Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_multiarm_DicerNOK_Multihit_bulgeHIGH (32 loci)

sblock11965 [novel_lenNOK_multiarm_DicerNOK_Multihit_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	0.069	no	no	0.30/0.50	18/23/0.33	0.0 0.0 0.0	0.0 0.0 0.0	1 1 1	0 0 0	1 1 1	0 0 0	0 13 19	47 35 6	5arm 5arm 3arm	1 12 12	nd nd nd	0.47 0.50 0.30	7 6 4	3	2	0	-11

		reads	miRBase family seed
seed	-GAGACCC---------------------------------------------------------------------------------------------------------------	1	novel
seed	------------------------------------------------------------------------------AAAGCUU----------------------------------	1	novel
seed	--------------UUUUUGG--------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T4S2
	-----------------------------------------------------------------------------AAAAGCTTATAGAATTTCCAGTG-------------------	23	-	1
	TGAGACCCTTGGGTTTTTT----------------------------------------------------------------------------------------------------	19	1	-
	-------------TTTTTTGGGGGTGGTGGT----------------------------------------------------------------------------------------	18	1	-
rat	TGAGACCCTTGGGTTTTTTGGGGGTGGTGGTggtggtctatttatttttacagctgcgttttttgtgactaatgggaAAAAGCTTATAGAATTTCCAGTGccccaattccggtgtttca
	***********************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000012565 ENSRNOG00000008941 Ets1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000011925 ENSRNOG00000008941 Ets1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000012000 ENSRNOG00000008941 Ets1
rat	.(((((((..(((.......((((((.(((......(((((..........((((...((((..((.....))..)))).)))).)))))....))).))))))...))))).))))).	0.850 -33.30

rat

chromosome:8:32482159:32482277:1

Same_strand|Intronic_coding|ENSRNOT00000011925|ENSRNOG00000008941 ## ENSRNOG00000008941|protein_coding|Ets1|Protein C-ets-1 (p54). [Source:UniProtKB/Swiss-Prot;Acc:P41156]

novel_lenNOK_5varHIGH_randfoldOK (31 loci)

block71572 [novel_lenNOK_5varHIGH_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	0.40/0.47	19/20/0.50	1.5	1.0	2	0	1	0	22	1	3arm	1	nd	0.16	2	2	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------AGGCUGU------------------------------------	1	novel
seed	----------------------------------------------------CUGUGUA---------------------------------	1	novel
		len	cloning frequencies
			T2S1
	---------------------------------------------------GCTGTGTAGGAATGTTAGC----------------------	19	1
	------------------------------------------------AAGGCTGTGTAGGAATGTTA------------------------	20	1
rat	aagtccaaattccttggttaggctagcgatcctaccaagtgatcctagAAGGCTGTGTAGGAATGTTAGCccggcttcagggcttggtgctt
	********************************************************************************************
rat	((((((((..((((.(((..((((((((.((((((..(((..((...))..)))..)))))).))))))))..)))..)))).)))).))))	1.000 -35.90

rat

chromosome:10:40878469:40878560:1

intergenic

block79113 [novel_lenNOK_5varHIGH_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	0.001	no	no	0.50/0.57	18/23/0.60	1.2	3.6	5	0	3	0	23	3	3arm	2	nd	0.22	3	5	3	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------ACAAGCA----------------------------------------	3	novel
seed	----------------------------------------------------------------------AAGCACU--------------------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T5S2
	---------------------------------------------------------------------CAAGCACTTCCAACTGCAGAGCC-----------------------	23	-	-	2
	-------------------------------------------------------------------CACAAGCACTTCCAACTG------------------------------	18	1	1	-
	-------------------------------------------------------------------CACAAGCACTTCCAACTGCAG---------------------------	21	-	1	-
rat	gagttggagatgatggtgagcgtgagctggagttggaggtgatcgtgagcgtgaagactgtggttgcCACAAGCACTTCCAACTGCAGAGCCacgctctgctgtggctcccactt
	*******************************************************************************************************************
rat	((((.((((...((((((((((((..(((.(((((((((((...(((.(((.............))))))...))))))))))).)))...))))))).)))))..)))).))))	0.790 -53.82

rat

chromosome:10:57458820:57458934:1

intergenic

block117078 [novel_lenNOK_5varHIGH_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	0.010	no	no	0.67/0.70	18/20/0.20	1.6	0.6	5	0	4	0	22	2	5arm	1	nd	0.05	1	5	4	na	na

		reads	miRBase family seed
seed	-------------------------UGUAAGG-------------------------------------------------------------------------------------	4	novel
seed	-----------------------CCUGUAA---------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T2S1	T3S1	T4S1
	------------------------CTGTAAGGGGCTGGGGGAG--------------------------------------------------------------------------	19	1	1	1	-
	----------------------GCCTGTAAGGGGCTGGGGGA---------------------------------------------------------------------------	20	-	-	-	1
	------------------------CTGTAAGGGGCTGGGGGA---------------------------------------------------------------------------	18	-	1	-	-
rat	ggggcatgggtgagccttgtgtGCCTGTAAGGGGCTGGGGGAGagatacttctcactctcccagggcttcacagctcctttaattacaagcaaacattttgttttgccatctgttcc
	*********************************************************************************************************************
	-------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000046486 ENSRNOG00000021569 Tiam1
	-------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000002889 ENSRNOG00000021569 Tiam1
rat	((..((..((..((...(((.(((.((((((((((((.(((((((..........))))))).........)))))))).....)))).))).)))......))..))...))..))	0.470 -42.30

rat

chromosome:11:30181658:30181774:-1

Opposite_strand|Intronic_coding|ENSRNOT00000002889|ENSRNOG00000021569 ## ENSRNOG00000021569|protein_coding|Tiam1|T-cell lymphoma invasion and metastasis 1 Gene [Source:MGI (curated);Acc:Tiam1-001]

block475216 [novel_lenNOK_5varHIGH_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	0.001	no	no	0.53/0.62	19/21/0.50	1.5	2.5	2	0	2	0	23	15	3arm	1	nd	0.14	1	2	2	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------CCCUGUU------------------------------------	1	novel
seed	------------------------------------------------------------------------UUUCCCU---------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T3S2
	--------------------------------------------------------------------------TCCCTGTTTCTACCCCCAGCC-----------------------	21	1	-
	-----------------------------------------------------------------------GTTTCCCTGTTTCTACCCC----------------------------	19	-	1
rat	ggagagtattcagggtagagctgagggggaggacaggcaggaaggatgtccctaggagaggacagttacctGTTTCCCTGTTTCTACCCCCAGCCtgccgagctgagtgacattttca
	**********************************************************************************************************************
rat	(((((.((((((((((((.((((.((((.((((((((((((.....(((((((...)).)))))....))))....)))))).)).)))))))))))))...)))))))...))))).	1.000 -52.80

rat

chromosome:15:9805603:9805720:1

intergenic

block648531 [novel_lenNOK_5varHIGH_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	0.001	no	no	0.50/0.58	19/22/0.50	2.5	1.0	2	0	2	0	5	16	5arm	2	nd	0.26	2	2	2	na	na

		reads	miRBase family seed
seed	-----------CCCACUG-------------------------------------------------------------------------------	1	novel
seed	------UCAUUCC------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2	T5S1
	-----TTCATTCCCACTGGTGGTCAGA----------------------------------------------------------------------	22	1	-
	----------TCCCACTGGTGGTCAGAGA--------------------------------------------------------------------	19	-	1
rat	gcatgTTCATTCCCACTGGTGGTCAGAGAataaagagagacaagcacaaagcctgtctccttcctttgtgacctctcctggggagagacaccaagca
	*************************************************************************************************
rat	((.((((..((((((..((.(((((.(((...(((.((((((.((.....)).)))))))))..))).))))).))..))))))..))))....)).	1.000 -37.80

rat

chromosome:17:20763470:20763566:1

intergenic

block648785 [novel_lenNOK_5varHIGH_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	0.001	no	no	0.50/0.58	19/22/0.67	3.0	1.7	3	0	3	0	19	15	5arm	2	nd	0.23	2	3	3	na	na

		reads	miRBase family seed
seed	------------------------UCCCACU-----------------------------------------------------------------------------------------	1	novel
seed	-------------------------CCCACUG----------------------------------------------------------------------------------------	1	novel
seed	--------------------UCAUUCC---------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S1	T4S2	T5S1
	-------------------TTCATTCCCACTGGTGGTCAGA-------------------------------------------------------------------------------	22	-	1	-
	-----------------------TTCCCACTGGTGGTCAGAGAC----------------------------------------------------------------------------	21	1	-	-
	------------------------TCCCACTGGTGGTCAGAGA-----------------------------------------------------------------------------	19	-	-	1
rat	gcagccagagaagagcatgTTCATTCCCACTGGTGGTCAGAGACtaaagagagacaagcacaaagcccgtctccttcctttgtaacctcccctgggaagagacaccaagcagcctggctg
	************************************************************************************************************************
rat	.(((((((.........((((..((((((..((.((((((((....(((.(((((..((.....))..)))))))).)))))..))).))..))))))..)))).........)))))))	0.990 -43.47

rat

chromosome:17:20796007:20796126:1

intergenic

block798883 [novel_lenNOK_5varHIGH_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	0.44/0.47	18/19/0.00	1.5	1.2	4	0	3	0	11	7	5arm	1	43	0.21	2	4	3	na	na

		reads	miRBase family seed
seed	--------------GUGGGUA--------------------------------------------------------------------	3	novel
seed	------------CUGUGGG----------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1
	-------------TGTGGGTAGAATGACAGAG---------------------------------------------------------	19	-	1	1
	-------------TGTGGGTAGAATGACAGA----------------------------------------------------------	18	1	-	-
	-----------ACTGTGGGTAGAATGACAG-----------------------------------------------------------	19	1	-	-
rat	cttcggaattcACTGTGGGTAGAATGACAGAGcagacaggagactagagagtctgctttgccatctctcttgcaggcatgtgcctgggt
	*****************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>	ENSRNOT00000000828 ENSRNOG00000000663 Tfip11
rat	((..((......(((..((.((((((.((((((((((((....)).....)))))))))).))).)))))..))).......))..)).	0.960 -33.52

rat

chromosome:19:14316666:14316754:1

Same_strand|Intronic_coding|ENSRNOT00000000828|ENSRNOG00000000663 ## ENSRNOG00000000663|protein_coding|Tfip11|tuftelin interacting protein 11 [Source:RefSeq_peptide;Acc:NP_001008292]

block843938 [novel_lenNOK_5varHIGH_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	0.007	no	no	0.50/0.57	18/23/0.67	1.3	2.3	6	0	2	0	10	18	3arm	3	nd	0.30	3	6	2	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------GACAACC-------------------------	4	novel
seed	----------------------------------------------------------------------------UCUGACA----------------------------	1	novel
seed	--------------------------------------------------------------------------CUUCUGA------------------------------	1	novel
		len	cloning frequencies
			T4S2	T5S1
	------------------------------------------------------------------------------TGACAACCCACAGTGAGCAGGGT----------	23	-	2
	------------------------------------------------------------------------------TGACAACCCACAGTGAGC---------------	18	-	2
	-------------------------------------------------------------------------TCTTCTGACAACCCACAGTG------------------	20	1	-
	---------------------------------------------------------------------------TTCTGACAACCCACAGTGAG----------------	20	-	1
rat	caggggtacatcatcacctctgtgactgtcagcccatagtttggatttactttcagtaataggctaagctgtcTCTTCTGACAACCCACAGTGAGCAGGGTacacacctgc
	***************************************************************************************************************
rat	((((.((((....((((...((((..((((((...(((((((((..((((.....))))....))))))))).....))))))...)))))))).....))))...)))).	0.860 -35.20

rat

chromosome:1:50003063:50003173:-1

intergenic

block845241 [novel_lenNOK_5varHIGH_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	0.007	no	no	0.50/0.57	18/23/0.67	1.3	2.3	6	0	2	0	10	18	3arm	3	nd	0.30	3	6	2	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------GACAACC-------------------------	4	novel
seed	----------------------------------------------------------------------------UCUGACA----------------------------	1	novel
seed	--------------------------------------------------------------------------CUUCUGA------------------------------	1	novel
		len	cloning frequencies
			T4S2	T5S1
	------------------------------------------------------------------------------TGACAACCCACAGTGAGCAGGGT----------	23	-	2
	------------------------------------------------------------------------------TGACAACCCACAGTGAGC---------------	18	-	2
	-------------------------------------------------------------------------TCTTCTGACAACCCACAGTG------------------	20	1	-
	---------------------------------------------------------------------------TTCTGACAACCCACAGTGAG----------------	20	-	1
rat	caggggtacatcatcacctctgtgactgtcagcccatagtttggatttactttcagtaataggctaagctgtcTCTTCTGACAACCCACAGTGAGCAGGGTacacacctgc
	***************************************************************************************************************
rat	((((.((((....((((...((((..((((((...(((((((((..((((.....))))....))))))))).....))))))...)))))))).....))))...)))).	0.860 -35.20

rat

chromosome:1:50588044:50588154:-1

intergenic

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