Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
55	0.003921	0.237	b1781	yeaE	-12.93	0.026626	223 -- 235	47 -- 59	aldo-keto reductase methylglyoxal to acetol NADPH-dependent	_____________222___________236\n_____________\|_____________\|\n5'-GUU...UCAAU_____________CUCAC...CAG-3'\n______________UUAGUGGCGAUGU\n______________\|:\|\|\|\|\|\|:\|\|\|:\n______________AGUCACCGUUACG\n3'-UUU...CUUUU_____________UUACC...UUG-5'\n_____________\|_____________\|\n_____________60____________46\n	229 -- 235	47 -- 53	-19.9127 kcal/mol	3.5603 kcal/mol	3.42309 kcal/mol	222 236@LB@ \| \|@LB@5'-GUU...UCAAU CUCAC...CAG-3'@LB@ UUAGUGGCGAUGU@LB@ \|:\|\|\|\|\|\|:\|\|\|:@LB@ AGUCACCGUUACG@LB@3'-UUU...CUUUU UUACC...UUG-5'@LB@ \| \|@LB@ 60 46@LB@@LB@@LB@Energy -12.93 kcal/mol@LB@Hybridization Energy -19.9127 kcal/mol@LB@Unfolding Energy - mRNA 3.5603 kcal/mol@LB@Unfolding Energy - sRNA 3.42309 kcal/mol@LB@@LB@Position - mRNA 223 -- 235@LB@Position - sRNA 47 -- 59@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 47 -- 53@LB@
5	0.0001064	0.07159	b1784	yeaH	-10.63	0.089613	150 -- 205	1 -- 57	UPF0229 family protein	_____________149________________________________________________________206\n_____________\|__________________________________________________________\|\n5'-UGU...UGAGA__C_____CA_______G_____UACAGUUGGCAAA___AGUACG_____________CUGGU...CGA-3'\n______________AG_GGCAA__CA__GGC_UAGCA_____________UGU______GGGGGCAUAUGAC\n______________\|\|_\|\|\|\|\|__\|\|__\|\|\|_:\|:\|\|_____________\|\|\|______:::\|\|\|\|\|\|\|:\|\|\n______________UC_CCGUU__GU__CCG_GUUGU_____________ACA______UUUCCGUAUAUUG\n3'-UUU...UUUAG__A_____AC__UA___G_____CUUUUAUUUUAG____CUGUUA_____________-5'\n_____________\|_________________________________________________________\|\n_____________58________________________________________________________1\n	198 -- 204	2 -- 8	-36.8439 kcal/mol	14.0882 kcal/mol	12.1233 kcal/mol	149 206@LB@ \| \|@LB@5'-UGU...UGAGA C CA G UACAGUUGGCAAA AGUACG CUGGU...CGA-3'@LB@ AG GGCAA CA GGC UAGCA UGU GGGGGCAUAUGAC@LB@ \|\| \|\|\|\|\| \|\| \|\|\| :\|:\|\| \|\|\| :::\|\|\|\|\|\|\|:\|\|@LB@ UC CCGUU GU CCG GUUGU ACA UUUCCGUAUAUUG@LB@3'-UUU...UUUAG A AC UA G CUUUUAUUUUAG CUGUUA -5'@LB@ \| \|@LB@ 58 1@LB@@LB@@LB@Energy -10.63 kcal/mol@LB@Hybridization Energy -36.8439 kcal/mol@LB@Unfolding Energy - mRNA 14.0882 kcal/mol@LB@Unfolding Energy - sRNA 12.1233 kcal/mol@LB@@LB@Position - mRNA 150 -- 205@LB@Position - sRNA 1 -- 57@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 2 -- 8@LB@
94	0.008385	0.3	b1804	rnd	-8.17	0.271836	224 -- 238	41 -- 54	ribonuclease D	_____________223_____________239\n_____________\|_______________\|\n5'-GUC...ACCAC__A_______C____UUCUU...GUA-3'\n______________GG_CGAUGCG_UGGC\n______________\|\|_\|:\|\|\|\|:_\|\|\|\|\n______________CC_GUUACGU_ACCG\n3'-UUU...AGUCA__________U____GGUUG...UUG-5'\n_____________\|_______________\|\n_____________55______________40\n	227 -- 233	46 -- 52	-18.0571 kcal/mol	5.99437 kcal/mol	3.89026 kcal/mol	223 239@LB@ \| \|@LB@5'-GUC...ACCAC A C UUCUU...GUA-3'@LB@ GG CGAUGCG UGGC@LB@ \|\| \|:\|\|\|\|: \|\|\|\|@LB@ CC GUUACGU ACCG@LB@3'-UUU...AGUCA U GGUUG...UUG-5'@LB@ \| \|@LB@ 55 40@LB@@LB@@LB@Energy -8.17 kcal/mol@LB@Hybridization Energy -18.0571 kcal/mol@LB@Unfolding Energy - mRNA 5.99437 kcal/mol@LB@Unfolding Energy - sRNA 3.89026 kcal/mol@LB@@LB@Position - mRNA 224 -- 238@LB@Position - sRNA 41 -- 54@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 46 -- 52@LB@
196	0.02524	0.4256	b1805	fadD	-8.19	0.269381	280 -- 298	55 -- 72	acyl-CoA synthetase (long-chain-fatty-acid--CoA ligase)	_____________279_________________299\n_____________\|___________________\|\n5'-UUG...GGUAG_______U___C_______CG-3'\n______________AUAUGUU_GAG_AGUCGGU\n______________\|\|\|\|\|\|\|_\|\|:_\|:\|\|:\|\|\n______________UAUACAA_CUU_UUAGUCA\n3'-UUU...AAAAA_______C___________CCGUU...UUG-5'\n_____________\|___________________\|\n_____________73__________________54\n	292 -- 298	55 -- 61	-14.048 kcal/mol	3.20699 kcal/mol	2.64594 kcal/mol	279 299@LB@ \| \|@LB@5'-UUG...GGUAG U C CG-3'@LB@ AUAUGUU GAG AGUCGGU@LB@ \|\|\|\|\|\|\| \|\|: \|:\|\|:\|\|@LB@ UAUACAA CUU UUAGUCA@LB@3'-UUU...AAAAA C CCGUU...UUG-5'@LB@ \| \|@LB@ 73 54@LB@@LB@@LB@Energy -8.19 kcal/mol@LB@Hybridization Energy -14.048 kcal/mol@LB@Unfolding Energy - mRNA 3.20699 kcal/mol@LB@Unfolding Energy - sRNA 2.64594 kcal/mol@LB@@LB@Position - mRNA 280 -- 298@LB@Position - sRNA 55 -- 72@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 55 -- 61@LB@
123	0.01273	0.3462	b1817	manX	-9.41	0.160028	181 -- 191	9 -- 19	fused mannose-specific PTS enzymes: IIA component/IIB component	_____________180_________192\n_____________\|___________\|\n5'-UUA...UUAAC___________AGGUA...GGA-3'\n______________GAUAAUAAAGG\n______________\|\|:\|\|\|\|\|\|\|\|\n______________CUGUUAUUUCC\n3'-UUU...AGACA___________GUAUAUUG-5'\n_____________\|___________\|\n_____________20__________8\n	185 -- 191	9 -- 15	-11.4394 kcal/mol	1.08042 kcal/mol	0.949641 kcal/mol	180 192@LB@ \| \|@LB@5'-UUA...UUAAC AGGUA...GGA-3'@LB@ GAUAAUAAAGG@LB@ \|\|:\|\|\|\|\|\|\|\|@LB@ CUGUUAUUUCC@LB@3'-UUU...AGACA GUAUAUUG-5'@LB@ \| \|@LB@ 20 8@LB@@LB@@LB@Energy -9.41 kcal/mol@LB@Hybridization Energy -11.4394 kcal/mol@LB@Unfolding Energy - mRNA 1.08042 kcal/mol@LB@Unfolding Energy - sRNA 0.949641 kcal/mol@LB@@LB@Position - mRNA 181 -- 191@LB@Position - sRNA 9 -- 19@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 9 -- 15@LB@
189	0.02329	0.4145	b1823	cspC	-8.37	0.250499	214 -- 248	8 -- 63	stress protein member of the CspA-family	_____________213______________________________________________________249\n_____________\|________________________________________________________\|\n5'-UAU...GAUUA____________UA__________________________________________UUUGG...UCU-3'\n______________AAGGUCA__GGU_____AGUGGUUCAAC________GAGUC________UAAAGGU\n______________\|\|::\|\|\|__\|\|:_____\|:\|\|\|::\|\|\|\|________:\|:\|\|________\|\|\|\|\|\|:\n______________UUUUAGU__CCG_____UUACCGGGUUG________UUUAG________AUUUCCG\n3'-UUU...CAACC_______CA___UUACG___________UCUUUUAU_____ACACUGUU_______UAUAUUG-5'\n_____________\|________________________________________________________\|\n_____________64_______________________________________________________7\n	242 -- 248	8 -- 14	-25.9028 kcal/mol	5.39828 kcal/mol	12.1311 kcal/mol	213 249@LB@ \| \|@LB@5'-UAU...GAUUA UA UUUGG...UCU-3'@LB@ AAGGUCA GGU AGUGGUUCAAC GAGUC UAAAGGU@LB@ \|\|::\|\|\| \|\|: \|:\|\|\|::\|\|\|\| :\|:\|\| \|\|\|\|\|\|:@LB@ UUUUAGU CCG UUACCGGGUUG UUUAG AUUUCCG@LB@3'-UUU...CAACC CA UUACG UCUUUUAU ACACUGUU UAUAUUG-5'@LB@ \| \|@LB@ 64 7@LB@@LB@@LB@Energy -8.37 kcal/mol@LB@Hybridization Energy -25.9028 kcal/mol@LB@Unfolding Energy - mRNA 5.39828 kcal/mol@LB@Unfolding Energy - sRNA 12.1311 kcal/mol@LB@@LB@Position - mRNA 214 -- 248@LB@Position - sRNA 8 -- 63@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 8 -- 14@LB@
145	0.01667	0.3828	b1835	rsmF	-17.85	0.001164	186 -- 211	35 -- 58	16S rRNA m(5)C1407 methyltransferase SAM-dependent	_____________185________________________212\n_____________\|__________________________\|\n5'-CGC...UUUGC________C____UC___________CACCG...GUC-3'\n______________CAGUGGUA_AUGC__GUGGCCCAACA\n______________\|\|\|\|\|\|:\|_\|\|\|\|__:\|\|\|\|\|\|\|\|\|\|\n______________GUCACCGU_UACG__UACCGGGUUGU\n3'-UUU...UUUUA_____________U____________CUUUU...UUG-5'\n_____________\|__________________________\|\n_____________59_________________________34\n	205 -- 211	35 -- 41	-37.9392 kcal/mol	9.33395 kcal/mol	10.7541 kcal/mol	185 212@LB@ \| \|@LB@5'-CGC...UUUGC C UC CACCG...GUC-3'@LB@ CAGUGGUA AUGC GUGGCCCAACA@LB@ \|\|\|\|\|\|:\| \|\|\|\| :\|\|\|\|\|\|\|\|\|\|@LB@ GUCACCGU UACG UACCGGGUUGU@LB@3'-UUU...UUUUA U CUUUU...UUG-5'@LB@ \| \|@LB@ 59 34@LB@@LB@@LB@Energy -17.85 kcal/mol@LB@Hybridization Energy -37.9392 kcal/mol@LB@Unfolding Energy - mRNA 9.33395 kcal/mol@LB@Unfolding Energy - sRNA 10.7541 kcal/mol@LB@@LB@Position - mRNA 186 -- 211@LB@Position - sRNA 35 -- 58@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 35 -- 41@LB@
90	0.007755	0.2889	b1852	zwf	-12.23	0.039232	191 -- 223	38 -- 65	glucose-6-phosphate 1-dehydrogenase	_____________190_______________________________224\n_____________\|_________________________________\|\n5'-UCA...CUUAA_______G_CA_______AAC____ACA_____GGCCU...UGG-3'\n______________GGAGAAU_A__UGGCGGU___GCAA___GCCCA\n______________\|\|\|:\|\|\|_\|__\|\|\|\|::\|___\|\|\|\|___\|\|\|\|\|\n______________CCUUUUA_U__ACCGUUA___CGUU___CGGGU\n3'-UUU...UACAA_______G_C_______________AC______UGUCU...UUG-5'\n_____________\|_________________________________\|\n_____________66________________________________37\n	202 -- 208	49 -- 55	-27.1425 kcal/mol	8.24293 kcal/mol	6.67322 kcal/mol	190 224@LB@ \| \|@LB@5'-UCA...CUUAA G CA AAC ACA GGCCU...UGG-3'@LB@ GGAGAAU A UGGCGGU GCAA GCCCA@LB@ \|\|\|:\|\|\| \| \|\|\|\|::\| \|\|\|\| \|\|\|\|\|@LB@ CCUUUUA U ACCGUUA CGUU CGGGU@LB@3'-UUU...UACAA G C AC UGUCU...UUG-5'@LB@ \| \|@LB@ 66 37@LB@@LB@@LB@Energy -12.23 kcal/mol@LB@Hybridization Energy -27.1425 kcal/mol@LB@Unfolding Energy - mRNA 8.24293 kcal/mol@LB@Unfolding Energy - sRNA 6.67322 kcal/mol@LB@@LB@Position - mRNA 191 -- 223@LB@Position - sRNA 38 -- 65@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 49 -- 55@LB@
187	0.02306	0.4145	b1854	pykA	-9.88	0.128920	243 -- 268	12 -- 43	pyruvate kinase II	_____________242______________________________269\n_____________\|________________________________\|\n5'-GAA...CGUUA_________AC____________C________UCUUG...ACG-3'\n______________GGCCCAGCA_______AGAUC_G_GAUAAUAA\n______________\|\|\|\|\|\|:\|\|_______\|:\|\|\|_\|_\|\|:\|\|\|\|\|\n______________CCGGGUUGU_______UUUAG_C_CUGUUAUU\n3'-UUU...CGUUA_________CUUUUAU_____A_A________UCCGU...UUG-5'\n_____________\|________________________________\|\n_____________44_______________________________11\n	262 -- 268	12 -- 18	-24.7448 kcal/mol	4.16838 kcal/mol	10.6985 kcal/mol	242 269@LB@ \| \|@LB@5'-GAA...CGUUA AC C UCUUG...ACG-3'@LB@ GGCCCAGCA AGAUC G GAUAAUAA@LB@ \|\|\|\|\|\|:\|\| \|:\|\|\| \| \|\|:\|\|\|\|\|@LB@ CCGGGUUGU UUUAG C CUGUUAUU@LB@3'-UUU...CGUUA CUUUUAU A A UCCGU...UUG-5'@LB@ \| \|@LB@ 44 11@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -24.7448 kcal/mol@LB@Unfolding Energy - mRNA 4.16838 kcal/mol@LB@Unfolding Energy - sRNA 10.6985 kcal/mol@LB@@LB@Position - mRNA 243 -- 268@LB@Position - sRNA 12 -- 43@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 12 -- 18@LB@
87	0.007653	0.2889	b1881	cheZ	-13.56	0.018568	164 -- 190	2 -- 28	chemotaxis regulator protein phosphatase for CheY	_____________163_________________________191\n_____________\|___________________________\|\n5'-AUU...UCAAC_______U___G__ACU__________GGAUG...GGG-3'\n______________AAAAUCU_UGA_AA___GGGCAUGUGA\n______________\|\|\|\|\|\|\|_\|\|\|_\|\|___:\|\|\|\|\|:\|:\|\n______________UUUUAGA_ACU_UU___UCCGUAUAUU\n3'-UUU...UUUUA_______C___G__AUU__________G-5'\n_____________\|___________________________\|\n_____________29__________________________1\n	183 -- 189	3 -- 9	-22.696 kcal/mol	4.24203 kcal/mol	4.89261 kcal/mol	163 191@LB@ \| \|@LB@5'-AUU...UCAAC U G ACU GGAUG...GGG-3'@LB@ AAAAUCU UGA AA GGGCAUGUGA@LB@ \|\|\|\|\|\|\| \|\|\| \|\| :\|\|\|\|\|:\|:\|@LB@ UUUUAGA ACU UU UCCGUAUAUU@LB@3'-UUU...UUUUA C G AUU G-5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -13.56 kcal/mol@LB@Hybridization Energy -22.696 kcal/mol@LB@Unfolding Energy - mRNA 4.24203 kcal/mol@LB@Unfolding Energy - sRNA 4.89261 kcal/mol@LB@@LB@Position - mRNA 164 -- 190@LB@Position - sRNA 2 -- 28@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 3 -- 9@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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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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