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
40	0.007925	0.6129	b1109	ndh	-7.04	0.160101	187 -- 195	46 -- 54	respiratory NADH dehydrogenase 2/cupric reductase	_____________186_______196\n_____________\|_________\|\n5'-UGU...UAAAU_________UCACG...AAG-3'\n______________UUAAGGGGG\n______________\|:\|\|:\|:\|\|\n______________AGUUUCUCC\n3'-UUU...CGGGC_________UUAAA...ACA-5'\n_____________\|_________\|\n_____________55________45\n	189 -- 195	46 -- 52	-9.48398 kcal/mol	1.51964 kcal/mol	0.922697 kcal/mol	186 196@LB@ \| \|@LB@5'-UGU...UAAAU UCACG...AAG-3'@LB@ UUAAGGGGG@LB@ \|:\|\|:\|:\|\|@LB@ AGUUUCUCC@LB@3'-UUU...CGGGC UUAAA...ACA-5'@LB@ \| \|@LB@ 55 45@LB@@LB@@LB@Energy -7.04 kcal/mol@LB@Hybridization Energy -9.48398 kcal/mol@LB@Unfolding Energy - mRNA 1.51964 kcal/mol@LB@Unfolding Energy - sRNA 0.922697 kcal/mol@LB@@LB@Position - mRNA 187 -- 195@LB@Position - sRNA 46 -- 54@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 46 -- 52@LB@
12	0.002398	0.593	b1114	mfd	-13.52	0.007793	210 -- 241	45 -- 73	transcription-repair coupling factor	_____________209______________________________242\n_____________\|________________________________\|\n5'-UUC...CUGAA____________ACGCU___________C___UGAGC...AAA-3'\n______________CAAUAUCGUUAU_____GCCCGUCAAAG_GGG\n______________\|\|\|\|\|\|\|\|:\|\|\|_____\|\|\|\|\|\|\|\|\|\|\|_\|\|:\n______________GUUAUAGCGAUA_____CGGGCAGUUUC_CCU\n3'-UUU...UACCG____________AC______________U___UAAAG...ACA-5'\n_____________\|________________________________\|\n_____________74_______________________________44\n	231 -- 237	49 -- 55	-37.142 kcal/mol	12.2919 kcal/mol	11.3343 kcal/mol	209 242@LB@ \| \|@LB@5'-UUC...CUGAA ACGCU C UGAGC...AAA-3'@LB@ CAAUAUCGUUAU GCCCGUCAAAG GGG@LB@ \|\|\|\|\|\|\|\|:\|\|\| \|\|\|\|\|\|\|\|\|\|\| \|\|:@LB@ GUUAUAGCGAUA CGGGCAGUUUC CCU@LB@3'-UUU...UACCG AC U UAAAG...ACA-5'@LB@ \| \|@LB@ 74 44@LB@@LB@@LB@Energy -13.52 kcal/mol@LB@Hybridization Energy -37.142 kcal/mol@LB@Unfolding Energy - mRNA 12.2919 kcal/mol@LB@Unfolding Energy - sRNA 11.3343 kcal/mol@LB@@LB@Position - mRNA 210 -- 241@LB@Position - sRNA 45 -- 73@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 49 -- 55@LB@
122	0.02427	0.6177	b1116	lolC	-7.56	0.127136	206 -- 233	55 -- 74	lipoprotein-releasing system transmembrane protein	_____________205__________________________234\n_____________\|____________________________\|\n5'-GUA...AUGUA____CC_______CUAUUU_________CGUUA...GCA-3'\n______________CCAA__UGUCGCU______AUUGGCCUG\n______________\|\|\|\|__\|:\|\|\|\|\|______\|\|\|\|\|\|\|:\|\n______________GGUU__AUAGCGA______UAACCGGGC\n3'-UUU...UUACC____________________________AGUUU...ACA-5'\n_____________\|____________________________\|\n_____________75___________________________54\n	212 -- 218	64 -- 70	-24.394 kcal/mol	5.52374 kcal/mol	11.3119 kcal/mol	205 234@LB@ \| \|@LB@5'-GUA...AUGUA CC CUAUUU CGUUA...GCA-3'@LB@ CCAA UGUCGCU AUUGGCCUG@LB@ \|\|\|\| \|:\|\|\|\|\| \|\|\|\|\|\|\|:\|@LB@ GGUU AUAGCGA UAACCGGGC@LB@3'-UUU...UUACC AGUUU...ACA-5'@LB@ \| \|@LB@ 75 54@LB@@LB@@LB@Energy -7.56 kcal/mol@LB@Hybridization Energy -24.394 kcal/mol@LB@Unfolding Energy - mRNA 5.52374 kcal/mol@LB@Unfolding Energy - sRNA 11.3119 kcal/mol@LB@@LB@Position - mRNA 206 -- 233@LB@Position - sRNA 55 -- 74@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 64 -- 70@LB@
146	0.02871	0.6177	b1120	cobB	-8.56	0.080407	32 -- 40	43 -- 51	deacetylase of acs and cheY chemotaxis regulator	_____________31________41\n_____________\|_________\|\n5'-CGC...GAUGC_________GCGUG...AUC-3'\n______________GGGAGGAAU\n______________::\|\|\|\|\|\|\|\n______________UUCUCCUUA\n3'-UUU...GCAGU_________AAGUA...ACA-5'\n_____________\|_________\|\n_____________52________42\n	34 -- 40	43 -- 49	-11.3695 kcal/mol	1.94725 kcal/mol	0.859837 kcal/mol	31 41@LB@ \| \|@LB@5'-CGC...GAUGC GCGUG...AUC-3'@LB@ GGGAGGAAU@LB@ ::\|\|\|\|\|\|\|@LB@ UUCUCCUUA@LB@3'-UUU...GCAGU AAGUA...ACA-5'@LB@ \| \|@LB@ 52 42@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -11.3695 kcal/mol@LB@Unfolding Energy - mRNA 1.94725 kcal/mol@LB@Unfolding Energy - sRNA 0.859837 kcal/mol@LB@@LB@Position - mRNA 32 -- 40@LB@Position - sRNA 43 -- 51@LB@Position Seed - mRNA 34 -- 40@LB@Position Seed - sRNA 43 -- 49@LB@
134	0.02619	0.6177	b1126	potA	-9.47	0.052791	285 -- 299	37 -- 55	spermidine/putrescine ABC transporter ATPase	_____________284_________________300\n_____________\|___________________\|\n5'-CAA...UUGAU_GU________________C-3'\n______________G__AAAGAGG____UCAUU\n______________\|__\|\|\|\|\|\|\|____\|\|\|\|\|\n______________C__UUUCUCC____AGUAA\n3'-UUU...CCGGG_AG_______UUAA_____AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________36\n	288 -- 294	46 -- 52	-11.4861 kcal/mol	0.840334 kcal/mol	1.17789 kcal/mol	284 300@LB@ \| \|@LB@5'-CAA...UUGAU GU C-3'@LB@ G AAAGAGG UCAUU@LB@ \| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ C UUUCUCC AGUAA@LB@3'-UUU...CCGGG AG UUAA AAAAA...ACA-5'@LB@ \| \|@LB@ 56 36@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -11.4861 kcal/mol@LB@Unfolding Energy - mRNA 0.840334 kcal/mol@LB@Unfolding Energy - sRNA 1.17789 kcal/mol@LB@@LB@Position - mRNA 285 -- 299@LB@Position - sRNA 37 -- 55@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 46 -- 52@LB@
49	0.009604	0.6129	b1175	minD	-8.49	0.083180	191 -- 199	40 -- 48	inhibitor of FtsZ ring polymerization; chromosome-membrane tethering protein; membrane ATPase of the MinCDEE system	_____________190_______200\n_____________\|_________\|\n5'-CUG...UAACA_________UAUGG...AAA-3'\n______________AGGAAUUUC\n______________\|\|\|\|\|\|\|\|\|\n______________UCCUUAAAG\n3'-UUU...GUUUC_________UAAAA...ACA-5'\n_____________\|_________\|\n_____________49________39\n	193 -- 199	40 -- 46	-11.0161 kcal/mol	1.62901 kcal/mol	0.898161 kcal/mol	190 200@LB@ \| \|@LB@5'-CUG...UAACA UAUGG...AAA-3'@LB@ AGGAAUUUC@LB@ \|\|\|\|\|\|\|\|\|@LB@ UCCUUAAAG@LB@3'-UUU...GUUUC UAAAA...ACA-5'@LB@ \| \|@LB@ 49 39@LB@@LB@@LB@Energy -8.49 kcal/mol@LB@Hybridization Energy -11.0161 kcal/mol@LB@Unfolding Energy - mRNA 1.62901 kcal/mol@LB@Unfolding Energy - sRNA 0.898161 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 40 -- 48@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 40 -- 46@LB@
193	0.04043	0.6177	b1180	ycgM	-6.42	0.210248	289 -- 296	47 -- 54	putative isomerase/hydrolase	_____________288______297\n_____________\|________\|\n5'-GAU...ACAUA________AUGG-3'\n______________UUAAAGAG\n______________\|:\|\|\|\|\|\|\n______________AGUUUCUC\n3'-UUU...CGGGC________CUUAA...ACA-5'\n_____________\|________\|\n_____________55_______46\n	290 -- 296	47 -- 53	-7.63974 kcal/mol	0.325787 kcal/mol	0.897871 kcal/mol	288 297@LB@ \| \|@LB@5'-GAU...ACAUA AUGG-3'@LB@ UUAAAGAG@LB@ \|:\|\|\|\|\|\|@LB@ AGUUUCUC@LB@3'-UUU...CGGGC CUUAA...ACA-5'@LB@ \| \|@LB@ 55 46@LB@@LB@@LB@Energy -6.42 kcal/mol@LB@Hybridization Energy -7.63974 kcal/mol@LB@Unfolding Energy - mRNA 0.325787 kcal/mol@LB@Unfolding Energy - sRNA 0.897871 kcal/mol@LB@@LB@Position - mRNA 289 -- 296@LB@Position - sRNA 47 -- 54@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 47 -- 53@LB@
197	0.04129	0.6177	b1205	ychH	-8.72	0.074776	153 -- 162	43 -- 52	DUF2583 family putative inner membrane protein	_____________152________163\n_____________\|__________\|\n5'-CAA...AUAAG__________AUUCC...UAC-3'\n______________GAAGAGGGGU\n______________:\|\|\|\|\|\|::\|\n______________UUUCUCCUUA\n3'-UUU...GGCAG__________AAGUA...ACA-5'\n_____________\|__________\|\n_____________53_________42\n	156 -- 162	43 -- 49	-11.7568 kcal/mol	2.17132 kcal/mol	0.865937 kcal/mol	152 163@LB@ \| \|@LB@5'-CAA...AUAAG AUUCC...UAC-3'@LB@ GAAGAGGGGU@LB@ :\|\|\|\|\|\|::\|@LB@ UUUCUCCUUA@LB@3'-UUU...GGCAG AAGUA...ACA-5'@LB@ \| \|@LB@ 53 42@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -11.7568 kcal/mol@LB@Unfolding Energy - mRNA 2.17132 kcal/mol@LB@Unfolding Energy - sRNA 0.865937 kcal/mol@LB@@LB@Position - mRNA 153 -- 162@LB@Position - sRNA 43 -- 52@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 43 -- 49@LB@
173	0.03478	0.6177	b1234	rssA	-4.70	0.418234	181 -- 188	43 -- 50	putative patatin-like family phospholipase	_____________180______189\n_____________\|________\|\n5'-GAU...AUUCC________CUUGC...AAA-3'\n______________AGGGGAAU\n______________\|\|:\|\|\|\|\|\n______________UCUCCUUA\n3'-UUU...CAGUU________AAGUA...ACA-5'\n_____________\|________\|\n_____________51_______42\n	182 -- 188	43 -- 49	-9.05148 kcal/mol	3.5051 kcal/mol	0.845564 kcal/mol	180 189@LB@ \| \|@LB@5'-GAU...AUUCC CUUGC...AAA-3'@LB@ AGGGGAAU@LB@ \|\|:\|\|\|\|\|@LB@ UCUCCUUA@LB@3'-UUU...CAGUU AAGUA...ACA-5'@LB@ \| \|@LB@ 51 42@LB@@LB@@LB@Energy -4.70 kcal/mol@LB@Hybridization Energy -9.05148 kcal/mol@LB@Unfolding Energy - mRNA 3.5051 kcal/mol@LB@Unfolding Energy - sRNA 0.845564 kcal/mol@LB@@LB@Position - mRNA 181 -- 188@LB@Position - sRNA 43 -- 50@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 43 -- 49@LB@
163	0.03345	0.6177	b1235	rssB	-5.20	0.346272	186 -- 195	44 -- 55	PcnB-degradosome interaction factor; response regulator	_____________185__________196\n_____________\|____________\|\n5'-AAU...AGCCA____________AGAAC...CAA-3'\n______________GUC__AGGGGAG\n______________\|\|\|__\|\|:\|\|\|:\n______________CAG__UCUCCUU\n3'-UUU...CCGGG___UU_______AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	189 -- 195	44 -- 50	-10.1709 kcal/mol	4.02871 kcal/mol	0.941432 kcal/mol	185 196@LB@ \| \|@LB@5'-AAU...AGCCA AGAAC...CAA-3'@LB@ GUC AGGGGAG@LB@ \|\|\| \|\|:\|\|\|:@LB@ CAG UCUCCUU@LB@3'-UUU...CCGGG UU AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -5.20 kcal/mol@LB@Hybridization Energy -10.1709 kcal/mol@LB@Unfolding Energy - mRNA 4.02871 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 186 -- 195@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@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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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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