miR-Intess: classification

other hairpins

novel_loopOverlap_nonpairedHIGH_bulgeHIGH (20 loci)

block208 [novel_loopOverlap_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	0.229	no	no	0.55/0.55	22/22/1.00	0.0	0.0	1	0	1	0	28	-2	5arm_loop	1	nd	0.32	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------GAAUUUC-------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	----------------------------CGAATTTCGGTCGTCCATGTGC-----------------------------------------------------	22	1
cbriggsae	ctcccctttttatatttttcgtcctaatCGAATTTCGGTCGTCCATGTGCaatcaaatattggaatcttatgatcattttctgggaacggaacgagaatggga
	*******************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001030661
	-----------------------------------------------------------------------------------------------------------------	NM_065286
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001015867
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001083967
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_013685
	-----------------------------------------------------------------------------------------------------------------	NM_127719
	-----------------------------------------------------------------------------------------------------------------	NM_067629
cbriggsae	.((((.(((((.....((((((((((...(((....((((((((((((........)))).)))......)))))...)))))))).))))).))))).))))	0.670 -21.00

cbriggsae

chromosome:chrI:9724216:9724318:-1

Same_strand|Intronic_non-coding|NM_001030661|SETD1B ## Opposite_strand|Intronic_non-coding|NM_065286|Y53G8AR.6 ## {Repeats: no}

block296 [novel_loopOverlap_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	0.233	no	no	0.57/0.57	21/21/1.00	0.0	0.0	1	0	1	0	8	-2	5arm_loop	1	nd	0.52	4	1	1	na	na

		reads	miRBase family seed
seed	---------AUGCAGC-----------------------------------------	1	novel
		len	cloning frequencies
			AF16
	--------GATGCAGCAACTTCTCCTGGC----------------------------	21	1
cbriggsae	cactagagGATGCAGCAACTTCTCCTGGCatcactggatatggcagttcctaaagtg
	*********************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_026450
	-------------------------------------------------------------------	NM_001024290
	-------------------------------------------------------------------	NM_175692
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001087652
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001089360
	-------------------------------------------------------------------	NM_013920
	-------------------------------------------------------------------	NM_004133
	-------------------------------------------------------------------	NM_104594
	-------------------------------------------------------------------	NM_031795
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_115574
	-------------------------------------------------------------------	NM_205811
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001109628
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001109626
	-------------------------------------------------------------------	NM_001124041
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001853
	<<<<<<-------------------------------------------------------------	NM_060219
cbriggsae	((((..((((.((.((....(((..((....))..)))....)).))))))..))))	0.940 -12.90

cbriggsae

chromosome:chrI:3808260:3808316:1

Same_strand|Intronic_non-coding|NM_026450|Zfp169 ## Opposite_strand|Intronic_non-coding|NM_001024290|Gal3st3 ## Same_strand|Intronic_coding|NM_001087652|col18sv-a ## Opposite_strand|Intronic_coding|NM_013920|Hnf4g ## {Repeats: no}

block977 [novel_loopOverlap_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	0.646	no	no	0.40/0.40	20/20/1.00	0.0	0.0	2	0	1	0	15	-1	3arm	1	nd	0.35	4	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------CAGAGAU---------------------------	2	novel
		len	cloning frequencies
			AF16
	----------------------------------------------------------ACAGAGATTTAGAACCAAGC---------------	20	2
cbriggsae	atcaaaaacggtagaatcacggattctggggagagattctggggaaataagctatgaaACAGAGATTTAGAACCAAGCgtgatatgttggggg
	*********************************************************************************************
	-------------------------------------------------------------------------------------------------------	NM_177732
	-------------------------------------------------------------------------------------------------------	NM_121608
	-------------------------------------------------------------------------------------------------------	NM_214509
	-------------------------------------------------------------------------------------------------------	NM_001030843
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001101718
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001011629
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001056446
	-------------------------------------------------------------------------------------------------------	NM_001036812
	-------------------------------------------------------------------------------------------------------	NM_001125761
	.................................................................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	NM_001026860
	.................................................................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	NM_001026861
	.................................................................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	NM_001026859
cbriggsae	.((...((((.....((((((.....(((....((((((((..................))))).)))....)))..)))))).))))..)).	0.560 -13.87

cbriggsae

chromosome:chrII:7650727:7650819:1

Opposite_strand|Intronic_non-coding|NM_177732|Slc35d1 ## Opposite_strand|Intronic_coding|NM_121608|AT5G16030 ## Same_strand|Intronic_coding|NM_001101718|LOC100009540 ## Same_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Opposite_strand|Boundary_non-coding|NM_001026860|trr-1 ## {Repeats: no}

block990 [novel_loopOverlap_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	0.528	no	no	0.45/0.45	22/22/1.00	0.0	0.0	1	0	1	0	16	-2	5arm_loop	5	nd	0.45	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------AAUAUCG--------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	----------------GAATATCGAAACAACTGCCTCG------------------------------------------	22	1
cbriggsae	ccgtcccccgaagtccGAATATCGAAACAACTGCCTCGacgggcctggtcttctcgaagcactcggttcttctctagcga
	********************************************************************************
	------------------------------------------------------------------------------------------	NM_001047975
	------------------------------------------------------------------------------------------	NM_001047939
	------------------------------------------------------------------------------------------	NM_001047939
	------------------------------------------------------------------------------------------	NM_127141
	------------------------------------------------------------------------------------------	NM_001003414
	------------------------------------------------------------------------------------------	NM_182152
	------------------------------------------------------------------------------------------	NM_063631
	------------------------------------------------------------------------------------------	NM_063632
	------------------------------------------------------------------------------------------	NM_063623
	------------------------------------------------------------------------------------------	NM_063620
	------------------------------------------------------------------------------------------	NM_063619
	------------------------------------------------------------------------------------------	NM_063628
	------------------------------------------------------------------------------------------	NM_063626
	------------------------------------------------------------------------------------------	NM_063626
	------------------------------------------------------------------------------------------	NM_063625
	------------------------------------------------------------------------------------------	NM_064259
	------------------------------------------------------------------------------------------	NM_063630
	------------------------------------------------------------------------------------------	NM_063630
	------------------------------------------------------------------------------------------	NM_074369
	------------------------------------------------------------------------------------------	NM_063617
	------------------------------------------------------------------------------------------	NM_062054
	------------------------------------------------------------------------------------------	NM_074369
	------------------------------------------------------------------------------------------	NM_063618
	------------------------------------------------------------------------------------------	NM_068455
	------------------------------------------------------------------------------------------	NM_068454
cbriggsae	.(((.....((((.((((...((((....(((((((....))))..)))....)))).....))))..))))....))).	0.980 -18.10

cbriggsae

chromosome:chrII:8214659:8214738:1

Opposite_strand|Intronic_coding|NM_001047975|LOC683871 ## Opposite_strand|Intronic_non-coding|NM_127141|SQN ## {Repeats: no}

block1078 [novel_loopOverlap_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	0.416	no	no	0.58/0.58	24/24/1.00	0.0	0.0	2	0	1	0	7	-3	5arm_loop	1	nd	0.42	4	2	1	na	na

		reads	miRBase family seed
seed	--------GUCCUGA------------------------------------------------------	2	novel
		len	cloning frequencies
			AF16
	-------GGTCCTGACGCTGCATTTCCACAG--------------------------------------	24	2
cbriggsae	tcgtactGGTCCTGACGCTGCATTTCCACAGaacgattggacttctcagcgcgatgggatcttcttgag
	*********************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001030387
	-------------------------------------------------------------------------------	NM_062091
cbriggsae	(((....((((((..(((((....((((.........)))).....)))))....))))))....))).	0.970 -17.50

cbriggsae

chromosome:chrII:13134769:13134837:1

Same_strand|Intronic_non-coding|NM_001030387|ARIH1 ## Opposite_strand|Intronic_coding|NM_062091|F02E11.2 ## {Repeats: no}

block1642 [novel_loopOverlap_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	0.548	no	no	0.45/0.45	22/22/1.00	0.0	0.0	1	0	1	0	16	-2	5arm_loop	5	nd	0.45	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------AAUAUCG--------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	----------------GAATATCGAAACAACTGCCTCG------------------------------------------	22	1
cbriggsae	ccgtcccccgaagtccGAATATCGAAACAACTGCCTCGatgggcctggtcttctcgaagcactcggttcttctctagcga
	********************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001011629
	------------------------------------------------------------------------------------------	NM_006386
	------------------------------------------------------------------------------------------	NM_001093260
	------------------------------------------------------------------------------------------	NM_001093256
	------------------------------------------------------------------------------------------	NM_001045920
	------------------------------------------------------------------------------------------	NM_009573
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_065104
	------------------------------------------------------------------------------------------	NM_001098504
cbriggsae	.(((.....((((.((((...((((....(((((((....))))..)))....)))).....))))..))))....))).	0.940 -18.00

cbriggsae

chromosome:chrIII:2483382:2483461:1

Same_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Opposite_strand|Intronic_non-coding|NM_006386|DDX17 ## {Repeats: no}

block1674 [novel_loopOverlap_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	0.024	no	no	0.50/0.50	22/22/1.00	0.0	0.0	1	0	1	0	29	-1	5arm_loop	1	nd	0.32	4	1	1	na	na

		reads	miRBase family seed
seed	------------------------------UCAAACU-------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-----------------------------GTCAAACTGCCCGAGCATGATT-----------------------------------------------------------	22	1
cbriggsae	gagtatcctaatcagtcgaaaacgacaccGTCAAACTGCCCGAGCATGATTccagtctactgtgcttaccaggttttcacaatgttggttttgacagattaaatatattt
	**************************************************************************************************************
	------------------------------------------------------------------------------------------------------------------------	NM_134696
	------------------------------------------------------------------------------------------------------------------------	NM_068799
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_080378
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_175389
	------------------------------------------------------------------------------------------------------------------------	NM_104789
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_006914
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_202770
cbriggsae	((((((..(((((.(((((((.(((((..((.(((((....(((((((((....)))....))))))....)))))..))..))))).))))))).)))))...))))))	1.000 -26.30

cbriggsae

chromosome:chrIII:4582121:4582230:1

Opposite_strand|Intronic_coding|NM_134696|CG2839 ## Opposite_strand|Intronic_non-coding|NM_068799|rod-1 ## Same_strand|Intronic_non-coding|NM_080378|Mgat1 ## Same_strand|Intronic_coding|NM_202770|AT4G01985 ## {Repeats: no}

block1720 [novel_loopOverlap_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	0.260	no	no	0.38/0.38	21/21/1.00	0.0	0.0	1	0	1	0	9	-4	3arm_loop	1	nd	0.48	4	1	1	na	na

		reads	miRBase family seed
seed	------------------------------GACUUCA----------------------	1	novel
		len	cloning frequencies
			AF16
	-----------------------------AGACTTCATATGGTGTTTACC---------	21	1
cbriggsae	catggaagaactaaacataaatttggaacAGACTTCATATGGTGTTTACCcctgatatg
	***********************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001087791
	---------------------------------------------------------------------	NM_001047975
	---------------------------------------------------------------------	NM_001858
	---------------------------------------------------------------------	NM_213264
	---------------------------------------------------------------------	NM_131292
	---------------------------------------------------------------------	NM_080680
	---------------------------------------------------------------------	NM_001845
	---------------------------------------------------------------------	NM_007739
	---------------------------------------------------------------------	NM_181277
	---------------------------------------------------------------------	NM_001006951
	---------------------------------------------------------------------	NM_001081764
	---------------------------------------------------------------------	NM_001046199
	---------------------------------------------------------------------	NM_001005153
	---------------------------------------------------------------------	NM_001002980
	---------------------------------------------------------------------	NM_001014971
	---------------------------------------------------------------------	NM_204790
	---------------------------------------------------------------------	NM_001082666
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_079524
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_206442
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_206443
	---------------------------------------------------------------------	NM_001038742
	---------------------------------------------------------------------	NM_080338
	---------------------------------------------------------------------	NM_167026
	---------------------------------------------------------------------	NM_167027
	---------------------------------------------------------------------	NM_212528
	---------------------------------------------------------------------	NM_201478
	---------------------------------------------------------------------	NM_182968
	---------------------------------------------------------------------	NM_033150
	---------------------------------------------------------------------	NM_080629
	---------------------------------------------------------------------	NM_000089
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_005381
	---------------------------------------------------------------------	NM_001107100
	---------------------------------------------------------------------	NM_000393
	---------------------------------------------------------------------	NM_080681
	---------------------------------------------------------------------	NM_004845
	---------------------------------------------------------------------	NM_080680
	---------------------------------------------------------------------	NM_001844
	---------------------------------------------------------------------	NM_080679
	---------------------------------------------------------------------	NM_001854
	---------------------------------------------------------------------	NM_212579
	---------------------------------------------------------------------	NM_080630
	---------------------------------------------------------------------	NM_007736
	---------------------------------------------------------------------	NM_001083844
	---------------------------------------------------------------------	NM_007738
	---------------------------------------------------------------------	NM_031366
	---------------------------------------------------------------------	NM_199214
	---------------------------------------------------------------------	NM_009926
	---------------------------------------------------------------------	NM_031362
	---------------------------------------------------------------------	NM_031365
	---------------------------------------------------------------------	NM_134452
	---------------------------------------------------------------------	NM_000092
	---------------------------------------------------------------------	NM_000091
	---------------------------------------------------------------------	NM_078485
	---------------------------------------------------------------------	NM_001851
	---------------------------------------------------------------------	NM_001079992
	---------------------------------------------------------------------	NM_001130548
cbriggsae	((((..((...(((((((.....((((......))))....)))))))...))..))))	1.000 -9.40

cbriggsae

chromosome:chrIII:6844135:6844193:1

Same_strand|Intronic_coding|NM_001087791|col2a1b ## Opposite_strand|Intronic_coding|NM_001047975|LOC683871 ## Opposite_strand|Intronic_non-coding|NM_213264|col9a1 ## {Repeats: no}

block1985 [novel_loopOverlap_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	0.812	no	no	0.29/0.29	21/21/1.00	0.0	0.0	2	0	1	0	19	-2	5arm_loop	1	nd	0.48	4	2	1	na	na

		reads	miRBase family seed
seed	--------------------UAUAUUG------------------------------------------------	2	novel
		len	cloning frequencies
			AF16
	-------------------TTATATTGATCTAGCTTTTGG-----------------------------------	21	2
cbriggsae	gttgtttatttgatgttgaTTATATTGATCTAGCTTTTGGaaaaatggttttcttggtcacaaaaaactggtggc
	***************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_070351
	-------------------------------------------------------------------------------------	NM_182271
cbriggsae	((..((..(((..((.((((((....((...(((((((....))).)))).)).))))))))..)))..))..))	0.810 -10.00

cbriggsae

chromosome:chrIV:2126104:2126178:-1

Same_strand|Intronic_non-coding|NM_070351|LLC1.2 ## Opposite_strand|Intronic_coding|NM_182271|K02E7.4 ## {Repeats: no}

block1993 [novel_loopOverlap_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	0.241	no	no	0.30/0.30	20/20/1.00	0.0	0.0	1	0	1	0	18	-4	5arm_loop	1	nd	0.40	5	1	1	na	na

		reads	miRBase family seed
seed	-------------------AAUAGAU--------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	------------------TAATAGATAGTTGAACTTGG--------------------------------------------	20	1
cbriggsae	gagataaaagtaaaacaaTAATAGATAGTTGAACTTGGattcaaaaaaaccctataaacgttcgattcatcttgagatctcg
	**********************************************************************************
cbriggsae	(((((.................((((((((((((.........................)))))))).))))....))))).	0.490 -11.01