Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
22	0.001812	0.2633	b2566	era	-10.12	0.260747	283 -- 292	16 -- 26	membrane-associated 16S rRNA-binding GTPase	_____________282________________293\n_____________\|__________________\|\n5'-UUG...AAUGA_________AA_______UGCGG...UCU-3'\n______________GCAUCGAUA___AGUUAC\n______________:\|\|:\|:\|\|\|___\|\|\|:\|\|\n______________UGUGGUUAU___UCAGUG\n3'-UUU...UAAAA_________GAG______UGUAC...UAG-5'\n_____________\|__________________\|\n_____________27_________________15\n	205 -- 211	181 -- 187	-15.5423 kcal/mol	3.87874 kcal/mol	4.86686 kcal/mol	282 293@LB@ \| \|@LB@5'-UUG...AAUGA AA UGCGG...UCU-3'@LB@ GCAUCGAUA AGUUAC@LB@ :\|\|:\|:\|\|\| \|\|\|:\|\|@LB@ UGUGGUUAU UCAGUG@LB@3'-UUU...UAAAA GAG UGUAC...UAG-5'@LB@ \| \|@LB@ 27 15@LB@@LB@@LB@Energy -10.12 kcal/mol@LB@Hybridization Energy -15.5423 kcal/mol@LB@Unfolding Energy - mRNA 3.87874 kcal/mol@LB@Unfolding Energy - sRNA 4.86686 kcal/mol@LB@@LB@Position - mRNA 283 -- 292@LB@Position - sRNA 16 -- 26@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 181 -- 187@LB@
184	0.02128	0.3833	b2831	mutH	-12.07	0.107608	142 -- 230	114 -- 189	methyl-directed mismatch repair protein	_____________141______________231\n_____________\|________________\|\n5'-UUC...CUGCG________________AUUGC...CGG-3'\n______________AAUAUUCGG_CACAUA\n______________\|\|\|\|:\|\|:\|_\|\|\|\|:\|\n______________UUAUGAGUC_GUGUGU\n3'-UUU...UGUGG_________A______ACUAC...UAG-5'\n_____________\|________________\|\n_____________190______________113\n	154 -- 160	174 -- 180	-15.1193 kcal/mol	2.199 kcal/mol	0.596263 kcal/mol	141 231@LB@ \| \|@LB@5'-UUC...CUGCG AUUGC...CGG-3'@LB@ AAUAUUCGG CACAUA@LB@ \|\|\|\|:\|\|:\| \|\|\|\|:\|@LB@ UUAUGAGUC GUGUGU@LB@3'-UUU...UGUGG A ACUAC...UAG-5'@LB@ \| \|@LB@ 190 113@LB@@LB@@LB@Energy -12.07 kcal/mol@LB@Hybridization Energy -15.1193 kcal/mol@LB@Unfolding Energy - mRNA 2.199 kcal/mol@LB@Unfolding Energy - sRNA 0.596263 kcal/mol@LB@@LB@Position - mRNA 142 -- 230@LB@Position - sRNA 114 -- 189@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 174 -- 180@LB@
83	0.008941	0.3575	b3343	tusB	-13.46	0.055944	1 -- 14	190 -- 203	mnm(5)-s(2)U34-tRNA synthesis 2-thiolation protein	______________1_____________15\n______________\|_____________\|\n___________5'-_______C______ACAUU...GCG-3'\n______________GCUGGCG_GUGAUU\n______________\|\|\|\|\|\|\|_\|\|\|\|\|\|\n______________CGACCGC_CACUAA\n3'-UUU...UUAGA_______C______AAUGU...UAG-5'\n_____________\|______________\|\n_____________204____________189\n	1 -- 7	197 -- 203	-22.3351 kcal/mol	4.22102 kcal/mol	9.06745 kcal/mol	1 15@LB@ \| \|@LB@ 5'- C ACAUU...GCG-3'@LB@ GCUGGCG GUGAUU@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ CGACCGC CACUAA@LB@3'-UUU...UUAGA C AAUGU...UAG-5'@LB@ \| \|@LB@ 204 189@LB@@LB@@LB@Energy -13.46 kcal/mol@LB@Hybridization Energy -22.3351 kcal/mol@LB@Unfolding Energy - mRNA 4.22102 kcal/mol@LB@Unfolding Energy - sRNA 9.06745 kcal/mol@LB@@LB@Position - mRNA 1 -- 14@LB@Position - sRNA 190 -- 203@LB@Position Seed - mRNA 1 -- 7@LB@Position Seed - sRNA 197 -- 203@LB@
117	0.01283	0.3575	b3096	mzrA	-10.41	0.230387	15 -- 55	168 -- 208	modulator of EnvZ/OmpR regulon	_____________14________________________________________________________56\n_____________\|_________________________________________________________\|\n_____5'-UCAACU____G____________________________GAUCCUGA___CU__G________GCUCG...AGC-3'\n______________GGAU_AGCGG______UCUGCU_GUGGGU_AUU________CAA__CU_GGUUACAU\n______________::\|:_\|\|\|:\|______\|\|\|\|\|\|_\|:\|\|\|\|_\|\|\|________\|\|\|__\|\|_:\|\|:\|\|\|:\n______________UUUG_UCGUC______AGACGA_CGCCCA_UAA________GUU__GA_UCAGUGUG\n______3'-UUUUU____G_____CAUAUU______C______C___AAUGUG_____AU__G________UACUA...UAG-5'\n_____________\|_________________________________________________________\|\n_____________209_______________________________________________________167\n	49 -- 55	168 -- 174	-40.4023 kcal/mol	11.8856 kcal/mol	18.3074 kcal/mol	14 56@LB@ \| \|@LB@ 5'-UCAACU G GAUCCUGA CU G GCUCG...AGC-3'@LB@ GGAU AGCGG UCUGCU GUGGGU AUU CAA CU GGUUACAU@LB@ ::\|: \|\|\|:\| \|\|\|\|\|\| \|:\|\|\|\| \|\|\| \|\|\| \|\| :\|\|:\|\|\|:@LB@ UUUG UCGUC AGACGA CGCCCA UAA GUU GA UCAGUGUG@LB@ 3'-UUUUU G CAUAUU C C AAUGUG AU G UACUA...UAG-5'@LB@ \| \|@LB@ 209 167@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -40.4023 kcal/mol@LB@Unfolding Energy - mRNA 11.8856 kcal/mol@LB@Unfolding Energy - sRNA 18.3074 kcal/mol@LB@@LB@Position - mRNA 15 -- 55@LB@Position - sRNA 168 -- 208@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 168 -- 174@LB@
65	0.006332	0.3261	b3857	mobA	-11.59	0.134663	143 -- 181	126 -- 173	molybdopterin-guanine dinucleotide synthase	_____________142________________________________________________________182\n_____________\|__________________________________________________________\|\n5'-UCC...AUAGU_______C_____U_U___GA___A__C______AG______________A_______AAUAA...AAC-3'\n______________GAUGCUC__UUAC_C_UGA__CAG_CA_GUUAGC____________GGUC_AUCCCAC\n______________:\|\|:\|\|\|__\|:\|\|_\|_\|\|\|__\|\|\|_\|\|_\|\|:\|:\|____________\|\|\|\|_\|\|\|\|\|\|\|\n______________UUAUGAG__AGUG_G_ACU__GUC_GU_CAGUUG____________CCAG_UAGGGUG\n3'-UUU...UGUGG_______UC____U_U___AC___C__U______AAAGUCUUAACG____________ACGUA...UAG-5'\n_____________\|__________________________________________________________\|\n_____________174________________________________________________________125\n	175 -- 181	126 -- 132	-38.7055 kcal/mol	10.57 kcal/mol	15.6637 kcal/mol	142 182@LB@ \| \|@LB@5'-UCC...AUAGU C U U GA A C AG A AAUAA...AAC-3'@LB@ GAUGCUC UUAC C UGA CAG CA GUUAGC GGUC AUCCCAC@LB@ :\|\|:\|\|\| \|:\|\| \| \|\|\| \|\|\| \|\| \|\|:\|:\| \|\|\|\| \|\|\|\|\|\|\|@LB@ UUAUGAG AGUG G ACU GUC GU CAGUUG CCAG UAGGGUG@LB@3'-UUU...UGUGG UC U U AC C U AAAGUCUUAACG ACGUA...UAG-5'@LB@ \| \|@LB@ 174 125@LB@@LB@@LB@Energy -11.59 kcal/mol@LB@Hybridization Energy -38.7055 kcal/mol@LB@Unfolding Energy - mRNA 10.57 kcal/mol@LB@Unfolding Energy - sRNA 15.6637 kcal/mol@LB@@LB@Position - mRNA 143 -- 181@LB@Position - sRNA 126 -- 173@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 126 -- 132@LB@
100	0.01091	0.3575	b0123	cueO	-12.06	0.108476	211 -- 256	146 -- 195	multicopper oxidase (laccase)	_____________210________________________________________________257\n_____________\|__________________________________________________\|\n5'-CUG...ACGUC_______CUUAA________C_______UG_________U__________GCCGC...CGU-3'\n______________GUGAUUU______AAUAUUC_GUCGCGC__GGUGU_GGC___UCGGCUUU\n______________\|\|\|\|\|\|\|______\|\|\|\|:\|\|_\|\|\|:\|:\|__\|:\|\|:_\|\|\|___\|\|::\|\|\|\|\n______________CACUAAA______UUAUGAG_CAGUGUG__CUACG_CCG___AGUUGAAA\n3'-UUU...CCGCC_______AUGUGG_______U_______UA_____U___UUC________GUCUU...UAG-5'\n_____________\|__________________________________________________\|\n_____________196________________________________________________145\n	250 -- 256	146 -- 152	-42.9672 kcal/mol	13.2361 kcal/mol	12.9468 kcal/mol	210 257@LB@ \| \|@LB@5'-CUG...ACGUC CUUAA C UG U GCCGC...CGU-3'@LB@ GUGAUUU AAUAUUC GUCGCGC GGUGU GGC UCGGCUUU@LB@ \|\|\|\|\|\|\| \|\|\|\|:\|\| \|\|\|:\|:\| \|:\|\|: \|\|\| \|\|::\|\|\|\|@LB@ CACUAAA UUAUGAG CAGUGUG CUACG CCG AGUUGAAA@LB@3'-UUU...CCGCC AUGUGG U UA U UUC GUCUU...UAG-5'@LB@ \| \|@LB@ 196 145@LB@@LB@@LB@Energy -12.06 kcal/mol@LB@Hybridization Energy -42.9672 kcal/mol@LB@Unfolding Energy - mRNA 13.2361 kcal/mol@LB@Unfolding Energy - sRNA 12.9468 kcal/mol@LB@@LB@Position - mRNA 211 -- 256@LB@Position - sRNA 146 -- 195@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 146 -- 152@LB@
87	0.009479	0.3575	b1192	ldcA	-9.25	0.375459	184 -- 216	125 -- 154	murein tetrapeptide carboxypeptidase; LD-carboxypeptidase A	_____________183_______________217\n_____________\|_________________\|\n5'-UGC...AGCAC__CG_____________UCCAG...UCA-3'\n______________GC__CGCUG_CGUGGUA\n______________:\|__\|\|\|\|\|_\|\|:\|\|\|\|\n______________UG__GCGAC_GCGCCAU\n3'-UUU...CGUGU__AA_____A_______UUUAU...UAG-5'\n_____________\|_________________\|\n_____________155_______________124\n	261 -- 267	48 -- 54	-20.6657 kcal/mol	8.36057 kcal/mol	6.14531 kcal/mol	183 217@LB@ \| \|@LB@5'-UGC...AGCAC CG UCCAG...UCA-3'@LB@ GC CGCUG CGUGGUA@LB@ :\| \|\|\|\|\| \|\|:\|\|\|\|@LB@ UG GCGAC GCGCCAU@LB@3'-UUU...CGUGU AA A UUUAU...UAG-5'@LB@ \| \|@LB@ 155 124@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -20.6657 kcal/mol@LB@Unfolding Energy - mRNA 8.36057 kcal/mol@LB@Unfolding Energy - sRNA 6.14531 kcal/mol@LB@@LB@Position - mRNA 184 -- 216@LB@Position - sRNA 125 -- 154@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 48 -- 54@LB@
77	0.007981	0.3458	b1738	chbB	-9.80	0.299184	58 -- 71	174 -- 187	N N'-diacetylchitobiose-specific enzyme IIB component of PTS	_____________57_______________________________72\n_____________\|________________________________\|\n5'-AAU...UAUAA___CAAAGAA______U_______G__U____CGUAU...CGG-3'\n______________GGU_______AUACUA_UGCUCAG_UC_AUAC\n______________\|\|\|_______\|:\|\|:\|_\|:\|\|\|\|\|_\|\|_\|:\|\|\n______________CCA_______UGUGGU_AUGAGUC_AG_UGUG\n3'-UUU...ACCGC___CUAAAA_______U_______________UACUA...UAG-5'\n_____________\|________________________________\|\n_____________188______________________________173\n	65 -- 71	174 -- 180	-20.4225 kcal/mol	4.13376 kcal/mol	5.03959 kcal/mol	57 72@LB@ \| \|@LB@5'-AAU...UAUAA CAAAGAA U G U CGUAU...CGG-3'@LB@ GGU AUACUA UGCUCAG UC AUAC@LB@ \|\|\| \|:\|\|:\| \|:\|\|\|\|\| \|\| \|:\|\|@LB@ CCA UGUGGU AUGAGUC AG UGUG@LB@3'-UUU...ACCGC CUAAAA U UACUA...UAG-5'@LB@ \| \|@LB@ 188 173@LB@@LB@@LB@Energy -9.80 kcal/mol@LB@Hybridization Energy -20.4225 kcal/mol@LB@Unfolding Energy - mRNA 4.13376 kcal/mol@LB@Unfolding Energy - sRNA 5.03959 kcal/mol@LB@@LB@Position - mRNA 58 -- 71@LB@Position - sRNA 174 -- 187@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 174 -- 180@LB@
123	0.01344	0.3575	b2615	nadK	-10.03	0.271821	99 -- 122	57 -- 77	NAD kinase	_____________98____________123\n_____________\|_____________\|\n5'-CUC...CCCAC________AC___ACUGA...AAG-3'\n______________GGCACCCC__UGC\n______________\|\|\|\|\|\|\|\|__\|\|\|\n______________CCGUGGGG__ACG\n3'-UUU...GUACC________GA___AAGUAG-5'\n_____________\|_____________\|\n_____________78____________56\n	245 -- 251	12 -- 18	-21.986 kcal/mol	5.26387 kcal/mol	8.16826 kcal/mol	98 123@LB@ \| \|@LB@5'-CUC...CCCAC AC ACUGA...AAG-3'@LB@ GGCACCCC UGC@LB@ \|\|\|\|\|\|\|\| \|\|\|@LB@ CCGUGGGG ACG@LB@3'-UUU...GUACC GA AAGUAG-5'@LB@ \| \|@LB@ 78 56@LB@@LB@@LB@Energy -10.03 kcal/mol@LB@Hybridization Energy -21.986 kcal/mol@LB@Unfolding Energy - mRNA 5.26387 kcal/mol@LB@Unfolding Energy - sRNA 8.16826 kcal/mol@LB@@LB@Position - mRNA 99 -- 122@LB@Position - sRNA 57 -- 77@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 12 -- 18@LB@
185	0.02128	0.3833	b2276	nuoN	-8.72	0.461673	62 -- 81	196 -- 211	NADH:ubiquinone oxidoreductase membrane subunit N	_____________61______________82\n_____________\|_______________\|\n5'-GUA...UAUGA__________U____GUGCU...AUC-3'\n______________UC_CUGUUGC_GGUG\n______________\|\|_\|\|\|\|:\|\|_\|\|\|:\n______________AG_GACAGCG_CCAU\n3'-UUU...GUUGA__C____________UUUAU...UAG-5'\n_____________\|_______________\|\n_____________212_____________195\n	69 -- 75	52 -- 58	-15.8669 kcal/mol	5.2118 kcal/mol	5.88061 kcal/mol	61 82@LB@ \| \|@LB@5'-GUA...UAUGA U GUGCU...AUC-3'@LB@ UC CUGUUGC GGUG@LB@ \|\| \|\|\|\|:\|\| \|\|\|:@LB@ AG GACAGCG CCAU@LB@3'-UUU...GUUGA C UUUAU...UAG-5'@LB@ \| \|@LB@ 212 195@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -15.8669 kcal/mol@LB@Unfolding Energy - mRNA 5.2118 kcal/mol@LB@Unfolding Energy - sRNA 5.88061 kcal/mol@LB@@LB@Position - mRNA 62 -- 81@LB@Position - sRNA 196 -- 211@LB@Position Seed - mRNA 69 -- 75@LB@Position Seed - sRNA 52 -- 58@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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