Input and runtime details for job 8257533 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 8257533 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:34:31 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:34:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:30:38 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:30:45 CET 2018
	Job Completed		@ Fri Feb 16 22:31:01 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=8257533&toolName=CopraRNA ( 30 days expiry )

Description of the job

LhrA2

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_003210 Listeria monocytogenes EGD-e

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation
30	0.00607	0.5445	lmo0619	N/A	-20.15	0.009257	186 -- 283	154 -- 223	lmo0619	_____________185_____________________________________________________________________________________________________284\n_____________\|_______________________________________________________________________________________________________\|\n5'-UAU...AACAG_____G__GC____CUU___________AAAAAG_____AGUAAAUUACUUCA_______AAAAAAGCGACCAAUU_________GUAUUA____________GGCGG...CAA-3'\n______________UCGGG_GU____GC___AU_GGAUGGGG______AGACA______________UGAAUUA________________UAC_GCCAA_______GAUGAAAACGA\n______________\|\|\|\|\|_\|:____\|\|___\|:_\|\|\|\|\|:\|\|______\|\|\|\|\|______________\|\|\|\|:\|\|________________:\|\|_\|\|\|\|\|_______:\|\|\|\|\|\|\|\|:\|\n______________AGCCC_CG____CG___UG_CCUACUCC______UCUGU______________ACUUGAU________________GUG_CGGUU_______UUACUUUUGUU\n3'-GUU...GUACA_____G__GAUA__UAU__C________GUA________________________________________________C_____ACUCUAC___________UAUUA...GGA-5'\n_____________\|_______________________________________________________________________________________________________\|\n_____________224_____________________________________________________________________________________________________153\n	277 -- 283	154 -- 160	-48.8019 kcal/mol	13.571 kcal/mol	22.2956 kcal/mol	185 284@LB@ \| \|@LB@5'-UAU...AACAG G GC CUU AAAAAG AGUAAAUUACUUCA AAAAAAGCGACCAAUU GUAUUA GGCGG...CAA-3'@LB@ UCGGG GU GC AU GGAUGGGG AGACA UGAAUUA UAC GCCAA GAUGAAAACGA@LB@ \|\|\|\|\| \|: \|\| \|: \|\|\|\|\|:\|\| \|\|\|\|\| \|\|\|\|:\|\| :\|\| \|\|\|\|\| :\|\|\|\|\|\|\|\|:\|@LB@ AGCCC CG CG UG CCUACUCC UCUGU ACUUGAU GUG CGGUU UUACUUUUGUU@LB@3'-GUU...GUACA G GAUA UAU C GUA C ACUCUAC UAUUA...GGA-5'@LB@ \| \|@LB@ 224 153@LB@@LB@@LB@Energy -20.15 kcal/mol@LB@Hybridization Energy -48.8019 kcal/mol@LB@Unfolding Energy - mRNA 13.571 kcal/mol@LB@Unfolding Energy - sRNA 22.2956 kcal/mol@LB@@LB@Position - mRNA 186 -- 283@LB@Position - sRNA 154 -- 223@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 154 -- 160@LB@
190	0.0551	0.7607	lmo0641	N/A	-14.65	0.112053	196 -- 245	175 -- 211	heavy metal-transporting ATPase	_____________195_____________________246\n_____________\|_______________________\|\n5'-AUU...GAGCA______AA__U____________GAAUU...ACU-3'\n______________UAAUGA__GA_UGGAUGAAG_CA\n______________:\|\|\|\|\|__\|\|_\|\|:\|\|\|\|\|:_\|\|\n______________GUUACU__CU_ACUUACUUU_GU\n3'-GUU...UGCCG____________________U__UUAUU...GGA-5'\n_____________\|_______________________\|\n_____________212_____________________174\n	212 -- 218	158 -- 164	-12.4633 kcal/mol	2.08827 kcal/mol	0.95817 kcal/mol	195 246@LB@ \| \|@LB@5'-AUU...GAGCA AA U GAAUU...ACU-3'@LB@ UAAUGA GA UGGAUGAAG CA@LB@ :\|\|\|\|\| \|\| \|\|:\|\|\|\|\|: \|\|@LB@ GUUACU CU ACUUACUUU GU@LB@3'-GUU...UGCCG U UUAUU...GGA-5'@LB@ \| \|@LB@ 212 174@LB@@LB@@LB@Energy -14.65 kcal/mol@LB@Hybridization Energy -12.4633 kcal/mol@LB@Unfolding Energy - mRNA 2.08827 kcal/mol@LB@Unfolding Energy - sRNA 0.95817 kcal/mol@LB@@LB@Position - mRNA 196 -- 245@LB@Position - sRNA 175 -- 211@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 158 -- 164@LB@
59	0.0137	0.6248	lmo0642	N/A	-14.84	0.103863	179 -- 256	168 -- 213	lmo0642	_____________178________257\n_____________\|__________\|\n5'-UUC...GAUUG__________CAUGA...CAA-3'\n______________GAGAUGAGUG\n______________\|\|\|\|\|\|\|:\|\|\n______________CUCUACUUAC\n3'-GUU...GGUUA__________UUUUG...GGA-5'\n_____________\|__________\|\n_____________214________167\n	193 -- 199	161 -- 167	-14.0942 kcal/mol	3.54513 kcal/mol	0.812237 kcal/mol	178 257@LB@ \| \|@LB@5'-UUC...GAUUG CAUGA...CAA-3'@LB@ GAGAUGAGUG@LB@ \|\|\|\|\|\|\|:\|\|@LB@ CUCUACUUAC@LB@3'-GUU...GGUUA UUUUG...GGA-5'@LB@ \| \|@LB@ 214 167@LB@@LB@@LB@Energy -14.84 kcal/mol@LB@Hybridization Energy -14.0942 kcal/mol@LB@Unfolding Energy - mRNA 3.54513 kcal/mol@LB@Unfolding Energy - sRNA 0.812237 kcal/mol@LB@@LB@Position - mRNA 179 -- 256@LB@Position - sRNA 168 -- 213@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 161 -- 167@LB@
36	0.007609	0.5562	lmo0649	N/A	-18.52	0.020396	192 -- 219	177 -- 204	transcriptional regulator	_____________191______220\n_____________\|________\|\n5'-UUU...AACGA________CAUGG...GUA-3'\n______________GGGAUGAG\n______________\|\|\|\|\|\|\|\|\n______________CCCUACUC\n3'-GUU...UAUUG________CGUAU...GGA-5'\n_____________\|________\|\n_____________205______176\n	193 -- 199	197 -- 203	-13.9784 kcal/mol	1.5957 kcal/mol	0.386531 kcal/mol	191 220@LB@ \| \|@LB@5'-UUU...AACGA CAUGG...GUA-3'@LB@ GGGAUGAG@LB@ \|\|\|\|\|\|\|\|@LB@ CCCUACUC@LB@3'-GUU...UAUUG CGUAU...GGA-5'@LB@ \| \|@LB@ 205 176@LB@@LB@@LB@Energy -18.52 kcal/mol@LB@Hybridization Energy -13.9784 kcal/mol@LB@Unfolding Energy - mRNA 1.5957 kcal/mol@LB@Unfolding Energy - sRNA 0.386531 kcal/mol@LB@@LB@Position - mRNA 192 -- 219@LB@Position - sRNA 177 -- 204@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 197 -- 203@LB@
118	0.03209	0.6968	lmo0654	N/A	-17.15	0.038336	200 -- 225	156 -- 180	lmo0654	_____________199________________________226\n_____________\|__________________________\|\n5'-GAA...GCGCG_______C______AUUUAA______UAGAA...CAC-3'\n______________UAUGGCC_AUGAGA______GAGAAC\n______________:\|:\|\|\|\|_\|\|\|\|\|\|______\|\|:\|\|\|\n______________GUGCCGG_UACUCU______CUUUUG\n3'-GUU...UUGAU_______U______ACUUA_______UUUAU...GGA-5'\n_____________\|__________________________\|\n_____________181________________________155\n	200 -- 206	174 -- 180	-23.3306 kcal/mol	3.96502 kcal/mol	8.29586 kcal/mol	199 226@LB@ \| \|@LB@5'-GAA...GCGCG C AUUUAA UAGAA...CAC-3'@LB@ UAUGGCC AUGAGA GAGAAC@LB@ :\|:\|\|\|\| \|\|\|\|\|\| \|\|:\|\|\|@LB@ GUGCCGG UACUCU CUUUUG@LB@3'-GUU...UUGAU U ACUUA UUUAU...GGA-5'@LB@ \| \|@LB@ 181 155@LB@@LB@@LB@Energy -17.15 kcal/mol@LB@Hybridization Energy -23.3306 kcal/mol@LB@Unfolding Energy - mRNA 3.96502 kcal/mol@LB@Unfolding Energy - sRNA 8.29586 kcal/mol@LB@@LB@Position - mRNA 200 -- 225@LB@Position - sRNA 156 -- 180@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 174 -- 180@LB@
147	0.03815	0.6968	lmo0655	N/A	-15.78	0.070044	227 -- 290	154 -- 212	phosphoprotein phosphatase	_____________226_____________291\n_____________\|_______________\|\n______5'-AACAA______UU_______CCACA...UUG-3'\n______________GAGA_G__UGAAGAC\n______________\|\|\|\|_\|__\|\|\|\|:\|\|\n______________CUCU_C__ACUUUUG\n3'-GUU...GGUUA____A_UU_______UUUAU...GGA-5'\n_____________\|_______________\|\n_____________213_____________153\n	13 -- 19	156 -- 162	-12.8457 kcal/mol	3.32795 kcal/mol	0.916023 kcal/mol	226 291@LB@ \| \|@LB@ 5'-AACAA UU CCACA...UUG-3'@LB@ GAGA G UGAAGAC@LB@ \|\|\|\| \| \|\|\|\|:\|\|@LB@ CUCU C ACUUUUG@LB@3'-GUU...GGUUA A UU UUUAU...GGA-5'@LB@ \| \|@LB@ 213 153@LB@@LB@@LB@Energy -15.78 kcal/mol@LB@Hybridization Energy -12.8457 kcal/mol@LB@Unfolding Energy - mRNA 3.32795 kcal/mol@LB@Unfolding Energy - sRNA 0.916023 kcal/mol@LB@@LB@Position - mRNA 227 -- 290@LB@Position - sRNA 154 -- 212@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 156 -- 162@LB@
88	0.02298	0.6733	lmo0666	N/A	-13.39	0.184164	127 -- 173	156 -- 211		_____________126__________________________________________________________________________________174\n_____________\|____________________________________________________________________________________\|\n5'-AAG...AUUCA____A__GAACC______AA__C___AGU____AC___A__AAA_____GUUA______G_____GC_________________UCGUU...AUG-3'\n______________GCCA_CA______GGCGC__AU_GCA___AUGG__GGU_AG___AUAGA____GA___A_ACGGC_________GAAUGGAGAC\n______________\|\|\|\|_\|\|______\|\|\|\|\|__\|\|_\|\|\|___\|:\|\|__\|:\|_\|\|___\|\|\|\|\|____\|\|___\|_\|\|\|\|\|_________\|\|\|\|\|:\|:\|\|\n______________CGGU_GU______CCGCG__UA_CGU___UGCC__CUA_UC___UAUCU____CU___U_UGCCG_________CUUACUUUUG\n3'-GUU...CGCAA____A__ACAAGC_____GA______AU__________C__CG______GUA___UGA_G_____GUUACUCUA__________UUUAU...GGA-5'\n_____________\|____________________________________________________________________________________\|\n_____________212__________________________________________________________________________________155\n	167 -- 173	156 -- 162	-45.3275 kcal/mol	14.8697 kcal/mol	22.6898 kcal/mol	126 174@LB@ \| \|@LB@5'-AAG...AUUCA A GAACC AA C AGU AC A AAA GUUA G GC UCGUU...AUG-3'@LB@ GCCA CA GGCGC AU GCA AUGG GGU AG AUAGA GA A ACGGC GAAUGGAGAC@LB@ \|\|\|\| \|\| \|\|\|\|\| \|\| \|\|\| \|:\|\| \|:\| \|\| \|\|\|\|\| \|\| \| \|\|\|\|\| \|\|\|\|\|:\|:\|\|@LB@ CGGU GU CCGCG UA CGU UGCC CUA UC UAUCU CU U UGCCG CUUACUUUUG@LB@3'-GUU...CGCAA A ACAAGC GA AU C CG GUA UGA G GUUACUCUA UUUAU...GGA-5'@LB@ \| \|@LB@ 212 155@LB@@LB@@LB@Energy -13.39 kcal/mol@LB@Hybridization Energy -45.3275 kcal/mol@LB@Unfolding Energy - mRNA 14.8697 kcal/mol@LB@Unfolding Energy - sRNA 22.6898 kcal/mol@LB@@LB@Position - mRNA 127 -- 173@LB@Position - sRNA 156 -- 211@LB@Position Seed - mRNA 167 -- 173@LB@Position Seed - sRNA 156 -- 162@LB@
9	0.002066	0.4469	lmo0669	N/A	-20.91	0.006284	33 -- 77	156 -- 211	oxidoreductase	_____________32__________________78\n_____________\|___________________\|\n5'-AAU...UAAAG___________________GGGAA...UUC-3'\n______________UAAUGGGG_GGAUGAAAAU\n______________:\|\|\|\|:\|:_\|:\|\|\|\|\|\|\|:\n______________GUUACUCU_CUUACUUUUG\n3'-GUU...UGCCG________A__________UUUAU...GGA-5'\n_____________\|___________________\|\n_____________212_________________155\n	71 -- 77	156 -- 162	-16.6504 kcal/mol	2.4241 kcal/mol	0.944687 kcal/mol	32 78@LB@ \| \|@LB@5'-AAU...UAAAG GGGAA...UUC-3'@LB@ UAAUGGGG GGAUGAAAAU@LB@ :\|\|\|\|:\|: \|:\|\|\|\|\|\|\|:@LB@ GUUACUCU CUUACUUUUG@LB@3'-GUU...UGCCG A UUUAU...GGA-5'@LB@ \| \|@LB@ 212 155@LB@@LB@@LB@Energy -20.91 kcal/mol@LB@Hybridization Energy -16.6504 kcal/mol@LB@Unfolding Energy - mRNA 2.4241 kcal/mol@LB@Unfolding Energy - sRNA 0.944687 kcal/mol@LB@@LB@Position - mRNA 33 -- 77@LB@Position - sRNA 156 -- 211@LB@Position Seed - mRNA 71 -- 77@LB@Position Seed - sRNA 156 -- 162@LB@
26	0.004866	0.5029	lmo0682	flgG	-18.63	0.019297	177 -- 239	156 -- 207	flagellar basal body rod protein FlgG	_____________176__________________________________________240\n_____________\|____________________________________________\|\n5'-GAA...ACCAA_______GU_______CGGA__G___________AC____A___GGCAG...UCA-3'\n______________AGA_GUC__UGGCUAG____GC_G_UUUGUUGGA__GGAU_GGA\n______________\|\|\|_\|\|\|__\|\|:\|\|\|\|____\|\|_:_\|:\|:\|\|\|\|\|__:\|\|\|_\|\|\|\n______________UCU_CAG__ACUGAUC____CG_U_AGAUAACCU__UCUA_CCU\n3'-GUU...AUUUG___A____________AA____G_A___________________AUGUG...GGA-5'\n_____________\|____________________________________________\|\n_____________208__________________________________________155\n	171 -- 177	102 -- 108	-30.3451 kcal/mol	11.2986 kcal/mol	9.4836 kcal/mol	176 240@LB@ \| \|@LB@5'-GAA...ACCAA GU CGGA G AC A GGCAG...UCA-3'@LB@ AGA GUC UGGCUAG GC G UUUGUUGGA GGAU GGA@LB@ \|\|\| \|\|\| \|\|:\|\|\|\| \|\| : \|:\|:\|\|\|\|\| :\|\|\| \|\|\|@LB@ UCU CAG ACUGAUC CG U AGAUAACCU UCUA CCU@LB@3'-GUU...AUUUG A AA G A AUGUG...GGA-5'@LB@ \| \|@LB@ 208 155@LB@@LB@@LB@Energy -18.63 kcal/mol@LB@Hybridization Energy -30.3451 kcal/mol@LB@Unfolding Energy - mRNA 11.2986 kcal/mol@LB@Unfolding Energy - sRNA 9.4836 kcal/mol@LB@@LB@Position - mRNA 177 -- 239@LB@Position - sRNA 156 -- 207@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 102 -- 108@LB@
129	0.03464	0.6968	lmo0756	N/A	-20.18	0.009099	160 -- 214	175 -- 223	ABC transporter ATP-binding protein	_____________159__________215\n_____________\|____________\|\n5'-AGU...AUAGA_______G____AGAAG...UUU-3'\n______________GACGGGA_GGGG\n______________:\|\|\|\|\|\|_\|:\|\|\n______________UUGCCCU_CUCC\n3'-GUU...ACGUA_______A____GUAUC...GGA-5'\n_____________\|____________\|\n_____________224__________174\n	181 -- 187	201 -- 207	-16.8336 kcal/mol	1.76926 kcal/mol	3.58567 kcal/mol	159 215@LB@ \| \|@LB@5'-AGU...AUAGA G AGAAG...UUU-3'@LB@ GACGGGA GGGG@LB@ :\|\|\|\|\|\| \|:\|\|@LB@ UUGCCCU CUCC@LB@3'-GUU...ACGUA A GUAUC...GGA-5'@LB@ \| \|@LB@ 224 174@LB@@LB@@LB@Energy -20.18 kcal/mol@LB@Hybridization Energy -16.8336 kcal/mol@LB@Unfolding Energy - mRNA 1.76926 kcal/mol@LB@Unfolding Energy - sRNA 3.58567 kcal/mol@LB@@LB@Position - mRNA 160 -- 214@LB@Position - sRNA 175 -- 223@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 201 -- 207@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:

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service.

When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

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