Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
60	0.004583	0.2539	b0674	asnB	-9.07	0.186262	281 -- 298	39 -- 51	asparagine synthetase B	_____________280________________299\n_____________\|__________________\|\n5'-ACA...CGCCU______UCAUC_______GG-3'\n______________GAUGCG_____GUGGCCC\n______________:\|\|\|\|:_____:\|\|\|\|\|\|\n______________UUACGU_____UACCGGG\n3'-UUU...CACCG__________________UUGUC...UUG-5'\n_____________\|__________________\|\n_____________52_________________38\n	292 -- 298	39 -- 45	-18.7239 kcal/mol	4.90882 kcal/mol	4.74571 kcal/mol	280 299@LB@ \| \|@LB@5'-ACA...CGCCU UCAUC GG-3'@LB@ GAUGCG GUGGCCC@LB@ :\|\|\|\|: :\|\|\|\|\|\|@LB@ UUACGU UACCGGG@LB@3'-UUU...CACCG UUGUC...UUG-5'@LB@ \| \|@LB@ 52 38@LB@@LB@@LB@Energy -9.07 kcal/mol@LB@Hybridization Energy -18.7239 kcal/mol@LB@Unfolding Energy - mRNA 4.90882 kcal/mol@LB@Unfolding Energy - sRNA 4.74571 kcal/mol@LB@@LB@Position - mRNA 281 -- 298@LB@Position - sRNA 39 -- 51@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 39 -- 45@LB@
99	0.009334	0.3118	b0675	umpH	-9.49	0.153954	143 -- 172	39 -- 66	UMP phosphatase	_____________142____________________________173\n_____________\|______________________________\|\n5'-AGC...UUUGC__________A__U__UUUUA_______G_UUAUU...AUA-3'\n______________UGGAAAAUUA_UG_GC_____UAGUGGC_C\n______________\|\|\|\|\|\|\|\|:\|_\|\|_\|\|_____:\|:\|\|\|\|_\|\n______________ACCUUUUAGU_AC_CG_____GUUACCG_G\n3'-UUU...AUACA__________C_____UUAC________G_UUGUC...UUG-5'\n_____________\|______________________________\|\n_____________67_____________________________38\n	145 -- 151	58 -- 64	-25.171 kcal/mol	9.00393 kcal/mol	6.67256 kcal/mol	142 173@LB@ \| \|@LB@5'-AGC...UUUGC A U UUUUA G UUAUU...AUA-3'@LB@ UGGAAAAUUA UG GC UAGUGGC C@LB@ \|\|\|\|\|\|\|\|:\| \|\| \|\| :\|:\|\|\|\| \|@LB@ ACCUUUUAGU AC CG GUUACCG G@LB@3'-UUU...AUACA C UUAC G UUGUC...UUG-5'@LB@ \| \|@LB@ 67 38@LB@@LB@@LB@Energy -9.49 kcal/mol@LB@Hybridization Energy -25.171 kcal/mol@LB@Unfolding Energy - mRNA 9.00393 kcal/mol@LB@Unfolding Energy - sRNA 6.67256 kcal/mol@LB@@LB@Position - mRNA 143 -- 172@LB@Position - sRNA 39 -- 66@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 58 -- 64@LB@
166	0.01968	0.3987	b0784	moaD	-8.29	0.259720	116 -- 144	39 -- 53	molybdopterin synthase small subunit	_____________115___________________________145\n_____________\|_____________________________\|\n5'-GCA...GCAAA_________AAAGAUAUGGUGAU______GGUAC...AGC-3'\n______________GCGGUGCAA______________UGGUCC\n______________\|\|::\|\|\|\|\|______________\|\|\|:\|\|\n______________CGUUACGUU______________ACCGGG\n3'-UUU...GUCAC_____________________________UUGUC...UUG-5'\n_____________\|_____________________________\|\n_____________54____________________________38\n	118 -- 124	45 -- 51	-19.827 kcal/mol	6.7839 kcal/mol	4.75794 kcal/mol	115 145@LB@ \| \|@LB@5'-GCA...GCAAA AAAGAUAUGGUGAU GGUAC...AGC-3'@LB@ GCGGUGCAA UGGUCC@LB@ \|\|::\|\|\|\|\| \|\|\|:\|\|@LB@ CGUUACGUU ACCGGG@LB@3'-UUU...GUCAC UUGUC...UUG-5'@LB@ \| \|@LB@ 54 38@LB@@LB@@LB@Energy -8.29 kcal/mol@LB@Hybridization Energy -19.827 kcal/mol@LB@Unfolding Energy - mRNA 6.7839 kcal/mol@LB@Unfolding Energy - sRNA 4.75794 kcal/mol@LB@@LB@Position - mRNA 116 -- 144@LB@Position - sRNA 39 -- 53@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 45 -- 51@LB@
83	0.007014	0.2822	b0815	opgE	-11.11	0.070482	164 -- 204	2 -- 58	OPG biosynthetic transmembrane phosphoethanolamine transferase	_____________163________________________________________________________205\n_____________\|__________________________________________________________\|\n5'-UUU...GACGC_____________C__________________________U_______U_________AUUUA...GCU-3'\n______________CAG_GGUAA_GCA_AUGGC_______________GUUUGU_ACGAUAG_GGCAUAUGA\n______________\|\|\|_\|\|:\|\|_\|\|\|_\|\|\|\|\|_______________:\|:\|\|\|_\|\|:\|\|\|:_\|\|\|\|\|\|\|:\|\n______________GUC_CCGUU_CGU_UACCG_______________UAGACA_UGUUAUU_CCGUAUAUU\n3'-UUU...UUUUA___A_____A_________GGUUGUCUUUUAUUU______C_______U_________G-5'\n_____________\|__________________________________________________________\|\n_____________59_________________________________________________________1\n	197 -- 203	3 -- 9	-40.5172 kcal/mol	17.2586 kcal/mol	12.1475 kcal/mol	163 205@LB@ \| \|@LB@5'-UUU...GACGC C U U AUUUA...GCU-3'@LB@ CAG GGUAA GCA AUGGC GUUUGU ACGAUAG GGCAUAUGA@LB@ \|\|\| \|\|:\|\| \|\|\| \|\|\|\|\| :\|:\|\|\| \|\|:\|\|\|: \|\|\|\|\|\|\|:\|@LB@ GUC CCGUU CGU UACCG UAGACA UGUUAUU CCGUAUAUU@LB@3'-UUU...UUUUA A A GGUUGUCUUUUAUUU C U G-5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -11.11 kcal/mol@LB@Hybridization Energy -40.5172 kcal/mol@LB@Unfolding Energy - mRNA 17.2586 kcal/mol@LB@Unfolding Energy - sRNA 12.1475 kcal/mol@LB@@LB@Position - mRNA 164 -- 204@LB@Position - sRNA 2 -- 58@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 3 -- 9@LB@
69	0.005697	0.2777	b0829	gsiA	-9.42	0.158982	246 -- 287	28 -- 64	glutathione ABC transporter ATPase	_____________245__________________________________________288\n_____________\|____________________________________________\|\n5'-CGG...CGGUU_______UGAAUAUU__CUUU_________A_____________GCUGC...GCA-3'\n______________GAAAAUC________GC____AUGCA__GG_CCAGCAGAAAAUA\n______________\|\|\|\|\|\|\|________\|\|____\|\|\|\|\|__\|\|_\|\|\|:\|\|\|\|\|\|\|\|\|\n______________CUUUUAG________CG____UACGU__CC_GGUUGUCUUUUAU\n3'-UUU...ACAAC_______UCAC______U________UA__G_____________UUUAG...UUG-5'\n_____________\|____________________________________________\|\n_____________65___________________________________________27\n	246 -- 252	58 -- 64	-27.8415 kcal/mol	7.44564 kcal/mol	10.972 kcal/mol	245 288@LB@ \| \|@LB@5'-CGG...CGGUU UGAAUAUU CUUU A GCUGC...GCA-3'@LB@ GAAAAUC GC AUGCA GG CCAGCAGAAAAUA@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|\| \|\| \|\|\|:\|\|\|\|\|\|\|\|\|@LB@ CUUUUAG CG UACGU CC GGUUGUCUUUUAU@LB@3'-UUU...ACAAC UCAC U UA G UUUAG...UUG-5'@LB@ \| \|@LB@ 65 27@LB@@LB@@LB@Energy -9.42 kcal/mol@LB@Hybridization Energy -27.8415 kcal/mol@LB@Unfolding Energy - mRNA 7.44564 kcal/mol@LB@Unfolding Energy - sRNA 10.972 kcal/mol@LB@@LB@Position - mRNA 246 -- 287@LB@Position - sRNA 28 -- 64@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 58 -- 64@LB@
107	0.009921	0.3118	b0836	bssR	-14.44	0.011050	12 -- 65	14 -- 65	repressor of biofilm formation by indole transport regulation	_____________11____________________________________________________________66\n_____________\|_____________________________________________________________\|\n5'-AUU...UUACA_____G___________________A___U______UUCUG____________AUC_____CUCAU...ACA-3'\n______________GGAAA_GUCAG_GGCAG______GG_UUC_ACAGAG_____GAUAAAAUUUGU___GCAAU\n______________\|\|\|\|\|_:\|\|\|\|_\|\|\|\|:______\|\|_::\|_\|\|\|\|\|:_____:\|\|\|\|\|\|\|:\|\|\|___:\|\|\|\|\n______________CCUUU_UAGUC_CCGUU______CC_GGG_UGUCUU_____UUAUUUUAGACA___UGUUA\n3'-UUU...UACAA___________A_____ACGUUA______U_______________________C_______UUUCC...UUG-5'\n_____________\|_____________________________________________________________\|\n_____________66____________________________________________________________13\n	46 -- 52	25 -- 31	-37.4064 kcal/mol	11.8508 kcal/mol	11.1173 kcal/mol	11 66@LB@ \| \|@LB@5'-AUU...UUACA G A U UUCUG AUC CUCAU...ACA-3'@LB@ GGAAA GUCAG GGCAG GG UUC ACAGAG GAUAAAAUUUGU GCAAU@LB@ \|\|\|\|\| :\|\|\|\| \|\|\|\|: \|\| ::\| \|\|\|\|\|: :\|\|\|\|\|\|\|:\|\|\| :\|\|\|\|@LB@ CCUUU UAGUC CCGUU CC GGG UGUCUU UUAUUUUAGACA UGUUA@LB@3'-UUU...UACAA A ACGUUA U C UUUCC...UUG-5'@LB@ \| \|@LB@ 66 13@LB@@LB@@LB@Energy -14.44 kcal/mol@LB@Hybridization Energy -37.4064 kcal/mol@LB@Unfolding Energy - mRNA 11.8508 kcal/mol@LB@Unfolding Energy - sRNA 11.1173 kcal/mol@LB@@LB@Position - mRNA 12 -- 65@LB@Position - sRNA 14 -- 65@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 25 -- 31@LB@
2	3.183e-05	0.03921	b0889	lrp	-15.78	0.004789	150 -- 212	1 -- 70	leucine-responsive global transcriptional regulator	_____________149__________________________________________________________________________213\n_____________\|____________________________________________________________________________\|\n5'-GUG...CAGUG_____UC________ACA______A_G__A__AAU___________________________UAAU____G_____AAGAA...AGC-3'\n______________AUGUU__AGGGUCAG___GG_AGU_G_GA_GG____ACAGAGA___________GACAAUAA____GGUA_AUAGC\n______________\|\|\|\|\|__\|:::\|\|\|\|___\|\|_\|:\|_\|_:\|_\|\|____\|\|\|\|\|:\|___________\|\|\|\|\|\|\|\|____\|\|:\|_\|\|\|:\|\n______________UACAA__UUUUAGUC___CC_UUA_C_UU_CC____UGUCUUU___________CUGUUAUU____CCGU_UAUUG\n3'-UUU...AAAUA_____CC________A____G_____G__A__GGGU_______UAUUUUAGACA________U_______A_____-5'\n_____________\|___________________________________________________________________________\|\n_____________71__________________________________________________________________________1\n	192 -- 198	12 -- 18	-35.9997 kcal/mol	8.06188 kcal/mol	12.1618 kcal/mol	149 213@LB@ \| \|@LB@5'-GUG...CAGUG UC ACA A G A AAU UAAU G AAGAA...AGC-3'@LB@ AUGUU AGGGUCAG GG AGU G GA GG ACAGAGA GACAAUAA GGUA AUAGC@LB@ \|\|\|\|\| \|:::\|\|\|\| \|\| \|:\| \| :\| \|\| \|\|\|\|\|:\| \|\|\|\|\|\|\|\| \|\|:\| \|\|\|:\|@LB@ UACAA UUUUAGUC CC UUA C UU CC UGUCUUU CUGUUAUU CCGU UAUUG@LB@3'-UUU...AAAUA CC A G G A GGGU UAUUUUAGACA U A -5'@LB@ \| \|@LB@ 71 1@LB@@LB@@LB@Energy -15.78 kcal/mol@LB@Hybridization Energy -35.9997 kcal/mol@LB@Unfolding Energy - mRNA 8.06188 kcal/mol@LB@Unfolding Energy - sRNA 12.1618 kcal/mol@LB@@LB@Position - mRNA 150 -- 212@LB@Position - sRNA 1 -- 70@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 12 -- 18@LB@
104	0.009649	0.3118	b0910	cmk	-9.70	0.140357	282 -- 294	41 -- 53	cytidylate kinase	_____________281___________295\n_____________\|_____________\|\n5'-CCG...CGGAA___U_________AUCUGC-3'\n______________GCG_UGCAAUGGC\n______________\|\|:_\|\|\|\|\|\|\|\|\|\n______________CGU_ACGUUACCG\n3'-UUU...GUCAC___U_________GGUUG...UUG-5'\n_____________\|_____________\|\n_____________54____________40\n	288 -- 294	41 -- 47	-19.191 kcal/mol	5.61932 kcal/mol	3.8759 kcal/mol	281 295@LB@ \| \|@LB@5'-CCG...CGGAA U AUCUGC-3'@LB@ GCG UGCAAUGGC@LB@ \|\|: \|\|\|\|\|\|\|\|\|@LB@ CGU ACGUUACCG@LB@3'-UUU...GUCAC U GGUUG...UUG-5'@LB@ \| \|@LB@ 54 40@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -19.191 kcal/mol@LB@Unfolding Energy - mRNA 5.61932 kcal/mol@LB@Unfolding Energy - sRNA 3.8759 kcal/mol@LB@@LB@Position - mRNA 282 -- 294@LB@Position - sRNA 41 -- 53@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 41 -- 47@LB@
53	0.003903	0.237	b0946	zapC	-7.74	0.322468	177 -- 206	45 -- 76	FtsZ stabilizer	_____________176_________________________________207\n_____________\|___________________________________\|\n5'-AUU...UGCGG_______GG__AG______________A_______AUUAA...GUU-3'\n______________UUUUAUA__GU__GGGAGA_____GGC_GAUGCGA\n______________\|\|\|\|\|\|\|__\|\|__\|\|:\|:\|_____\|\|\|_:\|\|\|\|:\|\n______________AAAAUAU__CA__CCUUUU_____CCG_UUACGUU\n3'-UUU...ACAGA_______A___A_______AGUCA___________ACCGG...UUG-5'\n_____________\|___________________________________\|\n_____________77__________________________________44\n	200 -- 206	45 -- 51	-19.1898 kcal/mol	6.23804 kcal/mol	5.21532 kcal/mol	176 207@LB@ \| \|@LB@5'-AUU...UGCGG GG AG A AUUAA...GUU-3'@LB@ UUUUAUA GU GGGAGA GGC GAUGCGA@LB@ \|\|\|\|\|\|\| \|\| \|\|:\|:\| \|\|\| :\|\|\|\|:\|@LB@ AAAAUAU CA CCUUUU CCG UUACGUU@LB@3'-UUU...ACAGA A A AGUCA ACCGG...UUG-5'@LB@ \| \|@LB@ 77 44@LB@@LB@@LB@Energy -7.74 kcal/mol@LB@Hybridization Energy -19.1898 kcal/mol@LB@Unfolding Energy - mRNA 6.23804 kcal/mol@LB@Unfolding Energy - sRNA 5.21532 kcal/mol@LB@@LB@Position - mRNA 177 -- 206@LB@Position - sRNA 45 -- 76@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 45 -- 51@LB@
176	0.02144	0.4097	b0948	rlmL	-6.91	0.434425	184 -- 201	13 -- 33	23S rRNA m(2)G2445 and m(7)G2069 methyltransferases SAM-dependent	_____________183___________________202\n_____________\|_____________________\|\n5'-GAC...CUCUU_____________________UGAAU...GUG-3'\n______________AGAGUAAAA___GUGACGAUA\n______________\|:\|:\|\|\|\|\|___\|\|\|\|\|:\|\|\|\n______________UUUUAUUUU___CACUGUUAU\n3'-UUU...UUGUC_________AGA_________UUCCG...UUG-5'\n_____________\|_____________________\|\n_____________34____________________12\n	195 -- 201	13 -- 19	-14.282 kcal/mol	2.4415 kcal/mol	4.9341 kcal/mol	183 202@LB@ \| \|@LB@5'-GAC...CUCUU UGAAU...GUG-3'@LB@ AGAGUAAAA GUGACGAUA@LB@ \|:\|:\|\|\|\|\| \|\|\|\|\|:\|\|\|@LB@ UUUUAUUUU CACUGUUAU@LB@3'-UUU...UUGUC AGA UUCCG...UUG-5'@LB@ \| \|@LB@ 34 12@LB@@LB@@LB@Energy -6.91 kcal/mol@LB@Hybridization Energy -14.282 kcal/mol@LB@Unfolding Energy - mRNA 2.4415 kcal/mol@LB@Unfolding Energy - sRNA 4.9341 kcal/mol@LB@@LB@Position - mRNA 184 -- 201@LB@Position - sRNA 13 -- 33@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 13 -- 19@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:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching