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
58	0.01235	0.6177	b3903	rhaA	-9.27	0.057813	267 -- 276	46 -- 55	L-rhamnose isomerase		_____________266________277\n_____________\|__________\|\n5'-GCC...UUGAU__________CGCUG...UAC-3'\n______________GUCGAGGAGG\n______________\|\|\|:\|:\|\|\|\|\n______________CAGUUUCUCC\n3'-UUU...CCGGG__________UUAAA...ACA-5'\n_____________\|__________\|\n_____________56_________45\n	270 -- 276	46 -- 52	-15.3197 kcal/mol	5.12197 kcal/mol	0.924411 kcal/mol	266 277@LB@ \| \|@LB@5'-GCC...UUGAU CGCUG...UAC-3'@LB@ GUCGAGGAGG@LB@ \|\|\|:\|:\|\|\|\|@LB@ CAGUUUCUCC@LB@3'-UUU...CCGGG UUAAA...ACA-5'@LB@ \| \|@LB@ 56 45@LB@@LB@@LB@Energy -9.27 kcal/mol@LB@Hybridization Energy -15.3197 kcal/mol@LB@Unfolding Energy - mRNA 5.12197 kcal/mol@LB@Unfolding Energy - sRNA 0.924411 kcal/mol@LB@@LB@Position - mRNA 267 -- 276@LB@Position - sRNA 46 -- 55@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 46 -- 52@LB@
36	0.007218	0.6129	b3938	metJ	-9.22	0.059290	181 -- 189	45 -- 53	transcriptional repressor S-adenosylmethionine-binding		_____________180_______190\n_____________\|_________\|\n5'-UCU...AUUGA_________UUAAG...UGU-3'\n______________CGAAGAGGA\n______________\|:\|\|\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	183 -- 189	45 -- 51	-12.478 kcal/mol	2.34125 kcal/mol	0.917553 kcal/mol	180 190@LB@ \| \|@LB@5'-UCU...AUUGA UUAAG...UGU-3'@LB@ CGAAGAGGA@LB@ \|:\|\|\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.22 kcal/mol@LB@Hybridization Energy -12.478 kcal/mol@LB@Unfolding Energy - mRNA 2.34125 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 181 -- 189@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 45 -- 51@LB@
167	0.03387	0.6177	b3980	tufB	-7.70	0.119070	183 -- 194	44 -- 55	translation elongation factor EF-Tu 2	b3339	_____________182__________195\n_____________\|____________\|\n5'-UCC...UCCGU___UU_______CAAUC...CUA-3'\n______________GUC__AGAGGGA\n______________\|\|\|__\|\|\|\|\|:\|\n______________CAG__UCUCCUU\n3'-UUU...CCGGG___UU_______AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	188 -- 194	44 -- 50	-14.3886 kcal/mol	5.74361 kcal/mol	0.941432 kcal/mol	182 195@LB@ \| \|@LB@5'-UCC...UCCGU UU CAAUC...CUA-3'@LB@ GUC AGAGGGA@LB@ \|\|\| \|\|\|\|\|:\|@LB@ CAG UCUCCUU@LB@3'-UUU...CCGGG UU AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -7.70 kcal/mol@LB@Hybridization Energy -14.3886 kcal/mol@LB@Unfolding Energy - mRNA 5.74361 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 183 -- 194@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
165	0.0337	0.6177	b3983	rplK	-8.80	0.071896	189 -- 197	41 -- 49	50S ribosomal subunit protein L11		_____________188_______198\n_____________\|_________\|\n5'-ACC...AACUU_________AUAAU...UAA-3'\n______________GAGGAAUUU\n______________\|\|\|\|\|\|\|\|\|\n______________CUCCUUAAA\n3'-UUU...AGUUU_________GUAAA...ACA-5'\n_____________\|_________\|\n_____________50________40\n	191 -- 197	41 -- 47	-11.4231 kcal/mol	1.76644 kcal/mol	0.852225 kcal/mol	188 198@LB@ \| \|@LB@5'-ACC...AACUU AUAAU...UAA-3'@LB@ GAGGAAUUU@LB@ \|\|\|\|\|\|\|\|\|@LB@ CUCCUUAAA@LB@3'-UUU...AGUUU GUAAA...ACA-5'@LB@ \| \|@LB@ 50 40@LB@@LB@@LB@Energy -8.80 kcal/mol@LB@Hybridization Energy -11.4231 kcal/mol@LB@Unfolding Energy - mRNA 1.76644 kcal/mol@LB@Unfolding Energy - sRNA 0.852225 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 41 -- 49@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 41 -- 47@LB@
52	0.01005	0.6177	b3985	rplJ	-10.76	0.028819	17 -- 26	48 -- 57	50S ribosomal subunit protein L10		_____________16_________27\n_____________\|__________\|\n5'-UGG...GGCCU__________CCGCA...UAA-3'\n______________CCGUCGAAGA\n______________\|\|\|\|\|:\|\|\|\|\n______________GGCAGUUUCU\n3'-UUU...AACCG__________CCUUA...ACA-5'\n_____________\|__________\|\n_____________58_________47\n	20 -- 26	48 -- 54	-14.4896 kcal/mol	0.999171 kcal/mol	2.73483 kcal/mol	16 27@LB@ \| \|@LB@5'-UGG...GGCCU CCGCA...UAA-3'@LB@ CCGUCGAAGA@LB@ \|\|\|\|\|:\|\|\|\|@LB@ GGCAGUUUCU@LB@3'-UUU...AACCG CCUUA...ACA-5'@LB@ \| \|@LB@ 58 47@LB@@LB@@LB@Energy -10.76 kcal/mol@LB@Hybridization Energy -14.4896 kcal/mol@LB@Unfolding Energy - mRNA 0.999171 kcal/mol@LB@Unfolding Energy - sRNA 2.73483 kcal/mol@LB@@LB@Position - mRNA 17 -- 26@LB@Position - sRNA 48 -- 57@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 48 -- 54@LB@
100	0.01963	0.6177	b4001	yjaH	-9.93	0.042585	215 -- 230	39 -- 53	DUF1481 family putative lipoprotein		_____________214______________231\n_____________\|________________\|\n5'-UGG...UUUAA________U_______CCCCU...AUA-3'\n______________CGAAGGGG_GGUUUCA\n______________\|:\|\|\|:\|\|_::\|\|\|\|\|\n______________GUUUCUCC_UUAAAGU\n3'-UUU...GGGCA________________AAAAA...ACA-5'\n_____________\|________________\|\n_____________54_______________38\n	216 -- 222	46 -- 52	-15.2589 kcal/mol	4.19806 kcal/mol	1.13439 kcal/mol	214 231@LB@ \| \|@LB@5'-UGG...UUUAA U CCCCU...AUA-3'@LB@ CGAAGGGG GGUUUCA@LB@ \|:\|\|\|:\|\| ::\|\|\|\|\|@LB@ GUUUCUCC UUAAAGU@LB@3'-UUU...GGGCA AAAAA...ACA-5'@LB@ \| \|@LB@ 54 38@LB@@LB@@LB@Energy -9.93 kcal/mol@LB@Hybridization Energy -15.2589 kcal/mol@LB@Unfolding Energy - mRNA 4.19806 kcal/mol@LB@Unfolding Energy - sRNA 1.13439 kcal/mol@LB@@LB@Position - mRNA 215 -- 230@LB@Position - sRNA 39 -- 53@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 46 -- 52@LB@
70	0.01448	0.6177	b4012	yjaB	-8.12	0.098308	234 -- 242	44 -- 52	GNAT-family putative N-acetyltransferase; acetyl coenzyme A-binding protein		_____________233_______243\n_____________\|_________\|\n5'-AAG...AUGAG_________GAACU...CAG-3'\n______________GAAGGGGAG\n______________:\|\|\|:\|\|\|:\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	236 -- 242	44 -- 50	-9.78668 kcal/mol	0.80114 kcal/mol	0.860683 kcal/mol	233 243@LB@ \| \|@LB@5'-AAG...AUGAG GAACU...CAG-3'@LB@ GAAGGGGAG@LB@ :\|\|\|:\|\|\|:@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -9.78668 kcal/mol@LB@Unfolding Energy - mRNA 0.80114 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 234 -- 242@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 44 -- 50@LB@
62	0.01306	0.6177	b4034	malE	-9.62	0.049140	112 -- 120	45 -- 53	maltose transporter subunit		_____________111_______121\n_____________\|_________\|\n5'-AGG...AGGGG_________UGGAA...UGG-3'\n______________CAAGGAGGA\n______________\|\|\|:\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	114 -- 120	45 -- 51	-12.5673 kcal/mol	2.02865 kcal/mol	0.917553 kcal/mol	111 121@LB@ \| \|@LB@5'-AGG...AGGGG UGGAA...UGG-3'@LB@ CAAGGAGGA@LB@ \|\|\|:\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.62 kcal/mol@LB@Hybridization Energy -12.5673 kcal/mol@LB@Unfolding Energy - mRNA 2.02865 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 112 -- 120@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 45 -- 51@LB@
166	0.03384	0.6177	b4035	malK	-4.35	0.473183	186 -- 196	44 -- 53	maltose ABC transportor ATPase		_____________185_________197\n_____________\|___________\|\n5'-CGC...UGUUA_______A___GGGCA...UGU-3'\n______________CAAAGGG_GAA\n______________\|\|\|\|\|:\|_\|\|\|\n______________GUUUCUC_CUU\n3'-UUU...GGGCA___________AAAGU...ACA-5'\n_____________\|___________\|\n_____________54__________43\n	186 -- 192	47 -- 53	-9.12531 kcal/mol	3.84302 kcal/mol	0.927997 kcal/mol	185 197@LB@ \| \|@LB@5'-CGC...UGUUA A GGGCA...UGU-3'@LB@ CAAAGGG GAA@LB@ \|\|\|\|\|:\| \|\|\|@LB@ GUUUCUC CUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -4.35 kcal/mol@LB@Hybridization Energy -9.12531 kcal/mol@LB@Unfolding Energy - mRNA 3.84302 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 186 -- 196@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 47 -- 53@LB@
136	0.02642	0.6177	b4036	lamB	-8.19	0.095416	26 -- 54	55 -- 84	maltose outer membrane porin (maltoporin)		_____________25_____________________________55\n_____________\|______________________________\|\n5'-CGC...GGUAG_____________CAU_______C______CCGCC...GUU-3'\n______________AAGAAGGU_GCCA___UCGCUAU_GGCCUG\n______________\|\|:\|\|::\|_\|\|\|\|___\|\|\|\|\|\|\|_\|\|\|\|:\|\n______________UUUUUUUA_CGGU___AGCGAUA_CCGGGC\n___________3'-________C____UAU_______A______AGUUU...ACA-5'\n______________\|_____________________________\|\n______________84____________________________54\n	41 -- 47	62 -- 68	-32.2235 kcal/mol	10.7352 kcal/mol	13.2983 kcal/mol	25 55@LB@ \| \|@LB@5'-CGC...GGUAG CAU C CCGCC...GUU-3'@LB@ AAGAAGGU GCCA UCGCUAU GGCCUG@LB@ \|\|:\|\|::\| \|\|\|\| \|\|\|\|\|\|\| \|\|\|\|:\|@LB@ UUUUUUUA CGGU AGCGAUA CCGGGC@LB@ 3'- C UAU A AGUUU...ACA-5'@LB@ \| \|@LB@ 84 54@LB@@LB@@LB@Energy -8.19 kcal/mol@LB@Hybridization Energy -32.2235 kcal/mol@LB@Unfolding Energy - mRNA 10.7352 kcal/mol@LB@Unfolding Energy - sRNA 13.2983 kcal/mol@LB@@LB@Position - mRNA 26 -- 54@LB@Position - sRNA 55 -- 84@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 62 -- 68@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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