miR-Intess: classification

other hairpins

novel_Multihit_loopOverlap_randfoldOK_nonpairedHIGH (40 loci)

block846604 [novel_Multihit_loopOverlap_randfoldOK_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	0.008	no	no	0.64/0.64	22/22/1.00	0.0	0.0	1	0	1	0	15	-3	3arm_loop	46	nd	0.41	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------CUGGGAG-----------------------------	1	novel
		len	cloning frequencies
			T3S1
	-------------------------------GCTGGGAGTTAGGCTGGATGCC---------------	22	1
rat	ggctcatccacagacatctcacactctccctGCTGGGAGTTAGGCTGGATGCCtgctgtgtgggagct
	********************************************************************
rat	(((((.(((((((.((((.((..(((((((....)))))..))..))))))....))))).)))))))	0.410 -27.80

rat

chromosome:1:51367555:51367622:-1

intergenic

block847045 [novel_Multihit_loopOverlap_randfoldOK_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	0.008	no	no	0.64/0.64	22/22/1.00	0.0	0.0	1	0	1	0	15	-3	3arm_loop	46	nd	0.41	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------CUGGGAG-----------------------------	1	novel
		len	cloning frequencies
			T3S1
	-------------------------------GCTGGGAGTTAGGCTGGATGCC---------------	22	1
rat	ggctcatccacagacatctcacactctccctGCTGGGAGTTAGGCTGGATGCCtgctgtgtgggagct
	********************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000059938 ENSRNOG00000039174 RGD1563865_predicted
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000048246 ENSRNOG00000039174 RGD1563865_predicted
rat	(((((.(((((((.((((.((..(((((((....)))))..))..))))))....))))).)))))))	0.410 -27.80

rat

chromosome:1:51794924:51794991:-1

block1611401 [novel_Multihit_loopOverlap_randfoldOK_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	0.008	no	no	0.60/0.60	20/20/1.00	0.0	0.0	2	0	1	0	37	-2	5arm_loop	32	nd	0.45	3	2	1	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------------------GAGCCGG-------------------------------------------	1	novel
seed	--------------------------------------GAGCCGG---------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------------------TGAGCCGGGAACACTGTGAG---------------------------------------------------------------	20	1
	---------------------------------------------------------------------TGAGCCGGGAACACTGTGAG-------------------------------	20	1
rat	cactgtgagctgagaacactgtgagctgggaacactgTGAGCCGGGAACACTGTGAGccgagaacactgTGAGCCGGGAACACTGTGAGccgggaacactgtgagctgggaacactgtga
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000021306 ENSRNOG00000015910 Ifltd1_predicted
rat	(((.(((..((.((..(((.(((..((.((..(((.(((..((.((..(((.(((.........))).)))..)).))..))).)))..)).))..))).)))..)).))..))).))).	1.000 -47.00

rat

chromosome:4:183058282:183058401:-1

Same_strand|Intronic_coding|ENSRNOT00000021306|ENSRNOG00000015910 ## ENSRNOG00000015910|protein_coding|Ifltd1_predicted| ## {Repeats: trf 1465 1485 0 class=trf}

block1611403 [novel_Multihit_loopOverlap_randfoldOK_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	0.008	no	no	0.60/0.60	20/20/1.00	0.0	0.0	2	0	1	0	37	-2	5arm_loop	32	nd	0.45	3	2	1	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------------------GAGCCGG-------------------------------------------	1	novel
seed	--------------------------------------GAGCCGG---------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------------------TGAGCCGGGAACACTGTGAG---------------------------------------------------------------	20	1
	---------------------------------------------------------------------TGAGCCGGGAACACTGTGAG-------------------------------	20	1
rat	cactgtgagctgagaacactgtgagctgggaacactgTGAGCCGGGAACACTGTGAGccgagaacactgTGAGCCGGGAACACTGTGAGccgggaacactgtgagctgggaacactgtga
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000021306 ENSRNOG00000015910 Ifltd1_predicted
rat	(((.(((..((.((..(((.(((..((.((..(((.(((..((.((..(((.(((.........))).)))..)).))..))).)))..)).))..))).)))..)).))..))).))).	1.000 -47.00

rat

chromosome:4:183058282:183058401:-1

Same_strand|Intronic_coding|ENSRNOT00000021306|ENSRNOG00000015910 ## ENSRNOG00000015910|protein_coding|Ifltd1_predicted| ## {Repeats: trf 1513 1533 0 class=trf}

block595535 [novel_Multihit_loopOverlap_randfoldOK_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	0.001	no	no	0.57/0.57	21/21/1.00	0.0	0.0	2	0	1	0	40	-4	3arm_loop	14	nd	0.33	3	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------------CCUGUGG---------------------	1	novel
seed	------------------------------------------------------------CCUGUGG-----------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	-------------------------------------------------------------------------------------------GCCTGTGGTGTGTGTGTCACA--------	21	1
	-----------------------------------------------------------GCCTGTGGTGTGTGTGTCACA----------------------------------------	21	1
rat	tgtggtgtgtgtgtcacagacttcactgtacctgtggtgtgtgtcacagacttcactgtGCCTGTGGTGTGTGTGTCACAgacttcactggGCCTGTGGTGTGTGTGTCACAgacttcac
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000025914 ENSRNOG00000028871 RGD1561537_predicted
rat	.((((.((.((((.((((.((.((((....((.(((((.((((.((((.((.((((.......)))).)).)))).)))).))..))).))....)))).)).)))).)))).)).))))	1.000 -51.50

rat

chromosome:17:6769544:6769663:-1

Same_strand|Intronic_coding|ENSRNOT00000025914|ENSRNOG00000028871 ## ENSRNOG00000028871|protein_coding|RGD1561537_predicted| ## {Repeats: trf 313 334 0 class=trf,trf 337 358 0 class=trf,dust 6769556 6769573 0 class=dust}

block595536 [novel_Multihit_loopOverlap_randfoldOK_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	0.001	no	no	0.57/0.57	21/21/1.00	0.0	0.0	2	0	1	0	41	-4	3arm_loop	14	nd	0.33	3	2	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------------------CCUGUGG----------------------	1	novel
seed	-----------------------------------------------------------CCUGUGG------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	------------------------------------------------------------------------------------------GCCTGTGGTGTGTGTGTCACA---------	21	1
	----------------------------------------------------------GCCTGTGGTGTGTGTGTCACA-----------------------------------------	21	1
rat	gtggtgtgtgtgtcacagacttcactgtacctgtggtgtgtgtcacagacttcactgtGCCTGTGGTGTGTGTGTCACAgacttcactggGCCTGTGGTGTGTGTGTCACAgacttcact
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000025914 ENSRNOG00000028871 RGD1561537_predicted
rat	((((.((.((((.((((.((.((((....((.(((((.((((.((((.((.((((.......)))).)).)))).)))).))..))).))....)))).)).)))).)))).)).)))).	1.000 -52.70

rat

chromosome:17:6769543:6769662:-1

Same_strand|Intronic_coding|ENSRNOT00000025914|ENSRNOG00000028871 ## ENSRNOG00000028871|protein_coding|RGD1561537_predicted| ## {Repeats: trf 369 390 0 class=trf,dust 6769584 6769605 0 class=dust,trf 345 366 0 class=trf}

novel_Multihit_loopOverlap_randfoldOK_nonpairedHIGH_bulgeHIGH (40 loci)

block90517 [novel_Multihit_loopOverlap_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	0.59/0.59	22/22/1.00	0.0	0.0	1	0	1	0	25	-4	5arm_loop	112	nd	0.36	5	1	1	na	na

		reads	miRBase family seed
seed	--------------------------UCAGUUG---------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	-------------------------CTCAGTTGCTGAGGAGTCCCCA-------------------------------------------------	22	1
rat	ggatattgaaagcaagaaagaggccCTCAGTTGCTGAGGAGTCCCCAtcccaactcggctcccaacactgagtatctccctcacaatttccatccc
	************************************************************************************************
rat	((((...((((....((..((((..(((((.((.((.((((((.............)))))))).)))))))..))))..))....)))).)))).	0.970 -28.12

rat

chromosome:10:80891071:80891166:1

intergenic

block353806 [novel_Multihit_loopOverlap_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	0.003	no	no	0.57/0.57	21/21/1.00	0.0	0.0	1	0	1	0	34	-1	5arm_loop	110	nd	0.43	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------UUCAGUC---------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	----------------------------------CTTCAGTCAGGCTCACTGGCT--------------------------------------------------------------	21	1
rat	gctcttcagttaggctcactggctagcctctgctCTTCAGTCAGGCTCACTGGCTagcctctgctcttcagcctggctcactggctagcctctgctcttcagtcagactcactggct
	*********************************************************************************************************************
rat	(((....((((.((((((..((((((((..((......(((((((((....(((........)))....)))))))))))..))))))))..))......)))).))))....))).	0.440 -42.40

rat

chromosome:14:49265337:49265453:-1

intergenic ## {Repeats: trf 403 424 0 class=trf}

block354464 [novel_Multihit_loopOverlap_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	0.57/0.57	21/21/1.00	0.0	0.0	1	0	1	0	34	-1	5arm_loop	110	nd	0.43	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------UUCAGUC---------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	----------------------------------CTTCAGTCAGGCTCACTGGCT--------------------------------------------------------------	21	1
rat	agccttcagcctggctcactggctagcctgtgctCTTCAGTCAGGCTCACTGGCTagcctctgctcttcagcctggctcactggctagcctgtgctcttcagtcagactcactggct
	*********************************************************************************************************************
	-------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000043791 ENSRNOG00000032207 LOC690700
rat	((((...((.(((((((((.((((((((.(((......(((((((((....(((........)))....)))))))))))).)))))))).)))......)))))).))....))))	0.920 -51.80

rat

chromosome:14:49732003:49732119:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000050021|ENSRNOG00000032207 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000043791|ENSRNOG00000032207 ## ENSRNOG00000032207|protein_coding|LOC690700|LOC501224 protein. [Source:UniProtKB/TrEMBL;Acc:Q0P5Q7] ## {Repeats: trf 434 455 0 class=trf}

block637238 [novel_Multihit_loopOverlap_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	0.59/0.59	22/22/1.00	0.0	0.0	1	0	1	0	20	-4	5arm_loop	112	nd	0.41	5	1	1	na	na

		reads	miRBase family seed
seed	---------------------UCAGUUG------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	--------------------CTCAGTTGCTGAGGAGTCCCCA----------------------------------------------------	22	1
rat	ctgagaggaagagagaggccCTCAGTTGCTGAGGAGTCCCCAtcccaactcaggccccaacactgaggatctccctcacaatttccatcccaga
	**********************************************************************************************
rat	(((.(((((((((.(((..((((((.((.((.((.(((..............))))))).))))))))..))).))).....)))).)).))).	0.980 -32.04