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
194	0.02335	0.3864	b4182	yjfJ	-9.08	0.030148	209 -- 238	10 -- 37	PspA/IM30 family protein	_____________208____________________________239\n_____________\|______________________________\|\n5'-GAA...GGAAU____________AU______UG________GUUUA...AGC-3'\n______________UUUAAAAAGUUU__UUACGC__GGGAAAUC\n______________:\|\|\|\|\|\|\|:\|\|:__\|\|\|\|:\|__:\|\|\|\|\|\|\|\n______________GAAUUUUUUAAG__AAUGUG__UCCUUUAG\n3'-UUU...UUCGU____________C_______G_________ACUAC...CAA-5'\n_____________\|______________________________\|\n_____________38_____________________________9\n	232 -- 238	10 -- 16	-23.4786 kcal/mol	5.49388 kcal/mol	8.90309 kcal/mol	208 239@LB@ \| \|@LB@5'-GAA...GGAAU AU UG GUUUA...AGC-3'@LB@ UUUAAAAAGUUU UUACGC GGGAAAUC@LB@ :\|\|\|\|\|\|\|:\|\|: \|\|\|\|:\| :\|\|\|\|\|\|\|@LB@ GAAUUUUUUAAG AAUGUG UCCUUUAG@LB@3'-UUU...UUCGU C G ACUAC...CAA-5'@LB@ \| \|@LB@ 38 9@LB@@LB@@LB@Energy -9.08 kcal/mol@LB@Hybridization Energy -23.4786 kcal/mol@LB@Unfolding Energy - mRNA 5.49388 kcal/mol@LB@Unfolding Energy - sRNA 8.90309 kcal/mol@LB@@LB@Position - mRNA 209 -- 238@LB@Position - sRNA 10 -- 37@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 10 -- 16@LB@
184	0.02168	0.3768	b4380	yjjI	-6.70	0.131310	12 -- 49	9 -- 40	DUF3029 family protein putative glycine radical enzyme	_____________11________________________________________50\n_____________\|_________________________________________\|\n5'-ACA...ACUCC___ACACAC_______A_____AUCACAAUUA_________ACUUA...UGG-3'\n______________GCA_________UUCG_UACAC__________AGGAAAUCU\n______________\|\|\|_________\|\|\|\|_\|\|\|\|\|__________\|\|\|\|\|\|\|\|\|\n______________CGU_________AAGC_AUGUG__________UCCUUUAGA\n3'-UUU...UUCUU___GAAUUUUUU____A_____G__________________CUACACAA-5'\n_____________\|_________________________________________\|\n_____________41________________________________________8\n	43 -- 49	9 -- 15	-18.7623 kcal/mol	2.84333 kcal/mol	9.22063 kcal/mol	11 50@LB@ \| \|@LB@5'-ACA...ACUCC ACACAC A AUCACAAUUA ACUUA...UGG-3'@LB@ GCA UUCG UACAC AGGAAAUCU@LB@ \|\|\| \|\|\|\| \|\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ CGU AAGC AUGUG UCCUUUAGA@LB@3'-UUU...UUCUU GAAUUUUUU A G CUACACAA-5'@LB@ \| \|@LB@ 41 8@LB@@LB@@LB@Energy -6.70 kcal/mol@LB@Hybridization Energy -18.7623 kcal/mol@LB@Unfolding Energy - mRNA 2.84333 kcal/mol@LB@Unfolding Energy - sRNA 9.22063 kcal/mol@LB@@LB@Position - mRNA 12 -- 49@LB@Position - sRNA 9 -- 40@LB@Position Seed - mRNA 43 -- 49@LB@Position Seed - sRNA 9 -- 15@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@
160	0.01746	0.3504	b4542	yohO	-11.65	0.004993	133 -- 150	23 -- 41	putative membrane protein	_____________132_________________151\n_____________\|___________________\|\n5'-UCG...CACUC_________U_________AACAA...GUG-3'\n______________GGCAUUUAA__GAUUCGUU\n______________:\|\|\|:\|\|\|\|__:\|\|\|\|\|\|\|\n______________UCGUGAAUU__UUAAGCAA\n3'-UUU...GUUCU_________UU________UGUGG...CAA-5'\n_____________\|___________________\|\n_____________42__________________22\n	144 -- 150	23 -- 29	-16.4387 kcal/mol	3.13759 kcal/mol	1.64896 kcal/mol	132 151@LB@ \| \|@LB@5'-UCG...CACUC U AACAA...GUG-3'@LB@ GGCAUUUAA GAUUCGUU@LB@ :\|\|\|:\|\|\|\| :\|\|\|\|\|\|\|@LB@ UCGUGAAUU UUAAGCAA@LB@3'-UUU...GUUCU UU UGUGG...CAA-5'@LB@ \| \|@LB@ 42 22@LB@@LB@@LB@Energy -11.65 kcal/mol@LB@Hybridization Energy -16.4387 kcal/mol@LB@Unfolding Energy - mRNA 3.13759 kcal/mol@LB@Unfolding Energy - sRNA 1.64896 kcal/mol@LB@@LB@Position - mRNA 133 -- 150@LB@Position - sRNA 23 -- 41@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 23 -- 29@LB@
30	0.0008402	0.09021	b2792	yqcC	-12.92	0.001907	10 -- 25	38 -- 53	DUF446 family protein	_____________9________________26\n_____________\|________________\|\n5'-AUC...GGGUG__G_____________AUAGU...AAU-3'\n______________GU_UGAGCAGGAAGCA\n______________\|:_\|:\|\|\|\|:\|\|\|\|\|\|\n______________CG_AUUCGUUCUUCGU\n3'-UUU...UUGAA__A_____________GAAUU...CAA-5'\n_____________\|________________\|\n_____________54_______________37\n	19 -- 25	38 -- 44	-21.2799 kcal/mol	2.27149 kcal/mol	6.09301 kcal/mol	9 26@LB@ \| \|@LB@5'-AUC...GGGUG G AUAGU...AAU-3'@LB@ GU UGAGCAGGAAGCA@LB@ \|: \|:\|\|\|\|:\|\|\|\|\|\|@LB@ CG AUUCGUUCUUCGU@LB@3'-UUU...UUGAA A GAAUU...CAA-5'@LB@ \| \|@LB@ 54 37@LB@@LB@@LB@Energy -12.92 kcal/mol@LB@Hybridization Energy -21.2799 kcal/mol@LB@Unfolding Energy - mRNA 2.27149 kcal/mol@LB@Unfolding Energy - sRNA 6.09301 kcal/mol@LB@@LB@Position - mRNA 10 -- 25@LB@Position - sRNA 38 -- 53@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 38 -- 44@LB@
177	0.02045	0.3721	b3148	yraN	-6.85	0.120614	263 -- 276	37 -- 54	UPF0102 family protein	_____________262________________277\n_____________\|__________________\|\n5'-GGU...GGCGA__________________AAGCG...GCA-3'\n______________UGC____GUGGGAAGCAC\n______________\|\|\|____\|:::\|\|\|\|\|\|\|\n______________ACG____CGUUCUUCGUG\n3'-UUU...UUUGA___AAUU___________AAUUU...CAA-5'\n_____________\|__________________\|\n_____________55_________________36\n	270 -- 276	37 -- 43	-17.1481 kcal/mol	4.14332 kcal/mol	6.1584 kcal/mol	262 277@LB@ \| \|@LB@5'-GGU...GGCGA AAGCG...GCA-3'@LB@ UGC GUGGGAAGCAC@LB@ \|\|\| \|:::\|\|\|\|\|\|\|@LB@ ACG CGUUCUUCGUG@LB@3'-UUU...UUUGA AAUU AAUUU...CAA-5'@LB@ \| \|@LB@ 55 36@LB@@LB@@LB@Energy -6.85 kcal/mol@LB@Hybridization Energy -17.1481 kcal/mol@LB@Unfolding Energy - mRNA 4.14332 kcal/mol@LB@Unfolding Energy - sRNA 6.1584 kcal/mol@LB@@LB@Position - mRNA 263 -- 276@LB@Position - sRNA 37 -- 54@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 37 -- 43@LB@
44	0.001875	0.1369	b4485	ytfR	-11.10	0.007490	215 -- 227	10 -- 22	putative sugar ABC transporter ATPase	_____________214___________228\n_____________\|_____________\|\n5'-CCU...GACCA_____________CUCCG...GCC-3'\n______________ACACCAGGAGAUC\n______________\|\|\|\|\|\|\|\|\|:\|\|\|\n______________UGUGGUCCUUUAG\n3'-UUU...AGCAA_____________ACUAC...CAA-5'\n_____________\|_____________\|\n_____________23____________9\n	221 -- 227	10 -- 16	-21.5971 kcal/mol	2.94097 kcal/mol	7.55838 kcal/mol	214 228@LB@ \| \|@LB@5'-CCU...GACCA CUCCG...GCC-3'@LB@ ACACCAGGAGAUC@LB@ \|\|\|\|\|\|\|\|\|:\|\|\|@LB@ UGUGGUCCUUUAG@LB@3'-UUU...AGCAA ACUAC...CAA-5'@LB@ \| \|@LB@ 23 9@LB@@LB@@LB@Energy -11.10 kcal/mol@LB@Hybridization Energy -21.5971 kcal/mol@LB@Unfolding Energy - mRNA 2.94097 kcal/mol@LB@Unfolding Energy - sRNA 7.55838 kcal/mol@LB@@LB@Position - mRNA 215 -- 227@LB@Position - sRNA 10 -- 22@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 10 -- 16@LB@
101	0.007657	0.2442	b3928	zapB	-6.83	0.122013	220 -- 239	38 -- 54	FtsZ stabilizer septal ring assembly factor cell division stimulator	_____________219__________________240\n_____________\|____________________\|\n5'-UUU...AGAAG________AAACU_______AAAGU...AAG-3'\n______________UGUUUGAG_____GGAAGCA\n______________\|\|:\|\|:\|\|_____:\|\|\|\|\|\|\n______________ACGAAUUC_____UCUUCGU\n3'-UUU...UUUGA________GU__________GAAUU...CAA-5'\n_____________\|____________________\|\n_____________55___________________37\n	233 -- 239	38 -- 44	-16.6983 kcal/mol	3.7204 kcal/mol	6.15149 kcal/mol	219 240@LB@ \| \|@LB@5'-UUU...AGAAG AAACU AAAGU...AAG-3'@LB@ UGUUUGAG GGAAGCA@LB@ \|\|:\|\|:\|\| :\|\|\|\|\|\|@LB@ ACGAAUUC UCUUCGU@LB@3'-UUU...UUUGA GU GAAUU...CAA-5'@LB@ \| \|@LB@ 55 37@LB@@LB@@LB@Energy -6.83 kcal/mol@LB@Hybridization Energy -16.6983 kcal/mol@LB@Unfolding Energy - mRNA 3.7204 kcal/mol@LB@Unfolding Energy - sRNA 6.15149 kcal/mol@LB@@LB@Position - mRNA 220 -- 239@LB@Position - sRNA 38 -- 54@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 38 -- 44@LB@
199	0.02405	0.3893	b2412	zipA	-4.86	0.342002	121 -- 136	25 -- 40	FtsZ stabilizer	_____________120______________137\n_____________\|________________\|\n5'-CAG...CACUU__________UAA___GCAAA...CUU-3'\n______________GCACUUGAGG___UCG\n______________\|\|\|\|\|\|:\|::___\|\|\|\n______________CGUGAAUUUU___AGC\n3'-UUU...UUCUU__________UUA___AAUGU...CAA-5'\n_____________\|________________\|\n_____________41_______________24\n	124 -- 130	31 -- 37	-13.2366 kcal/mol	6.7246 kcal/mol	1.64821 kcal/mol	120 137@LB@ \| \|@LB@5'-CAG...CACUU UAA GCAAA...CUU-3'@LB@ GCACUUGAGG UCG@LB@ \|\|\|\|\|\|:\|:: \|\|\|@LB@ CGUGAAUUUU AGC@LB@3'-UUU...UUCUU UUA AAUGU...CAA-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -4.86 kcal/mol@LB@Hybridization Energy -13.2366 kcal/mol@LB@Unfolding Energy - mRNA 6.7246 kcal/mol@LB@Unfolding Energy - sRNA 1.64821 kcal/mol@LB@@LB@Position - mRNA 121 -- 136@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 31 -- 37@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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service.

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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