Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
72	0.00375	0.1804	b0386	proC	-10.69	0.102749	216 -- 233	53 -- 70	pyrroline-5-carboxylate reductase NAD(P)-binding		_____________215________________234\n_____________\|__________________\|\n5'-CAU...AAAUC__UUUUA_________G_AAUAU...GGG-3'\n______________GG_____UUGGCUGCG_C\n______________\|\|_____\|\|\|\|\|\|\|\|\|_\|\n______________CC_____AACCGACGC_G\n3'-UUU...UGGUC__UUUAG_________G_CAUUU...GUG-5'\n_____________\|__________________\|\n_____________71_________________52\n	225 -- 231	55 -- 61	-21.889 kcal/mol	4.36146 kcal/mol	6.83419 kcal/mol	215 234@LB@ \| \|@LB@5'-CAU...AAAUC UUUUA G AAUAU...GGG-3'@LB@ GG UUGGCUGCG C@LB@ \|\| \|\|\|\|\|\|\|\|\| \|@LB@ CC AACCGACGC G@LB@3'-UUU...UGGUC UUUAG G CAUUU...GUG-5'@LB@ \| \|@LB@ 71 52@LB@@LB@@LB@Energy -10.69 kcal/mol@LB@Hybridization Energy -21.889 kcal/mol@LB@Unfolding Energy - mRNA 4.36146 kcal/mol@LB@Unfolding Energy - sRNA 6.83419 kcal/mol@LB@@LB@Position - mRNA 216 -- 233@LB@Position - sRNA 53 -- 70@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 55 -- 61@LB@
161	0.009429	0.2062	b1372	stfR	-7.17	0.431291	283 -- 297	69 -- 83	Rac prophage; putative tail fiber protein	b1547	_____________282_____________298\n_____________\|_______________\|\n5'-CAC...AAAAC__AA________C__UGG-3'\n______________GU__CAGCACCA_GG\n______________\|:__\|\|:\|\|\|\|\|_\|\|\n______________CG__GUUGUGGU_CC\n3'-UUU...UAUGA__CG________C__UUUAG...GUG-5'\n_____________\|_______________\|\n_____________84______________68\n	288 -- 294	72 -- 78	-17.3245 kcal/mol	2.81769 kcal/mol	7.33837 kcal/mol	282 298@LB@ \| \|@LB@5'-CAC...AAAAC AA C UGG-3'@LB@ GU CAGCACCA GG@LB@ \|: \|\|:\|\|\|\|\| \|\|@LB@ CG GUUGUGGU CC@LB@3'-UUU...UAUGA CG C UUUAG...GUG-5'@LB@ \| \|@LB@ 84 68@LB@@LB@@LB@Energy -7.17 kcal/mol@LB@Hybridization Energy -17.3245 kcal/mol@LB@Unfolding Energy - mRNA 2.81769 kcal/mol@LB@Unfolding Energy - sRNA 7.33837 kcal/mol@LB@@LB@Position - mRNA 283 -- 297@LB@Position - sRNA 69 -- 83@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 72 -- 78@LB@
100	0.00547	0.1855	b2451	eutA	-10.77	0.099200	8 -- 32	56 -- 86	reactivating factor for ethanolamine ammonia lyase		_____________7_______________________________33\n_____________\|_______________________________\|\n____5'-GUCAUCA________UU______________CC_____UUUCG...UGU-3'\n______________ACUGCGCC__CGCC______GUUU__GCUGC\n______________\|\|\|\|\|\|\|\|__\|:\|\|______:\|:\|__\|\|\|\|\|\n______________UGACGCGG__GUGG______UAGA__CGACG\n3'-UUU...GCUUA________UU____UCCCUU____AC_____CGGCA...GUG-5'\n_____________\|_______________________________\|\n_____________87______________________________55\n	9 -- 15	79 -- 85	-30.9169 kcal/mol	5.09004 kcal/mol	15.0537 kcal/mol	7 33@LB@ \| \|@LB@ 5'-GUCAUCA UU CC UUUCG...UGU-3'@LB@ ACUGCGCC CGCC GUUU GCUGC@LB@ \|\|\|\|\|\|\|\| \|:\|\| :\|:\| \|\|\|\|\|@LB@ UGACGCGG GUGG UAGA CGACG@LB@3'-UUU...GCUUA UU UCCCUU AC CGGCA...GUG-5'@LB@ \| \|@LB@ 87 55@LB@@LB@@LB@Energy -10.77 kcal/mol@LB@Hybridization Energy -30.9169 kcal/mol@LB@Unfolding Energy - mRNA 5.09004 kcal/mol@LB@Unfolding Energy - sRNA 15.0537 kcal/mol@LB@@LB@Position - mRNA 8 -- 32@LB@Position - sRNA 56 -- 86@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 79 -- 85@LB@
154	0.009082	0.2059	b2676	nrdF	-13.94	0.023769	159 -- 176	53 -- 69	ribonucleoside-diphosphate reductase 2 beta subunit ferritin-like protein		_____________158________________177\n_____________\|__________________\|\n5'-AAG...GCACU______GAA_________UCCUG...CAG-3'\n______________GAAAUU___GGCUGCGUC\n______________\|\|\|\|\|:___\|\|\|\|\|\|\|:\|\n______________CUUUAG___CCGACGCGG\n3'-UUU...GGUCC______AA__________CAUUU...GUG-5'\n_____________\|__________________\|\n_____________70_________________52\n	170 -- 176	53 -- 59	-23.1658 kcal/mol	2.38862 kcal/mol	6.83371 kcal/mol	158 177@LB@ \| \|@LB@5'-AAG...GCACU GAA UCCUG...CAG-3'@LB@ GAAAUU GGCUGCGUC@LB@ \|\|\|\|\|: \|\|\|\|\|\|\|:\|@LB@ CUUUAG CCGACGCGG@LB@3'-UUU...GGUCC AA CAUUU...GUG-5'@LB@ \| \|@LB@ 70 52@LB@@LB@@LB@Energy -13.94 kcal/mol@LB@Hybridization Energy -23.1658 kcal/mol@LB@Unfolding Energy - mRNA 2.38862 kcal/mol@LB@Unfolding Energy - sRNA 6.83371 kcal/mol@LB@@LB@Position - mRNA 159 -- 176@LB@Position - sRNA 53 -- 69@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 53 -- 59@LB@
36	0.001988	0.1727	b2573	rpoE	-9.66	0.161217	247 -- 255	64 -- 72	RNA polymerase sigma E factor		_____________246_______256\n_____________\|_________\|\n5'-ACA...CCAGA_________AGAAA...UGG-3'\n______________AGGGAGAUC\n______________\|\|\|\|\|:\|\|\|\n______________UCCCUUUAG\n3'-UUU...UGUGG_________AACCG...GUG-5'\n_____________\|_________\|\n_____________73________63\n	249 -- 255	64 -- 70	-13.5601 kcal/mol	1.40253 kcal/mol	2.50058 kcal/mol	246 256@LB@ \| \|@LB@5'-ACA...CCAGA AGAAA...UGG-3'@LB@ AGGGAGAUC@LB@ \|\|\|\|\|:\|\|\|@LB@ UCCCUUUAG@LB@3'-UUU...UGUGG AACCG...GUG-5'@LB@ \| \|@LB@ 73 63@LB@@LB@@LB@Energy -9.66 kcal/mol@LB@Hybridization Energy -13.5601 kcal/mol@LB@Unfolding Energy - mRNA 1.40253 kcal/mol@LB@Unfolding Energy - sRNA 2.50058 kcal/mol@LB@@LB@Position - mRNA 247 -- 255@LB@Position - sRNA 64 -- 72@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 64 -- 70@LB@
86	0.004777	0.1855	b3157	yhbT	-11.83	0.061936	277 -- 294	70 -- 85	SCP-2 sterol transfer family protein		_____________276________________295\n_____________\|__________________\|\n5'-CUG...GCCAU________AA________UUCUUG-3'\n______________UUGCGCUA__ACGCCAGG\n______________:\|\|\|\|\|:\|__\|\|:\|\|\|\|\|\n______________GACGCGGU__UGUGGUCC\n3'-UUU...CUUAU__________________CUUUA...GUG-5'\n_____________\|__________________\|\n_____________86_________________69\n	288 -- 294	70 -- 76	-24.8001 kcal/mol	5.69349 kcal/mol	7.27689 kcal/mol	276 295@LB@ \| \|@LB@5'-CUG...GCCAU AA UUCUUG-3'@LB@ UUGCGCUA ACGCCAGG@LB@ :\|\|\|\|\|:\| \|\|:\|\|\|\|\|@LB@ GACGCGGU UGUGGUCC@LB@3'-UUU...CUUAU CUUUA...GUG-5'@LB@ \| \|@LB@ 86 69@LB@@LB@@LB@Energy -11.83 kcal/mol@LB@Hybridization Energy -24.8001 kcal/mol@LB@Unfolding Energy - mRNA 5.69349 kcal/mol@LB@Unfolding Energy - sRNA 7.27689 kcal/mol@LB@@LB@Position - mRNA 277 -- 294@LB@Position - sRNA 70 -- 85@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 70 -- 76@LB@
101	0.005473	0.1855	b1129	phoQ	-8.66	0.244665	211 -- 219	79 -- 87	sensory histidine kinase in two-component regulatory system with PhoP		_____________210_______220\n_____________\|_________\|\n5'-AUG...AAAAU_________UUUUU...GAA-3'\n______________UACUGCGUC\n______________\|\|\|\|\|\|\|:\|\n______________AUGACGCGG\n3'-UUU...CGCUU_________UUGUG...GUG-5'\n_____________\|_________\|\n_____________88________78\n	213 -- 219	79 -- 85	-14.7172 kcal/mol	1.01485 kcal/mol	5.0453 kcal/mol	210 220@LB@ \| \|@LB@5'-AUG...AAAAU UUUUU...GAA-3'@LB@ UACUGCGUC@LB@ \|\|\|\|\|\|\|:\|@LB@ AUGACGCGG@LB@3'-UUU...CGCUU UUGUG...GUG-5'@LB@ \| \|@LB@ 88 78@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -14.7172 kcal/mol@LB@Unfolding Energy - mRNA 1.01485 kcal/mol@LB@Unfolding Energy - sRNA 5.0453 kcal/mol@LB@@LB@Position - mRNA 211 -- 219@LB@Position - sRNA 79 -- 87@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 79 -- 85@LB@
30	0.001614	0.1727	b3607	cysE	-13.31	0.031682	13 -- 32	63 -- 81	serine acetyltransferase		_____________12___________________33\n_____________\|____________________\|\n5'-CGG...GAAAU______A____A________AUCAA...CGA-3'\n______________GCCAAU_ACCG_GGAAAUUU\n______________\|\|\|\|\|:_\|\|\|:_\|\|\|\|\|\|:\|\n______________CGGUUG_UGGU_CCUUUAGA\n3'-UUU...UGACG___________C________ACCGA...GUG-5'\n_____________\|____________________\|\n_____________82___________________62\n	26 -- 32	63 -- 69	-21.8966 kcal/mol	1.53041 kcal/mol	7.0543 kcal/mol	12 33@LB@ \| \|@LB@5'-CGG...GAAAU A A AUCAA...CGA-3'@LB@ GCCAAU ACCG GGAAAUUU@LB@ \|\|\|\|\|: \|\|\|: \|\|\|\|\|\|:\|@LB@ CGGUUG UGGU CCUUUAGA@LB@3'-UUU...UGACG C ACCGA...GUG-5'@LB@ \| \|@LB@ 82 62@LB@@LB@@LB@Energy -13.31 kcal/mol@LB@Hybridization Energy -21.8966 kcal/mol@LB@Unfolding Energy - mRNA 1.53041 kcal/mol@LB@Unfolding Energy - sRNA 7.0543 kcal/mol@LB@@LB@Position - mRNA 13 -- 32@LB@Position - sRNA 63 -- 81@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 63 -- 69@LB@
186	0.01109	0.2089	b3234	degQ	-11.96	0.058310	267 -- 277	3 -- 13	serine endoprotease periplasmic		_____________266_________278\n_____________\|___________\|\n5'-CUG...CGUCA___________CGCGU...UUG-3'\n______________UUUCAGGCCGU\n______________\|\|\|\|\|\|\|\|\|\|:\n______________AAAGUCCGGCG\n3'-UUU...GACAA___________UG-5'\n_____________\|___________\|\n_____________14__________2\n	271 -- 277	3 -- 9	-19.4081 kcal/mol	1.79109 kcal/mol	5.63489 kcal/mol	266 278@LB@ \| \|@LB@5'-CUG...CGUCA CGCGU...UUG-3'@LB@ UUUCAGGCCGU@LB@ \|\|\|\|\|\|\|\|\|\|:@LB@ AAAGUCCGGCG@LB@3'-UUU...GACAA UG-5'@LB@ \| \|@LB@ 14 2@LB@@LB@@LB@Energy -11.96 kcal/mol@LB@Hybridization Energy -19.4081 kcal/mol@LB@Unfolding Energy - mRNA 1.79109 kcal/mol@LB@Unfolding Energy - sRNA 5.63489 kcal/mol@LB@@LB@Position - mRNA 267 -- 277@LB@Position - sRNA 3 -- 13@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 3 -- 9@LB@
49	0.00252	0.1727	b3452	ugpA	-14.40	0.019328	59 -- 78	52 -- 70	sn-glycerol-3-phosphate ABC transporter permease		_____________58___________________79\n_____________\|____________________\|\n5'-GAG...AGCGU_______AGUU_________CUUUG...CGG-3'\n______________GGAAAUC____GCUGCGCCG\n______________\|\|\|\|\|\|\|____\|\|\|\|\|\|\|\|\|\n______________CCUUUAG____CGACGCGGC\n3'-UUU...UGGUC_______AAC__________AUUUA...GUG-5'\n_____________\|____________________\|\n_____________71___________________51\n	72 -- 78	52 -- 58	-27.9409 kcal/mol	6.69662 kcal/mol	6.84683 kcal/mol	58 79@LB@ \| \|@LB@5'-GAG...AGCGU AGUU CUUUG...CGG-3'@LB@ GGAAAUC GCUGCGCCG@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ CCUUUAG CGACGCGGC@LB@3'-UUU...UGGUC AAC AUUUA...GUG-5'@LB@ \| \|@LB@ 71 51@LB@@LB@@LB@Energy -14.40 kcal/mol@LB@Hybridization Energy -27.9409 kcal/mol@LB@Unfolding Energy - mRNA 6.69662 kcal/mol@LB@Unfolding Energy - sRNA 6.84683 kcal/mol@LB@@LB@Position - mRNA 59 -- 78@LB@Position - sRNA 52 -- 70@LB@Position Seed - mRNA 72 -- 78@LB@Position Seed - sRNA 52 -- 58@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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