Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
141	0.01363	0.3114	b0767	pgl	-6.62	0.137481	178 -- 199	36 -- 55	6-phosphogluconolactonase	_____________177____________________200\n_____________\|______________________\|\n5'-UCA...GUCAG_____A__U__A__________CAUGA...AUG-3'\n______________UUGCU_AA_GC_AAGGAGCAUU\n______________\|\|\|\|\|_\|\|_\|\|_\|\|\|:\|\|\|\|:\|\n______________AACGA_UU_CG_UUCUUCGUGA\n3'-UUU...CUUUG_____A________________AUUUU...CAA-5'\n_____________\|______________________\|\n_____________56_____________________35\n	193 -- 199	36 -- 42	-19.0667 kcal/mol	6.27112 kcal/mol	6.17795 kcal/mol	177 200@LB@ \| \|@LB@5'-UCA...GUCAG A U A CAUGA...AUG-3'@LB@ UUGCU AA GC AAGGAGCAUU@LB@ \|\|\|\|\| \|\| \|\| \|\|\|:\|\|\|\|:\|@LB@ AACGA UU CG UUCUUCGUGA@LB@3'-UUU...CUUUG A AUUUU...CAA-5'@LB@ \| \|@LB@ 56 35@LB@@LB@@LB@Energy -6.62 kcal/mol@LB@Hybridization Energy -19.0667 kcal/mol@LB@Unfolding Energy - mRNA 6.27112 kcal/mol@LB@Unfolding Energy - sRNA 6.17795 kcal/mol@LB@@LB@Position - mRNA 178 -- 199@LB@Position - sRNA 36 -- 55@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 36 -- 42@LB@
142	0.01375	0.3119	b4166	queG	-9.76	0.019130	257 -- 284	36 -- 60	epoxyqueuosine reductase cobalamine-stimulated; queosine biosynthesis	_____________256__________________________285\n_____________\|____________________________\|\n5'-CGC...GGGCU______GG____UC______U_______ACCGA...UCA-3'\n______________GGAACU__GCUU__AGCAGG_AGGUAUU\n______________\|:\|\|\|\|__\|\|\|\|__\|\|\|\|:\|_\|:\|:\|:\|\n______________CUUUGA__CGAA__UCGUUC_UUCGUGA\n3'-UUU...CCCUA______A_____U_______________AUUUU...CAA-5'\n_____________\|____________________________\|\n_____________61___________________________35\n	278 -- 284	36 -- 42	-22.8123 kcal/mol	6.80174 kcal/mol	6.24973 kcal/mol	256 285@LB@ \| \|@LB@5'-CGC...GGGCU GG UC U ACCGA...UCA-3'@LB@ GGAACU GCUU AGCAGG AGGUAUU@LB@ \|:\|\|\|\| \|\|\|\| \|\|\|\|:\| \|:\|:\|:\|@LB@ CUUUGA CGAA UCGUUC UUCGUGA@LB@3'-UUU...CCCUA A U AUUUU...CAA-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -9.76 kcal/mol@LB@Hybridization Energy -22.8123 kcal/mol@LB@Unfolding Energy - mRNA 6.80174 kcal/mol@LB@Unfolding Energy - sRNA 6.24973 kcal/mol@LB@@LB@Position - mRNA 257 -- 284@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 36 -- 42@LB@
143	0.01412	0.3181	b0642	leuS	-6.82	0.122159	244 -- 266	37 -- 58	leucyl-tRNA synthetase	_____________243_____________________267\n_____________\|_______________________\|\n5'-AAU...AGUAC_____CA_____A__________ACAUU...AGA-3'\n______________AGCUU__UUGGG_UGAGAAGCGC\n______________\|:\|\|\|__\|\|::\|_::\|\|\|\|\|\|:\|\n______________UUGAA__AAUUC_GUUCUUCGUG\n3'-UUU...CUACU_____CG________________AAUUU...CAA-5'\n_____________\|_______________________\|\n_____________59______________________36\n	260 -- 266	37 -- 43	-20.1861 kcal/mol	7.11823 kcal/mol	6.24354 kcal/mol	243 267@LB@ \| \|@LB@5'-AAU...AGUAC CA A ACAUU...AGA-3'@LB@ AGCUU UUGGG UGAGAAGCGC@LB@ \|:\|\|\| \|\|::\| ::\|\|\|\|\|\|:\|@LB@ UUGAA AAUUC GUUCUUCGUG@LB@3'-UUU...CUACU CG AAUUU...CAA-5'@LB@ \| \|@LB@ 59 36@LB@@LB@@LB@Energy -6.82 kcal/mol@LB@Hybridization Energy -20.1861 kcal/mol@LB@Unfolding Energy - mRNA 7.11823 kcal/mol@LB@Unfolding Energy - sRNA 6.24354 kcal/mol@LB@@LB@Position - mRNA 244 -- 266@LB@Position - sRNA 37 -- 58@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 37 -- 43@LB@
144	0.01453	0.3231	b3614	yibQ	-4.49	0.404320	261 -- 267	34 -- 40	putative polysaccharide deacetylase	_____________260_____268\n_____________\|_______\|\n5'-UGG...CCCCC_______CUGGC...UUG-3'\n______________GUACUUG\n______________\|:\|\|\|\|:\n______________CGUGAAU\n3'-UUU...UUCUU_______UUUUU...CAA-5'\n_____________\|_______\|\n_____________41______33\n	261 -- 267	34 -- 40	-7.10274 kcal/mol	0.998159 kcal/mol	1.61352 kcal/mol	260 268@LB@ \| \|@LB@5'-UGG...CCCCC CUGGC...UUG-3'@LB@ GUACUUG@LB@ \|:\|\|\|\|:@LB@ CGUGAAU@LB@3'-UUU...UUCUU UUUUU...CAA-5'@LB@ \| \|@LB@ 41 33@LB@@LB@@LB@Energy -4.49 kcal/mol@LB@Hybridization Energy -7.10274 kcal/mol@LB@Unfolding Energy - mRNA 0.998159 kcal/mol@LB@Unfolding Energy - sRNA 1.61352 kcal/mol@LB@@LB@Position - mRNA 261 -- 267@LB@Position - sRNA 34 -- 40@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 34 -- 40@LB@
145	0.01456	0.3231	b1529	marC	-5.50	0.250589	206 -- 227	39 -- 59	UPF0056 family inner membrane protein	_____________205____________________228\n_____________\|______________________\|\n5'-UGG...AUGUU__________A______UU___CUGGG...GCA-3'\n______________AGAUUUGUUU_AAGCAA__GGC\n______________\|:\|:\|\|\|:\|\|_\|\|\|\|\|\|__:\|\|\n______________UUUGAACGAA_UUCGUU__UCG\n3'-UUU...CCUAC_________________CU___UGAAU...CAA-5'\n_____________\|______________________\|\n_____________60_____________________38\n	207 -- 213	52 -- 58	-17.1508 kcal/mol	5.49588 kcal/mol	6.15149 kcal/mol	205 228@LB@ \| \|@LB@5'-UGG...AUGUU A UU CUGGG...GCA-3'@LB@ AGAUUUGUUU AAGCAA GGC@LB@ \|:\|:\|\|\|:\|\| \|\|\|\|\|\| :\|\|@LB@ UUUGAACGAA UUCGUU UCG@LB@3'-UUU...CCUAC CU UGAAU...CAA-5'@LB@ \| \|@LB@ 60 38@LB@@LB@@LB@Energy -5.50 kcal/mol@LB@Hybridization Energy -17.1508 kcal/mol@LB@Unfolding Energy - mRNA 5.49588 kcal/mol@LB@Unfolding Energy - sRNA 6.15149 kcal/mol@LB@@LB@Position - mRNA 206 -- 227@LB@Position - sRNA 39 -- 59@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 52 -- 58@LB@
146	0.01469	0.3231	b0026	ileS	-7.82	0.067581	147 -- 206	2 -- 59	isoleucyl-tRNA synthetase	_____________146_____________________________________________________________207\n_____________\|_______________________________________________________________\|\n5'-AUG...UAACA____CG________CU_UUAU___AUCAAACC_____A__GA______A___________A__GACUA...CUG-3'\n______________AAAC__GCUUAAGC__G____GUA________GAAAU_CG____ACCG__GAAUCUGAUG_GU\n______________\|\|\|\|__\|\|\|\|\|\|\|\|__\|____\|:\|________:\|\|\|\|_\|\|____\|\|\|:__:\|\|\|\|\|\|\|\|\|_\|\|\n______________UUUG__CGAAUUCG__C____CGU________UUUUA_GC____UGGU__UUUAGACUAC_CA\n3'-UUU...CCUAC____AA________UU_UU_____GAAUU________A__AAUG____CC__________A__A-5'\n_____________\|_______________________________________________________________\|\n_____________60______________________________________________________________1\n	197 -- 203	5 -- 11	-33.6314 kcal/mol	11.9684 kcal/mol	13.8468 kcal/mol	146 207@LB@ \| \|@LB@5'-AUG...UAACA CG CU UUAU AUCAAACC A GA A A GACUA...CUG-3'@LB@ AAAC GCUUAAGC G GUA GAAAU CG ACCG GAAUCUGAUG GU@LB@ \|\|\|\| \|\|\|\|\|\|\|\| \| \|:\| :\|\|\|\| \|\| \|\|\|: :\|\|\|\|\|\|\|\|\| \|\|@LB@ UUUG CGAAUUCG C CGU UUUUA GC UGGU UUUAGACUAC CA@LB@3'-UUU...CCUAC AA UU UU GAAUU A AAUG CC A A-5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -7.82 kcal/mol@LB@Hybridization Energy -33.6314 kcal/mol@LB@Unfolding Energy - mRNA 11.9684 kcal/mol@LB@Unfolding Energy - sRNA 13.8468 kcal/mol@LB@@LB@Position - mRNA 147 -- 206@LB@Position - sRNA 2 -- 59@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 5 -- 11@LB@
147	0.01475	0.3231	b0084	ftsI	-4.75	0.360226	157 -- 172	24 -- 39	transpeptidase involved in septal peptidoglycan synthesis; penicillin-binding protein 3	_____________156_______________173\n_____________\|_________________\|\n5'-GUU...UCCGU___A________A____AGUGC...UGG-3'\n______________CAC__AGAAAAU_UCGU\n______________\|\|\|__\|:\|\|\|\|\|_\|\|\|\|\n______________GUG__UUUUUUA_AGCA\n3'-UUU...UCUUC___AA____________AUGUG...CAA-5'\n_____________\|_________________\|\n_____________40________________23\n	161 -- 167	28 -- 34	-7.76704 kcal/mol	1.36905 kcal/mol	1.64726 kcal/mol	156 173@LB@ \| \|@LB@5'-GUU...UCCGU A A AGUGC...UGG-3'@LB@ CAC AGAAAAU UCGU@LB@ \|\|\| \|:\|\|\|\|\| \|\|\|\|@LB@ GUG UUUUUUA AGCA@LB@3'-UUU...UCUUC AA AUGUG...CAA-5'@LB@ \| \|@LB@ 40 23@LB@@LB@@LB@Energy -4.75 kcal/mol@LB@Hybridization Energy -7.76704 kcal/mol@LB@Unfolding Energy - mRNA 1.36905 kcal/mol@LB@Unfolding Energy - sRNA 1.64726 kcal/mol@LB@@LB@Position - mRNA 157 -- 172@LB@Position - sRNA 24 -- 39@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 28 -- 34@LB@
148	0.01496	0.3255	b2202	napC	-5.47	0.254772	189 -- 211	26 -- 46	quinol dehydrogenase electron source for NapAB	_____________188_____________________212\n_____________\|_______________________\|\n5'-ACG...GGAAA_______U____A__________UGACC...GUU-3'\n______________UAAGAGG_UAUU_UGGGAAAUUC\n______________:\|\|\|\|:\|_:\|:\|_\|:::\|\|\|\|\|\|\n______________GUUCUUC_GUGA_AUUUUUUAAG\n3'-UUU...AAUUC_______________________CAAUG...CAA-5'\n_____________\|_______________________\|\n_____________47______________________25\n	205 -- 211	26 -- 32	-14.2639 kcal/mol	2.66276 kcal/mol	6.13041 kcal/mol	188 212@LB@ \| \|@LB@5'-ACG...GGAAA U A UGACC...GUU-3'@LB@ UAAGAGG UAUU UGGGAAAUUC@LB@ :\|\|\|\|:\| :\|:\| \|:::\|\|\|\|\|\|@LB@ GUUCUUC GUGA AUUUUUUAAG@LB@3'-UUU...AAUUC CAAUG...CAA-5'@LB@ \| \|@LB@ 47 25@LB@@LB@@LB@Energy -5.47 kcal/mol@LB@Hybridization Energy -14.2639 kcal/mol@LB@Unfolding Energy - mRNA 2.66276 kcal/mol@LB@Unfolding Energy - sRNA 6.13041 kcal/mol@LB@@LB@Position - mRNA 189 -- 211@LB@Position - sRNA 26 -- 46@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 26 -- 32@LB@
149	0.01515	0.3274	b4196	ulaD	-9.50	0.022893	140 -- 153	36 -- 49	3-keto-L-gulonate 6-phosphate decarboxylase	_____________139____________154\n_____________\|______________\|\n5'-CGA...GUACC______________GGAUC...AAG-3'\n______________GAGCAGGAAGUACU\n______________:\|\|\|\|:\|\|\|\|:\|\|\|\n______________UUCGUUCUUCGUGA\n3'-UUU...ACGAA______________AUUUU...CAA-5'\n_____________\|______________\|\n_____________50_____________35\n	147 -- 153	36 -- 42	-21.0071 kcal/mol	5.47534 kcal/mol	6.03645 kcal/mol	139 154@LB@ \| \|@LB@5'-CGA...GUACC GGAUC...AAG-3'@LB@ GAGCAGGAAGUACU@LB@ :\|\|\|\|:\|\|\|\|:\|\|\|@LB@ UUCGUUCUUCGUGA@LB@3'-UUU...ACGAA AUUUU...CAA-5'@LB@ \| \|@LB@ 50 35@LB@@LB@@LB@Energy -9.50 kcal/mol@LB@Hybridization Energy -21.0071 kcal/mol@LB@Unfolding Energy - mRNA 5.47534 kcal/mol@LB@Unfolding Energy - sRNA 6.03645 kcal/mol@LB@@LB@Position - mRNA 140 -- 153@LB@Position - sRNA 36 -- 49@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 36 -- 42@LB@
150	0.01547	0.3321	b3736	atpF	-5.86	0.208717	262 -- 272	37 -- 47	F0 sector of membrane-bound ATP synthase subunit b	_____________261_________273\n_____________\|___________\|\n5'-AUU...GUUCU___U_______GUAUG...UCG-3'\n______________GCA_GAAGUAC\n______________\|\|\|_\|\|\|\|:\|\|\n______________CGU_CUUCGUG\n3'-UUU...GAAUU___U_______AAUUU...CAA-5'\n_____________\|___________\|\n_____________48__________36\n	266 -- 272	37 -- 43	-12.6044 kcal/mol	1.50868 kcal/mol	5.23944 kcal/mol	261 273@LB@ \| \|@LB@5'-AUU...GUUCU U GUAUG...UCG-3'@LB@ GCA GAAGUAC@LB@ \|\|\| \|\|\|\|:\|\|@LB@ CGU CUUCGUG@LB@3'-UUU...GAAUU U AAUUU...CAA-5'@LB@ \| \|@LB@ 48 36@LB@@LB@@LB@Energy -5.86 kcal/mol@LB@Hybridization Energy -12.6044 kcal/mol@LB@Unfolding Energy - mRNA 1.50868 kcal/mol@LB@Unfolding Energy - sRNA 5.23944 kcal/mol@LB@@LB@Position - mRNA 262 -- 272@LB@Position - sRNA 37 -- 47@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 37 -- 43@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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