Input and runtime details for job 3202356 (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 3202356 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:02 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:03:47 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:03:55 CET 2018
	Job Completed		@ Sat Feb 17 02:04:28 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

Description of the job

GcvB

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_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

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
24	0.000609	0.08814	stm3510	yhgH	-18.34	0.033208	106 -- 153	42 -- 84	DNA utilization protein GntX	_____________105____________________________________154\n_____________\|______________________________________\|\n5'-CCG...UCCGU____________G__G___AUUUCCCUC__________UGCCA...GCG-3'\n______________GCAGCAGCACAA_AU_ACA_________GCCGUAGGUC\n______________:\|\|:\|\|:\|\|\|\|\|_\|\|_\|\|\|_________:\|\|\|\|\|:\|:\|\n______________UGUUGUUGUGUU_UA_UGU_________UGGCAUUCGG\n3'-UUU...GUUUG____________G__G______________________UUUUC...UCA-5'\n_____________\|______________________________________\|\n_____________85_____________________________________41\n	135 -- 141	58 -- 64	-35.7194 kcal/mol	10.0869 kcal/mol	11.5136 kcal/mol	105 154@LB@ \| \|@LB@5'-CCG...UCCGU G G AUUUCCCUC UGCCA...GCG-3'@LB@ GCAGCAGCACAA AU ACA GCCGUAGGUC@LB@ :\|\|:\|\|:\|\|\|\|\| \|\| \|\|\| :\|\|\|\|\|:\|:\|@LB@ UGUUGUUGUGUU UA UGU UGGCAUUCGG@LB@3'-UUU...GUUUG G G UUUUC...UCA-5'@LB@ \| \|@LB@ 85 41@LB@@LB@@LB@Energy -18.34 kcal/mol@LB@Hybridization Energy -35.7194 kcal/mol@LB@Unfolding Energy - mRNA 10.0869 kcal/mol@LB@Unfolding Energy - sRNA 11.5136 kcal/mol@LB@@LB@Position - mRNA 106 -- 153@LB@Position - sRNA 42 -- 84@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 58 -- 64@LB@
73	0.003444	0.1596	stm1437	ydhM	-18.33	0.033340	6 -- 47	35 -- 81	TetR family transcriptional regulator	_____________5_______________________48\n_____________\|_______________________\|\n5'-CGG...CAAAC___________CC___G______UGCUG...AGU-3'\n______________CGAACACGAUA__CGC_AACAUC\n______________\|:\|\|\|\|\|:\|:\|__\|:\|_\|\|\|\|\|\|\n______________GUUUGUGUUGU__GUG_UUGUAG\n3'-UUU...UUAAC___________U___________UGUUG...UCA-5'\n_____________\|_______________________\|\n_____________82______________________34\n	219 -- 225	79 -- 85	-19.8292 kcal/mol	2.08213 kcal/mol	4.32311 kcal/mol	5 48@LB@ \| \|@LB@5'-CGG...CAAAC CC G UGCUG...AGU-3'@LB@ CGAACACGAUA CGC AACAUC@LB@ \|:\|\|\|\|\|:\|:\| \|:\| \|\|\|\|\|\|@LB@ GUUUGUGUUGU GUG UUGUAG@LB@3'-UUU...UUAAC U UGUUG...UCA-5'@LB@ \| \|@LB@ 82 34@LB@@LB@@LB@Energy -18.33 kcal/mol@LB@Hybridization Energy -19.8292 kcal/mol@LB@Unfolding Energy - mRNA 2.08213 kcal/mol@LB@Unfolding Energy - sRNA 4.32311 kcal/mol@LB@@LB@Position - mRNA 6 -- 47@LB@Position - sRNA 35 -- 81@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 79 -- 85@LB@
49	0.001802	0.1291	stm1787	N/A	-18.29	0.033902	137 -- 202	34 -- 90	[Ni/Fe] hydrogenase large subunit	_____________136__________________203\n_____________\|____________________\|\n5'-GGC...CCAAC________C___________GUUAG...GCG-3'\n______________GUAAACGC_ACAA_ACAACA\n______________\|:\|\|\|\|:\|_\|\|\|\|_\|\|\|\|\|\|\n______________CGUUUGUG_UGUU_UGUUGU\n3'-UUU...GUUAA________U____G______AGUGU...UCA-5'\n_____________\|____________________\|\n_____________91___________________33\n	138 -- 144	83 -- 89	-18.7581 kcal/mol	1.39906 kcal/mol	3.80671 kcal/mol	136 203@LB@ \| \|@LB@5'-GGC...CCAAC C GUUAG...GCG-3'@LB@ GUAAACGC ACAA ACAACA@LB@ \|:\|\|\|\|:\| \|\|\|\| \|\|\|\|\|\|@LB@ CGUUUGUG UGUU UGUUGU@LB@3'-UUU...GUUAA U G AGUGU...UCA-5'@LB@ \| \|@LB@ 91 33@LB@@LB@@LB@Energy -18.29 kcal/mol@LB@Hybridization Energy -18.7581 kcal/mol@LB@Unfolding Energy - mRNA 1.39906 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 137 -- 202@LB@Position - sRNA 34 -- 90@LB@Position Seed - mRNA 138 -- 144@LB@Position Seed - sRNA 83 -- 89@LB@
102	0.005164	0.1728	stm0668	ybeY	-18.23	0.034693	146 -- 193	37 -- 81	rRNA maturation RNase YbeY	_____________145__________________________________________194\n_____________\|____________________________________________\|\n5'-UCC...AAAAC____________UUG____________G_______GU_______AGGAG...CGC-3'\n______________GCAAA_GCGGCG___GCGGCA____GA_CGUAAGC__GAAGCCC\n______________\|\|\|\|\|_:\|::\|:___:\|::\|\|____:\|_\|\|\|\|\|\|\|__:\|\|\|\|\|\|\n______________CGUUU_UGUUGU___UGUUGU____UU_GCAUUCG__UUUCGGG\n3'-UUU...GUUAA_____G______UG_______AGUG__G_______GU_______UAGUC...UCA-5'\n_____________\|____________________________________________\|\n_____________82___________________________________________36\n	178 -- 184	48 -- 54	-38.2699 kcal/mol	15.4401 kcal/mol	16.4278 kcal/mol	145 194@LB@ \| \|@LB@5'-UCC...AAAAC UUG G GU AGGAG...CGC-3'@LB@ GCAAA GCGGCG GCGGCA GA CGUAAGC GAAGCCC@LB@ \|\|\|\|\| :\|::\|: :\|::\|\| :\| \|\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ CGUUU UGUUGU UGUUGU UU GCAUUCG UUUCGGG@LB@3'-UUU...GUUAA G UG AGUG G GU UAGUC...UCA-5'@LB@ \| \|@LB@ 82 36@LB@@LB@@LB@Energy -18.23 kcal/mol@LB@Hybridization Energy -38.2699 kcal/mol@LB@Unfolding Energy - mRNA 15.4401 kcal/mol@LB@Unfolding Energy - sRNA 16.4278 kcal/mol@LB@@LB@Position - mRNA 146 -- 193@LB@Position - sRNA 37 -- 81@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 48 -- 54@LB@
93	0.004254	0.1596	stm0408	secF	-18.22	0.034847	7 -- 64	39 -- 91	protein-export membrane protein SecF	_____________6______________________________________65\n_____________\|______________________________________\|\n5'-CUU...GCACA_G__U____UGUUG______UA________________AGUCU...UGC-3'\n______________G_AA_ACAC_____AACAAC__AAC__CACGGCCGUAA\n______________\|_\|\|_\|\|\|\|_____\|\|\|\|\|\|__\|\|\|__\|\|\|::\|\|\|\|\|\|\n______________C_UU_UGUG_____UUGUUG__UUG__GUGUUGGCAUU\n3'-UUU...GUUAA_G__________________UG___UA___________CGGUU...UCA-5'\n_____________\|______________________________________\|\n_____________92_____________________________________38\n	238 -- 244	59 -- 65	-26.2573 kcal/mol	3.95572 kcal/mol	10.1648 kcal/mol	6 65@LB@ \| \|@LB@5'-CUU...GCACA G U UGUUG UA AGUCU...UGC-3'@LB@ G AA ACAC AACAAC AAC CACGGCCGUAA@LB@ \| \|\| \|\|\|\| \|\|\|\|\|\| \|\|\| \|\|\|::\|\|\|\|\|\|@LB@ C UU UGUG UUGUUG UUG GUGUUGGCAUU@LB@3'-UUU...GUUAA G UG UA CGGUU...UCA-5'@LB@ \| \|@LB@ 92 38@LB@@LB@@LB@Energy -18.22 kcal/mol@LB@Hybridization Energy -26.2573 kcal/mol@LB@Unfolding Energy - mRNA 3.95572 kcal/mol@LB@Unfolding Energy - sRNA 10.1648 kcal/mol@LB@@LB@Position - mRNA 7 -- 64@LB@Position - sRNA 39 -- 91@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 59 -- 65@LB@
187	0.01045	0.1967	stm4558	rimI	-18.19	0.035171	194 -- 252	42 -- 91	ribosomal-protein-alanine N-acetyltransferase	_____________193______________________________________253\n_____________\|________________________________________\|\n5'-GAC...AAAUC_________G__________UUCUAUCCUCAG________AUCUC...UCG-3'\n______________UGCGAACAU___AACACGAU____________CACGACCG\n______________\|\|\|:\|\|\|\|:___\|\|\|\|\|:\|:____________\|\|\|:\|\|\|\|\n______________ACGUUUGUG___UUGUGUUG____________GUGUUGGC\n3'-UUU...GGUUA_________UUG________UA__________________AUUCG...UCA-5'\n_____________\|________________________________________\|\n_____________92_______________________________________41\n	225 -- 231	62 -- 68	-28.9909 kcal/mol	5.96366 kcal/mol	8.62907 kcal/mol	193 253@LB@ \| \|@LB@5'-GAC...AAAUC G UUCUAUCCUCAG AUCUC...UCG-3'@LB@ UGCGAACAU AACACGAU CACGACCG@LB@ \|\|\|:\|\|\|\|: \|\|\|\|\|:\|: \|\|\|:\|\|\|\|@LB@ ACGUUUGUG UUGUGUUG GUGUUGGC@LB@3'-UUU...GGUUA UUG UA AUUCG...UCA-5'@LB@ \| \|@LB@ 92 41@LB@@LB@@LB@Energy -18.19 kcal/mol@LB@Hybridization Energy -28.9909 kcal/mol@LB@Unfolding Energy - mRNA 5.96366 kcal/mol@LB@Unfolding Energy - sRNA 8.62907 kcal/mol@LB@@LB@Position - mRNA 194 -- 252@LB@Position - sRNA 42 -- 91@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 62 -- 68@LB@
168	0.009144	0.1938	stm3609	yhjE	-18.08	0.036777	202 -- 261	35 -- 91	MFS transporter	_____________201__________________________________262\n_____________\|____________________________________\|\n5'-UAA...UAGUA_______A__C_____________U_____A_____AGGAA...UUG-3'\n______________UGCAAGC_AC_GC__CACAACA_C_CGACC_UGAGC\n______________\|\|\|\|\|:\|_\|\|_:\|__\|\|\|\|\|\|\|_\|_\|:\|\|\|_\|:\|\|\|\n______________ACGUUUG_UG_UG__GUGUUGU_G_GUUGG_AUUCG\n3'-UUU...GGUUA__________U__UU_______A_U_____C_____GUUUU...UCA-5'\n_____________\|____________________________________\|\n_____________92___________________________________34\n	215 -- 221	71 -- 77	-32.2191 kcal/mol	4.27941 kcal/mol	11.5198 kcal/mol	201 262@LB@ \| \|@LB@5'-UAA...UAGUA A C U A AGGAA...UUG-3'@LB@ UGCAAGC AC GC CACAACA C CGACC UGAGC@LB@ \|\|\|\|\|:\| \|\| :\| \|\|\|\|\|\|\| \| \|:\|\|\| \|:\|\|\|@LB@ ACGUUUG UG UG GUGUUGU G GUUGG AUUCG@LB@3'-UUU...GGUUA U UU A U C GUUUU...UCA-5'@LB@ \| \|@LB@ 92 34@LB@@LB@@LB@Energy -18.08 kcal/mol@LB@Hybridization Energy -32.2191 kcal/mol@LB@Unfolding Energy - mRNA 4.27941 kcal/mol@LB@Unfolding Energy - sRNA 11.5198 kcal/mol@LB@@LB@Position - mRNA 202 -- 261@LB@Position - sRNA 35 -- 91@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 71 -- 77@LB@
61	0.002902	0.1596	stm3567	livJ	-18.03	0.037474	150 -- 196	40 -- 87	high-affinity branched-chain amino acid transporter	_____________149_______________________197\n_____________\|_________________________\|\n5'-CGG...ACAAU_____C____________A______AGAAU...CCG-3'\n______________AACAC_ACAACACA_CGU_ACAACC\n______________\|\|\|\|\|_\|\|\|\|\|\|\|\|_\|:\|_\|\|\|\|\|\|\n______________UUGUG_UGUUGUGU_GUA_UGUUGG\n3'-UUU...AACGU_____U________U___G______CAUUC...UCA-5'\n_____________\|_________________________\|\n_____________88________________________39\n	157 -- 163	74 -- 80	-27.1738 kcal/mol	3.63117 kcal/mol	8.28637 kcal/mol	149 197@LB@ \| \|@LB@5'-CGG...ACAAU C A AGAAU...CCG-3'@LB@ AACAC ACAACACA CGU ACAACC@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\| \|:\| \|\|\|\|\|\|@LB@ UUGUG UGUUGUGU GUA UGUUGG@LB@3'-UUU...AACGU U U G CAUUC...UCA-5'@LB@ \| \|@LB@ 88 39@LB@@LB@@LB@Energy -18.03 kcal/mol@LB@Hybridization Energy -27.1738 kcal/mol@LB@Unfolding Energy - mRNA 3.63117 kcal/mol@LB@Unfolding Energy - sRNA 8.28637 kcal/mol@LB@@LB@Position - mRNA 150 -- 196@LB@Position - sRNA 40 -- 87@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 74 -- 80@LB@
140	0.007169	0.182	stm3126	N/A	-18.02	0.037639	66 -- 114	39 -- 91	putative amino acid transporter	_____________65_______________________________115\n_____________\|________________________________\|\n5'-AUU...GCGCA______G______U___________UU_____UAUCC...UGA-3'\n______________UGCGGG_ACGGCG_CACAACGUUAU__ACCGU\n______________\|\|\|:::_\|\|::\|:_\|\|\|\|\|\|:\|:\|:__\|\|\|\|\|\n______________ACGUUU_UGUUGU_GUGUUGUAGUG__UGGCA\n3'-UUU...GGUUA______G______U___________U______UUCGG...UCA-5'\n_____________\|________________________________\|\n_____________92_______________________________38\n	82 -- 88	69 -- 75	-33.8851 kcal/mol	10.4253 kcal/mol	9.42541 kcal/mol	65 115@LB@ \| \|@LB@5'-AUU...GCGCA G U UU UAUCC...UGA-3'@LB@ UGCGGG ACGGCG CACAACGUUAU ACCGU@LB@ \|\|\|::: \|\|::\|: \|\|\|\|\|\|:\|:\|: \|\|\|\|\|@LB@ ACGUUU UGUUGU GUGUUGUAGUG UGGCA@LB@3'-UUU...GGUUA G U U UUCGG...UCA-5'@LB@ \| \|@LB@ 92 38@LB@@LB@@LB@Energy -18.02 kcal/mol@LB@Hybridization Energy -33.8851 kcal/mol@LB@Unfolding Energy - mRNA 10.4253 kcal/mol@LB@Unfolding Energy - sRNA 9.42541 kcal/mol@LB@@LB@Position - mRNA 66 -- 114@LB@Position - sRNA 39 -- 91@LB@Position Seed - mRNA 82 -- 88@LB@Position Seed - sRNA 69 -- 75@LB@
47	0.001676	0.127	stm0637	dacA	-17.91	0.039191	14 -- 64	37 -- 92	serine-type D-Ala-D-Ala carboxypeptidase	_____________13____________________65\n_____________\|_____________________\|\n5'-GUU...AACGU_________GA__________UACAG...AUA-3'\n______________UUGCAAACA____AGCACAAU\n______________\|\|\|\|\|\|\|\|\|____\|:\|\|\|\|\|:\n______________AACGUUUGU____UUGUGUUG\n3'-UUU...UGGUU_________GUUG________UAGUG...UCA-5'\n_____________\|_____________________\|\n_____________93____________________36\n	26 -- 32	72 -- 78	-19.7119 kcal/mol	3.03223 kcal/mol	3.80821 kcal/mol	13 65@LB@ \| \|@LB@5'-GUU...AACGU GA UACAG...AUA-3'@LB@ UUGCAAACA AGCACAAU@LB@ \|\|\|\|\|\|\|\|\| \|:\|\|\|\|\|:@LB@ AACGUUUGU UUGUGUUG@LB@3'-UUU...UGGUU GUUG UAGUG...UCA-5'@LB@ \| \|@LB@ 93 36@LB@@LB@@LB@Energy -17.91 kcal/mol@LB@Hybridization Energy -19.7119 kcal/mol@LB@Unfolding Energy - mRNA 3.03223 kcal/mol@LB@Unfolding Energy - sRNA 3.80821 kcal/mol@LB@@LB@Position - mRNA 14 -- 64@LB@Position - sRNA 37 -- 92@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 72 -- 78@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