Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
89	0.002377	0.09395	b4136	dsbD	-10.47	0.032769	211 -- 231	1 -- 22	thiol:disulfide interchange protein and activator of DsbC	_____________210____________________232\n_____________\|______________________\|\n5'-UGC...UCAAC_______UA_G___________UACUU...CGG-3'\n______________GCAUCUU__C_CUG_AUCCUGC\n______________:\|\|\|\|\|\|__\|_\|\|\|_\|:\|\|\|:\|\n______________UGUAGAA__G_GAC_UGGGAUG\n3'-AUU...UAUCU_______UG_A___A_______-5'\n_____________\|_____________________\|\n_____________23____________________1\n	225 -- 231	1 -- 7	-23.5098 kcal/mol	5.0672 kcal/mol	7.99236 kcal/mol	210 232@LB@ \| \|@LB@5'-UGC...UCAAC UA G UACUU...CGG-3'@LB@ GCAUCUU C CUG AUCCUGC@LB@ :\|\|\|\|\|\| \| \|\|\| \|:\|\|\|:\|@LB@ UGUAGAA G GAC UGGGAUG@LB@3'-AUU...UAUCU UG A A -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.47 kcal/mol@LB@Hybridization Energy -23.5098 kcal/mol@LB@Unfolding Energy - mRNA 5.0672 kcal/mol@LB@Unfolding Energy - sRNA 7.99236 kcal/mol@LB@@LB@Position - mRNA 211 -- 231@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 1 -- 7@LB@
28	0.0002139	0.02687	b4174	hflK	-10.82	0.025576	125 -- 140	42 -- 58	modulator for HflB protease specific for phage lambda cII repressor	_____________124_______________141\n_____________\|_________________\|\n5'-AGA...GUAGC______A__________CAUAU...GUC-3'\n______________GUCUGA__GCGUGGAGU\n______________:\|\|:\|\|__:\|\|\|\|:\|\|\|\n______________UAGGCU__UGCACUUCA\n3'-AUU...CGGUU______AA_________UUUUC...AUG-5'\n_____________\|_________________\|\n_____________59________________41\n	134 -- 140	42 -- 48	-18.0833 kcal/mol	3.99428 kcal/mol	3.27972 kcal/mol	124 141@LB@ \| \|@LB@5'-AGA...GUAGC A CAUAU...GUC-3'@LB@ GUCUGA GCGUGGAGU@LB@ :\|\|:\|\| :\|\|\|\|:\|\|\|@LB@ UAGGCU UGCACUUCA@LB@3'-AUU...CGGUU AA UUUUC...AUG-5'@LB@ \| \|@LB@ 59 41@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -18.0833 kcal/mol@LB@Unfolding Energy - mRNA 3.99428 kcal/mol@LB@Unfolding Energy - sRNA 3.27972 kcal/mol@LB@@LB@Position - mRNA 125 -- 140@LB@Position - sRNA 42 -- 58@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 42 -- 48@LB@
155	0.00623	0.1406	b4178	nsrR	-8.53	0.114937	220 -- 228	48 -- 56	nitric oxide-sensitive repressor for NO regulon	_____________219_______229\n_____________\|_________\|\n5'-GGU...UUUCA_________GAUUA...ACG-3'\n______________CUGAUUACG\n______________\|:\|\|\|\|\|\|\|\n______________GGCUAAUGC\n3'-AUU...GUUUA_________ACUUC...AUG-5'\n_____________\|_________\|\n_____________57________47\n	222 -- 228	48 -- 54	-11.8869 kcal/mol	1.78283 kcal/mol	1.55919 kcal/mol	219 229@LB@ \| \|@LB@5'-GGU...UUUCA GAUUA...ACG-3'@LB@ CUGAUUACG@LB@ \|:\|\|\|\|\|\|\|@LB@ GGCUAAUGC@LB@3'-AUU...GUUUA ACUUC...AUG-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -8.53 kcal/mol@LB@Hybridization Energy -11.8869 kcal/mol@LB@Unfolding Energy - mRNA 1.78283 kcal/mol@LB@Unfolding Energy - sRNA 1.55919 kcal/mol@LB@@LB@Position - mRNA 220 -- 228@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 48 -- 54@LB@
185	0.008247	0.1556	b4195	ulaC	-8.57	0.111851	181 -- 191	40 -- 50	L-ascorbate-specific enzyme IIA component of PTS	_____________180_________192\n_____________\|___________\|\n5'-GCG...GCAGG___________GGACG...UGG-3'\n______________AUGUGAAGUAA\n______________\|:\|\|\|\|\|\|\|\|\|\n______________UGCACUUCAUU\n3'-AUU...GCUAA___________UUCCA...AUG-5'\n_____________\|___________\|\n_____________51__________39\n	185 -- 191	40 -- 46	-13.163 kcal/mol	1.2893 kcal/mol	3.32158 kcal/mol	180 192@LB@ \| \|@LB@5'-GCG...GCAGG GGACG...UGG-3'@LB@ AUGUGAAGUAA@LB@ \|:\|\|\|\|\|\|\|\|\|@LB@ UGCACUUCAUU@LB@3'-AUU...GCUAA UUCCA...AUG-5'@LB@ \| \|@LB@ 51 39@LB@@LB@@LB@Energy -8.57 kcal/mol@LB@Hybridization Energy -13.163 kcal/mol@LB@Unfolding Energy - mRNA 1.2893 kcal/mol@LB@Unfolding Energy - sRNA 3.32158 kcal/mol@LB@@LB@Position - mRNA 181 -- 191@LB@Position - sRNA 40 -- 50@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 40 -- 46@LB@
159	0.006413	0.1413	b4242	mgtA	-7.15	0.243258	247 -- 262	45 -- 58	magnesium transporter	_____________246______________263\n_____________\|________________\|\n5'-GGU...UUCCC________CAU_____UCCAU...UGG-3'\n______________GUCUGGUU___CGUGA\n______________:\|\|:\|:\|\|___\|\|\|\|\|\n______________UAGGCUAA___GCACU\n3'-AUU...CGGUU________U_______UCAUU...AUG-5'\n_____________\|________________\|\n_____________59_______________44\n	248 -- 254	51 -- 57	-12.639 kcal/mol	3.2244 kcal/mol	2.28003 kcal/mol	246 263@LB@ \| \|@LB@5'-GGU...UUCCC CAU UCCAU...UGG-3'@LB@ GUCUGGUU CGUGA@LB@ :\|\|:\|:\|\| \|\|\|\|\|@LB@ UAGGCUAA GCACU@LB@3'-AUU...CGGUU U UCAUU...AUG-5'@LB@ \| \|@LB@ 59 44@LB@@LB@@LB@Energy -7.15 kcal/mol@LB@Hybridization Energy -12.639 kcal/mol@LB@Unfolding Energy - mRNA 3.2244 kcal/mol@LB@Unfolding Energy - sRNA 2.28003 kcal/mol@LB@@LB@Position - mRNA 247 -- 262@LB@Position - sRNA 45 -- 58@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 51 -- 57@LB@
43	0.0004631	0.03766	b4346	mcrB	-12.47	0.007188	270 -- 300	1 -- 31	5-methylcytosine-specific restriction enzyme McrBC subunit McrB	_____________269_______________________________300\n_____________\|_________________________________\|\n5'-UUU...CCACU______UAUCC_________________A_____-3'\n______________AAAGAU_____AACGUCUUACC___GUA_CCUGC\n______________\|\|\|\|\|\|_____\|\|\|:\|\|\|\|\|\|\|___\|\|\|_\|\|\|:\|\n______________UUUCUA_____UUGUAGAAUGG___CAU_GGAUG\n3'-AUU...CAGAC______UC______________AGA___G_____-5'\n_____________\|_________________________________\|\n_____________32________________________________1\n	285 -- 291	13 -- 19	-24.3421 kcal/mol	3.83264 kcal/mol	8.05889 kcal/mol	269 300@LB@ \| \|@LB@5'-UUU...CCACU UAUCC A -3'@LB@ AAAGAU AACGUCUUACC GUA CCUGC@LB@ \|\|\|\|\|\| \|\|\|:\|\|\|\|\|\|\| \|\|\| \|\|\|:\|@LB@ UUUCUA UUGUAGAAUGG CAU GGAUG@LB@3'-AUU...CAGAC UC AGA G -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -12.47 kcal/mol@LB@Hybridization Energy -24.3421 kcal/mol@LB@Unfolding Energy - mRNA 3.83264 kcal/mol@LB@Unfolding Energy - sRNA 8.05889 kcal/mol@LB@@LB@Position - mRNA 270 -- 300@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 13 -- 19@LB@
184	0.00812	0.1553	b4371	rsmC	-7.50	0.203534	191 -- 216	4 -- 25	16S rRNA m(2)G1207 methyltransferase SAM-dependent	_____________190________________________217\n_____________\|__________________________\|\n5'-AUC...AUUGA________CC__G____CAUU_____CGGCA...UGC-3'\n______________GGAGCAUU__AU_UCUG____UACCC\n______________:\|\|:\|\|\|:__\|:_\|\|\|\|____\|\|\|\|\|\n______________UCUUGUAG__UG_AGAC____AUGGG\n3'-AUU...UUCUA________AA__G_____________AUG-5'\n_____________\|__________________________\|\n_____________26_________________________3\n	192 -- 198	18 -- 24	-20.5319 kcal/mol	5.03265 kcal/mol	8.0209 kcal/mol	190 217@LB@ \| \|@LB@5'-AUC...AUUGA CC G CAUU CGGCA...UGC-3'@LB@ GGAGCAUU AU UCUG UACCC@LB@ :\|\|:\|\|\|: \|: \|\|\|\| \|\|\|\|\|@LB@ UCUUGUAG UG AGAC AUGGG@LB@3'-AUU...UUCUA AA G AUG-5'@LB@ \| \|@LB@ 26 3@LB@@LB@@LB@Energy -7.50 kcal/mol@LB@Hybridization Energy -20.5319 kcal/mol@LB@Unfolding Energy - mRNA 5.03265 kcal/mol@LB@Unfolding Energy - sRNA 8.0209 kcal/mol@LB@@LB@Position - mRNA 191 -- 216@LB@Position - sRNA 4 -- 25@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 18 -- 24@LB@
91	0.002527	0.0977	b4393	trpR	-12.48	0.007130	9 -- 21	43 -- 55	transcriptional repressor tryptophan-binding	_____________8_____________22\n_____________\|_____________\|\n___5'-GAGACGCG_____________AACGU...AUC-3'\n______________CGGUUAUGUGAAG\n______________\|\|:\|\|\|:\|\|\|\|\|\|\n______________GCUAAUGCACUUC\n3'-AUU...UUUAG_____________AUUUU...AUG-5'\n_____________\|_____________\|\n_____________56____________42\n	15 -- 21	43 -- 49	-16.824 kcal/mol	1.08541 kcal/mol	3.2693 kcal/mol	8 22@LB@ \| \|@LB@ 5'-GAGACGCG AACGU...AUC-3'@LB@ CGGUUAUGUGAAG@LB@ \|\|:\|\|\|:\|\|\|\|\|\|@LB@ GCUAAUGCACUUC@LB@3'-AUU...UUUAG AUUUU...AUG-5'@LB@ \| \|@LB@ 56 42@LB@@LB@@LB@Energy -12.48 kcal/mol@LB@Hybridization Energy -16.824 kcal/mol@LB@Unfolding Energy - mRNA 1.08541 kcal/mol@LB@Unfolding Energy - sRNA 3.2693 kcal/mol@LB@@LB@Position - mRNA 9 -- 21@LB@Position - sRNA 43 -- 55@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 43 -- 49@LB@
199	0.008811	0.1558	b4515	cydX	-11.13	0.020449	151 -- 184	5 -- 31	cytochrome d (bd-I) ubiquinol oxidase subunit X	_____________150________________________________185\n_____________\|__________________________________\|\n5'-ACC...CCAAA_______UU______AAC___CACUC________AAGUA...GUC-3'\n______________GAAGAUA__GAACGU___ACC_____UCUGUACU\n______________:\|\|\|\|\|\|__\|\|\|\|:\|___\|\|\|_____\|\|\|\|\|\|\|:\n______________UUUCUAU__CUUGUA___UGG_____AGACAUGG\n3'-AUU...CAGAC_______________GAA________________GAUG-5'\n_____________\|__________________________________\|\n_____________32_________________________________4\n	178 -- 184	5 -- 11	-22.8813 kcal/mol	3.72257 kcal/mol	8.05162 kcal/mol	150 185@LB@ \| \|@LB@5'-ACC...CCAAA UU AAC CACUC AAGUA...GUC-3'@LB@ GAAGAUA GAACGU ACC UCUGUACU@LB@ :\|\|\|\|\|\| \|\|\|\|:\| \|\|\| \|\|\|\|\|\|\|:@LB@ UUUCUAU CUUGUA UGG AGACAUGG@LB@3'-AUU...CAGAC GAA GAUG-5'@LB@ \| \|@LB@ 32 4@LB@@LB@@LB@Energy -11.13 kcal/mol@LB@Hybridization Energy -22.8813 kcal/mol@LB@Unfolding Energy - mRNA 3.72257 kcal/mol@LB@Unfolding Energy - sRNA 8.05162 kcal/mol@LB@@LB@Position - mRNA 151 -- 184@LB@Position - sRNA 5 -- 31@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 5 -- 11@LB@
178	0.007695	0.1511	b4567	yjjZ	-7.25	0.231371	185 -- 218	2 -- 33	uncharacterized protein	_____________184_________________________________219\n_____________\|___________________________________\|\n5'-CGG...AUCAA_______GAU___AU___G____AA______G___GGCAG...GGA-3'\n______________UGAAAGA___GAA__CAU_UUGC__C_GUAC_CUG\n______________\|\|\|\|\|\|\|___\|\|\|__\|\|\|_\|\|:\|__\|_\|\|\|\|_\|\|:\n______________ACUUUCU___CUU__GUA_AAUG__G_CAUG_GAU\n3'-AUU...UCCAG_______AU_________G____GA_A____G___G-5'\n_____________\|___________________________________\|\n_____________34__________________________________1\n	185 -- 191	27 -- 33	-22.8177 kcal/mol	6.54395 kcal/mol	9.04499 kcal/mol	184 219@LB@ \| \|@LB@5'-CGG...AUCAA GAU AU G AA G GGCAG...GGA-3'@LB@ UGAAAGA GAA CAU UUGC C GUAC CUG@LB@ \|\|\|\|\|\|\| \|\|\| \|\|\| \|\|:\| \| \|\|\|\| \|\|:@LB@ ACUUUCU CUU GUA AAUG G CAUG GAU@LB@3'-AUU...UCCAG AU G GA A G G-5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -7.25 kcal/mol@LB@Hybridization Energy -22.8177 kcal/mol@LB@Unfolding Energy - mRNA 6.54395 kcal/mol@LB@Unfolding Energy - sRNA 9.04499 kcal/mol@LB@@LB@Position - mRNA 185 -- 218@LB@Position - sRNA 2 -- 33@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 27 -- 33@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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