miR-Intess: classification

other hairpins

block1038 [novel_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	0.074	no	no	0.43/0.43	21/21/1.00	0.0	0.0	1	0	1	0	19	11	5arm	9	nd	0.33	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------CAGAAGA--------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-------------------TCAGAAGAGATTGTGTGATGG-------------------------------------------------------	21	1
cbriggsae	atgcatacttcctagggacTCAGAAGAGATTGTGTGATGGaaaccccccagagacctagggtgtatcccgggaattttctgagctctgtgttgca
	***********************************************************************************************
	---------------------------------------------------------------------------------------------------------	NM_001039389
cbriggsae	.((((.((....(((((.(((((((((..((.((....(((.((.(((.((....)).))).)).))))).)).)))))))))))))).))))))	0.870 -29.80

cbriggsae

chromosome:chrII:11713843:11713937:1

Opposite_strand|Intronic_non-coding|NM_001039389|Wdr37 ## {Repeats: no}

block1141 [novel_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	0.055	no	no	0.43/0.43	21/21/1.00	0.0	0.0	1	0	1	0	19	0	5arm	9	nd	0.33	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------CAGAAGA-----------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-------------------TCAGAAGAGATTGTGTGATGG----------------------------------------------------	21	1
cbriggsae	atgcatactccctagagacTCAGAAGAGATTGTGTGATGGaaacccccgagatacctaggaattttctgagctctgaacggcctgtgttgca
	********************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_152394
cbriggsae	.(((((((..(((((((.(((((((((....((((..(((......)))..)))).......))))))))))))))...))...)))).)))	0.990 -26.90

cbriggsae

chromosome:chrII_random:605382:605473:-1

Same_strand|Intronic_coding|NM_152394|C3orf44 ## {Repeats: no}

block1322 [novel_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	0.280	no	no	0.46/0.46	24/24/1.00	0.0	0.0	1	0	1	0	12	9	5arm	1	nd	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	-------------CGUUUGU----------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	------------GCGTTTGTGTCACGTGTTCATTGT------------------------------------------------------------	24	1
cbriggsae	tcttacttctgtGCGTTTGTGTCACGTGTTCATTGTagagaatgctgaaaaatgtgtttttaacgatcacgaatagctaaaatcactttgttagaa
	************************************************************************************************
	----------------------------------------------------------------------------------------------------------	NM_001011629
	----------------------------------------------------------------------------------------------------------	NM_172925
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_065286
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001093260
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_009573
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_130279
cbriggsae	(((.((....(((..(((((....((((...(((((.((((((((........)))))))).)))))))))....)).)))..)))...)).))).	0.990 -18.60

cbriggsae

chromosome:chrIII:2282888:2282983:-1

Opposite_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Same_strand|Intronic_non-coding|NM_065286|Y53G8AR.6 ## {Repeats: no}

block1637 [novel_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	0.291	no	no	0.61/0.61	23/23/1.00	0.0	0.0	1	0	1	0	15	20	3arm	1	nd	0.39	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------AGCUGCG------------------------------	1	novel
		len	cloning frequencies
			AF16
	----------------------------------------------------------------------------------GAGCTGCGTGAACTTTGGTCGGC---------------	23	1
cbriggsae	attttttgtcgttgttgatttcttcaggttgagcgtagacgtaaggggggtaacatgagtttcgatatctccagaagttgatGAGCTGCGTGAACTTTGGTCGGCaaaccgattgagagc
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001011629
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_172925
	----------------------------------------------------------------------------------------------------------------------------------	NM_065286
	----------------------------------------------------------------------------------------------------------------------------------	NM_001093260
	----------------------------------------------------------------------------------------------------------------------------------	NM_009573
	----------------------------------------------------------------------------------------------------------------------------------	NM_130279
cbriggsae	.(((((.(((((((((((((..((((.((....(((.(((.....(((((((...((.....)).)))))))....))).)))....)).))))....)))))))))..)))).))))).	0.980 -29.80

cbriggsae

chromosome:chrIII:2263372:2263491:1

Same_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Opposite_strand|Intronic_non-coding|NM_065286|Y53G8AR.6 ## {Repeats: no}

block1962 [novel_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	0.127	no	no	0.52/0.52	21/21/1.00	0.0	0.0	1	0	1	0	26	4	5arm	1	nd	0.38	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------UGUCCAA------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	--------------------------GTGTCCAACAGCTTCCTTGAG-----------------------------------------------------------------	21	1
cbriggsae	acggctttctcagcgtggcatttggcGTGTCCAACAGCTTCCTTGAGctcgctgcccttctgagctcccgagcatcctggcttcacgtcggagaagacgcgctttcctccgt
	****************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_064155
	--------------------------------------------------------------------------------------------------------------------------	NM_113688
	-----------------------------------------<<<<<<<<<<<<<<<-----------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	NM_070415
	-----------------------------------------<<<<<<<<<<<<<<<-----------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	NM_001129339
cbriggsae	((((.......((((((...(((((((((.(((...((((....(((((((.........)))))))..))))....)))...))))))))).....)))))).....))))	0.960 -37.60

cbriggsae

chromosome:chrIV:1795140:1795251:-1

Same_strand|Intronic_non-coding|NM_064155|Y17G7B.3 ## Opposite_strand|Intronic_coding|NM_113688|AT3G27720 ## Opposite_strand|Boundary_coding|NM_070415|Y41E3.10 ## {Repeats: no}

block2137 [novel_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	0.088	no	no	0.35/0.35	20/20/1.00	0.0	0.0	1	0	1	0	17	20	5arm	1	nd	0.35	4	1	1	na	na

		reads	miRBase family seed
seed	------------------AGAUACU---------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-----------------TAGATACTCTAGGCTTATGT---------------------------------------------------------------------------	20	1
cbriggsae	aacgttgattgatttatTAGATACTCTAGGCTTATGTctgaaatacaatatctagtttagaaaactggagatgttaagcttacacatctgtttctaatatcccacgaacgtt
	****************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001028224
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001001614
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001028225
	--------------------------------------------------------------------------------------------------------------------------	NM_173611
	--------------------------------------------------------------------------------------------------------------------------	NM_001109807
	--------------------------------------------------------------------------------------------------------------------------	NM_200495
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_069815
	--------------------------------------------------------------------------------------------------------------------------	NM_026578
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_175389
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_068620
cbriggsae	((((((...((...(((((((.((..((((((((..........(((...(((((((.....)))))))..))))))))))).......)).)))))))...))..))))))	0.460 -22.30

cbriggsae

chromosome:chrIV:6436695:6436806:-1

Same_strand|Intronic_non-coding|NM_001028224|T22D1.3 ## Opposite_strand|Intronic_coding|NM_173611|FAM98B ## Same_strand|Intronic_coding|NM_069815|T22B3.3 ## {Repeats: no}

block2179 [novel_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	0.637	no	no	0.30/0.30	20/20/1.00	0.0	0.0	1	0	1	0	10	15	3arm	1	nd	0.35	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------AUUUUUU----------------------	1	novel
		len	cloning frequencies
			AF16
	----------------------------------------------------------------------TATTTTTTTGACGATAGGCT----------	20	1
cbriggsae	ttcaagtcacatcaaaagttttcaccgtttcaaatagttctcaaataaacttgttagtataattcagcatTATTTTTTTGACGATAGGCTaaccttgaat
	****************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001027775
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_068469
cbriggsae	((((((..........(((((....((((..(((((((.((.((.((.(((....))).)).)).)).)))))))....))))..)))))...)))))).	0.500 -10.72

cbriggsae

chromosome:chrIV:8223633:8223732:-1

Same_strand|Intronic_coding|NM_001027775|Y75B8A.37 ## {Repeats: no}

block2181 [novel_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	0.314	no	no	0.45/0.45	20/20/1.00	0.0	0.0	3	0	1	0	34	2	3arm	1	nd	0.45	4	3	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------UGACUGU----------------------------------------------	3	novel
		len	cloning frequencies
			AF16
	-------------------------------------------------------------TTGACTGTCTATGCCTCTTG----------------------------------	20	3
cbriggsae	acatttaaaattttacagtttaaaaaatgtctcataatttgcaaatcattcaattttctaaTTGACTGTCTATGCCTCTTGatcccaattctttaaaaaattcaaaacaatatgt
	*******************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001027775
	-----------------------------------------------------------------------------------------------------------------------------	NM_001111827
	-----------------------------------------------------------------------------------------------------------------------------	NM_001027894
	-----------------------------------------------------------------------------------------------------------------------------	NM_068459
cbriggsae	((((..............((((((.(((...(((......(((...((.((((((....)))))).))....)))....))).....))).))))))..............))))	0.650 -10.09

cbriggsae

chromosome:chrIV:8331228:8331342:-1

Same_strand|Intronic_coding|NM_001027775|Y75B8A.37 ## Opposite_strand|Intronic_non-coding|NM_001111827|LOC542215 ## Opposite_strand|Intronic_coding|NM_001027894|nhr-46 ## {Repeats: no}

block2205 [novel_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	0.280	no	no	0.48/0.48	21/21/1.00	0.0	0.0	1	0	1	0	13	10	5arm	2	nd	0.33	4	1	1	na	na

		reads	miRBase family seed
seed	--------------CCAUAUC----------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-------------TCCATATCCTGCCAGGTTTTG---------------------------------------------------------------------------	21	1
cbriggsae	tactcgttctcagTCCATATCCTGCCAGGTTTTGaaaagatcaagaaaattttattgtcctcattttcaaagtgtggtttttcattgtgttctctcatgcagtatgagt
	*************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------	NM_057270
	-----------------------------------------------------------------------------------------------------------------------	NM_164773
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_066961
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001001344
cbriggsae	.((((((.((.((..((((....((((..(((((((((((.(((..........)))...)).)))))))))..)))).......))))..)).......)).))))))	0.520 -19.10

cbriggsae

chromosome:chrIV:9028949:9029057:-1

Opposite_strand|Intronic_coding|NM_057270|LanB1 ## Same_strand|Intronic_non-coding|NM_066961|W09D10.4 ## Same_strand|Intronic_coding|NM_001001344|ATP2B3 ## {Repeats: no}

block2298 [novel_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	0.753	no	no	0.65/0.65	23/23/1.00	0.0	0.0	1	0	1	0	13	12	5arm	1	nd	0.35	4	1	1	na	na

		reads	miRBase family seed
seed	--------------GCCUCUG------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-------------AGCCTCTGGAACCACGACCGCGA---------------------------------------------------------------------	23	1
cbriggsae	tgggtcccagtagAGCCTCTGGAACCACGACCGCGAgctcctcctgattgttgtgtacgggttactgcttccgccctcgatgtttgaacacggctgctatgacct
	*********************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001026518
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_067755
	-------------------------------------------------------------------------------------------------------------------	NM_001047596
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_064510
	-------------------------------------------------------------------------------------------------------------------	NM_075282
cbriggsae	.(((((...((((((((....((((..(((..((((((....((((((......)).)))).....)))..)))..)))..))))......)))).)))))))))	0.740 -28.00

cbriggsae

chromosome:chrIV:12950723:12950827:-1

Same_strand|Intronic_coding|NM_001026518|Y105E8A.29 ## Same_strand|Intronic_non-coding|NM_067755|xpc-1 ## Opposite_strand|Intronic_non-coding|NM_001047596|tag-349 ## {Repeats: no}

Page 19

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Page 70

miR-Intess™

block1038 [novel_nonpairedHIGH_bulgeHIGH]

block1141 [novel_nonpairedHIGH_bulgeHIGH]

block1322 [novel_nonpairedHIGH_bulgeHIGH]

block1637 [novel_nonpairedHIGH_bulgeHIGH]

block1962 [novel_nonpairedHIGH_bulgeHIGH]

block2137 [novel_nonpairedHIGH_bulgeHIGH]

block2179 [novel_nonpairedHIGH_bulgeHIGH]

block2181 [novel_nonpairedHIGH_bulgeHIGH]

block2205 [novel_nonpairedHIGH_bulgeHIGH]

block2298 [novel_nonpairedHIGH_bulgeHIGH]