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
21	0.001755	0.2633	b3037	ygiB	-10.05	0.269263	126 -- 141	3 -- 15	DUF1190 family protein	_____________125______________142\n_____________\|________________\|\n5'-AAA...UUCUU_______CUC______AUUUC...UGC-3'\n______________CCCCCUU___GCUUCA\n______________\|\|\|\|\|\|\|___\|\|\|\|\|\|\n______________GGGGGAA___CGAAGU\n3'-UUU...CCCGU________________AG-5'\n_____________\|________________\|\n_____________16_______________2\n	126 -- 132	9 -- 15	-20.0074 kcal/mol	1.89647 kcal/mol	7.00663 kcal/mol	125 142@LB@ \| \|@LB@5'-AAA...UUCUU CUC AUUUC...UGC-3'@LB@ CCCCCUU GCUUCA@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GGGGGAA CGAAGU@LB@3'-UUU...CCCGU AG-5'@LB@ \| \|@LB@ 16 2@LB@@LB@@LB@Energy -10.05 kcal/mol@LB@Hybridization Energy -20.0074 kcal/mol@LB@Unfolding Energy - mRNA 1.89647 kcal/mol@LB@Unfolding Energy - sRNA 7.00663 kcal/mol@LB@@LB@Position - mRNA 126 -- 141@LB@Position - sRNA 3 -- 15@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 9 -- 15@LB@
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@
23	0.00185	0.2633	b3492	yhiN	-11.85	0.119629	108 -- 154	124 -- 161	putative oxidoreductase	_____________107_______________________________________155\n_____________\|_________________________________________\|\n5'-CGG...GGAAA_____G______U____AUAG____________________AUGUU...AUA-3'\n______________GGUUU_AUGCCA_UAUU_____GCGC_UGGUGC_GGCGGGU\n______________\|:\|\|\|_\|::\|\|\|_\|\|:\|_____:\|:\|_\|\|:\|\|\|_\|\|\|::\|\|\n______________CUAAA_UGUGGU_AUGA_____UGUG_ACUACG_CCGUUCA\n3'-UUU...GCCCA_____A______U____GUCAG____U______U_______GUUGA...UAG-5'\n_____________\|_________________________________________\|\n_____________162_______________________________________123\n	239 -- 245	153 -- 159	-35.0652 kcal/mol	11.4478 kcal/mol	11.9045 kcal/mol	107 155@LB@ \| \|@LB@5'-CGG...GGAAA G U AUAG AUGUU...AUA-3'@LB@ GGUUU AUGCCA UAUU GCGC UGGUGC GGCGGGU@LB@ \|:\|\|\| \|::\|\|\| \|\|:\| :\|:\| \|\|:\|\|\| \|\|\|::\|\|@LB@ CUAAA UGUGGU AUGA UGUG ACUACG CCGUUCA@LB@3'-UUU...GCCCA A U GUCAG U U GUUGA...UAG-5'@LB@ \| \|@LB@ 162 123@LB@@LB@@LB@Energy -11.85 kcal/mol@LB@Hybridization Energy -35.0652 kcal/mol@LB@Unfolding Energy - mRNA 11.4478 kcal/mol@LB@Unfolding Energy - sRNA 11.9045 kcal/mol@LB@@LB@Position - mRNA 108 -- 154@LB@Position - sRNA 124 -- 161@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 153 -- 159@LB@
24	0.001922	0.2633	b3017	ftsP	-19.79	0.002953	203 -- 291	63 -- 135	septal ring component that protects the divisome from stress; multicopy suppressor of ftsI(Ts)	_____________202__________________________________________________________________________________________292\n_____________\|____________________________________________________________________________________________\|\n5'-GAC...AAUAU_________GUCG__________A_________C__G______CACU_____CA______GUUCCCCUGAAG____________________AGCAA...CGC-3'\n______________GUCA_CUCA____GCGUCAGUUC_UUCAGGCAU_GG__GAUUG____UUGUG__GGCGCU____________GCCAGCGCAGCCGG_GCAAC\n______________\|\|\|\|_\|:\|\|____\|\|:\|\|\|\|\|:\|_\|\|\|\|:\|\|\|\|_\|\|__:\|\|:\|____\|\|\|\|\|__\|:\|\|\|\|____________:\|\|\|:\|\|\|\|:\|\|:\|_:\|\|\|\|\n______________CAGU_GGGU____CGUAGUCAGG_AAGUUCGUA_CC__UUAGC____AACAC__CUGCGA____________UGGUUGCGUUGGUC_UGUUG\n3'-UUU...AACGC____A____GA_________________________AA______________C_______AU________________________G_____AAGCG...UAG-5'\n_____________\|____________________________________________________________________________________________\|\n_____________136__________________________________________________________________________________________62\n	278 -- 284	71 -- 77	-82.7619 kcal/mol	32.3928 kcal/mol	37.2191 kcal/mol	202 292@LB@ \| \|@LB@5'-GAC...AAUAU GUCG A C G CACU CA GUUCCCCUGAAG AGCAA...CGC-3'@LB@ GUCA CUCA GCGUCAGUUC UUCAGGCAU GG GAUUG UUGUG GGCGCU GCCAGCGCAGCCGG GCAAC@LB@ \|\|\|\| \|:\|\| \|\|:\|\|\|\|\|:\| \|\|\|\|:\|\|\|\| \|\| :\|\|:\| \|\|\|\|\| \|:\|\|\|\| :\|\|\|:\|\|\|\|:\|\|:\| :\|\|\|\|@LB@ CAGU GGGU CGUAGUCAGG AAGUUCGUA CC UUAGC AACAC CUGCGA UGGUUGCGUUGGUC UGUUG@LB@3'-UUU...AACGC A GA AA C AU G AAGCG...UAG-5'@LB@ \| \|@LB@ 136 62@LB@@LB@@LB@Energy -19.79 kcal/mol@LB@Hybridization Energy -82.7619 kcal/mol@LB@Unfolding Energy - mRNA 32.3928 kcal/mol@LB@Unfolding Energy - sRNA 37.2191 kcal/mol@LB@@LB@Position - mRNA 203 -- 291@LB@Position - sRNA 63 -- 135@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 71 -- 77@LB@
25	0.002009	0.2633	b0134	panB	-9.88	0.290153	57 -- 67	176 -- 186	3-methyl-2-oxobutanoate hydroxymethyltransferase	_____________56__________68\n_____________\|___________\|\n5'-CAG...AAAGC___________UCCAG...UUG-3'\n______________CACCAGUACUU\n______________\|\|\|\|\|:\|\|\|\|:\n______________GUGGUUAUGAG\n3'-UUU...AAAAU___________UCAGU...UAG-5'\n_____________\|___________\|\n_____________187_________175\n	61 -- 67	176 -- 182	-15.2136 kcal/mol	0.973349 kcal/mol	3.38772 kcal/mol	56 68@LB@ \| \|@LB@5'-CAG...AAAGC UCCAG...UUG-3'@LB@ CACCAGUACUU@LB@ \|\|\|\|\|:\|\|\|\|:@LB@ GUGGUUAUGAG@LB@3'-UUU...AAAAU UCAGU...UAG-5'@LB@ \| \|@LB@ 187 175@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -15.2136 kcal/mol@LB@Unfolding Energy - mRNA 0.973349 kcal/mol@LB@Unfolding Energy - sRNA 3.38772 kcal/mol@LB@@LB@Position - mRNA 57 -- 67@LB@Position - sRNA 176 -- 186@LB@Position Seed - mRNA 61 -- 67@LB@Position Seed - sRNA 176 -- 182@LB@
26	0.002141	0.2633	b0183	rnhB	-16.17	0.015603	251 -- 292	123 -- 175	ribonuclease HII degrades RNA of DNA-RNA hybrids	______________251_______________________________________________________293\n______________\|_________________________________________________________\|\n___________5'-____________________________AG_G_______AAGAAUUAU__________AGUGU...UCC-3'\n______________AAUCUGCUGGCGGG___________CAG__A_UUAGUCA_________UGCAGG_AAG\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|\|___________\|\|:__\|_\|:\|\|\|\|\|_________\|\|\|\|\|\|_\|\|\|\n______________UUAGACGACCGCCC___________GUU__U_AGUCAGU_________ACGUCC_UUC\n3'-UUU...CCAUA______________ACUAAAAUGUG___A__G_______GUGUACU________G___AGUUG...UAG-5'\n_____________\|__________________________________________________________\|\n_____________176________________________________________________________122\n	22 -- 28	171 -- 177	-46.3072 kcal/mol	12.4456 kcal/mol	20.994 kcal/mol	251 293@LB@ \| \|@LB@ 5'- AG G AAGAAUUAU AGUGU...UCC-3'@LB@ AAUCUGCUGGCGGG CAG A UUAGUCA UGCAGG AAG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\|\| \|\|: \| \|:\|\|\|\|\| \|\|\|\|\|\| \|\|\|@LB@ UUAGACGACCGCCC GUU U AGUCAGU ACGUCC UUC@LB@3'-UUU...CCAUA ACUAAAAUGUG A G GUGUACU G AGUUG...UAG-5'@LB@ \| \|@LB@ 176 122@LB@@LB@@LB@Energy -16.17 kcal/mol@LB@Hybridization Energy -46.3072 kcal/mol@LB@Unfolding Energy - mRNA 12.4456 kcal/mol@LB@Unfolding Energy - sRNA 20.994 kcal/mol@LB@@LB@Position - mRNA 251 -- 292@LB@Position - sRNA 123 -- 175@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 171 -- 177@LB@
27	0.002233	0.2633	b3525	yhjH	-10.03	0.271118	185 -- 216	151 -- 171	cyclic-di-GMP phosphodiesterase FlhDC-regulated	_____________184_______________________________217\n_____________\|_________________________________\|\n5'-UUA...UUUAA__A___G_____CUU_____AUA__________UCCAG...CCU-3'\n______________AC_CAG__ACAU___UGAUG___AGGCAGGUUA\n______________\|\|_\|\|\|__\|\|\|:___\|\|\|\|\|___\|\|\|\|\|:\|\|:\|\n______________UG_GUC__UGUG___ACUAC___UCCGUUCAGU\n3'-UUU...GGUUA__A___AG____U_______G____________UGAAA...UAG-5'\n_____________\|_________________________________\|\n_____________172_______________________________150\n	209 -- 215	152 -- 158	-24.6278 kcal/mol	4.97701 kcal/mol	8.14531 kcal/mol	184 217@LB@ \| \|@LB@5'-UUA...UUUAA A G CUU AUA UCCAG...CCU-3'@LB@ AC CAG ACAU UGAUG AGGCAGGUUA@LB@ \|\| \|\|\| \|\|\|: \|\|\|\|\| \|\|\|\|\|:\|\|:\|@LB@ UG GUC UGUG ACUAC UCCGUUCAGU@LB@3'-UUU...GGUUA A AG U G UGAAA...UAG-5'@LB@ \| \|@LB@ 172 150@LB@@LB@@LB@Energy -10.03 kcal/mol@LB@Hybridization Energy -24.6278 kcal/mol@LB@Unfolding Energy - mRNA 4.97701 kcal/mol@LB@Unfolding Energy - sRNA 8.14531 kcal/mol@LB@@LB@Position - mRNA 185 -- 216@LB@Position - sRNA 151 -- 171@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 152 -- 158@LB@
28	0.002284	0.2633	b1114	mfd	-18.81	0.004608	253 -- 297	50 -- 95	transcription-repair coupling factor	_____________252______________298\n_____________\|________________\|\n5'-UUC...GCGUC___U____________CGGCG...AAA-3'\n______________UGC_GGGCGAGUUAAC\n______________\|\|\|_:\|\|\|:\|\|\|:\|\|\|\n______________ACG_UCCGUUCAGUUG\n3'-UUU...GUACU________________AAAGU...UAG-5'\n_____________\|________________\|\n_____________96_______________49\n	262 -- 268	149 -- 155	-20.6961 kcal/mol	4.60584 kcal/mol	7.12854 kcal/mol	252 298@LB@ \| \|@LB@5'-UUC...GCGUC U CGGCG...AAA-3'@LB@ UGC GGGCGAGUUAAC@LB@ \|\|\| :\|\|\|:\|\|\|:\|\|\|@LB@ ACG UCCGUUCAGUUG@LB@3'-UUU...GUACU AAAGU...UAG-5'@LB@ \| \|@LB@ 96 49@LB@@LB@@LB@Energy -18.81 kcal/mol@LB@Hybridization Energy -20.6961 kcal/mol@LB@Unfolding Energy - mRNA 4.60584 kcal/mol@LB@Unfolding Energy - sRNA 7.12854 kcal/mol@LB@@LB@Position - mRNA 253 -- 297@LB@Position - sRNA 50 -- 95@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 149 -- 155@LB@
29	0.002294	0.2633	b0624	flc	-16.49	0.013425	233 -- 293	118 -- 176	fluoride efflux channel dual topology membrane protein	_____________232_____________________294\n_____________\|_______________________\|\n5'-AAA...CGGCG_______UA______C_______AAUCA...UUC-3'\n______________UUACACU_____UCA_UCAUACA\n______________\|\|\|\|\|\|:_____\|\|\|_\|\|\|:\|\|\|\n______________AAUGUGG_____AGU_AGUGUGU\n3'-UUU...ACUAA_______UUAUG___C_______ACUAC...UAG-5'\n_____________\|_______________________\|\n_____________177_____________________117\n	172 -- 178	167 -- 173	-16.8792 kcal/mol	2.93634 kcal/mol	5.08824 kcal/mol	232 294@LB@ \| \|@LB@5'-AAA...CGGCG UA C AAUCA...UUC-3'@LB@ UUACACU UCA UCAUACA@LB@ \|\|\|\|\|\|: \|\|\| \|\|\|:\|\|\|@LB@ AAUGUGG AGU AGUGUGU@LB@3'-UUU...ACUAA UUAUG C ACUAC...UAG-5'@LB@ \| \|@LB@ 177 117@LB@@LB@@LB@Energy -16.49 kcal/mol@LB@Hybridization Energy -16.8792 kcal/mol@LB@Unfolding Energy - mRNA 2.93634 kcal/mol@LB@Unfolding Energy - sRNA 5.08824 kcal/mol@LB@@LB@Position - mRNA 233 -- 293@LB@Position - sRNA 118 -- 176@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 167 -- 173@LB@
30	0.002398	0.2633	b0494	tesA	-12.69	0.080698	14 -- 26	126 -- 138	acyl-CoA thioesterase 1 and protease I and lysophospholipase L1	_____________13____________27\n_____________\|_____________\|\n5'-UCC...AUGUA_____________CAGAC...UGG-3'\n______________GCGGUUGUCCCAC\n______________\|\|\|\|\|::\|\|\|\|\|\|\n______________CGCCAGUAGGGUG\n3'-UUU...CUUAA_____________ACGUA...UAG-5'\n_____________\|_____________\|\n_____________139___________125\n	20 -- 26	126 -- 132	-24.3083 kcal/mol	5.59054 kcal/mol	8.249 kcal/mol	13 27@LB@ \| \|@LB@5'-UCC...AUGUA CAGAC...UGG-3'@LB@ GCGGUUGUCCCAC@LB@ \|\|\|\|\|::\|\|\|\|\|\|@LB@ CGCCAGUAGGGUG@LB@3'-UUU...CUUAA ACGUA...UAG-5'@LB@ \| \|@LB@ 139 125@LB@@LB@@LB@Energy -12.69 kcal/mol@LB@Hybridization Energy -24.3083 kcal/mol@LB@Unfolding Energy - mRNA 5.59054 kcal/mol@LB@Unfolding Energy - sRNA 8.249 kcal/mol@LB@@LB@Position - mRNA 14 -- 26@LB@Position - sRNA 126 -- 138@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 126 -- 132@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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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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