Input and runtime details for job 3202356 (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 3202356 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:02 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:03:47 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:03:55 CET 2018
	Job Completed		@ Sat Feb 17 02:04:28 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

Description of the job

GcvB

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_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

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
76	0.003538	0.1596	stm3058	pepP	-14.75	0.129287	129 -- 167	36 -- 78	Xaa-Pro aminopeptidase	_____________128_________________168\n_____________\|___________________\|\n5'-CGA...CUGGC___________CCG_____GCCGC...GCA-3'\n______________GCAAAUGCAGC___GCAGC\n______________\|\|\|\|\|::\|\|:\|___:\|\|:\|\n______________CGUUUGUGUUG___UGUUG\n3'-UUU...GUUAA___________UUG_____UAGUG...UCA-5'\n_____________\|___________________\|\n_____________79__________________35\n	249 -- 255	80 -- 86	-18.5262 kcal/mol	6.77337 kcal/mol	3.80362 kcal/mol	128 168@LB@ \| \|@LB@5'-CGA...CUGGC CCG GCCGC...GCA-3'@LB@ GCAAAUGCAGC GCAGC@LB@ \|\|\|\|\|::\|\|:\| :\|\|:\|@LB@ CGUUUGUGUUG UGUUG@LB@3'-UUU...GUUAA UUG UAGUG...UCA-5'@LB@ \| \|@LB@ 79 35@LB@@LB@@LB@Energy -14.75 kcal/mol@LB@Hybridization Energy -18.5262 kcal/mol@LB@Unfolding Energy - mRNA 6.77337 kcal/mol@LB@Unfolding Energy - sRNA 3.80362 kcal/mol@LB@@LB@Position - mRNA 129 -- 167@LB@Position - sRNA 36 -- 78@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 80 -- 86@LB@
92	0.004229	0.1596	stm0669	phoL	-19.39	0.022083	221 -- 286	36 -- 89	putative phosphate starvation-inducible protein ATP-binding	_____________220__________________________________________________________________287\n_____________\|____________________________________________________________________\|\n5'-AAA...CGAUA_________G__GAACAGUUUGAAUAUA____C______AAUUAC___UU____________CA____CCGUC...GCC-3'\n______________CAGACACAA_AG________________GACA_UCGCGA_______CC__GAGCCCG_CAGA__ACGC\n______________\|\|:\|\|\|\|\|\|_\|:________________:\|\|\|_\|\|:\|:\|_______\|\|__:\|\|\|\|\|:_\|\|\|\|__\|\|\|\|\n______________GUUUGUGUU_UU________________UUGU_AGUGUU_______GG__UUCGGGU_GUCU__UGCG\n3'-UUU...UUAAC_________G__GUG________________________GGCAUUC__UU_______A____UG____UAAGG...UCA-5'\n_____________\|____________________________________________________________________\|\n_____________90___________________________________________________________________35\n	270 -- 276	47 -- 53	-43.5648 kcal/mol	9.30805 kcal/mol	22.4875 kcal/mol	220 287@LB@ \| \|@LB@5'-AAA...CGAUA G GAACAGUUUGAAUAUA C AAUUAC UU CA CCGUC...GCC-3'@LB@ CAGACACAA AG GACA UCGCGA CC GAGCCCG CAGA ACGC@LB@ \|\|:\|\|\|\|\|\| \|: :\|\|\| \|\|:\|:\| \|\| :\|\|\|\|\|: \|\|\|\| \|\|\|\|@LB@ GUUUGUGUU UU UUGU AGUGUU GG UUCGGGU GUCU UGCG@LB@3'-UUU...UUAAC G GUG GGCAUUC UU A UG UAAGG...UCA-5'@LB@ \| \|@LB@ 90 35@LB@@LB@@LB@Energy -19.39 kcal/mol@LB@Hybridization Energy -43.5648 kcal/mol@LB@Unfolding Energy - mRNA 9.30805 kcal/mol@LB@Unfolding Energy - sRNA 22.4875 kcal/mol@LB@@LB@Position - mRNA 221 -- 286@LB@Position - sRNA 36 -- 89@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 47 -- 53@LB@
90	0.004161	0.1596	stm1124	putA	-17.89	0.039481	159 -- 201	125 -- 168	trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase	_____________158______________________________________________202\n_____________\|________________________________________________\|\n5'-UAA...CGCUA____U___UUA________A_C____A_____________________UGGGA...UAA-3'\n______________ACUA_UGG___GCAGAUAG_G_GAAU__ACAGG_AGU___AGAGGGUA\n______________\|\|\|\|_\|\|\|___:\|\|\|\|:\|\|_\|_:\|\|\|__\|\|\|\|\|_\|\|\|___\|:\|\|\|\|\|\|\n______________UGAU_ACC___UGUCUGUC_C_UUUA__UGUCC_UCA___UUUCCCAU\n3'-UUU...AUUAG___________________C_A____CA_____U___CUU________CAGAG...UCA-5'\n_____________\|________________________________________________\|\n_____________169______________________________________________124\n	195 -- 201	125 -- 131	-33.9858 kcal/mol	7.26317 kcal/mol	8.4265 kcal/mol	158 202@LB@ \| \|@LB@5'-UAA...CGCUA U UUA A C A UGGGA...UAA-3'@LB@ ACUA UGG GCAGAUAG G GAAU ACAGG AGU AGAGGGUA@LB@ \|\|\|\| \|\|\| :\|\|\|\|:\|\| \| :\|\|\| \|\|\|\|\| \|\|\| \|:\|\|\|\|\|\|@LB@ UGAU ACC UGUCUGUC C UUUA UGUCC UCA UUUCCCAU@LB@3'-UUU...AUUAG C A CA U CUU CAGAG...UCA-5'@LB@ \| \|@LB@ 169 124@LB@@LB@@LB@Energy -17.89 kcal/mol@LB@Hybridization Energy -33.9858 kcal/mol@LB@Unfolding Energy - mRNA 7.26317 kcal/mol@LB@Unfolding Energy - sRNA 8.4265 kcal/mol@LB@@LB@Position - mRNA 159 -- 201@LB@Position - sRNA 125 -- 168@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 125 -- 131@LB@
87	0.004009	0.1596	stm2067	sbcB	-11.70	0.367652	220 -- 292	35 -- 90	exodeoxyribonuclease I	_____________219_____________________293\n_____________\|_______________________\|\n5'-AUU...AUGUA______U________________AUUGG...CCG-3'\n______________CGAACA_UAGCA__ACAAUAUCA\n______________\|:\|\|\|\|_:\|:\|\|__\|\|\|\|:\|\|\|\|\n______________GUUUGU_GUUGU__UGUUGUAGU\n3'-UUU...UUAAC____________UG_________GUUGG...UCA-5'\n_____________\|_______________________\|\n_____________91______________________34\n	110 -- 116	68 -- 74	-17.8808 kcal/mol	2.08887 kcal/mol	5.27986 kcal/mol	219 293@LB@ \| \|@LB@5'-AUU...AUGUA U AUUGG...CCG-3'@LB@ CGAACA UAGCA ACAAUAUCA@LB@ \|:\|\|\|\| :\|:\|\| \|\|\|\|:\|\|\|\|@LB@ GUUUGU GUUGU UGUUGUAGU@LB@3'-UUU...UUAAC UG GUUGG...UCA-5'@LB@ \| \|@LB@ 91 34@LB@@LB@@LB@Energy -11.70 kcal/mol@LB@Hybridization Energy -17.8808 kcal/mol@LB@Unfolding Energy - mRNA 2.08887 kcal/mol@LB@Unfolding Energy - sRNA 5.27986 kcal/mol@LB@@LB@Position - mRNA 220 -- 292@LB@Position - sRNA 35 -- 90@LB@Position Seed - mRNA 110 -- 116@LB@Position Seed - sRNA 68 -- 74@LB@
93	0.004254	0.1596	stm0408	secF	-18.22	0.034847	7 -- 64	39 -- 91	protein-export membrane protein SecF	_____________6______________________________________65\n_____________\|______________________________________\|\n5'-CUU...GCACA_G__U____UGUUG______UA________________AGUCU...UGC-3'\n______________G_AA_ACAC_____AACAAC__AAC__CACGGCCGUAA\n______________\|_\|\|_\|\|\|\|_____\|\|\|\|\|\|__\|\|\|__\|\|\|::\|\|\|\|\|\|\n______________C_UU_UGUG_____UUGUUG__UUG__GUGUUGGCAUU\n3'-UUU...GUUAA_G__________________UG___UA___________CGGUU...UCA-5'\n_____________\|______________________________________\|\n_____________92_____________________________________38\n	238 -- 244	59 -- 65	-26.2573 kcal/mol	3.95572 kcal/mol	10.1648 kcal/mol	6 65@LB@ \| \|@LB@5'-CUU...GCACA G U UGUUG UA AGUCU...UGC-3'@LB@ G AA ACAC AACAAC AAC CACGGCCGUAA@LB@ \| \|\| \|\|\|\| \|\|\|\|\|\| \|\|\| \|\|\|::\|\|\|\|\|\|@LB@ C UU UGUG UUGUUG UUG GUGUUGGCAUU@LB@3'-UUU...GUUAA G UG UA CGGUU...UCA-5'@LB@ \| \|@LB@ 92 38@LB@@LB@@LB@Energy -18.22 kcal/mol@LB@Hybridization Energy -26.2573 kcal/mol@LB@Unfolding Energy - mRNA 3.95572 kcal/mol@LB@Unfolding Energy - sRNA 10.1648 kcal/mol@LB@@LB@Position - mRNA 7 -- 64@LB@Position - sRNA 39 -- 91@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 59 -- 65@LB@
69	0.003278	0.1596	stm3675	sgbH	-16.55	0.065932	154 -- 200	33 -- 93	3-keto-L-gulonate-6-phosphate decarboxylase	_____________153_______________________201\n_____________\|_________________________\|\n5'-UUC...CAGUC__G_____GCC______________CCUGC...AGG-3'\n______________UG_AAGCA___CAACGCGAUGUCGC\n______________\|\|_\|\|:\|\|___\|\|\|\|:\|:\|::\|\|:\|\n______________AC_UUUGU___GUUGUGUUGUAGUG\n3'-UUU...GGUUA__G_____GUU______________UUGGC...UCA-5'\n_____________\|_________________________\|\n_____________94________________________32\n	258 -- 264	71 -- 77	-24.2274 kcal/mol	7.7572 kcal/mol	5.6854 kcal/mol	153 201@LB@ \| \|@LB@5'-UUC...CAGUC G GCC CCUGC...AGG-3'@LB@ UG AAGCA CAACGCGAUGUCGC@LB@ \|\| \|\|:\|\| \|\|\|\|:\|:\|::\|\|:\|@LB@ AC UUUGU GUUGUGUUGUAGUG@LB@3'-UUU...GGUUA G GUU UUGGC...UCA-5'@LB@ \| \|@LB@ 94 32@LB@@LB@@LB@Energy -16.55 kcal/mol@LB@Hybridization Energy -24.2274 kcal/mol@LB@Unfolding Energy - mRNA 7.7572 kcal/mol@LB@Unfolding Energy - sRNA 5.6854 kcal/mol@LB@@LB@Position - mRNA 154 -- 200@LB@Position - sRNA 33 -- 93@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 71 -- 77@LB@
70	0.003306	0.1596	stm2688	smpB	-12.25	0.308628	191 -- 230	36 -- 77	SsrA-binding protein	_____________190_________________231\n_____________\|___________________\|\n5'-AAU...GCAUA____UUCC__U________AUCGU...GUC-3'\n______________GCAA____CA_CAACAUAA\n______________\|\|\|\|____\|\|_\|\|\|\|\|:\|\|\n______________CGUU____GU_GUUGUGUU\n3'-UUU...GUUAA____UGU___U________GUAGU...UCA-5'\n_____________\|___________________\|\n_____________78__________________35\n	26 -- 32	73 -- 79	-12.551 kcal/mol	1.44298 kcal/mol	3.77104 kcal/mol	190 231@LB@ \| \|@LB@5'-AAU...GCAUA UUCC U AUCGU...GUC-3'@LB@ GCAA CA CAACAUAA@LB@ \|\|\|\| \|\| \|\|\|\|\|:\|\|@LB@ CGUU GU GUUGUGUU@LB@3'-UUU...GUUAA UGU U GUAGU...UCA-5'@LB@ \| \|@LB@ 78 35@LB@@LB@@LB@Energy -12.25 kcal/mol@LB@Hybridization Energy -12.551 kcal/mol@LB@Unfolding Energy - mRNA 1.44298 kcal/mol@LB@Unfolding Energy - sRNA 3.77104 kcal/mol@LB@@LB@Position - mRNA 191 -- 230@LB@Position - sRNA 36 -- 77@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 73 -- 79@LB@
64	0.003108	0.1596	stm4162	thiF	-13.53	0.200092	247 -- 294	34 -- 76	molybdopterin/thiamine biosynthesis adenylyltransferase	_____________246___________________295\n_____________\|_____________________\|\n5'-GCA...GCUCG_______________A_____AGCAA...UUG-3'\n______________GCGAUAUCGCGAUUG_AGGCC\n______________:\|:\|:\|\|\|:\|:\|::\|_\|:\|\|\|\n______________UGUUGUAGUGUUGGC_UUCGG\n3'-UUU...UGUUG_______________A_____UUUUC...UCA-5'\n_____________\|_____________________\|\n_____________77____________________33\n	248 -- 254	69 -- 75	-25.2172 kcal/mol	7.66984 kcal/mol	8.92374 kcal/mol	246 295@LB@ \| \|@LB@5'-GCA...GCUCG A AGCAA...UUG-3'@LB@ GCGAUAUCGCGAUUG AGGCC@LB@ :\|:\|:\|\|\|:\|:\|::\| \|:\|\|\|@LB@ UGUUGUAGUGUUGGC UUCGG@LB@3'-UUU...UGUUG A UUUUC...UCA-5'@LB@ \| \|@LB@ 77 33@LB@@LB@@LB@Energy -13.53 kcal/mol@LB@Hybridization Energy -25.2172 kcal/mol@LB@Unfolding Energy - mRNA 7.66984 kcal/mol@LB@Unfolding Energy - sRNA 8.92374 kcal/mol@LB@@LB@Position - mRNA 247 -- 294@LB@Position - sRNA 34 -- 76@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 69 -- 75@LB@
79	0.003723	0.1596	stm1723	trpE	-16.56	0.065817	202 -- 256	41 -- 91	anthranilate synthase subunit I	_____________201__________________257\n_____________\|____________________\|\n5'-UGA...AAAUG__________UU________CGGUU...CGG-3'\n______________GCAGCGACAU__GCAUUACA\n______________:\|\|:\|:\|\|\|:__:\|\|\|:\|\|\|\n______________UGUUGUUGUG__UGUAGUGU\n3'-UUU...GUUUG__________U_________UGGCA...UCA-5'\n_____________\|____________________\|\n_____________92___________________40\n	78 -- 84	66 -- 72	-20.8013 kcal/mol	5.41524 kcal/mol	5.89278 kcal/mol	201 257@LB@ \| \|@LB@5'-UGA...AAAUG UU CGGUU...CGG-3'@LB@ GCAGCGACAU GCAUUACA@LB@ :\|\|:\|:\|\|\|: :\|\|\|:\|\|\|@LB@ UGUUGUUGUG UGUAGUGU@LB@3'-UUU...GUUUG U UGGCA...UCA-5'@LB@ \| \|@LB@ 92 40@LB@@LB@@LB@Energy -16.56 kcal/mol@LB@Hybridization Energy -20.8013 kcal/mol@LB@Unfolding Energy - mRNA 5.41524 kcal/mol@LB@Unfolding Energy - sRNA 5.89278 kcal/mol@LB@@LB@Position - mRNA 202 -- 256@LB@Position - sRNA 41 -- 91@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 66 -- 72@LB@
71	0.003339	0.1596	stm0105	yabI	-14.10	0.163814	151 -- 168	141 -- 162	similar to E. coli orf hypothetical protein (AAC73176.1); Blastp hit to AAC73176.1 (254 aa) 89% identity in aa 1 - 253	_____________150____________________169\n_____________\|______________________\|\n5'-UGA...ACGAA__G___________________AAUCC...GGU-3'\n______________GG_GGACGGGGUAA____GCAG\n______________\|:_:\|\|\|:\|\|\|\|\|\|____:\|\|\|\n______________CU_UCUGUCCCAUU____UGUC\n3'-UUU...GAUAC__G___________UACA____CUUCA...UCA-5'\n_____________\|______________________\|\n_____________163____________________140\n	158 -- 164	149 -- 155	-23.8591 kcal/mol	5.26969 kcal/mol	3.68511 kcal/mol	150 169@LB@ \| \|@LB@5'-UGA...ACGAA G AAUCC...GGU-3'@LB@ GG GGACGGGGUAA GCAG@LB@ \|: :\|\|\|:\|\|\|\|\|\| :\|\|\|@LB@ CU UCUGUCCCAUU UGUC@LB@3'-UUU...GAUAC G UACA CUUCA...UCA-5'@LB@ \| \|@LB@ 163 140@LB@@LB@@LB@Energy -14.10 kcal/mol@LB@Hybridization Energy -23.8591 kcal/mol@LB@Unfolding Energy - mRNA 5.26969 kcal/mol@LB@Unfolding Energy - sRNA 3.68511 kcal/mol@LB@@LB@Position - mRNA 151 -- 168@LB@Position - sRNA 141 -- 162@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 149 -- 155@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

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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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