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
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@
113	0.01802	0.5155	b3910	yiiM	-13.90	0.013248	191 -- 239	40 -- 92	6-N-hydroxylaminopurine resistance protein	_____________190______________________________________________________240\n_____________\|________________________________________________________\|\n5'-UAA...GUGGA________A_____________________U_________C_______AGA_____GCUUA...UGC-3'\n______________GAGGGAAC__GAUGCGA__UAUCCGGUUGA_GUA____UA_ACAGGCA___UUCAG\n______________:\|:::\|\|\|__:\|\|\|\|\|\|__:\|\|\|\|\|\|\|\|\|\|_:\|\|____\|\|_\|\|\|\|:\|\|___\|\|\|\|\|\n______________UUUUUUUG__UUACGCU__GUAGGCCAACU_UAU____AU_UGUCUGU___AAGUC\n__________3'-U________GC_______CC___________U___CCCC__U_______________UUUAC...UCG-5'\n_____________\|________________________________________________________\|\n_____________93_______________________________________________________39\n	225 -- 231	45 -- 51	-43.4237 kcal/mol	10.1845 kcal/mol	19.3361 kcal/mol	190 240@LB@ \| \|@LB@5'-UAA...GUGGA A U C AGA GCUUA...UGC-3'@LB@ GAGGGAAC GAUGCGA UAUCCGGUUGA GUA UA ACAGGCA UUCAG@LB@ :\|:::\|\|\| :\|\|\|\|\|\| :\|\|\|\|\|\|\|\|\|\| :\|\| \|\| \|\|\|\|:\|\| \|\|\|\|\|@LB@ UUUUUUUG UUACGCU GUAGGCCAACU UAU AU UGUCUGU AAGUC@LB@ 3'-U GC CC U CCCC U UUUAC...UCG-5'@LB@ \| \|@LB@ 93 39@LB@@LB@@LB@Energy -13.90 kcal/mol@LB@Hybridization Energy -43.4237 kcal/mol@LB@Unfolding Energy - mRNA 10.1845 kcal/mol@LB@Unfolding Energy - sRNA 19.3361 kcal/mol@LB@@LB@Position - mRNA 191 -- 239@LB@Position - sRNA 40 -- 92@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 45 -- 51@LB@
149	0.02481	0.526	b2108	yehA	-13.80	0.014025	228 -- 241	1 -- 14	putative fimbrial-like adhesin protein	_____________227____________242\n_____________\|______________\|\n5'-GUU...UUAUA______________UAUGC...UUG-3'\n______________UUAAUGAUGAUGGU\n______________\|\|\|\|\|\|\|\|\|\|\|:\|:\n______________AAUUACUACUAUCG\n3'-UUU...AUUUC______________-5'\n_____________\|_____________\|\n_____________15____________1\n	235 -- 241	1 -- 7	-16.5389 kcal/mol	2.69058 kcal/mol	0.0473494 kcal/mol	227 242@LB@ \| \|@LB@5'-GUU...UUAUA UAUGC...UUG-3'@LB@ UUAAUGAUGAUGGU@LB@ \|\|\|\|\|\|\|\|\|\|\|:\|:@LB@ AAUUACUACUAUCG@LB@3'-UUU...AUUUC -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -13.80 kcal/mol@LB@Hybridization Energy -16.5389 kcal/mol@LB@Unfolding Energy - mRNA 2.69058 kcal/mol@LB@Unfolding Energy - sRNA 0.0473494 kcal/mol@LB@@LB@Position - mRNA 228 -- 241@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 1 -- 7@LB@
38	0.003831	0.3287	b3739	atpI	-13.67	0.015109	253 -- 271	1 -- 16	ATP synthase membrane-bound accessory factor	_____________252_________________272\n_____________\|___________________\|\n5'-GAA...CGUUC_____CUG___________AAGUG...ACC-3'\n______________AGUUA___GUGGUGAUAGC\n______________\|\|\|\|\|___:\|\|:\|\|\|\|\|\|\|\n______________UCAAU___UACUACUAUCG\n3'-UUU...UUAUU___________________-5'\n_____________\|__________________\|\n_____________17_________________1\n	265 -- 271	1 -- 7	-18.239 kcal/mol	4.52285 kcal/mol	0.0492804 kcal/mol	252 272@LB@ \| \|@LB@5'-GAA...CGUUC CUG AAGUG...ACC-3'@LB@ AGUUA GUGGUGAUAGC@LB@ \|\|\|\|\| :\|\|:\|\|\|\|\|\|\|@LB@ UCAAU UACUACUAUCG@LB@3'-UUU...UUAUU -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -13.67 kcal/mol@LB@Hybridization Energy -18.239 kcal/mol@LB@Unfolding Energy - mRNA 4.52285 kcal/mol@LB@Unfolding Energy - sRNA 0.0492804 kcal/mol@LB@@LB@Position - mRNA 253 -- 271@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 1 -- 7@LB@
58	0.008338	0.4523	b2280	nuoJ	-13.62	0.015495	7 -- 16	55 -- 64	NADH:ubiquinone oxidoreductase membrane subunit J	_____________6__________17\n_____________\|__________\|\n_____5'-GAUUUC__________AAUAC...UUA-3'\n______________GAAAUGGGGG\n______________\|\|\|\|\|:\|\|\|\|\n______________CUUUAUCCCC\n3'-UUU...GCCAA__________AUUUG...UCG-5'\n_____________\|__________\|\n_____________65_________54\n	10 -- 16	55 -- 61	-15.5198 kcal/mol	1.86933 kcal/mol	0.0291912 kcal/mol	6 17@LB@ \| \|@LB@ 5'-GAUUUC AAUAC...UUA-3'@LB@ GAAAUGGGGG@LB@ \|\|\|\|\|:\|\|\|\|@LB@ CUUUAUCCCC@LB@3'-UUU...GCCAA AUUUG...UCG-5'@LB@ \| \|@LB@ 65 54@LB@@LB@@LB@Energy -13.62 kcal/mol@LB@Hybridization Energy -15.5198 kcal/mol@LB@Unfolding Energy - mRNA 1.86933 kcal/mol@LB@Unfolding Energy - sRNA 0.0291912 kcal/mol@LB@@LB@Position - mRNA 7 -- 16@LB@Position - sRNA 55 -- 64@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 55 -- 61@LB@
22	0.001016	0.1516	b0734	cydB	-13.57	0.015928	285 -- 300	49 -- 64	cytochrome d terminal oxidase subunit II	_____________284_____________300\n_____________\|_______________\|\n5'-CGA...GUUUC__C_____________-3'\n______________GA_AUGGGGGUGGGCA\n______________\|\|_\|\|:\|\|\|\|\|:::\|\|\n______________CU_UAUCCCCAUUUGU\n3'-UUU...GCCAA__U_____________CUGUA...UCG-5'\n_____________\|________________\|\n_____________65_______________48\n	294 -- 300	49 -- 55	-19.142 kcal/mol	4.83222 kcal/mol	0.738518 kcal/mol	284 300@LB@ \| \|@LB@5'-CGA...GUUUC C -3'@LB@ GA AUGGGGGUGGGCA@LB@ \|\| \|\|:\|\|\|\|\|:::\|\|@LB@ CU UAUCCCCAUUUGU@LB@3'-UUU...GCCAA U CUGUA...UCG-5'@LB@ \| \|@LB@ 65 48@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -19.142 kcal/mol@LB@Unfolding Energy - mRNA 4.83222 kcal/mol@LB@Unfolding Energy - sRNA 0.738518 kcal/mol@LB@@LB@Position - mRNA 285 -- 300@LB@Position - sRNA 49 -- 64@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 49 -- 55@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@
35	0.003306	0.3101	b0551	quuD	-13.48	0.016718	188 -- 210	3 -- 24	DLP12 prophage; putative antitermination protein	_____________187_____________________211\n_____________\|_______________________\|\n5'-ACU...UUUUU_____GU_________C______UUCAG...GAU-3'\n______________GUGGA__AAGUUGAUG_GUGAUA\n______________:\|::\|__\|\|\|\|\|:\|\|\|_:\|\|\|\|\|\n______________UAUUU__UUCAAUUAC_UACUAU\n3'-UUU...GCCAU_____AU________________CG-5'\n_____________\|_______________________\|\n_____________25______________________2\n	197 -- 203	9 -- 15	-17.2545 kcal/mol	3.66311 kcal/mol	0.108279 kcal/mol	187 211@LB@ \| \|@LB@5'-ACU...UUUUU GU C UUCAG...GAU-3'@LB@ GUGGA AAGUUGAUG GUGAUA@LB@ :\|::\| \|\|\|\|\|:\|\|\| :\|\|\|\|\|@LB@ UAUUU UUCAAUUAC UACUAU@LB@3'-UUU...GCCAU AU CG-5'@LB@ \| \|@LB@ 25 2@LB@@LB@@LB@Energy -13.48 kcal/mol@LB@Hybridization Energy -17.2545 kcal/mol@LB@Unfolding Energy - mRNA 3.66311 kcal/mol@LB@Unfolding Energy - sRNA 0.108279 kcal/mol@LB@@LB@Position - mRNA 188 -- 210@LB@Position - sRNA 3 -- 24@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 9 -- 15@LB@
46	0.00512	0.3601	b2012	yeeD	-13.46	0.016912	185 -- 206	3 -- 23	putative TusA family sulfurtransferase	_____________184____________________207\n_____________\|______________________\|\n5'-GAU...CAAAU__________G___A_______AUUAA...UAG-3'\n______________UAAGUAAGGU_UAA_GAUGGUG\n______________\|\|\|:\|\|\|:\|\|_\|\|\|_\|\|\|\|:\|:\n______________AUUUAUUUCA_AUU_CUACUAU\n3'-UUU...CCAUU______________A_______CG-5'\n_____________\|______________________\|\n_____________24_____________________2\n	200 -- 206	3 -- 9	-15.4658 kcal/mol	1.89879 kcal/mol	0.104738 kcal/mol	184 207@LB@ \| \|@LB@5'-GAU...CAAAU G A AUUAA...UAG-3'@LB@ UAAGUAAGGU UAA GAUGGUG@LB@ \|\|\|:\|\|\|:\|\| \|\|\| \|\|\|\|:\|:@LB@ AUUUAUUUCA AUU CUACUAU@LB@3'-UUU...CCAUU A CG-5'@LB@ \| \|@LB@ 24 2@LB@@LB@@LB@Energy -13.46 kcal/mol@LB@Hybridization Energy -15.4658 kcal/mol@LB@Unfolding Energy - mRNA 1.89879 kcal/mol@LB@Unfolding Energy - sRNA 0.104738 kcal/mol@LB@@LB@Position - mRNA 185 -- 206@LB@Position - sRNA 3 -- 23@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 3 -- 9@LB@
20	0.0009027	0.1482	b2696	csrA	-13.42	0.017327	268 -- 280	48 -- 60	pleiotropic regulatory protein for carbon source metabolism	_____________267___________281\n_____________\|_____________\|\n5'-CGG...AGUUU__________G__CAACC...GCG-3'\n______________UAGGGGUAAA_GG\n______________\|\|\|\|\|\|\|\|\|\|_:\|\n______________AUCCCCAUUU_UC\n3'-UUU...ACUUU__________G__UGUAA...UCG-5'\n_____________\|_____________\|\n_____________61____________47\n	271 -- 277	51 -- 57	-17.9026 kcal/mol	2.43021 kcal/mol	2.05446 kcal/mol	267 281@LB@ \| \|@LB@5'-CGG...AGUUU G CAACC...GCG-3'@LB@ UAGGGGUAAA GG@LB@ \|\|\|\|\|\|\|\|\|\| :\|@LB@ AUCCCCAUUU UC@LB@3'-UUU...ACUUU G UGUAA...UCG-5'@LB@ \| \|@LB@ 61 47@LB@@LB@@LB@Energy -13.42 kcal/mol@LB@Hybridization Energy -17.9026 kcal/mol@LB@Unfolding Energy - mRNA 2.43021 kcal/mol@LB@Unfolding Energy - sRNA 2.05446 kcal/mol@LB@@LB@Position - mRNA 268 -- 280@LB@Position - sRNA 48 -- 60@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 51 -- 57@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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