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
116	0.01276	0.3575	b2989	yghU	-14.25	0.038539	247 -- 281	170 -- 208	putative S-transferase	_____________246______________________________________282\n_____________\|________________________________________\|\n5'-UUA...GGAUA____C________C_C_UU________________A____CCGGU...CGC-3'\n______________AAUC_GCUGGCGG_G_G______CGCCAAUA_UCA_UCGC\n______________\|\|\|\|_\|\|\|\|\|\|\|\|_\|_\|______\|:\|\|\|\|\|\|_\|\|\|_\|\|:\|\n______________UUAG_CGACCGCC_C_C______GUGGUUAU_AGU_AGUG\n3'-UUU...CCAUA____A__________A_UAAAAU________G___C____UGUAC...UAG-5'\n_____________\|________________________________________\|\n_____________209______________________________________169\n	267 -- 273	179 -- 185	-35.9489 kcal/mol	9.63265 kcal/mol	15.256 kcal/mol	246 282@LB@ \| \|@LB@5'-UUA...GGAUA C C C UU A CCGGU...CGC-3'@LB@ AAUC GCUGGCGG G G CGCCAAUA UCA UCGC@LB@ \|\|\|\| \|\|\|\|\|\|\|\| \| \| \|:\|\|\|\|\|\| \|\|\| \|\|:\|@LB@ UUAG CGACCGCC C C GUGGUUAU AGU AGUG@LB@3'-UUU...CCAUA A A UAAAAU G C UGUAC...UAG-5'@LB@ \| \|@LB@ 209 169@LB@@LB@@LB@Energy -14.25 kcal/mol@LB@Hybridization Energy -35.9489 kcal/mol@LB@Unfolding Energy - mRNA 9.63265 kcal/mol@LB@Unfolding Energy - sRNA 15.256 kcal/mol@LB@@LB@Position - mRNA 247 -- 281@LB@Position - sRNA 170 -- 208@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 179 -- 185@LB@
62	0.006126	0.3261	b3824	rhtB	-10.68	0.204362	7 -- 23	171 -- 187	homoserine homoserine lactone and S-methyl-methionine efflux pump	_____________6_________________24\n_____________\|_________________\|\n_____5'-ACGCUG_______AAA_______GCGGU...ACC-3'\n______________ACGCCAG___UCAGUCA\n______________\|\|:\|\|\|:___\|\|\|\|\|\|\|\n______________UGUGGUU___AGUCAGU\n3'-UUU...UAAAA_______AUG_______GUGUA...UAG-5'\n_____________\|_________________\|\n_____________188_______________170\n	17 -- 23	171 -- 177	-18.1223 kcal/mol	1.9449 kcal/mol	4.7016 kcal/mol	6 24@LB@ \| \|@LB@ 5'-ACGCUG AAA GCGGU...ACC-3'@LB@ ACGCCAG UCAGUCA@LB@ \|\|:\|\|\|: \|\|\|\|\|\|\|@LB@ UGUGGUU AGUCAGU@LB@3'-UUU...UAAAA AUG GUGUA...UAG-5'@LB@ \| \|@LB@ 188 170@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -18.1223 kcal/mol@LB@Unfolding Energy - mRNA 1.9449 kcal/mol@LB@Unfolding Energy - sRNA 4.7016 kcal/mol@LB@@LB@Position - mRNA 7 -- 23@LB@Position - sRNA 171 -- 187@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 171 -- 177@LB@
112	0.01232	0.3575	b1540	rspR	-15.19	0.024761	13 -- 44	171 -- 202	transcriptional repressor for rspAB	_____________12_________________________________________________________45\n_____________\|__________________________________________________________\|\n5'-CAG...GCCGU__________UCA_______GCC______C___A____CAAUACCCUGGAA_______CGGUU...GCA-3'\n______________CUGGUGGGUG_____ACGCU___UGCUCA_GUC_AUAU_____________AUGAUGC\n______________\|\|\|\|:\|\|\|\|\|_____\|\|:\|:___\|:\|\|\|\|_\|\|\|_\|:\|:_____________\|\|\|\|\|\|\|\n______________GACCGCCCAC_____UGUGG___AUGAGU_CAG_UGUG_____________UACUACG\n3'-UUU...UAGAC__________UAAAA_____UU____________________________________UCCGU...UAG-5'\n_____________\|__________________________________________________________\|\n_____________203________________________________________________________170\n	62 -- 68	161 -- 167	-40.6001 kcal/mol	15.8189 kcal/mol	17.3482 kcal/mol	12 45@LB@ \| \|@LB@5'-CAG...GCCGU UCA GCC C A CAAUACCCUGGAA CGGUU...GCA-3'@LB@ CUGGUGGGUG ACGCU UGCUCA GUC AUAU AUGAUGC@LB@ \|\|\|\|:\|\|\|\|\| \|\|:\|: \|:\|\|\|\| \|\|\| \|:\|: \|\|\|\|\|\|\|@LB@ GACCGCCCAC UGUGG AUGAGU CAG UGUG UACUACG@LB@3'-UUU...UAGAC UAAAA UU UCCGU...UAG-5'@LB@ \| \|@LB@ 203 170@LB@@LB@@LB@Energy -15.19 kcal/mol@LB@Hybridization Energy -40.6001 kcal/mol@LB@Unfolding Energy - mRNA 15.8189 kcal/mol@LB@Unfolding Energy - sRNA 17.3482 kcal/mol@LB@@LB@Position - mRNA 13 -- 44@LB@Position - sRNA 171 -- 202@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 161 -- 167@LB@
91	0.01018	0.3575	b1660	ydhC	-16.12	0.016020	223 -- 255	172 -- 209	putative arabinose efflux transporter	_____________222_____________________________________256\n_____________\|_______________________________________\|\n5'-GAA...AUUUU______G_________________A______________UUCUG...AGG-3'\n______________UAGUCU_GCUGGCGGGU____UUG_GC__GUACUCGGUU\n______________\|\|:\|\|\|_\|\|\|\|\|\|\|\|\|\|____\|\|:_:\|__:\|\|\|\|\|:\|\|:\n______________AUUAGA_CGACCGCCCA____AAU_UG__UAUGAGUCAG\n3'-UUU...UCCAU_________________CUAA___G__GU__________UGUGU...UAG-5'\n_____________\|_______________________________________\|\n_____________210_____________________________________171\n	249 -- 255	172 -- 178	-38.0361 kcal/mol	10.2504 kcal/mol	15.0669 kcal/mol	222 256@LB@ \| \|@LB@5'-GAA...AUUUU G A UUCUG...AGG-3'@LB@ UAGUCU GCUGGCGGGU UUG GC GUACUCGGUU@LB@ \|\|:\|\|\| \|\|\|\|\|\|\|\|\|\| \|\|: :\| :\|\|\|\|\|:\|\|:@LB@ AUUAGA CGACCGCCCA AAU UG UAUGAGUCAG@LB@3'-UUU...UCCAU CUAA G GU UGUGU...UAG-5'@LB@ \| \|@LB@ 210 171@LB@@LB@@LB@Energy -16.12 kcal/mol@LB@Hybridization Energy -38.0361 kcal/mol@LB@Unfolding Energy - mRNA 10.2504 kcal/mol@LB@Unfolding Energy - sRNA 15.0669 kcal/mol@LB@@LB@Position - mRNA 223 -- 255@LB@Position - sRNA 172 -- 209@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 172 -- 178@LB@
142	0.01524	0.3575	b0611	rna	-12.80	0.076457	138 -- 176	173 -- 202	ribonuclease I	_____________137_____________________________________177\n_____________\|_______________________________________\|\n5'-UAC...CCCAC________CUUUUUUA______A___GA___________GUAUG...AUU-3'\n______________CUGGCGGG________UGAUUU_AUA__UAGUAUUCAGU\n______________\|\|\|\|\|\|\|\|________\|\|\|\|\|\|_\|:\|__:\|:\|\|:\|\|\|\|\|\n______________GACCGCCC________ACUAAA_UGU__GUUAUGAGUCA\n3'-UUU...UAGAC______________________A___G____________GUGUG...UAG-5'\n_____________\|_______________________________________\|\n_____________203_____________________________________172\n	170 -- 176	173 -- 179	-31.7889 kcal/mol	9.30484 kcal/mol	14.6886 kcal/mol	137 177@LB@ \| \|@LB@5'-UAC...CCCAC CUUUUUUA A GA GUAUG...AUU-3'@LB@ CUGGCGGG UGAUUU AUA UAGUAUUCAGU@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\| \|:\| :\|:\|\|:\|\|\|\|\|@LB@ GACCGCCC ACUAAA UGU GUUAUGAGUCA@LB@3'-UUU...UAGAC A G GUGUG...UAG-5'@LB@ \| \|@LB@ 203 172@LB@@LB@@LB@Energy -12.80 kcal/mol@LB@Hybridization Energy -31.7889 kcal/mol@LB@Unfolding Energy - mRNA 9.30484 kcal/mol@LB@Unfolding Energy - sRNA 14.6886 kcal/mol@LB@@LB@Position - mRNA 138 -- 176@LB@Position - sRNA 173 -- 202@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 173 -- 179@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@
111	0.0122	0.3575	b1813	nudL	-9.44	0.347588	99 -- 131	174 -- 206	putative CoA pyrophosphohydrolase weak 3-phosphohydroxypyruvate phosphatase	_____________98________________________________132\n_____________\|_________________________________\|\n5'-CCU...UCUGC_____G_____UG__A__GU________GC___GAAGA...CUG-3'\n______________UCUGC_GGCGG__GA_UU__CGCCGAUA__CAG\n______________\|\|\|\|\|_\|\|\|\|\|__\|\|_\|\|__\|:\|\|:\|\|\|__\|\|\|\n______________AGACG_CCGCC__CU_AA__GUGGUUAU__GUC\n3'-UUU...AUAUU_____A_____CA__A__AU________GA___AGUGU...UAG-5'\n_____________\|_________________________________\|\n_____________207_______________________________173\n	120 -- 126	179 -- 185	-36.2385 kcal/mol	15.3331 kcal/mol	14.8345 kcal/mol	98 132@LB@ \| \|@LB@5'-CCU...UCUGC G UG A GU GC GAAGA...CUG-3'@LB@ UCUGC GGCGG GA UU CGCCGAUA CAG@LB@ \|\|\|\|\| \|\|\|\|\| \|\| \|\| \|:\|\|:\|\|\| \|\|\|@LB@ AGACG CCGCC CU AA GUGGUUAU GUC@LB@3'-UUU...AUAUU A CA A AU GA AGUGU...UAG-5'@LB@ \| \|@LB@ 207 173@LB@@LB@@LB@Energy -9.44 kcal/mol@LB@Hybridization Energy -36.2385 kcal/mol@LB@Unfolding Energy - mRNA 15.3331 kcal/mol@LB@Unfolding Energy - sRNA 14.8345 kcal/mol@LB@@LB@Position - mRNA 99 -- 131@LB@Position - sRNA 174 -- 206@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 179 -- 185@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@
153	0.01719	0.3749	b2997	hybO	-10.59	0.212773	44 -- 57	176 -- 189	hydrogenase 2 small subunit	_____________43_________________58\n_____________\|__________________\|\n5'-CUC...AUUAA______________CU__CCUUC...GCA-3'\n______________UUACACUAAUGCUU__UC\n______________\|\|\|\|\|\|:\|\|\|:\|\|:__\|\|\n______________AAUGUGGUUAUGAG__AG\n3'-UUU...ACUAA______________UC__UGUGU...UAG-5'\n_____________\|__________________\|\n_____________190________________175\n	51 -- 57	176 -- 182	-17.3647 kcal/mol	0.828093 kcal/mol	4.66778 kcal/mol	43 58@LB@ \| \|@LB@5'-CUC...AUUAA CU CCUUC...GCA-3'@LB@ UUACACUAAUGCUU UC@LB@ \|\|\|\|\|\|:\|\|\|:\|\|: \|\|@LB@ AAUGUGGUUAUGAG AG@LB@3'-UUU...ACUAA UC UGUGU...UAG-5'@LB@ \| \|@LB@ 190 175@LB@@LB@@LB@Energy -10.59 kcal/mol@LB@Hybridization Energy -17.3647 kcal/mol@LB@Unfolding Energy - mRNA 0.828093 kcal/mol@LB@Unfolding Energy - sRNA 4.66778 kcal/mol@LB@@LB@Position - mRNA 44 -- 57@LB@Position - sRNA 176 -- 189@LB@Position Seed - mRNA 51 -- 57@LB@Position Seed - sRNA 176 -- 182@LB@
32	0.002513	0.2642	b3456	livM	-11.89	0.117100	251 -- 271	186 -- 206	branched-chain amino acid ABC transporter permease	_____________250___________________________272\n_____________\|_____________________________\|\n5'-GCC...CUGCU______GCCG___________UG______CCGGA...CCA-3'\n______________GGUGAU_____ACCGGUAUUC__GGUCGC\n______________\|\|\|\|\|\|_____\|\|\|::\|\|:\|\|__:\|\|\|:\|\n______________CCACUA_____UGGUUAUGAG__UCAGUG\n3'-UUU...ACCGC______AAAUG__________________UGUAC...UAG-5'\n_____________\|_____________________________\|\n_____________207___________________________185\n	169 -- 175	176 -- 182	-27.5836 kcal/mol	14.0763 kcal/mol	5.03772 kcal/mol	250 272@LB@ \| \|@LB@5'-GCC...CUGCU GCCG UG CCGGA...CCA-3'@LB@ GGUGAU ACCGGUAUUC GGUCGC@LB@ \|\|\|\|\|\| \|\|\|::\|\|:\|\| :\|\|\|:\|@LB@ CCACUA UGGUUAUGAG UCAGUG@LB@3'-UUU...ACCGC AAAUG UGUAC...UAG-5'@LB@ \| \|@LB@ 207 185@LB@@LB@@LB@Energy -11.89 kcal/mol@LB@Hybridization Energy -27.5836 kcal/mol@LB@Unfolding Energy - mRNA 14.0763 kcal/mol@LB@Unfolding Energy - sRNA 5.03772 kcal/mol@LB@@LB@Position - mRNA 251 -- 271@LB@Position - sRNA 186 -- 206@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 176 -- 182@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:

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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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