miR-Intess: classification

other hairpins

novel_shortStem_nonpairedHIGH_bulgeHIGH (24 loci)

block2944 [novel_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	0.682	no	no	0.36/0.36	22/22/1.00	0.0	0.0	1	0	1	0	0	16	5arm	5	nd	0.55	4	1	1	na	na

		reads	miRBase family seed
seed	-UUGAAUA--------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	TTTGAATAAGGTGGTAACCTTG------------------------------------------------------	22	1
cbriggsae	TTTGAATAAGGTGGTAACCTTGaggtcactgtcacaaataggttttttaatagttactttgggtctaggtttgaga
	****************************************************************************
cbriggsae	((..(((....(((....((..((((.(((((...(((.....)))...))))).))))..)).))).)))..)).	0.720 -11.80

cbriggsae

chromosome:chrM:9433:9508:-1

{Repeats: no}

block3115 [novel_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	0.682	no	no	0.36/0.36	22/22/1.00	0.0	0.0	1	0	1	0	0	16	5arm	5	nd	0.55	4	1	1	na	na

		reads	miRBase family seed
seed	-UUGAAUA--------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	TTTGAATAAGGTGGTAACCTTG------------------------------------------------------	22	1
cbriggsae	TTTGAATAAGGTGGTAACCTTGaggtcactgtcacaaataggttttttaatagttactttgggtctaggtttgaga
	****************************************************************************
cbriggsae	((..(((....(((....((..((((.(((((...(((.....)))...))))).))))..)).))).)))..)).	0.720 -11.80

cbriggsae

chromosome:chrUn:4223496:4223571:-1

{Repeats: no}

block3120 [novel_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	0.682	no	no	0.36/0.36	22/22/1.00	0.0	0.0	1	0	1	0	0	16	5arm	5	nd	0.55	4	1	1	na	na

		reads	miRBase family seed
seed	-UUGAAUA--------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	TTTGAATAAGGTGGTAACCTTG------------------------------------------------------	22	1
cbriggsae	TTTGAATAAGGTGGTAACCTTGaggtcactgtcacaaataggttttttaatagttactttgggtctaggtttgaga
	****************************************************************************
cbriggsae	((..(((....(((....((..((((.(((((...(((.....)))...))))).))))..)).))).)))..)).	0.720 -11.80

cbriggsae

chromosome:chrUn:4427402:4427477:-1

{Repeats: no}

block3681 [novel_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	0.418	no	no	0.32/0.32	22/22/1.00	0.0	0.0	1	0	1	0	4	19	3arm	1	nd	0.32	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------AUGUCAA------------------	1	novel
		len	cloning frequencies
			AF16
	----------------------------------------------------------------------AATGTCAAGGATCTGATTCTTT----	22	1
cbriggsae	cgtggatcaggtgctcctggatggtcctatttatcattgcggctttggtactcgcgatataatcgataatAATGTCAAGGATCTGATTCTTTtcga
	************************************************************************************************
	----------------------------------------------------------------------------------------------------------	NM_075157
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_074754
	----------------------------------------------------------------------------------------------------------	NM_074932
	----------------------------------------------------------------------------------------------------------	NM_074581
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_074580
	----------------------------------------------------------------------------------------------------------	NM_074580
	----------------------------------------------------------------------------------------------------------	NM_074935
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_007590
	----------------------------------------------------------------------------------------------------------	NM_071059
	----------------------------------------------------------------------------------------------------------	NM_101553
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_071405
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_067315
cbriggsae	((.((((((((...((((.(((.(((....((((.(((((((.........)))))))))))..)))......))).))))))))))))....)).	0.440 -21.40

cbriggsae

chromosome:chrV:3373032:3373127:-1

Opposite_strand|Intronic_coding|NM_075157|F16H6.3 ## Same_strand|Intronic_coding|NM_074754|F26D2.13 ## Same_strand|Intronic_non-coding|NM_007590|Calm3 ## Opposite_strand|Intronic_non-coding|NM_101553|RAB11 ## {Repeats: no}

block4197 [novel_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	0.496	no	no	0.45/0.45	22/22/1.00	0.0	0.0	1	0	1	0	3	14	5arm	8	nd	0.50	5	1	1	na	na

		reads	miRBase family seed
seed	----CCAGCUA----------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	---TCCAGCTAGTGTGTGGTAGAAT--------------------------------------------------	22	1
cbriggsae	aatTCCAGCTAGTGTGTGGTAGAATgcttttactcgtgtagatgacacgtgtggtatctcaaacttgggtaatta
	***************************************************************************
	-------------------------------------------------------------------------------------	NM_001026206
	-------------------------------------------------------------------------------------	NM_071054
	-------------------------------------------------------------------------------------	NM_074620
	-------------------------------------------------------------------------------------	NM_074618
	-------------------------------------------------------------------------------------	NM_074614
	-------------------------------------------------------------------------------------	NM_077929
	-------------------------------------------------------------------------------------	NM_001028567
	-------------------------------------------------------------------------------------	NM_067949
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_063805
	-------------------------------------------------------------------------------------	NM_074647
	-------------------------------------------------------------------------------------	NM_074619
	-------------------------------------------------------------------------------------	NM_070063
cbriggsae	((((((....(((.((.((((........((((.(((((.....))))).)))))))).)).)))..)).)))).	0.820 -14.50

cbriggsae

chromosome:chrV:13781109:13781183:1

Opposite_strand|Intronic_coding|NM_001026206|nhr-50 ## Same_strand|Intronic_coding|NM_063805|srh-135 ## {Repeats: no}

block4727 [novel_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	0.496	no	no	0.45/0.45	22/22/1.00	0.0	0.0	1	0	1	0	3	14	5arm	8	nd	0.50	5	1	1	na	na

		reads	miRBase family seed
seed	----CCAGCUA----------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	---TCCAGCTAGTGTGTGGTAGAAT--------------------------------------------------	22	1
cbriggsae	aatTCCAGCTAGTGTGTGGTAGAATgcttttactcgtgtagatgacacgtgtggtatctcaaacttgggtaatta
	***************************************************************************
	-------------------------------------------------------------------------------------	NM_203923
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001111199
	-------------------------------------------------------------------------------------	NM_001030661
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001003666
cbriggsae	((((((....(((.((.((((........((((.(((((.....))))).)))))))).)).)))..)).)))).	0.820 -14.50

cbriggsae

chromosome:chrX:18774469:18774543:-1

Opposite_strand|Intronic_non-coding|NM_203923|abcb4 ## Same_strand|Intronic_non-coding|NM_001111199|zgc:173710 ## Same_strand|Intronic_coding|NM_001003666|Zfp457 ## {Repeats: no}

block5190 [novel_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	0.693	no	no	0.39/0.39	23/23/1.00	0.0	0.0	1	0	1	0	3	20	3arm	1	nd	0.48	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------GAGAGGU------------------	1	novel
		len	cloning frequencies
			AF16
	----------------------------------------------------------------------CGAGAGGTGAATCATTGAATAAC---	23	1
cbriggsae	cgggagaacatctttgtgcaccgatctggacacatcaagctggctgaattcgtgctcgtcagacgtatgcCGAGAGGTGAATCATTGAATAACccc
	************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001011629
	----------------------------------------------------------------------------------------------------------	NM_001003133
cbriggsae	.(((......((..((..((((..((.((..((.((..((.(((((....)).))).))..)).))...))))..))))...))..))....))).	0.790 -22.60

cbriggsae

chromosome:chrX:17294781:17294876:1

Same_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Opposite_strand|Intronic_non-coding|NM_001003133|MX2 ## {Repeats: no}

novel_bulgeHIGH (22 loci)

block182 [novel_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	0.764	no	no	0.48/0.48	23/23/1.00	0.0	0.0	1	0	1	0	23	2	5arm	1	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	------------------------UCUCUCG--------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-----------------------TTCTCTCGCTCCTGGTTATCTTC-----------------------------------------------	23	1
cbriggsae	ccgttcgactgctctcatcgtcaTTCTCTCGCTCCTGGTTATCTTCgtcaccaatacgctggctcagactgagaagaatggaacagattcgga
	*********************************************************************************************
	-------------------------------------------------------------------------------------------------------	NM_199320
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_061648
	-------------------------------------------------------------------------------------------------------	NM_060440
cbriggsae	(((.....(((.((.......((((((((((.((..(((((....(((.......))).)))))..)).))))).))))))).)))...))).	0.730 -18.11

cbriggsae

chromosome:chrI:8986506:8986598:-1

Opposite_strand|Intronic_non-coding|NM_199320|PHF17 ## Same_strand|Intronic_coding|NM_061648|sdz-18 ## Opposite_strand|Intronic_coding|NM_060440|srt-62 ## {Repeats: no}

block318 [novel_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	0.162	no	no	0.32/0.32	22/22/1.00	0.0	0.0	1	0	1	0	14	8	5arm	1	nd	0.27	4	1	1	na	na

		reads	miRBase family seed
seed	---------------UAACAUG----------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	--------------ATAACATGATGTATGGAAGGAT--------------------------------------------------------	22	1
cbriggsae	gagatcctttaattATAACATGATGTATGGAAGGATaaataacagatggtgaatgtgattcgaataaattatgttacaatatataggttttg
	********************************************************************************************
	------------------------------------------------------------------------------------------------------	NM_001011629
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001075022
	------------------------------------------------------------------------------------------------------	NM_205107
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_033488
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_033489
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_033486
	------------------------------------------------------------------------------------------------------	NM_001130548
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_033492
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_024011
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_033493
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_033529
	------------------------------------------------------------------------------------------------------	NM_031809
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_033487
	------------------------------------------------------------------------------------------------------	NM_214466
	------------------------------------------------------------------------------------------------------	NM_152888
	------------------------------------------------------------------------------------------------------	NM_007737
cbriggsae	((((.(((.(((((.(((((((((.(((....((((.....(((.........))).))))..))).))))))))).))).)).))))))).	0.640 -14.30

cbriggsae

chromosome:chrI:5101184:5101275:1

Opposite_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Same_strand|Intronic_coding|NM_001075022|Os11g0689400 ## Opposite_strand|Intronic_coding|NM_205107|COL6A1 ## {Repeats: no}

block799 [novel_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	0.666	no	no	0.62/0.62	21/21/1.00	0.0	0.0	1	0	1	0	19	4	5arm	1	nd	0.24	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------CUGACGA----------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-------------------GCTGACGATGCCTCCGAATCC---------------------------------------------	21	1
cbriggsae	cggcggtgtcttttccttcGCTGACGATGCCTCCGAATCCgcctcagagtgtggagattccatttggagcaccggcggtccgtcg
	*************************************************************************************
cbriggsae	((((((...........((((((....((.((((((((((((((...)).))))).......))))))))).)))))).))))))	0.490 -26.41