miR-Intess™

other hairpins

miRNAunknown_rep_cloningOK_multiarm_DicerNOK_Multihit_5varHIGH_loopOverlap_randfoldOK (2 loci)

sblock12820 (miRNA) [miRNAunknown_rep_cloningOK_multiarm_DicerNOK_Multihit_5varHIGH_loopOverlap_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

Ensembl miRNA

0.001

no

SINE

0.50/0.63

19/23/0.83

2.7 0.4 1.1

2.2 0.9 0.0

6 10 14

0 0 0

3 4 6

0 0 0

28 23 2

-2 0 22

5arm 3arm 3arm

358 358 358

nd nd nd

0.00 0.00 0.35

0 0 3

30

8

2

5

		reads	miRBase family seed
seed	---------------------------------------------------------GCACACA--------------------------------------	6	novel
seed	---------------------------------------------------------------------------------ACACACA--------------	5	novel
seed	-------------------------------------------------------------------------------ACACACA----------------	4	novel
seed	--------------------------------------------------------------------------------CACACAC---------------	4	novel
seed	----------------------------------------------------------CACACAC-------------------------------------	3	novel
seed	-----------------------------------GUGUGUG------------------------------------------------------------	2	novel
seed	--------------------------------UGUGUGU---------------------------------------------------------------	1	novel
seed	------------------------------------------------------------------------------CACACAC-----------------	1	novel
seed	---------------------------------GUGUGUG--------------------------------------------------------------	1	novel
seed	--------------------------------------------------------UGCACAC---------------------------------------	1	novel
seed	------------------------------UGUGUGU-----------------------------------------------------------------	1	novel
seed	-----------------------------GUGUGUG------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1
	--------------------------------------------------------TGCACACACACACACACACA--------------------------	20	-	-	-	2	-	-	-	3
	--------------------------------------------------------------------------------CACACACACACACACACACC--	20	1	1	1	-	-	2	-	-
	------------------------------------------------------------------------------CACACACACACACACACACACC--	22	-	2	1	-	-	-	1	-
	-------------------------------------------------------------------------------ACACACACACACACACACACC--	21	1	-	-	-	1	-	2	-
	---------------------------------------------------------GCACACACACACACACACAC-------------------------	20	-	-	-	1	-	-	-	1
	----------------------------------TGTGTGTGTGTGTGCGCGC-------------------------------------------------	19	-	-	2	-	-	-	-	-
	--------------------------------------------------------TGCACACACACACACACACACA------------------------	22	-	-	-	-	-	-	-	1
	--------------------------------TGTGTGTGTGTGTGTGCGC---------------------------------------------------	19	-	-	-	-	-	1	-	-
	-------------------------------GTGTGTGTGTGTGTGTGCG----------------------------------------------------	19	-	-	-	1	-	-	-	-
	---------------------------------------------------------GCACACACACACACACACACAC-----------------------	22	-	1	-	-	-	-	-	-
	-----------------------------------------------------------------------------ACACACACACACACACACACACC--	23	1	-	-	-	-	-	-	-
	----------------------------TGTGTGTGTGTGTGTGTGTGC-----------------------------------------------------	21	-	-	-	-	-	1	-	-
	-----------------------------GTGTGTGTGTGTGTGTGTGC-----------------------------------------------------	20	-	-	-	1	-	-	-	-
	-------------------------------------------------------GTGCACACACACACACACA----------------------------	19	1	-	-	-	-	-	-	-
rat	tgggtgaaggtgtttcctgacctgagccTGTGTGTGTGTGTGTGTGTGCGCGCgcGTGCACACACACACACACACACACACACACACACACACACACACCta
	******************************************************************************************************
	----------------------------------------------------------------------------------------------------------------	ENSRNOT00000034925 ENSRNOG00000012194 Morc4_predicted
	.........................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<.......	ENSRNOT00000063027 ENSRNOG00000041274
rat	((((((...((((....((...((....(((((((((((((((((((((((....)))))))))))))))))))))))....))..)).))))...))))))	0.510 -53.80

rat

chromosome:X:127581808:127581909:1

Opposite_strand|Exonic_non-coding|ENSRNOT00000063027|ENSRNOG00000041274 ## Opposite_strand|Intronic_coding|ENSRNOT00000034925|ENSRNOG00000012194 ## ENSRNOG00000041274|miRNA|| ## ENSRNOG00000012194|protein_coding|Morc4_predicted| ## {Repeats: AT_rich 1 32 1 class=Low_complexity,dust 127581866 127581888 0 class=dust,(CA)n 1 21 1 class=Simple_repeat,(CA)n 19 41 1 class=Simple_repeat,trf 21 41 0 class=trf,(TG)n 1 25 1 class=Simple_repeat,RSINE1 1 50 1 class=SINE,trf 1 20 0 class=trf,(CA)n 1 41 1 class=Simple_repeat,dust 127581836 127581855 0 class=dust,(TG)n 27 30 1 class=Simple_repeat,dust 127581886 127581906 0 class=dust,trf 1 23 0 class=trf}

miRNAunknown_rep_lenNOK_Multihit (2 loci)

block1013002 (miRNA) [miRNAunknown_rep_lenNOK_Multihit]

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

Ensembl miRNA

0.042

no

LTR,LTR/ERVL

0.56/0.56

18/18/0.00

0.0

0.0

1

0

1

0

20

1

3arm

22

nd

0.22

3

1

1

na

na

		reads	miRBase family seed
seed	-----------------------------------------------UCUCUUC------------------------------	1	novel
		len	cloning frequencies
			T3S2
	----------------------------------------------CTCTCTTCTTTGCCTGCC--------------------	18	1
rat	tgctggagacctatataaggacattggaagaagaaagattctctctCTCTCTTCTTTGCCTGCCtgccttgtgggactgagcaa
	************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063224 ENSRNOG00000041471
rat	((((..((.((((((..(((.((...((((((((.(((.......))).))))))))...)))))....)))))).)).)))).	1.000 -24.70

rat

chromosome:1:165836288:165836371:1

Same_strand|Exonic_non-coding|ENSRNOT00000063224|ENSRNOG00000041471 ## ENSRNOG00000041471|miRNA|| ## {Repeats: MT2_Rat2 1 487 1 class=LTR,MT2_Rat2 268 286 1 class=LTR/ERVL}

block2495533 (miRNA) [miRNAunknown_rep_lenNOK_Multihit]

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

Ensembl miRNA

0.107

no

SINE

0.53/0.53

19/19/0.00

0.0

0.0

1

0

1

0

9

22

3arm

256

nd

0.26

2

1

1

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------UGAGCCU--------------------	1	novel
		len	cloning frequencies
			T3S2
	----------------------------------------------------------------------GTGAGCCTAGCCTTTAACG---------	19	1
rat	ggtttctcgaggaggggtagattatacttaatgatatagccactggtaagttgttcttatatttttggttGTGAGCCTAGCCTTTAACGgctgagcca
	**************************************************************************************************
	..............................................................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	ENSRNOT00000054653 ENSRNOG00000036547
rat	(((((.(((..(((((.(((.(((((.((((.((((((((.(((....))).))...)))))).)))).)))))..))).)))))..)))..))))).	0.710 -25.90

rat

chromosome:9:38199838:38199935:-1

Opposite_strand|Exonic_non-coding|ENSRNOT00000054653|ENSRNOG00000036547 ## ENSRNOG00000036547|miRNA|| ## {Repeats: B4 2 47 -1 class=SINE}

miRNAunknown_rep_lenNOK_Multihit_shortStem (2 loci)

block916743 (miRNA) [miRNAunknown_rep_lenNOK_Multihit_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

Ensembl miRNA

0.526

no

LTR,SINE,SINE/Alu

0.42/0.42

19/19/0.00

0.0

0.0

1

0

1

0

3

17

3arm

136

nd

0.21

3

1

1

na

na

		reads	miRBase family seed
seed	------------------------------------------------------------------UGGAUUU--------------	1	novel
		len	cloning frequencies
			T3S1
	-----------------------------------------------------------------GTGGATTTCTGTGAGTTCA---	19	1
rat	ccactataccatagcaaagaatttagtacacgcctttaaccccagcacttgggaagcagaggcagGTGGATTTCTGTGAGTTCAagg
	***************************************************************************************
	-------------------------------------------------------------------------------------------------	ENSRNOT00000054813 ENSRNOG00000020702 Cybasc3
	-------------------------------------------------------------------------------------------------	ENSRNOT00000028094 ENSRNOG00000020702 Cybasc3
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<...	ENSRNOT00000063559 ENSRNOG00000041806
rat	...((..(((((((....(((((...(((..((((((...(((((...)))))....))))))..))))))))))))).))...)).	0.810 -18.50

rat

chromosome:1:213073842:213073928:-1

Opposite_strand|Intronic_coding|ENSRNOT00000028094|ENSRNOG00000020702 ## Opposite_strand|Exonic_non-coding|ENSRNOT00000063559|ENSRNOG00000041806 ## ENSRNOG00000041806|miRNA|| ## ENSRNOG00000020702|protein_coding|Cybasc3|Cytochrome b ascorbate-dependent protein 3 (EC 1.-.-.-). [Source:UniProtKB/Swiss-Prot;Acc:Q5U2W7] ## {Repeats: B1_Mur2 -57 92 1 class=SINE,B1_Mur4 55 74 1 class=SINE/Alu,MT2B -356 245 1 class=LTR}

block2137421 (miRNA) [miRNAunknown_rep_lenNOK_Multihit_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

Ensembl miRNA

0.162

no

SINE,SINE/Alu

0.47/0.50

19/20/0.50

0.5

0.0

2

0

2

0

0

16

3arm

258

nd

0.17

1

2

2

na

na

		reads	miRBase family seed
seed	--------------------------------------------------------UGGAUCU-----------	1	novel
seed	-------------------------------------------------------GUGGAUC------------	1	novel
		len	cloning frequencies
			T4S2	T5S2
	------------------------------------------------------GGTGGATCTCTGTGAGTTCA	20	-	1
	-------------------------------------------------------GTGGATCTCTGTGAGTTCA	19	1	-
rat	gagctgggtacggtggtgcatgcctttaatcccagcacttgggaggaagagacaGGTGGATCTCTGTGAGTTCA
	**************************************************************************
	------------------------------------------------------------------------------------	ENSRNOT00000005722 ENSRNOG00000004328 RGD1561030_predicted
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<...................	ENSRNOT00000063338 ENSRNOG00000041585
rat	(((((...(((((.(((.((((.((((..((((((...))))))...)))).))..)).))).)))))))))).	0.960 -22.90

rat

chromosome:7:91688578:91688651:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000063338|ENSRNOG00000041585 ## Opposite_strand|Intronic_coding|ENSRNOT00000005722|ENSRNOG00000004328 ## ENSRNOG00000041585|miRNA|| ## ENSRNOG00000004328|protein_coding|RGD1561030_predicted| ## {Repeats: B1_Mur3 53 73 1 class=SINE/Alu,B1_Mur3 -1 148 1 class=SINE}

miRNAunknown_rep_lenNOK_Multihit_shortStem_nonpairedHIGH (2 loci)

block942841 (miRNA) [miRNAunknown_rep_lenNOK_Multihit_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

Ensembl miRNA

0.319

no

SINE,SINE/Alu

0.67/0.67

18/18/0.00

0.0

0.0

1

0

1

0

0

16

3arm

50

nd

0.35

2

1

1

na

na

		reads	miRBase family seed
seed	-------------------------------------------------------------------GCCUUCU----------	1	novel
		len	cloning frequencies
			T1S2
	------------------------------------------------------------------TGCCTTCTGGGTGCTGGG	18	1
rat	ccctggctgttctggaacttgctctgtagaccaggttggcctcaaaattagggatccacctgcctcTGCCTTCTGGGTGCTGGG
	************************************************************************************
	...........................................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063382 ENSRNOG00000041629
rat	.((..((...((..(((........(((((.(((((.(((((........))).)).)))))..))))).)))..)).))..))	0.930 -25.60

rat

chromosome:1:9157052:9157135:1

Same_strand|Exonic_non-coding|ENSRNOT00000063382|ENSRNOG00000041629 ## ENSRNOG00000041629|miRNA|| ## {Repeats: B1_Rn -9 139 -1 class=SINE,B1_Rn 31 49 -1 class=SINE/Alu}

block2254370 (miRNA) [miRNAunknown_rep_lenNOK_Multihit_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

Ensembl miRNA

0.547

no

SINE

0.53/0.53

19/19/0.00

0.0

0.0

1

0

1

0

3

18

3arm

256

nd

0.32

3

1

1

na

na

		reads	miRBase family seed
seed	---------------------------------------------------------------------UGAGCCU--------------	1	novel
		len	cloning frequencies
			T3S2
	--------------------------------------------------------------------GTGAGCCTAGCCTTTAACG---	19	1
rat	ggcctacagagtgagttccgggtcagctagtactacagagatgaaatcctgtctcttatattttggttGTGAGCCTAGCCTTTAACGgct
	******************************************************************************************
	.............................................................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	ENSRNOT00000054625 ENSRNOG00000036518
rat	((((...((((...(((..(((((((((((......((((((........))))))......)))))))...)))))))))))...))))	0.460 -20.90

rat

chromosome:7:119593151:119593240:1

Opposite_strand|Exonic_non-coding|ENSRNOT00000054625|ENSRNOG00000036518 ## ENSRNOG00000036518|miRNA|| ## {Repeats: B4 -245 47 -1 class=SINE}

miRNAunknown_rep_lenNOK_cloningHIGH_multiarm_DicerNOK_randfoldOK (2 loci)

sblock10447 (miRNA) [miRNAunknown_rep_lenNOK_cloningHIGH_multiarm_DicerNOK_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

Ensembl miRNA

0.009

no

SINE,SINE/MIR

0.59/0.75

18/24/0.56

0.0 1.2

0.9 1.4

136 39

0 0

2 2

0 0

10 12

7 5

5arm 3arm

1 2

nd nd

0.20 0.28

2 2

206

2

0

2

		reads	miRBase family seed
seed	-----------GGUGUGA----------------------------------------------------------------	158	novel
seed	-------------------------------------------------GAGGCUC--------------------------	27	novel
seed	-----------------------------------------------CCGAGGC----------------------------	20	novel
seed	------------------------------------------------CGAGGCU---------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2
	----------TGGTGTGAGGTTGGGCCAG-----------------------------------------------------	19	40	27
	----------TGGTGTGAGGTTGGGCCAGGA---------------------------------------------------	21	31	26
	----------TGGTGTGAGGTTGGGCCAGG----------------------------------------------------	20	12	7
	----------TGGTGTGAGGTTGGGCCA------------------------------------------------------	18	7	2
	------------------------------------------------CGAGGCTCCCCACCACACCCT-------------	21	2	5
	----------------------------------------------TCCGAGGCTCCCCACCACACCCT-------------	23	5	2
	------------------------------------------------CGAGGCTCCCCACCACAC----------------	18	5	1
	------------------------------------------------CGAGGCTCCCCACCACACCCTG------------	22	4	1
	------------------------------------------------CGAGGCTCCCCACCACACCC--------------	20	3	2
	----------TGGTGTGAGGTTGGGCCAGGAT--------------------------------------------------	22	3	2
	----------------------------------------------TCCGAGGCTCCCCACCACACCC--------------	22	4	-
	----------------------------------------------TCCGAGGCTCCCCACCAC------------------	18	4	-
	------------------------------------------------CGAGGCTCCCCACCACACC---------------	19	-	3
	----------------------------------------------TCCGAGGCTCCCCACCACACC---------------	21	1	1
	----------TGGTGTGAGGTTGGGCCAGGATG-------------------------------------------------	23	-	1
	----------------------------------------------TCCGAGGCTCCCCACCACAC----------------	20	-	1
	----------------------------------------------TCCGAGGCTCCCCACCACACCCTG------------	24	1	-
	------------------------------------------------CGAGGCTCCCCACCACACCCTGC-----------	23	1	-
	-----------------------------------------------CCGAGGCTCCCCACCACACCCT-------------	22	-	1
	----------------------------------------------TCCGAGGCTCCCCACCACA-----------------	19	1	-
rat	gtctctcagcTGGTGTGAGGTTGGGCCAGGAtgaaacccaaggctctccgaggctccccaccacaccctgctgctgaagact
	**********************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063221 ENSRNOG00000041468
rat	((((.(((((.((((((.((..(((((.(((.((..((...)).)))))..))))).))..)))))).....))))))))).	0.920 -32.70

rat

chromosome:6:134203856:134203937:1

Same_strand|Exonic_non-coding|ENSRNOT00000063221|ENSRNOG00000041468 ## ENSRNOG00000041468|miRNA|| ## {Repeats: MIRb 23 48 -1 class=SINE/MIR,MIRb -113 155 -1 class=SINE,MIRb 61 84 -1 class=SINE/MIR}

sblock5001 (miRNA) [miRNAunknown_rep_lenNOK_cloningHIGH_multiarm_DicerNOK_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

Ensembl miRNA

0.001

no

LINE,LINE/L2

0.39/0.61

18/22/0.62

0.0 0.0 0.0

1.0 0.0 0.6

142 1 11

0 0 0

10 1 7

0 0 0

31 51 26

4 -12 6

5arm 5arm_loop_3arm 3arm

1 1 1

nd nd nd

0.10 0.33 0.11

1 4 1

196

10

2

0

		reads	miRBase family seed
seed	--------------------------------UUGGCAC--------------------------------------------------------------------------	184	miR-96
seed	--------------------------------------------------------------------GUGCCUG--------------------------------------	11	novel
seed	----------------------------------------------------AGUAACU------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-------------------------------CTTGGCACCTGGTAAGCACTCA------------------------------------------------------------	22	3	11	2	6	12	7	6	3	2	9
	-------------------------------CTTGGCACCTGGTAAGCACTC-------------------------------------------------------------	21	5	15	3	2	9	2	4	9	-	6
	-------------------------------CTTGGCACCTGGTAAGCAC---------------------------------------------------------------	19	1	10	2	-	13	9	8	3	-	7
	-------------------------------CTTGGCACCTGGTAAGCA----------------------------------------------------------------	18	-	2	1	-	4	2	1	1	-	-
	-------------------------------------------------------------------AGTGCCTGCTGTGTGCCA----------------------------	18	-	1	1	1	1	1	-	-	-	-
	-------------------------------CTTGGCACCTGGTAAGCACT--------------------------------------------------------------	20	-	-	-	-	1	-	1	2	-	-
	-------------------------------------------------------------------AGTGCCTGCTGTGTGCCAA---------------------------	19	-	-	-	-	2	-	-	-	1	1
	-------------------------------------------------------------------AGTGCCTGCTGTGTGCCAAG--------------------------	20	-	1	-	-	-	-	-	-	-	1
	---------------------------------------------------CAGTAACTACTTAGTGAG--------------------------------------------	18	-	1	-	-	-	-	-	-	-	-
rat	catttccctatccccagctcccacatcagtgCTTGGCACCTGGTAAGCACTCAgtaactacttagtgagtgcctgctgtgtgccaaggcattgtgctgaggctttggggggat
	*****************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000023200 ENSRNOG00000017229 Arl10
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000047738 ENSRNOG00000017229 Arl10
	........................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>..............	ENSRNOT00000063186 ENSRNOG00000041433
rat	.((..(((((..((((((........(((((((((((((.(((((.(((((((.(((....))).))))))).))))).)))))))).))))).)))).))...)))))..))	1.000 -54.70

rat

chromosome:17:16097392:16097504:-1

Same_strand|Intronic_coding|ENSRNOT00000047738|ENSRNOG00000017229 ## Same_strand|Exonic_non-coding|ENSRNOT00000063186|ENSRNOG00000041433 ## ENSRNOG00000017229|protein_coding|Arl10|ADP-ribosylation factor-like 10 [Source:RefSeq_peptide;Acc:NP_997048] ## ENSRNOG00000041433|miRNA|| ## {Repeats: L2 3260 3265 -1 class=LINE/L2,L2 3266 3286 1 class=LINE/L2,L2 3250 3268 1 class=LINE/L2,L2 3312 3371 -1 class=LINE,L2 3244 3262 -1 class=LINE/L2,L2 3230 3252 1 class=LINE/L2,L2 3226 3246 -1 class=LINE/L2,L2 -7 3412 1 class=LINE}

miRNAunknown_rep_lenNOK_cloningOK_multiarm_DicerNOK_Multihit_randfoldOK (2 loci)

sblock5207 (miRNA) [miRNAunknown_rep_lenNOK_cloningOK_multiarm_DicerNOK_Multihit_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

Ensembl miRNA

0.001

no

LTR

0.35/0.55

18/23/0.21

0.0 0.0 0.0

0.0 0.0 0.0

1 23 1

0 0 0

1 6 1

0 0 0

20 26 7

6 2 18

5arm 5arm 3arm

2 29 170

nd nd nd

0.24 0.21 0.32

3 3 5

34

7

16

19

		reads	miRBase family seed
seed	---------------------------GUGUAUG------------------------------------------------------------------	30	novel
seed	----------------------------UGUAUGU-----------------------------------------------------------------	2	miR-297
seed	---------------------GUGUUUG------------------------------------------------------------------------	1	novel
seed	------------------------------------------------------------------------CACACAC---------------------	1	novel
		len	cloning frequencies
			T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S2
	--------------------------TGTGTATGTCCATGTGTGT-------------------------------------------------------	19	7	10	3	-	-	3	-
	--------------------------TGTGTATGTCCATGTGTGTA------------------------------------------------------	20	2	1	-	-	-	-	-
	---------------------------GTGTATGTCCATGTGTGTA------------------------------------------------------	19	-	-	1	-	-	-	1
	--------------------------TGTGTATGTCCATGTGTG--------------------------------------------------------	18	1	-	-	1	-	-	-
	--------------------------TGTGTATGTCCATGTGTGTATAT---------------------------------------------------	23	1	-	-	-	-	-	-
	--------------------TGTGTTTGTGTATGTCCATGT-----------------------------------------------------------	21	1	-	-	-	-	-	-
	--------------------------TGTGTATGTCCATGTGTGTAT-----------------------------------------------------	21	-	-	1	-	-	-	-
	-----------------------------------------------------------------------ACACACACACGGACACACACAC-------	22	-	-	-	-	1	-	-
rat	tatgtgtgtttgtgtatatttgtgttTGTGTATGTCCATGTGTGTatatgagcatacacacacacacagacacacacacacggacacacacacacacata
	****************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042430 ENSRNOG00000029235 Sfmbt2
	...............>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>...........	ENSRNOT00000063037 ENSRNOG00000041284
rat	(((((((((.(((((.....(((((.(((((.(((...(((((((((......)))))))))...))).))))).))))).....))))).)))))))))	1.000 -42.70

rat

chromosome:17:79287182:79287281:-1

Same_strand|Exonic_non-coding|ENSRNOT00000063037|ENSRNOG00000041284 ## Same_strand|Boundary_non-coding|ENSRNOT00000051529|ENSRNOG00000029235 ## Same_strand|Intronic_coding|ENSRNOT00000042430|ENSRNOG00000029235 ## ENSRNOG00000041284|miRNA|| ## ENSRNOG00000029235|protein_coding|Sfmbt2|Scm-like with four mbt domains 2 Gene [Source:MGI (curated);Acc:Sfmbt2-001] ## {Repeats: (TG)n 38 60 -1 class=Simple_repeat,trf 38 60 0 class=trf,trf 1 14 0 class=trf,(TG)n 2 66 -1 class=Simple_repeat,RMER12 -471 851 1 class=LTR,dust 79287189 79287211 0 class=dust,(CA)n 2 31 -1 class=Simple_repeat}

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other hairpins:

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