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	Additional homologs
160	0.02589	0.526	b3297	rpsK	-10.33	0.083340	178 -- 193	52 -- 64	30S ribosomal subunit protein S11		_____________177______________194\n_____________\|________________\|\n5'-CGA...AUCAA______AUC_______UUGAA...CUA-3'\n______________GAAAUA___GGGGUGA\n______________\|\|\|\|\|\|___\|\|\|\|\|:\|\n______________CUUUAU___CCCCAUU\n3'-UUU...GCCAA________________UGUCU...UCG-5'\n_____________\|________________\|\n_____________65_______________51\n	187 -- 193	52 -- 58	-13.1856 kcal/mol	2.77978 kcal/mol	0.0778991 kcal/mol	177 194@LB@ \| \|@LB@5'-CGA...AUCAA AUC UUGAA...CUA-3'@LB@ GAAAUA GGGGUGA@LB@ \|\|\|\|\|\| \|\|\|\|\|:\|@LB@ CUUUAU CCCCAUU@LB@3'-UUU...GCCAA UGUCU...UCG-5'@LB@ \| \|@LB@ 65 51@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -13.1856 kcal/mol@LB@Unfolding Energy - mRNA 2.77978 kcal/mol@LB@Unfolding Energy - sRNA 0.0778991 kcal/mol@LB@@LB@Position - mRNA 178 -- 193@LB@Position - sRNA 52 -- 64@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 52 -- 58@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@
141	0.0236	0.526	b3339	tufA	-10.69	0.070202	69 -- 84	1 -- 19	translation elongation factor EF-Tu 1	b3980	_____________68__________________85\n_____________\|___________________\|\n5'-AAU...AUUCC___________________GCCGA...CCA-3'\n______________UGAAGU__AUGAUGA_AGC\n______________\|:\|\|\|\|__\|\|\|\|\|\|\|_\|\|\|\n______________AUUUCA__UACUACU_UCG\n3'-UUU...UAUUU______AU_______A___-5'\n_____________\|__________________\|\n_____________20_________________1\n	75 -- 81	5 -- 11	-13.5879 kcal/mol	2.83361 kcal/mol	0.0638423 kcal/mol	68 85@LB@ \| \|@LB@5'-AAU...AUUCC GCCGA...CCA-3'@LB@ UGAAGU AUGAUGA AGC@LB@ \|:\|\|\|\| \|\|\|\|\|\|\| \|\|\|@LB@ AUUUCA UACUACU UCG@LB@3'-UUU...UAUUU AU A -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -10.69 kcal/mol@LB@Hybridization Energy -13.5879 kcal/mol@LB@Unfolding Energy - mRNA 2.83361 kcal/mol@LB@Unfolding Energy - sRNA 0.0638423 kcal/mol@LB@@LB@Position - mRNA 69 -- 84@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 5 -- 11@LB@
116	0.01846	0.5155	b3349	slyD	-11.19	0.055067	245 -- 274	8 -- 47	FKBP-type peptidyl prolyl cis-trans isomerase (rotamase)		_____________244______________________________________275\n_____________\|________________________________________\|\n5'-UGU...CAGGU____A__________________UGUU_____________GUCUC...ACU-3'\n______________ACGU_CAGAA______GACGGUG________GGUUGAUGA\n______________\|\|:\|_\|\|\|\|\|______\|\|\|\|\|\|:________:\|\|\|:\|\|\|\|\n______________UGUA_GUCUU______CUGCCAU________UCAAUUACU\n3'-UUU...UUGUC____A_____UACUUA_______UAUUUAUU_________ACUAUCG-5'\n_____________\|________________________________________\|\n_____________48_______________________________________7\n	268 -- 274	8 -- 14	-23.1983 kcal/mol	5.6913 kcal/mol	6.31565 kcal/mol	244 275@LB@ \| \|@LB@5'-UGU...CAGGU A UGUU GUCUC...ACU-3'@LB@ ACGU CAGAA GACGGUG GGUUGAUGA@LB@ \|\|:\| \|\|\|\|\| \|\|\|\|\|\|: :\|\|\|:\|\|\|\|@LB@ UGUA GUCUU CUGCCAU UCAAUUACU@LB@3'-UUU...UUGUC A UACUUA UAUUUAUU ACUAUCG-5'@LB@ \| \|@LB@ 48 7@LB@@LB@@LB@Energy -11.19 kcal/mol@LB@Hybridization Energy -23.1983 kcal/mol@LB@Unfolding Energy - mRNA 5.6913 kcal/mol@LB@Unfolding Energy - sRNA 6.31565 kcal/mol@LB@@LB@Position - mRNA 245 -- 274@LB@Position - sRNA 8 -- 47@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 8 -- 14@LB@
101	0.01605	0.5059	b3360	pabA	-8.89	0.158482	100 -- 107	55 -- 62	aminodeoxychorismate synthase subunit II		_____________99_______108\n_____________\|________\|\n5'-GCG...GGGGC________AUCUC...CGU-3'\n______________AAUGGGGG\n______________\|\|\|:\|\|\|\|\n______________UUAUCCCC\n3'-UUU...CAACU________AUUUG...UCG-5'\n_____________\|________\|\n_____________63_______54\n	101 -- 107	55 -- 61	-11.7531 kcal/mol	2.8331 kcal/mol	0.0270923 kcal/mol	99 108@LB@ \| \|@LB@5'-GCG...GGGGC AUCUC...CGU-3'@LB@ AAUGGGGG@LB@ \|\|\|:\|\|\|\|@LB@ UUAUCCCC@LB@3'-UUU...CAACU AUUUG...UCG-5'@LB@ \| \|@LB@ 63 54@LB@@LB@@LB@Energy -8.89 kcal/mol@LB@Hybridization Energy -11.7531 kcal/mol@LB@Unfolding Energy - mRNA 2.8331 kcal/mol@LB@Unfolding Energy - sRNA 0.0270923 kcal/mol@LB@@LB@Position - mRNA 100 -- 107@LB@Position - sRNA 55 -- 62@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 55 -- 61@LB@
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@
48	0.005342	0.3653	b3380	yhfW	-15.20	0.006283	218 -- 233	1 -- 15	phosphopentomutase-related metalloenzyme superfamily protein		_____________217______________234\n_____________\|________________\|\n5'-CUC...GUGGU________U_______UUUGG...GUG-3'\n______________GUUAGUGA_UGAUAGC\n______________\|\|\|\|:\|\|\|_\|\|\|\|\|\|\|\n______________CAAUUACU_ACUAUCG\n3'-UUU...UAUUU________________-5'\n_____________\|_______________\|\n_____________16______________1\n	227 -- 233	1 -- 7	-17.7091 kcal/mol	2.46465 kcal/mol	0.0474282 kcal/mol	217 234@LB@ \| \|@LB@5'-CUC...GUGGU U UUUGG...GUG-3'@LB@ GUUAGUGA UGAUAGC@LB@ \|\|\|\|:\|\|\| \|\|\|\|\|\|\|@LB@ CAAUUACU ACUAUCG@LB@3'-UUU...UAUUU -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -15.20 kcal/mol@LB@Hybridization Energy -17.7091 kcal/mol@LB@Unfolding Energy - mRNA 2.46465 kcal/mol@LB@Unfolding Energy - sRNA 0.0474282 kcal/mol@LB@@LB@Position - mRNA 218 -- 233@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 1 -- 7@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@
8	0.0001978	0.08119	b3391	hofQ	-22.13	0.000045	16 -- 73	27 -- 88	DNA catabolic putative fimbrial transporter		_____________15________________________________________________________________74\n_____________\|_________________________________________________________________\|\n5'-CUA...AUGGU___G__________C_____AU____GU_____AA____________AA_________C______GUGCA...UAG-3'\n______________AGG_CGAG_GCGAG_GCAUC__CGGU___AAUA_____AGACGGGCA___AGAAAUGG__GACGG\n______________\|::_\|\|\|:_\|\|\|\|\|_\|\|\|\|\|__\|\|\|\|___\|\|\|\|_____\|:\|\|:\|:\|\|___\|\|\|\|\|\|\|:__\|\|\|\|\|\n______________UUU_GCUU_CGCUC_CGUAG__GCCA___UUAU_____UUUGUCUGU___UCUUUACU__CUGCC\n______3'-UUUUU___G____A_________________ACU____CCCCA_________AAG________UA_____AUUAU...UCG-5'\n_____________\|_________________________________________________________________\|\n_____________89________________________________________________________________26\n	60 -- 66	35 -- 41	-51.8767 kcal/mol	10.3742 kcal/mol	19.3742 kcal/mol	15 74@LB@ \| \|@LB@5'-CUA...AUGGU G C AU GU AA AA C GUGCA...UAG-3'@LB@ AGG CGAG GCGAG GCAUC CGGU AAUA AGACGGGCA AGAAAUGG GACGG@LB@ \|:: \|\|\|: \|\|\|\|\| \|\|\|\|\| \|\|\|\| \|\|\|\| \|:\|\|:\|:\|\| \|\|\|\|\|\|\|: \|\|\|\|\|@LB@ UUU GCUU CGCUC CGUAG GCCA UUAU UUUGUCUGU UCUUUACU CUGCC@LB@ 3'-UUUUU G A ACU CCCCA AAG UA AUUAU...UCG-5'@LB@ \| \|@LB@ 89 26@LB@@LB@@LB@Energy -22.13 kcal/mol@LB@Hybridization Energy -51.8767 kcal/mol@LB@Unfolding Energy - mRNA 10.3742 kcal/mol@LB@Unfolding Energy - sRNA 19.3742 kcal/mol@LB@@LB@Position - mRNA 16 -- 73@LB@Position - sRNA 27 -- 88@LB@Position Seed - mRNA 60 -- 66@LB@Position Seed - sRNA 35 -- 41@LB@
144	0.02445	0.526	b3441	yhhY	-11.04	0.059403	187 -- 218	22 -- 53	aminoacyl nucleotide detoxifying acetyltransferase		_____________186________________________________219\n_____________\|__________________________________\|\n5'-CCC...CCCCA__GA_____A______________GAUA______CGCCA...UGC-3'\n______________AA__GGACA___AGGAAUGAGUGA____GUAAUA\n______________\|\|__:\|\|\|\|___\|\|:\|\|\|\|\|:\|\|\|____\|\|\|\|\|\|\n______________UU__UCUGU___UCUUUACUUACU____CAUUAU\n3'-UUU...CCCCA__UG_____AAG____________GC________UUAUU...UCG-5'\n_____________\|__________________________________\|\n_____________54_________________________________21\n	202 -- 208	30 -- 36	-22.9472 kcal/mol	5.59747 kcal/mol	6.31329 kcal/mol	186 219@LB@ \| \|@LB@5'-CCC...CCCCA GA A GAUA CGCCA...UGC-3'@LB@ AA GGACA AGGAAUGAGUGA GUAAUA@LB@ \|\| :\|\|\|\| \|\|:\|\|\|\|\|:\|\|\| \|\|\|\|\|\|@LB@ UU UCUGU UCUUUACUUACU CAUUAU@LB@3'-UUU...CCCCA UG AAG GC UUAUU...UCG-5'@LB@ \| \|@LB@ 54 21@LB@@LB@@LB@Energy -11.04 kcal/mol@LB@Hybridization Energy -22.9472 kcal/mol@LB@Unfolding Energy - mRNA 5.59747 kcal/mol@LB@Unfolding Energy - sRNA 6.31329 kcal/mol@LB@@LB@Position - mRNA 187 -- 218@LB@Position - sRNA 22 -- 53@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 30 -- 36@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

Use the following button if you want to resubmit the job with altered input or parameterization:

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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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