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
181	0.05165	0.7607	lmo2287	N/A	-16.24	0.057456	190 -- 241	154 -- 199	tape-measure	_____________189________________________________________________242\n_____________\|__________________________________________________\|\n5'-UGA...CUGAA________AUAA___AAAA______AG__G_GAACAU_____C_______CAGUA...CAA-3'\n______________AAACAGAU____GUU____GAUUAG__GU_A________GAG_GAUGGAU\n______________\|\|\|\|\|\|\|\|____\|\|:____\|\|:\|\|\|__\|:_\|________\|\|:_\|\|\|\|\|\|\|\n______________UUUGUCUA____CAG____CUGAUC__CG_U________CUU_CUACCUA\n3'-GUU...ACAGA_______________A_________AA__G_AAGAUAAC___________UGUGG...GGA-5'\n_____________\|__________________________________________________\|\n_____________200________________________________________________153\n	207 -- 213	94 -- 100	-23.404 kcal/mol	6.71689 kcal/mol	9.49359 kcal/mol	189 242@LB@ \| \|@LB@5'-UGA...CUGAA AUAA AAAA AG G GAACAU C CAGUA...CAA-3'@LB@ AAACAGAU GUU GAUUAG GU A GAG GAUGGAU@LB@ \|\|\|\|\|\|\|\| \|\|: \|\|:\|\|\| \|: \| \|\|: \|\|\|\|\|\|\|@LB@ UUUGUCUA CAG CUGAUC CG U CUU CUACCUA@LB@3'-GUU...ACAGA A AA G AAGAUAAC UGUGG...GGA-5'@LB@ \| \|@LB@ 200 153@LB@@LB@@LB@Energy -16.24 kcal/mol@LB@Hybridization Energy -23.404 kcal/mol@LB@Unfolding Energy - mRNA 6.71689 kcal/mol@LB@Unfolding Energy - sRNA 9.49359 kcal/mol@LB@@LB@Position - mRNA 190 -- 241@LB@Position - sRNA 154 -- 199@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 94 -- 100@LB@
182	0.05242	0.7607	lmo2028	N/A	-14.74	0.108099	169 -- 210	158 -- 185		_____________168_________211\n_____________\|___________\|\n5'-CUU...AUUAU___________UUUAU...AAC-3'\n______________GAUGGAUGGAA\n______________\|\|\|\|:\|\|\|:\|\|\n______________CUACUUACUUU\n3'-GUU...UUACU___________UGUUU...GGA-5'\n_____________\|___________\|\n_____________186_________157\n	204 -- 210	158 -- 164	-12.4441 kcal/mol	2.18802 kcal/mol	0.806249 kcal/mol	168 211@LB@ \| \|@LB@5'-CUU...AUUAU UUUAU...AAC-3'@LB@ GAUGGAUGGAA@LB@ \|\|\|\|:\|\|\|:\|\|@LB@ CUACUUACUUU@LB@3'-GUU...UUACU UGUUU...GGA-5'@LB@ \| \|@LB@ 186 157@LB@@LB@@LB@Energy -14.74 kcal/mol@LB@Hybridization Energy -12.4441 kcal/mol@LB@Unfolding Energy - mRNA 2.18802 kcal/mol@LB@Unfolding Energy - sRNA 0.806249 kcal/mol@LB@@LB@Position - mRNA 169 -- 210@LB@Position - sRNA 158 -- 185@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 158 -- 164@LB@
183	0.0534	0.7607	lmo2583	N/A	-16.44	0.052604	178 -- 212	151 -- 181	DNA-binding response regulator	_____________177___________________________213\n_____________\|_____________________________\|\n5'-UAA...AAAUA_G_____AA______C_____________AACAA...AUG-3'\n______________A_ACGGU__GGUGAG___GGUGAAAAUGA\n______________\|_\|\|\|\|:__::\|\|\|\|___::\|\|\|\|\|\|::\|\n______________U_UGCCG__UUACUC___UUACUUUUGUU\n3'-GUU...CUUGA_G_____G_______UAC___________UAUUA...GGA-5'\n_____________\|_____________________________\|\n_____________182___________________________150\n	197 -- 203	155 -- 161	-21.6156 kcal/mol	3.93053 kcal/mol	8.33518 kcal/mol	177 213@LB@ \| \|@LB@5'-UAA...AAAUA G AA C AACAA...AUG-3'@LB@ A ACGGU GGUGAG GGUGAAAAUGA@LB@ \| \|\|\|\|: ::\|\|\|\| ::\|\|\|\|\|\|::\|@LB@ U UGCCG UUACUC UUACUUUUGUU@LB@3'-GUU...CUUGA G G UAC UAUUA...GGA-5'@LB@ \| \|@LB@ 182 150@LB@@LB@@LB@Energy -16.44 kcal/mol@LB@Hybridization Energy -21.6156 kcal/mol@LB@Unfolding Energy - mRNA 3.93053 kcal/mol@LB@Unfolding Energy - sRNA 8.33518 kcal/mol@LB@@LB@Position - mRNA 178 -- 212@LB@Position - sRNA 151 -- 181@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 155 -- 161@LB@
184	0.05355	0.7607	lmo2119	N/A	-15.99	0.064071	3 -- 81	95 -- 171		_____________2_________________________82\n_____________\|_________________________\|\n_________5'-CU______U______GU__________AUUAC...CCA-3'\n______________UGGGAU_AGUGAA__GACAGAUAGU\n______________\|\|:\|\|\|_\|:\|\|\|\|__:\|\|\|:\|\|\|:\|\n______________ACUCUA_UUACUU__UUGUUUAUUA\n3'-GUU...CGGUU______C__________________CUAAA...GGA-5'\n_____________\|_________________________\|\n_____________172_______________________94\n	18 -- 24	152 -- 158	-18.6088 kcal/mol	3.83703 kcal/mol	5.55637 kcal/mol	2 82@LB@ \| \|@LB@ 5'-CU U GU AUUAC...CCA-3'@LB@ UGGGAU AGUGAA GACAGAUAGU@LB@ \|\|:\|\|\| \|:\|\|\|\| :\|\|\|:\|\|\|:\|@LB@ ACUCUA UUACUU UUGUUUAUUA@LB@3'-GUU...CGGUU C CUAAA...GGA-5'@LB@ \| \|@LB@ 172 94@LB@@LB@@LB@Energy -15.99 kcal/mol@LB@Hybridization Energy -18.6088 kcal/mol@LB@Unfolding Energy - mRNA 3.83703 kcal/mol@LB@Unfolding Energy - sRNA 5.55637 kcal/mol@LB@@LB@Position - mRNA 3 -- 81@LB@Position - sRNA 95 -- 171@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 152 -- 158@LB@
185	0.05367	0.7607	lmo1631	trpD	-14.92	0.100424	142 -- 163	148 -- 170	anthranilate phosphoribosyltransferase	_____________141__________________164\n_____________\|____________________\|\n5'-UUC...UACGA____CG______________GAAAA...AAA-3'\n______________AUGA__GAAAACAAAUGAUG\n______________\|\|\|\|__\|\|\|\|\|\|\|\|\|\|:\|\|\|\n______________UACU__CUUUUGUUUAUUAC\n3'-GUU...UACUC____UA______________UAAAA...GGA-5'\n_____________\|____________________\|\n_____________171__________________147\n	153 -- 159	152 -- 158	-19.3831 kcal/mol	2.89443 kcal/mol	5.80116 kcal/mol	141 164@LB@ \| \|@LB@5'-UUC...UACGA CG GAAAA...AAA-3'@LB@ AUGA GAAAACAAAUGAUG@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|\|:\|\|\|@LB@ UACU CUUUUGUUUAUUAC@LB@3'-GUU...UACUC UA UAAAA...GGA-5'@LB@ \| \|@LB@ 171 147@LB@@LB@@LB@Energy -14.92 kcal/mol@LB@Hybridization Energy -19.3831 kcal/mol@LB@Unfolding Energy - mRNA 2.89443 kcal/mol@LB@Unfolding Energy - sRNA 5.80116 kcal/mol@LB@@LB@Position - mRNA 142 -- 163@LB@Position - sRNA 148 -- 170@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 152 -- 158@LB@
186	0.05422	0.7607	lmo2356	N/A	-15.92	0.066009	162 -- 205	129 -- 170	lmo2356	_____________161___________________206\n_____________\|_____________________\|\n5'-CUC...AAAGA_______AUUGAU________UUUGA...UUG-3'\n______________GAGAUGA______GUGAGGAU\n______________\|\|\|\|\|\|\|______:\|\|\|::\|:\n______________CUCUACU______UACUUUUG\n3'-GUU...GGUUA_____________________UUUAU...GGA-5'\n_____________\|_____________________\|\n_____________171___________________128\n	176 -- 182	156 -- 162	-14.0636 kcal/mol	2.1522 kcal/mol	0.916023 kcal/mol	161 206@LB@ \| \|@LB@5'-CUC...AAAGA AUUGAU UUUGA...UUG-3'@LB@ GAGAUGA GUGAGGAU@LB@ \|\|\|\|\|\|\| :\|\|\|::\|:@LB@ CUCUACU UACUUUUG@LB@3'-GUU...GGUUA UUUAU...GGA-5'@LB@ \| \|@LB@ 171 128@LB@@LB@@LB@Energy -15.92 kcal/mol@LB@Hybridization Energy -14.0636 kcal/mol@LB@Unfolding Energy - mRNA 2.1522 kcal/mol@LB@Unfolding Energy - sRNA 0.916023 kcal/mol@LB@@LB@Position - mRNA 162 -- 205@LB@Position - sRNA 129 -- 170@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 156 -- 162@LB@
187	0.05427	0.7607	lmo2654	fus	-15.17	0.090605	196 -- 212	168 -- 184	elongation factor G	_____________195____________213\n_____________\|______________\|\n5'-GAG...AUACA__________A___UUCUC...AUA-3'\n______________ACAUGGCUAG_GAG\n______________\|\|\|:\|\|\|:\|:_\|\|\|\n______________UGUGCCGGUU_CUC\n3'-GUU...CUUGA__________A___UACUU...GGA-5'\n_____________\|______________\|\n_____________185____________167\n	202 -- 208	172 -- 178	-17.9516 kcal/mol	0.731619 kcal/mol	6.23346 kcal/mol	195 213@LB@ \| \|@LB@5'-GAG...AUACA A UUCUC...AUA-3'@LB@ ACAUGGCUAG GAG@LB@ \|\|\|:\|\|\|:\|: \|\|\|@LB@ UGUGCCGGUU CUC@LB@3'-GUU...CUUGA A UACUU...GGA-5'@LB@ \| \|@LB@ 185 167@LB@@LB@@LB@Energy -15.17 kcal/mol@LB@Hybridization Energy -17.9516 kcal/mol@LB@Unfolding Energy - mRNA 0.731619 kcal/mol@LB@Unfolding Energy - sRNA 6.23346 kcal/mol@LB@@LB@Position - mRNA 196 -- 212@LB@Position - sRNA 168 -- 184@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 172 -- 178@LB@
188	0.05492	0.7607	lmo1246	N/A	-15.64	0.074442	171 -- 206	183 -- 211	ATP-dependent RNA helicase	_____________170_______________207\n_____________\|_________________\|\n5'-GCC...AUGAU______A__________UGACA...CCU-3'\n______________AUGAGG__AAUGAGGAC\n______________\|\|\|\|\|:__\|\|\|\|\|::\|\|\n______________UACUCU__UUACUUUUG\n3'-GUU...CCGGU______AC_________UUUAU...GGA-5'\n_____________\|_________________\|\n_____________212_______________182\n	190 -- 196	156 -- 162	-13.5081 kcal/mol	2.39769 kcal/mol	0.922045 kcal/mol	170 207@LB@ \| \|@LB@5'-GCC...AUGAU A UGACA...CCU-3'@LB@ AUGAGG AAUGAGGAC@LB@ \|\|\|\|\|: \|\|\|\|\|::\|\|@LB@ UACUCU UUACUUUUG@LB@3'-GUU...CCGGU AC UUUAU...GGA-5'@LB@ \| \|@LB@ 212 182@LB@@LB@@LB@Energy -15.64 kcal/mol@LB@Hybridization Energy -13.5081 kcal/mol@LB@Unfolding Energy - mRNA 2.39769 kcal/mol@LB@Unfolding Energy - sRNA 0.922045 kcal/mol@LB@@LB@Position - mRNA 171 -- 206@LB@Position - sRNA 183 -- 211@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 156 -- 162@LB@
189	0.05497	0.7607	lmo1156	N/A	-15.46	0.080118	37 -- 70	155 -- 186	diol dehydratase-reactivating factor large subunit	_____________36________________71\n_____________\|_________________\|\n5'-UAU...AAAUG______A__________UAUAU...CUA-3'\n______________CGGUGA_AUGAAUGAAG\n______________\|::\|\|\|_\|\|\|\|\|\|\|\|\|:\n______________GUUACU_UACUUACUUU\n3'-GUU...UGCCG______C__________UGUUU...GGA-5'\n_____________\|_________________\|\n_____________187_______________154\n	200 -- 206	158 -- 164	-15.35 kcal/mol	3.5534 kcal/mol	0.871719 kcal/mol	36 71@LB@ \| \|@LB@5'-UAU...AAAUG A UAUAU...CUA-3'@LB@ CGGUGA AUGAAUGAAG@LB@ \|::\|\|\| \|\|\|\|\|\|\|\|\|:@LB@ GUUACU UACUUACUUU@LB@3'-GUU...UGCCG C UGUUU...GGA-5'@LB@ \| \|@LB@ 187 154@LB@@LB@@LB@Energy -15.46 kcal/mol@LB@Hybridization Energy -15.35 kcal/mol@LB@Unfolding Energy - mRNA 3.5534 kcal/mol@LB@Unfolding Energy - sRNA 0.871719 kcal/mol@LB@@LB@Position - mRNA 37 -- 70@LB@Position - sRNA 155 -- 186@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 158 -- 164@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@

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)

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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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