Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
90	0.004009	0.1538	b3152	yraR	-13.99	0.037452	47 -- 72	45 -- 75	putative nucleoside-diphosphate-sugar epimerase	_____________46______________________________73\n_____________\|_______________________________\|\n5'-ACU...UCAGU_____AA___________UC___________UGCUU...CGA-3'\n______________GAUUA___ACGGCAAUUU______UUACUCA\n______________\|\|:\|\|___\|\|:\|\|\|\|\|\|:______\|:\|\|\|\|\|\n______________CUGAU___UGUCGUUAAG______AGUGAGU\n3'-UUU...CGUUU_____GUG__________CAACAA_______CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	66 -- 72	45 -- 51	-19.6514 kcal/mol	1.92306 kcal/mol	3.74078 kcal/mol	46 73@LB@ \| \|@LB@5'-ACU...UCAGU AA UC UGCUU...CGA-3'@LB@ GAUUA ACGGCAAUUU UUACUCA@LB@ \|\|:\|\| \|\|:\|\|\|\|\|\|: \|:\|\|\|\|\|@LB@ CUGAU UGUCGUUAAG AGUGAGU@LB@3'-UUU...CGUUU GUG CAACAA CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -13.99 kcal/mol@LB@Hybridization Energy -19.6514 kcal/mol@LB@Unfolding Energy - mRNA 1.92306 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 47 -- 72@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 66 -- 72@LB@Position Seed - sRNA 45 -- 51@LB@
140	0.006445	0.1605	b0325	yahK	-13.93	0.038719	67 -- 79	43 -- 55	broad specificity NADPH-dependent aldehyde reductase Zn-containing	_____________66____________80\n_____________\|_____________\|\n5'-UUA...UGCUC_____________CUCGC...AAA-3'\n______________UGUUUCAUUCAGG\n______________\|\|\|\|\|\|\|:\|\|\|\|\|\n______________ACAAAGUGAGUCC\n3'-UUU...AAGCA_____________CCUAA...GCA-5'\n_____________\|_____________\|\n_____________56____________42\n	73 -- 79	43 -- 49	-18.9036 kcal/mol	3.47822 kcal/mol	1.49792 kcal/mol	66 80@LB@ \| \|@LB@5'-UUA...UGCUC CUCGC...AAA-3'@LB@ UGUUUCAUUCAGG@LB@ \|\|\|\|\|\|\|:\|\|\|\|\|@LB@ ACAAAGUGAGUCC@LB@3'-UUU...AAGCA CCUAA...GCA-5'@LB@ \| \|@LB@ 56 42@LB@@LB@@LB@Energy -13.93 kcal/mol@LB@Hybridization Energy -18.9036 kcal/mol@LB@Unfolding Energy - mRNA 3.47822 kcal/mol@LB@Unfolding Energy - sRNA 1.49792 kcal/mol@LB@@LB@Position - mRNA 67 -- 79@LB@Position - sRNA 43 -- 55@LB@Position Seed - mRNA 73 -- 79@LB@Position Seed - sRNA 43 -- 49@LB@
13	0.0001005	0.0245	b1921	fliZ	-13.92	0.038869	246 -- 263	63 -- 78	RpoS antagonist; putative regulator of FliA activity	_____________245________________264\n_____________\|__________________\|\n5'-UGC...AUCUU_______UUAA_______CAGAC...AUC-3'\n______________AAAGACU____ACACAGC\n______________\|\|\|\|\|\|\|____\|\|\|\|\|\|\|\n______________UUUCUGA____UGUGUCG\n3'-UUU...ACCCG_______UG_________UUAAG...GCA-5'\n_____________\|__________________\|\n_____________79_________________62\n	257 -- 263	63 -- 69	-17.8578 kcal/mol	0.69523 kcal/mol	3.24195 kcal/mol	245 264@LB@ \| \|@LB@5'-UGC...AUCUU UUAA CAGAC...AUC-3'@LB@ AAAGACU ACACAGC@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UUUCUGA UGUGUCG@LB@3'-UUU...ACCCG UG UUAAG...GCA-5'@LB@ \| \|@LB@ 79 62@LB@@LB@@LB@Energy -13.92 kcal/mol@LB@Hybridization Energy -17.8578 kcal/mol@LB@Unfolding Energy - mRNA 0.69523 kcal/mol@LB@Unfolding Energy - sRNA 3.24195 kcal/mol@LB@@LB@Position - mRNA 246 -- 263@LB@Position - sRNA 63 -- 78@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 63 -- 69@LB@
135	0.006184	0.1605	b0637	rsfS	-13.92	0.038847	179 -- 195	40 -- 56	ribosomal silencing factor	_____________178_______________196\n_____________\|_________________\|\n5'-AUU...UCUAU___A_____C_______AAAAC...UCA-3'\n______________UUG_UUCAC_CAGGGGG\n______________\|\|\|_\|\|\|\|\|_\|\|\|\|\|\|:\n______________AAC_AAGUG_GUCCCCU\n3'-UUU...UAAGC___A_____A_______AAAGG...GCA-5'\n_____________\|_________________\|\n_____________57________________39\n	189 -- 195	40 -- 46	-20.5369 kcal/mol	4.69018 kcal/mol	1.92548 kcal/mol	178 196@LB@ \| \|@LB@5'-AUU...UCUAU A C AAAAC...UCA-3'@LB@ UUG UUCAC CAGGGGG@LB@ \|\|\| \|\|\|\|\| \|\|\|\|\|\|:@LB@ AAC AAGUG GUCCCCU@LB@3'-UUU...UAAGC A A AAAGG...GCA-5'@LB@ \| \|@LB@ 57 39@LB@@LB@@LB@Energy -13.92 kcal/mol@LB@Hybridization Energy -20.5369 kcal/mol@LB@Unfolding Energy - mRNA 4.69018 kcal/mol@LB@Unfolding Energy - sRNA 1.92548 kcal/mol@LB@@LB@Position - mRNA 179 -- 195@LB@Position - sRNA 40 -- 56@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 40 -- 46@LB@
21	0.0001827	0.02926	b1937	fliE	-13.91	0.039102	192 -- 221	38 -- 77	flagellar basal-body component	_____________191________________________________________222\n_____________\|__________________________________________\|\n5'-CUG...UCCGG_____GAGA___U_______A_____________________GAAGG...GUU-3'\n______________GAGAC____AUG_CAGCGAU_____________CAGGGGAUU\n______________:\|\|\|\|____\|::_\|\|\|\|:\|\|_____________\|\|\|\|\|\|\|\|\|\n______________UUCUG____UGU_GUCGUUA_____________GUCCCCUAA\n3'-UUU...CCCGU_____AUG____________AGCAACAAAGUGA_________AGGUA...GCA-5'\n_____________\|__________________________________________\|\n_____________78_________________________________________37\n	215 -- 221	38 -- 44	-25.7557 kcal/mol	7.06678 kcal/mol	4.77969 kcal/mol	191 222@LB@ \| \|@LB@5'-CUG...UCCGG GAGA U A GAAGG...GUU-3'@LB@ GAGAC AUG CAGCGAU CAGGGGAUU@LB@ :\|\|\|\| \|:: \|\|\|\|:\|\| \|\|\|\|\|\|\|\|\|@LB@ UUCUG UGU GUCGUUA GUCCCCUAA@LB@3'-UUU...CCCGU AUG AGCAACAAAGUGA AGGUA...GCA-5'@LB@ \| \|@LB@ 78 37@LB@@LB@@LB@Energy -13.91 kcal/mol@LB@Hybridization Energy -25.7557 kcal/mol@LB@Unfolding Energy - mRNA 7.06678 kcal/mol@LB@Unfolding Energy - sRNA 4.77969 kcal/mol@LB@@LB@Position - mRNA 192 -- 221@LB@Position - sRNA 38 -- 77@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 38 -- 44@LB@
4	8.9e-06	0.006694	b3281	aroE	-13.87	0.039990	230 -- 259	45 -- 75	dehydroshikimate reductase NAD(P)-binding	_____________229_____________________________260\n_____________\|_______________________________\|\n5'-UUU...AAUCC___A__C________A___CCA_________UCAGC...AUG-3'\n______________GAU_GC_CACAGCAA_UCG____UUCAUUCA\n______________\|\|:_:\|_\|\|\|\|\|\|\|\|_\|\|\|____\|\|\|\|:\|\|\|\n______________CUG_UG_GUGUCGUU_AGC____AAGUGAGU\n3'-UUU...CGUUU___A__U________A___AACA________CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	253 -- 259	45 -- 51	-26.2723 kcal/mol	8.66309 kcal/mol	3.74078 kcal/mol	229 260@LB@ \| \|@LB@5'-UUU...AAUCC A C A CCA UCAGC...AUG-3'@LB@ GAU GC CACAGCAA UCG UUCAUUCA@LB@ \|\|: :\| \|\|\|\|\|\|\|\| \|\|\| \|\|\|\|:\|\|\|@LB@ CUG UG GUGUCGUU AGC AAGUGAGU@LB@3'-UUU...CGUUU A U A AACA CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -13.87 kcal/mol@LB@Hybridization Energy -26.2723 kcal/mol@LB@Unfolding Energy - mRNA 8.66309 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 230 -- 259@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 45 -- 51@LB@
152	0.007399	0.1668	b0591	entS	-13.87	0.039944	258 -- 287	45 -- 70	enterobactin exporter iron-regulated	_____________257____________________________288\n_____________\|______________________________\|\n5'-AAU...CGUUU_________UUCC___CUC______U____AUUGU...UGG-3'\n______________CGCGCAGUA____UCG___GUUUCA_CUCA\n______________\|:\|:\|\|\|:\|____\|\|\|___\|\|\|\|\|\|_\|\|\|\|\n______________GUGUGUCGU____AGC___CAAAGU_GAGU\n3'-UUU...CUGAU_________UA_____AA____________CCCCU...GCA-5'\n_____________\|______________________________\|\n_____________71_____________________________44\n	260 -- 266	62 -- 68	-23.1768 kcal/mol	5.59312 kcal/mol	3.71317 kcal/mol	257 288@LB@ \| \|@LB@5'-AAU...CGUUU UUCC CUC U AUUGU...UGG-3'@LB@ CGCGCAGUA UCG GUUUCA CUCA@LB@ \|:\|:\|\|\|:\| \|\|\| \|\|\|\|\|\| \|\|\|\|@LB@ GUGUGUCGU AGC CAAAGU GAGU@LB@3'-UUU...CUGAU UA AA CCCCU...GCA-5'@LB@ \| \|@LB@ 71 44@LB@@LB@@LB@Energy -13.87 kcal/mol@LB@Hybridization Energy -23.1768 kcal/mol@LB@Unfolding Energy - mRNA 5.59312 kcal/mol@LB@Unfolding Energy - sRNA 3.71317 kcal/mol@LB@@LB@Position - mRNA 258 -- 287@LB@Position - sRNA 45 -- 70@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 62 -- 68@LB@
120	0.005393	0.1553	b0523	purE	-13.83	0.040764	102 -- 146	30 -- 75	N5-carboxyaminoimidazole ribonucleotide mutase	_____________101________________________________________________147\n_____________\|__________________________________________________\|\n5'-UGG...UUGCU____U____GC__C____C_____UUCC______UC______________AUUCU...UGA-3'\n______________GAUU_CACA__CA_GCAA__CGUU____UUGCUC______UUUCCGUGCU\n______________\|\|:\|_\|\|\|\|__\|\|_\|\|\|\|__\|\|\|\|____\|::\|\|\|______\|\|\|\|\|:\|\|\|\|\n______________CUGA_GUGU__GU_CGUU__GCAA____AGUGAG______AAAGGUACGA\n3'-UUU...CGUUU____U_____________AA____CAA_______UCCCCU__________AUAUU...GCA-5'\n_____________\|__________________________________________________\|\n_____________76_________________________________________________29\n	140 -- 146	30 -- 36	-29.2897 kcal/mol	7.36654 kcal/mol	8.08958 kcal/mol	101 147@LB@ \| \|@LB@5'-UGG...UUGCU U GC C C UUCC UC AUUCU...UGA-3'@LB@ GAUU CACA CA GCAA CGUU UUGCUC UUUCCGUGCU@LB@ \|\|:\| \|\|\|\| \|\| \|\|\|\| \|\|\|\| \|::\|\|\| \|\|\|\|\|:\|\|\|\|@LB@ CUGA GUGU GU CGUU GCAA AGUGAG AAAGGUACGA@LB@3'-UUU...CGUUU U AA CAA UCCCCU AUAUU...GCA-5'@LB@ \| \|@LB@ 76 29@LB@@LB@@LB@Energy -13.83 kcal/mol@LB@Hybridization Energy -29.2897 kcal/mol@LB@Unfolding Energy - mRNA 7.36654 kcal/mol@LB@Unfolding Energy - sRNA 8.08958 kcal/mol@LB@@LB@Position - mRNA 102 -- 146@LB@Position - sRNA 30 -- 75@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 30 -- 36@LB@
17	0.0001292	0.02674	b1854	pykA	-13.69	0.043994	133 -- 157	36 -- 68	pyruvate kinase II	_____________132_______________________________158\n_____________\|_________________________________\|\n5'-GAA...GCCAU______________A__________________AUGUU...ACG-3'\n______________CGCGGC_____GUU_UUUCAUUC___GGAUUUC\n______________\|:\|:\|\|_____\|\|\|_\|\|\|\|\|:\|\|___\|\|\|\|\|\|\|\n______________GUGUCG_____CAA_AAAGUGAG___CCUAAAG\n3'-UUU...GAUGU______UUAAG___C________UCC_______GUACG...GCA-5'\n_____________\|_________________________________\|\n_____________69________________________________35\n	151 -- 157	36 -- 42	-24.2432 kcal/mol	5.79946 kcal/mol	4.75078 kcal/mol	132 158@LB@ \| \|@LB@5'-GAA...GCCAU A AUGUU...ACG-3'@LB@ CGCGGC GUU UUUCAUUC GGAUUUC@LB@ \|:\|:\|\| \|\|\| \|\|\|\|\|:\|\| \|\|\|\|\|\|\|@LB@ GUGUCG CAA AAAGUGAG CCUAAAG@LB@3'-UUU...GAUGU UUAAG C UCC GUACG...GCA-5'@LB@ \| \|@LB@ 69 35@LB@@LB@@LB@Energy -13.69 kcal/mol@LB@Hybridization Energy -24.2432 kcal/mol@LB@Unfolding Energy - mRNA 5.79946 kcal/mol@LB@Unfolding Energy - sRNA 4.75078 kcal/mol@LB@@LB@Position - mRNA 133 -- 157@LB@Position - sRNA 36 -- 68@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 36 -- 42@LB@
25	0.0002079	0.02926	b4064	ghxP	-13.58	0.046769	115 -- 151	38 -- 73	guanine/hypoxanthine permease high affinity; guanine/hypoxanthine:H+ symporter	_____________114____________________________________152\n_____________\|______________________________________\|\n5'-UCG...CAAAC___GA_____G__GAUAAC________GG_________GUCCG...UAA-3'\n______________CUG___GCAG_AA______GUUUCGCU__CAGGGGAUU\n______________\|\|:___:\|\|\|_\|\|______\|\|\|\|\|:\|\|__\|\|\|\|\|\|\|\|\|\n______________GAU___UGUC_UU______CAAAGUGA__GUCCCCUAA\n3'-UUU...UUUCU___GUG____G__AAGCAA___________________AGGUA...GCA-5'\n_____________\|______________________________________\|\n_____________74_____________________________________37\n	145 -- 151	38 -- 44	-32.2199 kcal/mol	13.8672 kcal/mol	4.77333 kcal/mol	114 152@LB@ \| \|@LB@5'-UCG...CAAAC GA G GAUAAC GG GUCCG...UAA-3'@LB@ CUG GCAG AA GUUUCGCU CAGGGGAUU@LB@ \|\|: :\|\|\| \|\| \|\|\|\|\|:\|\| \|\|\|\|\|\|\|\|\|@LB@ GAU UGUC UU CAAAGUGA GUCCCCUAA@LB@3'-UUU...UUUCU GUG G AAGCAA AGGUA...GCA-5'@LB@ \| \|@LB@ 74 37@LB@@LB@@LB@Energy -13.58 kcal/mol@LB@Hybridization Energy -32.2199 kcal/mol@LB@Unfolding Energy - mRNA 13.8672 kcal/mol@LB@Unfolding Energy - sRNA 4.77333 kcal/mol@LB@@LB@Position - mRNA 115 -- 151@LB@Position - sRNA 38 -- 73@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 38 -- 44@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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service.

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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