Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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	Additional homologs
118	0.01863	0.5155	b0738	tolR	-11.80	0.040697	190 -- 199	50 -- 59	membrane spanning protein in TolA-TolQ-TolR complex		_____________189________200\n_____________\|__________\|\n5'-UGG...CAACA__________CAUGG...UGG-3'\n______________AGGGGUAAGC\n______________\|\|\|\|\|\|\|\|:\|\n______________UCCCCAUUUG\n3'-UUU...CUUUA__________UCUGU...UCG-5'\n_____________\|__________\|\n_____________60_________49\n	193 -- 199	50 -- 56	-16.6396 kcal/mol	4.1136 kcal/mol	0.728772 kcal/mol	189 200@LB@ \| \|@LB@5'-UGG...CAACA CAUGG...UGG-3'@LB@ AGGGGUAAGC@LB@ \|\|\|\|\|\|\|\|:\|@LB@ UCCCCAUUUG@LB@3'-UUU...CUUUA UCUGU...UCG-5'@LB@ \| \|@LB@ 60 49@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -16.6396 kcal/mol@LB@Unfolding Energy - mRNA 4.1136 kcal/mol@LB@Unfolding Energy - sRNA 0.728772 kcal/mol@LB@@LB@Position - mRNA 190 -- 199@LB@Position - sRNA 50 -- 59@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 50 -- 56@LB@
162	0.02632	0.526	b1886	tar	-10.00	0.096892	244 -- 251	53 -- 60	methyl-accepting chemotaxis protein II		_____________243______252\n_____________\|________\|\n5'-UGC...GGUGC________UUCGC...UUC-3'\n______________UGGGGGUA\n______________\|:\|\|\|\|\|\|\n______________AUCCCCAU\n3'-UUU...ACUUU________UUGUC...UCG-5'\n_____________\|________\|\n_____________61_______52\n	245 -- 251	53 -- 59	-12.2006 kcal/mol	2.12623 kcal/mol	0.0710089 kcal/mol	243 252@LB@ \| \|@LB@5'-UGC...GGUGC UUCGC...UUC-3'@LB@ UGGGGGUA@LB@ \|:\|\|\|\|\|\|@LB@ AUCCCCAU@LB@3'-UUU...ACUUU UUGUC...UCG-5'@LB@ \| \|@LB@ 61 52@LB@@LB@@LB@Energy -10.00 kcal/mol@LB@Hybridization Energy -12.2006 kcal/mol@LB@Unfolding Energy - mRNA 2.12623 kcal/mol@LB@Unfolding Energy - sRNA 0.0710089 kcal/mol@LB@@LB@Position - mRNA 244 -- 251@LB@Position - sRNA 53 -- 60@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 53 -- 59@LB@
183	0.03025	0.5427	b0999	cbpM	-7.72	0.255487	289 -- 296	53 -- 60	modulator of CbpA co-chaperone		_____________288______297\n_____________\|________\|\n5'-AUC...CGGUU________GUUG-3'\n______________UGGGGGUG\n______________\|:\|\|\|\|\|:\n______________AUCCCCAU\n3'-UUU...ACUUU________UUGUC...UCG-5'\n_____________\|________\|\n_____________61_______52\n	290 -- 296	53 -- 59	-12.779 kcal/mol	4.99203 kcal/mol	0.0710089 kcal/mol	288 297@LB@ \| \|@LB@5'-AUC...CGGUU GUUG-3'@LB@ UGGGGGUG@LB@ \|:\|\|\|\|\|:@LB@ AUCCCCAU@LB@3'-UUU...ACUUU UUGUC...UCG-5'@LB@ \| \|@LB@ 61 52@LB@@LB@@LB@Energy -7.72 kcal/mol@LB@Hybridization Energy -12.779 kcal/mol@LB@Unfolding Energy - mRNA 4.99203 kcal/mol@LB@Unfolding Energy - sRNA 0.0710089 kcal/mol@LB@@LB@Position - mRNA 289 -- 296@LB@Position - sRNA 53 -- 60@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 53 -- 59@LB@
11	0.0003561	0.1063	b3857	mobA	-16.95	0.002119	239 -- 276	15 -- 59	molybdopterin-guanine dinucleotide synthase		_____________238_______________________________________________277\n_____________\|_________________________________________________\|\n5'-UCC...CUGGC___C______GC___________________G_____C___________GAUUG...AAC-3'\n______________AGG_GGUAAA__CAGAC__________GAAU_GGCGG__GUAGAUAAAG\n______________\|\|\|_\|\|\|\|\|\|__\|\|\|\|\|__________\|\|\|\|_\|:\|\|\|__:\|\|:\|\|\|\|\|\|\n______________UCC_CCAUUU__GUCUG__________CUUA_CUGCC__UAUUUAUUUC\n3'-UUU...CUUUA_________________UAAGUCUUUA__________AU__________AAUUA...UCG-5'\n_____________\|_________________________________________________\|\n_____________60________________________________________________14\n	270 -- 276	15 -- 21	-31.2728 kcal/mol	7.99479 kcal/mol	6.32587 kcal/mol	238 277@LB@ \| \|@LB@5'-UCC...CUGGC C GC G C GAUUG...AAC-3'@LB@ AGG GGUAAA CAGAC GAAU GGCGG GUAGAUAAAG@LB@ \|\|\| \|\|\|\|\|\| \|\|\|\|\| \|\|\|\| \|:\|\|\| :\|\|:\|\|\|\|\|\|@LB@ UCC CCAUUU GUCUG CUUA CUGCC UAUUUAUUUC@LB@3'-UUU...CUUUA UAAGUCUUUA AU AAUUA...UCG-5'@LB@ \| \|@LB@ 60 14@LB@@LB@@LB@Energy -16.95 kcal/mol@LB@Hybridization Energy -31.2728 kcal/mol@LB@Unfolding Energy - mRNA 7.99479 kcal/mol@LB@Unfolding Energy - sRNA 6.32587 kcal/mol@LB@@LB@Position - mRNA 239 -- 276@LB@Position - sRNA 15 -- 59@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 15 -- 21@LB@
128	0.0201	0.5155	b2782	mazF	-10.78	0.067406	32 -- 50	1 -- 23	mRNA interferase toxin antitoxin is MazE	b4225	_____________31______________________51\n_____________\|_______________________\|\n5'-AUC...CAAUC_______________________GAAGA...UCC-3'\n______________UGAAUA___UUGAUGAUGA_AGU\n______________\|:\|\|\|\|___\|\|:\|\|\|\|\|\|\|_\|\|:\n______________AUUUAU___AAUUACUACU_UCG\n3'-UUU...CCAUU______UUC__________A___-5'\n_____________\|______________________\|\n_____________24_____________________1\n	41 -- 47	5 -- 11	-13.6359 kcal/mol	2.75565 kcal/mol	0.105066 kcal/mol	31 51@LB@ \| \|@LB@5'-AUC...CAAUC GAAGA...UCC-3'@LB@ UGAAUA UUGAUGAUGA AGU@LB@ \|:\|\|\|\| \|\|:\|\|\|\|\|\|\| \|\|:@LB@ AUUUAU AAUUACUACU UCG@LB@3'-UUU...CCAUU UUC A -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -10.78 kcal/mol@LB@Hybridization Energy -13.6359 kcal/mol@LB@Unfolding Energy - mRNA 2.75565 kcal/mol@LB@Unfolding Energy - sRNA 0.105066 kcal/mol@LB@@LB@Position - mRNA 32 -- 50@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 5 -- 11@LB@
109	0.01701	0.5123	b2075	mdtB	-10.10	0.092694	6 -- 26	38 -- 56	multidrug efflux system subunit B		_____________5_____________________27\n_____________\|_____________________\|\n______5'-CAUCU_____CGC_____________CAGUC...CCG-3'\n______________GGUGA___CGGGCAUUCAGGA\n______________\|\|\|:\|___\|:\|:\|\|\|\|\|\|\|:\|\n______________CCAUU___GUCUGUAAGUCUU\n3'-UUU...UAUCC_____U_______________UACUU...UCG-5'\n_____________\|_____________________\|\n_____________57____________________37\n	18 -- 24	40 -- 46	-22.2525 kcal/mol	5.90254 kcal/mol	6.25055 kcal/mol	5 27@LB@ \| \|@LB@ 5'-CAUCU CGC CAGUC...CCG-3'@LB@ GGUGA CGGGCAUUCAGGA@LB@ \|\|\|:\| \|:\|:\|\|\|\|\|\|\|:\|@LB@ CCAUU GUCUGUAAGUCUU@LB@3'-UUU...UAUCC U UACUU...UCG-5'@LB@ \| \|@LB@ 57 37@LB@@LB@@LB@Energy -10.10 kcal/mol@LB@Hybridization Energy -22.2525 kcal/mol@LB@Unfolding Energy - mRNA 5.90254 kcal/mol@LB@Unfolding Energy - sRNA 6.25055 kcal/mol@LB@@LB@Position - mRNA 6 -- 26@LB@Position - sRNA 38 -- 56@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 40 -- 46@LB@
139	0.0229	0.526	b3958	argC	-10.25	0.086580	11 -- 36	23 -- 56	N-acetyl-gamma-glutamylphosphate reductase NAD(P)-binding		_____________10___________________________________37\n_____________\|____________________________________\|\n5'-AUC...AGCGC_______CUC__________________________UUGUU...CUG-3'\n______________GGUAAAU___GAUA__________AAUGGCGGUAAU\n______________\|\|\|\|\|\|:___\|\|:\|__________\|\|\|\|:\|\|\|\|\|\|\|\n______________CCAUUUG___CUGU__________UUACUGCCAUUA\n3'-UUU...UAUCC_______U______AAGUCUUUAC____________UUUAU...UCG-5'\n_____________\|____________________________________\|\n_____________57___________________________________22\n	30 -- 36	23 -- 29	-21.8632 kcal/mol	5.30467 kcal/mol	6.31216 kcal/mol	10 37@LB@ \| \|@LB@5'-AUC...AGCGC CUC UUGUU...CUG-3'@LB@ GGUAAAU GAUA AAUGGCGGUAAU@LB@ \|\|\|\|\|\|: \|\|:\| \|\|\|\|:\|\|\|\|\|\|\|@LB@ CCAUUUG CUGU UUACUGCCAUUA@LB@3'-UUU...UAUCC U AAGUCUUUAC UUUAU...UCG-5'@LB@ \| \|@LB@ 57 22@LB@@LB@@LB@Energy -10.25 kcal/mol@LB@Hybridization Energy -21.8632 kcal/mol@LB@Unfolding Energy - mRNA 5.30467 kcal/mol@LB@Unfolding Energy - sRNA 6.31216 kcal/mol@LB@@LB@Position - mRNA 11 -- 36@LB@Position - sRNA 23 -- 56@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 23 -- 29@LB@
3	3.826e-06	0.004187	b0090	murG	-16.88	0.002220	177 -- 235	1 -- 51	N-acetylglucosaminyl transferase		_____________176_________________________________________________________236\n_____________\|___________________________________________________________\|\n5'-AUU...AAAGC___________UAC_____UCAC____A_____C___G____CGA______________AGGCG...GUU-3'\n______________GCAGGCGUUUG___GAGGU____GAUG_GUGGU_AAG_AAAG___UUAAUGGUGAUGGC\n______________:\|\|\|:\|:\|\|::___\|\|::\|____\|\|:\|_\|\|::\|_\|\|:_\|\|\|\|___\|\|\|\|\|\|:\|\|\|\|:\|\|\n______________UGUCUGUAAGU___CUUUA____CUGC_CAUUA_UUU_UUUC___AAUUACUACUAUCG\n3'-UUU...CCAUU___________________CUUA______________A_____________________-5'\n_____________\|__________________________________________________________\|\n_____________52_________________________________________________________1\n	229 -- 235	1 -- 7	-39.4015 kcal/mol	16.1862 kcal/mol	6.33528 kcal/mol	176 236@LB@ \| \|@LB@5'-AUU...AAAGC UAC UCAC A C G CGA AGGCG...GUU-3'@LB@ GCAGGCGUUUG GAGGU GAUG GUGGU AAG AAAG UUAAUGGUGAUGGC@LB@ :\|\|\|:\|:\|\|:: \|\|::\| \|\|:\| \|\|::\| \|\|: \|\|\|\| \|\|\|\|\|\|:\|\|\|\|:\|\|@LB@ UGUCUGUAAGU CUUUA CUGC CAUUA UUU UUUC AAUUACUACUAUCG@LB@3'-UUU...CCAUU CUUA A -5'@LB@ \| \|@LB@ 52 1@LB@@LB@@LB@Energy -16.88 kcal/mol@LB@Hybridization Energy -39.4015 kcal/mol@LB@Unfolding Energy - mRNA 16.1862 kcal/mol@LB@Unfolding Energy - sRNA 6.33528 kcal/mol@LB@@LB@Position - mRNA 177 -- 235@LB@Position - sRNA 1 -- 51@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 1 -- 7@LB@
58	0.008338	0.4523	b2280	nuoJ	-13.62	0.015495	7 -- 16	55 -- 64	NADH:ubiquinone oxidoreductase membrane subunit J		_____________6__________17\n_____________\|__________\|\n_____5'-GAUUUC__________AAUAC...UUA-3'\n______________GAAAUGGGGG\n______________\|\|\|\|\|:\|\|\|\|\n______________CUUUAUCCCC\n3'-UUU...GCCAA__________AUUUG...UCG-5'\n_____________\|__________\|\n_____________65_________54\n	10 -- 16	55 -- 61	-15.5198 kcal/mol	1.86933 kcal/mol	0.0291912 kcal/mol	6 17@LB@ \| \|@LB@ 5'-GAUUUC AAUAC...UUA-3'@LB@ GAAAUGGGGG@LB@ \|\|\|\|\|:\|\|\|\|@LB@ CUUUAUCCCC@LB@3'-UUU...GCCAA AUUUG...UCG-5'@LB@ \| \|@LB@ 65 54@LB@@LB@@LB@Energy -13.62 kcal/mol@LB@Hybridization Energy -15.5198 kcal/mol@LB@Unfolding Energy - mRNA 1.86933 kcal/mol@LB@Unfolding Energy - sRNA 0.0291912 kcal/mol@LB@@LB@Position - mRNA 7 -- 16@LB@Position - sRNA 55 -- 64@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 55 -- 61@LB@
7	0.0001529	0.07172	b0687	seqA	-15.48	0.005290	212 -- 226	5 -- 19	negative modulator of initiation of replication		_____________211_____________227\n_____________\|_______________\|\n5'-GGA...ACGAU_______________ACUCU...UGA-3'\n______________UGAAGUUGAUGAUGA\n______________\|:\|\|\|\|\|:\|\|\|\|\|\|\|\n______________AUUUCAAUUACUACU\n3'-UUU...UAUUU_______________AUCG-5'\n_____________\|_______________\|\n_____________20______________4\n	220 -- 226	5 -- 11	-18.3215 kcal/mol	2.77487 kcal/mol	0.0620344 kcal/mol	211 227@LB@ \| \|@LB@5'-GGA...ACGAU ACUCU...UGA-3'@LB@ UGAAGUUGAUGAUGA@LB@ \|:\|\|\|\|\|:\|\|\|\|\|\|\|@LB@ AUUUCAAUUACUACU@LB@3'-UUU...UAUUU AUCG-5'@LB@ \| \|@LB@ 20 4@LB@@LB@@LB@Energy -15.48 kcal/mol@LB@Hybridization Energy -18.3215 kcal/mol@LB@Unfolding Energy - mRNA 2.77487 kcal/mol@LB@Unfolding Energy - sRNA 0.0620344 kcal/mol@LB@@LB@Position - mRNA 212 -- 226@LB@Position - sRNA 5 -- 19@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 5 -- 11@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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