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	Additional homologs
194	0.01081	0.197	stm1954	fliY	-13.82	0.181182	183 -- 228	153 -- 193	cystine ABC transporter substrate-binding protein		_____________182________________________229\n_____________\|__________________________\|\n5'-CAG...GUCUA_________AC____AUAUU______UACUA...UGC-3'\n______________UGGUCAUUA__GGCA_____CGGGGU\n______________\|::\|\|\|:\|\|__\|:\|\|_____\|:\|\|\|\|\n______________AUUAGUGAU__CUGU_____GUCCCA\n3'-UUU...AUGUA_________AC____CU_________UUUAC...UCA-5'\n_____________\|__________________________\|\n_____________194________________________152\n	173 -- 179	165 -- 171	-18.5851 kcal/mol	4.12345 kcal/mol	4.10259 kcal/mol	182 229@LB@ \| \|@LB@5'-CAG...GUCUA AC AUAUU UACUA...UGC-3'@LB@ UGGUCAUUA GGCA CGGGGU@LB@ \|::\|\|\|:\|\| \|:\|\| \|:\|\|\|\|@LB@ AUUAGUGAU CUGU GUCCCA@LB@3'-UUU...AUGUA AC CU UUUAC...UCA-5'@LB@ \| \|@LB@ 194 152@LB@@LB@@LB@Energy -13.82 kcal/mol@LB@Hybridization Energy -18.5851 kcal/mol@LB@Unfolding Energy - mRNA 4.12345 kcal/mol@LB@Unfolding Energy - sRNA 4.10259 kcal/mol@LB@@LB@Position - mRNA 183 -- 228@LB@Position - sRNA 153 -- 193@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 165 -- 171@LB@
199	0.01101	0.197	stm3346	yhcM	-12.83	0.254909	186 -- 228	33 -- 82	cell division protein ZapE		_____________185____________________229\n_____________\|______________________\|\n5'-CAG...UUCAA_G__UA__________UAU___AAGCC...AAA-3'\n______________G_AA__ACAAUAACAU___GCA\n______________\|_\|\|__\|\|\|\|:\|\|\|\|:___:\|\|\n______________C_UU__UGUUGUUGUG___UGU\n3'-UUU...GUUAA_G__UG__________U_____AGUGU...UCA-5'\n_____________\|______________________\|\n_____________83_____________________32\n	193 -- 199	75 -- 81	-14.0954 kcal/mol	2.45302 kcal/mol	3.80671 kcal/mol	185 229@LB@ \| \|@LB@5'-CAG...UUCAA G UA UAU AAGCC...AAA-3'@LB@ G AA ACAAUAACAU GCA@LB@ \| \|\| \|\|\|\|:\|\|\|\|: :\|\|@LB@ C UU UGUUGUUGUG UGU@LB@3'-UUU...GUUAA G UG U AGUGU...UCA-5'@LB@ \| \|@LB@ 83 32@LB@@LB@@LB@Energy -12.83 kcal/mol@LB@Hybridization Energy -14.0954 kcal/mol@LB@Unfolding Energy - mRNA 2.45302 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 186 -- 228@LB@Position - sRNA 33 -- 82@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 75 -- 81@LB@
177	0.009665	0.1945	stm0079	yaaU	-14.30	0.152587	187 -- 218	40 -- 79	MFS transporter		_____________186___________219\n_____________\|_____________\|\n5'-GAA...GUUGA____G________CAUGC...UGC-3'\n______________AACA_GACAUCAC\n______________\|\|\|\|_:\|\|\|\|\|\|\|\n______________UUGU_UUGUAGUG\n3'-UUU...UGUUG____G________UUGGC...UCA-5'\n_____________\|_____________\|\n_____________80____________39\n	193 -- 199	67 -- 73	-15.1412 kcal/mol	3.61479 kcal/mol	3.57243 kcal/mol	186 219@LB@ \| \|@LB@5'-GAA...GUUGA G CAUGC...UGC-3'@LB@ AACA GACAUCAC@LB@ \|\|\|\| :\|\|\|\|\|\|\|@LB@ UUGU UUGUAGUG@LB@3'-UUU...UGUUG G UUGGC...UCA-5'@LB@ \| \|@LB@ 80 39@LB@@LB@@LB@Energy -14.30 kcal/mol@LB@Hybridization Energy -15.1412 kcal/mol@LB@Unfolding Energy - mRNA 3.61479 kcal/mol@LB@Unfolding Energy - sRNA 3.57243 kcal/mol@LB@@LB@Position - mRNA 187 -- 218@LB@Position - sRNA 40 -- 79@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 67 -- 73@LB@
101	0.005112	0.1728	stm0113	leuA	-13.72	0.187230	187 -- 230	37 -- 84	2-isopropylmalate synthase		_____________186_____________________231\n_____________\|_______________________\|\n5'-AUA...UGGAG____G_____________G____AGCAA...UGG-3'\n______________ACAA_GAC_C_ACAUCAU_AGCC\n______________\|\|\|\|_:\|\|_\|_\|\|\|\|\|\|:_\|:\|\|\n______________UGUU_UUG_G_UGUAGUG_UUGG\n3'-UUU...GUUUG____G___U_U____________CAUUC...UCA-5'\n_____________\|_______________________\|\n_____________85______________________36\n	196 -- 202	67 -- 73	-19.8594 kcal/mol	2.76514 kcal/mol	8.15907 kcal/mol	186 231@LB@ \| \|@LB@5'-AUA...UGGAG G G AGCAA...UGG-3'@LB@ ACAA GAC C ACAUCAU AGCC@LB@ \|\|\|\| :\|\| \| \|\|\|\|\|\|: \|:\|\|@LB@ UGUU UUG G UGUAGUG UUGG@LB@3'-UUU...GUUUG G U U CAUUC...UCA-5'@LB@ \| \|@LB@ 85 36@LB@@LB@@LB@Energy -13.72 kcal/mol@LB@Hybridization Energy -19.8594 kcal/mol@LB@Unfolding Energy - mRNA 2.76514 kcal/mol@LB@Unfolding Energy - sRNA 8.15907 kcal/mol@LB@@LB@Position - mRNA 187 -- 230@LB@Position - sRNA 37 -- 84@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 67 -- 73@LB@
192	0.01067	0.197	stm2650	yfiP	-13.22	0.223534	188 -- 232	36 -- 90	DTW domain-containing protein		_____________187_________________________233\n_____________\|___________________________\|\n5'-UCA...UCUCC________UUUCUAUGACC________UGUCC...GCU-3'\n______________GCAAACGC___________AAUAACGC\n______________\|\|\|\|\|\|:\|___________\|\|:\|\|\|:\|\n______________CGUUUGUG___________UUGUUGUG\n3'-UUU...GUUAA___________________________UUGUA...UCA-5'\n_____________\|___________________________\|\n_____________91__________________________35\n	208 -- 214	75 -- 81	-16.7007 kcal/mol	3.95203 kcal/mol	3.72363 kcal/mol	187 233@LB@ \| \|@LB@5'-UCA...UCUCC UUUCUAUGACC UGUCC...GCU-3'@LB@ GCAAACGC AAUAACGC@LB@ \|\|\|\|\|\|:\| \|\|:\|\|\|:\|@LB@ CGUUUGUG UUGUUGUG@LB@3'-UUU...GUUAA UUGUA...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -13.22 kcal/mol@LB@Hybridization Energy -16.7007 kcal/mol@LB@Unfolding Energy - mRNA 3.95203 kcal/mol@LB@Unfolding Energy - sRNA 3.72363 kcal/mol@LB@@LB@Position - mRNA 188 -- 232@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 75 -- 81@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@
144	0.00736	0.182	stm4559	yjjG	-11.80	0.356804	189 -- 218	128 -- 159	putative haloacid dehalogenase-like hydrolase		_____________188_________________________________219\n_____________\|___________________________________\|\n5'-UUG...AUAAA_G_____A____U__________________CU__AUUUU...UCA-3'\n______________A_AGGCA_GGUG_AAUG_AU__GAAGUGGGA__GG\n______________\|_\|\|:\|\|_\|\|\|:_\|\|\|\|_\|:__\|\|\|\|\|\|::\|__\|\|\n______________U_UCUGU_CCAU_UUAC_UG__CUUCACUUU__CC\n3'-UUU...AUACC_G_____C_________A__UC_________UU__CAUCA...UCA-5'\n_____________\|___________________________________\|\n_____________160_________________________________127\n	208 -- 214	132 -- 138	-24.694 kcal/mol	5.33554 kcal/mol	7.83417 kcal/mol	188 219@LB@ \| \|@LB@5'-UUG...AUAAA G A U CU AUUUU...UCA-3'@LB@ A AGGCA GGUG AAUG AU GAAGUGGGA GG@LB@ \| \|\|:\|\| \|\|\|: \|\|\|\| \|: \|\|\|\|\|\|::\| \|\|@LB@ U UCUGU CCAU UUAC UG CUUCACUUU CC@LB@3'-UUU...AUACC G C A UC UU CAUCA...UCA-5'@LB@ \| \|@LB@ 160 127@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -24.694 kcal/mol@LB@Unfolding Energy - mRNA 5.33554 kcal/mol@LB@Unfolding Energy - sRNA 7.83417 kcal/mol@LB@@LB@Position - mRNA 189 -- 218@LB@Position - sRNA 128 -- 159@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 132 -- 138@LB@
74	0.003449	0.1596	stm1129	N/A	-19.64	0.020096	190 -- 238	139 -- 186	N-acetylmannosamine-6-phosphate 2-epimerase	stm3337	_____________189__________________________________239\n_____________\|____________________________________\|\n5'-AUA...UGGAU________UAGC_____U__AACA_________C__AAACG...AAA-3'\n______________GUCACUAU____CAGGC_GG____AAGUGUACA_GA\n______________:\|\|\|\|\|\|\|____\|\|\|:\|_\|\|____\|\|:\|\|\|\|\|\|_\|\|\n______________UAGUGAUA____GUCUG_CC____UUUACAUGU_CU\n3'-UUU...GUAAU________CCU______U__CA___________C__UCACU...UCA-5'\n_____________\|____________________________________\|\n_____________187__________________________________138\n	229 -- 235	142 -- 148	-26.4502 kcal/mol	8.56913 kcal/mol	5.67007 kcal/mol	189 239@LB@ \| \|@LB@5'-AUA...UGGAU UAGC U AACA C AAACG...AAA-3'@LB@ GUCACUAU CAGGC GG AAGUGUACA GA@LB@ :\|\|\|\|\|\|\| \|\|\|:\| \|\| \|\|:\|\|\|\|\|\| \|\|@LB@ UAGUGAUA GUCUG CC UUUACAUGU CU@LB@3'-UUU...GUAAU CCU U CA C UCACU...UCA-5'@LB@ \| \|@LB@ 187 138@LB@@LB@@LB@Energy -19.64 kcal/mol@LB@Hybridization Energy -26.4502 kcal/mol@LB@Unfolding Energy - mRNA 8.56913 kcal/mol@LB@Unfolding Energy - sRNA 5.67007 kcal/mol@LB@@LB@Position - mRNA 190 -- 238@LB@Position - sRNA 139 -- 186@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 142 -- 148@LB@
122	0.00604	0.1758	stm2353	hisQ	-14.65	0.134227	190 -- 212	140 -- 163	amino acid ABC transporter permease		_____________189______________________213\n_____________\|________________________\|\n5'-GAU...CAACA________UGCAUGU_________UUUUC...UCG-3'\n______________GGACAGGC________UGUACGGG\n______________\|\|\|\|\|\|:\|________\|\|\|\|\|:\|\|\n______________CCUGUCUG________ACAUGUCC\n3'-UUU...UGAUA________UCCCAUUU________UUCAC...UCA-5'\n_____________\|________________________\|\n_____________164______________________139\n	206 -- 212	140 -- 146	-25.7393 kcal/mol	6.65037 kcal/mol	3.70771 kcal/mol	189 213@LB@ \| \|@LB@5'-GAU...CAACA UGCAUGU UUUUC...UCG-3'@LB@ GGACAGGC UGUACGGG@LB@ \|\|\|\|\|\|:\| \|\|\|\|\|:\|\|@LB@ CCUGUCUG ACAUGUCC@LB@3'-UUU...UGAUA UCCCAUUU UUCAC...UCA-5'@LB@ \| \|@LB@ 164 139@LB@@LB@@LB@Energy -14.65 kcal/mol@LB@Hybridization Energy -25.7393 kcal/mol@LB@Unfolding Energy - mRNA 6.65037 kcal/mol@LB@Unfolding Energy - sRNA 3.70771 kcal/mol@LB@@LB@Position - mRNA 190 -- 212@LB@Position - sRNA 140 -- 163@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 140 -- 146@LB@
25	0.0006298	0.08814	stm3161	metC	-13.21	0.223681	190 -- 249	35 -- 90	cystathionine beta-lyase		_____________189__________________250\n_____________\|____________________\|\n5'-CAA...AACUG_________G__________AAAAA...CAC-3'\n______________GUAAACGCA__GACGCAGCA\n______________\|:\|\|\|\|:\|\|__:\|\|:\|\|:\|\|\n______________CGUUUGUGU__UUGUGUUGU\n3'-UUU...GUUAA_________UG_________AGUGU...UCA-5'\n_____________\|____________________\|\n_____________91___________________34\n	243 -- 249	71 -- 77	-21.5854 kcal/mol	5.07977 kcal/mol	3.80671 kcal/mol	189 250@LB@ \| \|@LB@5'-CAA...AACUG G AAAAA...CAC-3'@LB@ GUAAACGCA GACGCAGCA@LB@ \|:\|\|\|\|:\|\| :\|\|:\|\|:\|\|@LB@ CGUUUGUGU UUGUGUUGU@LB@3'-UUU...GUUAA UG AGUGU...UCA-5'@LB@ \| \|@LB@ 91 34@LB@@LB@@LB@Energy -13.21 kcal/mol@LB@Hybridization Energy -21.5854 kcal/mol@LB@Unfolding Energy - mRNA 5.07977 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 190 -- 249@LB@Position - sRNA 35 -- 90@LB@Position Seed - mRNA 243 -- 249@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

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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

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