Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
124	0.01089	0.2829	b0186	ldcC	-10.51	0.011388	34 -- 66	24 -- 58	lysine decarboxylase 2 constitutive	_____________33___________________________________67\n_____________\|____________________________________\|\n5'-AAA...AUCUC___G__________CU____________________CGUUA...UUA-3'\n______________GAC_UG_UUAAGCA__GAAG_AUUUAAAAAA_UCGU\n______________:\|\|_\|\|_\|\|\|\|\|\|\|__\|\|\|\|_\|:\|\|\|\|\|\|\|\|_\|\|\|\|\n______________UUG_AC_AAUUCGU__CUUC_UGAAUUUUUU_AGCA\n3'-UUU...CUACU___A__G_______U_____G__________A____AUGUG...CAA-5'\n_____________\|____________________________________\|\n_____________59___________________________________23\n	53 -- 59	32 -- 38	-24.2219 kcal/mol	7.43557 kcal/mol	6.27608 kcal/mol	33 67@LB@ \| \|@LB@5'-AAA...AUCUC G CU CGUUA...UUA-3'@LB@ GAC UG UUAAGCA GAAG AUUUAAAAAA UCGU@LB@ :\|\| \|\| \|\|\|\|\|\|\| \|\|\|\| \|:\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UUG AC AAUUCGU CUUC UGAAUUUUUU AGCA@LB@3'-UUU...CUACU A G U G A AUGUG...CAA-5'@LB@ \| \|@LB@ 59 23@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -24.2219 kcal/mol@LB@Unfolding Energy - mRNA 7.43557 kcal/mol@LB@Unfolding Energy - sRNA 6.27608 kcal/mol@LB@@LB@Position - mRNA 34 -- 66@LB@Position - sRNA 24 -- 58@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 32 -- 38@LB@
139	0.01338	0.3093	b3765	yifB	-8.91	0.033732	103 -- 139	26 -- 57	magnesium chelatase family protein and putative transcriptional regulator	_____________102______________________________________140\n_____________\|________________________________________\|\n5'-AAA...ACUUC______ACAAA___A_____AUC__C______________ACGAA...CGA-3'\n______________ACUUGC_____UAA_CAGGA___AG_CACU___AAAAUUC\n______________\|\|\|\|\|\|_____\|\|\|_\|\|:\|\|___\|\|_\|\|\|\|___\|\|\|\|\|\|\|\n______________UGAACG_____AUU_GUUCU___UC_GUGA___UUUUAAG\n3'-UUU...UACUU______A_______C_______________AUU_______CAAUG...CAA-5'\n_____________\|________________________________________\|\n_____________58_______________________________________25\n	133 -- 139	26 -- 32	-18.0428 kcal/mol	2.85625 kcal/mol	6.27605 kcal/mol	102 140@LB@ \| \|@LB@5'-AAA...ACUUC ACAAA A AUC C ACGAA...CGA-3'@LB@ ACUUGC UAA CAGGA AG CACU AAAAUUC@LB@ \|\|\|\|\|\| \|\|\| \|\|:\|\| \|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ UGAACG AUU GUUCU UC GUGA UUUUAAG@LB@3'-UUU...UACUU A C AUU CAAUG...CAA-5'@LB@ \| \|@LB@ 58 25@LB@@LB@@LB@Energy -8.91 kcal/mol@LB@Hybridization Energy -18.0428 kcal/mol@LB@Unfolding Energy - mRNA 2.85625 kcal/mol@LB@Unfolding Energy - sRNA 6.27605 kcal/mol@LB@@LB@Position - mRNA 103 -- 139@LB@Position - sRNA 26 -- 57@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 26 -- 32@LB@
189	0.02233	0.3796	b3417	malP	-8.63	0.040366	227 -- 245	35 -- 53	maltodextrin phosphorylase	_____________226_________________246\n_____________\|___________________\|\n5'-ACA...GAUAA__AAUUU____________UCACG...GCC-3'\n______________GC_____CAGGAAGCGCUU\n______________\|\|_____\|\|:\|\|\|\|\|:\|\|\|\n______________CG_____GUUCUUCGUGAA\n3'-UUU...UUGAA__AAUUC____________UUUUU...CAA-5'\n_____________\|___________________\|\n_____________54__________________34\n	239 -- 245	35 -- 41	-18.4249 kcal/mol	3.68713 kcal/mol	6.10399 kcal/mol	226 246@LB@ \| \|@LB@5'-ACA...GAUAA AAUUU UCACG...GCC-3'@LB@ GC CAGGAAGCGCUU@LB@ \|\| \|\|:\|\|\|\|\|:\|\|\|@LB@ CG GUUCUUCGUGAA@LB@3'-UUU...UUGAA AAUUC UUUUU...CAA-5'@LB@ \| \|@LB@ 54 34@LB@@LB@@LB@Energy -8.63 kcal/mol@LB@Hybridization Energy -18.4249 kcal/mol@LB@Unfolding Energy - mRNA 3.68713 kcal/mol@LB@Unfolding Energy - sRNA 6.10399 kcal/mol@LB@@LB@Position - mRNA 227 -- 245@LB@Position - sRNA 35 -- 53@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 35 -- 41@LB@
50	0.002273	0.1465	b4159	mscM	-6.32	0.162358	72 -- 90	16 -- 34	mechanosensitive channel protein miniconductance	_____________71__________________91\n_____________\|___________________\|\n5'-AAG...CUACC____CC_____________ACGCU...AGC-3'\n______________GAAA__UUUGUUACGCCAG\n______________:\|\|\|__\|\|:\|\|\|\|\|:\|\|\|\|\n______________UUUU__AAGCAAUGUGGUC\n3'-UUU...GUGAA____UU_____________CUUUA...CAA-5'\n_____________\|___________________\|\n_____________35__________________15\n	84 -- 90	16 -- 22	-19.9467 kcal/mol	4.98786 kcal/mol	8.63814 kcal/mol	71 91@LB@ \| \|@LB@5'-AAG...CUACC CC ACGCU...AGC-3'@LB@ GAAA UUUGUUACGCCAG@LB@ :\|\|\| \|\|:\|\|\|\|\|:\|\|\|\|@LB@ UUUU AAGCAAUGUGGUC@LB@3'-UUU...GUGAA UU CUUUA...CAA-5'@LB@ \| \|@LB@ 35 15@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -19.9467 kcal/mol@LB@Unfolding Energy - mRNA 4.98786 kcal/mol@LB@Unfolding Energy - sRNA 8.63814 kcal/mol@LB@@LB@Position - mRNA 72 -- 90@LB@Position - sRNA 16 -- 34@LB@Position Seed - mRNA 84 -- 90@LB@Position Seed - sRNA 16 -- 22@LB@
120	0.01039	0.2788	b2314	dedD	-6.27	0.167184	42 -- 54	45 -- 58	membrane-anchored periplasmic protein involved in septation	_____________41_____________55\n_____________\|______________\|\n5'-UUG...AGAAC______________UUUGG...AUU-3'\n______________AAC_UGCUUGAGCA\n______________\|\|\|_\|\|\|\|\|:\|\|\|\|\n______________UUG_ACGAAUUCGU\n3'-UUU...CUACU___A__________UCUUC...CAA-5'\n_____________\|______________\|\n_____________59_____________44\n	47 -- 53	46 -- 52	-15.7533 kcal/mol	3.46622 kcal/mol	6.01947 kcal/mol	41 55@LB@ \| \|@LB@5'-UUG...AGAAC UUUGG...AUU-3'@LB@ AAC UGCUUGAGCA@LB@ \|\|\| \|\|\|\|\|:\|\|\|\|@LB@ UUG ACGAAUUCGU@LB@3'-UUU...CUACU A UCUUC...CAA-5'@LB@ \| \|@LB@ 59 44@LB@@LB@@LB@Energy -6.27 kcal/mol@LB@Hybridization Energy -15.7533 kcal/mol@LB@Unfolding Energy - mRNA 3.46622 kcal/mol@LB@Unfolding Energy - sRNA 6.01947 kcal/mol@LB@@LB@Position - mRNA 42 -- 54@LB@Position - sRNA 45 -- 58@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 46 -- 52@LB@
42	0.001686	0.1293	b2733	mutS	-6.21	0.172669	203 -- 222	25 -- 42	methyl-directed mismatch repair protein	_____________202__________________223\n_____________\|____________________\|\n5'-GAU...CCCAU______AA_________U__ACGCC...UGG-3'\n______________GAGUGC__UAGAAAAUU_CG\n______________:\|\|::\|__\|\|:\|\|\|\|\|\|_\|\|\n______________UUCGUG__AUUUUUUAA_GC\n3'-UUU...CGUUC______A_____________AAUGU...CAA-5'\n_____________\|____________________\|\n_____________43___________________24\n	213 -- 219	27 -- 33	-10.4027 kcal/mol	2.54535 kcal/mol	1.64855 kcal/mol	202 223@LB@ \| \|@LB@5'-GAU...CCCAU AA U ACGCC...UGG-3'@LB@ GAGUGC UAGAAAAUU CG@LB@ :\|\|::\| \|\|:\|\|\|\|\|\| \|\|@LB@ UUCGUG AUUUUUUAA GC@LB@3'-UUU...CGUUC A AAUGU...CAA-5'@LB@ \| \|@LB@ 43 24@LB@@LB@@LB@Energy -6.21 kcal/mol@LB@Hybridization Energy -10.4027 kcal/mol@LB@Unfolding Energy - mRNA 2.54535 kcal/mol@LB@Unfolding Energy - sRNA 1.64855 kcal/mol@LB@@LB@Position - mRNA 203 -- 222@LB@Position - sRNA 25 -- 42@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 27 -- 33@LB@
15	0.0003116	0.06692	b2149	mglA	-7.01	0.109495	281 -- 289	33 -- 41	methyl-galactoside ABC transporter ATPase	_____________280_______290\n_____________\|_________\|\n5'-CGA...GUUAA_________UAACG...AUU-3'\n______________GGCACUUGA\n______________:\|\|\|\|\|\|:\|\n______________UCGUGAAUU\n3'-UUU...GUUCU_________UUUUA...CAA-5'\n_____________\|_________\|\n_____________42________32\n	283 -- 289	33 -- 39	-11.227 kcal/mol	2.59529 kcal/mol	1.6188 kcal/mol	280 290@LB@ \| \|@LB@5'-CGA...GUUAA UAACG...AUU-3'@LB@ GGCACUUGA@LB@ :\|\|\|\|\|\|:\|@LB@ UCGUGAAUU@LB@3'-UUU...GUUCU UUUUA...CAA-5'@LB@ \| \|@LB@ 42 32@LB@@LB@@LB@Energy -7.01 kcal/mol@LB@Hybridization Energy -11.227 kcal/mol@LB@Unfolding Energy - mRNA 2.59529 kcal/mol@LB@Unfolding Energy - sRNA 1.6188 kcal/mol@LB@@LB@Position - mRNA 281 -- 289@LB@Position - sRNA 33 -- 41@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 33 -- 39@LB@
34	0.001265	0.1198	b0826	moeB	-10.82	0.009172	276 -- 295	26 -- 46	molybdopterin synthase sulfurylase	_____________275___________________296\n_____________\|_____________________\|\n5'-CUU...ACGGC_____________________UCGCG-3'\n______________CAGGAGGCGC_UGAAAGAUUC\n______________\|\|:\|\|:\|\|:\|_\|:\|\|\|:\|\|\|\|\n______________GUUCUUCGUG_AUUUUUUAAG\n3'-UUU...AAUUC__________A__________CAAUG...CAA-5'\n_____________\|_____________________\|\n_____________47____________________25\n	289 -- 295	26 -- 32	-23.0973 kcal/mol	6.15128 kcal/mol	6.13041 kcal/mol	275 296@LB@ \| \|@LB@5'-CUU...ACGGC UCGCG-3'@LB@ CAGGAGGCGC UGAAAGAUUC@LB@ \|\|:\|\|:\|\|:\| \|:\|\|\|:\|\|\|\|@LB@ GUUCUUCGUG AUUUUUUAAG@LB@3'-UUU...AAUUC A CAAUG...CAA-5'@LB@ \| \|@LB@ 47 25@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -23.0973 kcal/mol@LB@Unfolding Energy - mRNA 6.15128 kcal/mol@LB@Unfolding Energy - sRNA 6.13041 kcal/mol@LB@@LB@Position - mRNA 276 -- 295@LB@Position - sRNA 26 -- 46@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 26 -- 32@LB@
157	0.01701	0.3489	b3856	mobB	-4.94	0.329991	189 -- 197	52 -- 60	molybdopterin-guanine dinucleotide biosynthesis protein B	_____________188_______198\n_____________\|_________\|\n5'-GUG...CCAGA_________CCGAU...CCA-3'\n______________GGAGCUUGC\n______________\|:\|:\|\|\|\|\|\n______________CUUUGAACG\n3'-UUU...CCCUA_________AAUUC...CAA-5'\n_____________\|_________\|\n_____________61________51\n	191 -- 197	52 -- 58	-10.6989 kcal/mol	2.59286 kcal/mol	3.16562 kcal/mol	188 198@LB@ \| \|@LB@5'-GUG...CCAGA CCGAU...CCA-3'@LB@ GGAGCUUGC@LB@ \|:\|:\|\|\|\|\|@LB@ CUUUGAACG@LB@3'-UUU...CCCUA AAUUC...CAA-5'@LB@ \| \|@LB@ 61 51@LB@@LB@@LB@Energy -4.94 kcal/mol@LB@Hybridization Energy -10.6989 kcal/mol@LB@Unfolding Energy - mRNA 2.59286 kcal/mol@LB@Unfolding Energy - sRNA 3.16562 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 52 -- 60@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 52 -- 58@LB@
158	0.01725	0.3504	b3857	mobA	-11.09	0.007545	184 -- 212	5 -- 35	molybdopterin-guanine dinucleotide synthase	_____________183_____________________________213\n_____________\|_______________________________\|\n5'-UCC...CACAA_______GG___________U__________ACGAC...AAC-3'\n______________UAAAAGA__CG__AUAUCGG_GAAUCUGAUG\n______________\|\|\|\|\|:\|__\|\|__\|:\|:\|:\|_:\|\|\|\|\|\|\|\|\|\n______________AUUUUUU__GC__UGUGGUC_UUUAGACUAC\n3'-UUU...CGUGA_______AA__AA_______C__________ACAA-5'\n_____________\|_______________________________\|\n_____________36______________________________4\n	184 -- 190	29 -- 35	-25.0811 kcal/mol	5.24608 kcal/mol	8.74745 kcal/mol	183 213@LB@ \| \|@LB@5'-UCC...CACAA GG U ACGAC...AAC-3'@LB@ UAAAAGA CG AUAUCGG GAAUCUGAUG@LB@ \|\|\|\|\|:\| \|\| \|:\|:\|:\| :\|\|\|\|\|\|\|\|\|@LB@ AUUUUUU GC UGUGGUC UUUAGACUAC@LB@3'-UUU...CGUGA AA AA C ACAA-5'@LB@ \| \|@LB@ 36 4@LB@@LB@@LB@Energy -11.09 kcal/mol@LB@Hybridization Energy -25.0811 kcal/mol@LB@Unfolding Energy - mRNA 5.24608 kcal/mol@LB@Unfolding Energy - sRNA 8.74745 kcal/mol@LB@@LB@Position - mRNA 184 -- 212@LB@Position - sRNA 5 -- 35@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 29 -- 35@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