Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
192	0.02246	0.3833	b4340	yjiR	-11.68	0.128907	36 -- 62	126 -- 153	putative DNA-binding transcriptional regulator/putative aminotransferase	_____________35_______63\n_____________\|________\|\n5'-AGC...CAGAG________AUCCA...GUC-3'\n______________GCUUCAUC\n______________\|\|\|\|\|\|\|\|\n______________CGAAGUAG\n3'-UUU...GGGAA________-5'\n_____________\|_______\|\n_____________154_____126\n	50 -- 56	1 -- 7	-12.7164 kcal/mol	1.73081 kcal/mol	0.703102 kcal/mol	35 63@LB@ \| \|@LB@5'-AGC...CAGAG AUCCA...GUC-3'@LB@ GCUUCAUC@LB@ \|\|\|\|\|\|\|\|@LB@ CGAAGUAG@LB@3'-UUU...GGGAA -5'@LB@ \| \|@LB@ 154 126@LB@@LB@@LB@Energy -11.68 kcal/mol@LB@Hybridization Energy -12.7164 kcal/mol@LB@Unfolding Energy - mRNA 1.73081 kcal/mol@LB@Unfolding Energy - sRNA 0.703102 kcal/mol@LB@@LB@Position - mRNA 36 -- 62@LB@Position - sRNA 126 -- 153@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 1 -- 7@LB@
189	0.02188	0.3833	b4033	malF	-11.66	0.130598	273 -- 284	194 -- 205	maltose transporter subunit	_____________272__________285\n_____________\|____________\|\n5'-CUG...UCGGC____________UACCU...UAA-3'\n______________CUGCUGGUGGGU\n______________\|\|\|\|\|\|\|:\|\|\|\|\n______________GACGACCGCCCA\n3'-UUU...UAUUA____________CUAAA...UAG-5'\n_____________\|____________\|\n_____________206__________193\n	278 -- 284	194 -- 200	-24.1506 kcal/mol	7.59361 kcal/mol	9.05892 kcal/mol	272 285@LB@ \| \|@LB@5'-CUG...UCGGC UACCU...UAA-3'@LB@ CUGCUGGUGGGU@LB@ \|\|\|\|\|\|\|:\|\|\|\|@LB@ GACGACCGCCCA@LB@3'-UUU...UAUUA CUAAA...UAG-5'@LB@ \| \|@LB@ 206 193@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -24.1506 kcal/mol@LB@Unfolding Energy - mRNA 7.59361 kcal/mol@LB@Unfolding Energy - sRNA 9.05892 kcal/mol@LB@@LB@Position - mRNA 273 -- 284@LB@Position - sRNA 194 -- 205@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 194 -- 200@LB@
157	0.01768	0.3749	b1216	chaA	-11.60	0.134178	242 -- 292	18 -- 65	calcium/sodium:proton antiporter	_____________241_______________293\n_____________\|_________________\|\n5'-AUU...AAUGU_________C___A___UUUCU...GCC-3'\n______________UACCGAUAU_CAG_CAC\n______________:\|\|\|:\|\|\|:_\|\|\|_\|\|\|\n______________GUGGUUAUG_GUC_GUG\n3'-UUU...AAAAU_________A___A___UGUAC...UAG-5'\n_____________\|_________________\|\n_____________66________________17\n	120 -- 126	178 -- 184	-16.2011 kcal/mol	3.68451 kcal/mol	4.86651 kcal/mol	241 293@LB@ \| \|@LB@5'-AUU...AAUGU C A UUUCU...GCC-3'@LB@ UACCGAUAU CAG CAC@LB@ :\|\|\|:\|\|\|: \|\|\| \|\|\|@LB@ GUGGUUAUG GUC GUG@LB@3'-UUU...AAAAU A A UGUAC...UAG-5'@LB@ \| \|@LB@ 66 17@LB@@LB@@LB@Energy -11.60 kcal/mol@LB@Hybridization Energy -16.2011 kcal/mol@LB@Unfolding Energy - mRNA 3.68451 kcal/mol@LB@Unfolding Energy - sRNA 4.86651 kcal/mol@LB@@LB@Position - mRNA 242 -- 292@LB@Position - sRNA 18 -- 65@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 178 -- 184@LB@
65	0.006332	0.3261	b3857	mobA	-11.59	0.134663	143 -- 181	126 -- 173	molybdopterin-guanine dinucleotide synthase	_____________142________________________________________________________182\n_____________\|__________________________________________________________\|\n5'-UCC...AUAGU_______C_____U_U___GA___A__C______AG______________A_______AAUAA...AAC-3'\n______________GAUGCUC__UUAC_C_UGA__CAG_CA_GUUAGC____________GGUC_AUCCCAC\n______________:\|\|:\|\|\|__\|:\|\|_\|_\|\|\|__\|\|\|_\|\|_\|\|:\|:\|____________\|\|\|\|_\|\|\|\|\|\|\|\n______________UUAUGAG__AGUG_G_ACU__GUC_GU_CAGUUG____________CCAG_UAGGGUG\n3'-UUU...UGUGG_______UC____U_U___AC___C__U______AAAGUCUUAACG____________ACGUA...UAG-5'\n_____________\|__________________________________________________________\|\n_____________174________________________________________________________125\n	175 -- 181	126 -- 132	-38.7055 kcal/mol	10.57 kcal/mol	15.6637 kcal/mol	142 182@LB@ \| \|@LB@5'-UCC...AUAGU C U U GA A C AG A AAUAA...AAC-3'@LB@ GAUGCUC UUAC C UGA CAG CA GUUAGC GGUC AUCCCAC@LB@ :\|\|:\|\|\| \|:\|\| \| \|\|\| \|\|\| \|\| \|\|:\|:\| \|\|\|\| \|\|\|\|\|\|\|@LB@ UUAUGAG AGUG G ACU GUC GU CAGUUG CCAG UAGGGUG@LB@3'-UUU...UGUGG UC U U AC C U AAAGUCUUAACG ACGUA...UAG-5'@LB@ \| \|@LB@ 174 125@LB@@LB@@LB@Energy -11.59 kcal/mol@LB@Hybridization Energy -38.7055 kcal/mol@LB@Unfolding Energy - mRNA 10.57 kcal/mol@LB@Unfolding Energy - sRNA 15.6637 kcal/mol@LB@@LB@Position - mRNA 143 -- 181@LB@Position - sRNA 126 -- 173@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 126 -- 132@LB@
128	0.01397	0.3575	b2440	eutC	-11.59	0.134682	23 -- 48	126 -- 153	ethanolamine ammonia-lyase small subunit (light chain)	_____________22______________________________49\n_____________\|_______________________________\|\n______5'-CCGCU_______G_______________AC______GACCA...ACU-3'\n______________GGGUGAU___ACAUC_AUGCUCA__UAC_CA\n______________\|\|\|\|\|\|\|___\|\|\|:\|_\|\|:\|\|\|\|__:\|\|_\|\|\n______________CCCACUA___UGUGG_UAUGAGU__GUG_GU\n3'-UUU...GACCG_______AAA_____U_______CA___U__ACUAC...UAG-5'\n_____________\|_______________________________\|\n_____________154_____________________________125\n	19 -- 25	175 -- 181	-25.4577 kcal/mol	6.00586 kcal/mol	5.22711 kcal/mol	22 49@LB@ \| \|@LB@ 5'-CCGCU G AC GACCA...ACU-3'@LB@ GGGUGAU ACAUC AUGCUCA UAC CA@LB@ \|\|\|\|\|\|\| \|\|\|:\| \|\|:\|\|\|\| :\|\| \|\|@LB@ CCCACUA UGUGG UAUGAGU GUG GU@LB@3'-UUU...GACCG AAA U CA U ACUAC...UAG-5'@LB@ \| \|@LB@ 154 125@LB@@LB@@LB@Energy -11.59 kcal/mol@LB@Hybridization Energy -25.4577 kcal/mol@LB@Unfolding Energy - mRNA 6.00586 kcal/mol@LB@Unfolding Energy - sRNA 5.22711 kcal/mol@LB@@LB@Position - mRNA 23 -- 48@LB@Position - sRNA 126 -- 153@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 175 -- 181@LB@
141	0.01524	0.3575	b0133	panC	-11.57	0.136229	4 -- 24	142 -- 162	pantothenate synthetase	_____________3_________25\n_____________\|_________\|\n5'-GGC...ACCGG_________UCCUA...UGC-3'\n______________CGGUCACAU\n______________\|:\|\|\|\|\|\|:\n______________GUCAGUGUG\n3'-UUU...UAUGA_________UACUA...UAG-5'\n_____________\|_________\|\n_____________163_______141\n	65 -- 71	168 -- 174	-12.1402 kcal/mol	2.67616 kcal/mol	0.276974 kcal/mol	3 25@LB@ \| \|@LB@5'-GGC...ACCGG UCCUA...UGC-3'@LB@ CGGUCACAU@LB@ \|:\|\|\|\|\|\|:@LB@ GUCAGUGUG@LB@3'-UUU...UAUGA UACUA...UAG-5'@LB@ \| \|@LB@ 163 141@LB@@LB@@LB@Energy -11.57 kcal/mol@LB@Hybridization Energy -12.1402 kcal/mol@LB@Unfolding Energy - mRNA 2.67616 kcal/mol@LB@Unfolding Energy - sRNA 0.276974 kcal/mol@LB@@LB@Position - mRNA 4 -- 24@LB@Position - sRNA 142 -- 162@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 168 -- 174@LB@
120	0.01317	0.3575	b1158	pinE	-11.56	0.136715	30 -- 59	115 -- 145	e14 prophage; site-specific DNA recombinase	_____________29_____________________60\n_____________\|______________________\|\n5'-AGC...CCGGG______________GUA_____GAGCC...ACA-3'\n______________ACACCAA____CAG___AUGCA\n______________\|\|\|\|\|\|\|____\|\|\|___\|::\|\|\n______________UGUGGUU____GUC___UGUGU\n3'-UUU...UAAAA_______AUGA___AG______ACUAC...UAG-5'\n_____________\|______________________\|\n_____________146____________________114\n	98 -- 104	181 -- 187	-13.8739 kcal/mol	4.34554 kcal/mol	5.05492 kcal/mol	29 60@LB@ \| \|@LB@5'-AGC...CCGGG GUA GAGCC...ACA-3'@LB@ ACACCAA CAG AUGCA@LB@ \|\|\|\|\|\|\| \|\|\| \|::\|\|@LB@ UGUGGUU GUC UGUGU@LB@3'-UUU...UAAAA AUGA AG ACUAC...UAG-5'@LB@ \| \|@LB@ 146 114@LB@@LB@@LB@Energy -11.56 kcal/mol@LB@Hybridization Energy -13.8739 kcal/mol@LB@Unfolding Energy - mRNA 4.34554 kcal/mol@LB@Unfolding Energy - sRNA 5.05492 kcal/mol@LB@@LB@Position - mRNA 30 -- 59@LB@Position - sRNA 115 -- 145@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 181 -- 187@LB@
90	0.01008	0.3575	b3994	thiC	-11.53	0.138483	145 -- 158	1 -- 14	phosphomethylpyrimidine synthase	_____________144_________159\n_____________\|___________\|\n5'-AUG...CGUCU___________CGUCG...UUU-3'\n______________CUUGCUUCAUC\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________GAACGAAGUAG\n3'-UUU...UGGGG___________-5'\n_____________\|__________\|\n_____________15_________1\n	152 -- 158	1 -- 7	-17.5294 kcal/mol	1.22878 kcal/mol	1.03329 kcal/mol	144 159@LB@ \| \|@LB@5'-AUG...CGUCU CGUCG...UUU-3'@LB@ CUUGCUUCAUC@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ GAACGAAGUAG@LB@3'-UUU...UGGGG -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -11.53 kcal/mol@LB@Hybridization Energy -17.5294 kcal/mol@LB@Unfolding Energy - mRNA 1.22878 kcal/mol@LB@Unfolding Energy - sRNA 1.03329 kcal/mol@LB@@LB@Position - mRNA 145 -- 158@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 1 -- 7@LB@
86	0.009326	0.3575	b0899	ycaM	-11.50	0.140486	23 -- 68	127 -- 173	putative transporter	_____________22_______________________________________________________69\n_____________\|________________________________________________________\|\n5'-AGC...GAACU____GUU______UC_____UUUUUU___UCUU__A__U__C____U_________AAUUU...AUG-3'\n______________UACU___UCACAC____UGC______GUU____CU_UC_GA_UUGC__UUAUUCCA\n______________\|\|\|\|___\|\|\|\|\|\|____\|\|\|______\|\|:____\|\|_\|\|_\|\|_\|\|\|\|__\|:\|\|:\|\|\|\n______________AUGA___AGUGUG____ACG______CAG____GA_AG_CU_AACG__AGUAGGGU\n3'-UUU...UGGUU____GUC______UACU___UCCGUU___UU____A__U__U____CC________GACGU...UAG-5'\n_____________\|________________________________________________________\|\n_____________174______________________________________________________126\n	62 -- 68	127 -- 133	-29.7478 kcal/mol	2.56458 kcal/mol	15.6497 kcal/mol	22 69@LB@ \| \|@LB@5'-AGC...GAACU GUU UC UUUUUU UCUU A U C U AAUUU...AUG-3'@LB@ UACU UCACAC UGC GUU CU UC GA UUGC UUAUUCCA@LB@ \|\|\|\| \|\|\|\|\|\| \|\|\| \|\|: \|\| \|\| \|\| \|\|\|\| \|:\|\|:\|\|\|@LB@ AUGA AGUGUG ACG CAG GA AG CU AACG AGUAGGGU@LB@3'-UUU...UGGUU GUC UACU UCCGUU UU A U U CC GACGU...UAG-5'@LB@ \| \|@LB@ 174 126@LB@@LB@@LB@Energy -11.50 kcal/mol@LB@Hybridization Energy -29.7478 kcal/mol@LB@Unfolding Energy - mRNA 2.56458 kcal/mol@LB@Unfolding Energy - sRNA 15.6497 kcal/mol@LB@@LB@Position - mRNA 23 -- 68@LB@Position - sRNA 127 -- 173@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 127 -- 133@LB@
79	0.008119	0.3458	b0945	pyrD	-11.48	0.141710	30 -- 41	191 -- 202	dihydro-orotate oxidase FMN-linked	_____________29______________________42\n_____________\|_______________________\|\n5'-UGU...AGCAA_____________A___GA____CGU-3'\n______________UUACGCCG_UAUU_CAG__ACGC\n______________\|\|\|\|:\|\|:_\|\|:\|_\|\|\|__\|\|:\|\n______________AAUGUGGU_AUGA_GUC__UGUG\n3'-UUU...ACUAA________U________AG____UACUA...UAG-5'\n_____________\|_______________________\|\n_____________203_____________________190\n	277 -- 283	182 -- 188	-20.4941 kcal/mol	3.55802 kcal/mol	4.91485 kcal/mol	29 42@LB@ \| \|@LB@5'-UGU...AGCAA A GA CGU-3'@LB@ UUACGCCG UAUU CAG ACGC@LB@ \|\|\|\|:\|\|: \|\|:\| \|\|\| \|\|:\|@LB@ AAUGUGGU AUGA GUC UGUG@LB@3'-UUU...ACUAA U AG UACUA...UAG-5'@LB@ \| \|@LB@ 203 190@LB@@LB@@LB@Energy -11.48 kcal/mol@LB@Hybridization Energy -20.4941 kcal/mol@LB@Unfolding Energy - mRNA 3.55802 kcal/mol@LB@Unfolding Energy - sRNA 4.91485 kcal/mol@LB@@LB@Position - mRNA 30 -- 41@LB@Position - sRNA 191 -- 202@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 182 -- 188@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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