miR-Intess: classification

other hairpins

block2350 [novel_lenNOK_shortStem]

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	0.699	no	no	0.26/0.26	19/19/0.00	0.0	0.0	1	0	1	0	4	35	3arm	1	nd	0.26	2	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------------------------------------UUUUUUU---------------	1	novel
		len	cloning frequencies
			AF16
	-----------------------------------------------------------------------------------------------TTTTTTTTTGATGTCCTGT----	19	1
cbriggsae	aattagagtttacgataaaatgagtgaatcatgaagataataaaaattctcagtttcaatgaattcgtatttttcccaattcctctcttctgtgaTTTTTTTTTGATGTCCTGTagtt
	**********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_071218
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_067556
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001083250
	--------------------------------------------------------------------------------------------------------------------------------	NM_001085890
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_070819
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_002710
	--------------------------------------------------------------------------------------------------------------------------------	NM_070646
cbriggsae	(((((.((...(((.(((((.....((((((((((((.((((..(((((...........)))))..))))..............))))).)))))))..))))).))).)).)))))	0.850 -15.56

cbriggsae

chromosome:chrIV:142501:142618:1

Same_strand|Intronic_coding|NM_071218|str-253 ## Same_strand|Intronic_non-coding|NM_001083250|rom-4 ## Opposite_strand|Intronic_non-coding|NM_001085890|MGC52856 ## Opposite_strand|Intronic_coding|NM_070646|C52D10.3 ## {Repeats: no}

block2674 [novel_lenNOK_shortStem]

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	0.702	no	no	0.33/0.33	18/18/0.00	0.0	0.0	1	0	1	0	0	30	5arm	1	nd	0.28	3	1	1	na	na

		reads	miRBase family seed
seed	-CUUGUUU-----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	TCTTGTTTTGCTTTGGAT-------------------------------------------------------------------------	18	1
cbriggsae	TCTTGTTTTGCTTTGGATaataagaaaaaaaaactaaccttttcagcactattcttgttgtttctcatatttttctgtcgtagaaaataag
	*******************************************************************************************
	-----------------------------------------------------------------------------------------------------	NM_066961
	-----------------------------------------------------------------------------------------------------	NM_001001344
	-------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	NM_171332
cbriggsae	.((((((((.((.(((......(((((((..............(((((.......))))).........))))))).))).))))))))))	0.470 -10.00

cbriggsae

chromosome:chrIV:8993064:8993154:1

Opposite_strand|Intronic_non-coding|NM_066961|W09D10.4 ## Opposite_strand|Intronic_coding|NM_001001344|ATP2B3 ## {Repeats: no}

block3699 [novel_lenNOK_shortStem]

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	0.603	no	no	0.39/0.39	18/18/0.00	0.0	0.0	1	0	1	0	4	22	5arm	7	nd	0.11	1	1	1	na	na

		reads	miRBase family seed
seed	-----AAUUGAC------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	----CAATTGACACTGAAGAAC--------------------------------------------------------------------	18	1
cbriggsae	ggtcCAATTGACACTGAAGAACctgagtgactacgtcttcggcgtccactcgcctcttgtatactgttctgcgtcacgtcgttagtgcct
	******************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001038399
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_071206
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_070871
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_071201
	----------------------------------------------------------------------------------------------------	NM_073477
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_071221
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001029049
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_071906
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001038399
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001038398
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_070813
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001038398
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_071229
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_071229
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_070818
	----------------------------------------------------------------------------------------------------	NM_072677
	----------------------------------------------------------------------------------------------------	NM_073545
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_071059
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_009024
	----------------------------------------------------------------------------------------------------	NM_142040
	----------------------------------------------------------------------------------------------------	NM_001064034
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_071377
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_071696
	----------------------------------------------------------------------------------------------------	NM_071709
	----------------------------------------------------------------------------------------------------	NM_071708
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_070810
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_070809
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_070809
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_070808
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_070806
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_070807
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_070814
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_070813
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_070813
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_070807
cbriggsae	(((...((((((((((((((((...((((..((((.....((((......))))...)))))))))))))...))).)).))))))))).	0.640 -20.60

cbriggsae

chromosome:chrV:4491320:4491409:-1

Same_strand|Intronic_coding|NM_001038399|nhr-56 ## Opposite_strand|Intronic_coding|NM_073477|str-141 ## {Repeats: no}

block3945 [novel_lenNOK_shortStem]

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	0.429	no	no	0.56/0.56	18/18/0.00	0.0	0.0	1	0	1	0	4	12	3arm	1	nd	0.11	1	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------CUGUGGA--------------	1	novel
		len	cloning frequencies
			AF16
	------------------------------------------------------------------------TCTGTGGAGTCCTTGCTG----	18	1
cbriggsae	gttgtcgttgtgggacctttgaccacttccacagctccgatttttcatagcaaaattatatgctcacctcgtTCTGTGGAGTCCTTGCTGccgc
	**********************************************************************************************
	--------------------------------------------------------------------------------------------------------	NM_001847
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001028815
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_170227
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001012945
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001114052
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001130158
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_012223
cbriggsae	((.((.((...(((((...........(((((((...(((........((((........))))....)))..)))))))))))).)).)).))	0.400 -20.00

cbriggsae

chromosome:chrV:570978:571071:1

Opposite_strand|Intronic_coding|NM_001847|COL4A6 ## Same_strand|Intronic_coding|NM_001028815|F56H9.6 ## Same_strand|Intronic_non-coding|NM_001012945|DNAJA1 ## {Repeats: no}

block4131 [novel_lenNOK_shortStem]

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	0.586	no	no	0.37/0.37	27/27/0.00	0.0	0.0	1	0	1	0	0	19	5arm	1	nd	0.22	3	1	1	na	na

		reads	miRBase family seed
seed	-UAUUCGG------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	GTATTCGGATTGTGAATTCTGAAAGGT-----------------------------------------------------------------------	27	1
cbriggsae	GTATTCGGATTGTGAATTCTGAAAGGTgtggaagtcagaacagaaataagggttttcagttagatgctcacctcatgaagaaatttagaattgcgtgc
	**************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001011629
	------------------------------------------------------------------------------------------------------------	NM_070507
	------------------------------------------------------------------------------------------------------------	NM_001022613
	------------------------------------------------------------------------------------------------------------	NM_001047733
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001069016
	------------------------------------------------------------------------------------------------------------	NM_003299
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_212567
cbriggsae	((((.((.(((.((((((((...(((((.....(((..(((.((((.......)))).))).)))...))))).....)))).)))).))))).))))	0.940 -17.70

cbriggsae

chromosome:chrV:11721162:11721259:1

Same_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Opposite_strand|Intronic_non-coding|NM_070507|Y105C5B.19 ## Opposite_strand|Intronic_coding|NM_001022613|SPBC215.13 ## Same_strand|Intronic_coding|NM_001069016|Os08g0557100 ## {Repeats: no}

block4312 [novel_lenNOK_shortStem]

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	0.269	no	no	0.39/0.39	18/18/0.00	0.0	0.0	1	0	1	0	4	21	5arm	7	nd	0.22	2	1	1	na	na

		reads	miRBase family seed
seed	-----AAUUGAC------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	----CAATTGACACTGAAGAAC--------------------------------------------------------------------	18	1
cbriggsae	ggtcCAATTGACACTGAAGAACtgagtgactacgtcttcggcgtccactcgcctcttgtagtactgttctgcgtcacatcgttagtgcct
	******************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_072005
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_072002
cbriggsae	(((...((((((..((((((((..(((.((((((.....((((......))))...))))))))))))))...)))....))))))))).	0.700 -23.10

cbriggsae

chromosome:chrV_random:1962074:1962163:1

Same_strand|Intronic_coding|NM_072005|srt-70 ## {Repeats: no}

block4379 [novel_lenNOK_shortStem]

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	0.074	no	no	0.42/0.42	19/19/0.00	0.0	0.0	2	0	1	0	0	5	5arm	1	nd	0.26	3	2	1	na	na

		reads	miRBase family seed
seed	-AGCAUCC------------------------------------------------	2	novel
		len	cloning frequencies
			AF16
	GAGCATCCATTGGAAAGAA-------------------------------------	19	2
cbriggsae	GAGCATCCATTGGAAAGAAgtccttcgagcaacgggagtactttcggagtggatct
	********************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_076104
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_029999
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_022410
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_031169
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001027419
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_175605
	------------------------------------------------------------------	NM_181850
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_022416
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_006531
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001110786
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_033509
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001122952
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001122953
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_010905
cbriggsae	.((.(((((((.(((((...((((.........))))...))))).)).)))))))	0.960 -14.20

cbriggsae

chromosome:chrX:3802323:3802378:-1

Same_strand|Intronic_non-coding|NM_076104|Y71H10A.2 ## Same_strand|Intronic_coding|NM_175605|IFT88 ## Opposite_strand|Intronic_non-coding|NM_181850|Grm3 ## {Repeats: no}

block4492 [novel_lenNOK_shortStem]

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	0.090	no	no	0.47/0.47	19/19/0.00	0.0	0.0	1	0	1	0	3	1	3arm	1	nd	0.05	1	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------UGAAGUU--------------	1	novel
		len	cloning frequencies
			AF16
	------------------------------------------------CTGAAGTTTGTCGTGGATG---	19	1
cbriggsae	catattcaaaatattttgaaagacattagaaatttccagctcgaaacgCTGAAGTTTGTCGTGGATGtgg
	**********************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_129875
	--------------------------------------------------------------------------------	NM_007789
cbriggsae	((((((((.............((((.....(((((.((((.......))))))))))))).)))))))).	0.470 -14.64

cbriggsae

chromosome:chrX:9427471:9427540:-1

Same_strand|Intronic_non-coding|NM_129875|ARA4 ## Opposite_strand|Intronic_non-coding|NM_007789|Ncan ## {Repeats: no}

block4858 [novel_lenNOK_shortStem]

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	0.424	no	no	0.58/0.58	19/19/0.00	0.0	0.0	1	0	1	0	2	4	3arm	1	nd	0.26	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------UAUUCCA-------------	1	novel
		len	cloning frequencies
			AF16
	----------------------------------------------CTATTCCATCCACCTGGCC--	19	1
cbriggsae	gcagccaaattgttttttttttgatgtatagttttagttgtactgaCTATTCCATCCACCTGGCCgt
	*******************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001105250
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_004796
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_138970
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001087279
	-----------------------------------------------------------------------------	NM_166414
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001086648
cbriggsae	((.((((...((..........((((.((((((..((.....))))))))..))))))..)))).))	0.640 -9.60

cbriggsae

chromosome:chrX:5036590:5036656:1

Same_strand|Intronic_non-coding|NM_001105250|NRXN3 ## Opposite_strand|Intronic_coding|NM_166414|Act57B ## {Repeats: no}

block5156 [novel_lenNOK_shortStem]

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	0.161	no	no	0.39/0.39	18/18/0.00	0.0	0.0	1	0	1	0	4	21	5arm	7	nd	0.11	1	1	1	na	na

		reads	miRBase family seed
seed	-----AAUUGAC------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	----CAATTGACACTGAAGAAC--------------------------------------------------------------------	18	1
cbriggsae	ggtcCAATTGACACTGAAGAACtgagtgactacgtcttcggcgtccactcgcctcttgtagtactgttctgcgtcacgtcgttagtgcct
	******************************************************************************************
cbriggsae	(((...((((((((((((((((..(((.((((((.....((((......))))...))))))))))))))...))).)).))))))))).	0.960 -25.60