Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
111	0.004903	0.1545	b1735	chbR	-11.17	0.151186	109 -- 138	30 -- 50	repressor of chb operon for N N'-diacetylchitobiose utilization	_____________108____________________________139\n_____________\|______________________________\|\n5'-GAU...GUCCA________AUCAUUUAAU__CG________UGCGC...CUG-3'\n______________CGCUCAGG__________GA__UCCAUGCU\n______________\|:\|\|\|\|\|\|__________\|\|__\|\|\|\|\|\|\|\|\n______________GUGAGUCC__________CU__AGGUACGA\n3'-UUU...ACAAA________C___________AA________AUAUU...GCA-5'\n_____________\|______________________________\|\n_____________51_____________________________29\n	132 -- 138	30 -- 36	-23.5874 kcal/mol	7.28235 kcal/mol	5.13509 kcal/mol	108 139@LB@ \| \|@LB@5'-GAU...GUCCA AUCAUUUAAU CG UGCGC...CUG-3'@LB@ CGCUCAGG GA UCCAUGCU@LB@ \|:\|\|\|\|\|\| \|\| \|\|\|\|\|\|\|\|@LB@ GUGAGUCC CU AGGUACGA@LB@3'-UUU...ACAAA C AA AUAUU...GCA-5'@LB@ \| \|@LB@ 51 29@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -23.5874 kcal/mol@LB@Unfolding Energy - mRNA 7.28235 kcal/mol@LB@Unfolding Energy - sRNA 5.13509 kcal/mol@LB@@LB@Position - mRNA 109 -- 138@LB@Position - sRNA 30 -- 50@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 30 -- 36@LB@
112	0.004986	0.1545	b0118	acnB	-15.18	0.018766	221 -- 251	38 -- 71	aconitate hydratase 2; aconitase B; 2-methyl-cis-aconitate hydratase	_____________220________________________________252\n_____________\|__________________________________\|\n5'-GAG...CGUAA_________UGAG___GC_______G________GCGCC...UGC-3'\n______________GCACGUAGC____CGU_____CGCU_AGGGGAUU\n______________:\|\|\|::\|\|\|____\|\|\|_____\|:\|\|_\|\|\|\|\|\|\|\|\n______________UGUGUGUCG____GCA_____GUGA_UCCCCUAA\n3'-UUU...UCUGA_________UUAA___ACAAA____G________AGGUA...GCA-5'\n_____________\|__________________________________\|\n_____________72_________________________________37\n	245 -- 251	38 -- 44	-33.2374 kcal/mol	13.3072 kcal/mol	4.74986 kcal/mol	220 252@LB@ \| \|@LB@5'-GAG...CGUAA UGAG GC G GCGCC...UGC-3'@LB@ GCACGUAGC CGU CGCU AGGGGAUU@LB@ :\|\|\|::\|\|\| \|\|\| \|:\|\| \|\|\|\|\|\|\|\|@LB@ UGUGUGUCG GCA GUGA UCCCCUAA@LB@3'-UUU...UCUGA UUAA ACAAA G AGGUA...GCA-5'@LB@ \| \|@LB@ 72 37@LB@@LB@@LB@Energy -15.18 kcal/mol@LB@Hybridization Energy -33.2374 kcal/mol@LB@Unfolding Energy - mRNA 13.3072 kcal/mol@LB@Unfolding Energy - sRNA 4.74986 kcal/mol@LB@@LB@Position - mRNA 221 -- 251@LB@Position - sRNA 38 -- 71@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 38 -- 44@LB@
113	0.004991	0.1545	b0888	trxB	-9.59	0.285839	209 -- 223	61 -- 75	thioredoxin reductase FAD/NAD(P)-binding	_____________208_____________224\n_____________\|_______________\|\n5'-AAC...GGCAC___CAA_________ACUGC...UGC-3'\n______________GAC___ACACAGUAA\n______________\|\|\|___\|\|\|\|\|\|:\|\|\n______________CUG___UGUGUCGUU\n3'-UUU...CGUUU___AUG_________AAGCA...GCA-5'\n_____________\|_______________\|\n_____________76______________60\n	217 -- 223	61 -- 67	-15.4977 kcal/mol	2.65453 kcal/mol	3.25399 kcal/mol	208 224@LB@ \| \|@LB@5'-AAC...GGCAC CAA ACUGC...UGC-3'@LB@ GAC ACACAGUAA@LB@ \|\|\| \|\|\|\|\|\|:\|\|@LB@ CUG UGUGUCGUU@LB@3'-UUU...CGUUU AUG AAGCA...GCA-5'@LB@ \| \|@LB@ 76 60@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -15.4977 kcal/mol@LB@Unfolding Energy - mRNA 2.65453 kcal/mol@LB@Unfolding Energy - sRNA 3.25399 kcal/mol@LB@@LB@Position - mRNA 209 -- 223@LB@Position - sRNA 61 -- 75@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 61 -- 67@LB@
114	0.005004	0.1545	b0025	ribF	-11.63	0.123109	210 -- 237	43 -- 71	bifunctional riboflavin kinase/FAD synthetase	_____________209___________________________238\n_____________\|_____________________________\|\n5'-UGG...AGCUG__________UACAUAAUC____GC____CCCCG...GCG-3'\n______________AUACGCGGCA__________UCA__CAGG\n______________\|:\|\|:\|:\|\|\|__________\|\|\|__\|\|\|\|\n______________UGUGUGUCGU__________AGU__GUCC\n3'-UUU...UCUGA__________UAAGCAACAA___GA____CCUAA...GCA-5'\n_____________\|_____________________________\|\n_____________72____________________________42\n	213 -- 219	62 -- 68	-21.1915 kcal/mol	5.23887 kcal/mol	4.32409 kcal/mol	209 238@LB@ \| \|@LB@5'-UGG...AGCUG UACAUAAUC GC CCCCG...GCG-3'@LB@ AUACGCGGCA UCA CAGG@LB@ \|:\|\|:\|:\|\|\| \|\|\| \|\|\|\|@LB@ UGUGUGUCGU AGU GUCC@LB@3'-UUU...UCUGA UAAGCAACAA GA CCUAA...GCA-5'@LB@ \| \|@LB@ 72 42@LB@@LB@@LB@Energy -11.63 kcal/mol@LB@Hybridization Energy -21.1915 kcal/mol@LB@Unfolding Energy - mRNA 5.23887 kcal/mol@LB@Unfolding Energy - sRNA 4.32409 kcal/mol@LB@@LB@Position - mRNA 210 -- 237@LB@Position - sRNA 43 -- 71@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 62 -- 68@LB@
115	0.005088	0.155	b4131	cadA	-16.57	0.007707	197 -- 237	37 -- 75	lysine decarboxylase acid-inducible	_____________196__________________________________________238\n_____________\|____________________________________________\|\n5'-CUC...GAUAU______GA___UUAUU_____A_____AA____AU_________AUUUU...UUG-3'\n______________GACUAU__ACG_____GCAAU___UUG__UCAC___GGGGGUUU\n______________\|\|\|\|\|:__\|\|:_____\|\|\|\|\|___\|\|\|__\|\|\|\|___\|\|\|\|:\|\|\|\n______________CUGAUG__UGU_____CGUUA___AAC__AGUG___CCCCUAAA\n3'-UUU...CGUUU______UG_____________AGC___AA____AGU________GGUAC...GCA-5'\n_____________\|____________________________________________\|\n_____________76___________________________________________36\n	231 -- 237	37 -- 43	-27.1465 kcal/mol	5.79755 kcal/mol	4.77966 kcal/mol	196 238@LB@ \| \|@LB@5'-CUC...GAUAU GA UUAUU A AA AU AUUUU...UUG-3'@LB@ GACUAU ACG GCAAU UUG UCAC GGGGGUUU@LB@ \|\|\|\|\|: \|\|: \|\|\|\|\| \|\|\| \|\|\|\| \|\|\|\|:\|\|\|@LB@ CUGAUG UGU CGUUA AAC AGUG CCCCUAAA@LB@3'-UUU...CGUUU UG AGC AA AGU GGUAC...GCA-5'@LB@ \| \|@LB@ 76 36@LB@@LB@@LB@Energy -16.57 kcal/mol@LB@Hybridization Energy -27.1465 kcal/mol@LB@Unfolding Energy - mRNA 5.79755 kcal/mol@LB@Unfolding Energy - sRNA 4.77966 kcal/mol@LB@@LB@Position - mRNA 197 -- 237@LB@Position - sRNA 37 -- 75@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 37 -- 43@LB@
116	0.005119	0.155	b2513	yfgM	-8.84	0.371642	84 -- 101	60 -- 75	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________83_________________102\n_____________\|__________________\|\n5'-GGC...GAAGU_____ACG__________AGUGA...UUG-3'\n______________GGCUA___GCACAGCAGU\n______________\|:\|\|\|___:\|\|\|\|\|\|\|:\|\n______________CUGAU___UGUGUCGUUA\n3'-UUU...CGUUU_____G____________AGCAA...GCA-5'\n_____________\|__________________\|\n_____________76_________________59\n	95 -- 101	60 -- 66	-19.484 kcal/mol	7.35825 kcal/mol	3.28851 kcal/mol	83 102@LB@ \| \|@LB@5'-GGC...GAAGU ACG AGUGA...UUG-3'@LB@ GGCUA GCACAGCAGU@LB@ \|:\|\|\| :\|\|\|\|\|\|\|:\|@LB@ CUGAU UGUGUCGUUA@LB@3'-UUU...CGUUU G AGCAA...GCA-5'@LB@ \| \|@LB@ 76 59@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -19.484 kcal/mol@LB@Unfolding Energy - mRNA 7.35825 kcal/mol@LB@Unfolding Energy - sRNA 3.28851 kcal/mol@LB@@LB@Position - mRNA 84 -- 101@LB@Position - sRNA 60 -- 75@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 60 -- 66@LB@
117	0.005152	0.155	b2235	nrdB	-9.05	0.346139	190 -- 222	48 -- 77	ribonucleoside-diphosphate reductase 1 beta subunit ferritin-like protein	_____________189_______________________________223\n_____________\|_________________________________\|\n5'-UCC...CCAAC_____AC__U_______UAUACCACCU______AGACG...AAU-3'\n______________AGGAC__AC_CAUGGCA__________UUUCAC\n______________\|:\|\|\|__\|\|_\|\|::\|\|\|__________\|\|\|\|\|\|\n______________UUCUG__UG_GUGUCGU__________AAAGUG\n3'-UUU...CCCGU_____A___U_______UAAGCAAC________AGUCC...GCA-5'\n_____________\|_________________________________\|\n_____________78________________________________47\n	200 -- 206	62 -- 68	-18.188 kcal/mol	5.45206 kcal/mol	3.68729 kcal/mol	189 223@LB@ \| \|@LB@5'-UCC...CCAAC AC U UAUACCACCU AGACG...AAU-3'@LB@ AGGAC AC CAUGGCA UUUCAC@LB@ \|:\|\|\| \|\| \|\|::\|\|\| \|\|\|\|\|\|@LB@ UUCUG UG GUGUCGU AAAGUG@LB@3'-UUU...CCCGU A U UAAGCAAC AGUCC...GCA-5'@LB@ \| \|@LB@ 78 47@LB@@LB@@LB@Energy -9.05 kcal/mol@LB@Hybridization Energy -18.188 kcal/mol@LB@Unfolding Energy - mRNA 5.45206 kcal/mol@LB@Unfolding Energy - sRNA 3.68729 kcal/mol@LB@@LB@Position - mRNA 190 -- 222@LB@Position - sRNA 48 -- 77@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 62 -- 68@LB@
118	0.005291	0.1553	b0481	ybaK	-9.02	0.349126	203 -- 225	45 -- 75	Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase	_____________202_____________________________226\n_____________\|_______________________________\|\n5'-AAU...ACCAU______C______UAAA______________AAAAA...UCG-3'\n______________GAC_AC_CGCAGU___________UUACUCG\n______________\|\|\|_\|\|_\|:\|\|\|:___________\|:\|\|\|\|:\n______________CUG_UG_GUGUCG___________AGUGAGU\n3'-UUU...CGUUU___A__U______UUAAGCAACAA_______CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	219 -- 225	45 -- 51	-15.8984 kcal/mol	3.13427 kcal/mol	3.74078 kcal/mol	202 226@LB@ \| \|@LB@5'-AAU...ACCAU C UAAA AAAAA...UCG-3'@LB@ GAC AC CGCAGU UUACUCG@LB@ \|\|\| \|\| \|:\|\|\|: \|:\|\|\|\|:@LB@ CUG UG GUGUCG AGUGAGU@LB@3'-UUU...CGUUU A U UUAAGCAACAA CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -9.02 kcal/mol@LB@Hybridization Energy -15.8984 kcal/mol@LB@Unfolding Energy - mRNA 3.13427 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 203 -- 225@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 45 -- 51@LB@
119	0.005328	0.1553	b3417	malP	-6.58	0.680720	220 -- 257	42 -- 71	maltodextrin phosphorylase	_____________219____________________________________258\n_____________\|______________________________________\|\n5'-ACA...UUUUA___AUA________CAG_AAGCGC______G____U__CAGCG...GCC-3'\n______________ACG___AGCAAUUU___G______UUUCAC_UCAG_GG\n______________\|\|:___\|\|\|\|\|\|\|:___\|______\|\|\|\|\|\|_\|\|\|\|_\|\|\n______________UGU___UCGUUAAG___C______AAAGUG_AGUC_CC\n3'-UUU...UCUGA___GUG________CAA_____________________CUAAA...GCA-5'\n_____________\|______________________________________\|\n_____________72_____________________________________41\n	227 -- 233	58 -- 64	-19.6486 kcal/mol	8.3321 kcal/mol	4.73391 kcal/mol	219 258@LB@ \| \|@LB@5'-ACA...UUUUA AUA CAG AAGCGC G U CAGCG...GCC-3'@LB@ ACG AGCAAUUU G UUUCAC UCAG GG@LB@ \|\|: \|\|\|\|\|\|\|: \| \|\|\|\|\|\| \|\|\|\| \|\|@LB@ UGU UCGUUAAG C AAAGUG AGUC CC@LB@3'-UUU...UCUGA GUG CAA CUAAA...GCA-5'@LB@ \| \|@LB@ 72 41@LB@@LB@@LB@Energy -6.58 kcal/mol@LB@Hybridization Energy -19.6486 kcal/mol@LB@Unfolding Energy - mRNA 8.3321 kcal/mol@LB@Unfolding Energy - sRNA 4.73391 kcal/mol@LB@@LB@Position - mRNA 220 -- 257@LB@Position - sRNA 42 -- 71@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 58 -- 64@LB@
120	0.005393	0.1553	b0523	purE	-13.83	0.040764	102 -- 146	30 -- 75	N5-carboxyaminoimidazole ribonucleotide mutase	_____________101________________________________________________147\n_____________\|__________________________________________________\|\n5'-UGG...UUGCU____U____GC__C____C_____UUCC______UC______________AUUCU...UGA-3'\n______________GAUU_CACA__CA_GCAA__CGUU____UUGCUC______UUUCCGUGCU\n______________\|\|:\|_\|\|\|\|__\|\|_\|\|\|\|__\|\|\|\|____\|::\|\|\|______\|\|\|\|\|:\|\|\|\|\n______________CUGA_GUGU__GU_CGUU__GCAA____AGUGAG______AAAGGUACGA\n3'-UUU...CGUUU____U_____________AA____CAA_______UCCCCU__________AUAUU...GCA-5'\n_____________\|__________________________________________________\|\n_____________76_________________________________________________29\n	140 -- 146	30 -- 36	-29.2897 kcal/mol	7.36654 kcal/mol	8.08958 kcal/mol	101 147@LB@ \| \|@LB@5'-UGG...UUGCU U GC C C UUCC UC AUUCU...UGA-3'@LB@ GAUU CACA CA GCAA CGUU UUGCUC UUUCCGUGCU@LB@ \|\|:\| \|\|\|\| \|\| \|\|\|\| \|\|\|\| \|::\|\|\| \|\|\|\|\|:\|\|\|\|@LB@ CUGA GUGU GU CGUU GCAA AGUGAG AAAGGUACGA@LB@3'-UUU...CGUUU U AA CAA UCCCCU AUAUU...GCA-5'@LB@ \| \|@LB@ 76 29@LB@@LB@@LB@Energy -13.83 kcal/mol@LB@Hybridization Energy -29.2897 kcal/mol@LB@Unfolding Energy - mRNA 7.36654 kcal/mol@LB@Unfolding Energy - sRNA 8.08958 kcal/mol@LB@@LB@Position - mRNA 102 -- 146@LB@Position - sRNA 30 -- 75@LB@Position Seed - mRNA 140 -- 146@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:

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