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: https://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	Additional homologs
116	0.005629	0.1728	stm2662	rluD	-17.46	0.046576	204 -- 257	36 -- 86	23S rRNA pseudouridine(1911/1915/1917) synthase		_____________203____________________258\n_____________\|______________________\|\n5'-UGA...UAUAU__________G___________CGCAA...GUU-3'\n______________GGCACAACGA_UACAAC_UCAC\n______________::\|\|\|\|\|\|:\|_:\|\|\|\|\|_\|\|\|\|\n______________UUGUGUUGUU_GUGUUG_AGUG\n3'-UUU...AACGU_________________U____UUGGC...UCA-5'\n_____________\|______________________\|\n_____________87_____________________35\n	206 -- 212	78 -- 84	-22.2469 kcal/mol	4.97176 kcal/mol	5.3513 kcal/mol	203 258@LB@ \| \|@LB@5'-UGA...UAUAU G CGCAA...GUU-3'@LB@ GGCACAACGA UACAAC UCAC@LB@ ::\|\|\|\|\|\|:\| :\|\|\|\|\| \|\|\|\|@LB@ UUGUGUUGUU GUGUUG AGUG@LB@3'-UUU...AACGU U UUGGC...UCA-5'@LB@ \| \|@LB@ 87 35@LB@@LB@@LB@Energy -17.46 kcal/mol@LB@Hybridization Energy -22.2469 kcal/mol@LB@Unfolding Energy - mRNA 4.97176 kcal/mol@LB@Unfolding Energy - sRNA 5.3513 kcal/mol@LB@@LB@Position - mRNA 204 -- 257@LB@Position - sRNA 36 -- 86@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 78 -- 84@LB@
80	0.003756	0.1596	stm0132	ftsA	-17.45	0.046754	189 -- 236	139 -- 186	cell division protein FtsA		_____________188_______________________________________237\n_____________\|_________________________________________\|\n5'-AAU...GAACA___A______AG___C_________AAAACUG___G_____CUGGA...UCA-3'\n______________ACA_UGAUCA____G_GACGGACAG_______GUA_UAGGA\n______________\|\|\|_\|:\|\|\|\|____\|_\|\|\|:\|\|\|\|\|_______\|\|\|_:\|\|\|\|\n______________UGU_AUUAGU____C_CUGUCUGUC_______CAU_GUCCU\n3'-UUU...CACGA___A______GAUA___________CCAUUUA_________UCACU...UCA-5'\n_____________\|_________________________________________\|\n_____________187_______________________________________138\n	214 -- 220	154 -- 160	-27.6527 kcal/mol	5.88434 kcal/mol	5.72652 kcal/mol	188 237@LB@ \| \|@LB@5'-AAU...GAACA A AG C AAAACUG G CUGGA...UCA-3'@LB@ ACA UGAUCA G GACGGACAG GUA UAGGA@LB@ \|\|\| \|:\|\|\|\| \| \|\|\|:\|\|\|\|\| \|\|\| :\|\|\|\|@LB@ UGU AUUAGU C CUGUCUGUC CAU GUCCU@LB@3'-UUU...CACGA A GAUA CCAUUUA UCACU...UCA-5'@LB@ \| \|@LB@ 187 138@LB@@LB@@LB@Energy -17.45 kcal/mol@LB@Hybridization Energy -27.6527 kcal/mol@LB@Unfolding Energy - mRNA 5.88434 kcal/mol@LB@Unfolding Energy - sRNA 5.72652 kcal/mol@LB@@LB@Position - mRNA 189 -- 236@LB@Position - sRNA 139 -- 186@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 154 -- 160@LB@
134	0.006725	0.1774	stm0546	fimD	-17.45	0.046766	176 -- 200	37 -- 60	outer membrane usher protein	stm0301 stm0175 stm4593 stm3638 stm0023	_____________175_____________201\n_____________\|_______________\|\n5'-UCA...AAGCC______G________GAAGA...CGA-3'\n______________ACACGA_AACACGAU\n______________\|\|\|\|:\|_\|\|\|\|\|:\|:\n______________UGUGUU_UUGUGUUG\n3'-UUU...ACGUU______G________UAGUG...UCA-5'\n_____________\|_______________\|\n_____________61______________36\n	196 -- 202	72 -- 78	-17.1314 kcal/mol	2.16166 kcal/mol	3.50587 kcal/mol	175 201@LB@ \| \|@LB@5'-UCA...AAGCC G GAAGA...CGA-3'@LB@ ACACGA AACACGAU@LB@ \|\|\|\|:\| \|\|\|\|\|:\|:@LB@ UGUGUU UUGUGUUG@LB@3'-UUU...ACGUU G UAGUG...UCA-5'@LB@ \| \|@LB@ 61 36@LB@@LB@@LB@Energy -17.45 kcal/mol@LB@Hybridization Energy -17.1314 kcal/mol@LB@Unfolding Energy - mRNA 2.16166 kcal/mol@LB@Unfolding Energy - sRNA 3.50587 kcal/mol@LB@@LB@Position - mRNA 176 -- 200@LB@Position - sRNA 37 -- 60@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 72 -- 78@LB@
103	0.005167	0.1728	stm2670	aroF	-17.31	0.049328	173 -- 242	25 -- 90	3-deoxy-7-phosphoheptulonate synthase		_____________172______________________________________________________________________243\n_____________\|________________________________________________________________________\|\n5'-CUU...CUAUC_______AGAA__G____G_____C___AU____A_____A_G____U___UAACG_______CA_______ACAGG...AGG-3'\n______________GCAAACA____AA_ACAG_AUCGC_AUC____GC_AAAAG_C_CG_C_GAA_____UACGUAU__CCGAUGA\n______________\|\|\|\|\|\|\|____\|\|_\|\|\|:_\|\|\|:\|_\|:\|____\|\|_\|\|\|\|\|_\|_\|:_\|_\|\|\|_____:\|\|\|:\|\|__\|\|\|\|\|:\|\n______________CGUUUGU____UU_UGUU_UAGUG_UGG____CG_UUUUC_G_GU_G_CUU_____GUGCGUA__GGCUAUU\n3'-UUU...GUUAA_______GUUG__G____G_____U___CAUU__G_______G__A_U_______________A________UUGAA...UCA-5'\n_____________\|________________________________________________________________________\|\n_____________91_______________________________________________________________________24\n	226 -- 232	34 -- 40	-46.7665 kcal/mol	10.372 kcal/mol	24.1795 kcal/mol	172 243@LB@ \| \|@LB@5'-CUU...CUAUC AGAA G G C AU A A G U UAACG CA ACAGG...AGG-3'@LB@ GCAAACA AA ACAG AUCGC AUC GC AAAAG C CG C GAA UACGUAU CCGAUGA@LB@ \|\|\|\|\|\|\| \|\| \|\|\|: \|\|\|:\| \|:\| \|\| \|\|\|\|\| \| \|: \| \|\|\| :\|\|\|:\|\| \|\|\|\|\|:\|@LB@ CGUUUGU UU UGUU UAGUG UGG CG UUUUC G GU G CUU GUGCGUA GGCUAUU@LB@3'-UUU...GUUAA GUUG G G U CAUU G G A U A UUGAA...UCA-5'@LB@ \| \|@LB@ 91 24@LB@@LB@@LB@Energy -17.31 kcal/mol@LB@Hybridization Energy -46.7665 kcal/mol@LB@Unfolding Energy - mRNA 10.372 kcal/mol@LB@Unfolding Energy - sRNA 24.1795 kcal/mol@LB@@LB@Position - mRNA 173 -- 242@LB@Position - sRNA 25 -- 90@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 34 -- 40@LB@
43	0.001574	0.1267	stm4453	treC	-17.28	0.050040	221 -- 269	37 -- 81	trehalose- 6-P hydrolase		_____________220____________________270\n_____________\|______________________\|\n5'-CGU...CGCAC_______AA_____________UAUUC...GCG-3'\n______________UUGCAGG__ACAACAAU__GAC\n______________\|\|\|\|\|::__\|\|\|\|\|\|\|:__:\|\|\n______________AACGUUU__UGUUGUUG__UUG\n3'-UUU...UGGUU_______G_________UG___UAGUG...UCA-5'\n_____________\|______________________\|\n_____________82_____________________36\n	196 -- 202	77 -- 83	-15.8671 kcal/mol	3.0955 kcal/mol	3.80821 kcal/mol	220 270@LB@ \| \|@LB@5'-CGU...CGCAC AA UAUUC...GCG-3'@LB@ UUGCAGG ACAACAAU GAC@LB@ \|\|\|\|\|:: \|\|\|\|\|\|\|: :\|\|@LB@ AACGUUU UGUUGUUG UUG@LB@3'-UUU...UGGUU G UG UAGUG...UCA-5'@LB@ \| \|@LB@ 82 36@LB@@LB@@LB@Energy -17.28 kcal/mol@LB@Hybridization Energy -15.8671 kcal/mol@LB@Unfolding Energy - mRNA 3.0955 kcal/mol@LB@Unfolding Energy - sRNA 3.80821 kcal/mol@LB@@LB@Position - mRNA 221 -- 269@LB@Position - sRNA 37 -- 81@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 77 -- 83@LB@
120	0.006002	0.1758	stm2925	nlpD	-17.26	0.050371	258 -- 274	153 -- 170	lipoprotein NlpD		_____________257________________275\n_____________\|__________________\|\n5'-GUU...UGGUU___________U______UUGUA...CGG-3'\n______________UCACUAUGG_C_GGCAGG\n______________\|\|\|\|\|\|\|\|\|_\|_\|:\|\|\|\|\n______________AGUGAUACC_G_CUGUCC\n3'-UUU...UAAUU_________U_U______CAUUU...UCA-5'\n_____________\|__________________\|\n_____________171________________152\n	260 -- 266	162 -- 168	-24.411 kcal/mol	4.59255 kcal/mol	3.4766 kcal/mol	257 275@LB@ \| \|@LB@5'-GUU...UGGUU U UUGUA...CGG-3'@LB@ UCACUAUGG C GGCAGG@LB@ \|\|\|\|\|\|\|\|\| \| \|:\|\|\|\|@LB@ AGUGAUACC G CUGUCC@LB@3'-UUU...UAAUU U U CAUUU...UCA-5'@LB@ \| \|@LB@ 171 152@LB@@LB@@LB@Energy -17.26 kcal/mol@LB@Hybridization Energy -24.411 kcal/mol@LB@Unfolding Energy - mRNA 4.59255 kcal/mol@LB@Unfolding Energy - sRNA 3.4766 kcal/mol@LB@@LB@Position - mRNA 258 -- 274@LB@Position - sRNA 153 -- 170@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 162 -- 168@LB@
54	0.002071	0.1363	stm1429	ydhB	-17.23	0.050879	3 -- 45	36 -- 79	putative LysR family transcriptional regulator		_____________2___________________________________46\n_____________\|___________________________________\|\n5'-CAA...UAUCA________UU__CGCA___________________UUACG...UCA-3'\n______________GACAGACA__GU____GAGUGU__AGGGAGUGAAA\n______________\|\|\|\|\|\|\|\|__\|\|____:\|:\|\|\|__\|\|\|:\|\|\|\|\|\|\|\n______________CUGUCUGU__CA____UUUACA__UCCUUCACUUU\n3'-UUU...GAUAC________CC____________UG___________UUCCC...UCA-5'\n_____________\|___________________________________\|\n_____________80__________________________________35\n	136 -- 142	132 -- 138	-30.0385 kcal/mol	9.87391 kcal/mol	6.0649 kcal/mol	2 46@LB@ \| \|@LB@5'-CAA...UAUCA UU CGCA UUACG...UCA-3'@LB@ GACAGACA GU GAGUGU AGGGAGUGAAA@LB@ \|\|\|\|\|\|\|\| \|\| :\|:\|\|\| \|\|\|:\|\|\|\|\|\|\|@LB@ CUGUCUGU CA UUUACA UCCUUCACUUU@LB@3'-UUU...GAUAC CC UG UUCCC...UCA-5'@LB@ \| \|@LB@ 80 35@LB@@LB@@LB@Energy -17.23 kcal/mol@LB@Hybridization Energy -30.0385 kcal/mol@LB@Unfolding Energy - mRNA 9.87391 kcal/mol@LB@Unfolding Energy - sRNA 6.0649 kcal/mol@LB@@LB@Position - mRNA 3 -- 45@LB@Position - sRNA 36 -- 79@LB@Position Seed - mRNA 136 -- 142@LB@Position Seed - sRNA 132 -- 138@LB@
46	0.001637	0.1267	stm2313	elaC	-17.21	0.051329	250 -- 300	51 -- 90	ribonuclease Z	stm1109	_____________249_____________________________________________301\n_____________\|_______________________________________________\|\n5'-UCG...CUCAC____UGUA________UUUAUUACAUCU________CAAC_______GGAG-3'\n______________GCAA____ACGGCAAU____________GCAACAUC____GCAGCCG\n______________\|\|\|\|____\|\|::\|\|\|:____________:\|\|\|\|\|\|\|____:\|\|:\|\|\|\n______________CGUU____UGUUGUUG____________UGUUGUAG____UGUUGGC\n3'-UUU...GUUAA____UG_________________________________________AUUCG...UCA-5'\n_____________\|_______________________________________________\|\n_____________91______________________________________________50\n	290 -- 296	62 -- 68	-28.5454 kcal/mol	7.10881 kcal/mol	8.62576 kcal/mol	249 301@LB@ \| \|@LB@5'-UCG...CUCAC UGUA UUUAUUACAUCU CAAC GGAG-3'@LB@ GCAA ACGGCAAU GCAACAUC GCAGCCG@LB@ \|\|\|\| \|\|::\|\|\|: :\|\|\|\|\|\|\| :\|\|:\|\|\|@LB@ CGUU UGUUGUUG UGUUGUAG UGUUGGC@LB@3'-UUU...GUUAA UG AUUCG...UCA-5'@LB@ \| \|@LB@ 91 50@LB@@LB@@LB@Energy -17.21 kcal/mol@LB@Hybridization Energy -28.5454 kcal/mol@LB@Unfolding Energy - mRNA 7.10881 kcal/mol@LB@Unfolding Energy - sRNA 8.62576 kcal/mol@LB@@LB@Position - mRNA 250 -- 300@LB@Position - sRNA 51 -- 90@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 62 -- 68@LB@
52	0.001934	0.1324	stm0653	ybeL	-17.18	0.051878	262 -- 299	155 -- 188	similar to E. coli putative alpha helical protein (AAC73744.1); Blastp hit to AAC73744.1 (160 aa) 91% identity in aa 1 - 160		_____________261________________________300\n_____________\|__________________________\|\n5'-AUU...GCGCG________G____G_____G______C-3'\n______________ACAUUGAU_CGCU_GUGGA_CAGGCG\n______________\|\|\|\|\|:\|\|_\|:\|\|_:\|\|\|\|_\|\|\|:\|:\n______________UGUAAUUA_GUGA_UACCU_GUCUGU\n3'-UUU...CACGA__________________________CCCAU...UCA-5'\n_____________\|__________________________\|\n_____________189________________________154\n	275 -- 281	170 -- 176	-23.9532 kcal/mol	9.91713 kcal/mol	4.10825 kcal/mol	261 300@LB@ \| \|@LB@5'-AUU...GCGCG G G G C-3'@LB@ ACAUUGAU CGCU GUGGA CAGGCG@LB@ \|\|\|\|\|:\|\| \|:\|\| :\|\|\|\| \|\|\|:\|:@LB@ UGUAAUUA GUGA UACCU GUCUGU@LB@3'-UUU...CACGA CCCAU...UCA-5'@LB@ \| \|@LB@ 189 154@LB@@LB@@LB@Energy -17.18 kcal/mol@LB@Hybridization Energy -23.9532 kcal/mol@LB@Unfolding Energy - mRNA 9.91713 kcal/mol@LB@Unfolding Energy - sRNA 4.10825 kcal/mol@LB@@LB@Position - mRNA 262 -- 299@LB@Position - sRNA 155 -- 188@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 170 -- 176@LB@
10	0.0001468	0.05229	stm0680	asnB	-17.15	0.052408	158 -- 224	32 -- 90	asparagine synthetase B		_____________157________________________225\n_____________\|__________________________\|\n5'-CAU...GUCAA_________AAAAGU___________GAUUA...CGG-3'\n______________GCAAAUACA______ACGACGCAACA\n______________\|\|\|\|\|:\|\|\|______\|\|:\|\|:\|\|\|\|\|\n______________CGUUUGUGU______UGUUGUGUUGU\n3'-UUU...GUUAA__________________________AGUGU...UCA-5'\n_____________\|__________________________\|\n_____________91_________________________31\n	177 -- 183	71 -- 77	-23.872 kcal/mol	3.8402 kcal/mol	3.80671 kcal/mol	157 225@LB@ \| \|@LB@5'-CAU...GUCAA AAAAGU GAUUA...CGG-3'@LB@ GCAAAUACA ACGACGCAACA@LB@ \|\|\|\|\|:\|\|\| \|\|:\|\|:\|\|\|\|\|@LB@ CGUUUGUGU UGUUGUGUUGU@LB@3'-UUU...GUUAA AGUGU...UCA-5'@LB@ \| \|@LB@ 91 31@LB@@LB@@LB@Energy -17.15 kcal/mol@LB@Hybridization Energy -23.872 kcal/mol@LB@Unfolding Energy - mRNA 3.8402 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 158 -- 224@LB@Position - sRNA 32 -- 90@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 71 -- 77@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