------TGGGAAGGACAAAGTACAAAGG--------------------------------------------------------	22	-	1
rat	tggaaaacagagccagaggaagaatgagcacagagcaaacTGGGAAGGACAAAGTACAAAGGcacgtgtgttttgccatctgcgtgttctctggacaatctcccttggcctcatttct
	**********************************************************************************************************************
rat	.(((((..((.((((..((.(((.((....(((((...((..(((.((.(((((((((........))))))))))).)))..))...)))))..)).)))))..))))))..)))))	1.000 -34.20

rat

chromosome:1:51421435:51421552:1

intergenic

block962690 [novel_Multihit_loopOverlap_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	0.087	no	no	0.43/0.45	20/22/1.00	0.3	0.3	3	0	2	0	40	-4	5arm_loop	36	nd	0.30	4	3	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------GGGAAGG----------------------------------------------------------------------	2	novel
seed	------------------------------------------GGAAGGA---------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	-----------------------------------------GGGAAGGACAAAGTACAAAG---------------------------------------------------------	20	1	-
	----------------------------------------TGGGAAGGACAAAGTACAAAG---------------------------------------------------------	21	-	1
	----------------------------------------TGGGAAGGACAAAGTACAAAGG--------------------------------------------------------	22	-	1
rat	tggaaaacagagccagaggaagaatgagcacagagcaaacTGGGAAGGACAAAGTACAAAGGcacgtgtgttttgccatctgcgtgttctctggacaatctcccttggcctcatttct
	**********************************************************************************************************************
	--------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000059938 ENSRNOG00000039174 RGD1563865_predicted
rat	.(((((..((.((((..((.(((.((....(((((...((..(((.((.(((((((((........))))))))))).)))..))...)))))..)).)))))..))))))..)))))	1.000 -34.20

rat

chromosome:1:51536163:51536280:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000059936|ENSRNOG00000039174 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000059938|ENSRNOG00000039174 ## ENSRNOG00000039174|protein_coding|RGD1563865_predicted|

block1326780 [novel_Multihit_loopOverlap_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	0.699	no	no	0.67/0.67	21/21/1.00	0.0	0.0	1	0	1	0	16	-1	5arm_loop	11	nd	0.29	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------CUUUCCG-------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	----------------CCTTTCCGCTCGGCCGTTCTC------------------------------------------------	21	1
rat	ctttgcggtgcccggtCCTTTCCGCTCGGCCGTTCTCccatacccagccggaatggcatgatcctgaagccccacttccaaaagg
	*************************************************************************************
rat	((((..((.....((..((((....(((((((((((.............)))))))).)))....))))..))....)).)))).	0.650 -19.12

rat

chromosome:2:212252968:212253052:1

intergenic

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