Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
177	0.02886	0.5353	b2206	napA	-7.95	0.233634	77 -- 89	1 -- 13	nitrate reductase periplasmic large subunit	_____________76____________90\n_____________\|_____________\|\n5'-GAC...GAUUG_________A___AGAAG...UUG-3'\n______________UGGUGGUGG_AGC\n______________\|::\|\|:\|\|:_\|\|\|\n______________AUUACUACU_UCG\n3'-UUU...UUUCA_________A___-5'\n_____________\|____________\|\n_____________14___________1\n	79 -- 85	5 -- 11	-12.9311 kcal/mol	4.9403 kcal/mol	0.0446954 kcal/mol	76 90@LB@ \| \|@LB@5'-GAC...GAUUG A AGAAG...UUG-3'@LB@ UGGUGGUGG AGC@LB@ \|::\|\|:\|\|: \|\|\|@LB@ AUUACUACU UCG@LB@3'-UUU...UUUCA A -5'@LB@ \| \|@LB@ 14 1@LB@@LB@@LB@Energy -7.95 kcal/mol@LB@Hybridization Energy -12.9311 kcal/mol@LB@Unfolding Energy - mRNA 4.9403 kcal/mol@LB@Unfolding Energy - sRNA 0.0446954 kcal/mol@LB@@LB@Position - mRNA 77 -- 89@LB@Position - sRNA 1 -- 13@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 5 -- 11@LB@
71	0.01035	0.4523	b3365	nirB	-13.52	0.016420	166 -- 211	14 -- 63	nitrite reductase large subunit NAD(P)H-binding	_____________165_________________________________________________212\n_____________\|___________________________________________________\|\n5'-AUC...CGUUA_______C__________AA_________C______AAA______C_____CAGAC...UUA-3'\n______________AGGUAGG_GGU_AAUAGA_____AGAAAU_GA_GGC___AAUGAG_AAAGU\n______________\|::\|\|\|\|_\|\|\|_\|\|:\|\|\|_____\|\|\|\|\|\|_:\|_\|:\|___\|\|\|:\|:_\|\|\|\|\|\n______________UUUAUCC_CCA_UUGUCU_____UCUUUA_UU_CUG___UUAUUU_UUUCA\n3'-UUU...CCAAC___________U______GUAAG______C__A___CCA______A_____AUUAC...UCG-5'\n_____________\|___________________________________________________\|\n_____________64__________________________________________________13\n	166 -- 172	57 -- 63	-27.6903 kcal/mol	7.84168 kcal/mol	6.33269 kcal/mol	165 212@LB@ \| \|@LB@5'-AUC...CGUUA C AA C AAA C CAGAC...UUA-3'@LB@ AGGUAGG GGU AAUAGA AGAAAU GA GGC AAUGAG AAAGU@LB@ \|::\|\|\|\| \|\|\| \|\|:\|\|\| \|\|\|\|\|\| :\| \|:\| \|\|\|:\|: \|\|\|\|\|@LB@ UUUAUCC CCA UUGUCU UCUUUA UU CUG UUAUUU UUUCA@LB@3'-UUU...CCAAC U GUAAG C A CCA A AUUAC...UCG-5'@LB@ \| \|@LB@ 64 13@LB@@LB@@LB@Energy -13.52 kcal/mol@LB@Hybridization Energy -27.6903 kcal/mol@LB@Unfolding Energy - mRNA 7.84168 kcal/mol@LB@Unfolding Energy - sRNA 6.33269 kcal/mol@LB@@LB@Position - mRNA 166 -- 211@LB@Position - sRNA 14 -- 63@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 57 -- 63@LB@
2	1.932e-06	0.003171	b1243	oppA	-16.40	0.003005	12 -- 82	1 -- 59	oligopeptide ABC transporter periplasmic binding protein	_____________11__________________________________________________________________________83\n_____________\|___________________________________________________________________________\|\n5'-UGU...UCGAC___________CAGUACGAAUC_____AA__U__UCGUC_____C__CAG____________C____________AAUAC...UCA-3'\n______________AGGGG_AGACA___________GACAU__GG_GA_____UGAAU_AC___AAUAAAUAAAGU____GGUGAUAGU\n______________\|\|\|\|\|_\|:\|\|\|___________\|\|\|\|\|__:\|_:\|_____\|\|\|\|\|_\|\|___\|\|\|\|\|\|\|\|\|\|\|\|____\|:\|\|\|\|\|\|:\n______________UCCCC_UUUGU___________CUGUA__UC_UU_____ACUUA_UG___UUAUUUAUUUCA____CUACUAUCG\n3'-UUU...CUUUA_____A_____________________AG__U____________C__CCA____________AUUA_________-5'\n_____________\|__________________________________________________________________________\|\n_____________60_________________________________________________________________________1\n	76 -- 82	1 -- 7	-40.1642 kcal/mol	17.4223 kcal/mol	6.33764 kcal/mol	11 83@LB@ \| \|@LB@5'-UGU...UCGAC CAGUACGAAUC AA U UCGUC C CAG C AAUAC...UCA-3'@LB@ AGGGG AGACA GACAU GG GA UGAAU AC AAUAAAUAAAGU GGUGAUAGU@LB@ \|\|\|\|\| \|:\|\|\| \|\|\|\|\| :\| :\| \|\|\|\|\| \|\| \|\|\|\|\|\|\|\|\|\|\|\| \|:\|\|\|\|\|\|:@LB@ UCCCC UUUGU CUGUA UC UU ACUUA UG UUAUUUAUUUCA CUACUAUCG@LB@3'-UUU...CUUUA A AG U C CCA AUUA -5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -16.40 kcal/mol@LB@Hybridization Energy -40.1642 kcal/mol@LB@Unfolding Energy - mRNA 17.4223 kcal/mol@LB@Unfolding Energy - sRNA 6.33764 kcal/mol@LB@@LB@Position - mRNA 12 -- 82@LB@Position - sRNA 1 -- 59@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 1 -- 7@LB@
133	0.02154	0.526	b1105	lpoB	-10.17	0.089721	187 -- 196	50 -- 59	OM lipoprotein stimulator of MrcB transpeptidase	_____________186________197\n_____________\|__________\|\n5'-UUA...UUGUA__________CUUGA...AAC-3'\n______________AGGGGUGAAU\n______________\|\|\|\|\|\|:\|\|:\n______________UCCCCAUUUG\n3'-UUU...CUUUA__________UCUGU...UCG-5'\n_____________\|__________\|\n_____________60_________49\n	190 -- 196	50 -- 56	-15.1396 kcal/mol	4.24097 kcal/mol	0.728772 kcal/mol	186 197@LB@ \| \|@LB@5'-UUA...UUGUA CUUGA...AAC-3'@LB@ AGGGGUGAAU@LB@ \|\|\|\|\|\|:\|\|:@LB@ UCCCCAUUUG@LB@3'-UUU...CUUUA UCUGU...UCG-5'@LB@ \| \|@LB@ 60 49@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -15.1396 kcal/mol@LB@Unfolding Energy - mRNA 4.24097 kcal/mol@LB@Unfolding Energy - sRNA 0.728772 kcal/mol@LB@@LB@Position - mRNA 187 -- 196@LB@Position - sRNA 50 -- 59@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 50 -- 56@LB@
137	0.02279	0.526	b1739	osmE	-8.84	0.162198	202 -- 246	21 -- 65	osmotically-inducible lipoprotein	_____________201____________________________________________247\n_____________\|______________________________________________\|\n5'-GAA...GAAUA____CA__AAUAU______A____U______C__C_______U___CCAUG...AGC-3'\n______________UGAA__AG_____GGCAGG_AUUC__GAGUG_AG_GGCGGUA_UAA\n______________\|\|\|\|__\|\|_____::\|\|\|:_\|\|\|\|__:\|:\|\|_\|:_\|:\|\|\|\|\|_\|\|\|\n______________ACUU__UC_____UUGUCU_UAAG__UUUAC_UU_CUGCCAU_AUU\n3'-UUU...GGCCA____UA__CCCAU______G____UC________A_______U___UAUUU...UCG-5'\n_____________\|______________________________________________\|\n_____________66_____________________________________________20\n	236 -- 242	25 -- 31	-25.0909 kcal/mol	9.03477 kcal/mol	7.21767 kcal/mol	201 247@LB@ \| \|@LB@5'-GAA...GAAUA CA AAUAU A U C C U CCAUG...AGC-3'@LB@ UGAA AG GGCAGG AUUC GAGUG AG GGCGGUA UAA@LB@ \|\|\|\| \|\| ::\|\|\|: \|\|\|\| :\|:\|\| \|: \|:\|\|\|\|\| \|\|\|@LB@ ACUU UC UUGUCU UAAG UUUAC UU CUGCCAU AUU@LB@3'-UUU...GGCCA UA CCCAU G UC A U UAUUU...UCG-5'@LB@ \| \|@LB@ 66 20@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -25.0909 kcal/mol@LB@Unfolding Energy - mRNA 9.03477 kcal/mol@LB@Unfolding Energy - sRNA 7.21767 kcal/mol@LB@@LB@Position - mRNA 202 -- 246@LB@Position - sRNA 21 -- 65@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 25 -- 31@LB@
80	0.01119	0.4523	b0241	phoE	-11.22	0.054424	189 -- 234	2 -- 43	outer membrane phosphoporin protein E	_____________188____________________________________________235\n_____________\|______________________________________________\|\n5'-AGC...UAAAA__________AA____AAAAGAGCACUCU__CA_____________GCAUU...AUG-3'\n______________UCAGGAAUGA__AUGA_____________GG__UUAGUGGUGAUGG\n______________\|\|\|\|:\|\|\|\|\|__\|\|\|\|_____________:\|__\|\|\|:\|\|:\|\|\|\|:\|\n______________AGUCUUUACU__UACU_____________UC__AAUUACUACUAUC\n3'-UUU...CUGUA________________GCCAUUAUUUAUU_________________G-5'\n_____________\|______________________________________________\|\n_____________44_____________________________________________1\n	228 -- 234	2 -- 8	-27.55 kcal/mol	10.0434 kcal/mol	6.29139 kcal/mol	188 235@LB@ \| \|@LB@5'-AGC...UAAAA AA AAAAGAGCACUCU CA GCAUU...AUG-3'@LB@ UCAGGAAUGA AUGA GG UUAGUGGUGAUGG@LB@ \|\|\|\|:\|\|\|\|\| \|\|\|\| :\| \|\|\|:\|\|:\|\|\|\|:\|@LB@ AGUCUUUACU UACU UC AAUUACUACUAUC@LB@3'-UUU...CUGUA GCCAUUAUUUAUU G-5'@LB@ \| \|@LB@ 44 1@LB@@LB@@LB@Energy -11.22 kcal/mol@LB@Hybridization Energy -27.55 kcal/mol@LB@Unfolding Energy - mRNA 10.0434 kcal/mol@LB@Unfolding Energy - sRNA 6.29139 kcal/mol@LB@@LB@Position - mRNA 189 -- 234@LB@Position - sRNA 2 -- 43@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 2 -- 8@LB@
4	6.512e-06	0.005344	b0929	ompF	-18.50	0.000749	185 -- 210	1 -- 33	outer membrane porin 1a (Ia;b;F)	_____________184_______________________________211\n_____________\|_________________________________\|\n5'-GUU...AAACC____G____________________________GCAAU...UAG-3'\n______________AUGA_GGUAAUAAAUA______AUGAUGA_AGC\n______________\|\|\|\|_\|\|\|\|\|\|\|\|\|\|\|______\|\|\|\|\|\|\|_\|\|\|\n______________UACU_CCAUUAUUUAU______UACUACU_UCG\n3'-UUU...UUACU____G___________UUCAAU_______A___-5'\n_____________\|________________________________\|\n_____________34_______________________________1\n	201 -- 207	5 -- 11	-27.1062 kcal/mol	3.13427 kcal/mol	5.47105 kcal/mol	184 211@LB@ \| \|@LB@5'-GUU...AAACC G GCAAU...UAG-3'@LB@ AUGA GGUAAUAAAUA AUGAUGA AGC@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|@LB@ UACU CCAUUAUUUAU UACUACU UCG@LB@3'-UUU...UUACU G UUCAAU A -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -18.50 kcal/mol@LB@Hybridization Energy -27.1062 kcal/mol@LB@Unfolding Energy - mRNA 3.13427 kcal/mol@LB@Unfolding Energy - sRNA 5.47105 kcal/mol@LB@@LB@Position - mRNA 185 -- 210@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 5 -- 11@LB@
127	0.01998	0.5155	b2922	yggE	-8.69	0.172995	232 -- 253	1 -- 26	oxidative stress defense protein	_____________231________________________254\n_____________\|__________________________\|\n5'-GCA...GGCAU________________C_________AGCGC...CCG-3'\n______________UAAUGGGUA___UUAG_GG_GAUGGC\n______________\|\|\|\|:::\|\|___\|\|\|:_\|:_\|\|\|:\|\|\n______________AUUAUUUAU___AAUU_CU_CUAUCG\n3'-UUU...CUGCC_________UUC____A__A______-5'\n_____________\|_________________________\|\n_____________27________________________1\n	234 -- 240	18 -- 24	-12.7828 kcal/mol	3.51669 kcal/mol	0.580494 kcal/mol	231 254@LB@ \| \|@LB@5'-GCA...GGCAU C AGCGC...CCG-3'@LB@ UAAUGGGUA UUAG GG GAUGGC@LB@ \|\|\|\|:::\|\| \|\|\|: \|: \|\|\|:\|\|@LB@ AUUAUUUAU AAUU CU CUAUCG@LB@3'-UUU...CUGCC UUC A A -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -8.69 kcal/mol@LB@Hybridization Energy -12.7828 kcal/mol@LB@Unfolding Energy - mRNA 3.51669 kcal/mol@LB@Unfolding Energy - sRNA 0.580494 kcal/mol@LB@@LB@Position - mRNA 232 -- 253@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 18 -- 24@LB@
106	0.01645	0.5059	b2416	ptsI	-13.93	0.013056	96 -- 143	1 -- 59	PEP-protein phosphotransferase of PTS system (enzyme I)	_____________95__________________________________________________________144\n_____________\|___________________________________________________________\|\n5'-GUG...GCAGA___CGA_________AG_________________UGAACAUCU______AC________GGAAC...CCG-3'\n______________AGG_______AGACG__CAGAAA______GCGGU_________GGUUAA___UGAUGGC\n______________\|\|\|_______\|\|\|\|:__\|\|\|\|\|\|______:\|\|\|\|_________:\|\|\|\|\|___\|\|\|\|:\|\|\n______________UCC_______UCUGU__GUCUUU______UGCCA_________UCAAUU___ACUAUCG\n3'-UUU...CUUUA___CCAUUUG_____AA______ACUUAC_____UUAUUUAUU______ACU_______-5'\n_____________\|__________________________________________________________\|\n_____________60_________________________________________________________1\n	137 -- 143	1 -- 7	-30.8595 kcal/mol	10.5928 kcal/mol	6.33764 kcal/mol	95 144@LB@ \| \|@LB@5'-GUG...GCAGA CGA AG UGAACAUCU AC GGAAC...CCG-3'@LB@ AGG AGACG CAGAAA GCGGU GGUUAA UGAUGGC@LB@ \|\|\| \|\|\|\|: \|\|\|\|\|\| :\|\|\|\| :\|\|\|\|\| \|\|\|\|:\|\|@LB@ UCC UCUGU GUCUUU UGCCA UCAAUU ACUAUCG@LB@3'-UUU...CUUUA CCAUUUG AA ACUUAC UUAUUUAUU ACU -5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -13.93 kcal/mol@LB@Hybridization Energy -30.8595 kcal/mol@LB@Unfolding Energy - mRNA 10.5928 kcal/mol@LB@Unfolding Energy - sRNA 6.33764 kcal/mol@LB@@LB@Position - mRNA 96 -- 143@LB@Position - sRNA 1 -- 59@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 1 -- 7@LB@
49	0.00563	0.3739	b2239	glpQ	-9.17	0.140723	61 -- 103	1 -- 49	periplasmic glycerophosphodiester phosphodiesterase	_____________60__________________________________________________104\n_____________\|___________________________________________________\|\n5'-CGG...ACCGU____UUC_____CUG__________CUU______U________________GGCAG...UCA-3'\n______________GGAC___UUCGG____GGAUGGCGG_______UA_GG_UAAUGAU__UGGC\n______________:\|\|\|___\|\|\|:\|____\|:\|\|\|:\|\|\|_______\|\|_:\|_\|\|\|\|\|\|\|__\|:\|\|\n______________UCUG___AAGUC____CUUACUGCC_______AU_UC_AUUACUA__AUCG\n3'-UUU...AUUUG____U_______UUUA_________AUUAUUU__U__A_______CU____-5'\n_____________\|__________________________________________________\|\n_____________50_________________________________________________1\n	93 -- 99	7 -- 13	-28.1898 kcal/mol	12.697 kcal/mol	6.32371 kcal/mol	60 104@LB@ \| \|@LB@5'-CGG...ACCGU UUC CUG CUU U GGCAG...UCA-3'@LB@ GGAC UUCGG GGAUGGCGG UA GG UAAUGAU UGGC@LB@ :\|\|\| \|\|\|:\| \|:\|\|\|:\|\|\| \|\| :\| \|\|\|\|\|\|\| \|:\|\|@LB@ UCUG AAGUC CUUACUGCC AU UC AUUACUA AUCG@LB@3'-UUU...AUUUG U UUUA AUUAUUU U A CU -5'@LB@ \| \|@LB@ 50 1@LB@@LB@@LB@Energy -9.17 kcal/mol@LB@Hybridization Energy -28.1898 kcal/mol@LB@Unfolding Energy - mRNA 12.697 kcal/mol@LB@Unfolding Energy - sRNA 6.32371 kcal/mol@LB@@LB@Position - mRNA 61 -- 103@LB@Position - sRNA 1 -- 49@LB@Position Seed - mRNA 93 -- 99@LB@Position Seed - sRNA 7 -- 13@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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