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
157	0.008234	0.1845	stm0693	fur	-16.04	0.080078	199 -- 253	31 -- 90	ferric iron uptake transcriptional regulator	_____________198________________________254\n_____________\|__________________________\|\n5'-GCA...AUUCC___U___UG__________C______AAGAA...ACG-3'\n______________GCA_GAC__ACAACAAUAC_GCAUUA\n______________\|\|\|_:\|\|__\|\|\|\|\|\|\|:\|\|_:\|\|\|:\|\n______________CGU_UUG__UGUUGUUGUG_UGUAGU\n3'-UUU...GUUAA___________________U______GUUGG...UCA-5'\n_____________\|__________________________\|\n_____________91_________________________30\n	211 -- 217	75 -- 81	-20.9388 kcal/mol	2.89423 kcal/mol	5.29697 kcal/mol	198 254@LB@ \| \|@LB@5'-GCA...AUUCC U UG C AAGAA...ACG-3'@LB@ GCA GAC ACAACAAUAC GCAUUA@LB@ \|\|\| :\|\| \|\|\|\|\|\|\|:\|\| :\|\|\|:\|@LB@ CGU UUG UGUUGUUGUG UGUAGU@LB@3'-UUU...GUUAA U GUUGG...UCA-5'@LB@ \| \|@LB@ 91 30@LB@@LB@@LB@Energy -16.04 kcal/mol@LB@Hybridization Energy -20.9388 kcal/mol@LB@Unfolding Energy - mRNA 2.89423 kcal/mol@LB@Unfolding Energy - sRNA 5.29697 kcal/mol@LB@@LB@Position - mRNA 199 -- 253@LB@Position - sRNA 31 -- 90@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 75 -- 81@LB@
82	0.003783	0.1596	stm0710	ybgH	-19.90	0.018103	103 -- 151	33 -- 90	MFS transporter	_____________102__________________152\n_____________\|____________________\|\n5'-GCG...UUUAA_G__________________GGCUU...UUC-3'\n______________G_AAACACGGCGAUACGGCA\n______________\|_\|\|\|\|\|\|::\|:\|:\|\|::\|\|\n______________C_UUUGUGUUGUUGUGUUGU\n3'-UUU...GUUAA_G__________________AGUGU...UCA-5'\n_____________\|____________________\|\n_____________91___________________32\n	116 -- 122	71 -- 77	-24.8461 kcal/mol	5.94354 kcal/mol	3.80671 kcal/mol	102 152@LB@ \| \|@LB@5'-GCG...UUUAA G GGCUU...UUC-3'@LB@ G AAACACGGCGAUACGGCA@LB@ \| \|\|\|\|\|\|::\|:\|:\|\|::\|\|@LB@ C UUUGUGUUGUUGUGUUGU@LB@3'-UUU...GUUAA G AGUGU...UCA-5'@LB@ \| \|@LB@ 91 32@LB@@LB@@LB@Energy -19.90 kcal/mol@LB@Hybridization Energy -24.8461 kcal/mol@LB@Unfolding Energy - mRNA 5.94354 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 103 -- 151@LB@Position - sRNA 33 -- 90@LB@Position Seed - mRNA 116 -- 122@LB@Position Seed - sRNA 71 -- 77@LB@
104	0.005232	0.1728	stm0744	ybgC	-16.85	0.058772	132 -- 175	54 -- 90	tol-pal system-associated acyl-CoA thioesterase	_____________131_____________________________176\n_____________\|_______________________________\|\n5'-CUU...ACAAG____U____________UCUUGA________GGCGG...AAA-3'\n______________GCGA_AUACAACGGCAU______GGCAUUAC\n______________\|\|:\|_\|:\|\|\|\|\|::\|\|:______::\|\|\|:\|\|\n______________CGUU_UGUGUUGUUGUG______UUGUAGUG\n3'-UUU...GUUAA_______________________________UUGGC...UCA-5'\n_____________\|_______________________________\|\n_____________91______________________________53\n	156 -- 162	67 -- 73	-23.8418 kcal/mol	6.2547 kcal/mol	5.68203 kcal/mol	131 176@LB@ \| \|@LB@5'-CUU...ACAAG U UCUUGA GGCGG...AAA-3'@LB@ GCGA AUACAACGGCAU GGCAUUAC@LB@ \|\|:\| \|:\|\|\|\|\|::\|\|: ::\|\|\|:\|\|@LB@ CGUU UGUGUUGUUGUG UUGUAGUG@LB@3'-UUU...GUUAA UUGGC...UCA-5'@LB@ \| \|@LB@ 91 53@LB@@LB@@LB@Energy -16.85 kcal/mol@LB@Hybridization Energy -23.8418 kcal/mol@LB@Unfolding Energy - mRNA 6.2547 kcal/mol@LB@Unfolding Energy - sRNA 5.68203 kcal/mol@LB@@LB@Position - mRNA 132 -- 175@LB@Position - sRNA 54 -- 90@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 67 -- 73@LB@
60	0.002585	0.1534	stm0758	ybgR	-11.90	0.345594	235 -- 293	32 -- 91	cation transporter	_____________234_________________________294\n_____________\|___________________________\|\n5'-GGU...ACACC___CG___G__________U_______CUGCU...UCC-3'\n______________UGC__AAA_AUAAUAAUGC__CGUCGC\n______________\|\|\|__\|\|\|_\|:\|\|:\|\|::\|__\|:\|\|:\|\n______________ACG__UUU_UGUUGUUGUG__GUAGUG\n3'-UUU...GGUUA________G__________UU______UUGGC...UCA-5'\n_____________\|___________________________\|\n_____________92__________________________31\n	247 -- 253	75 -- 81	-19.147 kcal/mol	4.2306 kcal/mol	5.6854 kcal/mol	234 294@LB@ \| \|@LB@5'-GGU...ACACC CG G U CUGCU...UCC-3'@LB@ UGC AAA AUAAUAAUGC CGUCGC@LB@ \|\|\| \|\|\| \|:\|\|:\|\|::\| \|:\|\|:\|@LB@ ACG UUU UGUUGUUGUG GUAGUG@LB@3'-UUU...GGUUA G UU UUGGC...UCA-5'@LB@ \| \|@LB@ 92 31@LB@@LB@@LB@Energy -11.90 kcal/mol@LB@Hybridization Energy -19.147 kcal/mol@LB@Unfolding Energy - mRNA 4.2306 kcal/mol@LB@Unfolding Energy - sRNA 5.6854 kcal/mol@LB@@LB@Position - mRNA 235 -- 293@LB@Position - sRNA 32 -- 91@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 75 -- 81@LB@
124	0.006123	0.1758	stm0794	bioB	-18.46	0.031660	1 -- 37	38 -- 79	biotin synthase	______________1________________38\n______________\|________________\|\n___________5'-_________________UUCGG...AGC-3'\n______________AAC_CAGC_UCGCAGCC\n______________\|\|\|_\|\|:\|_\|\|:\|\|:\|\|\n______________UUG_GUUG_AGUGUUGG\n3'-UUU...UGUUG___U____U________CAUUC...UCA-5'\n_____________\|_________________\|\n_____________80________________37\n	9 -- 15	63 -- 69	-17.7754 kcal/mol	2.27351 kcal/mol	6.48115 kcal/mol	1 38@LB@ \| \|@LB@ 5'- UUCGG...AGC-3'@LB@ AAC CAGC UCGCAGCC@LB@ \|\|\| \|\|:\| \|\|:\|\|:\|\|@LB@ UUG GUUG AGUGUUGG@LB@3'-UUU...UGUUG U U CAUUC...UCA-5'@LB@ \| \|@LB@ 80 37@LB@@LB@@LB@Energy -18.46 kcal/mol@LB@Hybridization Energy -17.7754 kcal/mol@LB@Unfolding Energy - mRNA 2.27351 kcal/mol@LB@Unfolding Energy - sRNA 6.48115 kcal/mol@LB@@LB@Position - mRNA 1 -- 37@LB@Position - sRNA 38 -- 79@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 63 -- 69@LB@
183	0.01015	0.1966	stm0813	ybhP	-18.40	0.032407	2 -- 54	36 -- 90	similar to E. coli orf hypothetical protein (AAC73877.1); Blastp hit to AAC73877.1 (253 aa) 86% identity in aa 1 - 253	_____________1____________________________________55\n_____________\|____________________________________\|\n__________5'-A____________UA__CU__CA______________GGUUG...UGC-3'\n______________GUAAAUGCAACA__AU__GC___ACAACCG_AGGCC\n______________\|:\|\|\|::\|\|\|\|\|__\|:__:\|___\|\|\|\|\|\|\|_\|:\|\|\|\n______________CGUUUGUGUUGU__UG__UG___UGUUGGC_UUCGG\n3'-UUU...GUUAA____________UG__U___UAG_______A_____UUUUC...UCA-5'\n_____________\|____________________________________\|\n_____________91___________________________________35\n	24 -- 30	62 -- 68	-32.6929 kcal/mol	6.87264 kcal/mol	11.8287 kcal/mol	1 55@LB@ \| \|@LB@ 5'-A UA CU CA GGUUG...UGC-3'@LB@ GUAAAUGCAACA AU GC ACAACCG AGGCC@LB@ \|:\|\|\|::\|\|\|\|\| \|: :\| \|\|\|\|\|\|\| \|:\|\|\|@LB@ CGUUUGUGUUGU UG UG UGUUGGC UUCGG@LB@3'-UUU...GUUAA UG U UAG A UUUUC...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -18.40 kcal/mol@LB@Hybridization Energy -32.6929 kcal/mol@LB@Unfolding Energy - mRNA 6.87264 kcal/mol@LB@Unfolding Energy - sRNA 11.8287 kcal/mol@LB@@LB@Position - mRNA 2 -- 54@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 62 -- 68@LB@
139	0.007115	0.182	stm0826	ybiN	-18.61	0.029895	232 -- 282	36 -- 90	23S rRNA (adenine(1618)-N(6))-methyltransferase	_____________231___________________283\n_____________\|_____________________\|\n5'-CUC...GAGCC_____AACGAGCG________AAUUC...UUC-3'\n______________GAUCA________AGGCAGGG\n______________:\|\|\|\|________\|\|:\|\|\|\|\|\n______________UUAGU________UCUGUCCC\n3'-UUU...UGUAA_____GAUACCUG________AUUUA...UCA-5'\n_____________\|_____________________\|\n_____________91____________________35\n	124 -- 130	152 -- 158	-17.5433 kcal/mol	4.82059 kcal/mol	3.53427 kcal/mol	231 283@LB@ \| \|@LB@5'-CUC...GAGCC AACGAGCG AAUUC...UUC-3'@LB@ GAUCA AGGCAGGG@LB@ :\|\|\|\| \|\|:\|\|\|\|\|@LB@ UUAGU UCUGUCCC@LB@3'-UUU...UGUAA GAUACCUG AUUUA...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -18.61 kcal/mol@LB@Hybridization Energy -17.5433 kcal/mol@LB@Unfolding Energy - mRNA 4.82059 kcal/mol@LB@Unfolding Energy - sRNA 3.53427 kcal/mol@LB@@LB@Position - mRNA 232 -- 282@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 152 -- 158@LB@
65	0.003171	0.1596	stm0830	glnH	-11.06	0.446113	180 -- 193	153 -- 165	glutamine ABC transporter substrate-binding protein GlnH	_____________179____________194\n_____________\|______________\|\n5'-AGA...GCCCC_________AA___AAAUG...CGG-3'\n______________GUGGAUAGA__AGG\n______________:\|\|\|\|:\|\|\|__\|\|\|\n______________UACCUGUCU__UCC\n3'-UUU...AGUGA_________G____CAUUU...UCA-5'\n_____________\|______________\|\n_____________166____________152\n	182 -- 188	157 -- 163	-15.2236 kcal/mol	3.11192 kcal/mol	2.82582 kcal/mol	179 194@LB@ \| \|@LB@5'-AGA...GCCCC AA AAAUG...CGG-3'@LB@ GUGGAUAGA AGG@LB@ :\|\|\|\|:\|\|\| \|\|\|@LB@ UACCUGUCU UCC@LB@3'-UUU...AGUGA G CAUUU...UCA-5'@LB@ \| \|@LB@ 166 152@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -15.2236 kcal/mol@LB@Unfolding Energy - mRNA 3.11192 kcal/mol@LB@Unfolding Energy - sRNA 2.82582 kcal/mol@LB@@LB@Position - mRNA 180 -- 193@LB@Position - sRNA 153 -- 165@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 157 -- 163@LB@
133	0.006689	0.1774	stm0831	dps	-13.05	0.236755	141 -- 176	159 -- 184	DNA starvation/stationary phase protection protein Dps	_____________140________________________177\n_____________\|__________________________\|\n5'-CAU...UUACC___CA_______AACU__________AAUUG...UUA-3'\n______________CAC__AACAGCA____CGUC_UAACC\n______________\|\|\|__\|\|\|\|:\|\|____\|:\|\|_:\|\|\|\|\n______________GUG__UUGUUGU____GUAG_GUUGG\n3'-UUU...CGUUU____________GUU_____U_____CAUUC...UCA-5'\n_____________\|__________________________\|\n_____________185________________________158\n	37 -- 43	76 -- 82	-18.4678 kcal/mol	1.39739 kcal/mol	8.25195 kcal/mol	140 177@LB@ \| \|@LB@5'-CAU...UUACC CA AACU AAUUG...UUA-3'@LB@ CAC AACAGCA CGUC UAACC@LB@ \|\|\| \|\|\|\|:\|\| \|:\|\| :\|\|\|\|@LB@ GUG UUGUUGU GUAG GUUGG@LB@3'-UUU...CGUUU GUU U CAUUC...UCA-5'@LB@ \| \|@LB@ 185 158@LB@@LB@@LB@Energy -13.05 kcal/mol@LB@Hybridization Energy -18.4678 kcal/mol@LB@Unfolding Energy - mRNA 1.39739 kcal/mol@LB@Unfolding Energy - sRNA 8.25195 kcal/mol@LB@@LB@Position - mRNA 141 -- 176@LB@Position - sRNA 159 -- 184@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 76 -- 82@LB@
97	0.004849	0.1728	stm0832	ybiF	-11.58	0.382043	25 -- 72	45 -- 91	threonine/homoserine exporter RhtA	_____________24______________________73\n_____________\|_______________________\|\n5'-GGC...GCGCG_________________U_____CAGAU...CGU-3'\n______________UGC_GGCGCGAUA_CAU__CAUC\n______________\|\|\|_::\|:\|:\|:\|_\|\|:__\|\|\|\|\n______________ACG_UUGUGUUGU_GUG__GUAG\n3'-UUU...GGUUA___U_________U___UU____UGUUG...UCA-5'\n_____________\|_______________________\|\n_____________92______________________44\n	30 -- 36	79 -- 85	-16.3644 kcal/mol	3.58897 kcal/mol	4.34303 kcal/mol	24 73@LB@ \| \|@LB@5'-GGC...GCGCG U CAGAU...CGU-3'@LB@ UGC GGCGCGAUA CAU CAUC@LB@ \|\|\| ::\|:\|:\|:\| \|\|: \|\|\|\|@LB@ ACG UUGUGUUGU GUG GUAG@LB@3'-UUU...GGUUA U U UU UGUUG...UCA-5'@LB@ \| \|@LB@ 92 44@LB@@LB@@LB@Energy -11.58 kcal/mol@LB@Hybridization Energy -16.3644 kcal/mol@LB@Unfolding Energy - mRNA 3.58897 kcal/mol@LB@Unfolding Energy - sRNA 4.34303 kcal/mol@LB@@LB@Position - mRNA 25 -- 72@LB@Position - sRNA 45 -- 91@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 79 -- 85@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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