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
21	0.0009862	0.1579	b2572	rseA	-10.60	0.091224	9 -- 29	44 -- 65	anti-sigma factor	_____________8______________________30\n_____________\|______________________\|\n___5'-UCCCUCCC________UAC____UG_____AACCU...GGG-3'\n______________GGAAGAUU____GCA__GCAAU\n______________\|\|\|\|:\|\|:____\|\|\|__\|\|\|\|\|\n______________CCUUUUAG____CGU__CGUUA\n3'-UUU...UACAA________UCAC___UA_____CCGGG...UUG-5'\n_____________\|______________________\|\n_____________66_____________________43\n	10 -- 16	58 -- 64	-18.0609 kcal/mol	3.14057 kcal/mol	4.32401 kcal/mol	8 30@LB@ \| \|@LB@ 5'-UCCCUCCC UAC UG AACCU...GGG-3'@LB@ GGAAGAUU GCA GCAAU@LB@ \|\|\|\|:\|\|: \|\|\| \|\|\|\|\|@LB@ CCUUUUAG CGU CGUUA@LB@3'-UUU...UACAA UCAC UA CCGGG...UUG-5'@LB@ \| \|@LB@ 66 43@LB@@LB@@LB@Energy -10.60 kcal/mol@LB@Hybridization Energy -18.0609 kcal/mol@LB@Unfolding Energy - mRNA 3.14057 kcal/mol@LB@Unfolding Energy - sRNA 4.32401 kcal/mol@LB@@LB@Position - mRNA 9 -- 29@LB@Position - sRNA 44 -- 65@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 58 -- 64@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@
25	0.001369	0.1841	b2599	pheA	-10.09	0.116571	180 -- 205	1 -- 20	chorismate mutase and prephenate dehydratase P-protein	_____________179________________________206\n_____________\|__________________________\|\n5'-UGA...UUUAU______CAA_______ACAC______AUCGG...UCG-3'\n______________UGAUAA___AAAGGCA____UAUGAC\n______________\|\|\|:\|\|___\|\|\|\|\|\|\|____\|\|\|:\|\|\n______________ACUGUU___UUUCCGU____AUAUUG\n3'-UUU...UAGAC______A___________________-5'\n_____________\|_________________________\|\n_____________21________________________1\n	189 -- 195	7 -- 13	-16.49 kcal/mol	2.17136 kcal/mol	4.22784 kcal/mol	179 206@LB@ \| \|@LB@5'-UGA...UUUAU CAA ACAC AUCGG...UCG-3'@LB@ UGAUAA AAAGGCA UAUGAC@LB@ \|\|\|:\|\| \|\|\|\|\|\|\| \|\|\|:\|\|@LB@ ACUGUU UUUCCGU AUAUUG@LB@3'-UUU...UAGAC A -5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -10.09 kcal/mol@LB@Hybridization Energy -16.49 kcal/mol@LB@Unfolding Energy - mRNA 2.17136 kcal/mol@LB@Unfolding Energy - sRNA 4.22784 kcal/mol@LB@@LB@Position - mRNA 180 -- 205@LB@Position - sRNA 1 -- 20@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 7 -- 13@LB@
154	0.01792	0.3828	b2610	ffh	-8.53	0.234957	246 -- 258	48 -- 60	Signal Recognition Particle (SRP) component with 4.5S RNA (ffs)	_____________245___________259\n_____________\|_____________\|\n5'-AGG...GCAAU_________C___GACGC...AAG-3'\n______________AUCAGUGGC_GUG\n______________\|\|\|\|\|\|\|\|\|_:\|\|\n______________UAGUCACCG_UAC\n3'-UUU...CCUUU_________U___GUUAC...UUG-5'\n_____________\|_____________\|\n_____________61____________47\n	248 -- 254	52 -- 58	-18.214 kcal/mol	6.29175 kcal/mol	3.39422 kcal/mol	245 259@LB@ \| \|@LB@5'-AGG...GCAAU C GACGC...AAG-3'@LB@ AUCAGUGGC GUG@LB@ \|\|\|\|\|\|\|\|\| :\|\|@LB@ UAGUCACCG UAC@LB@3'-UUU...CCUUU U GUUAC...UUG-5'@LB@ \| \|@LB@ 61 47@LB@@LB@@LB@Energy -8.53 kcal/mol@LB@Hybridization Energy -18.214 kcal/mol@LB@Unfolding Energy - mRNA 6.29175 kcal/mol@LB@Unfolding Energy - sRNA 3.39422 kcal/mol@LB@@LB@Position - mRNA 246 -- 258@LB@Position - sRNA 48 -- 60@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 52 -- 58@LB@
93	0.008233	0.2977	b2669	stpA	-8.51	0.236304	244 -- 255	39 -- 50	DNA binding protein nucleoid-associated	_____________243__________256\n_____________\|____________\|\n5'-UUC...CCUCC____________GCGAA...UCA-3'\n______________GUGCGAUGGCUC\n______________:\|\|\|:\|\|\|\|\|:\|\n______________UACGUUACCGGG\n3'-UUU...ACCGU____________UUGUC...UUG-5'\n_____________\|____________\|\n_____________51___________38\n	249 -- 255	39 -- 45	-19.1222 kcal/mol	5.86982 kcal/mol	4.73799 kcal/mol	243 256@LB@ \| \|@LB@5'-UUC...CCUCC GCGAA...UCA-3'@LB@ GUGCGAUGGCUC@LB@ :\|\|\|:\|\|\|\|\|:\|@LB@ UACGUUACCGGG@LB@3'-UUU...ACCGU UUGUC...UUG-5'@LB@ \| \|@LB@ 51 38@LB@@LB@@LB@Energy -8.51 kcal/mol@LB@Hybridization Energy -19.1222 kcal/mol@LB@Unfolding Energy - mRNA 5.86982 kcal/mol@LB@Unfolding Energy - sRNA 4.73799 kcal/mol@LB@@LB@Position - mRNA 244 -- 255@LB@Position - sRNA 39 -- 50@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 39 -- 45@LB@
146	0.01679	0.3828	b2699	recA	-5.90	0.590167	190 -- 206	40 -- 58	DNA recombination and repair protein; ssDNA-dependent ATPase; synaptase; ssDNA and dsDNA binding protein; ATP-dependent homologous DNA strand exchanger; recombinase A; LexA autocleavage cofactor	_____________189_________________207\n_____________\|___________________\|\n5'-UGC...CAUGA___GA____A_________AUCGA...ACC-3'\n______________CAG__GUAA___AAUGGCU\n______________\|\|\|__\|:\|\|___\|\|\|\|\|\|:\n______________GUC__CGUU___UUACCGG\n3'-UUU...UUUUA___AC____ACG_______GUUGU...UUG-5'\n_____________\|___________________\|\n_____________59__________________39\n	200 -- 206	40 -- 46	-15.424 kcal/mol	3.45581 kcal/mol	6.06808 kcal/mol	189 207@LB@ \| \|@LB@5'-UGC...CAUGA GA A AUCGA...ACC-3'@LB@ CAG GUAA AAUGGCU@LB@ \|\|\| \|:\|\| \|\|\|\|\|\|:@LB@ GUC CGUU UUACCGG@LB@3'-UUU...UUUUA AC ACG GUUGU...UUG-5'@LB@ \| \|@LB@ 59 39@LB@@LB@@LB@Energy -5.90 kcal/mol@LB@Hybridization Energy -15.424 kcal/mol@LB@Unfolding Energy - mRNA 3.45581 kcal/mol@LB@Unfolding Energy - sRNA 6.06808 kcal/mol@LB@@LB@Position - mRNA 190 -- 206@LB@Position - sRNA 40 -- 58@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 40 -- 46@LB@
9	0.0003848	0.1262	b2708	srlQ	-10.45	0.097910	5 -- 28	40 -- 60	D-arabinose 5-phosphate isomerase	_____________4_________________________29\n_____________\|_________________________\|\n_______5'-UACC______AA____AU___________GCGCG...GCG-3'\n______________GUCAGU__GGCA__GUGCAAUG_CC\n______________:\|\|\|\|\|__\|\|\|\|__:\|\|\|\|\|\|\|_\|\|\n______________UAGUCA__CCGU__UACGUUAC_GG\n3'-UUU...CCUUU______________________C__GUUGU...UUG-5'\n_____________\|_________________________\|\n_____________61________________________39\n	20 -- 26	43 -- 49	-23.8159 kcal/mol	7.25851 kcal/mol	6.10522 kcal/mol	4 29@LB@ \| \|@LB@ 5'-UACC AA AU GCGCG...GCG-3'@LB@ GUCAGU GGCA GUGCAAUG CC@LB@ :\|\|\|\|\| \|\|\|\| :\|\|\|\|\|\|\| \|\|@LB@ UAGUCA CCGU UACGUUAC GG@LB@3'-UUU...CCUUU C GUUGU...UUG-5'@LB@ \| \|@LB@ 61 39@LB@@LB@@LB@Energy -10.45 kcal/mol@LB@Hybridization Energy -23.8159 kcal/mol@LB@Unfolding Energy - mRNA 7.25851 kcal/mol@LB@Unfolding Energy - sRNA 6.10522 kcal/mol@LB@@LB@Position - mRNA 5 -- 28@LB@Position - sRNA 40 -- 60@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 43 -- 49@LB@
186	0.02292	0.4143	b2717	hycI	-8.63	0.225035	220 -- 254	38 -- 70	protease involved in processing C-terminal end of HycE	_____________219___________________________________255\n_____________\|_____________________________________\|\n5'-AGC...ACUCU_______C__UAG__UGAUG______________G__GGUCC...ACU-3'\n______________GUGUUGG_AA___CA_____GGCGAUG__AUGGC_CA\n______________:\|\|\|\|\|\|_\|\|___\|\|_____\|\|\|:\|\|\|__\|\|\|\|\|_\|\|\n______________UACAACC_UU___GU_____CCGUUAC__UACCG_GU\n3'-UUU...AAAUA__________UUA__CA__________GU_____G__UGUCU...UUG-5'\n_____________\|_____________________________________\|\n_____________71____________________________________37\n	240 -- 246	48 -- 54	-27.127 kcal/mol	11.1995 kcal/mol	7.29667 kcal/mol	219 255@LB@ \| \|@LB@5'-AGC...ACUCU C UAG UGAUG G GGUCC...ACU-3'@LB@ GUGUUGG AA CA GGCGAUG AUGGC CA@LB@ :\|\|\|\|\|\| \|\| \|\| \|\|\|:\|\|\| \|\|\|\|\| \|\|@LB@ UACAACC UU GU CCGUUAC UACCG GU@LB@3'-UUU...AAAUA UUA CA GU G UGUCU...UUG-5'@LB@ \| \|@LB@ 71 37@LB@@LB@@LB@Energy -8.63 kcal/mol@LB@Hybridization Energy -27.127 kcal/mol@LB@Unfolding Energy - mRNA 11.1995 kcal/mol@LB@Unfolding Energy - sRNA 7.29667 kcal/mol@LB@@LB@Position - mRNA 220 -- 254@LB@Position - sRNA 38 -- 70@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 48 -- 54@LB@
143	0.01651	0.3828	b2793	syd	-11.91	0.046390	192 -- 225	39 -- 65	SecY-interacting protein	_____________191________________________________226\n_____________\|__________________________________\|\n5'-UCA...GAAGA_A___________A____UUGACC___CAA____UGAAA...UGU-3'\n______________G_GAAAUUAGUGG_CGAU______GCA___GCCC\n______________\|_:\|\|\|\|:\|\|\|\|\|_\|:\|\|______\|\|\|___\|\|\|\|\n______________C_UUUUAGUCACC_GUUA______CGU___CGGG\n3'-UUU...UACAA_C_________________________UAC____UUGUC...UUG-5'\n_____________\|__________________________________\|\n_____________66_________________________________38\n	198 -- 204	53 -- 59	-24.7129 kcal/mol	6.12952 kcal/mol	6.66922 kcal/mol	191 226@LB@ \| \|@LB@5'-UCA...GAAGA A A UUGACC CAA UGAAA...UGU-3'@LB@ G GAAAUUAGUGG CGAU GCA GCCC@LB@ \| :\|\|\|\|:\|\|\|\|\| \|:\|\| \|\|\| \|\|\|\|@LB@ C UUUUAGUCACC GUUA CGU CGGG@LB@3'-UUU...UACAA C UAC UUGUC...UUG-5'@LB@ \| \|@LB@ 66 38@LB@@LB@@LB@Energy -11.91 kcal/mol@LB@Hybridization Energy -24.7129 kcal/mol@LB@Unfolding Energy - mRNA 6.12952 kcal/mol@LB@Unfolding Energy - sRNA 6.66922 kcal/mol@LB@@LB@Position - mRNA 192 -- 225@LB@Position - sRNA 39 -- 65@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 53 -- 59@LB@
124	0.01277	0.3462	b2812	tcdA	-10.63	0.089790	208 -- 228	41 -- 66	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA	_____________207________________________229\n_____________\|__________________________\|\n5'-GUG...GUCUG___U______________________GUCAG...UUU-3'\n______________UGG__AAUUAGUG___AUGC_AUGGC\n______________\|\|\|__\|\|\|:\|\|\|\|___\|\|\|\|_\|\|\|\|\|\n______________ACC__UUAGUCAC___UACG_UACCG\n3'-UUU...AUACA___UU________CGU____U_____GGUUG...UUG-5'\n_____________\|__________________________\|\n_____________67_________________________40\n	213 -- 219	54 -- 60	-21.2123 kcal/mol	4.76037 kcal/mol	5.82355 kcal/mol	207 229@LB@ \| \|@LB@5'-GUG...GUCUG U GUCAG...UUU-3'@LB@ UGG AAUUAGUG AUGC AUGGC@LB@ \|\|\| \|\|\|:\|\|\|\| \|\|\|\| \|\|\|\|\|@LB@ ACC UUAGUCAC UACG UACCG@LB@3'-UUU...AUACA UU CGU U GGUUG...UUG-5'@LB@ \| \|@LB@ 67 40@LB@@LB@@LB@Energy -10.63 kcal/mol@LB@Hybridization Energy -21.2123 kcal/mol@LB@Unfolding Energy - mRNA 4.76037 kcal/mol@LB@Unfolding Energy - sRNA 5.82355 kcal/mol@LB@@LB@Position - mRNA 208 -- 228@LB@Position - sRNA 41 -- 66@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 54 -- 60@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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