Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
119	0.01215	0.3104	b3691	dgoT	-8.17	0.239341	58 -- 68	8 -- 21	D-galactonate transporter	_____________57_____________69\n_____________\|______________\|\n5'-GUG...AUGAA______________AGCAG...CCA-3'\n______________GAUAACA___GCGU\n______________\|\|\|\|\|\|\|___\|\|\|:\n______________CUAUUGU___CGCG\n3'-UUU...UACUA_______UUA____CAGAAAG-5'\n_____________\|______________\|\n_____________22_____________7\n	58 -- 64	15 -- 21	-12.2033 kcal/mol	2.79285 kcal/mol	1.23638 kcal/mol	57 69@LB@ \| \|@LB@5'-GUG...AUGAA AGCAG...CCA-3'@LB@ GAUAACA GCGU@LB@ \|\|\|\|\|\|\| \|\|\|:@LB@ CUAUUGU CGCG@LB@3'-UUU...UACUA UUA CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -8.17 kcal/mol@LB@Hybridization Energy -12.2033 kcal/mol@LB@Unfolding Energy - mRNA 2.79285 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 58 -- 68@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 15 -- 21@LB@
102	0.01008	0.3104	b3500	gor	-8.16	0.240292	285 -- 295	4 -- 15	glutathione oxidoreductase	_____________284__________296\n_____________\|____________\|\n5'-GGC...GCCAG____________GAUUG-3'\n______________AAAUGUGCG_CU\n______________\|\|\|\|\|:\|\|\|_\|\|\n______________UUUACGCGC_GA\n3'-UUU...UAUUG_________A__AAG-5'\n_____________\|____________\|\n_____________16___________3\n	287 -- 293	7 -- 13	-12.6909 kcal/mol	3.32128 kcal/mol	1.20666 kcal/mol	284 296@LB@ \| \|@LB@5'-GGC...GCCAG GAUUG-3'@LB@ AAAUGUGCG CU@LB@ \|\|\|\|\|:\|\|\| \|\|@LB@ UUUACGCGC GA@LB@3'-UUU...UAUUG A AAG-5'@LB@ \| \|@LB@ 16 3@LB@@LB@@LB@Energy -8.16 kcal/mol@LB@Hybridization Energy -12.6909 kcal/mol@LB@Unfolding Energy - mRNA 3.32128 kcal/mol@LB@Unfolding Energy - sRNA 1.20666 kcal/mol@LB@@LB@Position - mRNA 285 -- 295@LB@Position - sRNA 4 -- 15@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 7 -- 13@LB@
141	0.01345	0.3104	b3311	rpsQ	-8.13	0.242987	140 -- 150	8 -- 18	30S ribosomal subunit protein S17	_____________139_________151\n_____________\|___________\|\n5'-GGU...GUUGA___________CGCGA...UCU-3'\n______________AGCAAGUGCGU\n______________\|:\|\|\|:\|\|\|\|:\n______________UUGUUUACGCG\n3'-UUU...UACUA___________CAGAAAG-5'\n_____________\|___________\|\n_____________19__________7\n	144 -- 150	8 -- 14	-14.6725 kcal/mol	5.33741 kcal/mol	1.20363 kcal/mol	139 151@LB@ \| \|@LB@5'-GGU...GUUGA CGCGA...UCU-3'@LB@ AGCAAGUGCGU@LB@ \|:\|\|\|:\|\|\|\|:@LB@ UUGUUUACGCG@LB@3'-UUU...UACUA CAGAAAG-5'@LB@ \| \|@LB@ 19 7@LB@@LB@@LB@Energy -8.13 kcal/mol@LB@Hybridization Energy -14.6725 kcal/mol@LB@Unfolding Energy - mRNA 5.33741 kcal/mol@LB@Unfolding Energy - sRNA 1.20363 kcal/mol@LB@@LB@Position - mRNA 140 -- 150@LB@Position - sRNA 8 -- 18@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 8 -- 14@LB@
38	0.002512	0.2224	b0436	tig	-7.88	0.265562	192 -- 204	10 -- 21	peptidyl-prolyl cis/trans isomerase (trigger factor)	_____________191___________205\n_____________\|_____________\|\n5'-UAC...UUUGA_______A_____AAGUU...UCA-3'\n______________GGUAACA_GAUGC\n______________\|:\|\|\|\|\|_:\|\|\|\|\n______________CUAUUGU_UUACG\n3'-UUU...UACUA_____________CGCAG...AAG-5'\n_____________\|_____________\|\n_____________22____________9\n	192 -- 198	15 -- 21	-12.2618 kcal/mol	3.15229 kcal/mol	1.23076 kcal/mol	191 205@LB@ \| \|@LB@5'-UAC...UUUGA A AAGUU...UCA-3'@LB@ GGUAACA GAUGC@LB@ \|:\|\|\|\|\| :\|\|\|\|@LB@ CUAUUGU UUACG@LB@3'-UUU...UACUA CGCAG...AAG-5'@LB@ \| \|@LB@ 22 9@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -12.2618 kcal/mol@LB@Unfolding Energy - mRNA 3.15229 kcal/mol@LB@Unfolding Energy - sRNA 1.23076 kcal/mol@LB@@LB@Position - mRNA 192 -- 204@LB@Position - sRNA 10 -- 21@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 15 -- 21@LB@
92	0.009361	0.3104	b3652	recG	-7.88	0.265686	265 -- 278	7 -- 20	ATP-dependent DNA helicase	_____________264_____________279\n_____________\|_______________\|\n5'-CAA...ACUUA________C______AAAAU...UGC-3'\n______________GUAACAAA_UG_GCG\n______________:\|\|\|\|\|\|\|_\|\|_\|\|\|\n______________UAUUGUUU_AC_CGC\n3'-UUU...ACUAC___________G___AGAAAG-5'\n_____________\|_______________\|\n_____________21______________6\n	266 -- 272	13 -- 19	-11.4583 kcal/mol	2.34189 kcal/mol	1.23906 kcal/mol	264 279@LB@ \| \|@LB@5'-CAA...ACUUA C AAAAU...UGC-3'@LB@ GUAACAAA UG GCG@LB@ :\|\|\|\|\|\|\| \|\| \|\|\|@LB@ UAUUGUUU AC CGC@LB@3'-UUU...ACUAC G AGAAAG-5'@LB@ \| \|@LB@ 21 6@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -11.4583 kcal/mol@LB@Unfolding Energy - mRNA 2.34189 kcal/mol@LB@Unfolding Energy - sRNA 1.23906 kcal/mol@LB@@LB@Position - mRNA 265 -- 278@LB@Position - sRNA 7 -- 20@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 13 -- 19@LB@
189	0.01853	0.3104	b3743	asnC	-7.74	0.278830	255 -- 266	5 -- 18	transcriptional activator of asnA; autorepressor	_____________254____________267\n_____________\|______________\|\n5'-AUU...UAAUG______________ACCGC...GCG-3'\n______________GGC_AAUGCGCG_C\n______________::\|_\|\|\|\|\|\|\|\|_\|\n______________UUG_UUACGCGC_G\n3'-UUU...UACUA___U________A_AAAG-5'\n_____________\|______________\|\n_____________19_____________4\n	259 -- 265	7 -- 13	-14.4034 kcal/mol	5.44099 kcal/mol	1.2243 kcal/mol	254 267@LB@ \| \|@LB@5'-AUU...UAAUG ACCGC...GCG-3'@LB@ GGC AAUGCGCG C@LB@ ::\| \|\|\|\|\|\|\|\| \|@LB@ UUG UUACGCGC G@LB@3'-UUU...UACUA U A AAAG-5'@LB@ \| \|@LB@ 19 4@LB@@LB@@LB@Energy -7.74 kcal/mol@LB@Hybridization Energy -14.4034 kcal/mol@LB@Unfolding Energy - mRNA 5.44099 kcal/mol@LB@Unfolding Energy - sRNA 1.2243 kcal/mol@LB@@LB@Position - mRNA 255 -- 266@LB@Position - sRNA 5 -- 18@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 7 -- 13@LB@
123	0.01235	0.3104	b0097	secM	-7.65	0.286972	189 -- 203	7 -- 21	regulator of secA translation	_____________188_____________204\n_____________\|_______________\|\n5'-UGG...AUCGG________UAA____AGUGG...CGC-3'\n______________GAUGGCAA___CGUG\n______________\|\|\|::\|\|\|___\|\|:\|\n______________CUAUUGUU___GCGC\n3'-UUU...UACUA________UAC____AGAAAG-5'\n_____________\|_______________\|\n_____________22______________6\n	190 -- 196	14 -- 20	-12.5088 kcal/mol	3.61266 kcal/mol	1.24179 kcal/mol	188 204@LB@ \| \|@LB@5'-UGG...AUCGG UAA AGUGG...CGC-3'@LB@ GAUGGCAA CGUG@LB@ \|\|\|::\|\|\| \|\|:\|@LB@ CUAUUGUU GCGC@LB@3'-UUU...UACUA UAC AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -7.65 kcal/mol@LB@Hybridization Energy -12.5088 kcal/mol@LB@Unfolding Energy - mRNA 3.61266 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 189 -- 203@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 14 -- 20@LB@
83	0.007683	0.3104	b4244	pyrI	-7.62	0.290375	210 -- 222	10 -- 21	aspartate carbamoyltransferase regulatory subunit	_____________209___________223\n_____________\|_____________\|\n5'-UUC...CACAC__________U__AGGUU...UCA-3'\n______________GAUAAUAAAU_GC\n______________\|\|\|\|\|:\|\|\|\|_\|\|\n______________CUAUUGUUUA_CG\n3'-UUU...UACUA_____________CGCAG...AAG-5'\n_____________\|_____________\|\n_____________22____________9\n	213 -- 219	12 -- 18	-11.1174 kcal/mol	2.26673 kcal/mol	1.23076 kcal/mol	209 223@LB@ \| \|@LB@5'-UUC...CACAC U AGGUU...UCA-3'@LB@ GAUAAUAAAU GC@LB@ \|\|\|\|\|:\|\|\|\| \|\|@LB@ CUAUUGUUUA CG@LB@3'-UUU...UACUA CGCAG...AAG-5'@LB@ \| \|@LB@ 22 9@LB@@LB@@LB@Energy -7.62 kcal/mol@LB@Hybridization Energy -11.1174 kcal/mol@LB@Unfolding Energy - mRNA 2.26673 kcal/mol@LB@Unfolding Energy - sRNA 1.23076 kcal/mol@LB@@LB@Position - mRNA 210 -- 222@LB@Position - sRNA 10 -- 21@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 12 -- 18@LB@
188	0.0185	0.3104	b3364	tsgA	-7.52	0.300608	282 -- 299	12 -- 29	putative transporter	_____________281________________300\n_____________\|__________________\|\n5'-CCA...UCACC_____________G____A-3'\n______________GGGAUGGUGAUGG_AAAU\n______________\|\|\|\|\|\|:\|\|\|\|::_\|\|\|\|\n______________CCCUACUACUAUU_UUUA\n3'-UUU...UAAGU_____________G____CGCGC...AAG-5'\n_____________\|__________________\|\n_____________30_________________11\n	282 -- 288	23 -- 29	-23.3156 kcal/mol	8.39977 kcal/mol	7.39774 kcal/mol	281 300@LB@ \| \|@LB@5'-CCA...UCACC G A-3'@LB@ GGGAUGGUGAUGG AAAU@LB@ \|\|\|\|\|\|:\|\|\|\|:: \|\|\|\|@LB@ CCCUACUACUAUU UUUA@LB@3'-UUU...UAAGU G CGCGC...AAG-5'@LB@ \| \|@LB@ 30 11@LB@@LB@@LB@Energy -7.52 kcal/mol@LB@Hybridization Energy -23.3156 kcal/mol@LB@Unfolding Energy - mRNA 8.39977 kcal/mol@LB@Unfolding Energy - sRNA 7.39774 kcal/mol@LB@@LB@Position - mRNA 282 -- 299@LB@Position - sRNA 12 -- 29@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 23 -- 29@LB@
143	0.01362	0.3104	b3284	smg	-7.50	0.302399	64 -- 82	5 -- 21	DUF494 family putative periplasmic protein	_____________63__________________83\n_____________\|___________________\|\n5'-UUC...GAUGA_______CC__U__A____GUCGC...CAG-3'\n______________GGUAACA__UG_UG_CGUC\n______________\|:\|\|\|\|\|__\|\|_:\|_\|\|\|\|\n______________CUAUUGU__AC_GC_GCAG\n3'-UUU...UACUA_______UU__________AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	64 -- 70	15 -- 21	-13.2614 kcal/mol	4.51132 kcal/mol	1.24955 kcal/mol	63 83@LB@ \| \|@LB@5'-UUC...GAUGA CC U A GUCGC...CAG-3'@LB@ GGUAACA UG UG CGUC@LB@ \|:\|\|\|\|\| \|\| :\| \|\|\|\|@LB@ CUAUUGU AC GC GCAG@LB@3'-UUU...UACUA UU AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -7.50 kcal/mol@LB@Hybridization Energy -13.2614 kcal/mol@LB@Unfolding Energy - mRNA 4.51132 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 64 -- 82@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 15 -- 21@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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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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