Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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	Additional homologs
11	9.086e-05	0.0245	b3337	bfd	-12.11	0.098410	247 -- 280	34 -- 76	bacterioferritin-associated ferredoxin		_____________246_________________________________________281\n_____________\|___________________________________________\|\n5'-GCG...UCGUC___________________UCCCC___________________GCAAU...UUC-3'\n______________AGGCUGUGCGC__CAGUUU______UCACUCG______UUCCA\n______________\|\|:\|\|:::\|:\|__\|\|:\|\|:______\|\|\|\|\|\|:______\|\|\|\|\|\n______________UCUGAUGUGUG__GUUAAG______AGUGAGU______AAGGU\n3'-UUU...CCGUU___________UC______CAACAA_______CCCCUA_____ACGAA...GCA-5'\n_____________\|___________________________________________\|\n_____________77__________________________________________33\n	269 -- 275	45 -- 51	-24.9474 kcal/mol	8.02269 kcal/mol	4.816 kcal/mol	246 281@LB@ \| \|@LB@5'-GCG...UCGUC UCCCC GCAAU...UUC-3'@LB@ AGGCUGUGCGC CAGUUU UCACUCG UUCCA@LB@ \|\|:\|\|:::\|:\| \|\|:\|\|: \|\|\|\|\|\|: \|\|\|\|\|@LB@ UCUGAUGUGUG GUUAAG AGUGAGU AAGGU@LB@3'-UUU...CCGUU UC CAACAA CCCCUA ACGAA...GCA-5'@LB@ \| \|@LB@ 77 33@LB@@LB@@LB@Energy -12.11 kcal/mol@LB@Hybridization Energy -24.9474 kcal/mol@LB@Unfolding Energy - mRNA 8.02269 kcal/mol@LB@Unfolding Energy - sRNA 4.816 kcal/mol@LB@@LB@Position - mRNA 247 -- 280@LB@Position - sRNA 34 -- 76@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 45 -- 51@LB@
12	9.939e-05	0.0245	b2308	hisQ	-13.21	0.056865	186 -- 218	34 -- 75	histidine ABC transporter permease		_____________185__________________________________________219\n_____________\|____________________________________________\|\n5'-GAU...CACAC___AGG___G_______________AU_________________GGUGU...UUG-3'\n______________GAC___ACA_GCAGCA___UGUUGU__________GGGUUUUCA\n______________\|\|\|___\|\|\|_:\|\|\|\|\|___:\|\|\|\|\|__________\|\|:\|\|\|:\|\|\n______________CUG___UGU_UGUCGU___GCAACA__________CCUAAAGGU\n3'-UUU...CGUUU___A_____G______UAA______AAGUGAGUCC_________ACGAA...GCA-5'\n_____________\|____________________________________________\|\n_____________76___________________________________________33\n	212 -- 218	34 -- 40	-26.3199 kcal/mol	8.29445 kcal/mol	4.816 kcal/mol	185 219@LB@ \| \|@LB@5'-GAU...CACAC AGG G AU GGUGU...UUG-3'@LB@ GAC ACA GCAGCA UGUUGU GGGUUUUCA@LB@ \|\|\| \|\|\| :\|\|\|\|\| :\|\|\|\|\| \|\|:\|\|\|:\|\|@LB@ CUG UGU UGUCGU GCAACA CCUAAAGGU@LB@3'-UUU...CGUUU A G UAA AAGUGAGUCC ACGAA...GCA-5'@LB@ \| \|@LB@ 76 33@LB@@LB@@LB@Energy -13.21 kcal/mol@LB@Hybridization Energy -26.3199 kcal/mol@LB@Unfolding Energy - mRNA 8.29445 kcal/mol@LB@Unfolding Energy - sRNA 4.816 kcal/mol@LB@@LB@Position - mRNA 186 -- 218@LB@Position - sRNA 34 -- 75@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 34 -- 40@LB@
13	0.0001005	0.0245	b1921	fliZ	-13.92	0.038869	246 -- 263	63 -- 78	RpoS antagonist; putative regulator of FliA activity		_____________245________________264\n_____________\|__________________\|\n5'-UGC...AUCUU_______UUAA_______CAGAC...AUC-3'\n______________AAAGACU____ACACAGC\n______________\|\|\|\|\|\|\|____\|\|\|\|\|\|\|\n______________UUUCUGA____UGUGUCG\n3'-UUU...ACCCG_______UG_________UUAAG...GCA-5'\n_____________\|__________________\|\n_____________79_________________62\n	257 -- 263	63 -- 69	-17.8578 kcal/mol	0.69523 kcal/mol	3.24195 kcal/mol	245 264@LB@ \| \|@LB@5'-UGC...AUCUU UUAA CAGAC...AUC-3'@LB@ AAAGACU ACACAGC@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UUUCUGA UGUGUCG@LB@3'-UUU...ACCCG UG UUAAG...GCA-5'@LB@ \| \|@LB@ 79 62@LB@@LB@@LB@Energy -13.92 kcal/mol@LB@Hybridization Energy -17.8578 kcal/mol@LB@Unfolding Energy - mRNA 0.69523 kcal/mol@LB@Unfolding Energy - sRNA 3.24195 kcal/mol@LB@@LB@Position - mRNA 246 -- 263@LB@Position - sRNA 63 -- 78@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 63 -- 69@LB@
14	0.0001025	0.0245	b4051	qorA	-14.73	0.024599	192 -- 224	48 -- 76	quinone oxidoreductase NADPH-dependent		_____________191_______________________________225\n_____________\|_________________________________\|\n5'-CGC...GUUCU___GG___________CA__AA___AA______AAGCA...UCG-3'\n______________GGA__ACACAUGGCAA__CG__UUG__UUUCAC\n______________:\|\|__\|\|\|\|\|::\|\|\|\|__\|\|__\|\|\|__\|\|\|\|\|\|\n______________UCU__UGUGUGUCGUU__GC__AAC__AAAGUG\n3'-UUU...CCGUU___GA___________AA_______________AGUCC...GCA-5'\n_____________\|_________________________________\|\n_____________77________________________________47\n	201 -- 207	61 -- 67	-23.6874 kcal/mol	5.27405 kcal/mol	3.68714 kcal/mol	191 225@LB@ \| \|@LB@5'-CGC...GUUCU GG CA AA AA AAGCA...UCG-3'@LB@ GGA ACACAUGGCAA CG UUG UUUCAC@LB@ :\|\| \|\|\|\|\|::\|\|\|\| \|\| \|\|\| \|\|\|\|\|\|@LB@ UCU UGUGUGUCGUU GC AAC AAAGUG@LB@3'-UUU...CCGUU GA AA AGUCC...GCA-5'@LB@ \| \|@LB@ 77 47@LB@@LB@@LB@Energy -14.73 kcal/mol@LB@Hybridization Energy -23.6874 kcal/mol@LB@Unfolding Energy - mRNA 5.27405 kcal/mol@LB@Unfolding Energy - sRNA 3.68714 kcal/mol@LB@@LB@Position - mRNA 192 -- 224@LB@Position - sRNA 48 -- 76@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 61 -- 67@LB@
15	0.0001044	0.0245	b0741	pal	-16.61	0.007509	30 -- 75	30 -- 71	peptidoglycan-associated outer membrane lipoprotein		_____________29_____________________________________________76\n_____________\|______________________________________________\|\n5'-GGA...UAACG____U________CUACAGCUCUU__________GGGA________GAAUU...GCG-3'\n______________GCAC_AUGGUAAU___________CUCAGGGGAU____UCCGUGCU\n______________:\|\|\|_\|::\|:\|\|\|___________\|\|\|\|\|\|\|\|\|\|____\|\|\|:\|\|\|\|\n______________UGUG_UGUCGUUA___________GAGUCCCCUA____AGGUACGA\n3'-UUU...UCUGA_____________AGCAACAAAGU__________A___________AUAUU...GCA-5'\n_____________\|______________________________________________\|\n_____________72_____________________________________________29\n	69 -- 75	30 -- 36	-38.4662 kcal/mol	13.7923 kcal/mol	8.066 kcal/mol	29 76@LB@ \| \|@LB@5'-GGA...UAACG U CUACAGCUCUU GGGA GAAUU...GCG-3'@LB@ GCAC AUGGUAAU CUCAGGGGAU UCCGUGCU@LB@ :\|\|\| \|::\|:\|\|\| \|\|\|\|\|\|\|\|\|\| \|\|\|:\|\|\|\|@LB@ UGUG UGUCGUUA GAGUCCCCUA AGGUACGA@LB@3'-UUU...UCUGA AGCAACAAAGU A AUAUU...GCA-5'@LB@ \| \|@LB@ 72 29@LB@@LB@@LB@Energy -16.61 kcal/mol@LB@Hybridization Energy -38.4662 kcal/mol@LB@Unfolding Energy - mRNA 13.7923 kcal/mol@LB@Unfolding Energy - sRNA 8.066 kcal/mol@LB@@LB@Position - mRNA 30 -- 75@LB@Position - sRNA 30 -- 71@LB@Position Seed - mRNA 69 -- 75@LB@Position Seed - sRNA 30 -- 36@LB@
16	0.00012	0.02638	b3089	sstT	-15.87	0.012233	203 -- 224	42 -- 75	sodium:serine/threonine symporter		_____________202________________________________225\n_____________\|__________________________________\|\n5'-CAC...AAAAU_________ACG______________________CUAUU...CAU-3'\n______________GACUACGCA______________UUCAC_CGGGG\n______________\|\|\|\|\|\|:\|\|______________\|\|\|\|\|_\|:\|\|\|\n______________CUGAUGUGU______________AAGUG_GUCCC\n3'-UUU...CGUUU_________GUCGUUAAGCAACA_____A_____CUAAA...GCA-5'\n_____________\|__________________________________\|\n_____________76_________________________________41\n	205 -- 211	67 -- 73	-24.6329 kcal/mol	4.00159 kcal/mol	4.76397 kcal/mol	202 225@LB@ \| \|@LB@5'-CAC...AAAAU ACG CUAUU...CAU-3'@LB@ GACUACGCA UUCAC CGGGG@LB@ \|\|\|\|\|\|:\|\| \|\|\|\|\| \|:\|\|\|@LB@ CUGAUGUGU AAGUG GUCCC@LB@3'-UUU...CGUUU GUCGUUAAGCAACA A CUAAA...GCA-5'@LB@ \| \|@LB@ 76 41@LB@@LB@@LB@Energy -15.87 kcal/mol@LB@Hybridization Energy -24.6329 kcal/mol@LB@Unfolding Energy - mRNA 4.00159 kcal/mol@LB@Unfolding Energy - sRNA 4.76397 kcal/mol@LB@@LB@Position - mRNA 203 -- 224@LB@Position - sRNA 42 -- 75@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 67 -- 73@LB@
17	0.0001292	0.02674	b1854	pykA	-13.69	0.043994	133 -- 157	36 -- 68	pyruvate kinase II		_____________132_______________________________158\n_____________\|_________________________________\|\n5'-GAA...GCCAU______________A__________________AUGUU...ACG-3'\n______________CGCGGC_____GUU_UUUCAUUC___GGAUUUC\n______________\|:\|:\|\|_____\|\|\|_\|\|\|\|\|:\|\|___\|\|\|\|\|\|\|\n______________GUGUCG_____CAA_AAAGUGAG___CCUAAAG\n3'-UUU...GAUGU______UUAAG___C________UCC_______GUACG...GCA-5'\n_____________\|_________________________________\|\n_____________69________________________________35\n	151 -- 157	36 -- 42	-24.2432 kcal/mol	5.79946 kcal/mol	4.75078 kcal/mol	132 158@LB@ \| \|@LB@5'-GAA...GCCAU A AUGUU...ACG-3'@LB@ CGCGGC GUU UUUCAUUC GGAUUUC@LB@ \|:\|:\|\| \|\|\| \|\|\|\|\|:\|\| \|\|\|\|\|\|\|@LB@ GUGUCG CAA AAAGUGAG CCUAAAG@LB@3'-UUU...GAUGU UUAAG C UCC GUACG...GCA-5'@LB@ \| \|@LB@ 69 35@LB@@LB@@LB@Energy -13.69 kcal/mol@LB@Hybridization Energy -24.2432 kcal/mol@LB@Unfolding Energy - mRNA 5.79946 kcal/mol@LB@Unfolding Energy - sRNA 4.75078 kcal/mol@LB@@LB@Position - mRNA 133 -- 157@LB@Position - sRNA 36 -- 68@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 36 -- 42@LB@
18	0.0001516	0.02826	b2817	amiC	-14.62	0.026197	167 -- 204	31 -- 70	N-acetylmuramoyl-L-alanine amidase		_____________166______________________________________205\n_____________\|________________________________________\|\n5'-AGU...CUUGU________UUAGAUUUC___________A__GG_______CAGGA...UCA-3'\n______________UACACAGC_________UUUUGCUCGGG_GA____CAUGU\n______________:\|\|\|\|\|\|\|_________\|\|\|::\|\|\|:\|\|_\|\|____\|\|\|\|:\n______________GUGUGUCG_________AAAGUGAGUCC_CU____GUACG\n3'-UUU...CUGAU________UUAAGCAAC___________C__AAAG_____AAUAU...GCA-5'\n_____________\|________________________________________\|\n_____________71_______________________________________30\n	188 -- 194	43 -- 49	-32.0387 kcal/mol	10.1821 kcal/mol	7.23824 kcal/mol	166 205@LB@ \| \|@LB@5'-AGU...CUUGU UUAGAUUUC A GG CAGGA...UCA-3'@LB@ UACACAGC UUUUGCUCGGG GA CAUGU@LB@ :\|\|\|\|\|\|\| \|\|\|::\|\|\|:\|\| \|\| \|\|\|\|:@LB@ GUGUGUCG AAAGUGAGUCC CU GUACG@LB@3'-UUU...CUGAU UUAAGCAAC C AAAG AAUAU...GCA-5'@LB@ \| \|@LB@ 71 30@LB@@LB@@LB@Energy -14.62 kcal/mol@LB@Hybridization Energy -32.0387 kcal/mol@LB@Unfolding Energy - mRNA 10.1821 kcal/mol@LB@Unfolding Energy - sRNA 7.23824 kcal/mol@LB@@LB@Position - mRNA 167 -- 204@LB@Position - sRNA 31 -- 70@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 43 -- 49@LB@
19	0.0001526	0.02826	b1040	csgD	-18.47	0.001904	103 -- 117	60 -- 74	csgBAC operon transcriptional regulator	b3520	_____________102_____________118\n_____________\|_______________\|\n5'-UUA...UUAUU_______________GCAAC...CGC-3'\n______________ACUACACACAGCAGU\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|:\|\n______________UGAUGUGUGUCGUUA\n3'-UUU...GUUUC_______________AGCAA...GCA-5'\n_____________\|_______________\|\n_____________75______________59\n	111 -- 117	60 -- 66	-23.4761 kcal/mol	1.72592 kcal/mol	3.27997 kcal/mol	102 118@LB@ \| \|@LB@5'-UUA...UUAUU GCAAC...CGC-3'@LB@ ACUACACACAGCAGU@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\|:\|@LB@ UGAUGUGUGUCGUUA@LB@3'-UUU...GUUUC AGCAA...GCA-5'@LB@ \| \|@LB@ 75 59@LB@@LB@@LB@Energy -18.47 kcal/mol@LB@Hybridization Energy -23.4761 kcal/mol@LB@Unfolding Energy - mRNA 1.72592 kcal/mol@LB@Unfolding Energy - sRNA 3.27997 kcal/mol@LB@@LB@Position - mRNA 103 -- 117@LB@Position - sRNA 60 -- 74@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 60 -- 66@LB@
20	0.0001757	0.02926	b4175	hflC	-15.67	0.013919	175 -- 193	40 -- 75	HflB protease modulator specific for phage lambda cII repressor		_____________174__________________________________194\n_____________\|____________________________________\|\n5'-UUA...GUAAC____________________________________AAUAA...GUU-3'\n______________GACUAC___CAGCG______________UCAGGGGG\n______________\|\|\|\|\|\|___\|\|\|\|:______________\|\|\|\|\|\|\|:\n______________CUGAUG___GUCGU______________AGUCCCCU\n3'-UUU...CGUUU______UGU_____UAAGCAACAAAGUG________AAAGG...GCA-5'\n_____________\|____________________________________\|\n_____________76___________________________________39\n	187 -- 193	40 -- 46	-24.7611 kcal/mol	4.31935 kcal/mol	4.77786 kcal/mol	174 194@LB@ \| \|@LB@5'-UUA...GUAAC AAUAA...GUU-3'@LB@ GACUAC CAGCG UCAGGGGG@LB@ \|\|\|\|\|\| \|\|\|\|: \|\|\|\|\|\|\|:@LB@ CUGAUG GUCGU AGUCCCCU@LB@3'-UUU...CGUUU UGU UAAGCAACAAAGUG AAAGG...GCA-5'@LB@ \| \|@LB@ 76 39@LB@@LB@@LB@Energy -15.67 kcal/mol@LB@Hybridization Energy -24.7611 kcal/mol@LB@Unfolding Energy - mRNA 4.31935 kcal/mol@LB@Unfolding Energy - sRNA 4.77786 kcal/mol@LB@@LB@Position - mRNA 175 -- 193@LB@Position - sRNA 40 -- 75@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 40 -- 46@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

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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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