miR-Intess: classification

other hairpins

block3263 [novel_loopOverlap_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	0.442	no	no	0.52/0.52	21/21/1.00	0.0	0.0	2	0	1	0	11	-4	5arm_loop_3arm	8	nd	0.24	4	2	1	na	na

		reads	miRBase family seed
seed	------------UCCGAUC------------------------------------------------------	2	novel
		len	cloning frequencies
			AF16
	-----------GTCCGATCTGGCAAGTTAAGC-----------------------------------------	21	2
cbriggsae	cacgccatcccGTCCGATCTGGCAAGTTAAGCaacgttgagtccagttagtacttggatcggagacggcctgg
	*************************************************************************
cbriggsae	((.(((.((((((((((.((((((((((....))).)))...)))).......))))).))).)).))).)).	0.790 -20.40

cbriggsae

chromosome:chrUn:5165581:5165653:-1

{Repeats: no}

novel_lenNOK_loopOverlap (4 loci)

block382 [novel_lenNOK_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	0.028	no	no	0.32/0.32	19/19/0.00	0.0	0.0	1	0	1	0	34	-3	3arm_loop	1	nd	0.26	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------UAUUGUG---------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	----------------------------------------------------TTATTGTGAGAAGTGTACT----------------------------------	19	1
cbriggsae	tttttactgttccagaggtaagtttactaaaagagatacttctccgagctaaTTATTGTGAGAAGTGTACTaatcgcagaattcgggactttggaaggttagaaa
	*********************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_199320
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_060440
cbriggsae	((((.(((.((((((((...(((((........((((((((((((((........))).))))))))).)).......))))).....))))))))))).)))).	0.640 -25.56

cbriggsae

chromosome:chrI:8928096:8928200:1

Same_strand|Intronic_non-coding|NM_199320|PHF17 ## Same_strand|Intronic_coding|NM_060440|srt-62 ## {Repeats: no}

block1522 [novel_lenNOK_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	0.102	no	no	0.69/0.69	26/26/0.00	0.0	0.0	1	0	1	0	36	-1	3arm	1	nd	0.27	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------AUGGAGC------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	----------------------------------------------------------GATGGAGCTTGCCGGCCGGGATGGTG------------------------------------	26	1
cbriggsae	tcatgcggtcctgtggtgcattccaatgacgccaggtggctcggcggggacgtgggatGATGGAGCTTGCCGGCCGGGATGGTGagacggtctggaatgtaagagttagagtctgttgag
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_000209
	----------------------------------------------------------------------------------------------------------------------------------	NM_170975
	----------------------------------------------------------------------------------------------------------------------------------	NM_001027762
	----------------------------------------------------------------------------------------------------------------------------------	NM_007723
	----------------------------------------------------------------------------------------------------------------------------------	NM_001011571
	----------------------------------------------------------------------------------------------------------------------------------	NM_001056446
	----------------------------------------------------------------------------------------------------------------------------------	NM_001027705
	----------------------------------------------------------------------------------------------------------------------------------	NM_013665
	----------------------------------------------------------------------------------------------------------------------------------	NM_075505
	----------------------------------------------------------------------------------------------------------------------------------	NM_010466
	----------------------------------------------------------------------------------------------------------------------------------	NM_068079
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_075402
	----------------------------------------------------------------------------------------------------------------------------------	NM_065139
	----------------------------------------------------------------------------------------------------------------------------------	NM_001025933
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001039276
	----------------------------------------------------------------------------------------------------------------------------------	NM_001027777
	----------------------------------------------------------------------------------------------------------------------------------	NM_065222
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_065455
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_067633
cbriggsae	(((.((((..(((...(((((((((.((.(((((..((((.(((((((..(((......)))...)))))))))))...)))))...))...))))))))).....)))...))))))).	0.860 -41.60

cbriggsae

chromosome:chrIII:10575798:10575917:-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}

block3605 [novel_lenNOK_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	0.300	no	no	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	24	-2	5arm_loop	1	nd	0.22	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------------UUCUUGA--------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	------------------------GTTCTTGAACACGTGTAC----------------------------------------------------------	18	1
cbriggsae	ggcgcattctcagaagtgccgtccGTTCTTGAACACGTGTACacaaggacacgacgatgttccacaagactggccatccacttctccacaattacagctc
	****************************************************************************************************
cbriggsae	(((........(((((((....(((.((((((((((((((........)))))....)))))...)))).))).....)))))))...........))).	0.670 -21.81

cbriggsae

chromosome:chrUn:6894367:6894466:1

{Repeats: no}

block4852 [novel_lenNOK_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	0.354	no	no	0.40/0.40	25/25/0.00	0.0	0.0	2	0	1	0	12	-1	5arm_loop	1	nd	0.28	3	2	1	na	na

		reads	miRBase family seed
seed	-------------UUUCCCG--------------------------------------------------------------------	2	novel
		len	cloning frequencies
			AF16
	------------GTTTCCCGTGATTTTGAACTTGTGT---------------------------------------------------	25	2
cbriggsae	caattcgtccatGTTTCCCGTGATTTTGAACTTGTGTacgcacagctttccaaataaaaaaatctcggagccgctaatttcaaattga
	****************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001087279
	--------------------------------------------------------------------------------------------------	NM_166414
	--------------------------------------------------------------------------------------------------	NM_001046332
cbriggsae	(((((.......((...(((.(((((((((.(((((....))))).))).........)))))).)))....))........))))).	0.830 -12.26

cbriggsae

chromosome:chrX:4767264:4767351:1

Same_strand|Intronic_non-coding|NM_001087279|fbxl5 ## Opposite_strand|Intronic_non-coding|NM_166414|Act57B ## {Repeats: no}

novel_lenNOK_loopOverlap_bulgeHIGH (4 loci)

block1784 [novel_lenNOK_loopOverlap_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	0.364	no	no	0.48/0.48	25/25/0.00	0.0	0.0	1	0	1	0	34	-3	3arm_loop	1	nd	0.28	4	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------UAUCUAU---------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-----------------------------------------------------------GTATCTATCAAGACGCCCATTGTGG----------------------------------	25	1
cbriggsae	tcgagatgaattggtcgaacctcgagacctttaaccgcggcattgaggtctgatagaacGTATCTATCAAGACGCCCATTGTGGtaatcctcttcaaactttttccagctcttccgga
	**********************************************************************************************************************
	--------------------------------------------------------------------------------------------------------------------------------	NM_075282
	--------------------------------------------------------------------------------------------------------------------------------	NM_133381
	--------------------------------------------------------------------------------------------------------------------------------	NM_008273
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001094712
	--------------------------------------------------------------------------------------------------------------------------------	NM_199449
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_065202
cbriggsae	(((.((.((.((((..(((....((((...((.((((((((......((((((((((.....))))))).))))))....)))))))...)))).....)))..)))).)).))))).	0.710 -27.10

cbriggsae

chromosome:chrIII:10225892:10226009:1

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

block2939 [novel_lenNOK_loopOverlap_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	0.527	no	no	0.24/0.24	25/25/0.00	0.0	0.0	1	0	1	0	25	-1	3arm	3	nd	0.16	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------UGCAAAU------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	------------------------------------------------------TTGCAAATTAAATGGTTATGGTTTT-------------------------	25	1
cbriggsae	tagtactactagtttaaaaaattagaaatcatagtataattttagtatatttaaTTGCAAATTAAATGGTTATGGTTTTtagtaagataggataatatagtcta
	********************************************************************************************************
cbriggsae	(((.((((....((((....(((((((((((((((.((((((..(((........)))))))))....)))))))))))))))....))))......)))))))	0.490 -12.90

cbriggsae

chromosome:chrM:4370:4473:-1

{Repeats: no}

block3110 [novel_lenNOK_loopOverlap_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	0.527	no	no	0.24/0.24	25/25/0.00	0.0	0.0	1	0	1	0	25	-1	3arm	3	nd	0.16	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------UGCAAAU------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	------------------------------------------------------TTGCAAATTAAATGGTTATGGTTTT-------------------------	25	1
cbriggsae	tagtactactagtttaaaaaattagaaatcatagtataattttagtatatttaaTTGCAAATTAAATGGTTATGGTTTTtagtaagataggataatatagtcta
	********************************************************************************************************
cbriggsae	(((.((((....((((....(((((((((((((((.((((((..(((........)))))))))....)))))))))))))))....))))......)))))))	0.490 -12.90

cbriggsae

chromosome:chrUn:4218433:4218536:-1

{Repeats: no}

block3482 [novel_lenNOK_loopOverlap_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	0.527	no	no	0.24/0.24	25/25/0.00	0.0	0.0	1	0	1	0	25	-1	3arm	3	nd	0.16	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------UGCAAAU------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	------------------------------------------------------TTGCAAATTAAATGGTTATGGTTTT-------------------------	25	1
cbriggsae	tagtactactagtttaaaaaattagaaatcatagtataattttagtatatttaaTTGCAAATTAAATGGTTATGGTTTTtagtaagataggataatatagtcta
	********************************************************************************************************
cbriggsae	(((.((((....((((....(((((((((((((((.((((((..(((........)))))))))....)))))))))))))))....))))......)))))))	0.490 -12.90

cbriggsae

chromosome:chrUn:4250699:4250802:1

{Repeats: no}

novel_shortStem_bulgeHIGH (4 loci)

block1813 [novel_shortStem_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	0.132	no	no	0.50/0.50	24/24/1.00	0.0	0.0	1	0	1	0	2	0	3arm	1	nd	0.25	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------UUAAUGC------------------	1	novel
		len	cloning frequencies
			AF16
	----------------------------------GTTAATGCTGACGCAACTTGGAGG--	24	1
cbriggsae	ttttctaaaaatgtcaaaaaacattcgctcacctGTTAATGCTGACGCAACTTGGAGGaa
	************************************************************
	----------------------------------------------------------------------	NM_001028998
	----------------------------------------------------------------------	NM_001028999
	----------------------------------------------------------------------	NM_001029004
	----------------------------------------------------------------------	NM_001029003
	----------------------------------------------------------------------	NM_001029002
	----------------------------------------------------------------------	NM_001029001
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_064155
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001122952
	----------------------------------------------------------------------	NM_028763
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_065922
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_010905
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_065923
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_068002
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_065190
	----------------------------------------------------------------------	NM_067159
	----------------------------------------------------------------------	NM_175692
	----------------------------------------------------------------------	NM_061965
	----------------------------------------------------------------------	NM_061817
	----------------------------------------------------------------------	NM_075459
	----------------------------------------------------------------------	NM_067160
	----------------------------------------------------------------------	NM_067659
cbriggsae	((((((((...(((((.....((((.((......)).)))).)))))....)))))))).	0.860 -9.90

cbriggsae

chromosome:chrIII:11299660:11299719:1

Opposite_strand|Intronic_non-coding|NM_001028998|unc-62 ## Same_strand|Intronic_non-coding|NM_064155|Y17G7B.3 ## Same_strand|Intronic_coding|NM_065922|C05D10.4 ## Opposite_strand|Intronic_coding|NM_067659|Y104H12BL.1 ## {Repeats: no}

Page 60

miR-Intess™

block3263 [novel_loopOverlap_bulgeHIGH]

block382 [novel_lenNOK_loopOverlap]

block1522 [novel_lenNOK_loopOverlap]

block3605 [novel_lenNOK_loopOverlap]

block4852 [novel_lenNOK_loopOverlap]

block1784 [novel_lenNOK_loopOverlap_bulgeHIGH]

block2939 [novel_lenNOK_loopOverlap_bulgeHIGH]

block3110 [novel_lenNOK_loopOverlap_bulgeHIGH]

block3482 [novel_lenNOK_loopOverlap_bulgeHIGH]

block1813 [novel_shortStem_bulgeHIGH]