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
33	0.006504	0.6129	b1937	fliE	-6.45	0.207626	119 -- 135	24 -- 40	flagellar basal-body component		_____________118_______________136\n_____________\|_________________\|\n5'-CUG...AAACC_____________C___UUAGC...GUU-3'\n______________CGUUUUUUUGUUG_UAU\n______________\|:\|\|\|\|\|\|\|:\|\|:_\|\|\|\n______________GUAAAAAAAUAAU_AUA\n3'-UUU...UUAAA_____________A___CGGCA...ACA-5'\n_____________\|_________________\|\n_____________41________________23\n	124 -- 130	29 -- 35	-10.2961 kcal/mol	2.85244 kcal/mol	0.998368 kcal/mol	118 136@LB@ \| \|@LB@5'-CUG...AAACC C UUAGC...GUU-3'@LB@ CGUUUUUUUGUUG UAU@LB@ \|:\|\|\|\|\|\|\|:\|\|: \|\|\|@LB@ GUAAAAAAAUAAU AUA@LB@3'-UUU...UUAAA A CGGCA...ACA-5'@LB@ \| \|@LB@ 41 23@LB@@LB@@LB@Energy -6.45 kcal/mol@LB@Hybridization Energy -10.2961 kcal/mol@LB@Unfolding Energy - mRNA 2.85244 kcal/mol@LB@Unfolding Energy - sRNA 0.998368 kcal/mol@LB@@LB@Position - mRNA 119 -- 135@LB@Position - sRNA 24 -- 40@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 29 -- 35@LB@
139	0.02683	0.6177	b1474	fdnG	-8.74	0.074199	188 -- 196	44 -- 52	formate dehydrogenase-N alpha subunit nitrate-inducible	b3894	_____________187_______197\n_____________\|_________\|\n5'-AUU...UGAAA_________AGCAA...CUC-3'\n______________AAAGAGGAA\n______________\|\|\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	190 -- 196	44 -- 50	-11.3772 kcal/mol	1.78024 kcal/mol	0.860683 kcal/mol	187 197@LB@ \| \|@LB@5'-AUU...UGAAA AGCAA...CUC-3'@LB@ AAAGAGGAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -11.3772 kcal/mol@LB@Unfolding Energy - mRNA 1.78024 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 188 -- 196@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 44 -- 50@LB@
177	0.03616	0.6177	b1474	fdnG	-8.74	0.074199	188 -- 196	44 -- 52	formate dehydrogenase-N alpha subunit nitrate-inducible	b3894	_____________187_______197\n_____________\|_________\|\n5'-AUU...UGAAA_________AGCAA...CUC-3'\n______________AAAGAGGAA\n______________\|\|\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	190 -- 196	44 -- 50	-11.3772 kcal/mol	1.78024 kcal/mol	0.860683 kcal/mol	187 197@LB@ \| \|@LB@5'-AUU...UGAAA AGCAA...CUC-3'@LB@ AAAGAGGAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -11.3772 kcal/mol@LB@Unfolding Energy - mRNA 1.78024 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 188 -- 196@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 44 -- 50@LB@
11	0.002274	0.593	b1476	fdnI	-10.73	0.029150	152 -- 175	44 -- 69	formate dehydrogenase-N cytochrome B556 (gamma) subunit nitrate-inducible		_____________151________________________176\n_____________\|__________________________\|\n5'-CGU...ACUAC____G______________UA_____GUGGA...UUU-3'\n______________AUCG_UAUUGGCCCG__AA__AGGAA\n______________\|\|\|\|_\|\|\|\|\|\|\|\|\|\|__\|\|__\|\|\|\|\|\n______________UAGC_AUAACCGGGC__UU__UCCUU\n3'-UUU...GGUUA____G__________AG__UC_____AAAGU...ACA-5'\n_____________\|__________________________\|\n_____________70_________________________43\n	160 -- 166	55 -- 61	-29.2423 kcal/mol	7.20098 kcal/mol	11.3099 kcal/mol	151 176@LB@ \| \|@LB@5'-CGU...ACUAC G UA GUGGA...UUU-3'@LB@ AUCG UAUUGGCCCG AA AGGAA@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|\| \|\| \|\|\|\|\|@LB@ UAGC AUAACCGGGC UU UCCUU@LB@3'-UUU...GGUUA G AG UC AAAGU...ACA-5'@LB@ \| \|@LB@ 70 43@LB@@LB@@LB@Energy -10.73 kcal/mol@LB@Hybridization Energy -29.2423 kcal/mol@LB@Unfolding Energy - mRNA 7.20098 kcal/mol@LB@Unfolding Energy - sRNA 11.3099 kcal/mol@LB@@LB@Position - mRNA 152 -- 175@LB@Position - sRNA 44 -- 69@LB@Position Seed - mRNA 160 -- 166@LB@Position Seed - sRNA 55 -- 61@LB@
10	0.001925	0.593	b2910	zapA	-12.97	0.010115	44 -- 65	38 -- 56	FtsZ stabilizer		_____________43_____________________66\n_____________\|______________________\|\n5'-GUU...UUCGU______AG________A_____GAUAU...AUC-3'\n______________CGUCAA__GGAGGAAU_UUCAU\n______________\|\|\|\|\|\|__:\|\|\|\|\|\|\|_\|\|\|\|\|\n______________GCAGUU__UCUCCUUA_AAGUA\n3'-UUU...ACCGG______________________AAAAA...ACA-5'\n_____________\|______________________\|\n_____________57_____________________37\n	53 -- 59	43 -- 49	-19.9082 kcal/mol	5.76295 kcal/mol	1.17918 kcal/mol	43 66@LB@ \| \|@LB@5'-GUU...UUCGU AG A GAUAU...AUC-3'@LB@ CGUCAA GGAGGAAU UUCAU@LB@ \|\|\|\|\|\| :\|\|\|\|\|\|\| \|\|\|\|\|@LB@ GCAGUU UCUCCUUA AAGUA@LB@3'-UUU...ACCGG AAAAA...ACA-5'@LB@ \| \|@LB@ 57 37@LB@@LB@@LB@Energy -12.97 kcal/mol@LB@Hybridization Energy -19.9082 kcal/mol@LB@Unfolding Energy - mRNA 5.76295 kcal/mol@LB@Unfolding Energy - sRNA 1.17918 kcal/mol@LB@@LB@Position - mRNA 44 -- 65@LB@Position - sRNA 38 -- 56@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 43 -- 49@LB@
108	0.0217	0.6177	b0243	proA	-8.76	0.073409	183 -- 193	47 -- 57	gamma-glutamylphosphate reductase		_____________182_________194\n_____________\|___________\|\n5'-AAU...AUUAC___________CAGGC...AUG-3'\n______________CCGUUAAGGAG\n______________\|\|\|\|:\|\|:\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	187 -- 193	47 -- 53	-14.7866 kcal/mol	3.29159 kcal/mol	2.73556 kcal/mol	182 194@LB@ \| \|@LB@5'-AAU...AUUAC CAGGC...AUG-3'@LB@ CCGUUAAGGAG@LB@ \|\|\|\|:\|\|:\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -14.7866 kcal/mol@LB@Unfolding Energy - mRNA 3.29159 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 183 -- 193@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 47 -- 53@LB@
140	0.02703	0.6177	b3447	ggt	-5.41	0.319095	66 -- 81	38 -- 54	gamma-glutamyltranspeptidase		_____________65________________82\n_____________\|_________________\|\n5'-GUU...AAGAA________UC_______CGCGU...CGU-3'\n______________UCAGA_AG__GUUUCAU\n______________\|\|\|:\|_\|\|__:\|\|\|\|\|\|\n______________AGUUU_UC__UAAAGUA\n3'-UUU...CGGGC_____C__CU_______AAAAA...ACA-5'\n_____________\|_________________\|\n_____________55________________37\n	75 -- 81	38 -- 44	-8.61894 kcal/mol	2.03989 kcal/mol	1.17036 kcal/mol	65 82@LB@ \| \|@LB@5'-GUU...AAGAA UC CGCGU...CGU-3'@LB@ UCAGA AG GUUUCAU@LB@ \|\|\|:\| \|\| :\|\|\|\|\|\|@LB@ AGUUU UC UAAAGUA@LB@3'-UUU...CGGGC C CU AAAAA...ACA-5'@LB@ \| \|@LB@ 55 37@LB@@LB@@LB@Energy -5.41 kcal/mol@LB@Hybridization Energy -8.61894 kcal/mol@LB@Unfolding Energy - mRNA 2.03989 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 66 -- 81@LB@Position - sRNA 38 -- 54@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 38 -- 44@LB@
200	0.04173	0.6177	b3155	yhbQ	-7.74	0.117248	9 -- 16	50 -- 57	GIY-YIG nuclease superfamily protein		_____________8________17\n_____________\|________\|\n___5'-UUUUUCUU________AUGUA...GCG-3'\n______________CCGUCAAA\n______________\|\|\|\|\|\|\|\|\n______________GGCAGUUU\n3'-UUU...AACCG________CUCCU...ACA-5'\n_____________\|________\|\n_____________58_______49\n	10 -- 16	50 -- 56	-10.5697 kcal/mol	0.110673 kcal/mol	2.72137 kcal/mol	8 17@LB@ \| \|@LB@ 5'-UUUUUCUU AUGUA...GCG-3'@LB@ CCGUCAAA@LB@ \|\|\|\|\|\|\|\|@LB@ GGCAGUUU@LB@3'-UUU...AACCG CUCCU...ACA-5'@LB@ \| \|@LB@ 58 49@LB@@LB@@LB@Energy -7.74 kcal/mol@LB@Hybridization Energy -10.5697 kcal/mol@LB@Unfolding Energy - mRNA 0.110673 kcal/mol@LB@Unfolding Energy - sRNA 2.72137 kcal/mol@LB@@LB@Position - mRNA 9 -- 16@LB@Position - sRNA 50 -- 57@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 50 -- 56@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@
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@

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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