miR-Intess: classification

other hairpins

novel_loopOverlap_nonpairedHIGH_bulgeHIGH (20 loci)

block154 [novel_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	0.218	no	no	0.45/0.45	20/20/1.00	0.0	0.0	1	0	1	0	0	13	3arm	1	nd	0.32	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------AAUCGUC------------	1	novel
		len	cloning frequencies
			AF16
	--------------------------------------------------------TAATCGTCGCTCAAGTAGGT	20	1
cbriggsae	ccaactttttctgttttatgttagtcataaatcctgaaaaatctcaggttttccatTAATCGTCGCTCAAGTAGGT
	****************************************************************************
	--------------------------------------------------------------------------------------	NM_001087279
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_176035
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_205985
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_205986
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_102365
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001084127
cbriggsae	((.((((.....((...((((((((...(((.(((((......))))))))...))))).))).))..)))).)).	0.520 -10.60

cbriggsae

chromosome:chrI:7998697:7998772:-1

Opposite_strand|Intronic_non-coding|NM_001087279|fbxl5 ## Same_strand|Intronic_coding|NM_176035|nAcRalpha-34E ## {Repeats: no}

block363 [novel_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	0.820	no	no	0.48/0.48	21/21/1.00	0.0	0.0	1	0	1	0	1	19	3arm	1	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------CUCUUGG--------------	1	novel
		len	cloning frequencies
			AF16
	--------------------------------------------------------------------------GCTCTTGGGTGAATCTATCGT-	21	1
cbriggsae	atgtttgatgtgaacctgtatattgtgagcatcctccgccggcgcatagtcaggaataatgtcttttggaacatGCTCTTGGGTGAATCTATCGTa
	************************************************************************************************
	----------------------------------------------------------------------------------------------------------	NM_001103403
	----------------------------------------------------------------------------------------------------------	NM_012772
	----------------------------------------------------------------------------------------------------------	NM_007723
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_171630
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_008855
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_171940
	.....................................................................................................<<<<<	NM_001025856
	.....................................................................................................<<<<<	NM_001025857
cbriggsae	(((...(((....(((((........((((((..((((..((.((((.((.....)).))))))..))))..)))))).)))))..)))...))).	0.410 -19.20

cbriggsae

chromosome:chrI:8309679:8309774:1

Opposite_strand|Intronic_coding|NM_001103403|tlk ## Same_strand|Intronic_non-coding|NM_171630|toca-1 ## {Repeats: no}

block590 [novel_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	0.171	no	no	0.48/0.48	21/21/1.00	0.0	0.0	1	0	1	0	4	20	5arm	1	nd	0.38	3	1	1	na	na

		reads	miRBase family seed
seed	-----AAUUCCA--------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	----CAATTCCAGAGTGCCATCGTT-------------------------------------------------------------------------	21	1
cbriggsae	cctcCAATTCCAGAGTGCCATCGTTtgccgaatattttgtgagtcttcgttgattgtcgaaattggccttggcatcgttgcggagtctgaaatttgag
	**************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001005457
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_058490
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_075282
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_182230
cbriggsae	.(((.((((.((((...((..((..((((((..((((((..((((......))))..)))))).....)))))).))....))..)))).)))).)))	0.690 -23.80

cbriggsae

chromosome:chrII:2014585:2014682:-1

Same_strand|Intronic_coding|NM_001005457|adsl ## Same_strand|Intronic_non-coding|NM_058490|Y71G12B.8 ## {Repeats: no}

block595 [novel_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	0.144	no	no	0.50/0.50	22/22/1.00	0.0	0.0	1	0	1	0	2	13	3arm	1	nd	0.36	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------UGAUCCU----------------	1	novel
		len	cloning frequencies
			AF16
	------------------------------------------------------------------ATGATCCTGGGTAGCTGGTTTG--	22	1
cbriggsae	actctccagaaagccatacgaatcaaacattctgccgaacatcacaaccttcagagtatcggctccATGATCCTGGGTAGCTGGTTTGag
	******************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_075282
	----------------------------------------------------------------------------------------------------	NM_011794
cbriggsae	.(((.((((...(((....((.(((........(((((...((..........))...)))))....)))))...)))..))))...)))	0.410 -19.60

cbriggsae

chromosome:chrII:2351214:2351303:-1

Same_strand|Intronic_non-coding|NM_075282|wrs-1 ## Opposite_strand|Intronic_non-coding|NM_011794|Bpnt1 ## {Repeats: no}

block871 [novel_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	0.120	no	no	0.52/0.52	23/23/1.00	0.0	0.0	1	0	1	0	0	11	5arm	1	nd	0.35	3	1	1	na	na

		reads	miRBase family seed
seed	-GCAGGCG---------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	CGCAGGCGATCGAACCATTGTTT------------------------------------------------------	23	1
cbriggsae	CGCAGGCGATCGAACCATTGTTTaaacttttcgccgaagcggaaaaacagaagaagtcgacacggttctatcgaggc
	*****************************************************************************
	---------------------------------------------------------------------------------------	NM_001005457
	---------------------------------------------------------------------------------------	NM_058490
	---------------------------------------------------------------------------------------	NM_075282
	---------------------------------------------------------------------------------------	NM_182230
cbriggsae	.((...((((.(((((..((((...(((((((((....))))))..........))).)))).))))).))))..))	0.410 -19.00

cbriggsae

chromosome:chrII:2013903:2013979:1

Opposite_strand|Intronic_coding|NM_001005457|adsl ## Opposite_strand|Intronic_non-coding|NM_058490|Y71G12B.8 ## {Repeats: no}

block1325 [novel_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	0.598	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	0	11	3arm	8	nd	0.42	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------UUUGAAU------------	1	novel
		len	cloning frequencies
			AF16
	--------------------------------------------------GTTTGAATGCAGGCCGTTGG	20	1
cbriggsae	attggtggagtgtacgcacgagacgcttaaaactggtgacgttggcgggaGTTTGAATGCAGGCCGTTGG
	**********************************************************************
	--------------------------------------------------------------------------------	NM_001011629
	--------------------------------------------------------------------------------	NM_172925
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_065286
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001093260
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_009573
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_130279
cbriggsae	.((..(((..((((..((.....((((......((....))..))))......))..))))..)))..))	0.620 -14.80

cbriggsae

chromosome:chrIII:2310492:2310561:-1

Opposite_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Same_strand|Intronic_non-coding|NM_065286|Y53G8AR.6 ## {Repeats: no}

block1539 [novel_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	0.334	no	no	0.35/0.35	23/23/1.00	0.0	0.0	1	0	1	0	3	4	3arm	2	nd	0.39	3	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------GAUAUGU------------------	1	miR-50/62/90
		len	cloning frequencies
			AF16
	-----------------------------------TGATATGTAGATAATGCACCAAC---	23	1
cbriggsae	ctctttgtagcagtcaatgcacacaattaactgggTGATATGTAGATAATGCACCAACgag
	*************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001028998
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001028999
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001029004
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001029003
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001029002
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001029001
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001039389
	-----------------------------------------------------------------------	NM_135472
	-----------------------------------------------------------------------	NM_164874
	-----------------------------------------------------------------------	NM_205951
	-----------------------------------------------------------------------	NM_205952
	-----------------------------------------------------------------------	NM_205953
	-----------------------------------------------------------------------	NM_001092606
	-----------------------------------------------------------------------	NM_001004296
	-----------------------------------------------------------------------	NM_064155
	-----------------------------------------------------------------------	NM_001122952
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_075505
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_028763
	-----------------------------------------------------------------------	NM_065922
	-----------------------------------------------------------------------	NM_010905
	-----------------------------------------------------------------------	NM_065923
	-----------------------------------------------------------------------	NM_068002
	-----------------------------------------------------------------------	NM_067755
	-----------------------------------------------------------------------	NM_067378
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001031045
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001102968
cbriggsae	(((.(((..((((((.((((((.((......)).))).)))...)))..)))..))).)))	0.450 -10.80

cbriggsae

chromosome:chrIII:11509518:11509578:-1

Same_strand|Intronic_non-coding|NM_001028998|unc-62 ## Opposite_strand|Intronic_non-coding|NM_135472|nAcRalpha-30D ## Opposite_strand|Intronic_coding|NM_001004296|rdx ## {Repeats: no}

block1541 [novel_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	0.334	no	no	0.35/0.35	23/23/1.00	0.0	0.0	1	0	1	0	3	4	3arm	2	nd	0.39	3	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------GAUAUGU------------------	1	miR-50/62/90
		len	cloning frequencies
			AF16
	-----------------------------------TGATATGTAGATAATGCACCAAC---	23	1
cbriggsae	ctctttgtagcagtcaatgcacacaattaactgggTGATATGTAGATAATGCACCAACgag
	*************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001028998
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001028999
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001029004
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001029003
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001029002
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001029001
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001039389
	-----------------------------------------------------------------------	NM_135472
	-----------------------------------------------------------------------	NM_164874
	-----------------------------------------------------------------------	NM_205951
	-----------------------------------------------------------------------	NM_205952
	-----------------------------------------------------------------------	NM_205953
	-----------------------------------------------------------------------	NM_001092606
	-----------------------------------------------------------------------	NM_001004296
	-----------------------------------------------------------------------	NM_064155
	-----------------------------------------------------------------------	NM_001122952
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_075505
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_028763
	-----------------------------------------------------------------------	NM_065922
	-----------------------------------------------------------------------	NM_010905
	-----------------------------------------------------------------------	NM_065923
	-----------------------------------------------------------------------	NM_068002
	-----------------------------------------------------------------------	NM_067755
	-----------------------------------------------------------------------	NM_067378
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001031045
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001102968
cbriggsae	(((.(((..((((((.((((((.((......)).))).)))...)))..)))..))).)))	0.450 -10.80

cbriggsae

chromosome:chrIII:11517004:11517064:-1

Same_strand|Intronic_non-coding|NM_001028998|unc-62 ## Opposite_strand|Intronic_non-coding|NM_135472|nAcRalpha-30D ## Opposite_strand|Intronic_coding|NM_001004296|rdx ## {Repeats: no}

block2522 [novel_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	0.673	no	no	0.40/0.40	20/20/1.00	0.0	0.0	3	0	1	0	0	27	5arm	1	nd	0.35	3	3	1	na	na

		reads	miRBase family seed
seed	-CGAGUAU---------------------------------------------------------------------------------------------------	3	novel
		len	cloning frequencies
			AF16
	TCGAGTATTGTGTCAAGAAC---------------------------------------------------------------------------------------	20	3
cbriggsae	TCGAGTATTGTGTCAAGAACatgatgtgatgtaatcaaaaacaactaaattgctaattgtgagtgggttacagatgcttttctaaatgttcaaaccgagagaattga
	***********************************************************************************************************
	---------------------------------------------------------------------------------------------------------------------	NM_001105717
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_198022
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_112886
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_020066
cbriggsae	((((...(((.((...((((((((.((..(((((((....((((.((......)).)))).....)))))))...))...))...))))))..))))).....))))	0.730 -16.70

cbriggsae

chromosome:chrIV:3318277:3318383:1

Opposite_strand|Intronic_non-coding|NM_001105717|Dpysl2 ## Same_strand|Intronic_non-coding|NM_198022|Tnrc6c ## Same_strand|Intronic_coding|NM_020066|FMN2 ## {Repeats: no}

block2960 [novel_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	0.524	no	no	0.20/0.20	20/20/1.00	0.0	0.0	1	0	1	0	0	28	5arm	2	nd	0.35	3	1	1	na	na

		reads	miRBase family seed
seed	-ACUAAGA-----------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	TACTAAGATATTATTACTGA-----------------------------------------------------------------------------	20	1
cbriggsae	TACTAAGATATTATTACTGAtagaatttttagtttaatttagaatgtatcacttacaatgatagggtttaaaattctataattaagttattttttgt
	*************************************************************************************************
cbriggsae	.((.((((((...(((...((((((((((.........(((...((((.....)))).)))........))))))))))...)))..))))))..))	0.420 -11.53