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	Additional homologs
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@
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@
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@
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@
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@
189	0.01049	0.1967	stm0871	ybjM	-13.57	0.197684	34 -- 53	71 -- 89	similar to E. coli orf hypothetical protein (AAC73935.1); Blastp hit to AAC73935.1 (125 aa) 72% identity in aa 1 - 125		_____________33___________________54\n_____________\|____________________\|\n5'-AAU...GCAUC______AA____________AUAUA...GCG-3'\n______________CAAAUA__AACAACACAACA\n______________\|\|\|\|:\|__\|\|\|\|\|\|\|\|\|\|\|\|\n______________GUUUGU__UUGUUGUGUUGU\n3'-UUU...UUAAC______G_____________AGUGU...UCA-5'\n_____________\|____________________\|\n_____________90___________________70\n	47 -- 53	71 -- 77	-19.7565 kcal/mol	2.01075 kcal/mol	3.79866 kcal/mol	33 54@LB@ \| \|@LB@5'-AAU...GCAUC AA AUAUA...GCG-3'@LB@ CAAAUA AACAACACAACA@LB@ \|\|\|\|:\| \|\|\|\|\|\|\|\|\|\|\|\|@LB@ GUUUGU UUGUUGUGUUGU@LB@3'-UUU...UUAAC G AGUGU...UCA-5'@LB@ \| \|@LB@ 90 70@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -19.7565 kcal/mol@LB@Unfolding Energy - mRNA 2.01075 kcal/mol@LB@Unfolding Energy - sRNA 3.79866 kcal/mol@LB@@LB@Position - mRNA 34 -- 53@LB@Position - sRNA 71 -- 89@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 71 -- 77@LB@
75	0.003517	0.1596	stm1214	ycfR	-14.36	0.148951	168 -- 212	35 -- 81	multiple stress resistance protein BhsA	stm0823	_____________167______________213\n_____________\|________________\|\n5'-AAA...ACCAC_________CA_____AUUCA...AAC-3'\n______________UUCUGGCUC___GAGU\n______________\|\|\|:\|\|\|\|\|___:\|\|\|\n______________AAGGCCGAG___UUCA\n3'-UUU...AAAGC_________UCC____-5'\n_____________\|_______________\|\n_____________82______________35\n	15 -- 21	8 -- 14	-15.9373 kcal/mol	4.12962 kcal/mol	4.82557 kcal/mol	167 213@LB@ \| \|@LB@5'-AAA...ACCAC CA AUUCA...AAC-3'@LB@ UUCUGGCUC GAGU@LB@ \|\|\|:\|\|\|\|\| :\|\|\|@LB@ AAGGCCGAG UUCA@LB@3'-UUU...AAAGC UCC -5'@LB@ \| \|@LB@ 82 35@LB@@LB@@LB@Energy -14.36 kcal/mol@LB@Hybridization Energy -15.9373 kcal/mol@LB@Unfolding Energy - mRNA 4.12962 kcal/mol@LB@Unfolding Energy - sRNA 4.82557 kcal/mol@LB@@LB@Position - mRNA 168 -- 212@LB@Position - sRNA 35 -- 81@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 8 -- 14@LB@
156	0.008228	0.1845	stm1715	yciN	-28.69	0.000575	104 -- 163	36 -- 90	similar to E. coli orf hypothetical protein (AAC74355.1); Blastp hit to AAC74355.1 (83 aa) 92% identity in aa 1 - 83		_____________103___________________________________________________________164\n_____________\|_____________________________________________________________\|\n5'-UCG...UGCCA____________UG____AUC_____AUUUC_______AAUAUUU___________G____UCAGC...CCA-3'\n______________GUGAACGCAACA__ACAA___CAUCA_____CUGUGAG_______GCCCAUCAGAA__UGC\n______________\|::\|\|\|:\|\|\|\|\|__\|\|\|\|___\|\|\|\|\|_____\|:\|\|:\|\|_______\|\|\|\|\|\|\|\|\|\|\|__:\|\|\n______________CGUUUGUGUUGU__UGUU___GUAGU_____GGCAUUC_______CGGGUAGUCUU__GCG\n3'-UUU...GUUAA____________UG____________GUU_________GGUUUU____________GU___UAAGG...UCA-5'\n_____________\|_____________________________________________________________\|\n_____________91____________________________________________________________35\n	152 -- 158	42 -- 48	-53.6458 kcal/mol	9.96696 kcal/mol	22.5 kcal/mol	103 164@LB@ \| \|@LB@5'-UCG...UGCCA UG AUC AUUUC AAUAUUU G UCAGC...CCA-3'@LB@ GUGAACGCAACA ACAA CAUCA CUGUGAG GCCCAUCAGAA UGC@LB@ \|::\|\|\|:\|\|\|\|\| \|\|\|\| \|\|\|\|\| \|:\|\|:\|\| \|\|\|\|\|\|\|\|\|\|\| :\|\|@LB@ CGUUUGUGUUGU UGUU GUAGU GGCAUUC CGGGUAGUCUU GCG@LB@3'-UUU...GUUAA UG GUU GGUUUU GU UAAGG...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -28.69 kcal/mol@LB@Hybridization Energy -53.6458 kcal/mol@LB@Unfolding Energy - mRNA 9.96696 kcal/mol@LB@Unfolding Energy - sRNA 22.5 kcal/mol@LB@@LB@Position - mRNA 104 -- 163@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 42 -- 48@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@
146	0.007509	0.1831	stm1510	ydfH	-14.80	0.126744	211 -- 261	32 -- 88	GntR family transcriptional regulator		_____________210_____________________________________________________262\n_____________\|_______________________________________________________\|\n5'-UGA...AAAAA__AA____GAAU_____UCG___________UUAACCCU_______CUGU_____AGCAA...GCA-3'\n______________GU__GAAU____GACCG_____AAACGCAGC________ACACAGC____CAACC\n______________\|\|__\|\|\|\|____\|\|\|\|:_____\|\|\|\|:\|\|:\|________\|\|\|\|\|:\|____\|\|\|\|\|\n______________CA__CUUA____CUGGU_____UUUGUGUUG________UGUGUUG____GUUGG\n3'-UUU...GGCAC__GA____GCGU_____UAACG_________U______________UAGU_____CAUUC...UCA-5'\n_____________\|_______________________________________________________\|\n_____________89______________________________________________________31\n	228 -- 234	72 -- 78	-34.0267 kcal/mol	5.39256 kcal/mol	17.9909 kcal/mol	210 262@LB@ \| \|@LB@5'-UGA...AAAAA AA GAAU UCG UUAACCCU CUGU AGCAA...GCA-3'@LB@ GU GAAU GACCG AAACGCAGC ACACAGC CAACC@LB@ \|\| \|\|\|\| \|\|\|\|: \|\|\|\|:\|\|:\| \|\|\|\|\|:\| \|\|\|\|\|@LB@ CA CUUA CUGGU UUUGUGUUG UGUGUUG GUUGG@LB@3'-UUU...GGCAC GA GCGU UAACG U UAGU CAUUC...UCA-5'@LB@ \| \|@LB@ 89 31@LB@@LB@@LB@Energy -14.80 kcal/mol@LB@Hybridization Energy -34.0267 kcal/mol@LB@Unfolding Energy - mRNA 5.39256 kcal/mol@LB@Unfolding Energy - sRNA 17.9909 kcal/mol@LB@@LB@Position - mRNA 211 -- 261@LB@Position - sRNA 32 -- 88@LB@Position Seed - mRNA 228 -- 234@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)

Job resubmission

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

usability assessment

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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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