Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_Multihit_loopOverlap_nonpairedHIGH (327 loci)

block2123158 [novel_lenNOK_Multihit_loopOverlap_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	0.848	no	no	0.74/0.74	19/19/0.00	0.0	0.0	1	0	1	0	20	-4	3arm_loop	25	nd	0.37	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------AGAGCCG-------------------------------	1	novel
		len	cloning frequencies
			T1S1
	------------------------------------------GAGAGCCGGACGGGCACTG--------------------	19	1
rat	ttgcagtacattgagctccatagagacagcaccggggcgagcGAGAGCCGGACGGGCACTGggcgactctgtacctcgcag
	*********************************************************************************
	.................................................................................>>>>>>>>>>	ENSRNOT00000044144 ENSRNOG00000034186
rat	.(((.(((((....((.(((........((.(((...((.((....))))..)))))..))))).....)))))...))).	0.530 -22.00

rat

chromosome:7:67915123:67915203:-1

intergenic

block2558102 [novel_lenNOK_Multihit_loopOverlap_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	0.594	no	no	0.53/0.53	19/19/0.00	0.0	0.0	2	0	2	0	21	-2	3arm_loop	14	nd	0.42	3	2	2	na	na

		reads	miRBase family seed
seed	---------------------------------------GGCAAGC--------------------------------	2	novel
		len	cloning frequencies
			T3S2	T5S1
	--------------------------------------AGGCAAGCTCCAAAGTTGC---------------------	19	1	1
rat	gctctctgtcctgccgttgaattctctgaggcatgttcAGGCAAGCTCCAAAGTTGCgacatggtgagcactggggcg
	******************************************************************************
rat	(((((..((.(((((((((....((.((..((.(((....))).))..)).))...))))..))).)).)).))))).	0.790 -22.10

rat

chromosome:9:112719015:112719092:-1

intergenic

block2593556 [novel_lenNOK_Multihit_loopOverlap_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	0.099	no	no	0.74/0.74	19/19/0.00	0.0	0.0	1	0	1	0	17	-4	3arm_loop	25	nd	0.42	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------AGAGCCG----------------------------	1	novel
		len	cloning frequencies
			T1S1
	------------------------------GAGAGCCGGACGGGCACTG-----------------	19	1
rat	gagctccacagagacagcgccctggcaagcGAGAGCCGGACGGGCACTGggcgactctgtgcctcg
	******************************************************************
rat	(((...(((((((.(((.((((((((........))))...)))).))).....))))))).))).	1.000 -28.50

rat

chromosome:9:43337002:43337067:1

intergenic

block2652060 [novel_lenNOK_Multihit_loopOverlap_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	0.205	no	no	0.53/0.53	19/19/0.00	0.0	0.0	2	0	2	0	21	-2	3arm_loop	14	nd	0.42	3	2	2	na	na

		reads	miRBase family seed
seed	---------------------------------------GGCAAGC--------------------------------	2	novel
		len	cloning frequencies
			T3S2	T5S1
	--------------------------------------AGGCAAGCTCCAAAGTTGC---------------------	19	1	1
rat	gctctctgtcctgccgttgaattctctgaggcatgttcAGGCAAGCTCCAAAGTTGCgacatggtgagcacaggggcg
	******************************************************************************
rat	((.((((((.(((((((((....((.((..((.(((....))).))..)).))...))))..))).)).)))))))).	0.980 -25.80

rat

chromosome:9:112887868:112887945:1

intergenic

block2652898 [novel_lenNOK_Multihit_loopOverlap_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	0.114	no	no	0.53/0.53	19/19/0.00	0.0	0.0	2	0	2	0	37	-2	3arm_loop	14	nd	0.42	3	2	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------GGCAAGC------------------------------------------------	2	novel
		len	cloning frequencies
			T3S2	T5S1
	----------------------------------------------------AGGCAAGCTCCAAAGTTGC-------------------------------------	19	1	1
rat	gtcctggctgctgtgctctgagtcctgcggttggattctgtgaggcatgctcAGGCAAGCTCCAAAGTTGCgacatggtgagcacagggtcacggcacacaaagggca
	************************************************************************************************************
rat	(((((...((((((((((((.((((....((((....((.((..((.(((....))).))..)).))...))))..))...)).))))).))))))).....))))).	0.450 -39.70

rat

chromosome:9:113426343:113426450:1

intergenic

block939053 [novel_lenNOK_Multihit_loopOverlap_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	0.348	no	no	0.53/0.53	19/19/0.00	0.0	0.0	2	0	2	0	37	-2	3arm_loop	14	nd	0.42	3	2	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------GGCAAGC------------------------------------------------	2	novel
		len	cloning frequencies
			T3S2	T5S1
	----------------------------------------------------AGGCAAGCTCCAAAGTTGC-------------------------------------	19	1	1
rat	gtcctggttgctatgctctgtgtccctcggttggattctgtgaggcatgctcAGGCAAGCTCCAAAGTTGCgacatggtgagcacattgtcagggcacacaaaggggc
	************************************************************************************************************
rat	(((((.((((((..((..((((((((...((((....((.((..((.(((....))).))..)).))...))))..)).)).))))..))...)))).))...)))))	0.980 -34.60

rat

chromosome:1:165755:165862:1

intergenic

block823004 [novel_lenNOK_Multihit_loopOverlap_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	0.348	no	no	0.53/0.53	19/19/0.00	0.0	0.0	2	0	2	0	37	-2	3arm_loop	14	nd	0.42	3	2	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------GGCAAGC------------------------------------------------	2	novel
		len	cloning frequencies
			T3S2	T5S1
	----------------------------------------------------AGGCAAGCTCCAAAGTTGC-------------------------------------	19	1	1
rat	gtcctggttgctatgctctgtgtccctcggttggattctgtgaggcatgctcAGGCAAGCTCCAAAGTTGCgacatggtgagcacattgtcagggcacacaaaggggc
	************************************************************************************************************
rat	(((((.((((((..((..((((((((...((((....((.((..((.(((....))).))..)).))...))))..)).)).))))..))...)))).))...)))))	0.980 -34.60

rat

chromosome:1:881845:881952:-1

intergenic

novel_lenNOK_5varHIGH (326 loci)

block2411 [novel_lenNOK_5varHIGH]

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	0.724	no	no	0.67/0.67	18/21/0.50	2.5	1.0	2	0	1	0	6	9	3arm	1	nd	0.29	2	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------CCACCUG---------------------	1	novel
seed	----------------------------------------------------------------------UGGGCAU----------------	1	novel
		len	cloning frequencies
			T3S1
	----------------------------------------------------------------CCCACCTGGGCATCTGAGGAC--------	21	1
	---------------------------------------------------------------------CTGGGCATCTGAGGACCG------	18	1
rat	ctaactgggcttggtaggctcctaactggtataggaggcatgtgaggcatgaggctgcctgcttCCCACCTGGGCATCTGAGGACCGtcttgg
	*********************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000003572 ENSRNOG00000002659 C2ta
rat	((((.(((.(((((...((.((.....(((...((((((.....(((((......))))))))))).))).))))..)))))..)))..))))	0.750 -28.00

rat

chromosome:10:5126103:5126195:-1

Same_strand|Boundary_non-coding|ENSRNOT00000030118|ENSRNOG00000002659 ## Same_strand|Intronic_coding|ENSRNOT00000003572|ENSRNOG00000002659 ## ENSRNOG00000002659|protein_coding|C2ta|class II, major histocompatibility complex, transactivator [Source:RefSeq_peptide;Acc:NP_445981]

block3511 [novel_lenNOK_5varHIGH]

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	0.078	no	no	0.78/0.83	18/18/0.00	1.2	1.2	5	0	4	0	12	18	3arm	1	nd	0.22	2	5	4	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------UCGGGGU------------------------	3	novel
seed	----------------------------------------------------------------------------------------GGGGUGG----------------------	2	novel
		len	cloning frequencies
			T2S1	T2S2	T3S1	T4S2
	-------------------------------------------------------------------------------------CTCGGGGTGGGGGGGAGC--------------	18	1	-	1	1
	---------------------------------------------------------------------------------------CGGGGTGGGGGGGAGCAA------------	18	-	2	-	-
rat	gcccaaggtcacacataaagctgctgctttacatcccaggtgaagagctggatgagtgaagctaagaatctgtctgtttctcaagCTCGGGGTGGGGGGGAGCAAgctggtggaggg
	*********************************************************************************************************************
	-------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000003749 ENSRNOG00000002768 RGD1560593_predicted
rat	.(((....((.(((....(((((((.(((..((((((..((..((((..((((..((..........))..))))..))))...))..))))))..))).)))).))).))))))))	0.980 -40.20

rat

chromosome:10:7220153:7220269:-1

Opposite_strand|Intronic_coding|ENSRNOT00000003749|ENSRNOG00000002768 ## ENSRNOG00000002768|protein_coding|RGD1560593_predicted|

block6233 [novel_lenNOK_5varHIGH]

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	0.012	no	no	0.68/0.68	19/22/0.50	1.5	0.0	2	0	2	0	13	1	5arm	1	nd	0.16	2	2	2	na	na

		reads	miRBase family seed
seed	--------------GUGGGCC--------------------------------------------------------------------	1	novel
seed	-----------------GGCCUAG-----------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S2	T3S1
	----------------GGGCCTAGCAGCCACGTGA------------------------------------------------------	19	-	1
	-------------CGTGGGCCTAGCAGCCACGTGA------------------------------------------------------	22	1	-
rat	gtggcctcaatcaCGTGGGCCTAGCAGCCACGTGAtagccccttcatctgagtcacgtggtgcggcctggccggcttccgattaccact
	*****************************************************************************************
	...................................................................................>>>>>>>>>>>>>>>>	ENSRNOT00000008537 ENSRNOG00000006460 RGD1304601
rat	((((....((((..((.((((..((.((((((((((...............))))))))))...))..)))).))....)))).)))).	0.990 -35.76

rat

chromosome:10:13415517:13415605:-1

intergenic

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