miR-Intess: classification

other hairpins

novel_lenNOK_loopOverlap_nonpairedHIGH_bulgeHIGH (10 loci)

block4878 [novel_lenNOK_loopOverlap_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	0.501	no	no	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	29	-3	5arm_loop	2	nd	0.67	4	1	1	na	na

		reads	miRBase family seed
seed	------------------------------CUGUUAC--------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-----------------------------TCTGTTACGGTTTCCTTG----------------------------------------	18	1
cbriggsae	gtttctggaacaagttctctagaatcggcTCTGTTACGGTTTCCTTGagcggtccattccaaagtcgtcgttgaacaaaccagttgc
	***************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_172925
	-------------------------------------------------------------------------------------------------	NM_007496
	-------------------------------------------------------------------------------------------------	NM_001110231
	-------------------------------------------------------------------------------------------------	NM_004119
	-------------------------------------------------------------------------------------------------	NM_001110232
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_007736
	-------------------------------------------------------------------------------------------------	NM_001110229
	-------------------------------------------------------------------------------------------------	NM_011058
	-------------------------------------------------------------------------------------------------	NM_006206
	-------------------------------------------------------------------------------------------------	NM_010160
	-------------------------------------------------------------------------------------------------	NM_001110228
	-------------------------------------------------------------------------------------------------	NM_001110230
	-------------------------------------------------------------------------------------------------	NM_001090075
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001087789
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001079250
	-------------------------------------------------------------------------------------------------	NM_001020811
	-------------------------------------------------------------------------------------------------	NM_001083316
	-------------------------------------------------------------------------------------------------	NM_077435
cbriggsae	((..((((.....((((....((..(((((.((....((...((......)).))....)).)))))))...))))...))))..))	0.880 -18.00

cbriggsae

chromosome:chrX:5876123:5876209:1

Same_strand|Intronic_non-coding|NM_172925|Klhl31 ## Opposite_strand|Intronic_non-coding|NM_007496|Zfhx3 ## Opposite_strand|Intronic_coding|NM_004119|FLT3 ## Same_strand|Intronic_coding|NM_007736|Col4a5 ## {Repeats: no}

novel_Multihit_nonpairedHIGH (9 loci)

block1395 [novel_Multihit_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	0.397	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	11	4	5arm	49	nd	0.35	3	1	1	na	na

		reads	miRBase family seed
seed	------------CGUUCGU------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-----------GCGTTCGTGGTGTAATGGTC------------------------------------------	20	1
cbriggsae	ggaaaccatccGCGTTCGTGGTGTAATGGTCagcatggatgccttccaagcattcgacgggggttcgattccc
	*************************************************************************
	-----------------------------------------------------------------------------------	NM_138944
	-----------------------------------------------------------------------------------	NM_199029
	-----------------------------------------------------------------------------------	NM_001087791
	-----------------------------------------------------------------------------------	NM_203889
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001027397
	-----------------------------------------------------------------------------------	NM_121936
cbriggsae	((((...((((.((.(((.(((((..(((...(((....)))...))).)))))))))).))))....)))).	0.720 -21.40

cbriggsae

chromosome:chrIII:6237695:6237767:-1

Opposite_strand|Intronic_coding|NM_138944|Pou4f2 ## Opposite_strand|Intronic_non-coding|NM_199029|Zfp395 ## Same_strand|Intronic_coding|NM_001027397|rbf-1 ## {Repeats: no}

block2362 [novel_Multihit_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	0.776	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	12	4	3arm	49	nd	0.35	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------CGUUCGU------------------------	1	novel
		len	cloning frequencies
			AF16
	--------------------------------------------------------------------GCGTTCGTGGTGTAATGGTC------------	20	1
cbriggsae	gcgtctctcccgccgccgccactttccccctccttcttatacgccgttcccctccctccccgccatgcGCGTTCGTGGTGTAATGGTCagcatggatgcc
	****************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_123965
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_024349
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_008091
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_019034
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001016369
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001032772
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001040602
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001093711
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001095157
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_199692
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001033835
	--------------------------------------------------------------------------------------------------------------	NM_001047948
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_175092
	--------------------------------------------------------------------------------------------------------------	NM_065286
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001123190
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001126828
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001010953
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001127285
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_070587
cbriggsae	((((((.....((((.((((((..................(((((((.................))).))))..))))))...))))......)))))).	0.900 -19.38

cbriggsae

chromosome:chrIV:686298:686397:1

Same_strand|Intronic_coding|NM_123965|ARAC2 ## Same_strand|Intronic_non-coding|NM_024349|Ak1 ## Opposite_strand|Intronic_coding|NM_001047948|LOC499584 ## Opposite_strand|Intronic_non-coding|NM_065286|Y53G8AR.6 ## {Repeats: no}

block4044 [novel_Multihit_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	0.465	no	no	0.52/0.52	21/21/1.00	0.0	0.0	1	0	1	0	29	5	3arm	47	nd	0.33	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------UAAUGGU------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	----------------------------------------------------------------GTAATGGTCAGCATGGATGCC-----------------------------	21	1
cbriggsae	cggtttcaagtttttgtggattgtgtacgtgaaggcgcattgttcatttcaacgcgttcgtggtGTAATGGTCAGCATGGATGCCttccaagcattcgacgggggttcgattcc
	******************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_002474
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_068772
	----------------------------------------------------------------------------------------------------------------------------	NM_000393
	----------------------------------------------------------------------------------------------------------------------------	NM_001855
	----------------------------------------------------------------------------------------------------------------------------	NM_033150
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_021371
	----------------------------------------------------------------------------------------------------------------------------	NM_201478
	----------------------------------------------------------------------------------------------------------------------------	NM_007732
	----------------------------------------------------------------------------------------------------------------------------	NM_001106366
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001008159
	----------------------------------------------------------------------------------------------------------------------------	NM_001113224
	----------------------------------------------------------------------------------------------------------------------------	NM_001081764
	----------------------------------------------------------------------------------------------------------------------------	NM_001006951
	----------------------------------------------------------------------------------------------------------------------------	NM_001844
	----------------------------------------------------------------------------------------------------------------------------	NM_009928
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_181045
	----------------------------------------------------------------------------------------------------------------------------	NM_001858
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001040113
	----------------------------------------------------------------------------------------------------------------------------	NM_009936
	----------------------------------------------------------------------------------------------------------------------------	NM_001101980
	----------------------------------------------------------------------------------------------------------------------------	NM_000494
	----------------------------------------------------------------------------------------------------------------------------	NM_000089
	----------------------------------------------------------------------------------------------------------------------------	NM_001080091
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001040114
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_073745
	----------------------------------------------------------------------------------------------------------------------------	NM_001001135
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_022844
	----------------------------------------------------------------------------------------------------------------------------	NM_073729
cbriggsae	.((..((.((..(((((.((.(((......((((((((((((..((((.((.(((....))).)).))))..))..)))..)))))))...))).)).)))))..)).))..))	0.680 -31.00

cbriggsae

chromosome:chrV:5897264:5897377:1

Same_strand|Intronic_coding|NM_002474|MYH11 ## Opposite_strand|Intronic_coding|NM_000393|COL5A2 ## Same_strand|Intronic_non-coding|NM_021371|Caln1 ## {Repeats: no}

block4549 [novel_Multihit_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	0.515	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	8	4	5arm	49	nd	0.35	3	1	1	na	na

		reads	miRBase family seed
seed	---------CGUUCGU------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	--------GCGTTCGTGGTGTAATGGTC------------------------------------	20	1
cbriggsae	gaaatccaGCGTTCGTGGTGTAATGGTCagcatggatgccttccaagcattcgacgggggttcg
	****************************************************************
	--------------------------------------------------------------------------	NM_001108848
	--------------------------------------------------------------------------	NM_136816
	--------------------------------------------------------------------------	NM_136816
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_008260
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_008499
cbriggsae	((.((((..((.(((.(((((..(((...(((....)))...))).)))))))))).)))))).	0.710 -16.80

cbriggsae

chromosome:chrX:12706324:12706387:-1

Opposite_strand|Intronic_non-coding|NM_001108848|Elavl1 ## Opposite_strand|Intronic_coding|NM_136816|Cpr47Ef ## Same_strand|Intronic_non-coding|NM_008260|Foxa3 ## {Repeats: no}

block4562 [novel_Multihit_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	0.749	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	8	9	3arm	49	nd	0.35	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------CGUUCGU--------------------	1	novel
		len	cloning frequencies
			AF16
	--------------------------------------------GCGTTCGTGGTGTAATGGTC--------	20	1
cbriggsae	tccaggattatcatccccggcatccttttttctgaagaaagccaGCGTTCGTGGTGTAATGGTCagcatgga
	************************************************************************
	----------------------------------------------------------------------------------	NM_001108848
	----------------------------------------------------------------------------------	NM_133381
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001045626
	----------------------------------------------------------------------------------	NM_004845
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001086847
	----------------------------------------------------------------------------------	NM_001065160
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001082087
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001017762
cbriggsae	((((.((((((.((.((((((...((((((.....))))))...))...)).)).)).))))))....))))	0.480 -14.40

cbriggsae

chromosome:chrX:13290230:13290301:-1

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

block45 [novel_Multihit_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	0.407	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	12	2	3arm	49	nd	0.40	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------CGUUCGU------------------------	1	novel
		len	cloning frequencies
			AF16
	----------------------------------------------GCGTTCGTGGTGTAATGGTC------------	20	1
cbriggsae	ggcagccaccgcaatatgtacgccttggaagctttaatgagtgtgcGCGTTCGTGGTGTAATGGTCagcatggatgcc
	******************************************************************************
	----------------------------------------------------------------------------------------	NM_001011629
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_199320
	----------------------------------------------------------------------------------------	NM_014333
	----------------------------------------------------------------------------------------	NM_001098517
	----------------------------------------------------------------------------------------	NM_061553
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_067080
cbriggsae	((((.(((..((.((...((((((.((((.((............))...)))).))))))...))..)).))).))))	0.710 -22.60

cbriggsae

chromosome:chrI:1368004:1368081:-1

Opposite_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Same_strand|Intronic_non-coding|NM_199320|PHF17 ## Opposite_strand|Intronic_coding|NM_061553|C13A10.1 ## Same_strand|Intronic_coding|NM_067080|Y66D12A.21 ## {Repeats: no}

block559 [novel_Multihit_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	0.813	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	8	6	3arm	49	nd	0.40	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------CGUUCGU--------------------	1	novel
		len	cloning frequencies
			AF16
	----------------------------------------------GCGTTCGTGGTGTAATGGTC--------	20	1
cbriggsae	ccttgtcgccttcatatcattgccctccgctaccttctccgtcgcaGCGTTCGTGGTGTAATGGTCagcatgga
	**************************************************************************
	------------------------------------------------------------------------------------	NM_012655
	------------------------------------------------------------------------------------	NM_001012534
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_075505
	------------------------------------------------------------------------------------	NM_013672
	------------------------------------------------------------------------------------	NM_214128
cbriggsae	((.(((.(((...(((((((.((.((..((.((.......)).)))).))..)))))))...)))..))).)).	0.950 -13.90

cbriggsae

chromosome:chrI_random:2960407:2960480:1

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

block3470 [novel_Multihit_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	0.031	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	12	5	3arm	49	nd	0.40	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------CGUUCGU------------------------	1	novel
		len	cloning frequencies
			AF16
	------------------------------------------------GCGTTCGTGGTGTAATGGTC------------	20	1
cbriggsae	cggcagccgccgcgatatgtacaccttgttagtttatgttgaacgtggGCGTTCGTGGTGTAATGGTCagcatggatgcc
	********************************************************************************
cbriggsae	.((((.(((..(((((...((((((.((...(((((((.....)))))))...)).))))))...))).)).))).))))	0.990 -29.60

cbriggsae

chromosome:chrUn:4078063:4078142:1

{Repeats: no}

block4560 [novel_Multihit_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	0.696	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	8	4	5arm	49	nd	0.35	3	1	1	na	na

		reads	miRBase family seed
seed	---------CGUUCGU------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	--------GCGTTCGTGGTGTAATGGTC------------------------------------	20	1
cbriggsae	gacatccaGCGTTCGTGGTGTAATGGTCagcatggatgccttccaagcattcgacgggggttcg
	****************************************************************
	--------------------------------------------------------------------------	NM_001108848
	--------------------------------------------------------------------------	NM_133381
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001045626
	--------------------------------------------------------------------------	NM_004845
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001086847
	--------------------------------------------------------------------------	NM_001065160
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001082087
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001017762
cbriggsae	((.((((..((.(((.(((((..(((...(((....)))...))).)))))))))).)))))).	0.710 -16.80