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
88	0.007723	0.2889	b4403	yjtD	-13.82	0.016006	193 -- 211	1 -- 21	putative methyltransferase	_____________192___________________212\n_____________\|_____________________\|\n5'-AUU...GAAGA_________U___________GAUUA...UUG-3'\n______________GUGGCAAUA___GCGUAUAAC\n______________\|\|\|:\|\|\|\|\|___\|\|:\|\|\|\|\|\|\n______________CACUGUUAU___CGUAUAUUG\n3'-UUU...UUAGA_________UUC_________-5'\n_____________\|____________________\|\n_____________22___________________1\n	205 -- 211	1 -- 7	-21.8234 kcal/mol	3.59402 kcal/mol	4.41334 kcal/mol	192 212@LB@ \| \|@LB@5'-AUU...GAAGA U GAUUA...UUG-3'@LB@ GUGGCAAUA GCGUAUAAC@LB@ \|\|\|:\|\|\|\|\| \|\|:\|\|\|\|\|\|@LB@ CACUGUUAU CGUAUAUUG@LB@3'-UUU...UUAGA UUC -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -13.82 kcal/mol@LB@Hybridization Energy -21.8234 kcal/mol@LB@Unfolding Energy - mRNA 3.59402 kcal/mol@LB@Unfolding Energy - sRNA 4.41334 kcal/mol@LB@@LB@Position - mRNA 193 -- 211@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 1 -- 7@LB@
89	0.007733	0.2889	b3426	glpD	-8.48	0.239884	186 -- 234	7 -- 64	sn-glycerol-3-phosphate dehydrogenase aerobic FAD/NAD(P)-binding	_____________185__________________________________________________________235\n_____________\|____________________________________________________________\|\n5'-AAC...CGAAA_U____G________________AAA________UCU_______________________GCAUC...AGG-3'\n______________G_GAAU_AG_GGCA__GC_AUGG___CCAA_AGA______GA_UUGUGAUAG__GGGGCG\n______________\|_:\|\|\|_\|\|_\|\|\|\|__\|\|_\|\|\|\|___\|\|\|\|_\|\|\|______:\|_:\|\|\|\|\|:\|:__::\|\|\|:\n______________C_UUUA_UC_CCGU__CG_UACC___GGUU_UCU______UU_GACACUGUU__UUCCGU\n3'-UUU...ACAAC_U____G__A____UA__U____G______G___UUUAUU__A_________AU______AUAUUG-5'\n_____________\|____________________________________________________________\|\n_____________65___________________________________________________________6\n	222 -- 228	15 -- 21	-34.508 kcal/mol	13.8761 kcal/mol	12.1536 kcal/mol	185 235@LB@ \| \|@LB@5'-AAC...CGAAA U G AAA UCU GCAUC...AGG-3'@LB@ G GAAU AG GGCA GC AUGG CCAA AGA GA UUGUGAUAG GGGGCG@LB@ \| :\|\|\| \|\| \|\|\|\| \|\| \|\|\|\| \|\|\|\| \|\|\| :\| :\|\|\|\|\|:\|: ::\|\|\|:@LB@ C UUUA UC CCGU CG UACC GGUU UCU UU GACACUGUU UUCCGU@LB@3'-UUU...ACAAC U G A UA U G G UUUAUU A AU AUAUUG-5'@LB@ \| \|@LB@ 65 6@LB@@LB@@LB@Energy -8.48 kcal/mol@LB@Hybridization Energy -34.508 kcal/mol@LB@Unfolding Energy - mRNA 13.8761 kcal/mol@LB@Unfolding Energy - sRNA 12.1536 kcal/mol@LB@@LB@Position - mRNA 186 -- 234@LB@Position - sRNA 7 -- 64@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 15 -- 21@LB@
90	0.007755	0.2889	b1852	zwf	-12.23	0.039232	191 -- 223	38 -- 65	glucose-6-phosphate 1-dehydrogenase	_____________190_______________________________224\n_____________\|_________________________________\|\n5'-UCA...CUUAA_______G_CA_______AAC____ACA_____GGCCU...UGG-3'\n______________GGAGAAU_A__UGGCGGU___GCAA___GCCCA\n______________\|\|\|:\|\|\|_\|__\|\|\|\|::\|___\|\|\|\|___\|\|\|\|\|\n______________CCUUUUA_U__ACCGUUA___CGUU___CGGGU\n3'-UUU...UACAA_______G_C_______________AC______UGUCU...UUG-5'\n_____________\|_________________________________\|\n_____________66________________________________37\n	202 -- 208	49 -- 55	-27.1425 kcal/mol	8.24293 kcal/mol	6.67322 kcal/mol	190 224@LB@ \| \|@LB@5'-UCA...CUUAA G CA AAC ACA GGCCU...UGG-3'@LB@ GGAGAAU A UGGCGGU GCAA GCCCA@LB@ \|\|\|:\|\|\| \| \|\|\|\|::\| \|\|\|\| \|\|\|\|\|@LB@ CCUUUUA U ACCGUUA CGUU CGGGU@LB@3'-UUU...UACAA G C AC UGUCU...UUG-5'@LB@ \| \|@LB@ 66 37@LB@@LB@@LB@Energy -12.23 kcal/mol@LB@Hybridization Energy -27.1425 kcal/mol@LB@Unfolding Energy - mRNA 8.24293 kcal/mol@LB@Unfolding Energy - sRNA 6.67322 kcal/mol@LB@@LB@Position - mRNA 191 -- 223@LB@Position - sRNA 38 -- 65@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 49 -- 55@LB@
91	0.007817	0.2889	b3380	yhfW	-10.82	0.081759	179 -- 205	41 -- 67	phosphopentomutase-related metalloenzyme superfamily protein	_____________178_________________________206\n_____________\|___________________________\|\n5'-CUC...CAGUC_______C__UC___G__C________GCGAU...GUG-3'\n______________UUGGAAA_UC__UGG_GG_GUAAUGGC\n______________\|\|\|\|\|\|\|_\|\|__\|\|\|_::_\|:\|\|\|\|\|\|\n______________AACCUUU_AG__ACC_UU_CGUUACCG\n3'-UUU...UAUAC_______U__UC___G__A________GGUUG...UUG-5'\n_____________\|___________________________\|\n_____________68__________________________40\n	199 -- 205	41 -- 47	-26.7792 kcal/mol	10.1319 kcal/mol	5.83043 kcal/mol	178 206@LB@ \| \|@LB@5'-CUC...CAGUC C UC G C GCGAU...GUG-3'@LB@ UUGGAAA UC UGG GG GUAAUGGC@LB@ \|\|\|\|\|\|\| \|\| \|\|\| :: \|:\|\|\|\|\|\|@LB@ AACCUUU AG ACC UU CGUUACCG@LB@3'-UUU...UAUAC U UC G A GGUUG...UUG-5'@LB@ \| \|@LB@ 68 40@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -26.7792 kcal/mol@LB@Unfolding Energy - mRNA 10.1319 kcal/mol@LB@Unfolding Energy - sRNA 5.83043 kcal/mol@LB@@LB@Position - mRNA 179 -- 205@LB@Position - sRNA 41 -- 67@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 41 -- 47@LB@
92	0.007983	0.2918	b2513	yfgM	-8.87	0.203113	70 -- 109	9 -- 65	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________69___________________________________________________________110\n_____________\|____________________________________________________________\|\n5'-GGC...UGCUG__U_____UGA_____________C___A_______________________________AUUUG...UUG-3'\n______________GG_GAGUC___AGUGGC____UAA_GGC_CAGCAG________________UAGUGAAGG\n______________\|\|_:\|:\|\|___\|\|\|\|\|\|____:\|\|_\|\|\|_\|\|:\|\|\|________________:\|:\|:\|\|\|\|\n______________CC_UUUAG___UCACCG____GUU_CCG_GUUGUC________________GUUAUUUCC\n3'-UUU...UACAA__U______________UUAC___A___G______UUUUAUUUUAGACACU_________GUAUAUUG-5'\n_____________\|____________________________________________________________\|\n_____________66___________________________________________________________8\n	103 -- 109	9 -- 15	-31.9345 kcal/mol	11.9273 kcal/mol	11.1365 kcal/mol	69 110@LB@ \| \|@LB@5'-GGC...UGCUG U UGA C A AUUUG...UUG-3'@LB@ GG GAGUC AGUGGC UAA GGC CAGCAG UAGUGAAGG@LB@ \|\| :\|:\|\| \|\|\|\|\|\| :\|\| \|\|\| \|\|:\|\|\| :\|:\|:\|\|\|\|@LB@ CC UUUAG UCACCG GUU CCG GUUGUC GUUAUUUCC@LB@3'-UUU...UACAA U UUAC A G UUUUAUUUUAGACACU GUAUAUUG-5'@LB@ \| \|@LB@ 66 8@LB@@LB@@LB@Energy -8.87 kcal/mol@LB@Hybridization Energy -31.9345 kcal/mol@LB@Unfolding Energy - mRNA 11.9273 kcal/mol@LB@Unfolding Energy - sRNA 11.1365 kcal/mol@LB@@LB@Position - mRNA 70 -- 109@LB@Position - sRNA 9 -- 65@LB@Position Seed - mRNA 103 -- 109@LB@Position Seed - sRNA 9 -- 15@LB@
93	0.008233	0.2977	b2669	stpA	-8.51	0.236304	244 -- 255	39 -- 50	DNA binding protein nucleoid-associated	_____________243__________256\n_____________\|____________\|\n5'-UUC...CCUCC____________GCGAA...UCA-3'\n______________GUGCGAUGGCUC\n______________:\|\|\|:\|\|\|\|\|:\|\n______________UACGUUACCGGG\n3'-UUU...ACCGU____________UUGUC...UUG-5'\n_____________\|____________\|\n_____________51___________38\n	249 -- 255	39 -- 45	-19.1222 kcal/mol	5.86982 kcal/mol	4.73799 kcal/mol	243 256@LB@ \| \|@LB@5'-UUC...CCUCC GCGAA...UCA-3'@LB@ GUGCGAUGGCUC@LB@ :\|\|\|:\|\|\|\|\|:\|@LB@ UACGUUACCGGG@LB@3'-UUU...ACCGU UUGUC...UUG-5'@LB@ \| \|@LB@ 51 38@LB@@LB@@LB@Energy -8.51 kcal/mol@LB@Hybridization Energy -19.1222 kcal/mol@LB@Unfolding Energy - mRNA 5.86982 kcal/mol@LB@Unfolding Energy - sRNA 4.73799 kcal/mol@LB@@LB@Position - mRNA 244 -- 255@LB@Position - sRNA 39 -- 50@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 39 -- 45@LB@
94	0.008385	0.3	b1804	rnd	-8.17	0.271836	224 -- 238	41 -- 54	ribonuclease D	_____________223_____________239\n_____________\|_______________\|\n5'-GUC...ACCAC__A_______C____UUCUU...GUA-3'\n______________GG_CGAUGCG_UGGC\n______________\|\|_\|:\|\|\|\|:_\|\|\|\|\n______________CC_GUUACGU_ACCG\n3'-UUU...AGUCA__________U____GGUUG...UUG-5'\n_____________\|_______________\|\n_____________55______________40\n	227 -- 233	46 -- 52	-18.0571 kcal/mol	5.99437 kcal/mol	3.89026 kcal/mol	223 239@LB@ \| \|@LB@5'-GUC...ACCAC A C UUCUU...GUA-3'@LB@ GG CGAUGCG UGGC@LB@ \|\| \|:\|\|\|\|: \|\|\|\|@LB@ CC GUUACGU ACCG@LB@3'-UUU...AGUCA U GGUUG...UUG-5'@LB@ \| \|@LB@ 55 40@LB@@LB@@LB@Energy -8.17 kcal/mol@LB@Hybridization Energy -18.0571 kcal/mol@LB@Unfolding Energy - mRNA 5.99437 kcal/mol@LB@Unfolding Energy - sRNA 3.89026 kcal/mol@LB@@LB@Position - mRNA 224 -- 238@LB@Position - sRNA 41 -- 54@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 46 -- 52@LB@
95	0.008588	0.304	b4551	yheV	-11.20	0.067476	257 -- 273	47 -- 65	DUF2387 family putative metal-binding protein	_____________256_________________274\n_____________\|___________________\|\n5'-AUC...GCGCA___U_____A_________GGCGC...UUG-3'\n______________GGA___UCA_UGGCGAUGU\n______________\|\|\|___\|\|\|_\|\|\|\|:\|\|\|:\n______________CCU___AGU_ACCGUUACG\n3'-UUU...UACAA___UUU___C_________UUACC...UUG-5'\n_____________\|___________________\|\n_____________66__________________46\n	267 -- 273	47 -- 53	-19.3348 kcal/mol	4.06987 kcal/mol	4.06844 kcal/mol	256 274@LB@ \| \|@LB@5'-AUC...GCGCA U A GGCGC...UUG-3'@LB@ GGA UCA UGGCGAUGU@LB@ \|\|\| \|\|\| \|\|\|\|:\|\|\|:@LB@ CCU AGU ACCGUUACG@LB@3'-UUU...UACAA UUU C UUACC...UUG-5'@LB@ \| \|@LB@ 66 46@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -19.3348 kcal/mol@LB@Unfolding Energy - mRNA 4.06987 kcal/mol@LB@Unfolding Energy - sRNA 4.06844 kcal/mol@LB@@LB@Position - mRNA 257 -- 273@LB@Position - sRNA 47 -- 65@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 47 -- 53@LB@
96	0.009004	0.3118	b3981	secE	-8.82	0.207803	253 -- 270	42 -- 57	preprotein translocase membrane subunit	_____________252________________271\n_____________\|__________________\|\n5'-UAA...GAUGA_____GUCGU________CAUUG...ACU-3'\n______________AGUGG_____UGUGGUGG\n______________\|\|\|\|\|_____\|\|:::\|\|\|\n______________UCACC_____ACGUUACC\n3'-UUU...UUUAG_____GUU__________GGGUU...UUG-5'\n_____________\|__________________\|\n_____________58_________________41\n	264 -- 270	42 -- 48	-15.0916 kcal/mol	2.64473 kcal/mol	3.62906 kcal/mol	252 271@LB@ \| \|@LB@5'-UAA...GAUGA GUCGU CAUUG...ACU-3'@LB@ AGUGG UGUGGUGG@LB@ \|\|\|\|\| \|\|:::\|\|\|@LB@ UCACC ACGUUACC@LB@3'-UUU...UUUAG GUU GGGUU...UUG-5'@LB@ \| \|@LB@ 58 41@LB@@LB@@LB@Energy -8.82 kcal/mol@LB@Hybridization Energy -15.0916 kcal/mol@LB@Unfolding Energy - mRNA 2.64473 kcal/mol@LB@Unfolding Energy - sRNA 3.62906 kcal/mol@LB@@LB@Position - mRNA 253 -- 270@LB@Position - sRNA 42 -- 57@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 42 -- 48@LB@
97	0.009098	0.3118	b3221	yhcH	-21.73	0.000051	38 -- 71	30 -- 66	DUF386 family protein cupin superfamily	_____________37____________________________________72\n_____________\|_____________________________________\|\n5'-AUC...GUGCG___U_________________U_______________GUAUC...AAG-3'\n______________UGG__GGUCGGUGGCA__GCG_UGGUCUGGCAGAAGG\n______________\|\|\|__::\|\|:\|\|\|\|\|\|__\|\|:_\|\|\|:\|:::\|\|\|\|\|::\n______________ACC__UUAGUCACCGU__CGU_ACCGGGUUGUCUUUU\n3'-UUU...AUACA___UU___________UA___U_______________AUUUU...UUG-5'\n_____________\|_____________________________________\|\n_____________67____________________________________29\n	57 -- 63	38 -- 44	-43.4799 kcal/mol	10.7586 kcal/mol	10.9916 kcal/mol	37 72@LB@ \| \|@LB@5'-AUC...GUGCG U U GUAUC...AAG-3'@LB@ UGG GGUCGGUGGCA GCG UGGUCUGGCAGAAGG@LB@ \|\|\| ::\|\|:\|\|\|\|\|\| \|\|: \|\|\|:\|:::\|\|\|\|\|::@LB@ ACC UUAGUCACCGU CGU ACCGGGUUGUCUUUU@LB@3'-UUU...AUACA UU UA U AUUUU...UUG-5'@LB@ \| \|@LB@ 67 29@LB@@LB@@LB@Energy -21.73 kcal/mol@LB@Hybridization Energy -43.4799 kcal/mol@LB@Unfolding Energy - mRNA 10.7586 kcal/mol@LB@Unfolding Energy - sRNA 10.9916 kcal/mol@LB@@LB@Position - mRNA 38 -- 71@LB@Position - sRNA 30 -- 66@LB@Position Seed - mRNA 57 -- 63@LB@Position Seed - sRNA 38 -- 44@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