Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_cloningHIGH_nonpairedHIGH_bulgeHIGH (187 loci)

novel_Multihit_loopOverlap (184 loci)

block5262 [novel_Multihit_loopOverlap]

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	0.107	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	6	-1	3arm	34	nd	0.25	2	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------CUGGCCA------------------	1	novel
		len	cloning frequencies
			T2S2
	------------------------------------ACTGGCCACTGTCAGAACCA------	20	1
rat	gctctgggttgacaaatggtggggtaacaggaaggaACTGGCCACTGTCAGAACCAtgtgca
	**************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000009409 ENSRNOG00000007117 LOC363544
rat	((..(((.((((((..((((.((..............)).)))).))))))..)))...)).	1.000 -17.24

rat

chromosome:10:11871022:11871083:-1

Same_strand|Intronic_coding|ENSRNOT00000009409|ENSRNOG00000007117 ## ENSRNOG00000007117|protein_coding|LOC363544|Clusterin-associated protein 1. [Source:UniProtKB/Swiss-Prot;Acc:Q6AYJ5]

block187784 [novel_Multihit_loopOverlap]

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	0.107	no	no	0.38/0.38	21/21/1.00	0.0	0.0	1	0	1	0	13	-2	3arm_loop	12	nd	0.19	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------AUGUCUA--------------------------	1	novel
		len	cloning frequencies
			T1S2
	--------------------------------------------------CATGTCTACTCTGTCTTAACA-------------	21	1
rat	agcagacaacatgttaaaggcagtgatagctataaaaaaaagacacctccCATGTCTACTCTGTCTTAACAtttgatagtcagc
	************************************************************************************
rat	.((.(((...(((((.(((((((.................(((((.......)))))...))))))))))))......))).))	0.440 -14.25

rat

chromosome:12:19167105:19167188:-1

intergenic

block188597 [novel_Multihit_loopOverlap]

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	0.193	no	no	0.57/0.57	23/23/1.00	0.0	0.0	1	0	1	0	5	-2	3arm_loop	14	nd	0.17	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------CCACAGC--------------------	1	novel
		len	cloning frequencies
			T3S1
	--------------------------------------------------CCCACAGCCTTCCATGTCTTCTC-----	23	1
rat	accagggaggcaagtttacatcaaagtagttgtgattataaaccctgcatCCCACAGCCTTCCATGTCTTCTCgctgg
	******************************************************************************
rat	.((((.((((..((...((((..(((..((((((..................)))))))))..)))))))))).))))	0.730 -17.47

rat

chromosome:12:20511177:20511254:-1

intergenic

block188599 [novel_Multihit_loopOverlap]

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	0.193	no	no	0.57/0.57	23/23/1.00	0.0	0.0	1	0	1	0	5	-2	3arm_loop	14	nd	0.17	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------CCACAGC--------------------	1	novel
		len	cloning frequencies
			T3S1
	--------------------------------------------------CCCACAGCCTTCCATGTCTTCTC-----	23	1
rat	accagggaggcaagtttacatcaaagtagttgtgattataaaccctgcatCCCACAGCCTTCCATGTCTTCTCgctgg
	******************************************************************************
rat	.((((.((((..((...((((..(((..((((((..................)))))))))..)))))))))).))))	0.730 -17.47

rat

chromosome:12:20512190:20512267:-1

intergenic

block188650 [novel_Multihit_loopOverlap]

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	0.164	no	no	0.38/0.38	21/21/1.00	0.0	0.0	1	0	1	0	13	-2	3arm_loop	12	nd	0.19	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------AUGUCUA--------------------------	1	novel
		len	cloning frequencies
			T1S2
	--------------------------------------------------CATGTCTACTCTGTCTTAACA-------------	21	1
rat	gcagacaacatgttaaaggcagtgatagctataaaaaaagagacacctccCATGTCTACTCTGTCTTAACAtttgatagtcagc
	************************************************************************************
rat	((.(((...(((((.(((((((..................(((((.......)))))...))))))))))))......))).))	0.730 -15.10

rat

chromosome:12:20609400:20609483:-1

intergenic

block218029 [novel_Multihit_loopOverlap]

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	0.107	no	no	0.38/0.38	21/21/1.00	0.0	0.0	1	0	1	0	13	-2	3arm_loop	12	nd	0.19	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------AUGUCUA--------------------------	1	novel
		len	cloning frequencies
			T1S2
	--------------------------------------------------CATGTCTACTCTGTCTTAACA-------------	21	1
rat	agcagacaacatgttaaaggcagtgatagctataaaaaaaagacacctccCATGTCTACTCTGTCTTAACAtttgatagtcagc
	************************************************************************************
rat	.((.(((...(((((.(((((((.................(((((.......)))))...))))))))))))......))).))	0.440 -14.25

rat

chromosome:12:19061612:19061695:1

intergenic

block218744 [novel_Multihit_loopOverlap]

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	0.193	no	no	0.57/0.57	23/23/1.00	0.0	0.0	1	0	1	0	5	-2	3arm_loop	14	nd	0.17	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------CCACAGC--------------------	1	novel
		len	cloning frequencies
			T3S1
	--------------------------------------------------CCCACAGCCTTCCATGTCTTCTC-----	23	1
rat	accagggaggcaagtttacatcaaagtagttgtgattataaaccctgcatCCCACAGCCTTCCATGTCTTCTCgctgg
	******************************************************************************
rat	.((((.((((..((...((((..(((..((((((..................)))))))))..)))))))))).))))	0.730 -17.47

rat

chromosome:12:20104136:20104213:1

intergenic

block353451 [novel_Multihit_loopOverlap]

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	0.67/0.67	24/24/1.00	0.0	0.0	3	0	1	0	6	-3	3arm_loop	14	nd	0.25	2	3	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------CACCUCC----------------------	3	novel
		len	cloning frequencies
			T2S1
	----------------------------------------GCACCTCCTCCCCTCAGGAGAGTC------	24	3
rat	cagagggcataactatgtttgacagggaagaggatttataGCACCTCCTCCCCTCAGGAGAGTCctgtgt
	**********************************************************************
rat	((.(((((....((....((((..((((.((((..........)))).)))).)))).)).))))).)).	0.710 -20.10

rat

chromosome:14:49035523:49035592:-1

intergenic

block353532 [novel_Multihit_loopOverlap]

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	0.018	no	no	0.68/0.68	22/22/1.00	0.0	0.0	1	0	1	0	22	-1	3arm	13	nd	0.18	1	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------CAGGACC------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	-----------------------------------------------------------CCAGGACCAGTGCCAGCAGCAG----------------------	22	1
rat	cagctctgaatcgggacaaaccatgtgctccttgctcatcatgcttttggccctgaacgCCAGGACCAGTGCCAGCAGCAGcccatggagagtcccaggctga
	*******************************************************************************************************
rat	((((.((.....(((((...(((((.(((.((.(((......((..((((.((((.....)))).)))).)).))))).))).)))))...))))))))))).	0.990 -38.40

rat

chromosome:14:49078263:49078365:-1

intergenic

block353539 [novel_Multihit_loopOverlap]

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	0.170	no	no	0.67/0.67	24/24/1.00	0.0	0.0	3	0	1	0	6	-3	3arm_loop	14	nd	0.29	2	3	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------CACCUCC----------------------	3	novel
		len	cloning frequencies
			T2S1
	------------------------------------------GCACCTCCTCCCCTCAGGAGAGTC------	24	3
rat	cccagagggcataactaagtttgacagggaagaggatttgtaGCACCTCCTCCCCTCAGGAGAGTCctgggt
	************************************************************************
rat	(((((........(((...(((((..((((.((((..........)))).)))).)))))..))).))))).	0.680 -21.00

rat

chromosome:14:49089980:49090051:-1

intergenic

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