miR-Intess: classification

other hairpins

novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH (14 loci)

block2625 [novel_lenNOK_shortStem_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	0.071	no	no	0.22/0.22	18/18/0.00	0.0	0.0	2	0	1	0	1	13	5arm	1	nd	0.39	4	2	1	na	na

		reads	miRBase family seed
seed	--UUUAUAU--------------------------------------------------------	2	novel
		len	cloning frequencies
			AF16
	-TTTTATATACAACAGTTC----------------------------------------------	18	2
cbriggsae	gTTTTATATACAACAGTTCaaacaatggtttaataattaggaattgttttgggctgatagaagca
	*****************************************************************
	---------------------------------------------------------------------------	NM_001094577
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_134696
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_026485
	---------------------------------------------------------------------------	NM_001083551
cbriggsae	(((((.(((....(((..((((((((..((((.....)))).)))))).))..))))))))))).	0.970 -12.40

cbriggsae

chromosome:chrIV:7077176:7077240:1

Opposite_strand|Intronic_non-coding|NM_001094577|LOC494739 ## Same_strand|Intronic_coding|NM_134696|CG2839 ## Same_strand|Intronic_non-coding|NM_026485|Trabd ## {Repeats: no}

block2941 [novel_lenNOK_shortStem_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	0.594	no	no	0.52/0.52	29/29/0.00	0.0	0.0	1	0	1	0	2	6	5arm	3	nd	0.41	4	1	1	na	na

		reads	miRBase family seed
seed	---UGGUUAC------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	--ATGGTTACCTAAGGCTCATGTTGAGGCCC---------------------------------------------	29	1
cbriggsae	ctATGGTTACCTAAGGCTCATGTTGAGGCCCccactacagctagtatacttttagcaggccttttattaaaattgg
	****************************************************************************
cbriggsae	(((...(((...((((((..((((((((.....((((....))))....))))))))))))))....)))...)))	0.640 -12.80

cbriggsae

chromosome:chrM:6759:6834:-1

{Repeats: no}

block3112 [novel_lenNOK_shortStem_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	0.594	no	no	0.52/0.52	29/29/0.00	0.0	0.0	1	0	1	0	2	6	5arm	3	nd	0.41	4	1	1	na	na

		reads	miRBase family seed
seed	---UGGUUAC------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	--ATGGTTACCTAAGGCTCATGTTGAGGCCC---------------------------------------------	29	1
cbriggsae	ctATGGTTACCTAAGGCTCATGTTGAGGCCCccactacagctagtatacttttagcaggccttttattaaaattgg
	****************************************************************************
cbriggsae	(((...(((...((((((..((((((((.....((((....))))....))))))))))))))....)))...)))	0.640 -12.80

cbriggsae

chromosome:chrUn:4220822:4220897:-1

{Repeats: no}

block3480 [novel_lenNOK_shortStem_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	0.594	no	no	0.52/0.52	29/29/0.00	0.0	0.0	1	0	1	0	2	6	5arm	3	nd	0.41	4	1	1	na	na

		reads	miRBase family seed
seed	---UGGUUAC------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	--ATGGTTACCTAAGGCTCATGTTGAGGCCC---------------------------------------------	29	1
cbriggsae	ctATGGTTACCTAAGGCTCATGTTGAGGCCCccactacagctagtatacttttagcaggccttttattaaaattgg
	****************************************************************************
cbriggsae	(((...(((...((((((..((((((((.....((((....))))....))))))))))))))....)))...)))	0.640 -12.80

cbriggsae

chromosome:chrUn:4248337:4248412:1

{Repeats: no}

block4004 [novel_lenNOK_shortStem_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	0.876	no	no	0.50/0.50	18/18/0.00	0.0	0.0	3	0	1	0	4	12	3arm	1	nd	0.33	4	3	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------ACAAGAA--------------	3	novel
		len	cloning frequencies
			AF16
	--------------------------------------------------------GACAAGAAGAGTCCCATG----	18	3
cbriggsae	agttcagcttgaaatttgtccagatttccgggaaagttacggtattcctcgacgttGACAAGAAGAGTCCCATGacct
	******************************************************************************
	----------------------------------------------------------------------------------------	NM_007590
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_101553
	----------------------------------------------------------------------------------------	NM_067315
cbriggsae	((.(((((((....((((((..(((.((.(((((..........))))).)).)))))))))..))))....))).))	0.400 -12.70

cbriggsae

chromosome:chrV:3457329:3457406:1

Opposite_strand|Intronic_non-coding|NM_007590|Calm3 ## Same_strand|Intronic_non-coding|NM_101553|RAB11 ## Opposite_strand|Intronic_coding|NM_067315|Y39E4B.10 ## {Repeats: no}

block4498 [novel_lenNOK_shortStem_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	0.425	no	no	0.47/0.47	19/19/0.00	0.0	0.0	1	0	1	0	3	17	5arm	1	nd	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	----CCAGCUA----------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	---TCCAGCTAGTGTGTGGTAA-----------------------------------------------------	19	1
cbriggsae	aatTCCAGCTAGTGTGTGGTAAaatggttttactcgtgtagatgacacgtgtggtatctcaaacttgggtaatta
	***************************************************************************
	-------------------------------------------------------------------------------------	NM_007789
	-------------------------------------------------------------------------------------	NM_001047210
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_076367
cbriggsae	((((((....(((.((.((((........((((.(((((.....))))).)))))))).)).)))..)).)))).	0.820 -14.50

cbriggsae

chromosome:chrX:9574709:9574783:-1

Opposite_strand|Intronic_non-coding|NM_007789|Ncan ## Same_strand|Intronic_coding|NM_076367|atg-16.1 ## {Repeats: no}

block4776 [novel_lenNOK_shortStem_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	0.734	no	no	0.50/0.50	26/26/0.00	0.0	0.0	1	0	1	0	1	13	5arm	1	nd	0.50	4	1	1	na	na

		reads	miRBase family seed
seed	--UUUGACC------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-GTTTGACCCCCAAAGGCTGTAAATGG------------------------------------------------------	26	1
cbriggsae	cGTTTGACCCCCAAAGGCTGTAAATGGaaccatcggcatcgcaagatttttttttccagacggaagtggctgcccattcgg
	*********************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001031326
cbriggsae	((..((....(((....((((...(((((........(((....)))......))))).))))...))).....))..)).	0.480 -17.44

cbriggsae

chromosome:chrX:19975759:19975839:-1

Same_strand|Intronic_non-coding|NM_001031326|CLK2 ## {Repeats: no}

novel_Multihit (12 loci)

block87 [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	0.188	no	no	0.55/0.55	22/22/1.00	0.0	0.0	1	0	1	0	21	13	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	taaatgtaggccagtgaacccGTTTCGAGTGTGTGTGCGCCTTtaaccccttcgtggcgacacctcaacgatagggcgcgcttgcacgaagagagagaaaattggcgggaatttga
	********************************************************************************************************************
	------------------------------------------------------------------------------------------------------------------------------	NM_020177
	------------------------------------------------------------------------------------------------------------------------------	NM_001032736
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_122649
	------------------------------------------------------------------------------------------------------------------------------	NM_059191
	------------------------------------------------------------------------------------------------------------------------------	NM_115574
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_120834
cbriggsae	(((((....((((((.......((((..(((((.(((((((((..........(((....))).........))))))))).)))))...))))......))))))....))))).	0.990 -37.13

cbriggsae

chromosome:chrI:3460902:3461017:-1

Opposite_strand|Intronic_non-coding|NM_020177|FEM1C ## Opposite_strand|Intronic_coding|NM_001032736|cnp-3 ## Same_strand|Intronic_non-coding|NM_122649|HTA7 ## Same_strand|Intronic_coding|NM_120834|GRP18 ## {Repeats: no}

block262 [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	0.220	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	12	8	3arm	49	nd	0.30	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------CGUUCGU------------------------	1	novel
		len	cloning frequencies
			AF16
	-------------------------------------------------------------GCGTTCGTGGTGTAATGGTC------------	20	1
cbriggsae	gcggccaggcgcggcggcagccaccgcaatatgtacgccttggaagcttagaacatagcgtGCGTTCGTGGTGTAATGGTCagcatggatgcc
	*********************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001011629
	-------------------------------------------------------------------------------------------------------	NM_199320
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_014333
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001098517
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_061553
	-------------------------------------------------------------------------------------------------------	NM_067080
cbriggsae	(((.(((.((..(((..((..((((((...((((((((..((...........))..))))))))..))))))...))))).)).))).))).	0.540 -33.60

cbriggsae

chromosome:chrI:1372473:1372565:1

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

block1620 [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	0.117	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	12	2	3arm	49	nd	0.30	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------CGUUCGU------------------------	1	novel
		len	cloning frequencies
			AF16
	----------------------------------------------------------GCGTTCGTGGTGTAATGGTC------------	20	1
cbriggsae	gcgtctctctgccacgccctcgctttatctacgcgtttccccccttctctctcactgcGCGTTCGTGGTGTAATGGTCagcatggatgcc
	******************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001027762
	----------------------------------------------------------------------------------------------------	NM_075282
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_061817
	----------------------------------------------------------------------------------------------------	NM_071129
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_071129
	----------------------------------------------------------------------------------------------------	NM_068002
	----------------------------------------------------------------------------------------------------	NM_001129219
	----------------------------------------------------------------------------------------------------	NM_003107
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001026513
	----------------------------------------------------------------------------------------------------	NM_001027762
	----------------------------------------------------------------------------------------------------	NM_001090026
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001079600
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_172541
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_064860
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_067650
	----------------------------------------------------------------------------------------------------	NM_067787
	----------------------------------------------------------------------------------------------------	NM_067659
	----------------------------------------------------------------------------------------------------	NM_075459
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_061965
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_075282
	----------------------------------------------------------------------------------------------------	NM_070558
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_075513
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001037901
	----------------------------------------------------------------------------------------------------	NM_064510
	----------------------------------------------------------------------------------------------------	NM_072208
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_065010
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_065104
	----------------------------------------------------------------------------------------------------	NM_077859
	----------------------------------------------------------------------------------------------------	NM_001129266
	----------------------------------------------------------------------------------------------------	NM_001027789
cbriggsae	((((((..((((((((((..((........((((((....................)))))).)).)))))...)).)))...)))))).	0.940 -23.55

cbriggsae

chromosome:chrIII:1725529:1725618:1

Same_strand|Intronic_coding|NM_001027762|smr-1 ## Opposite_strand|Intronic_non-coding|NM_075282|wrs-1 ## Same_strand|Intronic_non-coding|NM_061817|cct-3 ## Opposite_strand|Intronic_coding|NM_071129|Y32G9A.10 ## {Repeats: no}

Page 52

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miR-Intess™

block2625 [novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH]

block2941 [novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH]

block3112 [novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH]

block3480 [novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH]

block4004 [novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH]

block4498 [novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH]

block4776 [novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH]

block87 [novel_Multihit]

block262 [novel_Multihit]

block1620 [novel_Multihit]