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: https://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
148	0.007836	0.1845	stm2318	nuoL	-12.84	0.254324	144 -- 178	37 -- 76	NADH-quinone oxidoreductase subunit L	_____________143___________________179\n_____________\|_____________________\|\n5'-GGG...AGACC_____U____U__________UUCUC...UUG-3'\n______________GAUGG_CAGG___GAUGUACA\n______________\|\|::\|_\|\|\|\|___:\|\|\|\|\|\|\|\n______________CUGUC_GUCC___UUACAUGU\n3'-UUU...GAUAC_____U____CAU________CCUUC...UCA-5'\n_____________\|_____________________\|\n_____________77____________________36\n	82 -- 88	142 -- 148	-19.9967 kcal/mol	7.20144 kcal/mol	3.50251 kcal/mol	143 179@LB@ \| \|@LB@5'-GGG...AGACC U U UUCUC...UUG-3'@LB@ GAUGG CAGG GAUGUACA@LB@ \|\|::\| \|\|\|\| :\|\|\|\|\|\|\|@LB@ CUGUC GUCC UUACAUGU@LB@3'-UUU...GAUAC U CAU CCUUC...UCA-5'@LB@ \| \|@LB@ 77 36@LB@@LB@@LB@Energy -12.84 kcal/mol@LB@Hybridization Energy -19.9967 kcal/mol@LB@Unfolding Energy - mRNA 7.20144 kcal/mol@LB@Unfolding Energy - sRNA 3.50251 kcal/mol@LB@@LB@Position - mRNA 144 -- 178@LB@Position - sRNA 37 -- 76@LB@Position Seed - mRNA 82 -- 88@LB@Position Seed - sRNA 142 -- 148@LB@
102	0.005164	0.1728	stm0668	ybeY	-18.23	0.034693	146 -- 193	37 -- 81	rRNA maturation RNase YbeY	_____________145__________________________________________194\n_____________\|____________________________________________\|\n5'-UCC...AAAAC____________UUG____________G_______GU_______AGGAG...CGC-3'\n______________GCAAA_GCGGCG___GCGGCA____GA_CGUAAGC__GAAGCCC\n______________\|\|\|\|\|_:\|::\|:___:\|::\|\|____:\|_\|\|\|\|\|\|\|__:\|\|\|\|\|\|\n______________CGUUU_UGUUGU___UGUUGU____UU_GCAUUCG__UUUCGGG\n3'-UUU...GUUAA_____G______UG_______AGUG__G_______GU_______UAGUC...UCA-5'\n_____________\|____________________________________________\|\n_____________82___________________________________________36\n	178 -- 184	48 -- 54	-38.2699 kcal/mol	15.4401 kcal/mol	16.4278 kcal/mol	145 194@LB@ \| \|@LB@5'-UCC...AAAAC UUG G GU AGGAG...CGC-3'@LB@ GCAAA GCGGCG GCGGCA GA CGUAAGC GAAGCCC@LB@ \|\|\|\|\| :\|::\|: :\|::\|\| :\| \|\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ CGUUU UGUUGU UGUUGU UU GCAUUCG UUUCGGG@LB@3'-UUU...GUUAA G UG AGUG G GU UAGUC...UCA-5'@LB@ \| \|@LB@ 82 36@LB@@LB@@LB@Energy -18.23 kcal/mol@LB@Hybridization Energy -38.2699 kcal/mol@LB@Unfolding Energy - mRNA 15.4401 kcal/mol@LB@Unfolding Energy - sRNA 16.4278 kcal/mol@LB@@LB@Position - mRNA 146 -- 193@LB@Position - sRNA 37 -- 81@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 48 -- 54@LB@
186	0.01044	0.1967	stm1725	trpC	-12.00	0.335236	146 -- 174	55 -- 86	bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase	_____________145_______________175\n_____________\|_________________\|\n5'-AAA...GUUCU____________C____AUGAC...AGC-3'\n______________GCGCAACGGCAC_GCAU\n______________:\|:\|\|\|\|::\|\|\|_:\|\|\|\n______________UGUGUUGUUGUG_UGUA\n3'-UUU...ACGUU____________U____GUGUU...UCA-5'\n_____________\|_________________\|\n_____________87________________54\n	151 -- 157	75 -- 81	-20.8979 kcal/mol	6.12922 kcal/mol	3.85824 kcal/mol	145 175@LB@ \| \|@LB@5'-AAA...GUUCU C AUGAC...AGC-3'@LB@ GCGCAACGGCAC GCAU@LB@ :\|:\|\|\|\|::\|\|\| :\|\|\|@LB@ UGUGUUGUUGUG UGUA@LB@3'-UUU...ACGUU U GUGUU...UCA-5'@LB@ \| \|@LB@ 87 54@LB@@LB@@LB@Energy -12.00 kcal/mol@LB@Hybridization Energy -20.8979 kcal/mol@LB@Unfolding Energy - mRNA 6.12922 kcal/mol@LB@Unfolding Energy - sRNA 3.85824 kcal/mol@LB@@LB@Position - mRNA 146 -- 174@LB@Position - sRNA 55 -- 86@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 75 -- 81@LB@
110	0.005337	0.1728	stm1920	cheW	-12.58	0.277263	149 -- 192	51 -- 90	chemotaxis protein CheW	_____________148__________193\n_____________\|____________\|\n5'-GUC...UGAUU____________AAUAA...UCC-3'\n______________GAGUGAGAAGGG\n______________:\|\|\|\|\|:\|\|:\|\|\n______________UUCACUUUUUCC\n3'-UUU...UGUCC____________CAUCA...UCA-5'\n_____________\|____________\|\n_____________91___________50\n	188 -- 194	128 -- 134	-15.4894 kcal/mol	2.64754 kcal/mol	3.77328 kcal/mol	148 193@LB@ \| \|@LB@5'-GUC...UGAUU AAUAA...UCC-3'@LB@ GAGUGAGAAGGG@LB@ :\|\|\|\|\|:\|\|:\|\|@LB@ UUCACUUUUUCC@LB@3'-UUU...UGUCC CAUCA...UCA-5'@LB@ \| \|@LB@ 91 50@LB@@LB@@LB@Energy -12.58 kcal/mol@LB@Hybridization Energy -15.4894 kcal/mol@LB@Unfolding Energy - mRNA 2.64754 kcal/mol@LB@Unfolding Energy - sRNA 3.77328 kcal/mol@LB@@LB@Position - mRNA 149 -- 192@LB@Position - sRNA 51 -- 90@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 128 -- 134@LB@
61	0.002902	0.1596	stm3567	livJ	-18.03	0.037474	150 -- 196	40 -- 87	high-affinity branched-chain amino acid transporter	_____________149_______________________197\n_____________\|_________________________\|\n5'-CGG...ACAAU_____C____________A______AGAAU...CCG-3'\n______________AACAC_ACAACACA_CGU_ACAACC\n______________\|\|\|\|\|_\|\|\|\|\|\|\|\|_\|:\|_\|\|\|\|\|\|\n______________UUGUG_UGUUGUGU_GUA_UGUUGG\n3'-UUU...AACGU_____U________U___G______CAUUC...UCA-5'\n_____________\|_________________________\|\n_____________88________________________39\n	157 -- 163	74 -- 80	-27.1738 kcal/mol	3.63117 kcal/mol	8.28637 kcal/mol	149 197@LB@ \| \|@LB@5'-CGG...ACAAU C A AGAAU...CCG-3'@LB@ AACAC ACAACACA CGU ACAACC@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\| \|:\| \|\|\|\|\|\|@LB@ UUGUG UGUUGUGU GUA UGUUGG@LB@3'-UUU...AACGU U U G CAUUC...UCA-5'@LB@ \| \|@LB@ 88 39@LB@@LB@@LB@Energy -18.03 kcal/mol@LB@Hybridization Energy -27.1738 kcal/mol@LB@Unfolding Energy - mRNA 3.63117 kcal/mol@LB@Unfolding Energy - sRNA 8.28637 kcal/mol@LB@@LB@Position - mRNA 150 -- 196@LB@Position - sRNA 40 -- 87@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 74 -- 80@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@
83	0.003855	0.1596	stm1680	ycjI	-14.22	0.156552	151 -- 200	34 -- 86	murein peptide amidase A	_____________150_________201\n_____________\|___________\|\n5'-GAA...CUGAA___________UUCGC...CGG-3'\n______________CAUUAUGGACG\n______________\|\|:\|\|\|\|\|\|\|:\n______________GUGAUACCUGU\n3'-UUU...AAUUA___________CUGUC...UCA-5'\n_____________\|___________\|\n_____________87__________33\n	259 -- 265	159 -- 165	-14.9153 kcal/mol	1.6295 kcal/mol	3.40995 kcal/mol	150 201@LB@ \| \|@LB@5'-GAA...CUGAA UUCGC...CGG-3'@LB@ CAUUAUGGACG@LB@ \|\|:\|\|\|\|\|\|\|:@LB@ GUGAUACCUGU@LB@3'-UUU...AAUUA CUGUC...UCA-5'@LB@ \| \|@LB@ 87 33@LB@@LB@@LB@Energy -14.22 kcal/mol@LB@Hybridization Energy -14.9153 kcal/mol@LB@Unfolding Energy - mRNA 1.6295 kcal/mol@LB@Unfolding Energy - sRNA 3.40995 kcal/mol@LB@@LB@Position - mRNA 151 -- 200@LB@Position - sRNA 34 -- 86@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 159 -- 165@LB@
18	0.0003131	0.06194	stm0112	leuB	-16.29	0.072835	153 -- 217	44 -- 93	3-isopropylmalate dehydrogenase	_____________152___________218\n_____________\|_____________\|\n5'-AAA...AAAGA_____________AGCUC...GUU-3'\n______________AUUGC_AACGCAA\n______________\|\|\|\|\|_\|\|\|:\|\|\|\n______________UAACG_UUGUGUU\n3'-UUU...CUGGU_____U_______GUUGU...UCA-5'\n_____________\|_____________\|\n_____________94____________43\n	158 -- 164	81 -- 87	-11.6192 kcal/mol	1.90811 kcal/mol	3.57619 kcal/mol	152 218@LB@ \| \|@LB@5'-AAA...AAAGA AGCUC...GUU-3'@LB@ AUUGC AACGCAA@LB@ \|\|\|\|\| \|\|\|:\|\|\|@LB@ UAACG UUGUGUU@LB@3'-UUU...CUGGU U GUUGU...UCA-5'@LB@ \| \|@LB@ 94 43@LB@@LB@@LB@Energy -16.29 kcal/mol@LB@Hybridization Energy -11.6192 kcal/mol@LB@Unfolding Energy - mRNA 1.90811 kcal/mol@LB@Unfolding Energy - sRNA 3.57619 kcal/mol@LB@@LB@Position - mRNA 153 -- 217@LB@Position - sRNA 44 -- 93@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 81 -- 87@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@
115	0.005604	0.1728	stm0982	himD	-16.93	0.057154	154 -- 192	37 -- 75	integration host factor subunit beta	______________154________193\n______________\|__________\|\n___________5'-___________GGCUG...UGG-3'\n______________AACAACGCAAU\n______________\|\|\|\|\|\|:\|\|\|:\n______________UUGUUGUGUUG\n3'-UUU...UUGUG___________UAGUG...UCA-5'\n_____________\|___________\|\n_____________76__________36\n	5 -- 11	72 -- 78	-12.1177 kcal/mol	1.51678 kcal/mol	3.07616 kcal/mol	154 193@LB@ \| \|@LB@ 5'- GGCUG...UGG-3'@LB@ AACAACGCAAU@LB@ \|\|\|\|\|\|:\|\|\|:@LB@ UUGUUGUGUUG@LB@3'-UUU...UUGUG UAGUG...UCA-5'@LB@ \| \|@LB@ 76 36@LB@@LB@@LB@Energy -16.93 kcal/mol@LB@Hybridization Energy -12.1177 kcal/mol@LB@Unfolding Energy - mRNA 1.51678 kcal/mol@LB@Unfolding Energy - sRNA 3.07616 kcal/mol@LB@@LB@Position - mRNA 154 -- 192@LB@Position - sRNA 37 -- 75@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 72 -- 78@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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