Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
65	0.01408	0.6177	b3176	glmM	-9.74	0.046438	133 -- 141	48 -- 56	phosphoglucosamine mutase		_____________132_______142\n_____________\|_________\|\n5'-GUU...CAUGA_________AACCG...CGG-3'\n______________CGUCAAAGA\n______________\|\|\|\|\|\|\|\|\|\n______________GCAGUUUCU\n3'-UUU...ACCGG_________CCUUA...ACA-5'\n_____________\|_________\|\n_____________57________47\n	135 -- 141	48 -- 54	-11.8395 kcal/mol	1.20122 kcal/mol	0.896433 kcal/mol	132 142@LB@ \| \|@LB@5'-GUU...CAUGA AACCG...CGG-3'@LB@ CGUCAAAGA@LB@ \|\|\|\|\|\|\|\|\|@LB@ GCAGUUUCU@LB@3'-UUU...ACCGG CCUUA...ACA-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -11.8395 kcal/mol@LB@Unfolding Energy - mRNA 1.20122 kcal/mol@LB@Unfolding Energy - sRNA 0.896433 kcal/mol@LB@@LB@Position - mRNA 133 -- 141@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 48 -- 54@LB@
114	0.02277	0.6177	b4077	gltP	-4.92	0.386213	48 -- 56	47 -- 55	glutamate/aspartate:proton symporter		_____________47________57\n_____________\|_________\|\n5'-GCC...CUGUU_________UUGCG...GCG-3'\n______________GUUAAAGGG\n______________\|\|:\|\|\|\|:\|\n______________CAGUUUCUC\n3'-UUU...CCGGG_________CUUAA...ACA-5'\n_____________\|_________\|\n_____________56________46\n	50 -- 56	47 -- 53	-9.45392 kcal/mol	3.63887 kcal/mol	0.899516 kcal/mol	47 57@LB@ \| \|@LB@5'-GCC...CUGUU UUGCG...GCG-3'@LB@ GUUAAAGGG@LB@ \|\|:\|\|\|\|:\|@LB@ CAGUUUCUC@LB@3'-UUU...CCGGG CUUAA...ACA-5'@LB@ \| \|@LB@ 56 46@LB@@LB@@LB@Energy -4.92 kcal/mol@LB@Hybridization Energy -9.45392 kcal/mol@LB@Unfolding Energy - mRNA 3.63887 kcal/mol@LB@Unfolding Energy - sRNA 0.899516 kcal/mol@LB@@LB@Position - mRNA 48 -- 56@LB@Position - sRNA 47 -- 55@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 47 -- 53@LB@
150	0.03022	0.6177	b1285	gmr	-9.04	0.064446	208 -- 218	47 -- 57	cyclic-di-GMP phosphodiesterase; csgD regulator; modulator of RNase II stability		_____________207_________219\n_____________\|___________\|\n5'-UUU...GAAAA___________UCCAC...CUA-3'\n______________CCGUUAGGGAG\n______________\|\|\|\|:\|::\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	212 -- 218	47 -- 53	-14.7452 kcal/mol	2.96952 kcal/mol	2.73556 kcal/mol	207 219@LB@ \| \|@LB@5'-UUU...GAAAA UCCAC...CUA-3'@LB@ CCGUUAGGGAG@LB@ \|\|\|\|:\|::\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -9.04 kcal/mol@LB@Hybridization Energy -14.7452 kcal/mol@LB@Unfolding Energy - mRNA 2.96952 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 208 -- 218@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 47 -- 53@LB@
160	0.0322	0.6177	b1550	gnsB	-8.75	0.073686	189 -- 197	44 -- 52	Qin prophage; multicopy suppressor of secG(Cs) and fabA6(Ts)	b4517	_____________188_______198\n_____________\|_________\|\n5'-UGG...GACUA_________AUGAU...UUA-3'\n______________AAAGAGGAA\n______________\|\|\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	191 -- 197	44 -- 50	-11.5466 kcal/mol	1.93458 kcal/mol	0.860683 kcal/mol	188 198@LB@ \| \|@LB@5'-UGG...GACUA AUGAU...UUA-3'@LB@ AAAGAGGAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.75 kcal/mol@LB@Hybridization Energy -11.5466 kcal/mol@LB@Unfolding Energy - mRNA 1.93458 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 44 -- 50@LB@
111	0.02245	0.6177	b3413	gntX	-10.38	0.034336	253 -- 267	41 -- 55	DNA catabolic protein		_____________252_____________268\n_____________\|_______________\|\n5'-CCC...GUUAG____UU_________GUUCG...AUA-3'\n______________GUCA__GGGGGAUUU\n______________\|\|\|\|__\|:\|\|:\|\|\|\|\n______________CAGU__CUCCUUAAA\n3'-UUU...CCGGG____UU_________GUAAA...ACA-5'\n_____________\|_______________\|\n_____________56______________40\n	261 -- 267	41 -- 47	-16.783 kcal/mol	5.45091 kcal/mol	0.947844 kcal/mol	252 268@LB@ \| \|@LB@5'-CCC...GUUAG UU GUUCG...AUA-3'@LB@ GUCA GGGGGAUUU@LB@ \|\|\|\| \|:\|\|:\|\|\|\|@LB@ CAGU CUCCUUAAA@LB@3'-UUU...CCGGG UU GUAAA...ACA-5'@LB@ \| \|@LB@ 56 40@LB@@LB@@LB@Energy -10.38 kcal/mol@LB@Hybridization Energy -16.783 kcal/mol@LB@Unfolding Energy - mRNA 5.45091 kcal/mol@LB@Unfolding Energy - sRNA 0.947844 kcal/mol@LB@@LB@Position - mRNA 253 -- 267@LB@Position - sRNA 41 -- 55@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 41 -- 47@LB@
125	0.02442	0.6177	b3181	greA	-6.11	0.239901	243 -- 260	40 -- 56	transcript cleavage factor		_____________242_________________261\n_____________\|___________________\|\n5'-CGC...AAUUA__________CU_______CUGAA...UCG-3'\n______________CG_CGAAGAG__GGAUUUU\n______________\|\|_\|:\|\|\|\|\|__\|:\|\|\|\|:\n______________GC_GUUUCUC__CUUAAAG\n3'-UUU...ACCGG__A________________UAAAA...ACA-5'\n_____________\|___________________\|\n_____________57__________________39\n	245 -- 251	47 -- 53	-12.1125 kcal/mol	4.98158 kcal/mol	1.02557 kcal/mol	242 261@LB@ \| \|@LB@5'-CGC...AAUUA CU CUGAA...UCG-3'@LB@ CG CGAAGAG GGAUUUU@LB@ \|\| \|:\|\|\|\|\| \|:\|\|\|\|:@LB@ GC GUUUCUC CUUAAAG@LB@3'-UUU...ACCGG A UAAAA...ACA-5'@LB@ \| \|@LB@ 57 39@LB@@LB@@LB@Energy -6.11 kcal/mol@LB@Hybridization Energy -12.1125 kcal/mol@LB@Unfolding Energy - mRNA 4.98158 kcal/mol@LB@Unfolding Energy - sRNA 1.02557 kcal/mol@LB@@LB@Position - mRNA 243 -- 260@LB@Position - sRNA 40 -- 56@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 47 -- 53@LB@
30	0.005789	0.6127	b2688	gshA	-11.51	0.020183	254 -- 264	45 -- 55	glutamate-cysteine ligase		_____________253_________265\n_____________\|___________\|\n5'-UGU...CAGGC___________UACAG...UUA-3'\n______________GUUAAAGGGGA\n______________\|\|:\|\|\|\|:\|\|\|\n______________CAGUUUCUCCU\n3'-UUU...CCGGG___________UAAAG...ACA-5'\n_____________\|___________\|\n_____________56__________44\n	258 -- 264	45 -- 51	-13.8935 kcal/mol	1.45381 kcal/mol	0.930875 kcal/mol	253 265@LB@ \| \|@LB@5'-UGU...CAGGC UACAG...UUA-3'@LB@ GUUAAAGGGGA@LB@ \|\|:\|\|\|\|:\|\|\|@LB@ CAGUUUCUCCU@LB@3'-UUU...CCGGG UAAAG...ACA-5'@LB@ \| \|@LB@ 56 44@LB@@LB@@LB@Energy -11.51 kcal/mol@LB@Hybridization Energy -13.8935 kcal/mol@LB@Unfolding Energy - mRNA 1.45381 kcal/mol@LB@Unfolding Energy - sRNA 0.930875 kcal/mol@LB@@LB@Position - mRNA 254 -- 264@LB@Position - sRNA 45 -- 55@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 45 -- 51@LB@
20	0.00399	0.5992	b4175	hflC	-10.54	0.031960	184 -- 196	43 -- 56	HflB protease modulator specific for phage lambda cII repressor		_____________183____________197\n_____________\|______________\|\n5'-UUA...ACCAG______________AACGA...GUU-3'\n______________CGUCAGGG_GGAAU\n______________\|\|\|\|\|::\|_\|\|\|\|\|\n______________GCAGUUUC_CCUUA\n3'-UUU...ACCGG________U_____AAGUA...ACA-5'\n_____________\|______________\|\n_____________57_____________42\n	185 -- 191	49 -- 55	-15.8123 kcal/mol	4.32193 kcal/mol	0.953958 kcal/mol	183 197@LB@ \| \|@LB@5'-UUA...ACCAG AACGA...GUU-3'@LB@ CGUCAGGG GGAAU@LB@ \|\|\|\|\|::\| \|\|\|\|\|@LB@ GCAGUUUC CCUUA@LB@3'-UUU...ACCGG U AAGUA...ACA-5'@LB@ \| \|@LB@ 57 42@LB@@LB@@LB@Energy -10.54 kcal/mol@LB@Hybridization Energy -15.8123 kcal/mol@LB@Unfolding Energy - mRNA 4.32193 kcal/mol@LB@Unfolding Energy - sRNA 0.953958 kcal/mol@LB@@LB@Position - mRNA 184 -- 196@LB@Position - sRNA 43 -- 56@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 49 -- 55@LB@
35	0.00713	0.6129	b2025	hisF	-8.66	0.076851	182 -- 193	46 -- 57	imidazole glycerol phosphate synthase catalytic subunit with HisH		_____________181__________194\n_____________\|____________\|\n5'-UCG...AUUCA____G_______CCAUC...UGC-3'\n______________CCGU_AAGGAGG\n______________\|\|\|\|_\|\|:\|\|\|\|\n______________GGCA_UUUCUCC\n3'-UUU...AACCG____G_______UUAAA...ACA-5'\n_____________\|____________\|\n_____________58___________45\n	187 -- 193	46 -- 52	-16.1254 kcal/mol	4.72855 kcal/mol	2.7365 kcal/mol	181 194@LB@ \| \|@LB@5'-UCG...AUUCA G CCAUC...UGC-3'@LB@ CCGU AAGGAGG@LB@ \|\|\|\| \|\|:\|\|\|\|@LB@ GGCA UUUCUCC@LB@3'-UUU...AACCG G UUAAA...ACA-5'@LB@ \| \|@LB@ 58 45@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -16.1254 kcal/mol@LB@Unfolding Energy - mRNA 4.72855 kcal/mol@LB@Unfolding Energy - sRNA 2.7365 kcal/mol@LB@@LB@Position - mRNA 182 -- 193@LB@Position - sRNA 46 -- 57@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 46 -- 52@LB@
19	0.003501	0.593	b2019	hisG	-12.73	0.011332	183 -- 194	43 -- 54	ATP phosphoribosyltransferase		_____________182__________195\n_____________\|____________\|\n5'-UUU...CAGGU____________AACAA...AUC-3'\n______________UUAAAGAGGAAU\n______________\|:\|\|\|\|\|\|\|\|\|\|\n______________AGUUUCUCCUUA\n3'-UUU...CGGGC____________AAGUA...ACA-5'\n_____________\|____________\|\n_____________55___________42\n	188 -- 194	43 -- 49	-14.9017 kcal/mol	1.23041 kcal/mol	0.944705 kcal/mol	182 195@LB@ \| \|@LB@5'-UUU...CAGGU AACAA...AUC-3'@LB@ UUAAAGAGGAAU@LB@ \|:\|\|\|\|\|\|\|\|\|\|@LB@ AGUUUCUCCUUA@LB@3'-UUU...CGGGC AAGUA...ACA-5'@LB@ \| \|@LB@ 55 42@LB@@LB@@LB@Energy -12.73 kcal/mol@LB@Hybridization Energy -14.9017 kcal/mol@LB@Unfolding Energy - mRNA 1.23041 kcal/mol@LB@Unfolding Energy - sRNA 0.944705 kcal/mol@LB@@LB@Position - mRNA 183 -- 194@LB@Position - sRNA 43 -- 54@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 43 -- 49@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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