Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
88	0.01388	0.5059	b3809	dapF	-7.53	0.274407	192 -- 207	1 -- 17	diaminopimelate epimerase	_____________191_______________208\n_____________\|_________________\|\n5'-UCU...GAUUG____A_______C____UCUCG...UGG-3'\n______________GAGU_AAUGAUG__AGU\n______________:\|\|\|_\|\|\|\|\|\|\|__\|\|:\n______________UUCA_UUACUAC__UCG\n3'-UUU...UUUAU____A_______UA___-5'\n_____________\|________________\|\n_____________18_______________1\n	197 -- 203	6 -- 12	-9.99588 kcal/mol	2.41483 kcal/mol	0.0529402 kcal/mol	191 208@LB@ \| \|@LB@5'-UCU...GAUUG A C UCUCG...UGG-3'@LB@ GAGU AAUGAUG AGU@LB@ :\|\|\| \|\|\|\|\|\|\| \|\|:@LB@ UUCA UUACUAC UCG@LB@3'-UUU...UUUAU A UA -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -7.53 kcal/mol@LB@Hybridization Energy -9.99588 kcal/mol@LB@Unfolding Energy - mRNA 2.41483 kcal/mol@LB@Unfolding Energy - sRNA 0.0529402 kcal/mol@LB@@LB@Position - mRNA 192 -- 207@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 6 -- 12@LB@
89	0.01433	0.5059	b0636	rlmH	-12.18	0.033475	189 -- 207	1 -- 19	23S rRNA m(3)Psi1915 pseudouridine methyltransferase SAM-dependent	_____________188__________________208\n_____________\|____________________\|\n5'-CGG...AACUC___________C________UGCAA...UCG-3'\n______________UGGAGUUAAUG_GUGA_AGC\n______________\|::\|\|\|\|\|\|\|\|_:\|\|\|_\|\|\|\n______________AUUUCAAUUAC_UACU_UCG\n3'-UUU...UAUUU________________A___-5'\n_____________\|___________________\|\n_____________20__________________1\n	193 -- 199	9 -- 15	-16.4949 kcal/mol	4.25175 kcal/mol	0.0638423 kcal/mol	188 208@LB@ \| \|@LB@5'-CGG...AACUC C UGCAA...UCG-3'@LB@ UGGAGUUAAUG GUGA AGC@LB@ \|::\|\|\|\|\|\|\|\| :\|\|\| \|\|\|@LB@ AUUUCAAUUAC UACU UCG@LB@3'-UUU...UAUUU A -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -12.18 kcal/mol@LB@Hybridization Energy -16.4949 kcal/mol@LB@Unfolding Energy - mRNA 4.25175 kcal/mol@LB@Unfolding Energy - sRNA 0.0638423 kcal/mol@LB@@LB@Position - mRNA 189 -- 207@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 9 -- 15@LB@
90	0.01478	0.5059	b0740	tolB	-11.20	0.054749	186 -- 207	1 -- 21	periplasmic protein	_____________185_____________________208\n_____________\|_______________________\|\n5'-UCC...GUCCA_______GAGAU___________AGGCA...CCG-3'\n______________GAUAAGG_____AUGAUGA_AGC\n______________:\|\|\|\|:\|_____\|\|\|\|\|\|\|_\|\|\|\n______________UUAUUUC_____UACUACU_UCG\n3'-UUU...AUUAU_______AAU_________A___-5'\n_____________\|______________________\|\n_____________22_____________________1\n	198 -- 204	5 -- 11	-16.1118 kcal/mol	4.84175 kcal/mol	0.0669945 kcal/mol	185 208@LB@ \| \|@LB@5'-UCC...GUCCA GAGAU AGGCA...CCG-3'@LB@ GAUAAGG AUGAUGA AGC@LB@ :\|\|\|\|:\| \|\|\|\|\|\|\| \|\|\|@LB@ UUAUUUC UACUACU UCG@LB@3'-UUU...AUUAU AAU A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -16.1118 kcal/mol@LB@Unfolding Energy - mRNA 4.84175 kcal/mol@LB@Unfolding Energy - sRNA 0.0669945 kcal/mol@LB@@LB@Position - mRNA 186 -- 207@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 5 -- 11@LB@
92	0.01497	0.5059	b1902	ftnB	-10.62	0.072498	12 -- 36	1 -- 25	ferritin B putative ferrous iron reservoir	_____________11________________________37\n_____________\|_________________________\|\n5'-UGA...GUAAA____U_____C________UUA___AUUUU...AAC-3'\n______________AAUA_AUAAA_UUGAUGAU___AGC\n______________\|\|\|\|_\|\|\|\|\|_\|\|:\|\|\|\|\|___\|\|\|\n______________UUAU_UAUUU_AAUUACUA___UCG\n3'-UUU...UGCCA____U_____C________CUA___-5'\n_____________\|________________________\|\n_____________26_______________________1\n	24 -- 30	7 -- 13	-13.6335 kcal/mol	2.89836 kcal/mol	0.112205 kcal/mol	11 37@LB@ \| \|@LB@5'-UGA...GUAAA U C UUA AUUUU...AAC-3'@LB@ AAUA AUAAA UUGAUGAU AGC@LB@ \|\|\|\| \|\|\|\|\| \|\|:\|\|\|\|\| \|\|\|@LB@ UUAU UAUUU AAUUACUA UCG@LB@3'-UUU...UGCCA U C CUA -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -10.62 kcal/mol@LB@Hybridization Energy -13.6335 kcal/mol@LB@Unfolding Energy - mRNA 2.89836 kcal/mol@LB@Unfolding Energy - sRNA 0.112205 kcal/mol@LB@@LB@Position - mRNA 12 -- 36@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 7 -- 13@LB@
94	0.01566	0.5059	b3918	cdh	-10.38	0.081442	225 -- 238	1 -- 14	CDP-diacylglycerol phosphotidylhydrolase	_____________224____________239\n_____________\|______________\|\n5'-AUU...UUUUU______________UAUCG...CAU-3'\n______________UUGGUGAUGAUAGU\n______________\|\|::\|\|\|\|\|\|\|\|\|:\n______________AAUUACUACUAUCG\n3'-UUU...AUUUC______________-5'\n_____________\|_____________\|\n_____________15____________1\n	232 -- 238	1 -- 7	-16.1883 kcal/mol	5.76383 kcal/mol	0.0473494 kcal/mol	224 239@LB@ \| \|@LB@5'-AUU...UUUUU UAUCG...CAU-3'@LB@ UUGGUGAUGAUAGU@LB@ \|\|::\|\|\|\|\|\|\|\|\|:@LB@ AAUUACUACUAUCG@LB@3'-UUU...AUUUC -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -10.38 kcal/mol@LB@Hybridization Energy -16.1883 kcal/mol@LB@Unfolding Energy - mRNA 5.76383 kcal/mol@LB@Unfolding Energy - sRNA 0.0473494 kcal/mol@LB@@LB@Position - mRNA 225 -- 238@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 1 -- 7@LB@
98	0.01586	0.5059	b1860	ruvB	-8.95	0.154425	184 -- 211	1 -- 30	ATP-dependent DNA helicase component of RuvABC resolvasome	_____________183_____________________________212\n_____________\|_______________________________\|\n5'-ACG...GCGCC___U__UG_______________U_______AGACC...GUC-3'\n______________GCG_UA__AGGUAAAG__GAUGA_UGA_AGC\n______________:\|\|_\|\|__\|::\|\|\|\|\|__:\|\|\|\|_\|\|\|_\|\|\|\n______________UGC_AU__UUUAUUUC__UUACU_ACU_UCG\n3'-UUU...CUUAC___C__UA________AA_________A___-5'\n_____________\|______________________________\|\n_____________31_____________________________1\n	193 -- 199	15 -- 21	-17.0174 kcal/mol	5.93551 kcal/mol	2.12822 kcal/mol	183 212@LB@ \| \|@LB@5'-ACG...GCGCC U UG U AGACC...GUC-3'@LB@ GCG UA AGGUAAAG GAUGA UGA AGC@LB@ :\|\| \|\| \|::\|\|\|\|\| :\|\|\|\| \|\|\| \|\|\|@LB@ UGC AU UUUAUUUC UUACU ACU UCG@LB@3'-UUU...CUUAC C UA AA A -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -8.95 kcal/mol@LB@Hybridization Energy -17.0174 kcal/mol@LB@Unfolding Energy - mRNA 5.93551 kcal/mol@LB@Unfolding Energy - sRNA 2.12822 kcal/mol@LB@@LB@Position - mRNA 184 -- 211@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 15 -- 21@LB@
99	0.01587	0.5059	b2155	cirA	-12.92	0.022646	275 -- 290	1 -- 16	colicin IA outer membrane receptor and translocator; ferric iron-catecholate transporter	_____________274______________291\n_____________\|________________\|\n5'-GGA...UUAGC___C____________GAAAC...UGG-3'\n______________GGU_GAUGAUGAUGGC\n______________:\|\|_:\|\|\|\|\|\|\|\|:\|\|\n______________UCA_UUACUACUAUCG\n3'-UUU...UUAUU___A____________-5'\n_____________\|_______________\|\n_____________17______________1\n	284 -- 290	1 -- 7	-19.8516 kcal/mol	6.87927 kcal/mol	0.0492804 kcal/mol	274 291@LB@ \| \|@LB@5'-GGA...UUAGC C GAAAC...UGG-3'@LB@ GGU GAUGAUGAUGGC@LB@ :\|\| :\|\|\|\|\|\|\|\|:\|\|@LB@ UCA UUACUACUAUCG@LB@3'-UUU...UUAUU A -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -12.92 kcal/mol@LB@Hybridization Energy -19.8516 kcal/mol@LB@Unfolding Energy - mRNA 6.87927 kcal/mol@LB@Unfolding Energy - sRNA 0.0492804 kcal/mol@LB@@LB@Position - mRNA 275 -- 290@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 1 -- 7@LB@
102	0.01618	0.5059	b3306	rpsH	-10.04	0.095208	179 -- 210	1 -- 36	30S ribosomal subunit protein S8	_____________178____________________________________211\n_____________\|______________________________________\|\n5'-AGC...CCAAU_____C________________ACA_______GCAU__AAGAU...AAG-3'\n______________UGAAU_ACGG____GAGUAAAG_____GAUGA____GC\n______________\|\|\|\|\|_\|\|\|\|____:\|:\|\|\|\|\|_____\|\|\|\|\|____\|\|\n______________ACUUA_UGCC____UUUAUUUC_____CUACU____CG\n3'-UUU...UCUUU_____C____AUUA________AAUUA_____AU____-5'\n_____________\|_____________________________________\|\n_____________37____________________________________1\n	190 -- 196	15 -- 21	-20.3749 kcal/mol	4.57112 kcal/mol	5.76239 kcal/mol	178 211@LB@ \| \|@LB@5'-AGC...CCAAU C ACA GCAU AAGAU...AAG-3'@LB@ UGAAU ACGG GAGUAAAG GAUGA GC@LB@ \|\|\|\|\| \|\|\|\| :\|:\|\|\|\|\| \|\|\|\|\| \|\|@LB@ ACUUA UGCC UUUAUUUC CUACU CG@LB@3'-UUU...UCUUU C AUUA AAUUA AU -5'@LB@ \| \|@LB@ 37 1@LB@@LB@@LB@Energy -10.04 kcal/mol@LB@Hybridization Energy -20.3749 kcal/mol@LB@Unfolding Energy - mRNA 4.57112 kcal/mol@LB@Unfolding Energy - sRNA 5.76239 kcal/mol@LB@@LB@Position - mRNA 179 -- 210@LB@Position - sRNA 1 -- 36@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 15 -- 21@LB@
103	0.01627	0.5059	b3527	yhjJ	-12.72	0.025178	191 -- 250	1 -- 59	putative periplasmic M16 family chaperone	_____________190_____________________________________________________________________251\n_____________\|_______________________________________________________________________\|\n5'-CUC...UGAUC______UC___U___GGGCACAAAAA____ACUUUUAGCG____________________C__________CACUG...GGC-3'\n______________AGGGGU__ACA_GCA___________UUCG__________GGCGGU___________UUG_UGAUGAUGGC\n______________\|\|\|\|\|\|__\|\|\|_:\|\|___________\|\|\|:__________\|:\|\|\|\|___________\|\|:_\|\|\|\|\|\|\|:\|\|\n______________UCCCCA__UGU_UGU___________AAGU__________CUGCCA___________AAU_ACUACUAUCG\n3'-UUU...CUUUA______UU___C__________________CUUUACUUA_______UUAUUUAUUUC___U__________-5'\n_____________\|______________________________________________________________________\|\n_____________60_____________________________________________________________________1\n	244 -- 250	1 -- 7	-34.0873 kcal/mol	15.0257 kcal/mol	6.33764 kcal/mol	190 251@LB@ \| \|@LB@5'-CUC...UGAUC UC U GGGCACAAAAA ACUUUUAGCG C CACUG...GGC-3'@LB@ AGGGGU ACA GCA UUCG GGCGGU UUG UGAUGAUGGC@LB@ \|\|\|\|\|\| \|\|\| :\|\| \|\|\|: \|:\|\|\|\| \|\|: \|\|\|\|\|\|\|:\|\|@LB@ UCCCCA UGU UGU AAGU CUGCCA AAU ACUACUAUCG@LB@3'-UUU...CUUUA UU C CUUUACUUA UUAUUUAUUUC U -5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -12.72 kcal/mol@LB@Hybridization Energy -34.0873 kcal/mol@LB@Unfolding Energy - mRNA 15.0257 kcal/mol@LB@Unfolding Energy - sRNA 6.33764 kcal/mol@LB@@LB@Position - mRNA 191 -- 250@LB@Position - sRNA 1 -- 59@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 1 -- 7@LB@
106	0.01645	0.5059	b2416	ptsI	-13.93	0.013056	96 -- 143	1 -- 59	PEP-protein phosphotransferase of PTS system (enzyme I)	_____________95__________________________________________________________144\n_____________\|___________________________________________________________\|\n5'-GUG...GCAGA___CGA_________AG_________________UGAACAUCU______AC________GGAAC...CCG-3'\n______________AGG_______AGACG__CAGAAA______GCGGU_________GGUUAA___UGAUGGC\n______________\|\|\|_______\|\|\|\|:__\|\|\|\|\|\|______:\|\|\|\|_________:\|\|\|\|\|___\|\|\|\|:\|\|\n______________UCC_______UCUGU__GUCUUU______UGCCA_________UCAAUU___ACUAUCG\n3'-UUU...CUUUA___CCAUUUG_____AA______ACUUAC_____UUAUUUAUU______ACU_______-5'\n_____________\|__________________________________________________________\|\n_____________60_________________________________________________________1\n	137 -- 143	1 -- 7	-30.8595 kcal/mol	10.5928 kcal/mol	6.33764 kcal/mol	95 144@LB@ \| \|@LB@5'-GUG...GCAGA CGA AG UGAACAUCU AC GGAAC...CCG-3'@LB@ AGG AGACG CAGAAA GCGGU GGUUAA UGAUGGC@LB@ \|\|\| \|\|\|\|: \|\|\|\|\|\| :\|\|\|\| :\|\|\|\|\| \|\|\|\|:\|\|@LB@ UCC UCUGU GUCUUU UGCCA UCAAUU ACUAUCG@LB@3'-UUU...CUUUA CCAUUUG AA ACUUAC UUAUUUAUU ACU -5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -13.93 kcal/mol@LB@Hybridization Energy -30.8595 kcal/mol@LB@Unfolding Energy - mRNA 10.5928 kcal/mol@LB@Unfolding Energy - sRNA 6.33764 kcal/mol@LB@@LB@Position - mRNA 96 -- 143@LB@Position - sRNA 1 -- 59@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 1 -- 7@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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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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