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
186	0.02184	0.3768	b1256	ompW	-5.92	0.201836	13 -- 38	30 -- 57	outer membrane protein W	_____________12___________________________39\n_____________\|____________________________\|\n5'-GAC...UUAAU______GU______A_____________UUGAU...CUG-3'\n______________AUUUGC___AGCGA_AA_UAUUUAAAAA\n______________\|:\|\|\|\|___\|\|\|:\|_\|\|_:\|:\|\|\|\|\|\|\|\n______________UGAACG___UCGUU_UU_GUGAAUUUUU\n3'-UUU...UACUU______AAU_____C__C__________UAAGC...CAA-5'\n_____________\|____________________________\|\n_____________58___________________________29\n	32 -- 38	30 -- 36	-16.1426 kcal/mol	3.99952 kcal/mol	6.22352 kcal/mol	12 39@LB@ \| \|@LB@5'-GAC...UUAAU GU A UUGAU...CUG-3'@LB@ AUUUGC AGCGA AA UAUUUAAAAA@LB@ \|:\|\|\|\| \|\|\|:\| \|\| :\|:\|\|\|\|\|\|\|@LB@ UGAACG UCGUU UU GUGAAUUUUU@LB@3'-UUU...UACUU AAU C C UAAGC...CAA-5'@LB@ \| \|@LB@ 58 29@LB@@LB@@LB@Energy -5.92 kcal/mol@LB@Hybridization Energy -16.1426 kcal/mol@LB@Unfolding Energy - mRNA 3.99952 kcal/mol@LB@Unfolding Energy - sRNA 6.22352 kcal/mol@LB@@LB@Position - mRNA 13 -- 38@LB@Position - sRNA 30 -- 57@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 30 -- 36@LB@
10	0.0001005	0.03239	b1260	trpA	-10.26	0.013526	184 -- 203	5 -- 22	tryptophan synthase alpha subunit	_____________183__________________204\n_____________\|____________________\|\n5'-GCC...UGAAA____GAG_____________GAACG...CAU-3'\n______________GCAC___GGGAAAUCUGAUG\n______________:\|\|\|___:\|\|\|\|\|\|\|\|\|\|\|\|\n______________UGUG___UCCUUUAGACUAC\n3'-UUU...AGCAA____G_______________ACAA-5'\n_____________\|____________________\|\n_____________23___________________4\n	192 -- 198	10 -- 16	-23.1901 kcal/mol	5.35202 kcal/mol	7.57357 kcal/mol	183 204@LB@ \| \|@LB@5'-GCC...UGAAA GAG GAACG...CAU-3'@LB@ GCAC GGGAAAUCUGAUG@LB@ :\|\|\| :\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UGUG UCCUUUAGACUAC@LB@3'-UUU...AGCAA G ACAA-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -10.26 kcal/mol@LB@Hybridization Energy -23.1901 kcal/mol@LB@Unfolding Energy - mRNA 5.35202 kcal/mol@LB@Unfolding Energy - sRNA 7.57357 kcal/mol@LB@@LB@Position - mRNA 184 -- 203@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 10 -- 16@LB@
79	0.005218	0.2128	b1264	trpE	-7.84	0.066605	225 -- 250	34 -- 59	component I of anthranilate synthase	_____________224__________________________251\n_____________\|____________________________\|\n5'-UGU...CUCUC_________AACCU______________UCGCG...CGG-3'\n______________GAAC_UGCU_____GCGA_AGGCGCUUA\n______________:\|\|\|_\|\|\|\|_____\|\|:\|_\|:\|\|:\|\|\|\|\n______________UUUG_ACGA_____CGUU_UUCGUGAAU\n3'-UUU...CCUAC____A____AUU______C_________UUUUU...CAA-5'\n_____________\|____________________________\|\n_____________60___________________________33\n	244 -- 250	34 -- 40	-20.2106 kcal/mol	6.10702 kcal/mol	6.26371 kcal/mol	224 251@LB@ \| \|@LB@5'-UGU...CUCUC AACCU UCGCG...CGG-3'@LB@ GAAC UGCU GCGA AGGCGCUUA@LB@ :\|\|\| \|\|\|\| \|\|:\| \|:\|\|:\|\|\|\|@LB@ UUUG ACGA CGUU UUCGUGAAU@LB@3'-UUU...CCUAC A AUU C UUUUU...CAA-5'@LB@ \| \|@LB@ 60 33@LB@@LB@@LB@Energy -7.84 kcal/mol@LB@Hybridization Energy -20.2106 kcal/mol@LB@Unfolding Energy - mRNA 6.10702 kcal/mol@LB@Unfolding Energy - sRNA 6.26371 kcal/mol@LB@@LB@Position - mRNA 225 -- 250@LB@Position - sRNA 34 -- 59@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 34 -- 40@LB@
192	0.02295	0.3851	b1282	yciH	-4.88	0.338940	8 -- 32	15 -- 33	initiation factor function partial mimic SUI1 family	_____________7_________________________33\n_____________\|_________________________\|\n____5'-UUCGGUC________AAACUG___________CAUUC...UGC-3'\n______________AGGAGUUC______GUUACGCCGGG\n______________\|::\|:\|\|\|______\|\|\|\|\|:\|\|:\|\|\n______________UUUUUAAG______CAAUGUGGUCC\n3'-UUU...UGAAU_________________________UUUAG...CAA-5'\n_____________\|_________________________\|\n_____________34________________________14\n	9 -- 15	26 -- 32	-19.9664 kcal/mol	6.44674 kcal/mol	8.63649 kcal/mol	7 33@LB@ \| \|@LB@ 5'-UUCGGUC AAACUG CAUUC...UGC-3'@LB@ AGGAGUUC GUUACGCCGGG@LB@ \|::\|:\|\|\| \|\|\|\|\|:\|\|:\|\|@LB@ UUUUUAAG CAAUGUGGUCC@LB@3'-UUU...UGAAU UUUAG...CAA-5'@LB@ \| \|@LB@ 34 14@LB@@LB@@LB@Energy -4.88 kcal/mol@LB@Hybridization Energy -19.9664 kcal/mol@LB@Unfolding Energy - mRNA 6.44674 kcal/mol@LB@Unfolding Energy - sRNA 8.63649 kcal/mol@LB@@LB@Position - mRNA 8 -- 32@LB@Position - sRNA 15 -- 33@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 26 -- 32@LB@
94	0.006975	0.2379	b1284	yciT	-8.66	0.039674	34 -- 64	15 -- 42	global regulator of transcription; DeoR family	_____________33_______________________________65\n_____________\|________________________________\|\n5'-GCA...AUCUC___A________GCA___C_____________UUGCU...CCA-3'\n______________GAG_UACUUAAA___GAA_UC_UUGCGCCAGG\n______________:\|\|_:\|\|\|\|\|\|\|___:\|\|_\|\|_\|\|:\|:\|\|\|\|\|\n______________UUC_GUGAAUUU___UUU_AG_AAUGUGGUCC\n3'-UUU...CGUUC__________________A__C__________UUUAG...CAA-5'\n_____________\|________________________________\|\n_____________43_______________________________14\n	58 -- 64	15 -- 21	-23.4161 kcal/mol	5.55126 kcal/mol	9.20431 kcal/mol	33 65@LB@ \| \|@LB@5'-GCA...AUCUC A GCA C UUGCU...CCA-3'@LB@ GAG UACUUAAA GAA UC UUGCGCCAGG@LB@ :\|\| :\|\|\|\|\|\|\| :\|\| \|\| \|\|:\|:\|\|\|\|\|@LB@ UUC GUGAAUUU UUU AG AAUGUGGUCC@LB@3'-UUU...CGUUC A C UUUAG...CAA-5'@LB@ \| \|@LB@ 43 14@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -23.4161 kcal/mol@LB@Unfolding Energy - mRNA 5.55126 kcal/mol@LB@Unfolding Energy - sRNA 9.20431 kcal/mol@LB@@LB@Position - mRNA 34 -- 64@LB@Position - sRNA 15 -- 42@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 15 -- 21@LB@
62	0.00332	0.1645	b1305	pspB	-5.29	0.278747	189 -- 201	34 -- 46	psp operon transcription co-activator	_____________188___________202\n_____________\|_____________\|\n5'-AUU...UCGUC_____________UGAGC...GUG-3'\n______________UAAGGAGUACUUA\n______________:\|\|\|:\|\|:\|\|\|\|\|\n______________GUUCUUCGUGAAU\n3'-UUU...AAUUC_____________UUUUU...CAA-5'\n_____________\|_____________\|\n_____________47____________33\n	195 -- 201	34 -- 40	-14.7021 kcal/mol	3.41245 kcal/mol	5.99897 kcal/mol	188 202@LB@ \| \|@LB@5'-AUU...UCGUC UGAGC...GUG-3'@LB@ UAAGGAGUACUUA@LB@ :\|\|\|:\|\|:\|\|\|\|\|@LB@ GUUCUUCGUGAAU@LB@3'-UUU...AAUUC UUUUU...CAA-5'@LB@ \| \|@LB@ 47 33@LB@@LB@@LB@Energy -5.29 kcal/mol@LB@Hybridization Energy -14.7021 kcal/mol@LB@Unfolding Energy - mRNA 3.41245 kcal/mol@LB@Unfolding Energy - sRNA 5.99897 kcal/mol@LB@@LB@Position - mRNA 189 -- 201@LB@Position - sRNA 34 -- 46@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 34 -- 40@LB@
91	0.006547	0.2317	b1323	tyrR	-8.26	0.051378	202 -- 222	3 -- 23	aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase	_____________201___________________223\n_____________\|_____________________\|\n5'-UCG...UCCCA______U________UU____AAGAC...UUG-3'\n______________UGCGUC_GGAAGUCU__UGUG\n______________\|:\|::\|_\|\|\|\|:\|\|\|__\|\|\|\|\n______________AUGUGG_CCUUUAGA__ACAC\n3'-UUU...AAGCA______U________CU____AA-5'\n_____________\|_____________________\|\n_____________24____________________2\n	209 -- 215	10 -- 16	-19.6247 kcal/mol	3.79223 kcal/mol	7.5769 kcal/mol	201 223@LB@ \| \|@LB@5'-UCG...UCCCA U UU AAGAC...UUG-3'@LB@ UGCGUC GGAAGUCU UGUG@LB@ \|:\|::\| \|\|\|\|:\|\|\| \|\|\|\|@LB@ AUGUGG CCUUUAGA ACAC@LB@3'-UUU...AAGCA U CU AA-5'@LB@ \| \|@LB@ 24 2@LB@@LB@@LB@Energy -8.26 kcal/mol@LB@Hybridization Energy -19.6247 kcal/mol@LB@Unfolding Energy - mRNA 3.79223 kcal/mol@LB@Unfolding Energy - sRNA 7.5769 kcal/mol@LB@@LB@Position - mRNA 202 -- 222@LB@Position - sRNA 3 -- 23@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 10 -- 16@LB@
82	0.005534	0.2146	b1342	ydaN	-6.57	0.141434	180 -- 206	30 -- 54	putative Zn(II) transporter	_____________179_________________________207\n_____________\|___________________________\|\n5'-CGU...AAUAA___G____U_AU_________GU____GCGAU...AUG-3'\n______________UGC_UUGA_G__GGAGGCACU__GGAA\n______________\|\|\|_\|\|:\|_\|__:\|\|:\|\|\|\|\|__::\|\|\n______________ACG_AAUU_C__UCUUCGUGA__UUUU\n3'-UUU...UUUGA__________GU_________AU____UAAGC...CAA-5'\n_____________\|___________________________\|\n_____________55__________________________29\n	194 -- 200	36 -- 42	-19.056 kcal/mol	6.29262 kcal/mol	6.19579 kcal/mol	179 207@LB@ \| \|@LB@5'-CGU...AAUAA G U AU GU GCGAU...AUG-3'@LB@ UGC UUGA G GGAGGCACU GGAA@LB@ \|\|\| \|\|:\| \| :\|\|:\|\|\|\|\| ::\|\|@LB@ ACG AAUU C UCUUCGUGA UUUU@LB@3'-UUU...UUUGA GU AU UAAGC...CAA-5'@LB@ \| \|@LB@ 55 29@LB@@LB@@LB@Energy -6.57 kcal/mol@LB@Hybridization Energy -19.056 kcal/mol@LB@Unfolding Energy - mRNA 6.29262 kcal/mol@LB@Unfolding Energy - sRNA 6.19579 kcal/mol@LB@@LB@Position - mRNA 180 -- 206@LB@Position - sRNA 30 -- 54@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 36 -- 42@LB@
80	0.005376	0.2146	b1520	yneE	-6.66	0.134465	278 -- 284	34 -- 40	bestrophin family putative inner membrane protein	_____________277_____285\n_____________\|_______\|\n5'-CGU...UCCUC_______CUACU...UCU-3'\n______________GCGCUUA\n______________\|\|:\|\|\|\|\n______________CGUGAAU\n3'-UUU...UUCUU_______UUUUU...CAA-5'\n_____________\|_______\|\n_____________41______33\n	278 -- 284	34 -- 40	-8.65652 kcal/mol	0.386276 kcal/mol	1.61352 kcal/mol	277 285@LB@ \| \|@LB@5'-CGU...UCCUC CUACU...UCU-3'@LB@ GCGCUUA@LB@ \|\|:\|\|\|\|@LB@ CGUGAAU@LB@3'-UUU...UUCUU UUUUU...CAA-5'@LB@ \| \|@LB@ 41 33@LB@@LB@@LB@Energy -6.66 kcal/mol@LB@Hybridization Energy -8.65652 kcal/mol@LB@Unfolding Energy - mRNA 0.386276 kcal/mol@LB@Unfolding Energy - sRNA 1.61352 kcal/mol@LB@@LB@Position - mRNA 278 -- 284@LB@Position - sRNA 34 -- 40@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 34 -- 40@LB@
138	0.01322	0.3087	b1523	yneG	-4.22	0.452951	267 -- 281	24 -- 41	DUF4186 family protein	_____________266________________282\n_____________\|__________________\|\n5'-AUG...GUCUG_____________G____CAGUA...AAG-3'\n______________GGCA__UGAAAGA__CGU\n______________:\|\|\|__\|:\|\|\|:\|__\|\|\|\n______________UCGU__AUUUUUU__GCA\n3'-UUU...GUUCU____GA_______AA___AUGUG...CAA-5'\n_____________\|__________________\|\n_____________42_________________23\n	271 -- 277	29 -- 35	-8.58312 kcal/mol	2.71204 kcal/mol	1.64881 kcal/mol	266 282@LB@ \| \|@LB@5'-AUG...GUCUG G CAGUA...AAG-3'@LB@ GGCA UGAAAGA CGU@LB@ :\|\|\| \|:\|\|\|:\| \|\|\|@LB@ UCGU AUUUUUU GCA@LB@3'-UUU...GUUCU GA AA AUGUG...CAA-5'@LB@ \| \|@LB@ 42 23@LB@@LB@@LB@Energy -4.22 kcal/mol@LB@Hybridization Energy -8.58312 kcal/mol@LB@Unfolding Energy - mRNA 2.71204 kcal/mol@LB@Unfolding Energy - sRNA 1.64881 kcal/mol@LB@@LB@Position - mRNA 267 -- 281@LB@Position - sRNA 24 -- 41@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 29 -- 35@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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