miR-Intess: classification

other hairpins

block4848 [novel_rep_randfoldOK]

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	0.001	no	DNA	0.39/0.39	23/23/1.00	0.0	0.0	4	0	1	0	18	5	3arm	1	nd	0.22	2	4	1	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------------------------------AAGUGAA------------------------------------------------	4	miR-785/86
		len	cloning frequencies
			AF16
	---------------------------------------------------------------------------------TAAGTGAATTCTCTACCTTCGGT---------------------------------	23	4
cbriggsae	------GTGCTCACAGGCACAGCAGAAGTTAG--AGTATT------------TTCTCTTAGCCAACACATTGATTC---GCTAAGTGAATTCTCTACCTTCGGTTGTGTTG-------------ATTGAGGCATT--
celegans	TCTTGCGTCCCTAATAGTATTGCACTTCTTCGTTAGTATTGCAAACTCTTCATTCTTTTAGTCAAAAAAATTGTAC---GAAAAGTGAATTTGC-AGTTTCTATAGAGTTGCACTCTTAAATTAGCCGACACGTGGA
cjaponica	-------------AAGACGGTGAAGATTT-----------------------CTCTCCTTCCCAAGACCACGAAACCGAAGAAAGTGAA------AGATTAT-----------------------------CGTCCG
	* * * *** * *** * * ******* * ** * *
	+++++ ++++++++++++++++++++++++++ ++++++ ++++++++++++++++++++++++ ++++++++++++++++++++++++++++++++ +++++++++++ +++++	NM_001087279
	+++++ ++++++++++++++++++++++++++ ++++++ ++++++++++++++++++++++++ ++++++++++++++++++++++++++++++++ +++++++++++ +++++	NM_072843
	+++++ ++++++++++++++++++++++++++ ++++++ ++++++++++++++++++++++++ ++++++++++++++++++++++++++++++++ +++++++++++ +++++	NM_178655
	+++++ ++++++++++++++++++++++++++ ++++++ ++++++++++++++++++++++++ ++++++++++++++++++++++++++++++++ +++++++++++ +++++	NM_001034168
	----- -------------------------- ------ ------------------------ -------------------------------- ----------- -----	NM_001109816
	+++++ ++++++++++++++++++++++++++ ++++++ ++++++++++++++++++++++++ ++++++++++++++++++++++++++++++++ +++++++++++ +++++	NM_065440
	----- -------------------------- ------ ------------------------ -------------------------------- ----------- -----	NM_020367
cbriggsae	(((((((..((((((((.((((.((( ((.... (((.((((((.((........)). )))))).)))..))))).)))).)))))))). ..)))).))).	1.000 -36.40
celegans	((.((.(((.(((((((...((((.((((....(((.((((((((...((((..(((((.(((((.....))).)) .)))))))))))))) )))..))).)))).))))..))...)))))..))).)).)).	0.995 -26.20
cjaponica	..((((((((...((( (.((.((((................))))..)).))) )..)))) ))))..	0.968 -13.39

cbriggsae	chromosome:chrX:4488214:4488312:1	Same_strand\|Intronic_non-coding\|NM_001087279\|fbxl5 ## Opposite_strand\|Intronic_coding\|NM_001109816\|MHC ## Opposite_strand\|Intronic_non-coding\|NM_020367\|PARP11 ## {Repeats: no}
celegans	chromosome:chrI:5715360:5715492:-1	intergenic ## {Repeats: CELE12B 72 154 -1 class=DNA}
cjaponica	chromosome:chrUn:138859703:138859841:-1	intergenic

novel_shortStem_loopOverlap (2 loci)

block2046 [novel_shortStem_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	0.105	no	no	0.45/0.45	20/20/1.00	0.0	0.0	1	0	1	0	4	-3	3arm_loop	1	nd	0.30	3	1	1	na	na

		reads	miRBase family seed
seed	------------------------AUGGCAU----------------	1	novel
		len	cloning frequencies
			AF16
	-----------------------TATGGCATCTTCCAGTGTGT----	20	1
cbriggsae	tctataccatcaggacctgttaaTATGGCATCTTCCAGTGTGTagaa
	***********************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001105717
	---------------------------------------------------------	NM_198022
	---------------------------------------------------------	NM_020066
cbriggsae	((((((.(((..(((..((((.....))))...))).))))))))).	1.000 -9.50

cbriggsae

chromosome:chrIV:3220102:3220148:-1

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

block3457 [novel_shortStem_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	0.071	no	no	0.41/0.41	22/22/1.00	0.0	0.0	1	0	1	0	0	-2	3arm_loop	1	nd	0.24	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------GUUGAUU--------------	1	novel
		len	cloning frequencies
			AF16
	--------------------GGTTGATTTATCAATGGCCATG	22	1
cbriggsae	tatggttggagaagttagccGGTTGATTTATCAATGGCCATG
	******************************************
cbriggsae	(((((((.((.(((((((....))))))).))...)))))))	1.000 -10.10

cbriggsae

chromosome:chrUn:3716990:3717031:1

{Repeats: no}

novel_shortStem_loopOverlap_nonpairedHIGH (2 loci)

block1343 [novel_shortStem_loopOverlap_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	0.046	no	no	0.45/0.45	20/20/1.00	0.0	0.0	1	0	1	0	3	-1	5arm_loop	1	nd	0.35	3	1	1	na	na

		reads	miRBase family seed
seed	----AUUUGAU-----------------------------------	1	novel
		len	cloning frequencies
			AF16
	---GATTTGATCCAATGGTGTCG-----------------------	20	1
cbriggsae	catGATTTGATCCAATGGTGTCGacagacatatgagaggaaatctg
	**********************************************
	--------------------------------------------------------	NM_214211
	--------------------------------------------------------	NM_001011629
	--------------------------------------------------------	NM_001035248
	--------------------------------------------------------	NM_057428
	--------------------------------------------------------	NM_001062274
	--------------------------------------------------------	NM_001005123
	--------------------------------------------------------	NM_001091987
	--------------------------------------------------------	NM_001069872
	--------------------------------------------------------	NM_001069872
	--------------------------------------------------------	NM_205075
	--------------------------------------------------------	NM_001037113
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_133195
	--------------------------------------------------------	NM_001022613
	--------------------------------------------------------	NM_001019821
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_007496
	--------------------------------------------------------	NM_003333
	--------------------------------------------------------	NM_003333
	--------------------------------------------------------	NM_001033930
	--------------------------------------------------------	NM_001076363
	--------------------------------------------------------	NM_001124194
	--------------------------------------------------------	NM_001126212
	--------------------------------------------------------	NM_001009286
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_013743
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_065840
	--------------------------------------------------------	NM_080331
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_024149
	<<<<<<<<<<<<<<<<<<<<<-----------------------------------	NM_065897
cbriggsae	...(((((..((((...(((((....))))).)).))..)))))..	1.000 -11.30

cbriggsae

chromosome:chrIII:2882593:2882638:-1

Opposite_strand|Intronic_coding|NM_214211|UBA52 ## Opposite_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Same_strand|Intronic_non-coding|NM_133195|Brunol4 ## Same_strand|Intronic_coding|NM_065840|SR-famA ## Opposite_strand|Boundary_coding|NM_065897|F25B5.2 ## {Repeats: no}

block1691 [novel_shortStem_loopOverlap_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	0.200	no	no	0.35/0.35	20/20/1.00	0.0	0.0	1	0	1	0	1	-1	5arm_loop	1	nd	0.35	3	1	1	na	na

		reads	miRBase family seed
seed	--AUGGGUG---------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-AATGGGTGGAAAAGAAATGT---------------------------------------	20	1
cbriggsae	gAATGGGTGGAAAAGAAATGTatacatgaaataaaagaagactattggccgccggcattc
	************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_066813
	----------------------------------------------------------------------	NM_127796
	----------------------------------------------------------------------	NM_134696
	----------------------------------------------------------------------	NM_134696
	----------------------------------------------------------------------	NM_018785
	----------------------------------------------------------------------	NM_012760
	----------------------------------------------------------------------	NM_026275
	----------------------------------------------------------------------	NM_066760
	----------------------------------------------------------------------	NM_066759
	----------------------------------------------------------------------	NM_001129239
cbriggsae	((((((((((..((...(((....))).................))..)))))..)))))	0.470 -9.45

cbriggsae

chromosome:chrIII:5066011:5066070:1

Same_strand|Intronic_non-coding|NM_066813|R10E12.2 ## Opposite_strand|Intronic_non-coding|NM_127796|ATUBP4 ## Opposite_strand|Intronic_coding|NM_134696|CG2839 ## {Repeats: no}

novel_shortStem_loopOverlap_nonpairedHIGH_bulgeHIGH (2 loci)

block888 [novel_shortStem_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	0.054	no	no	0.46/0.46	24/24/1.00	0.0	0.0	1	0	1	0	4	-3	5arm_loop	1	nd	0.33	4	1	1	na	na

		reads	miRBase family seed
seed	-----UUGAUGG--------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	----GTTGATGGTCCATGAGAATGCTTC----------------------------------	24	1
cbriggsae	ttgaGTTGATGGTCCATGAGAATGCTTCaaaaatgtgtttcgctgggaccatttcgaatcga
	**************************************************************
	------------------------------------------------------------------------	NM_001017803
	------------------------------------------------------------------------	NM_077434
	------------------------------------------------------------------------	NM_171029
	------------------------------------------------------------------------	NM_171855
cbriggsae	((((.((((((((((....((((((.........)))))).....))))))..)))).))))	0.980 -16.40

cbriggsae

chromosome:chrII:2724288:2724349:1

Opposite_strand|Intronic_coding|NM_001017803|zgc:111983 ## {Repeats: no}

block4107 [novel_shortStem_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	0.278	no	no	0.65/0.65	20/20/1.00	0.0	0.0	1	0	1	0	1	-4	3arm_loop	5	nd	0.40	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------GUUCGAG-------------	1	novel
		len	cloning frequencies
			AF16
	-------------------------AGTTCGAGCCTGGCATGGGG-	20	1
cbriggsae	gtctatagggcatgccaaggtcgccAGTTCGAGCCTGGCATGGGGc
	**********************************************
	--------------------------------------------------------	NM_001011629
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_115403
	--------------------------------------------------------	NM_023868
	--------------------------------------------------------	NM_001087279
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001087279
	--------------------------------------------------------	NM_141224
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_214496
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001079883
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_021399
	--------------------------------------------------------	NM_001036
	--------------------------------------------------------	NM_009109
	--------------------------------------------------------	NM_001001534
	--------------------------------------------------------	NM_001042723
	--------------------------------------------------------	NM_072352
	--------------------------------------------------------	NM_001082762
	--------------------------------------------------------	NM_001101718
	--------------------------------------------------------	NM_001102571
	--------------------------------------------------------	NM_057643
	--------------------------------------------------------	NM_057644
	--------------------------------------------------------	NM_057645
	--------------------------------------------------------	NM_057646
	--------------------------------------------------------	NM_206874
	--------------------------------------------------------	NM_001082757
	--------------------------------------------------------	NM_177652
	--------------------------------------------------------	NM_001035
	--------------------------------------------------------	NM_000540
	--------------------------------------------------------	NM_032078
cbriggsae	..........((((((.((((((......))).)))))))))....	0.930 -15.50

cbriggsae

chromosome:chrV:10108769:10108814:1

Opposite_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Same_strand|Intronic_non-coding|NM_115403|AT3G55450 ## Opposite_strand|Intronic_coding|NM_023868|Ryr2 ## Same_strand|Intronic_coding|NM_214496|dlp ## {Repeats: no}

novel_Multihit_loopOverlap (1 loci)

block2028 [novel_Multihit_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	0.465	no	no	0.30/0.30	20/20/1.00	0.0	0.0	1	0	1	0	14	-3	3arm_loop	43	nd	0.30	2	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------ACUUUUC--------------------------	1	novel
		len	cloning frequencies
			AF16
	------------------------------------------TACTTTTCAAATGTGCCAAT--------------	20	1
cbriggsae	cgcttgccttaaaacccgcataggacaacttttcgaaaatgtTACTTTTCAAATGTGCCAATatgtgtttaatagc
	****************************************************************************
	--------------------------------------------------------------------------------------	NM_001047948
	--------------------------------------------------------------------------------------	NM_001047555
	--------------------------------------------------------------------------------------	NM_001047554
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_068260
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_068267
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_068270
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_060105
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_068253
cbriggsae	.(((....(((((...((((((((...((.(((.(((((......)))))))).)).))..))))))))))).)))	1.000 -10.50

cbriggsae

chromosome:chrIV:2874853:2874928:-1

Opposite_strand|Intronic_coding|NM_001047948|LOC499584 ## Same_strand|Intronic_coding|NM_068260|str-175 ## Same_strand|Intronic_non-coding|NM_060105|C17E4.9 ## {Repeats: no}

novel_Multihit_shortStem_loopOverlap (1 loci)

block4922 [novel_Multihit_shortStem_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	0.021	no	no	0.52/0.52	21/21/1.00	0.0	0.0	1	0	1	0	4	-3	3arm_loop	47	nd	0.29	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------UAAUGGU-----------------	1	novel
		len	cloning frequencies
			AF16
	--------------------------GTAATGGTCAGCATGGATGCC----	21	1
cbriggsae	gggaggttaatgtgtgcgttcgtggtGTAATGGTCAGCATGGATGCCttcc
	***************************************************
	-------------------------------------------------------------	NM_133381
	-------------------------------------------------------------	NM_002254
	-------------------------------------------------------------	NM_001059519
	-------------------------------------------------------------	NM_024598
	-------------------------------------------------------------	NM_175804
	-------------------------------------------------------------	NM_001089427
	-------------------------------------------------------------	NM_001110788
	-------------------------------------------------------------	NM_001005477
cbriggsae	(((((((..((.(((((..((((......))))...))))).)))))))))	0.990 -17.40

cbriggsae

chromosome:chrX:7915026:7915076:1

Opposite_strand|Intronic_non-coding|NM_133381|Crebbp ## Opposite_strand|Intronic_coding|NM_002254|KIF3C ## {Repeats: no}

novel_Multihit_shortStem_loopOverlap_nonpairedHIGH (1 loci)

block4559 [novel_Multihit_shortStem_loopOverlap_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	0.041	no	no	0.52/0.52	21/21/1.00	0.0	0.0	1	0	1	0	2	-3	3arm_loop	47	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	----------------------UAAUGGU---------------	1	novel
		len	cloning frequencies
			AF16
	---------------------GTAATGGTCAGCATGGATGCC--	21	1
cbriggsae	aagacatccagcgttcgtggtGTAATGGTCAGCATGGATGCCtt
	********************************************
	------------------------------------------------------	NM_001108848
	------------------------------------------------------	NM_133381
	++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001045626
	------------------------------------------------------	NM_004845
	++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001086847
	------------------------------------------------------	NM_001065160
	++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001082087
	++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001017762
cbriggsae	(((.((((((((..((((......))))...)).)))))).)))	1.000 -13.90

cbriggsae

chromosome:chrX:13287402:13287445:-1

Opposite_strand|Intronic_non-coding|NM_001108848|Elavl1 ## Same_strand|Intronic_coding|NM_001045626|galntl1 ## Same_strand|Intronic_non-coding|NM_001086847|MGC53595 ## Opposite_strand|Intronic_coding|NM_001065160|Os06g0725900 ## {Repeats: no}

Page 66

miR-Intess™

block4848 [novel_rep_randfoldOK]

block2046 [novel_shortStem_loopOverlap]

block3457 [novel_shortStem_loopOverlap]

block1343 [novel_shortStem_loopOverlap_nonpairedHIGH]

block1691 [novel_shortStem_loopOverlap_nonpairedHIGH]

block888 [novel_shortStem_loopOverlap_nonpairedHIGH_bulgeHIGH]

block4107 [novel_shortStem_loopOverlap_nonpairedHIGH_bulgeHIGH]

block2028 [novel_Multihit_loopOverlap]

block4922 [novel_Multihit_shortStem_loopOverlap]

block4559 [novel_Multihit_shortStem_loopOverlap_nonpairedHIGH]