Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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_000913 Escherichia coli str. K-12 substr. MG1655

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
163	0.02026	0.4072	b1283	osmB	-10.88	0.136535	231 -- 259	38 -- 61	osmotically and stress inducible lipoprotein	_____________230___________________________260\n_____________\|_____________________________\|\n5'-UAA...CCGCG____UUCU______UACUUU_________UCUGA...ACA-3'\n______________GCUG____GGCAAU______GGCAAUGUC\n______________:\|\|\|____:\|\|\|\|\|______:\|\|\|\|\|\|\|\|\n______________UGAC____UCGUUA______UCGUUACAG\n3'-UUU...CAUUA____CU________CAC____________CACGA...GCG-5'\n_____________\|_____________________________\|\n_____________62____________________________37\n	253 -- 259	38 -- 44	-21.4164 kcal/mol	7.23917 kcal/mol	3.30134 kcal/mol	230 260@LB@ \| \|@LB@5'-UAA...CCGCG UUCU UACUUU UCUGA...ACA-3'@LB@ GCUG GGCAAU GGCAAUGUC@LB@ :\|\|\| :\|\|\|\|\| :\|\|\|\|\|\|\|\|@LB@ UGAC UCGUUA UCGUUACAG@LB@3'-UUU...CAUUA CU CAC CACGA...GCG-5'@LB@ \| \|@LB@ 62 37@LB@@LB@@LB@Energy -10.88 kcal/mol@LB@Hybridization Energy -21.4164 kcal/mol@LB@Unfolding Energy - mRNA 7.23917 kcal/mol@LB@Unfolding Energy - sRNA 3.30134 kcal/mol@LB@@LB@Position - mRNA 231 -- 259@LB@Position - sRNA 38 -- 61@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 38 -- 44@LB@
184	0.02284	0.4113	b2512	bamB	-14.63	0.032048	112 -- 136	38 -- 58	BamABCDE complex OM biogenesis lipoprotein	_____________111_______________________137\n_____________\|_________________________\|\n5'-GCU...GCAUG________GC____AAA________ACUCC...CCC-3'\n______________GGAAGCAG__GUGA___GCGAUGUU\n______________\|\|\|\|\|\|\|:__\|\|\|\|___\|\|:\|\|\|\|:\n______________CCUUCGUU__CACU___CGUUACAG\n3'-UUU...UAUGA________A________________CACGA...GCG-5'\n_____________\|_________________________\|\n_____________59________________________37\n	130 -- 136	38 -- 44	-25.7462 kcal/mol	7.89766 kcal/mol	3.21639 kcal/mol	111 137@LB@ \| \|@LB@5'-GCU...GCAUG GC AAA ACUCC...CCC-3'@LB@ GGAAGCAG GUGA GCGAUGUU@LB@ \|\|\|\|\|\|\|: \|\|\|\| \|\|:\|\|\|\|:@LB@ CCUUCGUU CACU CGUUACAG@LB@3'-UUU...UAUGA A CACGA...GCG-5'@LB@ \| \|@LB@ 59 37@LB@@LB@@LB@Energy -14.63 kcal/mol@LB@Hybridization Energy -25.7462 kcal/mol@LB@Unfolding Energy - mRNA 7.89766 kcal/mol@LB@Unfolding Energy - sRNA 3.21639 kcal/mol@LB@@LB@Position - mRNA 112 -- 136@LB@Position - sRNA 38 -- 58@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 38 -- 44@LB@
6	0.0003052	0.1521	b4255	rraB	-18.72	0.006315	136 -- 158	39 -- 61	protein inhibitor of RNase E	_____________135_____________________159\n_____________\|_______________________\|\n5'-GAG...ACAAA_G____________C________GUGAC...CCA-3'\n______________G_UGGAGGCAAUGU_AGUGGUGU\n______________:_\|\|\|\|:\|\|\|\|\|\|\|_\|\|:::\|\|\|\n______________U_ACCUUCGUUACA_UCGUUACA\n3'-UUU...CAUUA_G____________C________GCACG...GCG-5'\n_____________\|_______________________\|\n_____________62______________________38\n	152 -- 158	39 -- 45	-27.5113 kcal/mol	5.49395 kcal/mol	3.30099 kcal/mol	135 159@LB@ \| \|@LB@5'-GAG...ACAAA G C GUGAC...CCA-3'@LB@ G UGGAGGCAAUGU AGUGGUGU@LB@ : \|\|\|\|:\|\|\|\|\|\|\| \|\|:::\|\|\|@LB@ U ACCUUCGUUACA UCGUUACA@LB@3'-UUU...CAUUA G C GCACG...GCG-5'@LB@ \| \|@LB@ 62 38@LB@@LB@@LB@Energy -18.72 kcal/mol@LB@Hybridization Energy -27.5113 kcal/mol@LB@Unfolding Energy - mRNA 5.49395 kcal/mol@LB@Unfolding Energy - sRNA 3.30099 kcal/mol@LB@@LB@Position - mRNA 136 -- 158@LB@Position - sRNA 39 -- 61@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 39 -- 45@LB@
55	0.005153	0.2905	b2727	hypB	-14.04	0.040392	194 -- 204	39 -- 49	GTP hydrolase involved in nickel liganding into hydrogenases	_____________193_________205\n_____________\|___________\|\n5'-GCC...CAGGA___________GUACA...CGG-3'\n______________GUGAGCGAUGU\n______________\|\|\|\|\|\|:\|\|\|\|\n______________CACUCGUUACA\n3'-UUU...CGUUA___________GCACG...GCG-5'\n_____________\|___________\|\n_____________50__________38\n	198 -- 204	39 -- 45	-18.0568 kcal/mol	2.85856 kcal/mol	1.15413 kcal/mol	193 205@LB@ \| \|@LB@5'-GCC...CAGGA GUACA...CGG-3'@LB@ GUGAGCGAUGU@LB@ \|\|\|\|\|\|:\|\|\|\|@LB@ CACUCGUUACA@LB@3'-UUU...CGUUA GCACG...GCG-5'@LB@ \| \|@LB@ 50 38@LB@@LB@@LB@Energy -14.04 kcal/mol@LB@Hybridization Energy -18.0568 kcal/mol@LB@Unfolding Energy - mRNA 2.85856 kcal/mol@LB@Unfolding Energy - sRNA 1.15413 kcal/mol@LB@@LB@Position - mRNA 194 -- 204@LB@Position - sRNA 39 -- 49@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 39 -- 45@LB@
140	0.01604	0.3851	b4022	rluF	-13.68	0.046602	82 -- 103	39 -- 60	23S rRNA pseudouridine(2604) synthase	_____________81______________________104\n_____________\|_______________________\|\n5'-UUA...UGCUU____A_______U__________AACGA...UGU-3'\n______________CUGG_AAGUGAU_UGAGCAG_GU\n______________\|\|\|\|_\|\|\|::\|\|_\|\|\|\|\|\|:_\|\|\n______________GACC_UUCGUUA_ACUCGUU_CA\n3'-UUU...AUUAU____________C_______A__GCACG...GCG-5'\n_____________\|_______________________\|\n_____________61______________________38\n	95 -- 101	42 -- 48	-22.0004 kcal/mol	5.021 kcal/mol	3.3001 kcal/mol	81 104@LB@ \| \|@LB@5'-UUA...UGCUU A U AACGA...UGU-3'@LB@ CUGG AAGUGAU UGAGCAG GU@LB@ \|\|\|\| \|\|\|::\|\| \|\|\|\|\|\|: \|\|@LB@ GACC UUCGUUA ACUCGUU CA@LB@3'-UUU...AUUAU C A GCACG...GCG-5'@LB@ \| \|@LB@ 61 38@LB@@LB@@LB@Energy -13.68 kcal/mol@LB@Hybridization Energy -22.0004 kcal/mol@LB@Unfolding Energy - mRNA 5.021 kcal/mol@LB@Unfolding Energy - sRNA 3.3001 kcal/mol@LB@@LB@Position - mRNA 82 -- 103@LB@Position - sRNA 39 -- 60@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 42 -- 48@LB@
179	0.02212	0.4113	b3317	rplB	-11.24	0.118994	191 -- 218	39 -- 68	50S ribosomal subunit protein L2	_____________190____________________________219\n_____________\|______________________________\|\n5'-GCA...CGGAG_________AAU__________UUA_____AAACC...UGC-3'\n______________GAGUAAUAC____GGCAGU_UG___AAUGU\n______________:\|\|\|\|\|\|\|\|____:\|\|\|:\|_\|\|___\|\|\|\|\|\n______________UUCAUUAUG____UCGUUA_AC___UUACA\n3'-UUU...ACCGA_________ACCU______C__UCG_____GCACG...GCG-5'\n_____________\|______________________________\|\n_____________69_____________________________38\n	193 -- 199	60 -- 66	-19.7264 kcal/mol	5.17772 kcal/mol	3.30515 kcal/mol	190 219@LB@ \| \|@LB@5'-GCA...CGGAG AAU UUA AAACC...UGC-3'@LB@ GAGUAAUAC GGCAGU UG AAUGU@LB@ :\|\|\|\|\|\|\|\| :\|\|\|:\| \|\| \|\|\|\|\|@LB@ UUCAUUAUG UCGUUA AC UUACA@LB@3'-UUU...ACCGA ACCU C UCG GCACG...GCG-5'@LB@ \| \|@LB@ 69 38@LB@@LB@@LB@Energy -11.24 kcal/mol@LB@Hybridization Energy -19.7264 kcal/mol@LB@Unfolding Energy - mRNA 5.17772 kcal/mol@LB@Unfolding Energy - sRNA 3.30515 kcal/mol@LB@@LB@Position - mRNA 191 -- 218@LB@Position - sRNA 39 -- 68@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 60 -- 66@LB@
27	0.002163	0.2692	b2563	acpS	-16.12	0.017802	179 -- 203	40 -- 65	holo-[acyl-carrier-protein] synthase 1	_____________178_________________________204\n_____________\|___________________________\|\n5'-GCC...GCGUC______________C_______U____GCAAU...GCG-3'\n______________UGAUGCUGGAAGCG__GUG_GC_AAUG\n______________\|:\|\|:\|\|\|\|\|\|\|\|:__\|\|\|_\|\|_\|\|\|\|\n______________AUUAUGACCUUCGU__CAC_CG_UUAC\n3'-UUU...GAUUC______________UA___U_______AGCAC...GCG-5'\n_____________\|___________________________\|\n_____________66__________________________39\n	186 -- 192	52 -- 58	-28.0575 kcal/mol	8.63593 kcal/mol	3.30476 kcal/mol	178 204@LB@ \| \|@LB@5'-GCC...GCGUC C U GCAAU...GCG-3'@LB@ UGAUGCUGGAAGCG GUG GC AAUG@LB@ \|:\|\|:\|\|\|\|\|\|\|\|: \|\|\| \|\| \|\|\|\|@LB@ AUUAUGACCUUCGU CAC CG UUAC@LB@3'-UUU...GAUUC UA U AGCAC...GCG-5'@LB@ \| \|@LB@ 66 39@LB@@LB@@LB@Energy -16.12 kcal/mol@LB@Hybridization Energy -28.0575 kcal/mol@LB@Unfolding Energy - mRNA 8.63593 kcal/mol@LB@Unfolding Energy - sRNA 3.30476 kcal/mol@LB@@LB@Position - mRNA 179 -- 203@LB@Position - sRNA 40 -- 65@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 52 -- 58@LB@
32	0.002983	0.2776	b3032	cpdA	-14.85	0.029357	133 -- 158	40 -- 64	3' 5' cAMP phosphodiesterase	_____________132_________________________159\n_____________\|___________________________\|\n5'-ACG...GUUGC_______UUU____C____________GCGAU...UGU-3'\n______________GAUACUG___AGCA_AUG_GAGCGAUG\n______________:\|\|\|\|\|\|___\|\|\|\|_\|\|\|_\|\|\|\|:\|\|\|\n______________UUAUGAC___UCGU_UAC_CUCGUUAC\n3'-UUU...AUUCA_______CU_________A________AGCAC...GCG-5'\n_____________\|___________________________\|\n_____________65__________________________39\n	152 -- 158	40 -- 46	-24.327 kcal/mol	6.1707 kcal/mol	3.30198 kcal/mol	132 159@LB@ \| \|@LB@5'-ACG...GUUGC UUU C GCGAU...UGU-3'@LB@ GAUACUG AGCA AUG GAGCGAUG@LB@ :\|\|\|\|\|\| \|\|\|\| \|\|\| \|\|\|\|:\|\|\|@LB@ UUAUGAC UCGU UAC CUCGUUAC@LB@3'-UUU...AUUCA CU A AGCAC...GCG-5'@LB@ \| \|@LB@ 65 39@LB@@LB@@LB@Energy -14.85 kcal/mol@LB@Hybridization Energy -24.327 kcal/mol@LB@Unfolding Energy - mRNA 6.1707 kcal/mol@LB@Unfolding Energy - sRNA 3.30198 kcal/mol@LB@@LB@Position - mRNA 133 -- 158@LB@Position - sRNA 40 -- 64@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 40 -- 46@LB@
37	0.003144	0.2776	b3743	asnC	-18.99	0.005660	240 -- 261	40 -- 60	transcriptional activator of asnA; autorepressor	_____________239____________________262\n_____________\|______________________\|\n5'-AUU...GCAUC_________UUAA_________CGCGC...GCG-3'\n______________CUGGAAGCA____UGGGCAAUG\n______________\|\|\|\|\|\|\|\|\|____\|\|:\|\|\|\|\|\|\n______________GACCUUCGU____ACUCGUUAC\n3'-UUU...AUUAU_________UAC__________AGCAC...GCG-5'\n_____________\|______________________\|\n_____________61_____________________39\n	255 -- 261	40 -- 46	-27.3577 kcal/mol	5.06736 kcal/mol	3.29985 kcal/mol	239 262@LB@ \| \|@LB@5'-AUU...GCAUC UUAA CGCGC...GCG-3'@LB@ CUGGAAGCA UGGGCAAUG@LB@ \|\|\|\|\|\|\|\|\| \|\|:\|\|\|\|\|\|@LB@ GACCUUCGU ACUCGUUAC@LB@3'-UUU...AUUAU UAC AGCAC...GCG-5'@LB@ \| \|@LB@ 61 39@LB@@LB@@LB@Energy -18.99 kcal/mol@LB@Hybridization Energy -27.3577 kcal/mol@LB@Unfolding Energy - mRNA 5.06736 kcal/mol@LB@Unfolding Energy - sRNA 3.29985 kcal/mol@LB@@LB@Position - mRNA 240 -- 261@LB@Position - sRNA 40 -- 60@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 40 -- 46@LB@
38	0.003171	0.2776	b0033	carB	-16.38	0.016045	157 -- 203	40 -- 88	carbamoyl-phosphate synthase large subunit	_____________156_________________________________________________204\n_____________\|___________________________________________________\|\n5'-GCA...UAAUU___________GUAAAACC____________A________AA_____C___CCAAA...CGU-3'\n______________GAG_CAGUACC________GCUAAGUAAU_C_GG_AGUAA___GAGC_AUG\n______________:\|\|_\|\|\|:\|\|\|________\|\|\|\|\|\|\|\|\|\|_\|_\|\|_\|\|:\|\|___\|\|\|\|_\|\|\|\n______________UUC_GUCGUGG________CGAUUCAUUA_G_CC_UCGUU___CUCG_UAC\n_________3'-UU___G_______GCCGAC____________U_A__U_____ACA____U___AGCAC...GCG-5'\n_____________\|___________________________________________________\|\n_____________89__________________________________________________39\n	178 -- 184	62 -- 68	-37.8454 kcal/mol	6.5567 kcal/mol	14.9104 kcal/mol	156 204@LB@ \| \|@LB@5'-GCA...UAAUU GUAAAACC A AA C CCAAA...CGU-3'@LB@ GAG CAGUACC GCUAAGUAAU C GG AGUAA GAGC AUG@LB@ :\|\| \|\|\|:\|\|\| \|\|\|\|\|\|\|\|\|\| \| \|\| \|\|:\|\| \|\|\|\| \|\|\|@LB@ UUC GUCGUGG CGAUUCAUUA G CC UCGUU CUCG UAC@LB@ 3'-UU G GCCGAC U A U ACA U AGCAC...GCG-5'@LB@ \| \|@LB@ 89 39@LB@@LB@@LB@Energy -16.38 kcal/mol@LB@Hybridization Energy -37.8454 kcal/mol@LB@Unfolding Energy - mRNA 6.5567 kcal/mol@LB@Unfolding Energy - sRNA 14.9104 kcal/mol@LB@@LB@Position - mRNA 157 -- 203@LB@Position - sRNA 40 -- 88@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 62 -- 68@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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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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