Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_multiarm_DicerNOK_5varHIGH_nonpairedHIGH_bulgeHIGH (8 loci)

sblock7193 [novel_lenNOK_multiarm_DicerNOK_5varHIGH_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	0.097	no	no	0.37/0.52	19/21/0.43	0.0 1.7	0.0 2.3	1 6	0 0	1 2	0 0	3 8	15 18	5arm 3arm	1 1	nd nd	0.33 0.57	4 10	7	2	0	0

		reads	miRBase family seed
seed	--------------------------------------------------------------GUGAGGC------------------------	4	novel
seed	-------------------------------------------------------------------GCCUUAG-------------------	2	novel
seed	----ACAAGCU----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2	T5S1
	------------------------------------------------------------------GGCCTTAGAGAATATTTAG--------	19	1	1
	-------------------------------------------------------------TGTGAGGCCTTAGAGAATATT-----------	21	-	2
	-------------------------------------------------------------TGTGAGGCCTTAGAGAATA-------------	19	-	2
	---CACAAGCTGCAGGGAGTTATG---------------------------------------------------------------------	21	-	1
rat	gctCACAAGCTGCAGGGAGTTATGgggctgggtggggtctgggggccactgtgccagccacTGTGAGGCCTTAGAGAATATTTAGcgaggggc
	*********************************************************************************************
rat	((((....((((.((((..((((((((((((..((((((....)))).))...)))))).))))))..))))..........))))...))))	0.620 -33.30

rat

chromosome:20:5554570:5554662:1

intergenic

sblock736 [novel_lenNOK_multiarm_DicerNOK_5varHIGH_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	0.034	no	no	0.26/0.41	19/22/0.33	0.0 1.5	0.0 1.5	1 2	0 0	1 1	0 0	5 8	0 6	5arm 3arm	1 1	nd nd	0.32 0.58	4 8	3	1	3	-5

		reads	miRBase family seed
seed	---------------------------------------------CUUAAGA-------------------	1	novel
seed	------------------------------------------CCUCUUA----------------------	1	novel
seed	------GACUAAU----------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-----TGACTAATCACTGTGAGGTTGA--------------------------------------------	22	1
	--------------------------------------------TCTTAAGATTCAAAGTAGT--------	19	1
	-----------------------------------------TCCTCTTAAGATTCAAAGT-----------	19	1
rat	tctagTGACTAATCACTGTGAGGTTGAtactatcctcaagtTCCTCTTAAGATTCAAAGTAGTcaccggat
	***********************************************************************
rat	((..(((((((....((..((((((((........))))...))))...))........)))))))..)).	0.410 -17.10

rat

chromosome:1:129006109:129006179:-1

intergenic

sblock754 [novel_lenNOK_multiarm_DicerNOK_5varHIGH_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	0.049	no	no	0.42/0.44	18/21/0.25	2.3 0.0	0.7 0.0	3 1	0 0	1 1	0 0	11 10	2 13	5arm 3arm	2 2	nd nd	0.38 0.37	4 5	4	1	9	10

		reads	miRBase family seed
seed	-----------------------------------------------------GGGAAAG---------------------	1	novel
seed	----------------AGGUCUC----------------------------------------------------------	1	novel
seed	---------------AAGGUCU-----------------------------------------------------------	1	novel
seed	------------GUUAAGG--------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	--------------TAAGGTCTCTGGGTAAGAA------------------------------------------------	19	1
	---------------AAGGTCTCTGGGTAAGAA------------------------------------------------	18	1
	----------------------------------------------------TGGGAAAGACATTAAGAGG----------	19	1
	-----------TGTTAAGGTCTCTGGGTAAGA-------------------------------------------------	21	1
rat	gagaggccaaaTGTTAAGGTCTCTGGGTAAGAAgcatgagcagtgatgcccaTGGGAAAGACATTAAGAGGgagagtctcc
	*********************************************************************************
rat	((((..((.((((((....((((((((((....((....)).....)))))).))))..)))))).....))....)))).	0.440 -21.30

rat

chromosome:1:129015027:129015107:-1

intergenic

sblock8942 [novel_lenNOK_multiarm_DicerNOK_5varHIGH_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	0.872	no	no	0.67/0.74	18/24/0.57	1.4 0.0	3.6 0.0	5 2	0 0	3 1	0 0	9 4	0 3	5arm 3arm	2 2	nd nd	0.45 0.38	4 4	7	4	5	5

		reads	miRBase family seed
seed	------------ACGCUGC------------------------------------------------	3	novel
seed	----------------------------------------UGCUCCU--------------------	2	novel
seed	----------CCACGCU--------------------------------------------------	1	novel
seed	-----------CACGCUG-------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S2	T3S1	T5S2
	---------------------------------------CTGCTCCTACAGTCGCCCCGAGTG----	24	-	-	-	2
	-----------CACGCTGCTCAGAGCCACC-------------------------------------	19	-	1	1	-
	---------CCCACGCTGCTCAGAGCC----------------------------------------	18	1	-	-	-
	-----------CACGCTGCTCAGAGCCACCCGC----------------------------------	22	-	-	1	-
	----------CCACGCTGCTCAGAGCCACCCGC----------------------------------	23	-	-	1	-
rat	tgtctgctcCCCACGCTGCTCAGAGCCACCCGCgccgcgCTGCTCCTACAGTCGCCCCGAGTGgtcg
	*******************************************************************
rat	((.((((((....(((((....((((....(((...)))..))))...))).))....)))))).))	0.490 -16.60

rat

chromosome:4:83509483:83509549:1

intergenic ## {SimpF: -1 Eponine}

novel_lenNOK_multiarm_DicerNOK_Multihit_loopOverlap_randfoldOK (8 loci)

sblock148 [novel_lenNOK_multiarm_DicerNOK_Multihit_loopOverlap_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	0.47/0.48	19/23/0.67	0.0 0.0 0.0	0.0 0.0 0.0	1 1 1	0 0 0	1 1 1	0 0 0	5 19 35	28 18 -1	5arm 5arm 3arm	22 23 23	nd nd nd	0.35 0.26 0.39	5 2 4	3	2	-20	-16

		reads	miRBase family seed
seed	--------------------UUGCUUG-------------------------------------------------------------------------------------------	1	novel
seed	-------------------------------------------------------------CCUAAUU--------------------------------------------------	1	novel
seed	------CCAGGAG---------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S1	T5S1
	-------------------CTTGCTTGATTGAGCACAG--------------------------------------------------------------------------------	19	-	1
	-----CCCAGGAGAGTTTTCTTGCTTGA------------------------------------------------------------------------------------------	23	-	1
	------------------------------------------------------------TCCTAATTTCTTGGTCCACCCTG-----------------------------------	23	1	-
rat	gctgtCCCAGGAGAGTTTTCTTGCTTGATTGAGCACAGgaatactgcttgatttggatatTCCTAATTTCTTGGTCCACCCTGtaaatcatctgagcatgctcctgcttgggacagtc
	**********************************************************************************************************************
rat	(((((((((((.((((.....((((((..(((..(((((...(((....((((.((.....)).))))....)))....)))))...)))..)))))).))))...))))))))))).	0.990 -42.30

rat

chromosome:1:48363114:48363231:-1

intergenic

sblock1644 [novel_lenNOK_multiarm_DicerNOK_Multihit_loopOverlap_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	0.47/0.50	19/23/0.50	0.0 0.0 0.0 0.0	0.0 0.0 0.0 0.0	1 1 1 1	0 0 0 0	1 1 1 1	0 0 0 0	25 31 21 12	10 -2 12 18	5arm 3arm_loop 3arm 3arm	25 25 25 25	nd nd nd nd	0.37 0.30 0.37 0.41	4 2 4 4	4	1	0	12

		reads	miRBase family seed
seed	--------------------------CUCAUUU----------------------------------------------------------------------------	1	novel
seed	----------------------------------------------------------------------UUGCUUG--------------------------------	1	novel
seed	--------------------------------------------------------CCAGGAG----------------------------------------------	1	novel
seed	----------------------------------------------------------------------------GAUUGAG--------------------------	1	novel
		len	cloning frequencies
			T5S1
	---------------------------------------------------------------------CTTGCTTGATTGAGCACAG---------------------	19	1
	---------------------------------------------------------------------------TGATTGAGCACAGGAACACTGC------------	22	1
	-------------------------CCTCATTTCTCAGGAGAGA-----------------------------------------------------------------	19	1
	-------------------------------------------------------CCCAGGAGAGTTTTCTTGCTTGA-------------------------------	23	1
rat	ttattttttggatgctgtctccagcCCTCATTTCTCAGGAGAGAtactgtcctgtCCCAGGAGAGTTTTCTTGCTTGATTGAGCACAGGAACACTGCttcctttggata
	*************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------	ENSRNOT00000059909 ENSRNOG00000030267 RGD1561185_predicted
rat	.(((((...(((.((.((.(((....((((....(((((..(((.(((.(((((...))))).)))..)))..))))).))))....)))..)).)).)))...)))))	0.960 -32.90

rat

chromosome:1:52652649:52652757:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000048991|ENSRNOG00000030267 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000059909|ENSRNOG00000030267 ## ENSRNOG00000030267|protein_coding|RGD1561185_predicted|

sblock203 [novel_lenNOK_multiarm_DicerNOK_Multihit_loopOverlap_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	0.47/0.48	19/23/0.50	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	0 5	10 -2	5arm 3arm_loop	25 25	nd nd	0.37 0.30	4 2	2	1	0	12

		reads	miRBase family seed
seed	-CUCAUUU--------------------------------------------------	1	novel
seed	-------------------------------CCAGGAG--------------------	1	novel
		len	cloning frequencies
			T5S1
	CCTCATTTCTCAGGAGAGA---------------------------------------	19	1
	------------------------------CCCAGGAGAGTTTTCTTGCTTGA-----	23	1
rat	CCTCATTTCTCAGGAGAGAtactgtcctgtCCCAGGAGAGTTTTCTTGCTTGAttgag
	**********************************************************
	--------------------------------------------------------------------	ENSRNOT00000049502 ENSRNOG00000031954 LOC678916
rat	.((((....(((((..(((.(((.(((((...))))).)))..)))..))))).))))	1.000 -21.10

rat

chromosome:1:49548348:49548405:-1

Opposite_strand|Intronic_non-coding|ENSRNOT00000049502|ENSRNOG00000031954 ## ENSRNOG00000031954|protein_coding|LOC678916|

sblock209 [novel_lenNOK_multiarm_DicerNOK_Multihit_loopOverlap_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	0.47/0.50	19/23/0.50	0.0 0.0 0.0 0.0	0.0 0.0 0.0 0.0	1 1 1 1	0 0 0 0	1 1 1 1	0 0 0 0	25 31 21 12	10 -2 12 18	5arm 3arm_loop 3arm 3arm	25 25 25 25	nd nd nd nd	0.37 0.30 0.37 0.36	4 2 3 3	4	1	0	12

		reads	miRBase family seed
seed	--------------------------CUCAUUU----------------------------------------------------------------------------	1	novel
seed	----------------------------------------------------------------------UUGCUUG--------------------------------	1	novel
seed	--------------------------------------------------------CCAGGAG----------------------------------------------	1	novel
seed	----------------------------------------------------------------------------GAUUGAG--------------------------	1	novel
		len	cloning frequencies
			T5S1
	---------------------------------------------------------------------CTTGCTTGATTGAGCACAG---------------------	19	1
	---------------------------------------------------------------------------TGATTGAGCACAGGAACACTGC------------	22	1
	-------------------------CCTCATTTCTCAGGAGAGA-----------------------------------------------------------------	19	1
	-------------------------------------------------------CCCAGGAGAGTTTTCTTGCTTGA-------------------------------	23	1
rat	ttattctttggatgctgtctctagcCCTCATTTCTCAGGAGAGAtactgtcctgtCCCAGGAGAGTTTTCTTGCTTGATTGAGCACAGGAACACTGCttcatttggata
	*************************************************************************************************************
rat	.(((((..((((.(((((..((....((((....(((((..(((.(((.(((((...))))).)))..)))..))))).))))...))..)))..))))))...)))))	0.880 -31.50

rat

chromosome:1:49859332:49859440:-1

intergenic

sblock371 [novel_lenNOK_multiarm_DicerNOK_Multihit_loopOverlap_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	0.37/0.58	18/20/0.17	0.0 0.0 0.0 0.0	0.3 0.0 0.0 0.0	3 1 1 1	0 0 0 0	2 1 1 1	0 0 0 0	11 21 7 0	-6 -14 1 9	5arm_loop 5arm_loop_3arm 3arm 3arm	38 38 38 38	nd nd nd nd	0.53 0.67 0.16 0.18	6 12 3 3	6	2	0	7

		reads	miRBase family seed
seed	------------GGUGUGU---------------------------------------------	3	novel
seed	-----------------------------------------------UCGGGAG----------	1	novel
seed	----------------------UAUGCUU-----------------------------------	1	novel
seed	---------------------------------------GCGUGUU------------------	1	novel
		len	cloning frequencies
			T3S1	T5S1
	-----------TGGTGTGTATGTATGCTTT----------------------------------	19	1	1
	---------------------GTATGCTTTGTTCACTGT-------------------------	18	-	1
	----------------------------------------------GTCGGGAGTGTCCTGAAA	18	-	1
	--------------------------------------TGCGTGTTGTCGGGAGTGT-------	19	-	1
	-----------TGGTGTGTATGTATGCTTTG---------------------------------	20	-	1
rat	caggacacttcTGGTGTGTATGTATGCTTTGTTCACTGTGCGTGTTGTCGGGAGTGTCCTGAAA
	****************************************************************
rat	((((((((((((((....(((((((............)))))))...))))))))))))))...	0.980 -26.00

rat

chromosome:1:50787246:50787309:-1

intergenic

sblock471 [novel_lenNOK_multiarm_DicerNOK_Multihit_loopOverlap_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	0.37/0.58	18/20/0.17	0.0 0.0 0.0 0.0	0.3 0.0 0.0 0.0	3 1 1 1	0 0 0 0	2 1 1 1	0 0 0 0	33 43 28 21	-6 -14 1 9	5arm_loop 5arm_loop_3arm 3arm 3arm	38 38 38 38	nd nd nd nd	0.53 0.67 0.16 0.22	6 12 3 4	6	2	0	7

		reads	miRBase family seed
seed	----------------------------------GGUGUGU------------------------------------------------------------------	3	novel
seed	-------------------------------------------------------------GCGUGUU---------------------------------------	1	novel
seed	---------------------------------------------------------------------UCGGGAG-------------------------------	1	novel
seed	--------------------------------------------UAUGCUU--------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T5S1
	---------------------------------TGGTGTGTATGTATGCTTT-------------------------------------------------------	19	1	1
	-------------------------------------------GTATGCTTTGTTCACTGT----------------------------------------------	18	-	1
	--------------------------------------------------------------------GTCGGGAGTGTCCTGAAA---------------------	18	-	1
	---------------------------------TGGTGTGTATGTATGCTTTG------------------------------------------------------	20	-	1
	------------------------------------------------------------TGCGTGTTGTCGGGAGTGT----------------------------	19	-	1
rat	ggctgatggttgagtgaagacacaggacacttcTGGTGTGTATGTATGCTTTGTTCACTGTGCGTGTTGTCGGGAGTGTCCTGAAAagnnnngcatgcccaatggct
	***********************************************************************************************************
	---------------------------------------------------------------------------------------------------------------------	ENSRNOT00000041486 ENSRNOG00000033456 LOC308198
rat	(((((.(((.((..........((((((((((((((....(((((((............)))))))...))))))))))))))..........))...))).)))))	0.670 -32.65

rat

chromosome:1:52395611:52395717:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000044415|ENSRNOG00000033456 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000041486|ENSRNOG00000033456 ## ENSRNOG00000033456|protein_coding|LOC308198|

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