Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
68	0.00659	0.3261	b4080	mdtP	-14.15	0.040423	195 -- 221	144 -- 172	outer membrane factor of efflux pump	_____________194_______________________________222\n_____________\|_________________________________\|\n5'-CUG...CAAGG__C_____A________AUC_____________CGUCU...CUC-3'\n______________AG_CACGC_AUGAU_CA_____GUCAACUUUCA\n______________\|\|_\|\|\|:\|_\|\|\|\|\|_\|\|_____\|\|\|\|\|\|\|\|\|\|\|\n______________UC_GUGUG_UACUA_GU_____CAGUUGAAAGU\n3'-UUU...AUGAG__A___________C__CCGUU___________CUUAA...UAG-5'\n_____________\|_________________________________\|\n_____________173_______________________________143\n	215 -- 221	144 -- 150	-24.8993 kcal/mol	3.71866 kcal/mol	8.07675 kcal/mol	194 222@LB@ \| \|@LB@5'-CUG...CAAGG C A AUC CGUCU...CUC-3'@LB@ AG CACGC AUGAU CA GUCAACUUUCA@LB@ \|\| \|\|\|:\| \|\|\|\|\| \|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ UC GUGUG UACUA GU CAGUUGAAAGU@LB@3'-UUU...AUGAG A C CCGUU CUUAA...UAG-5'@LB@ \| \|@LB@ 173 143@LB@@LB@@LB@Energy -14.15 kcal/mol@LB@Hybridization Energy -24.8993 kcal/mol@LB@Unfolding Energy - mRNA 3.71866 kcal/mol@LB@Unfolding Energy - sRNA 8.07675 kcal/mol@LB@@LB@Position - mRNA 195 -- 221@LB@Position - sRNA 144 -- 172@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 144 -- 150@LB@
188	0.0218	0.3833	b3357	crp	-15.41	0.022266	196 -- 257	123 -- 172	cAMP-activated global transcription factor mediator of catabolite repression	_____________195_________________258\n_____________\|___________________\|\n5'-GAC...AUAAC____________UU_____ACCGC...AGG-3'\n______________CGCGCAUGGUGC__GGCAA\n______________\|:\|:\|\|\|\|:\|\|\|__\|\|\|\|\|\n______________GUGUGUACUACG__CCGUU\n3'-UUU...AGUCA____________U______CAGUU...UAG-5'\n_____________\|___________________\|\n_____________173_________________122\n	201 -- 207	161 -- 167	-26.7729 kcal/mol	8.17538 kcal/mol	7.52835 kcal/mol	195 258@LB@ \| \|@LB@5'-GAC...AUAAC UU ACCGC...AGG-3'@LB@ CGCGCAUGGUGC GGCAA@LB@ \|:\|:\|\|\|\|:\|\|\| \|\|\|\|\|@LB@ GUGUGUACUACG CCGUU@LB@3'-UUU...AGUCA U CAGUU...UAG-5'@LB@ \| \|@LB@ 173 122@LB@@LB@@LB@Energy -15.41 kcal/mol@LB@Hybridization Energy -26.7729 kcal/mol@LB@Unfolding Energy - mRNA 8.17538 kcal/mol@LB@Unfolding Energy - sRNA 7.52835 kcal/mol@LB@@LB@Position - mRNA 196 -- 257@LB@Position - sRNA 123 -- 172@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 161 -- 167@LB@
9	0.0005653	0.1842	b3527	yhjJ	-12.58	0.084694	198 -- 237	133 -- 170	putative periplasmic M16 family chaperone	_____________197__________________________________________________238\n_____________\|____________________________________________________\|\n5'-CUC...GUUGA____GGGUU______CA_______CAAAAAU___________CGG_______UGCUG...GGC-3'\n______________UCAG_____CACAUG____GGGCA_______UCGACUUUUAG____GCGGUU\n______________\|\|\|\|_____\|\|\|\|\|\|____:\|\|\|\|_______\|\|:\|\|\|\|\|:\|\|____\|\|\|\|\|:\n______________AGUC_____GUGUAC____UCCGU_______AGUUGAAAGUC____CGCCAG\n3'-UUU...UUAUG____AGU________UACG_____UC________________UUAA______UAGGG...UAG-5'\n_____________\|____________________________________________________\|\n_____________171__________________________________________________132\n	222 -- 228	143 -- 149	-37.5898 kcal/mol	10.9006 kcal/mol	12.7286 kcal/mol	197 238@LB@ \| \|@LB@5'-CUC...GUUGA GGGUU CA CAAAAAU CGG UGCUG...GGC-3'@LB@ UCAG CACAUG GGGCA UCGACUUUUAG GCGGUU@LB@ \|\|\|\| \|\|\|\|\|\| :\|\|\|\| \|\|:\|\|\|\|\|:\|\| \|\|\|\|\|:@LB@ AGUC GUGUAC UCCGU AGUUGAAAGUC CGCCAG@LB@3'-UUU...UUAUG AGU UACG UC UUAA UAGGG...UAG-5'@LB@ \| \|@LB@ 171 132@LB@@LB@@LB@Energy -12.58 kcal/mol@LB@Hybridization Energy -37.5898 kcal/mol@LB@Unfolding Energy - mRNA 10.9006 kcal/mol@LB@Unfolding Energy - sRNA 12.7286 kcal/mol@LB@@LB@Position - mRNA 198 -- 237@LB@Position - sRNA 133 -- 170@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 143 -- 149@LB@
24	0.001922	0.2633	b3017	ftsP	-19.79	0.002953	203 -- 291	63 -- 135	septal ring component that protects the divisome from stress; multicopy suppressor of ftsI(Ts)	_____________202__________________________________________________________________________________________292\n_____________\|____________________________________________________________________________________________\|\n5'-GAC...AAUAU_________GUCG__________A_________C__G______CACU_____CA______GUUCCCCUGAAG____________________AGCAA...CGC-3'\n______________GUCA_CUCA____GCGUCAGUUC_UUCAGGCAU_GG__GAUUG____UUGUG__GGCGCU____________GCCAGCGCAGCCGG_GCAAC\n______________\|\|\|\|_\|:\|\|____\|\|:\|\|\|\|\|:\|_\|\|\|\|:\|\|\|\|_\|\|__:\|\|:\|____\|\|\|\|\|__\|:\|\|\|\|____________:\|\|\|:\|\|\|\|:\|\|:\|_:\|\|\|\|\n______________CAGU_GGGU____CGUAGUCAGG_AAGUUCGUA_CC__UUAGC____AACAC__CUGCGA____________UGGUUGCGUUGGUC_UGUUG\n3'-UUU...AACGC____A____GA_________________________AA______________C_______AU________________________G_____AAGCG...UAG-5'\n_____________\|____________________________________________________________________________________________\|\n_____________136__________________________________________________________________________________________62\n	278 -- 284	71 -- 77	-82.7619 kcal/mol	32.3928 kcal/mol	37.2191 kcal/mol	202 292@LB@ \| \|@LB@5'-GAC...AAUAU GUCG A C G CACU CA GUUCCCCUGAAG AGCAA...CGC-3'@LB@ GUCA CUCA GCGUCAGUUC UUCAGGCAU GG GAUUG UUGUG GGCGCU GCCAGCGCAGCCGG GCAAC@LB@ \|\|\|\| \|:\|\| \|\|:\|\|\|\|\|:\| \|\|\|\|:\|\|\|\| \|\| :\|\|:\| \|\|\|\|\| \|:\|\|\|\| :\|\|\|:\|\|\|\|:\|\|:\| :\|\|\|\|@LB@ CAGU GGGU CGUAGUCAGG AAGUUCGUA CC UUAGC AACAC CUGCGA UGGUUGCGUUGGUC UGUUG@LB@3'-UUU...AACGC A GA AA C AU G AAGCG...UAG-5'@LB@ \| \|@LB@ 136 62@LB@@LB@@LB@Energy -19.79 kcal/mol@LB@Hybridization Energy -82.7619 kcal/mol@LB@Unfolding Energy - mRNA 32.3928 kcal/mol@LB@Unfolding Energy - sRNA 37.2191 kcal/mol@LB@@LB@Position - mRNA 203 -- 291@LB@Position - sRNA 63 -- 135@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 71 -- 77@LB@
94	0.01043	0.3575	b4293	fecI	-12.90	0.072974	203 -- 229	60 -- 87	RNA polymerase sigma-19 factor fec operon-specific; ECF sigma factor	_____________202_______________________230\n_____________\|_________________________\|\n5'-AAU...AUCCC__________UAC_____UA_____UUAGA...AGU-3'\n______________AUUUUAUACC____CUUA___ACAC\n______________\|\|\|\|\|\|:\|\|\|____\|\|:\|___\|\|\|\|\n______________UAAAAUGUGG____GAGU___UGUG\n3'-UUU...CCCAC__________UUAU____CAG____UACUA...UAG-5'\n_____________\|_________________________\|\n_____________88________________________59\n	66 -- 72	183 -- 189	-15.6606 kcal/mol	1.17775 kcal/mol	4.92862 kcal/mol	202 230@LB@ \| \|@LB@5'-AAU...AUCCC UAC UA UUAGA...AGU-3'@LB@ AUUUUAUACC CUUA ACAC@LB@ \|\|\|\|\|\|:\|\|\| \|\|:\| \|\|\|\|@LB@ UAAAAUGUGG GAGU UGUG@LB@3'-UUU...CCCAC UUAU CAG UACUA...UAG-5'@LB@ \| \|@LB@ 88 59@LB@@LB@@LB@Energy -12.90 kcal/mol@LB@Hybridization Energy -15.6606 kcal/mol@LB@Unfolding Energy - mRNA 1.17775 kcal/mol@LB@Unfolding Energy - sRNA 4.92862 kcal/mol@LB@@LB@Position - mRNA 203 -- 229@LB@Position - sRNA 60 -- 87@LB@Position Seed - mRNA 66 -- 72@LB@Position Seed - sRNA 183 -- 189@LB@
115	0.01273	0.3575	b3440	yhhX	-9.67	0.316530	203 -- 215	123 -- 136	putative oxidoreductase	_____________202______________________________216\n_____________\|________________________________\|\n5'-GAC...CGUAU_______AC____AG____A__U____U____CGCAUA-3'\n______________GUACUUA__CGCA___GAU_GC_GGCA_GUCG\n______________:\|\|\|\|:\|__\|:\|\|___\|\|\|_\|\|_\|\|\|\|_\|\|\|:\n______________UAUGAGU__GUGU___CUA_CG_CCGU_CAGU\n3'-UUU...GUGGU_______CA____GUA______U____U____UGAAA...UAG-5'\n_____________\|________________________________\|\n_____________137______________________________122\n	264 -- 270	175 -- 181	-25.3028 kcal/mol	7.53441 kcal/mol	8.15082 kcal/mol	202 216@LB@ \| \|@LB@5'-GAC...CGUAU AC AG A U U CGCAUA-3'@LB@ GUACUUA CGCA GAU GC GGCA GUCG@LB@ :\|\|\|\|:\| \|:\|\| \|\|\| \|\| \|\|\|\| \|\|\|:@LB@ UAUGAGU GUGU CUA CG CCGU CAGU@LB@3'-UUU...GUGGU CA GUA U U UGAAA...UAG-5'@LB@ \| \|@LB@ 137 122@LB@@LB@@LB@Energy -9.67 kcal/mol@LB@Hybridization Energy -25.3028 kcal/mol@LB@Unfolding Energy - mRNA 7.53441 kcal/mol@LB@Unfolding Energy - sRNA 8.15082 kcal/mol@LB@@LB@Position - mRNA 203 -- 215@LB@Position - sRNA 123 -- 136@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 175 -- 181@LB@
136	0.01456	0.3575	b0369	hemB	-9.31	0.367566	203 -- 221	75 -- 90	5-aminolevulinate dehydratase (porphobilinogen synthase)	_____________202________________222\n_____________\|__________________\|\n5'-CCA...UAAAA_______ACCC_______GGUAU...UGC-3'\n______________CAUCCCU____UGCUUCA\n______________\|\|:\|\|\|:____\|\|\|\|\|\|\|\n______________GUGGGGG____ACGAAGU\n3'-UUU...ACCCC_______A__________AG-5'\n_____________\|__________________\|\n_____________91_________________74\n	153 -- 159	3 -- 9	-17.8942 kcal/mol	1.92924 kcal/mol	7.09151 kcal/mol	202 222@LB@ \| \|@LB@5'-CCA...UAAAA ACCC GGUAU...UGC-3'@LB@ CAUCCCU UGCUUCA@LB@ \|\|:\|\|\|: \|\|\|\|\|\|\|@LB@ GUGGGGG ACGAAGU@LB@3'-UUU...ACCCC A AG-5'@LB@ \| \|@LB@ 91 74@LB@@LB@@LB@Energy -9.31 kcal/mol@LB@Hybridization Energy -17.8942 kcal/mol@LB@Unfolding Energy - mRNA 1.92924 kcal/mol@LB@Unfolding Energy - sRNA 7.09151 kcal/mol@LB@@LB@Position - mRNA 203 -- 221@LB@Position - sRNA 75 -- 90@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 3 -- 9@LB@
75	0.007778	0.3458	b0766	ybhA	-9.49	0.341100	208 -- 245	124 -- 172	pyridoxal phosphate (PLP) phosphatase	_____________207___________________________246\n_____________\|_____________________________\|\n5'-GAA...UGGAA_______UG________________U___UCUCG...GCG-3'\n______________UACGCCA__AC_CA__CACGCGUGA_UGC\n______________\|\|\|:\|\|\|__\|\|_\|\|__\|\|\|:\|:\|\|\|_\|\|\|\n______________AUGUGGU__UG_GU__GUGUGUACU_ACG\n3'-UUU...CUAAA_______UA__A__CA_____________UCCGU...UAG-5'\n_____________\|_____________________________\|\n_____________173___________________________123\n	195 -- 201	182 -- 188	-28.0817 kcal/mol	7.23992 kcal/mol	7.72227 kcal/mol	207 246@LB@ \| \|@LB@5'-GAA...UGGAA UG U UCUCG...GCG-3'@LB@ UACGCCA AC CA CACGCGUGA UGC@LB@ \|\|\|:\|\|\| \|\| \|\| \|\|\|:\|:\|\|\| \|\|\|@LB@ AUGUGGU UG GU GUGUGUACU ACG@LB@3'-UUU...CUAAA UA A CA UCCGU...UAG-5'@LB@ \| \|@LB@ 173 123@LB@@LB@@LB@Energy -9.49 kcal/mol@LB@Hybridization Energy -28.0817 kcal/mol@LB@Unfolding Energy - mRNA 7.23992 kcal/mol@LB@Unfolding Energy - sRNA 7.72227 kcal/mol@LB@@LB@Position - mRNA 208 -- 245@LB@Position - sRNA 124 -- 172@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 182 -- 188@LB@
81	0.008673	0.3575	b1683	sufB	-9.84	0.294156	211 -- 257	124 -- 171	component of SufBCD Fe-S cluster assembly scaffold	_____________210_______________258\n_____________\|_________________\|\n5'-GUU...AAUCA________AAUU_____ACCCU...AGC-3'\n______________GAUAUUCA____UCACA\n______________:\|\|\|:\|\|\|____\|\|\|\|\|\n______________UUAUGAGU____AGUGU\n3'-UUU...UGUGG________C________GUACU...UAG-5'\n_____________\|_________________\|\n_____________172_______________123\n	127 -- 133	175 -- 181	-8.93573 kcal/mol	1.46068 kcal/mol	0.409577 kcal/mol	210 258@LB@ \| \|@LB@5'-GUU...AAUCA AAUU ACCCU...AGC-3'@LB@ GAUAUUCA UCACA@LB@ :\|\|\|:\|\|\| \|\|\|\|\|@LB@ UUAUGAGU AGUGU@LB@3'-UUU...UGUGG C GUACU...UAG-5'@LB@ \| \|@LB@ 172 123@LB@@LB@@LB@Energy -9.84 kcal/mol@LB@Hybridization Energy -8.93573 kcal/mol@LB@Unfolding Energy - mRNA 1.46068 kcal/mol@LB@Unfolding Energy - sRNA 0.409577 kcal/mol@LB@@LB@Position - mRNA 211 -- 257@LB@Position - sRNA 124 -- 171@LB@Position Seed - mRNA 127 -- 133@LB@Position Seed - sRNA 175 -- 181@LB@
100	0.01091	0.3575	b0123	cueO	-12.06	0.108476	211 -- 256	146 -- 195	multicopper oxidase (laccase)	_____________210________________________________________________257\n_____________\|__________________________________________________\|\n5'-CUG...ACGUC_______CUUAA________C_______UG_________U__________GCCGC...CGU-3'\n______________GUGAUUU______AAUAUUC_GUCGCGC__GGUGU_GGC___UCGGCUUU\n______________\|\|\|\|\|\|\|______\|\|\|\|:\|\|_\|\|\|:\|:\|__\|:\|\|:_\|\|\|___\|\|::\|\|\|\|\n______________CACUAAA______UUAUGAG_CAGUGUG__CUACG_CCG___AGUUGAAA\n3'-UUU...CCGCC_______AUGUGG_______U_______UA_____U___UUC________GUCUU...UAG-5'\n_____________\|__________________________________________________\|\n_____________196________________________________________________145\n	250 -- 256	146 -- 152	-42.9672 kcal/mol	13.2361 kcal/mol	12.9468 kcal/mol	210 257@LB@ \| \|@LB@5'-CUG...ACGUC CUUAA C UG U GCCGC...CGU-3'@LB@ GUGAUUU AAUAUUC GUCGCGC GGUGU GGC UCGGCUUU@LB@ \|\|\|\|\|\|\| \|\|\|\|:\|\| \|\|\|:\|:\| \|:\|\|: \|\|\| \|\|::\|\|\|\|@LB@ CACUAAA UUAUGAG CAGUGUG CUACG CCG AGUUGAAA@LB@3'-UUU...CCGCC AUGUGG U UA U UUC GUCUU...UAG-5'@LB@ \| \|@LB@ 196 145@LB@@LB@@LB@Energy -12.06 kcal/mol@LB@Hybridization Energy -42.9672 kcal/mol@LB@Unfolding Energy - mRNA 13.2361 kcal/mol@LB@Unfolding Energy - sRNA 12.9468 kcal/mol@LB@@LB@Position - mRNA 211 -- 256@LB@Position - sRNA 146 -- 195@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 146 -- 152@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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