miR-Intess: classification

other hairpins

block3473 [novel_Multihit]

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	0.149	no	no	0.55/0.55	22/22/1.00	0.0	0.0	1	0	1	0	12	17	5arm	15	nd	0.18	2	1	1	na	na

		reads	miRBase family seed
seed	-------------UUUCGAG------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	------------GTTTCGAGTGTGTGTGCGCCTT----------------------------------------------------------------	22	1
cbriggsae	gccagtgaacccGTTTCGAGTGTGTGTGCGCCTTtaaccccttcgtggcgagacctcaacgatagggcgcgcttgcacgaaggaagagggaaaaggcg
	**************************************************************************************************
cbriggsae	(((......(((.((((..(((((.(((((((((........((((...((....)).)))).))))))))).)))))...))))..)))....))).	0.950 -35.30

cbriggsae

chromosome:chrUn:4113492:4113589:1

{Repeats: no}

block4697 [novel_Multihit]

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	0.618	no	no	0.52/0.52	21/21/1.00	0.0	0.0	1	0	1	0	6	8	3arm	22	nd	0.29	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------UUGUUGU-------------------	1	novel
		len	cloning frequencies
			AF16
	------------------------------------------------------CTTGTTGTCAGCTGGGACCTT------	21	1
cbriggsae	gtcctcttggttctgtgttctggcttcgaactgttggccatcaccttggagaatCTTGTTGTCAGCTGGGACCTTcttggc
	*********************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_029869
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_020252
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_133906
	-------------------------------------------------------------------------------------------	NM_068376
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_020297
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_027016
	-------------------------------------------------------------------------------------------	NM_079863
	-------------------------------------------------------------------------------------------	NM_170535
	-------------------------------------------------------------------------------------------	NM_170536
	-------------------------------------------------------------------------------------------	NM_078585
	-------------------------------------------------------------------------------------------	NM_167331
	-------------------------------------------------------------------------------------------	NM_167332
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001087595
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_003262
	-------------------------------------------------------------------------------------------	NM_078127
	-------------------------------------------------------------------------------------------	NM_078127
	-------------------------------------------------------------------------------------------	NM_078127
cbriggsae	..((....(((((((....(((((..(((...(((..(((......)))..))).)))..))))).))))))).....)).	0.590 -17.90

cbriggsae

chromosome:chrX:17979583:17979663:-1

Same_strand|Intronic_non-coding|NM_029869|Zkscan1 ## Opposite_strand|Intronic_coding|NM_068376|ZK354.3 ## Same_strand|Intronic_coding|NM_027016|Sec62 ## Opposite_strand|Intronic_non-coding|NM_079863|dco ## {SimpF: trf}

block4699 [novel_Multihit]

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	0.929	no	no	0.52/0.52	21/21/1.00	0.0	0.0	1	0	1	0	11	9	3arm	22	nd	0.24	2	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------UUGUUGU------------------------	1	novel
		len	cloning frequencies
			AF16
	------------------------------------------------------------------CTTGTTGTCAGCTGGGACCTT-----------	21	1
cbriggsae	gatgtgagtaaagtcctctcggtcctgtgttctggcttcgaactgtaaacaatcaccttggagaatCTTGTTGTCAGCTGGGACCTTcttggcatatc
	**************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_029869
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_020252
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_133906
	------------------------------------------------------------------------------------------------------------	NM_068376
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_020297
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_027016
	------------------------------------------------------------------------------------------------------------	NM_079863
	------------------------------------------------------------------------------------------------------------	NM_170535
	------------------------------------------------------------------------------------------------------------	NM_170536
	------------------------------------------------------------------------------------------------------------	NM_078585
	------------------------------------------------------------------------------------------------------------	NM_167331
	------------------------------------------------------------------------------------------------------------	NM_167332
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001087595
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_003262
	------------------------------------------------------------------------------------------------------------	NM_078127
	<<<<<<<<<<<<------------------------------------------------------------------------------------------------	NM_078127
	<<<<<<<<<<<<------------------------------------------------------------------------------------------------	NM_078127
cbriggsae	((((((....(((.......(((((((....(((((..(((........(((.....))).......)))..))))).)))))))..)))..))))))	0.470 -19.26

cbriggsae

chromosome:chrX:17980977:17981074:-1

block4795 [novel_Multihit]

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	0.213	no	no	0.55/0.55	22/22/1.00	0.0	0.0	1	0	1	0	12	17	5arm	15	nd	0.18	2	1	1	na	na

		reads	miRBase family seed
seed	-------------UUUCGAG------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	------------GTTTCGAGTGTGTGTGCGCCTT----------------------------------------------------------------	22	1
cbriggsae	gccagtaaacccGTTTCGAGTGTGTGTGCGCCTTtaaccccttcgtggcgagacctcaacgatagggcgcgcttgcacgaaaagagagaaaattggcg
	**************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001095669
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001047906
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001047906
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_033381
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001844
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_007734
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_033380
	------------------------------------------------------------------------------------------------------------	NM_001122840
	------------------------------------------------------------------------------------------------------------	NM_033150
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_009930
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_032085
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001076831
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_053304
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_012929
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_000090
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_131292
	------------------------------------------------------------------------------------------------------------	NM_001090075
	------------------------------------------------------------------------------------------------------------	NM_214509
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001081764
	------------------------------------------------------------------------------------------------------------	NM_001031818
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_152660
	------------------------------------------------------------------------------------------------------------	NM_007734
	------------------------------------------------------------------------------------------------------------	NM_000090
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_009930
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_000495
cbriggsae	((((((.......((((..(((((.(((((((((........((((...((....)).)))).))))))))).))))).....))))....)))))).	0.940 -31.60

cbriggsae

chromosome:chrX:836939:837036:1

Same_strand|Intronic_coding|NM_001095669|foxp2a ## Opposite_strand|Intronic_coding|NM_001122840|si:ch211-212m21.5 ## Same_strand|Intronic_non-coding|NM_152660|FAM76A ## {Repeats: no}

block5189 [novel_Multihit]

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	0.273	no	no	0.55/0.55	22/22/1.00	0.0	0.0	1	0	1	0	31	14	5arm	15	nd	0.23	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------UUUCGAG---------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-------------------------------GTTTCGAGTGTGTGTGCGCCTT-------------------------------------------------------------------	22	1
cbriggsae	ccctagtgagtaaaaataggccagtaaatccGTTTCGAGTGTGTGTGCGCCTTtaacccctttgtggcgatacctcaacgatagggcgcgcttgcacaaagggagagaaaattggcggga
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001011629
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_205032
cbriggsae	(((................((((((...(((.(((...(((((.(((((((((........(((.((.....)).)))....))))))))).)))))))).)))......))))))))).	0.500 -34.89

cbriggsae

chromosome:chrX:17121268:17121387:1

Same_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## {Repeats: no}

block96 [novel_Multihit]

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	0.524	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	15	8	5arm	49	nd	0.25	2	1	1	na	na

		reads	miRBase family seed
seed	----------------CGUUCGU------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	---------------GCGTTCGTGGTGTAATGGTC------------------------------------------------------------------	20	1
cbriggsae	tgtctctgtttcgccGCGTTCGTGGTGTAATGGTCagcatggatgccttccaagcacacaggccaggcgcgactgctggataacgggcgaacgccggggcg
	*****************************************************************************************************
	---------------------------------------------------------------------------------------------------------------	NM_026450
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_175692
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001037394
	---------------------------------------------------------------------------------------------------------------	NM_001087652
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_104594
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_031795
	---------------------------------------------------------------------------------------------------------------	NM_115574
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001124041
	---------------------------------------------------------------------------------------------------------------	NM_001853
	---------------------------------------------------------------------------------------------------------------	NM_057771
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001031386
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001026315
cbriggsae	.(((((.((((((((.((((.((.((((..(((((.((.((((.....)))).)).....))))).)))).))........)))))))))).)).))))).	0.700 -36.90

cbriggsae

chromosome:chrI:3743779:3743879:-1

Opposite_strand|Intronic_non-coding|NM_026450|Zfp169 ## Same_strand|Intronic_non-coding|NM_175692|A930034L06Rik ## Opposite_strand|Intronic_coding|NM_001087652|col18sv-a ## Same_strand|Intronic_coding|NM_001031386|CIR ## {Repeats: no}

block3029 [novel_Multihit]

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	0.051	no	no	0.52/0.52	21/21/1.00	0.0	0.0	1	0	1	0	14	1	5arm	47	nd	0.00	0	1	1	na	na

		reads	miRBase family seed
seed	---------------UAAUGGU------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	--------------GTAATGGTCAGCATGGATGCC-----------------------------------------------------------	21	1
cbriggsae	tgtgcgttcgtggtGTAATGGTCAGCATGGATGCCttccaagcgcaggtgattcgtgattgaccaattacaggtatagggctataaacgaccaa
	**********************************************************************************************
cbriggsae	((..((((..((((((((((((((((((((((((((.........)))).))))))).))))))).)))).........))))..))))..)).	0.950 -29.10

cbriggsae

chromosome:chrUn:1921511:1921604:-1

{Repeats: no}

block3030 [novel_Multihit]

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	0.123	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	11	13	5arm	49	nd	0.10	2	1	1	na	na

		reads	miRBase family seed
seed	------------CGUUCGU------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-----------GCGTTCGTGGTGTAATGGTC------------------------------------------------------------------------------	20	1
cbriggsae	gaggaacatgtGCGTTCGTGGTGTAATGGTCagcatggatgccttccaagcgcaggtgattcgtgattgaccaattacaggtatagggctataaacgaccaattactta
	*************************************************************************************************************
cbriggsae	(((.....((..((((..((((((((((((((((((((((((((.........)))).))))))).))))))).)))).........))))..))))..))....))).	0.760 -29.90

cbriggsae

chromosome:chrUn:1921504:1921612:-1

{Repeats: no}

block98 [novel_Multihit]

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	0.524	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	15	8	5arm	49	nd	0.25	2	1	1	na	na

		reads	miRBase family seed
seed	----------------CGUUCGU------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	---------------GCGTTCGTGGTGTAATGGTC------------------------------------------------------------------	20	1
cbriggsae	tgtctctgtttcgccGCGTTCGTGGTGTAATGGTCagcatggatgccttccaagcacacaggccaggcgcgactgctggataacgggcgaacgccggggcg
	*****************************************************************************************************
	---------------------------------------------------------------------------------------------------------------	NM_026450
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_175692
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001037394
	---------------------------------------------------------------------------------------------------------------	NM_001087652
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_104594
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_031795
	---------------------------------------------------------------------------------------------------------------	NM_115574
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001124041
	---------------------------------------------------------------------------------------------------------------	NM_001853
	---------------------------------------------------------------------------------------------------------------	NM_057771
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001031386
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001026315
cbriggsae	.(((((.((((((((.((((.((.((((..(((((.((.((((.....)))).)).....))))).)))).))........)))))))))).)).))))).	0.700 -36.90

cbriggsae

chromosome:chrI:3748060:3748160:-1

novel_loopOverlap (12 loci)

block243 [novel_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	0.054	no	no	0.50/0.50	22/22/1.00	0.0	0.0	2	0	1	0	28	-3	3arm_loop	3	nd	0.23	2	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------UAUCCCA------------------------------------------	2	novel
		len	cloning frequencies
			AF16
	----------------------------------------GTATCCCAAGTGTCTCTTACGG----------------------------	22	2
cbriggsae	ttagatcgcttcgacaagccgaaaagccgcattgggaccaGTATCCCAAGTGTCTCTTACGGttccaccagttttatcggggcgaggcta
	******************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001011629
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001051257
	----------------------------------------------------------------------------------------------------	NM_026191
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_067594
	----------------------------------------------------------------------------------------------------	NM_184109
	----------------------------------------------------------------------------------------------------	NM_184109
cbriggsae	.(((.((((..(((..(((((((.((.(((.((((((......))))))))).)).)).)))))............)))..))))..)))	0.720 -28.94

cbriggsae

chromosome:chrI:421870:421959:1

Same_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Same_strand|Intronic_coding|NM_001051257|Os01g0834700 ## Opposite_strand|Intronic_non-coding|NM_026191|Dhx40 ## Opposite_strand|Intronic_coding|NM_184109|Rtl1 ## {Repeats: no}

Page 53

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Page 70

miR-Intess™

block3473 [novel_Multihit]

block4697 [novel_Multihit]

block4699 [novel_Multihit]

block4795 [novel_Multihit]

block5189 [novel_Multihit]

block96 [novel_Multihit]

block3029 [novel_Multihit]

block3030 [novel_Multihit]

block98 [novel_Multihit]

block243 [novel_loopOverlap]