miR-Intess: classification

other hairpins

novel_loopOverlap_nonpairedHIGH (16 loci)

block2876 [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	0.442	no	no	0.40/0.43	20/21/1.00	0.0	0.3	3	0	1	0	7	-3	3arm_loop	1	nd	0.33	3	3	1	na	na

		reads	miRBase family seed
seed	---------------------------------------UUCGUAG--------------------	3	novel
		len	cloning frequencies
			AF16
	--------------------------------------TTTCGTAGTCTTTTGTGTCGG-------	21	2
	--------------------------------------TTTCGTAGTCTTTTGTGTCG--------	20	1
cbriggsae	agtaatctcataaaatttatgcgtactaaaaaatgcaaTTTCGTAGTCTTTTGTGTCGGagaacta
	******************************************************************
cbriggsae	(((..((((((((((....((((..................))))...)))))))..)))..))).	0.820 -8.67

cbriggsae

chromosome:chrIV_random:464734:464799:-1

{Repeats: no}

block2919 [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	0.112	no	no	0.38/0.38	21/21/1.00	0.0	0.0	1	0	1	0	16	-1	5arm_loop	1	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------UCUCUUG----------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	----------------TTCTCTTGTGTTCCAAATTCG---------------------------------------------	21	1
cbriggsae	aaaatgtaaaatttacTTCTCTTGTGTTCCAAATTCGtccgaatttctggaaaattcgagtttttcgaaatttgaaaatttt
	**********************************************************************************
cbriggsae	(((((...((((((......((((..((((((((((....)))))..)))))....)))).......))))))....)))))	0.480 -13.42

cbriggsae

chromosome:chrIV_random:737221:737302:1

{Repeats: no}

block3028 [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	0.413	no	no	0.48/0.48	23/23/1.00	0.0	0.0	3	0	1	0	43	-1	5arm_loop	2	nd	0.43	3	3	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------UUUUUCG-------------------------------------------------------------------	3	novel
		len	cloning frequencies
			AF16
	-------------------------------------------GTTTTTCGATGGCTTCCGAATCC----------------------------------------------------	23	3
cbriggsae	ggacttctttagatgaaatcgagcattcagaatccttctccacGTTTTTCGATGGCTTCCGAATCCttttagatgacgtggctgatgacgtggatggttcagaatcttctataagttt
	**********************************************************************************************************************
cbriggsae	.(((((...((((........((.((((.(((.((...((((((((..((...((((..((.(((......)))..)).)))))).)))))))).))))).)))))))))).))))).	0.530 -26.20

cbriggsae

chromosome:chrUn:1740549:1740666:-1

{Repeats: no}

block3402 [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	0.413	no	no	0.48/0.48	23/23/1.00	0.0	0.0	3	0	1	0	43	-1	5arm_loop	2	nd	0.43	3	3	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------UUUUUCG-------------------------------------------------------------------	3	novel
		len	cloning frequencies
			AF16
	-------------------------------------------GTTTTTCGATGGCTTCCGAATCC----------------------------------------------------	23	3
cbriggsae	ggacttctttagatgaaatcgagcattcagaatccttctccacGTTTTTCGATGGCTTCCGAATCCttttagatgacgtggctgatgacgtggatggttcagaatcttctataagttt
	**********************************************************************************************************************
cbriggsae	.(((((...((((........((.((((.(((.((...((((((((..((...((((..((.(((......)))..)).)))))).)))))))).))))).)))))))))).))))).	0.530 -26.20

cbriggsae

chromosome:chrUn:1730148:1730265:1

{Repeats: no}

block3711 [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	0.873	no	no	0.50/0.50	22/22/1.00	0.0	0.0	1	0	1	0	18	-2	5arm_loop	1	nd	0.45	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------UUGUCCU---------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	------------------GTTGTCCTTGCTGTGCCACATT-------------------------------------	22	1
cbriggsae	cacgtactccagatgataGTTGTCCTTGCTGTGCCACATTtttgtttccactcgaatccacgccgtcagccatacgt
	*****************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_062569
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_062548
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_062490
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001027169
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_069339
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_069380
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_069341
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_062753
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_062505
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_062748
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_062764
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_062571
	---------------------------------------------------------------------------------------	NM_070877
	---------------------------------------------------------------------------------------	NM_071913
	---------------------------------------------------------------------------------------	NM_032435
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_112328
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001125155
	<<<<<----------------------------------------------------------------------------------	NM_058341
cbriggsae	.(((((.......(((..((((...(((..(((..(((....)))...))).)))...)).))..)))....)))))	0.430 -9.50

cbriggsae

chromosome:chrV:5355096:5355172:-1

Same_strand|Intronic_coding|NM_062569|msp-49 ## Same_strand|Intronic_non-coding|NM_001027169|nhr-109 ## Opposite_strand|Intronic_coding|NM_070877|ugt-42 ## Opposite_strand|Intronic_non-coding|NM_032435|KIAA1804 ## {Repeats: no}

block3753 [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	0.843	no	no	0.35/0.35	20/20/1.00	0.0	0.0	1	0	1	0	21	-1	5arm_loop	1	nd	0.45	3	1	1	na	na

		reads	miRBase family seed
seed	----------------------UUGAAUU----------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	---------------------ATTGAATTCAAGGCAACATG----------------------------------	20	1
cbriggsae	tttttgagtttaaaatcgcgtATTGAATTCAAGGCAACATGatgatgagttagggaaaaagtatgtacacgaaag
	***************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_070871
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_173095
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_010595
	-------------------------------------------------------------------------------------	NM_026039
	-------------------------------------------------------------------------------------	NM_001093159
	-------------------------------------------------------------------------------------	NM_064380
	-------------------------------------------------------------------------------------	NM_173979
	-------------------------------------------------------------------------------------	NM_076658
cbriggsae	.(((((.((........(((((((...(((..(((..(((....))).)))..)))...))))))))).))))).	0.710 -8.00

cbriggsae

chromosome:chrV:8230998:8231072:-1

Same_strand|Intronic_coding|NM_070871|nhr-83 ## Opposite_strand|Intronic_non-coding|NM_026039|Med18 ## Opposite_strand|Intronic_coding|NM_001093159|MGC78950 ## {Repeats: no}

block3810 [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	0.611	no	no	0.30/0.30	23/23/1.00	0.0	0.0	1	0	1	0	9	-3	3arm_loop	1	nd	0.35	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------AUGUCAA------------------------	1	novel
		len	cloning frequencies
			AF16
	----------------------------------------GATGTCAAGAGTTTGTATTCAAT---------	23	1
cbriggsae	gtcacatgaagagtaagaaaaggtaaagacaagtgaccatGATGTCAAGAGTTTGTATTCAATcaatgttac
	************************************************************************
	----------------------------------------------------------------------------------	NM_001011629
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_182351
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_011821
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_007904
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_134696
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001040230
	----------------------------------------------------------------------------------	NM_001041377
	----------------------------------------------------------------------------------	NM_001042144
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001079844
	----------------------------------------------------------------------------------	NM_207352
	----------------------------------------------------------------------------------	NM_073111
cbriggsae	((.((((((.(((((...........((((...((((......))))...)))).)))))..))).))).))	0.750 -8.80

cbriggsae

chromosome:chrV:11322552:11322623:-1

Opposite_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Same_strand|Intronic_coding|NM_182351|fipr-1 ## Same_strand|Intronic_non-coding|NM_011821|Gpc6 ## Opposite_strand|Intronic_coding|NM_001041377|ECU05_1680 ## {Repeats: no}

block3957 [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	0.540	no	no	0.65/0.65	20/20/1.00	0.0	0.0	1	0	1	0	11	-4	3arm_loop	1	nd	0.35	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------AGCGCCG-----------------------	1	novel
		len	cloning frequencies
			AF16
	----------------------------------GAGCGCCGGGATTCTACGCA-----------	20	1
cbriggsae	actctggatccttcaagtcacgatagtattcggtGAGCGCCGGGATTCTACGCAggagacggcag
	*****************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001106714
	---------------------------------------------------------------------------	NM_001028857
	---------------------------------------------------------------------------	NM_001028858
	---------------------------------------------------------------------------	NM_001062304
	---------------------------------------------------------------------------	NM_029761
	---------------------------------------------------------<<<<<<<<<<<<<<<<<<	NM_072808
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_072806
cbriggsae	.(((((..((((........((.(((..((((((....))))))...))))).))))..))).))	0.530 -15.20

cbriggsae

chromosome:chrV:1206963:1207027:1

Same_strand|Intronic_non-coding|NM_001106714|Slc7a15 ## Opposite_strand|Intronic_non-coding|NM_001028857|K04F1.14 ## Opposite_strand|Intronic_coding|NM_001028858|K04F1.14 ## Opposite_strand|Boundary_coding|NM_072808|F25G6.9 ## {Repeats: no}

novel_Multihit_shortStem (15 loci)

block48 [novel_Multihit_shortStem]

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	0.069	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	3	4	3arm	49	nd	0.15	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------CGUUCGU---------------	1	novel
		len	cloning frequencies
			AF16
	----------------------------------------GCGTTCGTGGTGTAATGGTC---	20	1
cbriggsae	cgctgatttatatacgacaagaggatgaaagtttcaacatGCGTTCGTGGTGTAATGGTCagc
	***************************************************************
	-------------------------------------------------------------------------	NM_001011629
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_199320
	-------------------------------------------------------------------------	NM_014333
	-------------------------------------------------------------------------	NM_001098517
	-------------------------------------------------------------------------	NM_061553
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_067080
cbriggsae	.(((((((..(((((.((....(((((...((....))...))))))).)))))..)))))))	0.860 -16.40

cbriggsae

chromosome:chrI:1372413:1372475:-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}

block72 [novel_Multihit_shortStem]

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	0.569	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	4	0	3arm	49	nd	0.25	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------CGUUCGU----------------	1	novel
		len	cloning frequencies
			AF16
	------------------------------------------GCGTTCGTGGTGTAATGGTC----	20	1
cbriggsae	gcgcccttgttttatacgcgaaccgctccctctcctctcgccGCGTTCGTGGTGTAATGGTCagca
	******************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_177366
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001069244
	----------------------------------------------------------------------------	NM_058481
	----------------------------------------------------------------------------	NM_014920
	----------------------------------------------------------------------------	NM_058496
	----------------------------------------------------------------------------	NM_016513
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_059707
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_010301
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_008139
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_059728
cbriggsae	((..((.....(((((((((((.(((................))))))))).))))).))...)).	0.700 -15.09

cbriggsae

chromosome:chrI:2304871:2304936:-1

Same_strand|Intronic_non-coding|NM_177366|Gpr157 ## Opposite_strand|Intronic_non-coding|NM_058481|ubc-3 ## Opposite_strand|Intronic_coding|NM_058496|Y71G12B.5 ## Same_strand|Intronic_coding|NM_059728|F26A3.1 ## {Repeats: no}

Page 46

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miR-Intess™

block2876 [novel_loopOverlap_nonpairedHIGH]

block2919 [novel_loopOverlap_nonpairedHIGH]

block3028 [novel_loopOverlap_nonpairedHIGH]

block3402 [novel_loopOverlap_nonpairedHIGH]

block3711 [novel_loopOverlap_nonpairedHIGH]

block3753 [novel_loopOverlap_nonpairedHIGH]

block3810 [novel_loopOverlap_nonpairedHIGH]

block3957 [novel_loopOverlap_nonpairedHIGH]

block48 [novel_Multihit_shortStem]

block72 [novel_Multihit_shortStem]