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
112	0.004986	0.1545	b0118	acnB	-15.18	0.018766	221 -- 251	38 -- 71	aconitate hydratase 2; aconitase B; 2-methyl-cis-aconitate hydratase	_____________220________________________________252\n_____________\|__________________________________\|\n5'-GAG...CGUAA_________UGAG___GC_______G________GCGCC...UGC-3'\n______________GCACGUAGC____CGU_____CGCU_AGGGGAUU\n______________:\|\|\|::\|\|\|____\|\|\|_____\|:\|\|_\|\|\|\|\|\|\|\|\n______________UGUGUGUCG____GCA_____GUGA_UCCCCUAA\n3'-UUU...UCUGA_________UUAA___ACAAA____G________AGGUA...GCA-5'\n_____________\|__________________________________\|\n_____________72_________________________________37\n	245 -- 251	38 -- 44	-33.2374 kcal/mol	13.3072 kcal/mol	4.74986 kcal/mol	220 252@LB@ \| \|@LB@5'-GAG...CGUAA UGAG GC G GCGCC...UGC-3'@LB@ GCACGUAGC CGU CGCU AGGGGAUU@LB@ :\|\|\|::\|\|\| \|\|\| \|:\|\| \|\|\|\|\|\|\|\|@LB@ UGUGUGUCG GCA GUGA UCCCCUAA@LB@3'-UUU...UCUGA UUAA ACAAA G AGGUA...GCA-5'@LB@ \| \|@LB@ 72 37@LB@@LB@@LB@Energy -15.18 kcal/mol@LB@Hybridization Energy -33.2374 kcal/mol@LB@Unfolding Energy - mRNA 13.3072 kcal/mol@LB@Unfolding Energy - sRNA 4.74986 kcal/mol@LB@@LB@Position - mRNA 221 -- 251@LB@Position - sRNA 38 -- 71@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 38 -- 44@LB@
73	0.00298	0.1437	b0474	adk	-13.48	0.049381	180 -- 198	34 -- 50	adenylate kinase	_____________179_________________199\n_____________\|___________________\|\n5'-ACC...CGACA_____UA____________CAAUG...AUA-3'\n______________CAUUU__AGGGGAUUUUCG\n______________\|\|:\|:__\|\|\|\|\|\|\|\|\|:\|:\n______________GUGAG__UCCCCUAAAGGU\n3'-UUU...ACAAA___________________ACGAA...GCA-5'\n_____________\|___________________\|\n_____________51__________________33\n	191 -- 197	35 -- 41	-19.9961 kcal/mol	4.64453 kcal/mol	1.87382 kcal/mol	179 199@LB@ \| \|@LB@5'-ACC...CGACA UA CAAUG...AUA-3'@LB@ CAUUU AGGGGAUUUUCG@LB@ \|\|:\|: \|\|\|\|\|\|\|\|\|:\|:@LB@ GUGAG UCCCCUAAAGGU@LB@3'-UUU...ACAAA ACGAA...GCA-5'@LB@ \| \|@LB@ 51 33@LB@@LB@@LB@Energy -13.48 kcal/mol@LB@Hybridization Energy -19.9961 kcal/mol@LB@Unfolding Energy - mRNA 4.64453 kcal/mol@LB@Unfolding Energy - sRNA 1.87382 kcal/mol@LB@@LB@Position - mRNA 180 -- 198@LB@Position - sRNA 34 -- 50@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 35 -- 41@LB@
18	0.0001516	0.02826	b2817	amiC	-14.62	0.026197	167 -- 204	31 -- 70	N-acetylmuramoyl-L-alanine amidase	_____________166______________________________________205\n_____________\|________________________________________\|\n5'-AGU...CUUGU________UUAGAUUUC___________A__GG_______CAGGA...UCA-3'\n______________UACACAGC_________UUUUGCUCGGG_GA____CAUGU\n______________:\|\|\|\|\|\|\|_________\|\|\|::\|\|\|:\|\|_\|\|____\|\|\|\|:\n______________GUGUGUCG_________AAAGUGAGUCC_CU____GUACG\n3'-UUU...CUGAU________UUAAGCAAC___________C__AAAG_____AAUAU...GCA-5'\n_____________\|________________________________________\|\n_____________71_______________________________________30\n	188 -- 194	43 -- 49	-32.0387 kcal/mol	10.1821 kcal/mol	7.23824 kcal/mol	166 205@LB@ \| \|@LB@5'-AGU...CUUGU UUAGAUUUC A GG CAGGA...UCA-3'@LB@ UACACAGC UUUUGCUCGGG GA CAUGU@LB@ :\|\|\|\|\|\|\| \|\|\|::\|\|\|:\|\| \|\| \|\|\|\|:@LB@ GUGUGUCG AAAGUGAGUCC CU GUACG@LB@3'-UUU...CUGAU UUAAGCAAC C AAAG AAUAU...GCA-5'@LB@ \| \|@LB@ 71 30@LB@@LB@@LB@Energy -14.62 kcal/mol@LB@Hybridization Energy -32.0387 kcal/mol@LB@Unfolding Energy - mRNA 10.1821 kcal/mol@LB@Unfolding Energy - sRNA 7.23824 kcal/mol@LB@@LB@Position - mRNA 167 -- 204@LB@Position - sRNA 31 -- 70@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 43 -- 49@LB@
121	0.005439	0.1553	b1640	anmK	-7.89	0.496680	290 -- 297	63 -- 70	anhydro-N-acetylmuramic acid kinase	_____________289______298\n_____________\|________\|\n5'-CCA...CGGGU________UGG-3'\n______________CGCACAGC\n______________\|:\|\|\|\|\|\|\n______________GUGUGUCG\n3'-UUU...CUGAU________UUAAG...GCA-5'\n_____________\|________\|\n_____________71_______62\n	291 -- 297	63 -- 69	-13.0848 kcal/mol	2.06561 kcal/mol	3.13161 kcal/mol	289 298@LB@ \| \|@LB@5'-CCA...CGGGU UGG-3'@LB@ CGCACAGC@LB@ \|:\|\|\|\|\|\|@LB@ GUGUGUCG@LB@3'-UUU...CUGAU UUAAG...GCA-5'@LB@ \| \|@LB@ 71 62@LB@@LB@@LB@Energy -7.89 kcal/mol@LB@Hybridization Energy -13.0848 kcal/mol@LB@Unfolding Energy - mRNA 2.06561 kcal/mol@LB@Unfolding Energy - sRNA 3.13161 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 63 -- 70@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 63 -- 69@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@
57	0.002011	0.1223	b3057	bacA	-16.67	0.007222	149 -- 193	41 -- 71	undecaprenyl pyrophosphate phosphatase	_____________148___________________________________________194\n_____________\|_____________________________________________\|\n5'-UUC...UGGUC_______________GACAAG_GGUACAUUUUAAUA_________UUUAU...UUG-3'\n______________AUACGCAGUAGUUCG______C______________AUUUAGGGG\n______________\|:\|\|:\|\|\|:\|:\|\|\|\|______\|______________\|:\|:\|\|\|\|\|\n______________UGUGUGUCGUUAAGC______G______________UGAGUCCCC\n3'-UUU...UCUGA_______________AACAAA________________________UAAAG...GCA-5'\n_____________\|_____________________________________________\|\n_____________72____________________________________________40\n	187 -- 193	41 -- 47	-30.087 kcal/mol	8.67993 kcal/mol	4.74226 kcal/mol	148 194@LB@ \| \|@LB@5'-UUC...UGGUC GACAAG GGUACAUUUUAAUA UUUAU...UUG-3'@LB@ AUACGCAGUAGUUCG C AUUUAGGGG@LB@ \|:\|\|:\|\|\|:\|:\|\|\|\| \| \|:\|:\|\|\|\|\|@LB@ UGUGUGUCGUUAAGC G UGAGUCCCC@LB@3'-UUU...UCUGA AACAAA UAAAG...GCA-5'@LB@ \| \|@LB@ 72 40@LB@@LB@@LB@Energy -16.67 kcal/mol@LB@Hybridization Energy -30.087 kcal/mol@LB@Unfolding Energy - mRNA 8.67993 kcal/mol@LB@Unfolding Energy - sRNA 4.74226 kcal/mol@LB@@LB@Position - mRNA 149 -- 193@LB@Position - sRNA 41 -- 71@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 41 -- 47@LB@
101	0.004534	0.1538	b2079	baeR	-10.16	0.230535	155 -- 191	34 -- 71	response regulator in two-component regulatory system with BaeS	_____________154_______________________________________192\n_____________\|_________________________________________\|\n5'-CAG...GGUAA___U________A_____AC______G_AAC______UA__GAGAG...CGA-3'\n______________GCA_UACAGUAG___GUU____CGCU_G___GGGAUU__CA\n______________:\|\|_:\|\|\|\|:\|:___\|\|\|____\|:\|\|_:___\|\|\|\|\|\|__\|\|\n______________UGU_GUGUCGUU___CAA____GUGA_U___CCCUAA__GU\n3'-UUU...UCUGA____________AAG___CAAA____G_C________AG__ACGAA...GCA-5'\n_____________\|_________________________________________\|\n_____________72________________________________________33\n	160 -- 166	61 -- 67	-23.4603 kcal/mol	8.51419 kcal/mol	4.79237 kcal/mol	154 192@LB@ \| \|@LB@5'-CAG...GGUAA U A AC G AAC UA GAGAG...CGA-3'@LB@ GCA UACAGUAG GUU CGCU G GGGAUU CA@LB@ :\|\| :\|\|\|\|:\|: \|\|\| \|:\|\| : \|\|\|\|\|\| \|\|@LB@ UGU GUGUCGUU CAA GUGA U CCCUAA GU@LB@3'-UUU...UCUGA AAG CAAA G C AG ACGAA...GCA-5'@LB@ \| \|@LB@ 72 33@LB@@LB@@LB@Energy -10.16 kcal/mol@LB@Hybridization Energy -23.4603 kcal/mol@LB@Unfolding Energy - mRNA 8.51419 kcal/mol@LB@Unfolding Energy - sRNA 4.79237 kcal/mol@LB@@LB@Position - mRNA 155 -- 191@LB@Position - sRNA 34 -- 71@LB@Position Seed - mRNA 160 -- 166@LB@Position Seed - sRNA 61 -- 67@LB@
11	9.086e-05	0.0245	b3337	bfd	-12.11	0.098410	247 -- 280	34 -- 76	bacterioferritin-associated ferredoxin	_____________246_________________________________________281\n_____________\|___________________________________________\|\n5'-GCG...UCGUC___________________UCCCC___________________GCAAU...UUC-3'\n______________AGGCUGUGCGC__CAGUUU______UCACUCG______UUCCA\n______________\|\|:\|\|:::\|:\|__\|\|:\|\|:______\|\|\|\|\|\|:______\|\|\|\|\|\n______________UCUGAUGUGUG__GUUAAG______AGUGAGU______AAGGU\n3'-UUU...CCGUU___________UC______CAACAA_______CCCCUA_____ACGAA...GCA-5'\n_____________\|___________________________________________\|\n_____________77__________________________________________33\n	269 -- 275	45 -- 51	-24.9474 kcal/mol	8.02269 kcal/mol	4.816 kcal/mol	246 281@LB@ \| \|@LB@5'-GCG...UCGUC UCCCC GCAAU...UUC-3'@LB@ AGGCUGUGCGC CAGUUU UCACUCG UUCCA@LB@ \|\|:\|\|:::\|:\| \|\|:\|\|: \|\|\|\|\|\|: \|\|\|\|\|@LB@ UCUGAUGUGUG GUUAAG AGUGAGU AAGGU@LB@3'-UUU...CCGUU UC CAACAA CCCCUA ACGAA...GCA-5'@LB@ \| \|@LB@ 77 33@LB@@LB@@LB@Energy -12.11 kcal/mol@LB@Hybridization Energy -24.9474 kcal/mol@LB@Unfolding Energy - mRNA 8.02269 kcal/mol@LB@Unfolding Energy - sRNA 4.816 kcal/mol@LB@@LB@Position - mRNA 247 -- 280@LB@Position - sRNA 34 -- 76@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 45 -- 51@LB@
86	0.003687	0.1509	b0774	bioA	-10.95	0.166636	92 -- 152	44 -- 98	7 8-diaminopelargonic acid synthase PLP-dependent	_____________91_____________________________________________________________153\n_____________\|______________________________________________________________\|\n5'-ACG...ACAAU_____G______C____A__CAU______UCUCCAAA___U__UU_________A_______UGUAG...AAG-3'\n______________GUCCA_CGUGGG_GGUG_GC___GGGGCU________ACG_GU__UUUGUUGUU__AUUCGG\n______________\|:\|\|\|_\|\|\|\|\|\|_\|:\|\|_\|\|___::\|:\|\|________\|\|:_\|:__\|\|:\|\|\|\|\|\|__\|:\|\|:\|\n______________CGGGU_GCACCC_CUAC_CG___UUCUGA________UGU_CG__AAGCAACAA__UGAGUC\n____3'-UUUUUUU_____A______U____C__U________UGUG__________UU_________AG______CCCUA...GCA-5'\n_____________\|______________________________________________________________\|\n_____________99_____________________________________________________________43\n	139 -- 145	52 -- 58	-48.0349 kcal/mol	20.1482 kcal/mol	16.9429 kcal/mol	91 153@LB@ \| \|@LB@5'-ACG...ACAAU G C A CAU UCUCCAAA U UU A UGUAG...AAG-3'@LB@ GUCCA CGUGGG GGUG GC GGGGCU ACG GU UUUGUUGUU AUUCGG@LB@ \|:\|\|\| \|\|\|\|\|\| \|:\|\| \|\| ::\|:\|\| \|\|: \|: \|\|:\|\|\|\|\|\| \|:\|\|:\|@LB@ CGGGU GCACCC CUAC CG UUCUGA UGU CG AAGCAACAA UGAGUC@LB@ 3'-UUUUUUU A U C U UGUG UU AG CCCUA...GCA-5'@LB@ \| \|@LB@ 99 43@LB@@LB@@LB@Energy -10.95 kcal/mol@LB@Hybridization Energy -48.0349 kcal/mol@LB@Unfolding Energy - mRNA 20.1482 kcal/mol@LB@Unfolding Energy - sRNA 16.9429 kcal/mol@LB@@LB@Position - mRNA 92 -- 152@LB@Position - sRNA 44 -- 98@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 52 -- 58@LB@
115	0.005088	0.155	b4131	cadA	-16.57	0.007707	197 -- 237	37 -- 75	lysine decarboxylase acid-inducible	_____________196__________________________________________238\n_____________\|____________________________________________\|\n5'-CUC...GAUAU______GA___UUAUU_____A_____AA____AU_________AUUUU...UUG-3'\n______________GACUAU__ACG_____GCAAU___UUG__UCAC___GGGGGUUU\n______________\|\|\|\|\|:__\|\|:_____\|\|\|\|\|___\|\|\|__\|\|\|\|___\|\|\|\|:\|\|\|\n______________CUGAUG__UGU_____CGUUA___AAC__AGUG___CCCCUAAA\n3'-UUU...CGUUU______UG_____________AGC___AA____AGU________GGUAC...GCA-5'\n_____________\|____________________________________________\|\n_____________76___________________________________________36\n	231 -- 237	37 -- 43	-27.1465 kcal/mol	5.79755 kcal/mol	4.77966 kcal/mol	196 238@LB@ \| \|@LB@5'-CUC...GAUAU GA UUAUU A AA AU AUUUU...UUG-3'@LB@ GACUAU ACG GCAAU UUG UCAC GGGGGUUU@LB@ \|\|\|\|\|: \|\|: \|\|\|\|\| \|\|\| \|\|\|\| \|\|\|\|:\|\|\|@LB@ CUGAUG UGU CGUUA AAC AGUG CCCCUAAA@LB@3'-UUU...CGUUU UG AGC AA AGU GGUAC...GCA-5'@LB@ \| \|@LB@ 76 36@LB@@LB@@LB@Energy -16.57 kcal/mol@LB@Hybridization Energy -27.1465 kcal/mol@LB@Unfolding Energy - mRNA 5.79755 kcal/mol@LB@Unfolding Energy - sRNA 4.77966 kcal/mol@LB@@LB@Position - mRNA 197 -- 237@LB@Position - sRNA 37 -- 75@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 37 -- 43@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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