Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
156	0.01801	0.3828	b1942	fliJ	-11.30	0.063944	187 -- 254	7 -- 65	flagellar protein	_____________186______________________________________________________________________255\n_____________\|________________________________________________________________________\|\n5'-UUC...ACCCA_____UAACGG___A_____GAACAUG_____C____GACCCU______________GCAGA__A_______GAGGA...AGC-3'\n______________GGAGA______CAG_UGGCA_______GUGCG_UGGC______GAAA____GAUCUG_____AA_AGAGGUA\n______________\|\|\|:\|______\|\|\|_\|\|\|\|\|_______:\|\|\|:_\|\|\|\|______\|\|\|\|____:\|\|\|\|\|_____\|\|_\|:\|\|\|:\|\n______________CCUUU______GUC_ACCGU_______UACGU_ACCG______CUUU____UUAGAC_____UU_UUUCCGU\n3'-UUU...UACAA_____UA_________________________U____GGUUGU____UAUU______ACUG___A_______AUAUUG-5'\n_____________\|________________________________________________________________________\|\n_____________66_______________________________________________________________________6\n	248 -- 254	7 -- 13	-39.8056 kcal/mol	16.3505 kcal/mol	12.1538 kcal/mol	186 255@LB@ \| \|@LB@5'-UUC...ACCCA UAACGG A GAACAUG C GACCCU GCAGA A GAGGA...AGC-3'@LB@ GGAGA CAG UGGCA GUGCG UGGC GAAA GAUCUG AA AGAGGUA@LB@ \|\|\|:\| \|\|\| \|\|\|\|\| :\|\|\|: \|\|\|\| \|\|\|\| :\|\|\|\|\| \|\| \|:\|\|\|:\|@LB@ CCUUU GUC ACCGU UACGU ACCG CUUU UUAGAC UU UUUCCGU@LB@3'-UUU...UACAA UA U GGUUGU UAUU ACUG A AUAUUG-5'@LB@ \| \|@LB@ 66 6@LB@@LB@@LB@Energy -11.30 kcal/mol@LB@Hybridization Energy -39.8056 kcal/mol@LB@Unfolding Energy - mRNA 16.3505 kcal/mol@LB@Unfolding Energy - sRNA 12.1538 kcal/mol@LB@@LB@Position - mRNA 187 -- 254@LB@Position - sRNA 7 -- 65@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 7 -- 13@LB@
74	0.006275	0.2822	b3298	rpsM	-14.03	0.014091	187 -- 207	39 -- 57	30S ribosomal subunit protein S13	_____________186___________________208\n_____________\|_____________________\|\n5'-GUC...UAAAU___A_G______UA_______GUAUA...UCC-3'\n______________AGU_G_AGUGCA__GUGGCCC\n______________\|\|\|_\|_\|:\|\|\|\|__:\|\|\|\|\|\|\n______________UCA_C_UUACGU__UACCGGG\n3'-UUU...UUUAG___C_G_______________UUGUC...UUG-5'\n_____________\|_____________________\|\n_____________58____________________38\n	201 -- 207	39 -- 45	-23.7565 kcal/mol	4.54468 kcal/mol	5.17956 kcal/mol	186 208@LB@ \| \|@LB@5'-GUC...UAAAU A G UA GUAUA...UCC-3'@LB@ AGU G AGUGCA GUGGCCC@LB@ \|\|\| \| \|:\|\|\|\| :\|\|\|\|\|\|@LB@ UCA C UUACGU UACCGGG@LB@3'-UUU...UUUAG C G UUGUC...UUG-5'@LB@ \| \|@LB@ 58 38@LB@@LB@@LB@Energy -14.03 kcal/mol@LB@Hybridization Energy -23.7565 kcal/mol@LB@Unfolding Energy - mRNA 4.54468 kcal/mol@LB@Unfolding Energy - sRNA 5.17956 kcal/mol@LB@@LB@Position - mRNA 187 -- 207@LB@Position - sRNA 39 -- 57@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 39 -- 45@LB@
7	0.0002249	0.1081	b4032	malG	-16.06	0.003987	187 -- 221	31 -- 65	maltose transporter subunit	_____________186_________________________________222\n_____________\|___________________________________\|\n5'-CGU...AUUAA_______AACAAAAAUG_____________C____UCGCA...UGG-3'\n______________GGGAGAU__________GCAAUGGUCCAAC_GAAA\n______________\|\|:\|:\|\|__________\|\|\|\|\|\|\|:\|\|\|\|\|_\|\|\|\|\n______________CCUUUUA__________CGUUACCGGGUUG_CUUU\n3'-UUU...UACAA_______GUCACCGUUA_____________U____UAUUU...UUG-5'\n_____________\|___________________________________\|\n_____________66__________________________________30\n	210 -- 216	36 -- 42	-33.4232 kcal/mol	6.39587 kcal/mol	10.9697 kcal/mol	186 222@LB@ \| \|@LB@5'-CGU...AUUAA AACAAAAAUG C UCGCA...UGG-3'@LB@ GGGAGAU GCAAUGGUCCAAC GAAA@LB@ \|\|:\|:\|\| \|\|\|\|\|\|\|:\|\|\|\|\| \|\|\|\|@LB@ CCUUUUA CGUUACCGGGUUG CUUU@LB@3'-UUU...UACAA GUCACCGUUA U UAUUU...UUG-5'@LB@ \| \|@LB@ 66 30@LB@@LB@@LB@Energy -16.06 kcal/mol@LB@Hybridization Energy -33.4232 kcal/mol@LB@Unfolding Energy - mRNA 6.39587 kcal/mol@LB@Unfolding Energy - sRNA 10.9697 kcal/mol@LB@@LB@Position - mRNA 187 -- 221@LB@Position - sRNA 31 -- 65@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 36 -- 42@LB@
26	0.00144	0.1863	b4406	yaeP	-8.75	0.213688	187 -- 204	2 -- 20	UPF0253 family protein	_____________186_________________205\n_____________\|___________________\|\n5'-ACC...AGUGC_____G_____________AAAAA...UGC-3'\n______________UGACA__GAGGGCAUGUGG\n______________\|\|\|\|\|__:\|:\|\|\|\|\|:\|::\n______________ACUGU__UUUCCGUAUAUU\n3'-UUU...UAGAC_____UA____________G-5'\n_____________\|___________________\|\n_____________21__________________1\n	197 -- 203	3 -- 9	-20.0716 kcal/mol	7.09254 kcal/mol	4.22649 kcal/mol	186 205@LB@ \| \|@LB@5'-ACC...AGUGC G AAAAA...UGC-3'@LB@ UGACA GAGGGCAUGUGG@LB@ \|\|\|\|\| :\|:\|\|\|\|\|:\|::@LB@ ACUGU UUUCCGUAUAUU@LB@3'-UUU...UAGAC UA G-5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -8.75 kcal/mol@LB@Hybridization Energy -20.0716 kcal/mol@LB@Unfolding Energy - mRNA 7.09254 kcal/mol@LB@Unfolding Energy - sRNA 4.22649 kcal/mol@LB@@LB@Position - mRNA 187 -- 204@LB@Position - sRNA 2 -- 20@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 3 -- 9@LB@
172	0.02065	0.4033	b1015	putP	-10.70	0.086688	188 -- 205	52 -- 67	proline:sodium symporter	_____________187________________206\n_____________\|__________________\|\n5'-AGA...AUUUU_______CU____A____UAUUA...ACG-3'\n______________UUGGAGA__UUAG_UGGC\n______________\|\|\|\|\|:\|__\|:\|\|_\|\|\|\|\n______________AACCUUU__AGUC_ACCG\n3'-UUU...UAUAC_______U__________UUACG...UUG-5'\n_____________\|__________________\|\n_____________68_________________51\n	188 -- 194	61 -- 67	-15.9795 kcal/mol	2.37428 kcal/mol	2.90583 kcal/mol	187 206@LB@ \| \|@LB@5'-AGA...AUUUU CU A UAUUA...ACG-3'@LB@ UUGGAGA UUAG UGGC@LB@ \|\|\|\|\|:\| \|:\|\| \|\|\|\|@LB@ AACCUUU AGUC ACCG@LB@3'-UUU...UAUAC U UUACG...UUG-5'@LB@ \| \|@LB@ 68 51@LB@@LB@@LB@Energy -10.70 kcal/mol@LB@Hybridization Energy -15.9795 kcal/mol@LB@Unfolding Energy - mRNA 2.37428 kcal/mol@LB@Unfolding Energy - sRNA 2.90583 kcal/mol@LB@@LB@Position - mRNA 188 -- 205@LB@Position - sRNA 52 -- 67@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 61 -- 67@LB@
46	0.003168	0.2306	b3066	dnaG	-7.10	0.407270	188 -- 205	41 -- 63	DNA primase	_____________187_____________________206\n_____________\|_______________________\|\n5'-ACC...UGCUA____________CU_________UGGAC...GCA-3'\n______________AAAAUCGG_GGC______AUGGC\n______________\|\|\|\|\|\|:\|_\|\|\|______\|\|\|\|\|\n______________UUUUAGUC_CCG______UACCG\n3'-UUU...CAACC________A___UUACGU_____GGUUG...UUG-5'\n_____________\|_______________________\|\n_____________64______________________40\n	189 -- 195	56 -- 62	-16.4791 kcal/mol	5.10709 kcal/mol	4.27657 kcal/mol	187 206@LB@ \| \|@LB@5'-ACC...UGCUA CU UGGAC...GCA-3'@LB@ AAAAUCGG GGC AUGGC@LB@ \|\|\|\|\|\|:\| \|\|\| \|\|\|\|\|@LB@ UUUUAGUC CCG UACCG@LB@3'-UUU...CAACC A UUACGU GGUUG...UUG-5'@LB@ \| \|@LB@ 64 40@LB@@LB@@LB@Energy -7.10 kcal/mol@LB@Hybridization Energy -16.4791 kcal/mol@LB@Unfolding Energy - mRNA 5.10709 kcal/mol@LB@Unfolding Energy - sRNA 4.27657 kcal/mol@LB@@LB@Position - mRNA 188 -- 205@LB@Position - sRNA 41 -- 63@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 56 -- 62@LB@
78	0.006706	0.2822	b3738	atpB	-10.93	0.077303	188 -- 216	28 -- 54	F0 sector of membrane-bound ATP synthase subunit a	_____________187_____________________________217\n_____________\|_______________________________\|\n5'-CAU...CAAAG_____AAG___UC__________________UGACG...ACC-3'\n______________GGUAA___GCA__AUGGCUU__CAGAAAAUA\n______________\|\|:\|\|___\|\|\|__\|\|\|\|\|::__\|\|\|\|\|\|\|\|\|\n______________CCGUU___CGU__UACCGGG__GUCUUUUAU\n3'-UUU...AGUCA_____A______________UU_________UUUAG...UUG-5'\n_____________\|_______________________________\|\n_____________55______________________________27\n	201 -- 207	39 -- 45	-24.7477 kcal/mol	4.83623 kcal/mol	8.98285 kcal/mol	187 217@LB@ \| \|@LB@5'-CAU...CAAAG AAG UC UGACG...ACC-3'@LB@ GGUAA GCA AUGGCUU CAGAAAAUA@LB@ \|\|:\|\| \|\|\| \|\|\|\|\|:: \|\|\|\|\|\|\|\|\|@LB@ CCGUU CGU UACCGGG GUCUUUUAU@LB@3'-UUU...AGUCA A UU UUUAG...UUG-5'@LB@ \| \|@LB@ 55 27@LB@@LB@@LB@Energy -10.93 kcal/mol@LB@Hybridization Energy -24.7477 kcal/mol@LB@Unfolding Energy - mRNA 4.83623 kcal/mol@LB@Unfolding Energy - sRNA 8.98285 kcal/mol@LB@@LB@Position - mRNA 188 -- 216@LB@Position - sRNA 28 -- 54@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 39 -- 45@LB@
120	0.01191	0.3337	b0354	yaiL	-10.86	0.080118	189 -- 207	50 -- 67	DUF2058 family protein	_____________188_________________208\n_____________\|___________________\|\n5'-GUA...CGGGU_______CAA__A______AACUU...UUC-3'\n______________UUGGAAA___AG_UGGCAA\n______________\|\|\|\|\|\|\|___\|\|_\|\|\|\|\|\|\n______________AACCUUU___UC_ACCGUU\n3'-UUU...UAUAC_______UAG_________ACGUU...UUG-5'\n_____________\|___________________\|\n_____________68__________________49\n	189 -- 195	61 -- 67	-16.0374 kcal/mol	2.05851 kcal/mol	3.12147 kcal/mol	188 208@LB@ \| \|@LB@5'-GUA...CGGGU CAA A AACUU...UUC-3'@LB@ UUGGAAA AG UGGCAA@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|\|\|@LB@ AACCUUU UC ACCGUU@LB@3'-UUU...UAUAC UAG ACGUU...UUG-5'@LB@ \| \|@LB@ 68 49@LB@@LB@@LB@Energy -10.86 kcal/mol@LB@Hybridization Energy -16.0374 kcal/mol@LB@Unfolding Energy - mRNA 2.05851 kcal/mol@LB@Unfolding Energy - sRNA 3.12147 kcal/mol@LB@@LB@Position - mRNA 189 -- 207@LB@Position - sRNA 50 -- 67@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 61 -- 67@LB@
20	0.0008987	0.1511	b2597	raiA	-11.08	0.071670	189 -- 211	11 -- 33	cold shock protein associated with 30S ribosomal subunit	_____________188_____________________212\n_____________\|_______________________\|\n5'-GCG...GACAA____________A__________CAUUA...AUC-3'\n______________GAGGUAAAAUUU_UGACAAUGAA\n______________:\|::\|\|\|\|\|\|:\|_\|\|\|\|\|\|\|:\|\|\n______________UUUUAUUUUAGA_ACUGUUAUUU\n3'-UUU...UUGUC____________C__________CCGUA...UUG-5'\n_____________\|_______________________\|\n_____________34______________________10\n	205 -- 211	11 -- 17	-19.0558 kcal/mol	3.03608 kcal/mol	4.94152 kcal/mol	188 212@LB@ \| \|@LB@5'-GCG...GACAA A CAUUA...AUC-3'@LB@ GAGGUAAAAUUU UGACAAUGAA@LB@ :\|::\|\|\|\|\|\|:\| \|\|\|\|\|\|\|:\|\|@LB@ UUUUAUUUUAGA ACUGUUAUUU@LB@3'-UUU...UUGUC C CCGUA...UUG-5'@LB@ \| \|@LB@ 34 10@LB@@LB@@LB@Energy -11.08 kcal/mol@LB@Hybridization Energy -19.0558 kcal/mol@LB@Unfolding Energy - mRNA 3.03608 kcal/mol@LB@Unfolding Energy - sRNA 4.94152 kcal/mol@LB@@LB@Position - mRNA 189 -- 211@LB@Position - sRNA 11 -- 33@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 11 -- 17@LB@
125	0.01291	0.3474	b3006	exbB	-11.08	0.071576	189 -- 220	46 -- 66	membrane spanning protein in TonB-ExbB-ExbD complex	_____________188______________________________221\n_____________\|________________________________\|\n5'-CGC...CGUCC______UACA______GUAAUAAUU_______GACGG...CCU-3'\n______________UGGAGA____CAGUGG_________UAAUGCA\n______________\|\|\|\|:\|____\|\|\|\|\|\|_________:\|\|\|\|\|\|\n______________ACCUUU____GUCACC_________GUUACGU\n3'-UUU...AUACA______UA________________________UACCG...UUG-5'\n_____________\|________________________________\|\n_____________67_______________________________45\n	214 -- 220	46 -- 52	-19.4381 kcal/mol	4.26886 kcal/mol	4.08842 kcal/mol	188 221@LB@ \| \|@LB@5'-CGC...CGUCC UACA GUAAUAAUU GACGG...CCU-3'@LB@ UGGAGA CAGUGG UAAUGCA@LB@ \|\|\|\|:\| \|\|\|\|\|\| :\|\|\|\|\|\|@LB@ ACCUUU GUCACC GUUACGU@LB@3'-UUU...AUACA UA UACCG...UUG-5'@LB@ \| \|@LB@ 67 45@LB@@LB@@LB@Energy -11.08 kcal/mol@LB@Hybridization Energy -19.4381 kcal/mol@LB@Unfolding Energy - mRNA 4.26886 kcal/mol@LB@Unfolding Energy - sRNA 4.08842 kcal/mol@LB@@LB@Position - mRNA 189 -- 220@LB@Position - sRNA 46 -- 66@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 46 -- 52@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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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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