Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
39	0.002105	0.1727	b3249	mreD	-13.67	0.026871	102 -- 115	74 -- 87	cell wall structural complex MreBCD transmembrane component MreD	_____________101____________116\n_____________\|______________\|\n5'-CCU...GCGCC______________AGCCU...UUU-3'\n______________UGCUGCGCCGACAC\n______________\|:\|\|\|\|\|\|\|:\|\|\|\|\n______________AUGACGCGGUUGUG\n3'-UUU...CGCUU______________GUCCC...GUG-5'\n_____________\|______________\|\n_____________88_____________73\n	109 -- 115	74 -- 80	-25.8251 kcal/mol	5.39353 kcal/mol	6.75739 kcal/mol	101 116@LB@ \| \|@LB@5'-CCU...GCGCC AGCCU...UUU-3'@LB@ UGCUGCGCCGACAC@LB@ \|:\|\|\|\|\|\|\|:\|\|\|\|@LB@ AUGACGCGGUUGUG@LB@3'-UUU...CGCUU GUCCC...GUG-5'@LB@ \| \|@LB@ 88 73@LB@@LB@@LB@Energy -13.67 kcal/mol@LB@Hybridization Energy -25.8251 kcal/mol@LB@Unfolding Energy - mRNA 5.39353 kcal/mol@LB@Unfolding Energy - sRNA 6.75739 kcal/mol@LB@@LB@Position - mRNA 102 -- 115@LB@Position - sRNA 74 -- 87@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 74 -- 80@LB@
14	0.0004762	0.1198	b2286	nuoC	-13.55	0.028468	156 -- 179	68 -- 87	NADH:ubiquinone oxidoreductase fused CD subunit	_____________155______________________180\n_____________\|________________________\|\n5'-AGG...AAGCU_____________GUCA___C___CCAUU...CCU-3'\n______________UACUGCGCCGACA____CCA_GGA\n______________\|\|\|\|\|\|\|\|\|:\|\|\|____\|\|\|_\|\|\|\n______________AUGACGCGGUUGU____GGU_CCU\n3'-UUU...CGCUU____________________C___UUAGA...GUG-5'\n_____________\|________________________\|\n_____________88_______________________67\n	162 -- 168	75 -- 81	-29.2495 kcal/mol	8.32219 kcal/mol	7.38006 kcal/mol	155 180@LB@ \| \|@LB@5'-AGG...AAGCU GUCA C CCAUU...CCU-3'@LB@ UACUGCGCCGACA CCA GGA@LB@ \|\|\|\|\|\|\|\|\|:\|\|\| \|\|\| \|\|\|@LB@ AUGACGCGGUUGU GGU CCU@LB@3'-UUU...CGCUU C UUAGA...GUG-5'@LB@ \| \|@LB@ 88 67@LB@@LB@@LB@Energy -13.55 kcal/mol@LB@Hybridization Energy -29.2495 kcal/mol@LB@Unfolding Energy - mRNA 8.32219 kcal/mol@LB@Unfolding Energy - sRNA 7.38006 kcal/mol@LB@@LB@Position - mRNA 156 -- 179@LB@Position - sRNA 68 -- 87@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 75 -- 81@LB@
148	0.008708	0.2059	b1754	ynjB	-13.35	0.031185	160 -- 171	50 -- 61	putative ABC transporter periplasmic binding protein	_____________159__________172\n_____________\|____________\|\n5'-CCG...UCAGG____________UUCCU...AAA-3'\n______________GGCUGUGCCGUA\n______________\|\|\|\|\|:\|\|\|\|\|\|\n______________CCGACGCGGCAU\n3'-UUU...UAGAA____________UUAAU...GUG-5'\n_____________\|____________\|\n_____________62___________49\n	165 -- 171	50 -- 56	-23.078 kcal/mol	3.86799 kcal/mol	5.86332 kcal/mol	159 172@LB@ \| \|@LB@5'-CCG...UCAGG UUCCU...AAA-3'@LB@ GGCUGUGCCGUA@LB@ \|\|\|\|\|:\|\|\|\|\|\|@LB@ CCGACGCGGCAU@LB@3'-UUU...UAGAA UUAAU...GUG-5'@LB@ \| \|@LB@ 62 49@LB@@LB@@LB@Energy -13.35 kcal/mol@LB@Hybridization Energy -23.078 kcal/mol@LB@Unfolding Energy - mRNA 3.86799 kcal/mol@LB@Unfolding Energy - sRNA 5.86332 kcal/mol@LB@@LB@Position - mRNA 160 -- 171@LB@Position - sRNA 50 -- 61@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 50 -- 56@LB@
30	0.001614	0.1727	b3607	cysE	-13.31	0.031682	13 -- 32	63 -- 81	serine acetyltransferase	_____________12___________________33\n_____________\|____________________\|\n5'-CGG...GAAAU______A____A________AUCAA...CGA-3'\n______________GCCAAU_ACCG_GGAAAUUU\n______________\|\|\|\|\|:_\|\|\|:_\|\|\|\|\|\|:\|\n______________CGGUUG_UGGU_CCUUUAGA\n3'-UUU...UGACG___________C________ACCGA...GUG-5'\n_____________\|____________________\|\n_____________82___________________62\n	26 -- 32	63 -- 69	-21.8966 kcal/mol	1.53041 kcal/mol	7.0543 kcal/mol	12 33@LB@ \| \|@LB@5'-CGG...GAAAU A A AUCAA...CGA-3'@LB@ GCCAAU ACCG GGAAAUUU@LB@ \|\|\|\|\|: \|\|\|: \|\|\|\|\|\|:\|@LB@ CGGUUG UGGU CCUUUAGA@LB@3'-UUU...UGACG C ACCGA...GUG-5'@LB@ \| \|@LB@ 82 62@LB@@LB@@LB@Energy -13.31 kcal/mol@LB@Hybridization Energy -21.8966 kcal/mol@LB@Unfolding Energy - mRNA 1.53041 kcal/mol@LB@Unfolding Energy - sRNA 7.0543 kcal/mol@LB@@LB@Position - mRNA 13 -- 32@LB@Position - sRNA 63 -- 81@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 63 -- 69@LB@
126	0.006849	0.1914	b2930	yggF	-13.28	0.032133	176 -- 191	68 -- 83	fructose 1 6 bisphosphatase isozyme	_____________175______________192\n_____________\|________________\|\n5'-AUC...AUUUG________________GGCCG...GCC-3'\n______________GCGUUGAUAUCGGGGA\n______________\|\|\|:::\|:\|:\|:\|\|\|\|\n______________CGCGGUUGUGGUCCCU\n3'-UUU...UAUGA________________UUAGA...GUG-5'\n_____________\|________________\|\n_____________84_______________67\n	185 -- 191	68 -- 74	-24.7766 kcal/mol	4.1491 kcal/mol	7.34657 kcal/mol	175 192@LB@ \| \|@LB@5'-AUC...AUUUG GGCCG...GCC-3'@LB@ GCGUUGAUAUCGGGGA@LB@ \|\|\|:::\|:\|:\|:\|\|\|\|@LB@ CGCGGUUGUGGUCCCU@LB@3'-UUU...UAUGA UUAGA...GUG-5'@LB@ \| \|@LB@ 84 67@LB@@LB@@LB@Energy -13.28 kcal/mol@LB@Hybridization Energy -24.7766 kcal/mol@LB@Unfolding Energy - mRNA 4.1491 kcal/mol@LB@Unfolding Energy - sRNA 7.34657 kcal/mol@LB@@LB@Position - mRNA 176 -- 191@LB@Position - sRNA 68 -- 83@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 68 -- 74@LB@
45	0.002234	0.1727	b0055	djlA	-13.22	0.033048	207 -- 250	35 -- 76	membrane-anchored DnaK co-chaperone DNA-binding protein	_____________206___________________________________________251\n_____________\|_____________________________________________\|\n5'-GAC...UGCAG_________AA____A_____GUG_______CCUUAC________CGGCG...UUG-3'\n______________UAUUGGGGA__AAUC_UUGGC___GCCGUGG_______UGAUGGG\n______________:\|:::\|\|\|\|__\|\|\|\|_\|\|\|\|\|___\|\|\|\|\|::_______\|\|\|\|\|:\|\n______________GUGGUCCCU__UUAG_AACCG___CGGCAUU_______ACUACUC\n3'-UUU...CGGUU_____________________ACG_______UAAUAAU_______AAUGU...GUG-5'\n_____________\|_____________________________________________\|\n_____________77____________________________________________34\n	244 -- 250	35 -- 41	-37.823 kcal/mol	15.2445 kcal/mol	9.3594 kcal/mol	206 251@LB@ \| \|@LB@5'-GAC...UGCAG AA A GUG CCUUAC CGGCG...UUG-3'@LB@ UAUUGGGGA AAUC UUGGC GCCGUGG UGAUGGG@LB@ :\|:::\|\|\|\| \|\|\|\| \|\|\|\|\| \|\|\|\|\|:: \|\|\|\|\|:\|@LB@ GUGGUCCCU UUAG AACCG CGGCAUU ACUACUC@LB@3'-UUU...CGGUU ACG UAAUAAU AAUGU...GUG-5'@LB@ \| \|@LB@ 77 34@LB@@LB@@LB@Energy -13.22 kcal/mol@LB@Hybridization Energy -37.823 kcal/mol@LB@Unfolding Energy - mRNA 15.2445 kcal/mol@LB@Unfolding Energy - sRNA 9.3594 kcal/mol@LB@@LB@Position - mRNA 207 -- 250@LB@Position - sRNA 35 -- 76@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 35 -- 41@LB@
138	0.007886	0.2012	b3991	thiG	-13.21	0.033127	237 -- 259	64 -- 85	thiamine biosynthesis ThiGH complex subunit	_____________236______________________260\n_____________\|________________________\|\n5'-GCA...CACAU____UUA_________________CGCUU...CCG-3'\n______________CUGU___CCGGCA_CAGGGAAAUU\n______________\|\|\|:___\|\|::\|\|_\|\|\|\|\|\|\|\|\|:\n______________GACG___GGUUGU_GUCCCUUUAG\n3'-UUU...CUUAU____C________G__________AACCG...GUG-5'\n_____________\|________________________\|\n_____________86_______________________63\n	253 -- 259	64 -- 70	-25.8634 kcal/mol	5.26561 kcal/mol	7.38387 kcal/mol	236 260@LB@ \| \|@LB@5'-GCA...CACAU UUA CGCUU...CCG-3'@LB@ CUGU CCGGCA CAGGGAAAUU@LB@ \|\|\|: \|\|::\|\| \|\|\|\|\|\|\|\|\|:@LB@ GACG GGUUGU GUCCCUUUAG@LB@3'-UUU...CUUAU C G AACCG...GUG-5'@LB@ \| \|@LB@ 86 63@LB@@LB@@LB@Energy -13.21 kcal/mol@LB@Hybridization Energy -25.8634 kcal/mol@LB@Unfolding Energy - mRNA 5.26561 kcal/mol@LB@Unfolding Energy - sRNA 7.38387 kcal/mol@LB@@LB@Position - mRNA 237 -- 259@LB@Position - sRNA 64 -- 85@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 64 -- 70@LB@
140	0.008117	0.2031	b3221	yhcH	-13.19	0.033484	158 -- 212	34 -- 73	DUF386 family protein cupin superfamily	_____________157_____________________________________________________213\n_____________\|_______________________________________________________\|\n5'-AUC...UGAUG____UUUAC__GG___________UGGCCCAGGGAGAA_______G_________GAAGU...AAG-3'\n______________CAGG_____UU__GGCUGCGCUGU______________AAAUUAU_AUGAUGGGU\n______________\|\|\|\|_____\|:__\|\|\|\|\|\|\|\|:\|\|______________\|\|\|\|\|\|\|_\|\|\|\|\|\|:\|\|\n______________GUCC_____AG__CCGACGCGGCA______________UUUAAUA_UACUACUCA\n3'-UUU...UUGUG____CUUU___AA________________________________A_________AUGUU...GUG-5'\n_____________\|_______________________________________________________\|\n_____________74______________________________________________________33\n	206 -- 212	34 -- 40	-41.3429 kcal/mol	18.8865 kcal/mol	9.26614 kcal/mol	157 213@LB@ \| \|@LB@5'-AUC...UGAUG UUUAC GG UGGCCCAGGGAGAA G GAAGU...AAG-3'@LB@ CAGG UU GGCUGCGCUGU AAAUUAU AUGAUGGGU@LB@ \|\|\|\| \|: \|\|\|\|\|\|\|\|:\|\| \|\|\|\|\|\|\| \|\|\|\|\|\|:\|\|@LB@ GUCC AG CCGACGCGGCA UUUAAUA UACUACUCA@LB@3'-UUU...UUGUG CUUU AA A AUGUU...GUG-5'@LB@ \| \|@LB@ 74 33@LB@@LB@@LB@Energy -13.19 kcal/mol@LB@Hybridization Energy -41.3429 kcal/mol@LB@Unfolding Energy - mRNA 18.8865 kcal/mol@LB@Unfolding Energy - sRNA 9.26614 kcal/mol@LB@@LB@Position - mRNA 158 -- 212@LB@Position - sRNA 34 -- 73@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 34 -- 40@LB@
42	0.002147	0.1727	b0082	rsmH	-13.18	0.033634	23 -- 49	70 -- 94	16S rRNA m(4)C1402 methyltransferase SAM-dependent	_____________22__________________________50\n_____________\|___________________________\|\n5'-UGG...UAAUC____C_________G____AU______CUGAC...GUC-3'\n______________GCGC_AGUACUGCG_CAAC__GCCGGG\n______________\|\|\|\|_\|:\|\|\|\|\|\|\|_\|\|\|\|__:\|\|:\|\|\n______________CGCG_UUAUGACGC_GUUG__UGGUCC\n3'-UUU...CCCCA____C_________G____________CUUUA...GUG-5'\n_____________\|___________________________\|\n_____________95__________________________69\n	30 -- 36	81 -- 87	-36.7334 kcal/mol	10.4772 kcal/mol	13.036 kcal/mol	22 50@LB@ \| \|@LB@5'-UGG...UAAUC C G AU CUGAC...GUC-3'@LB@ GCGC AGUACUGCG CAAC GCCGGG@LB@ \|\|\|\| \|:\|\|\|\|\|\|\| \|\|\|\| :\|\|:\|\|@LB@ CGCG UUAUGACGC GUUG UGGUCC@LB@3'-UUU...CCCCA C G CUUUA...GUG-5'@LB@ \| \|@LB@ 95 69@LB@@LB@@LB@Energy -13.18 kcal/mol@LB@Hybridization Energy -36.7334 kcal/mol@LB@Unfolding Energy - mRNA 10.4772 kcal/mol@LB@Unfolding Energy - sRNA 13.036 kcal/mol@LB@@LB@Position - mRNA 23 -- 49@LB@Position - sRNA 70 -- 94@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 81 -- 87@LB@
83	0.004611	0.1855	b1593	ynfK	-13.15	0.034145	276 -- 295	66 -- 83	putative dethiobiotin synthetase	_____________275__________________296\n_____________\|____________________\|\n5'-CAC...UACAA________CUC_________AACGG-3'\n______________GCGUUAGC___CCAGGGAAA\n______________\|\|\|::\|:\|___\|\|\|\|\|\|\|\|\|\n______________CGCGGUUG___GGUCCCUUU\n3'-UUU...UAUGA________U___________AGAAC...GUG-5'\n_____________\|____________________\|\n_____________84___________________65\n	289 -- 295	66 -- 72	-26.3491 kcal/mol	5.84339 kcal/mol	7.35847 kcal/mol	275 296@LB@ \| \|@LB@5'-CAC...UACAA CUC AACGG-3'@LB@ GCGUUAGC CCAGGGAAA@LB@ \|\|\|::\|:\| \|\|\|\|\|\|\|\|\|@LB@ CGCGGUUG GGUCCCUUU@LB@3'-UUU...UAUGA U AGAAC...GUG-5'@LB@ \| \|@LB@ 84 65@LB@@LB@@LB@Energy -13.15 kcal/mol@LB@Hybridization Energy -26.3491 kcal/mol@LB@Unfolding Energy - mRNA 5.84339 kcal/mol@LB@Unfolding Energy - sRNA 7.35847 kcal/mol@LB@@LB@Position - mRNA 276 -- 295@LB@Position - sRNA 66 -- 83@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 66 -- 72@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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