miR-Intess: classification

other hairpins

block2980 [novel_shortStem_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	0.195	no	no	0.58/0.58	24/24/1.00	0.0	0.0	1	0	1	0	2	12	3arm	10	nd	0.38	3	1	1	na	na

		reads	miRBase family seed
seed	----------------------------------------------------AUAACCC------------------	1	novel
		len	cloning frequencies
			AF16
	---------------------------------------------------CATAACCCAGAGGTCGGTGGATCG--	24	1
cbriggsae	tcgactcacagacatcggtagcagcgtggcgcagtggaagcgtgctgggccCATAACCCAGAGGTCGGTGGATCGaa
	*****************************************************************************
cbriggsae	((((..(((.(((.(((((....((.((((((.((....)))))))).)).....)))..)).))).)))..)))).	0.920 -27.10

cbriggsae

chromosome:chrUn:819342:819418:-1

{Repeats: no}

block3136 [novel_shortStem_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	0.524	no	no	0.20/0.20	20/20/1.00	0.0	0.0	1	0	1	0	0	28	5arm	2	nd	0.35	3	1	1	na	na

		reads	miRBase family seed
seed	-ACUAAGA-----------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	TACTAAGATATTATTACTGA-----------------------------------------------------------------------------	20	1
cbriggsae	TACTAAGATATTATTACTGAtagaatttttagtttaatttagaatgtatcacttacaatgatagggtttaaaattctataattaagttattttttgt
	*************************************************************************************************
cbriggsae	.((.((((((...(((...((((((((((.........(((...((((.....)))).)))........))))))))))...)))..))))))..))	0.420 -11.53

cbriggsae

chromosome:chrUn:4431924:4432020:-1

{Repeats: no}

block3370 [novel_shortStem_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	0.942	no	no	0.58/0.58	24/24/1.00	0.0	0.0	1	0	1	0	2	12	3arm	10	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------AUAACCC------------------	1	novel
		len	cloning frequencies
			AF16
	------------------------------------------------------CATAACCCAGAGGTCGGTGGATCG--	24	1
cbriggsae	tccctcccaactgtctcttgtcagcagcgtggcgcagtggaagcgtgctgggccCATAACCCAGAGGTCGGTGGATCGaa
	********************************************************************************
cbriggsae	((..(((..(((((((((.((.....((.((((((.((....)))))))).)).....))..))))).)))))))..)).	0.430 -21.50

cbriggsae

chromosome:chrUn:854032:854111:1

{Repeats: no}

block3455 [novel_shortStem_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	0.390	no	no	0.40/0.40	20/20/1.00	0.0	0.0	1	0	1	0	4	22	5arm	1	nd	0.40	2	1	1	na	na

		reads	miRBase family seed
seed	-----AUGGUCA----------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	----TATGGTCATCAAGGGATATG----------------------------------------------------------------------------	20	1
cbriggsae	cgggTATGGTCATCAAGGGATATGgtcatgaagcgggtaagctttttcttaaattgcgctcccatttcatgttcatcatttcagtgctgcgtagaatccc
	****************************************************************************************************
cbriggsae	.(((..((..((.((..(((.(((..(((((((.(((...((..((.....))..))...))).)))))))..)))...)))..)).))..))....)))	0.930 -24.00

cbriggsae

chromosome:chrUn:3692468:3692567:1

{Repeats: no}

block3775 [novel_shortStem_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	0.199	no	no	0.48/0.48	21/21/1.00	0.0	0.0	1	0	1	0	0	8	3arm	1	nd	0.40	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------CUUUCUG-------------	1	novel
		len	cloning frequencies
			AF16
	--------------------------------------------GCTTTCTGGCTTATTCCAAGG	21	1
cbriggsae	ccttcgtaaatcggctctgcgattgctgagggactttcttcatcGCTTTCTGGCTTATTCCAAGG
	*****************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001011629
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001082367
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001082235
	---------------------------------------------------------------------------	NM_005334
cbriggsae	((((.((((..(((....((((....((((((....))))))))))...)))..))))...))))	0.900 -15.10

cbriggsae

chromosome:chrV:9389538:9389602:-1

Same_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Same_strand|Intronic_coding|NM_001082367|ROCK1 ## Opposite_strand|Intronic_non-coding|NM_005334|HCFC1 ## {Repeats: no}

block3865 [novel_shortStem_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	0.306	no	no	0.50/0.50	20/20/1.00	0.0	0.0	1	0	1	0	0	17	3arm	2	nd	0.32	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------AAUAGCA------------	1	novel
		len	cloning frequencies
			AF16
	------------------------------------------------------------CAATAGCAGTCTGGGCATCT	20	1
cbriggsae	ggaaccgagatttcattgaatccagagaacggaagccttttgtggtgttccgatagtagtCAATAGCAGTCTGGGCATCT
	********************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_074329
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001046690
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_074820
	------------------------------------------------------------------------------------------	NM_001129524
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001061126
cbriggsae	(((.((.(((((..(((((..........((((((((......))).))))).......)))))...))))).))..)))	0.640 -18.73

cbriggsae

chromosome:chrV:13525888:13525967:-1

Same_strand|Intronic_coding|NM_074329|srj-27 ## Opposite_strand|Intronic_coding|NM_001129524|T03E6.9 ## Same_strand|Intronic_non-coding|NM_001061126|Os05g0138300 ## {Repeats: no}

block4294 [novel_shortStem_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	0.319	no	no	0.45/0.45	22/22/1.00	0.0	0.0	1	0	1	0	0	13	5arm	8	nd	0.41	3	1	1	na	na

		reads	miRBase family seed
seed	-CCAGCUA----------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	TCCAGCTAGTGTGTGGTAGAAT--------------------------------------------	22	1
cbriggsae	TCCAGCTAGTGTGTGGTAGAATgctttactcgtgtagatgacacgtgtggtatttcaaacttgggt
	******************************************************************
	----------------------------------------------------------------------------	NM_070863
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_062358
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_062003
cbriggsae	((((...(((...((...(((((((..((.(((((.....))))).))))))))))).))))))).	0.830 -15.10

cbriggsae

chromosome:chrV_random:1214653:1214718:1

Opposite_strand|Intronic_coding|NM_070863|nhr-250 ## Same_strand|Intronic_coding|NM_062358|srw-40 ## {Repeats: no}

block4428 [novel_shortStem_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	0.30/0.30	20/20/1.00	0.0	0.0	1	0	1	0	1	25	5arm	5	nd	0.35	3	1	1	na	na

		reads	miRBase family seed
seed	--AAAGUUU------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-GAAAGTTTGGTAAAAGAAAG------------------------------------------------------------------------	20	1
cbriggsae	tGAAAGTTTGGTAAAAGAAAGcattttccttcagatttacagtgatttttctttcacgtcactgagattttctttttcttcttaatttttcag
	*********************************************************************************************
	-------------------------------------------------------------------------------------------------------	NM_001105250
	-------------------------------------------------------------------------------------------------------	NM_004796
	-------------------------------------------------------------------------------------------------------	NM_138970
	-------------------------------------------------------------------------------------------------------	NM_001087279
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_007496
	-------------------------------------------------------------------------------------------------------	NM_001080396
	-------------------------------------------------------------------------------------------------------	NM_007736
	-------------------------------------------------------------------------------------------------------	NM_001092981
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001090075
	-------------------------------------------------------------------------------------------------------	NM_001087789
	-------------------------------------------------------------------------------------------------------	NM_001079250
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_008591
	-------------------------------------------------------------------------------------------------------	NM_030706
cbriggsae	((((((...((.(((((((..............(((((.(((((((...........)))))))))))))))))))....))....)))))).	0.440 -14.53

cbriggsae

chromosome:chrX:5610005:5610097:-1

Opposite_strand|Intronic_non-coding|NM_001105250|NRXN3 ## Same_strand|Intronic_non-coding|NM_007496|Zfhx3 ## Opposite_strand|Intronic_coding|NM_007736|Col4a5 ## Same_strand|Intronic_coding|NM_001090075|MGC69046 ## {Repeats: no}

block5098 [novel_shortStem_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	0.689	no	no	0.38/0.38	21/21/1.00	0.0	0.0	1	0	1	0	0	12	5arm	1	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	-UUGUUCU--------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	GTTGTTCTCAGTAGCTGTTAT-------------------------------------------------------	21	1
cbriggsae	GTTGTTCTCAGTAGCTGTTATgatactggtacgaaaaaactggagcggtagaaaagaaacgctggtggccatgact
	****************************************************************************
	--------------------------------------------------------------------------------------	NM_011978
cbriggsae	(((((..(((.((((.(((....(((((...((.......))...))))).......))))))).)))..))))).	0.740 -13.20

cbriggsae

chromosome:chrX:14752744:14752819:1

Opposite_strand|Intronic_non-coding|NM_011978|Slc27a2 ## {Repeats: no}

novel_lenNOK_loopOverlap_nonpairedHIGH (17 loci)

block138 [novel_lenNOK_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	0.891	no	no	0.42/0.42	26/26/0.00	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	-----------------------CAAACAA----------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	----------------------GCAAACAATCACGTCGAATATTGGTC----------------------------------------------------	26	1
cbriggsae	cattatttctagatgacaacacGCAAACAATCACGTCGAATATTGGTCttatcccaaattggcaatgggcggtttttttcggtttacacatggaaaagtg
	****************************************************************************************************
	--------------------------------------------------------------------------------------------------------------	NM_001087279
	--------------------------------------------------------------------------------------------------------------	NM_177732
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_007732
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_214466
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_199473
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_073882
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_007740
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_152890
	--------------------------------------------------------------------------------------------------------------	NM_001081345
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001087019
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001001458
	--------------------------------------------------------------------------------------------------------------	NM_069710
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_211230
	--------------------------------------------------------------------------------------------------------------	NM_001021292
cbriggsae	((((.((((((..((..(((.((.((((..(((.(((((...((((.......)))).)))))..)))...))))....)))))..))..))))))))))	0.810 -15.30

cbriggsae

chromosome:chrI:7165238:7165337:-1

Opposite_strand|Intronic_non-coding|NM_001087279|fbxl5 ## Same_strand|Intronic_coding|NM_007732|Col17a1 ## Opposite_strand|Intronic_coding|NM_001081345|Chd2 ## Same_strand|Intronic_non-coding|NM_001087019|nr2f2 ## {Repeats: no}

Page 41

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miR-Intess™

block2980 [novel_shortStem_nonpairedHIGH]

block3136 [novel_shortStem_nonpairedHIGH]

block3370 [novel_shortStem_nonpairedHIGH]

block3455 [novel_shortStem_nonpairedHIGH]

block3775 [novel_shortStem_nonpairedHIGH]

block3865 [novel_shortStem_nonpairedHIGH]

block4294 [novel_shortStem_nonpairedHIGH]

block4428 [novel_shortStem_nonpairedHIGH]

block5098 [novel_shortStem_nonpairedHIGH]

block138 [novel_lenNOK_loopOverlap_nonpairedHIGH]