miR-Intess: classification

other hairpins

novel_lenNOK_shortStem_nonpairedHIGH (15 loci)

block4538 [novel_lenNOK_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	0.791	no	no	0.68/0.68	19/19/0.00	0.0	0.0	3	0	1	0	2	9	5arm	2	nd	0.32	3	3	1	na	na

		reads	miRBase family seed
seed	---ACCAAGC----------------------------------------------------------	3	novel
		len	cloning frequencies
			AF16
	--CACCAAGCGTCCGCCCAGT-----------------------------------------------	19	3
cbriggsae	gcCACCAAGCGTCCGCCCAGTcaacggtgaaatggaaatcccagtgaaagtggagtcgatcgaggagg
	********************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_005235
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_174363
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001042599
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001092457
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_203998
	------------------------------------------------------------------------------	NM_001006317
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001045879
cbriggsae	.((.((...((((.(((((.(((..((.((........))))..)))...))).)).)).)).)).))	0.930 -14.60

cbriggsae

chromosome:chrX:12286728:12286795:-1

Same_strand|Intronic_non-coding|NM_005235|ERBB4 ## Same_strand|Intronic_coding|NM_001092457|MGC82829 ## Opposite_strand|Intronic_non-coding|NM_001006317|NFRKB ## {Repeats: no}

block4808 [novel_lenNOK_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	0.521	no	no	0.39/0.39	18/18/0.00	0.0	0.0	1	0	1	0	1	12	3arm	1	nd	0.33	2	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------UUUGCUA-----------	1	novel
		len	cloning frequencies
			AF16
	------------------------------------------------TTTTGCTACCTGTGAAGA-	18	1
cbriggsae	tctgttctagagtcacacgaactgagatcttgaattagttttttggttTTTTGCTACCTGTGAAGAg
	*******************************************************************
	-----------------------------------------------------------------------------	NM_001089360
	-----------------------------------------------------------------------------	NM_007496
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001011629
	-----------------------------------------------------------------------------	NM_001084210
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_134696
	-----------------------------------------------------------------------------	NM_103590
cbriggsae	.((.((((((.((..((.((((..(((.((......))..)))..))))..))..))))).))).))	0.850 -11.10

cbriggsae

chromosome:chrX:1414100:1414166:1

Opposite_strand|Intronic_coding|NM_001089360|zgc:162345 ## Opposite_strand|Intronic_non-coding|NM_007496|Zfhx3 ## Same_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Same_strand|Intronic_coding|NM_134696|CG2839 ## {Repeats: no}

block5203 [novel_lenNOK_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	0.695	no	no	0.17/0.17	18/18/0.00	0.0	0.0	1	0	1	0	0	18	5arm	1	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	-UGAUUGA-------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	TTGATTGAGTTTTTTTAA---------------------------------------------------------------------------	18	1
cbriggsae	TTGATTGAGTTTTTTTAAaatttttttttttgagttgatagacacagaacaacaaaacacaaaaatccatcaaaattcgaactattcaatgaa
	*********************************************************************************************
	-------------------------------------------------------------------------------------------------------	NM_029869
	-------------------------------------------------------------------------------------------------------	NM_020252
	-------------------------------------------------------------------------------------------------------	NM_133906
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_068376
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001014547
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_080381
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_021359
	-------------------------------------------------------------------------------------------------------	NM_001083297
	-------------------------------------------------------------------------------------------------------	NM_001083296
cbriggsae	((.(((((((..(((...((((((..((((((.(((...................))).))))))......)))))).)))..))))))).))	0.630 -8.11

cbriggsae

chromosome:chrX:17791732:17791824:1

Opposite_strand|Intronic_non-coding|NM_029869|Zkscan1 ## Same_strand|Intronic_coding|NM_068376|ZK354.3 ## Same_strand|Intronic_non-coding|NM_021359|Itgb6 ## Opposite_strand|Intronic_coding|NM_001083297|psa-3 ## {Repeats: AT_rich 1 22 1 class=Low_complexity}

novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH (14 loci)

block598 [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	0.912	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	0	16	5arm	1	nd	0.47	4	1	1	na	na

		reads	miRBase family seed
seed	-CUCAUCG--------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	GCTCATCGTTCCAGTTAGG---------------------------------------------------------------	19	1
cbriggsae	GCTCATCGTTCCAGTTAGGctccgcccctttttgctccaaatacatccgctcaaaaaaggttttgtctcgtttcgaaacgcc
	**********************************************************************************
	--------------------------------------------------------------------------------------------	NM_131262
	--------------------------------------------------------------------------------------------	NM_011341
	--------------------------------------------------------------------------------------------	NM_007697
	--------------------------------------------------------------------------------------------	NM_000767
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_077434
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_171029
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_171855
cbriggsae	((...(((....((..((((......(((((((((.............))...)))))))....))))..)).)))...)).	0.830 -9.22

cbriggsae

chromosome:chrII:2594910:2594991:-1

Opposite_strand|Intronic_non-coding|NM_131262|myod1 ## Same_strand|Intronic_coding|NM_077434|ver-4 ## {Repeats: no}

block1029 [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	0.627	no	no	0.36/0.36	25/25/0.00	0.0	0.0	1	0	1	0	0	0	5arm	1	nd	0.32	4	1	1	na	na

		reads	miRBase family seed
seed	-GAAAUUG------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	GGAAATTGGTTTACATTCCATTGTC-------------------------------------	25	1
cbriggsae	GGAAATTGGTTTACATTCCATTGTCgaagaagttatgggactggaacatgttatggtgtcca
	**************************************************************
	------------------------------------------------------------------------	NM_001038232
	------------------------------------------------------------------------	NM_062121
	------------------------------------------------------------------------	NM_061791
	------------------------------------------------------------------------	NM_001038233
	------------------------------------------------------------------------	NM_061723
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001123511
	----------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<------------------	NM_064193
cbriggsae	(((.((((....((((((((..(((.............)))))))..))))..)))).))).	0.760 -10.22

cbriggsae

chromosome:chrII:11231612:11231673:1

Opposite_strand|Intronic_coding|NM_001038232|bath-20 ## Same_strand|Intronic_non-coding|NM_001123511|rab7 ## Opposite_strand|Boundary_non-coding|NM_064193|pqn-87 ## {Repeats: no}

block1510 [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	0.044	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	3	11	3arm	1	nd	0.47	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------CAAUGCC--------------	1	novel
		len	cloning frequencies
			AF16
	--------------------------------------------TCAATGCCGCGGTTAAAGG---	19	1
cbriggsae	ggattaccacaatgggcgtcttgatagatacgttctatcagaccTCAATGCCGCGGTTAAAGGtct
	******************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_075282
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_133381
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_008273
	----------------------------------------------------------------------------	NM_001094712
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_199449
	----------------------------------------------------------------------------	NM_065202
cbriggsae	((((((((.((.((((.(((.(((((((.....)))))))))))))).))....)))....)))))	0.690 -18.90

cbriggsae

chromosome:chrIII:10225916:10225981:-1

Same_strand|Intronic_non-coding|NM_075282|wrs-1 ## Same_strand|Intronic_coding|NM_008273|Hoxd11 ## Opposite_strand|Intronic_non-coding|NM_001094712|LOC495006 ## {Repeats: no}

block1516 [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	0.135	no	no	0.58/0.58	19/19/0.00	0.0	0.0	1	0	1	0	1	2	5arm	1	nd	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	--CAUGGCC----------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-GCATGGCCAATGCCAACAG-----------------------------------------------	19	1
cbriggsae	tGCATGGCCAATGCCAACAGactcttcacatatccaatttccacttgtctgaacgcccacgccgtcg
	*******************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_000209
	-----------------------------------------------------------------------------	NM_170975
	-----------------------------------------------------------------------------	NM_001027762
	-----------------------------------------------------------------------------	NM_007723
	-----------------------------------------------------------------------------	NM_001011571
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_075282
	-----------------------------------------------------------------------------	NM_075505
	-----------------------------------------------------------------------------	NM_010466
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_133381
	-----------------------------------------------------------------------------	NM_065139
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_075413
	-----------------------------------------------------------------------------	NM_001067238
	-----------------------------------------------------------------------------	NM_001067238
	-----------------------------------------------------------------------------	NM_001067238
	-----------------------------------------------------------------------------	NM_181934
cbriggsae	...(((((....((...(((((........................)))))...))....)))))..	0.860 -11.86

cbriggsae

chromosome:chrIII:10423025:10423091:-1

Same_strand|Intronic_non-coding|NM_000209|PDX1 ## Opposite_strand|Intronic_non-coding|NM_170975|C33C12.10 ## Opposite_strand|Intronic_coding|NM_007723|Cnga1 ## {Repeats: no}

block1669 [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	0.133	no	no	0.39/0.39	18/18/0.00	0.0	0.0	1	0	1	0	0	17	5arm	1	nd	0.44	4	1	1	na	na

		reads	miRBase family seed
seed	-ACACAGA----------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	GACACAGAAGAACTAAAG------------------------------------------------------------	18	1
cbriggsae	GACACAGAAGAACTAAAGactgtattttttcgtagaagaaggagattacgaaatcagaataggtagtatttcttatca
	******************************************************************************
	----------------------------------------------------------------------------------------	NM_001016781
	----------------------------------------------------------------------------------------	NM_001005609
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001043354
	----------------------------------------------------------------------------------------	NM_111431
	----------------------------------------------------------------------------------------	NM_001399
	----------------------------------------------------------------------------------------	NM_212504
	----------------------------------------------------------------------------------------	NM_007473
	----------------------------------------------------------------------------------------	NM_136816
	----------------------------------------------------------------------------------------	NM_131262
	----------------------------------------------------------------------------------------	NM_001014761
cbriggsae	((...(((((.((((....((((....((((((((..........)))))))).....)))).)))).)))))..)).	0.870 -13.40

cbriggsae

chromosome:chrIII:3941538:3941615:1

Opposite_strand|Intronic_non-coding|NM_001016781|LOC549535 ## Opposite_strand|Intronic_coding|NM_001005609|EDA ## Same_strand|Intronic_non-coding|NM_001043354|Rorb ## {Repeats: no}

block2149 [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	0.059	no	no	0.26/0.26	19/19/0.00	0.0	0.0	1	0	1	0	2	16	5arm	1	nd	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	---UUAGCUA----------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	--TTTAGCTAAGACAAATATC-----------------------------------------------------------------	19	1
cbriggsae	gtTTTAGCTAAGACAAATATCaatttttacttttccattccttcgaaaataatctttggaaaaccaatttgtctacactttgaaca
	**************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001094577
	------------------------------------------------------------------------------------------------	NM_134696
	------------------------------------------------------------------------------------------------	NM_026485
	------------------------------------------------------------------------------------------------	NM_004845
cbriggsae	((((.((...((((((((............(((((((...................)))))))...))))))))...))..)))).	0.410 -11.57

cbriggsae

chromosome:chrIV:7003227:7003312:-1

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

block2206 [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	0.521	no	no	0.54/0.54	26/26/0.00	0.0	0.0	1	0	1	0	2	0	3arm	1	nd	0.35	4	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------AUAUCCU--------------------	1	novel
		len	cloning frequencies
			AF16
	-----------------------------------------GATATCCTCCTCCGATGGCCAGTAGT--	26	1
cbriggsae	ggcttttgccagaacttctatagtgggattccttcctcaatGATATCCTCCTCCGATGGCCAGTAGTcg
	*********************************************************************
	-------------------------------------------------------------------------------	NM_057270
	-------------------------------------------------------------------------------	NM_164773
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_066961
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001001344
cbriggsae	((((...((((.....((...((..((((....((......)).))))..))..))))))....)))).	0.610 -13.30

cbriggsae

chromosome:chrIV:9044325:9044393:-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}

Page 51

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miR-Intess™

block4538 [novel_lenNOK_shortStem_nonpairedHIGH]

block4808 [novel_lenNOK_shortStem_nonpairedHIGH]

block5203 [novel_lenNOK_shortStem_nonpairedHIGH]

block598 [novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH]

block1029 [novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH]

block1510 [novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH]

block1516 [novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH]

block1669 [novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH]

block2149 [novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH]

block2206 [novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH]