miR-Intess: classification

other hairpins

novel_Multihit_nonpairedHIGH_bulgeHIGH (16 loci)

block5018 [novel_Multihit_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	0.187	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	8	2	3arm	49	nd	0.35	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------CGUUCGU--------------------	1	novel
		len	cloning frequencies
			AF16
	-------------------------------------GCGTTCGTGGTGTAATGGTC--------	20	1
cbriggsae	ttcatataatattatacaggagagtgttagaatgtgcGCGTTCGTGGTGTAATGGTCagcatgga
	*****************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001108848
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_133381
	---------------------------------------------------------------------------	NM_001045626
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_004845
	---------------------------------------------------------------------------	NM_001086847
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001065160
	---------------------------------------------------------------------------	NM_001082087
	---------------------------------------------------------------------------	NM_001017762
cbriggsae	(((((....(((((((((.(((.((((........)))).))).)).)))))))......)))))	0.990 -13.40

cbriggsae

chromosome:chrX:13287567:13287631:1

Same_strand|Intronic_non-coding|NM_001108848|Elavl1 ## Opposite_strand|Intronic_coding|NM_001045626|galntl1 ## Opposite_strand|Intronic_non-coding|NM_001086847|MGC53595 ## Same_strand|Intronic_coding|NM_001065160|Os06g0725900 ## {Repeats: no}

block560 [novel_Multihit_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	0.761	no	no	0.52/0.52	21/21/1.00	0.0	0.0	1	0	1	0	8	12	3arm	47	nd	0.33	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------UAAUGGU---------------------	1	novel
		len	cloning frequencies
			AF16
	----------------------------------------------------------GTAATGGTCAGCATGGATGCC--------	21	1
cbriggsae	gccttgtcgccttcatatcattgccctccgctaccttctccgtcgcagcgttcgtggtGTAATGGTCAGCATGGATGCCttccaagc
	***************************************************************************************
	-------------------------------------------------------------------------------------------------	NM_012655
	-------------------------------------------------------------------------------------------------	NM_001012534
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_075505
	-------------------------------------------------------------------------------------------------	NM_013672
	-------------------------------------------------------------------------------------------------	NM_214128
cbriggsae	..((((..((.(((((((((((((((..((((..............)))).....)).))))))))....))))).))....)))).	0.590 -18.14

cbriggsae

chromosome:chrI_random:2960406:2960492:1

Opposite_strand|Intronic_non-coding|NM_012655|Sp1 ## Same_strand|Intronic_non-coding|NM_075505|psa-1 ## {Repeats: no}

novel_loopOverlap_nonpairedHIGH (16 loci)

block300 [novel_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	0.607	no	no	0.55/0.55	22/22/1.00	0.0	0.0	2	0	1	0	20	-3	3arm_loop	1	nd	0.41	3	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------ACACGAG----------------------------------	2	novel
		len	cloning frequencies
			AF16
	----------------------------------GACACGAGTTGTCGGACTGGTA--------------------	22	2
cbriggsae	ctatataacacaaaagaaacagttagaaacgagtGACACGAGTTGTCGGACTGGTAtcatcatggtggtctatatg
	****************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_026450
	--------------------------------------------------------------------------------------	NM_001093227
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_177350
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_009930
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_058794
	--------------------------------------------------------------------------------------	NM_001024290
	--------------------------------------------------------------------------------------	NM_175692
	--------------------------------------------------------------------------------------	NM_001078787
	--------------------------------------------------------------------------------------	NM_001109774
	--------------------------------------------------------------------------------------	NM_001114303
	--------------------------------------------------------------------------------------	NM_001114304
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001089360
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_059581
	--------------------------------------------------------------------------------------	NM_121223
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_115574
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_021399
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001079883
cbriggsae	.((((((.(((....((..(((((.(((((..((...))..))).)).)))))...))......)))...))))))	0.520 -11.40

cbriggsae

chromosome:chrI:4057087:4057162:1

Same_strand|Intronic_non-coding|NM_026450|Zfp169 ## Opposite_strand|Intronic_coding|NM_001093227|MGC80275 ## Same_strand|Intronic_coding|NM_009930|Col3a1 ## Opposite_strand|Intronic_non-coding|NM_001024290|Gal3st3 ## {Repeats: no}

block1109 [novel_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	0.122	no	no	0.45/0.45	22/22/1.00	0.0	0.0	1	0	1	0	8	-3	3arm_loop	2	nd	0.36	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------UUCGCGA----------------------	1	novel
		len	cloning frequencies
			AF16
	------------------------------------GTTCGCGATTCATCGTCTTCTT--------	22	1
cbriggsae	agaaggcttttgaggctcatcgatttcaatagtgtcGTTCGCGATTCATCGTCTTCTTcgtcttct
	******************************************************************
cbriggsae	(((((((....((((.....((((...(((.(((.....))).))).)))).))))...)))))))	0.580 -13.30

cbriggsae

chromosome:chrII:14511861:14511926:1

{Repeats: no}

block1231 [novel_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	0.710	no	no	0.36/0.36	22/22/1.00	0.0	0.0	1	0	1	0	6	-1	3arm	1	nd	0.32	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------CAGGUGG--------------------	1	novel
		len	cloning frequencies
			AF16
	----------------------------------------------------ACAGGTGGTAGTTGTCTTTTTA------	22	1
cbriggsae	atcatcaataatcacgatttccggctgctctaaaactttctcacactcttctACAGGTGGTAGTTGTCTTTTTAggcgat
	********************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_030676
	------------------------------------------------------------------------------------------	NM_062055
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_074739
	------------------------------------------------------------------------------------------	NM_204717
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001087841
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001097628
	------------------------------------------------------------------------------------------	NM_174951
	------------------------------------------------------------------------------------------	NM_001114294
	------------------------------------------------------------------------------------------	NM_061996
	------------------------------------------------------------------------------------------	NM_062047
	------------------------------------------------------------------------------------------	NM_061910
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001123635
cbriggsae	(((.((...((..((((((.(((.(((..........................))).))).))))))..))...)).)))	0.520 -9.87

cbriggsae

chromosome:chrII_random:1494664:1494743:1

Same_strand|Intronic_coding|NM_030676|Nr5a2 ## Opposite_strand|Intronic_coding|NM_062055|sri-54 ## Opposite_strand|Intronic_non-coding|NM_204717|ECE1 ## {Repeats: no}

block1535 [novel_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	0.461	no	no	0.48/0.48	23/23/1.00	0.0	0.0	1	0	1	0	17	-3	3arm_loop	1	nd	0.39	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------GAGUUGC--------------------------------	1	novel
		len	cloning frequencies
			AF16
	-------------------------------------------CGAGTTGCATGTGATATTCACCG-----------------	23	1
cbriggsae	tcagaaatgagttctgctgtgaagtgcgctccaacatattcttCGAGTTGCATGTGATATTCACCGtatccaccatgatttgg
	***********************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001028998
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001028999
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001029004
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001029003
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001029002
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001029001
	---------------------------------------------------------------------------------------------	NM_064155
	---------------------------------------------------------------------------------------------	NM_001122952
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_028763
	---------------------------------------------------------------------------------------------	NM_065922
	---------------------------------------------------------------------------------------------	NM_010905
	---------------------------------------------------------------------------------------------	NM_065923
	---------------------------------------------------------------------------------------------	NM_068002
	---------------------------------------------------------------------------------------------	NM_065190
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_067159
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_175692
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001093474
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_061965
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_061817
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_075459
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_067160
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_067659
cbriggsae	.((((.(((.((..(((.(((((...(((..((((...........))))...)))...))))).)))...)))))..)))).	0.610 -16.70

cbriggsae

chromosome:chrIII:11328918:11329000:-1

Same_strand|Intronic_non-coding|NM_001028998|unc-62 ## Opposite_strand|Intronic_non-coding|NM_064155|Y17G7B.3 ## Opposite_strand|Intronic_coding|NM_065922|C05D10.4 ## Same_strand|Intronic_coding|NM_067659|Y104H12BL.1 ## {Repeats: no}

block1696 [novel_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	0.184	no	no	0.43/0.43	21/21/1.00	0.0	0.0	1	0	1	0	13	-2	3arm_loop	1	nd	0.33	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------CUGCAGU--------------------------	1	novel
		len	cloning frequencies
			AF16
	----------------------------------------GCTGCAGTTGATTTTCTGGTT-------------	21	1
cbriggsae	tctgatgtaattatcaagaacatctcctccactttctttcGCTGCAGTTGATTTTCTGGTTtctgaattcagaa
	**************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_066813
	------------------------------------------------------------------------------------	NM_127796
	------------------------------------------------------------------------------------	NM_134696
	------------------------------------------------------------------------------------	NM_134696
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001077541
	------------------------------------------------------------------------------------	NM_018785
	------------------------------------------------------------------------------------	NM_012760
	------------------------------------------------------------------------------------	NM_026275
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001082235
	------------------------------------------------------------------------------------	NM_001111819
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	NM_066771
cbriggsae	(((((.......(((.((((.(((..((.((...........)).))..))).)))))))........))))).	0.840 -10.86

cbriggsae

chromosome:chrIII:5116872:5116945:1

Same_strand|Intronic_non-coding|NM_066813|R10E12.2 ## Opposite_strand|Intronic_non-coding|NM_127796|ATUBP4 ## Opposite_strand|Intronic_coding|NM_134696|CG2839 ## Same_strand|Intronic_coding|NM_001077541|clgn ## Opposite_strand|Boundary_coding|NM_066771|ZK632.2 ## {Repeats: no}

block1898 [novel_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	0.100	no	no	0.48/0.48	21/21/1.00	0.0	0.0	1	0	1	0	22	-2	5arm_loop	1	nd	0.38	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------GGAACUA-------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	----------------------TGGAACTAATGGCGAAGACGT------------------------------------------	21	1
cbriggsae	tccaaaaatcgataattggtgaTGGAACTAATGGCGAAGACGTtggttttcaaattttccgattatttctttatcttgttctgga
	*************************************************************************************
	-----------------------------------------------------------------------------------------------	NM_123965
	-----------------------------------------------------------------------------------------------	NM_024349
	-----------------------------------------------------------------------------------------------	NM_019034
	-----------------------------------------------------------------------------------------------	NM_001016369
	-----------------------------------------------------------------------------------------------	NM_001032772
	-----------------------------------------------------------------------------------------------	NM_001040602
	-----------------------------------------------------------------------------------------------	NM_001093711
	-----------------------------------------------------------------------------------------------	NM_001095157
	-----------------------------------------------------------------------------------------------	NM_199692
	-----------------------------------------------------------------------------------------------	NM_001033835
	-----------------------------------------------------------------------------------------------	NM_175092
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_065286
	-----------------------------------------------------------------------------------------------	NM_001123190
	-----------------------------------------------------------------------------------------------	NM_001126828
	-----------------------------------------------------------------------------------------------	NM_001010953
	-----------------------------------------------------------------------------------------------	NM_001127285
cbriggsae	((((.((...(((((..((((((((((..(((...((((((....))))))..))))))).))))))...)))))...)).))))	0.950 -18.20

cbriggsae

chromosome:chrIV:606058:606142:-1

Opposite_strand|Intronic_coding|NM_123965|ARAC2 ## Opposite_strand|Intronic_non-coding|NM_024349|Ak1 ## Same_strand|Intronic_non-coding|NM_065286|Y53G8AR.6 ## {Repeats: no}

block2710 [novel_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	0.497	no	no	0.43/0.43	21/21/1.00	0.0	0.0	1	0	1	0	37	-2	5arm_loop	1	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------GAGGUGA---------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-------------------------------------AGAGGTGAGTGATGAGTAGAT--------------------------------------------------------------	21	1
cbriggsae	tctcttatagattttggccggttctttgatcgaaaacAGAGGTGAGTGATGAGTAGATattgctggatcaggtggcttatgtttcggagtcgaagtgttaattgggaatgggtttgggat
	************************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------------------	NM_172632
	----------------------------------------------------------------------------------------------------------------------------------	NM_001007257
	----------------------------------------------------------------------------------------------------------------------------------	NM_001027635
	----------------------------------------------------------------------------------------------------------------------------------	NM_199501
	----------------------------------------------------------------------------------------------------------------------------------	NM_012231
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_133288
	----------------------------------------------------------------------------------------------------------------------------------	NM_001087019
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001032790
	----------------------------------------------------------------------------------------------------------------------------------	NM_015866
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_020367
	----------------------------------------------------------------------------------------------------------------------------------	NM_001046756
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_012963
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_011241
	----------------------------------------------------------------------------------------------------------------------------------	NM_001044304
cbriggsae	((((..((..((((...((((((((((((((((((...(((.((..((((.(((((...)))))..))))..)).)))...)))))..)))))))....))))))))))..))..)))).	0.960 -24.80

cbriggsae

chromosome:chrIV:10329967:10330086:1

Opposite_strand|Intronic_non-coding|NM_172632|Mapk4 ## Opposite_strand|Intronic_coding|NM_001007257|PRDM2 ## Same_strand|Intronic_coding|NM_133288|Atp2b3 ## Same_strand|Intronic_non-coding|NM_020367|PARP11 ## {Repeats: no}

block2873 [novel_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	0.169	no	no	0.71/0.71	21/21/1.00	0.0	0.0	1	0	1	0	20	-2	5arm_loop	1	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------UCCGCCC------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	--------------------GTCCGCCCGAGGAACGCGCAT-----------------------------------------------	21	1
cbriggsae	ctcgcaccgactgaccgcttGTCCGCCCGAGGAACGCGCATaaagaggcggtccctcgggtaacatcccatcgctccttaatgtcgag
	****************************************************************************************
cbriggsae	((((((..((.(((.....(((..((((((((.((.(((........))))).)))))))).))).....))).)).....)).))))	0.690 -28.10