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
71	0.01035	0.4523	b3365	nirB	-13.52	0.016420	166 -- 211	14 -- 63	nitrite reductase large subunit NAD(P)H-binding	_____________165_________________________________________________212\n_____________\|___________________________________________________\|\n5'-AUC...CGUUA_______C__________AA_________C______AAA______C_____CAGAC...UUA-3'\n______________AGGUAGG_GGU_AAUAGA_____AGAAAU_GA_GGC___AAUGAG_AAAGU\n______________\|::\|\|\|\|_\|\|\|_\|\|:\|\|\|_____\|\|\|\|\|\|_:\|_\|:\|___\|\|\|:\|:_\|\|\|\|\|\n______________UUUAUCC_CCA_UUGUCU_____UCUUUA_UU_CUG___UUAUUU_UUUCA\n3'-UUU...CCAAC___________U______GUAAG______C__A___CCA______A_____AUUAC...UCG-5'\n_____________\|___________________________________________________\|\n_____________64__________________________________________________13\n	166 -- 172	57 -- 63	-27.6903 kcal/mol	7.84168 kcal/mol	6.33269 kcal/mol	165 212@LB@ \| \|@LB@5'-AUC...CGUUA C AA C AAA C CAGAC...UUA-3'@LB@ AGGUAGG GGU AAUAGA AGAAAU GA GGC AAUGAG AAAGU@LB@ \|::\|\|\|\| \|\|\| \|\|:\|\|\| \|\|\|\|\|\| :\| \|:\| \|\|\|:\|: \|\|\|\|\|@LB@ UUUAUCC CCA UUGUCU UCUUUA UU CUG UUAUUU UUUCA@LB@3'-UUU...CCAAC U GUAAG C A CCA A AUUAC...UCG-5'@LB@ \| \|@LB@ 64 13@LB@@LB@@LB@Energy -13.52 kcal/mol@LB@Hybridization Energy -27.6903 kcal/mol@LB@Unfolding Energy - mRNA 7.84168 kcal/mol@LB@Unfolding Energy - sRNA 6.33269 kcal/mol@LB@@LB@Position - mRNA 166 -- 211@LB@Position - sRNA 14 -- 63@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 57 -- 63@LB@
72	0.01058	0.4523	b3458	livK	-8.91	0.157650	183 -- 215	28 -- 63	leucine transporter subunit	_____________182___________________________________216\n_____________\|_____________________________________\|\n5'-UGU...AUCAC________AUUUUU____UAU______CG________AAAAC...CGA-3'\n______________GAAUGGGG_______GAC_____GAAA__GAAUG_CG\n______________:\|\|\|:\|\|\|_______\|\|\|_____\|\|\|\|__\|\|\|\|\|_\|\|\n______________UUUAUCCC_______CUG_____CUUU__CUUAC_GC\n3'-UUU...CCAAC________CAUUUGU___UAAGU____A______U__CAUUA...UCG-5'\n_____________\|_____________________________________\|\n_____________64____________________________________27\n	184 -- 190	56 -- 62	-20.644 kcal/mol	5.44449 kcal/mol	6.29422 kcal/mol	182 216@LB@ \| \|@LB@5'-UGU...AUCAC AUUUUU UAU CG AAAAC...CGA-3'@LB@ GAAUGGGG GAC GAAA GAAUG CG@LB@ :\|\|\|:\|\|\| \|\|\| \|\|\|\| \|\|\|\|\| \|\|@LB@ UUUAUCCC CUG CUUU CUUAC GC@LB@3'-UUU...CCAAC CAUUUGU UAAGU A U CAUUA...UCG-5'@LB@ \| \|@LB@ 64 27@LB@@LB@@LB@Energy -8.91 kcal/mol@LB@Hybridization Energy -20.644 kcal/mol@LB@Unfolding Energy - mRNA 5.44449 kcal/mol@LB@Unfolding Energy - sRNA 6.29422 kcal/mol@LB@@LB@Position - mRNA 183 -- 215@LB@Position - sRNA 28 -- 63@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 56 -- 62@LB@
73	0.01069	0.4523	b1949	fliQ	-11.32	0.051762	219 -- 228	2 -- 11	flagellar biosynthesis protein	_____________218________229\n_____________\|__________\|\n5'-UUC...CGGUC__________GGACU...UUA-3'\n______________AUGAUGAUGG\n______________\|\|\|\|\|\|\|\|:\|\n______________UACUACUAUC\n3'-UUU...UCAAU__________G-5'\n_____________\|__________\|\n_____________12_________1\n	222 -- 228	2 -- 8	-12.2017 kcal/mol	0.859554 kcal/mol	0.0252227 kcal/mol	218 229@LB@ \| \|@LB@5'-UUC...CGGUC GGACU...UUA-3'@LB@ AUGAUGAUGG@LB@ \|\|\|\|\|\|\|\|:\|@LB@ UACUACUAUC@LB@3'-UUU...UCAAU G-5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -11.32 kcal/mol@LB@Hybridization Energy -12.2017 kcal/mol@LB@Unfolding Energy - mRNA 0.859554 kcal/mol@LB@Unfolding Energy - sRNA 0.0252227 kcal/mol@LB@@LB@Position - mRNA 219 -- 228@LB@Position - sRNA 2 -- 11@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 2 -- 8@LB@
74	0.0107	0.4523	b3385	gph	-12.85	0.023515	41 -- 77	8 -- 48	phosphoglycolate phosphatase	_____________40____________________________________________78\n_____________\|_____________________________________________\|\n5'-ACU...GCUUU_______GACU__________________C_______________ACAAC...UGU-3'\n______________GACAUUC____AGAAGUG___GACGGUGG___GUGAAG___GUGA\n______________\|\|\|\|\|\|\|____\|\|\|\|:\|\|___\|\|\|\|\|\|::___:\|:\|\|\|___:\|\|\|\n______________CUGUAAG____UCUUUAC___CUGCCAUU___UAUUUC___UACU\n3'-UUU...UUUGU__________________UUA________AUU______AAU____ACUAUCG-5'\n_____________\|_____________________________________________\|\n_____________49____________________________________________7\n	60 -- 66	24 -- 30	-29.3756 kcal/mol	10.2075 kcal/mol	6.31567 kcal/mol	40 78@LB@ \| \|@LB@5'-ACU...GCUUU GACU C ACAAC...UGU-3'@LB@ GACAUUC AGAAGUG GACGGUGG GUGAAG GUGA@LB@ \|\|\|\|\|\|\| \|\|\|\|:\|\| \|\|\|\|\|\|:: :\|:\|\|\| :\|\|\|@LB@ CUGUAAG UCUUUAC CUGCCAUU UAUUUC UACU@LB@3'-UUU...UUUGU UUA AUU AAU ACUAUCG-5'@LB@ \| \|@LB@ 49 7@LB@@LB@@LB@Energy -12.85 kcal/mol@LB@Hybridization Energy -29.3756 kcal/mol@LB@Unfolding Energy - mRNA 10.2075 kcal/mol@LB@Unfolding Energy - sRNA 6.31567 kcal/mol@LB@@LB@Position - mRNA 41 -- 77@LB@Position - sRNA 8 -- 48@LB@Position Seed - mRNA 60 -- 66@LB@Position Seed - sRNA 24 -- 30@LB@
75	0.01076	0.4523	b4291	fecA	-8.60	0.179326	183 -- 193	2 -- 12	TonB-dependent outer membrane ferric citrate transporter and signal transducer; ferric citrate extracelluar receptor; FecR-interacting protein	_____________182_________194\n_____________\|___________\|\n5'-AGC...ACAAA___________GGAAG...CUG-3'\n______________AAUGAUGAUGG\n______________\|\|\|\|\|\|\|\|\|:\|\n______________UUACUACUAUC\n3'-UUU...UUCAA___________G-5'\n_____________\|___________\|\n_____________13__________1\n	187 -- 193	2 -- 8	-12.8036 kcal/mol	4.16536 kcal/mol	0.0386655 kcal/mol	182 194@LB@ \| \|@LB@5'-AGC...ACAAA GGAAG...CUG-3'@LB@ AAUGAUGAUGG@LB@ \|\|\|\|\|\|\|\|\|:\|@LB@ UUACUACUAUC@LB@3'-UUU...UUCAA G-5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -12.8036 kcal/mol@LB@Unfolding Energy - mRNA 4.16536 kcal/mol@LB@Unfolding Energy - sRNA 0.0386655 kcal/mol@LB@@LB@Position - mRNA 183 -- 193@LB@Position - sRNA 2 -- 12@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 2 -- 8@LB@
76	0.01084	0.4523	b3990	thiH	-9.70	0.111440	16 -- 25	55 -- 64	tyrosine lyase involved in thiamine-thiazole moiety synthesis	_____________15_________26\n_____________\|__________\|\n5'-GCC...CGCUG__________CCGAC...AUG-3'\n______________GAAAUGGGGG\n______________\|\|\|\|\|:\|\|\|\|\n______________CUUUAUCCCC\n3'-UUU...GCCAA__________AUUUG...UCG-5'\n_____________\|__________\|\n_____________65_________54\n	19 -- 25	55 -- 61	-15.2995 kcal/mol	5.57445 kcal/mol	0.0291912 kcal/mol	15 26@LB@ \| \|@LB@5'-GCC...CGCUG CCGAC...AUG-3'@LB@ GAAAUGGGGG@LB@ \|\|\|\|\|:\|\|\|\|@LB@ CUUUAUCCCC@LB@3'-UUU...GCCAA AUUUG...UCG-5'@LB@ \| \|@LB@ 65 54@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -15.2995 kcal/mol@LB@Unfolding Energy - mRNA 5.57445 kcal/mol@LB@Unfolding Energy - sRNA 0.0291912 kcal/mol@LB@@LB@Position - mRNA 16 -- 25@LB@Position - sRNA 55 -- 64@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 55 -- 61@LB@
77	0.01108	0.4523	b2099	yegU	-9.55	0.118747	1 -- 10	2 -- 11	ADP-ribosylglycohydrolase family protein	______________1_________11\n______________\|_________\|\n___________5'-__________AAAAG...CAC-3'\n______________GUGAUGAUGG\n______________:\|\|\|\|\|\|\|:\|\n______________UACUACUAUC\n3'-UUU...UCAAU__________G-5'\n_____________\|__________\|\n_____________12_________1\n	4 -- 10	2 -- 8	-12.4903 kcal/mol	2.91076 kcal/mol	0.0252227 kcal/mol	1 11@LB@ \| \|@LB@ 5'- AAAAG...CAC-3'@LB@ GUGAUGAUGG@LB@ :\|\|\|\|\|\|\|:\|@LB@ UACUACUAUC@LB@3'-UUU...UCAAU G-5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -9.55 kcal/mol@LB@Hybridization Energy -12.4903 kcal/mol@LB@Unfolding Energy - mRNA 2.91076 kcal/mol@LB@Unfolding Energy - sRNA 0.0252227 kcal/mol@LB@@LB@Position - mRNA 1 -- 10@LB@Position - sRNA 2 -- 11@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 2 -- 8@LB@
78	0.01113	0.4523	b2678	proW	-13.08	0.020853	190 -- 200	49 -- 59	glycine betaine/proline ABC transporter permease	_____________189_________201\n_____________\|___________\|\n5'-GUU...CGUGA___________AUGGC...ACG-3'\n______________GGGGGUAAAUA\n______________:\|\|\|\|\|\|\|\|:\|\n______________UCCCCAUUUGU\n3'-UUU...CUUUA___________CUGUA...UCG-5'\n_____________\|___________\|\n_____________60__________48\n	194 -- 200	49 -- 55	-15.0309 kcal/mol	1.22377 kcal/mol	0.730523 kcal/mol	189 201@LB@ \| \|@LB@5'-GUU...CGUGA AUGGC...ACG-3'@LB@ GGGGGUAAAUA@LB@ :\|\|\|\|\|\|\|\|:\|@LB@ UCCCCAUUUGU@LB@3'-UUU...CUUUA CUGUA...UCG-5'@LB@ \| \|@LB@ 60 48@LB@@LB@@LB@Energy -13.08 kcal/mol@LB@Hybridization Energy -15.0309 kcal/mol@LB@Unfolding Energy - mRNA 1.22377 kcal/mol@LB@Unfolding Energy - sRNA 0.730523 kcal/mol@LB@@LB@Position - mRNA 190 -- 200@LB@Position - sRNA 49 -- 59@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 49 -- 55@LB@
79	0.01117	0.4523	b1593	ynfK	-13.04	0.021217	188 -- 210	1 -- 21	putative dethiobiotin synthetase	_____________187_____________________211\n_____________\|_______________________\|\n5'-CAC...AUAAC________________CUGA___GUUUC...CGG-3'\n______________GGUGGAGUUAGUGAUG____AGC\n______________::\|::\|\|\|\|\|:\|\|\|\|\|____\|\|\|\n______________UUAUUUCAAUUACUAC____UCG\n3'-UUU...AUUAU________________UA_____-5'\n_____________\|______________________\|\n_____________22_____________________1\n	197 -- 203	6 -- 12	-19.4081 kcal/mol	6.29658 kcal/mol	0.0669945 kcal/mol	187 211@LB@ \| \|@LB@5'-CAC...AUAAC CUGA GUUUC...CGG-3'@LB@ GGUGGAGUUAGUGAUG AGC@LB@ ::\|::\|\|\|\|\|:\|\|\|\|\| \|\|\|@LB@ UUAUUUCAAUUACUAC UCG@LB@3'-UUU...AUUAU UA -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -13.04 kcal/mol@LB@Hybridization Energy -19.4081 kcal/mol@LB@Unfolding Energy - mRNA 6.29658 kcal/mol@LB@Unfolding Energy - sRNA 0.0669945 kcal/mol@LB@@LB@Position - mRNA 188 -- 210@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 6 -- 12@LB@
80	0.01119	0.4523	b0241	phoE	-11.22	0.054424	189 -- 234	2 -- 43	outer membrane phosphoporin protein E	_____________188____________________________________________235\n_____________\|______________________________________________\|\n5'-AGC...UAAAA__________AA____AAAAGAGCACUCU__CA_____________GCAUU...AUG-3'\n______________UCAGGAAUGA__AUGA_____________GG__UUAGUGGUGAUGG\n______________\|\|\|\|:\|\|\|\|\|__\|\|\|\|_____________:\|__\|\|\|:\|\|:\|\|\|\|:\|\n______________AGUCUUUACU__UACU_____________UC__AAUUACUACUAUC\n3'-UUU...CUGUA________________GCCAUUAUUUAUU_________________G-5'\n_____________\|______________________________________________\|\n_____________44_____________________________________________1\n	228 -- 234	2 -- 8	-27.55 kcal/mol	10.0434 kcal/mol	6.29139 kcal/mol	188 235@LB@ \| \|@LB@5'-AGC...UAAAA AA AAAAGAGCACUCU CA GCAUU...AUG-3'@LB@ UCAGGAAUGA AUGA GG UUAGUGGUGAUGG@LB@ \|\|\|\|:\|\|\|\|\| \|\|\|\| :\| \|\|\|:\|\|:\|\|\|\|:\|@LB@ AGUCUUUACU UACU UC AAUUACUACUAUC@LB@3'-UUU...CUGUA GCCAUUAUUUAUU G-5'@LB@ \| \|@LB@ 44 1@LB@@LB@@LB@Energy -11.22 kcal/mol@LB@Hybridization Energy -27.55 kcal/mol@LB@Unfolding Energy - mRNA 10.0434 kcal/mol@LB@Unfolding Energy - sRNA 6.29139 kcal/mol@LB@@LB@Position - mRNA 189 -- 234@LB@Position - sRNA 2 -- 43@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 2 -- 8@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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