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
11	0.0001804	0.05681	stm0959	lrp	-12.80	0.257711	163 -- 181	139 -- 159	leucine-responsive transcriptional regulator		_____________162_______________________________________________182\n_____________\|_________________________________________________\|\n5'-UGA...AGAGU________A_____GA________UAC______ACAAUAAUAAU_____AUAGC...AGC-3'\n______________CAGGCAGG_GUAGG_____AGGAA___AGAGAG___________GGUAG\n______________\|\|\|:\|\|\|\|_\|\|\|::_____\|\|\|\|\|___\|:\|:\|\|___________\|\|\|\|\|\n______________GUCUGUCC_CAUUU_____UCCUU___UUUUUC___________CCAUC\n3'-UUU...UACCU______________ACAUG_____CAC______________________AGAGC...UCA-5'\n_____________\|_________________________________________________\|\n_____________160_______________________________________________138\n	163 -- 169	153 -- 159	-28.6161 kcal/mol	5.81197 kcal/mol	10.0349 kcal/mol	162 182@LB@ \| \|@LB@5'-UGA...AGAGU A GA UAC ACAAUAAUAAU AUAGC...AGC-3'@LB@ CAGGCAGG GUAGG AGGAA AGAGAG GGUAG@LB@ \|\|\|:\|\|\|\| \|\|\|:: \|\|\|\|\| \|:\|:\|\| \|\|\|\|\|@LB@ GUCUGUCC CAUUU UCCUU UUUUUC CCAUC@LB@3'-UUU...UACCU ACAUG CAC AGAGC...UCA-5'@LB@ \| \|@LB@ 160 138@LB@@LB@@LB@Energy -12.80 kcal/mol@LB@Hybridization Energy -28.6161 kcal/mol@LB@Unfolding Energy - mRNA 5.81197 kcal/mol@LB@Unfolding Energy - sRNA 10.0349 kcal/mol@LB@@LB@Position - mRNA 163 -- 181@LB@Position - sRNA 139 -- 159@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 153 -- 159@LB@
190	0.01053	0.1967	stm4032	N/A	-12.98	0.242168	37 -- 92	31 -- 85	lipase	stm0490	_____________36__________________93\n_____________\|___________________\|\n5'-CUU...UCGCG____G______G_______GAGGG...GCU-3'\n______________AACA_AAUAUU_AUGACCG\n______________\|\|\|\|_\|\|:\|\|:_\|::\|\|\|\|\n______________UUGU_UUGUAG_UGUUGGC\n3'-UUU...UGUUG____G______________AUUCG...UCA-5'\n_____________\|___________________\|\n_____________86__________________30\n	283 -- 289	62 -- 68	-14.8704 kcal/mol	1.51414 kcal/mol	6.51321 kcal/mol	36 93@LB@ \| \|@LB@5'-CUU...UCGCG G G GAGGG...GCU-3'@LB@ AACA AAUAUU AUGACCG@LB@ \|\|\|\| \|\|:\|\|: \|::\|\|\|\|@LB@ UUGU UUGUAG UGUUGGC@LB@3'-UUU...UGUUG G AUUCG...UCA-5'@LB@ \| \|@LB@ 86 30@LB@@LB@@LB@Energy -12.98 kcal/mol@LB@Hybridization Energy -14.8704 kcal/mol@LB@Unfolding Energy - mRNA 1.51414 kcal/mol@LB@Unfolding Energy - sRNA 6.51321 kcal/mol@LB@@LB@Position - mRNA 37 -- 92@LB@Position - sRNA 31 -- 85@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 62 -- 68@LB@
41	0.001426	0.1215	stm3718	rfaI	-15.09	0.114319	193 -- 209	157 -- 173	lipopolysaccharide 1 3-galactosyltransferase	stm3717	_____________192_______________210\n_____________\|_________________\|\n5'-AUG...AAAAG___________A_____AAAUA...GGA-3'\n______________UGAUCACUAUG_GCAGA\n______________\|:\|\|\|\|\|\|\|\|\|_:\|\|\|\|\n______________AUUAGUGAUAC_UGUCU\n3'-UUU...AUGUA___________C_____GUCCC...UCA-5'\n_____________\|_________________\|\n_____________174_______________156\n	197 -- 203	163 -- 169	-20.9664 kcal/mol	2.81615 kcal/mol	3.98136 kcal/mol	192 210@LB@ \| \|@LB@5'-AUG...AAAAG A AAAUA...GGA-3'@LB@ UGAUCACUAUG GCAGA@LB@ \|:\|\|\|\|\|\|\|\|\| :\|\|\|\|@LB@ AUUAGUGAUAC UGUCU@LB@3'-UUU...AUGUA C GUCCC...UCA-5'@LB@ \| \|@LB@ 174 156@LB@@LB@@LB@Energy -15.09 kcal/mol@LB@Hybridization Energy -20.9664 kcal/mol@LB@Unfolding Energy - mRNA 2.81615 kcal/mol@LB@Unfolding Energy - sRNA 3.98136 kcal/mol@LB@@LB@Position - mRNA 193 -- 209@LB@Position - sRNA 157 -- 173@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 163 -- 169@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@
130	0.00652	0.1774	stm4228	malF	-14.47	0.143021	162 -- 175	1 -- 15	maltose ABC transporter permease MalF		_____________161_____________176\n_____________\|_______________\|\n5'-AAC...ACAUC_______________UUCAA...UAA-3'\n______________UCCGGC_CAGGAAGU\n______________\|\|\|\|\|\|_\|\|\|\|\|\|\|\|\n______________AGGCCG_GUCCUUCA\n3'-UUU...AAGCA______A________-5'\n_____________\|______________\|\n_____________16_____________1\n	169 -- 175	1 -- 7	-25.2779 kcal/mol	6.67863 kcal/mol	4.81264 kcal/mol	161 176@LB@ \| \|@LB@5'-AAC...ACAUC UUCAA...UAA-3'@LB@ UCCGGC CAGGAAGU@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ AGGCCG GUCCUUCA@LB@3'-UUU...AAGCA A -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -14.47 kcal/mol@LB@Hybridization Energy -25.2779 kcal/mol@LB@Unfolding Energy - mRNA 6.67863 kcal/mol@LB@Unfolding Energy - sRNA 4.81264 kcal/mol@LB@@LB@Position - mRNA 162 -- 175@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 1 -- 7@LB@
59	0.00232	0.14	stm4105	metF	-16.51	0.066936	223 -- 245	40 -- 59	methylenetetrahydrofolate reductase [NAD(P)H]		_____________222__________________246\n_____________\|____________________\|\n5'-AAG...UUUAC__________AUA_______GCGAU...GCA-3'\n______________AACACAACAA___AUAACAU\n______________\|\|\|\|\|\|\|\|\|\|___\|:\|\|\|\|\|\n______________UUGUGUUGUU___UGUUGUA\n3'-UUU...AACGU__________G_________GUGUU...UCA-5'\n_____________\|____________________\|\n_____________60___________________39\n	175 -- 181	70 -- 76	-16.6304 kcal/mol	0.675865 kcal/mol	3.87174 kcal/mol	222 246@LB@ \| \|@LB@5'-AAG...UUUAC AUA GCGAU...GCA-3'@LB@ AACACAACAA AUAACAU@LB@ \|\|\|\|\|\|\|\|\|\| \|:\|\|\|\|\|@LB@ UUGUGUUGUU UGUUGUA@LB@3'-UUU...AACGU G GUGUU...UCA-5'@LB@ \| \|@LB@ 60 39@LB@@LB@@LB@Energy -16.51 kcal/mol@LB@Hybridization Energy -16.6304 kcal/mol@LB@Unfolding Energy - mRNA 0.675865 kcal/mol@LB@Unfolding Energy - sRNA 3.87174 kcal/mol@LB@@LB@Position - mRNA 223 -- 245@LB@Position - sRNA 40 -- 59@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 70 -- 76@LB@
82	0.003783	0.1596	stm0710	ybgH	-19.90	0.018103	103 -- 151	33 -- 90	MFS transporter		_____________102__________________152\n_____________\|____________________\|\n5'-GCG...UUUAA_G__________________GGCUU...UUC-3'\n______________G_AAACACGGCGAUACGGCA\n______________\|_\|\|\|\|\|\|::\|:\|:\|\|::\|\|\n______________C_UUUGUGUUGUUGUGUUGU\n3'-UUU...GUUAA_G__________________AGUGU...UCA-5'\n_____________\|____________________\|\n_____________91___________________32\n	116 -- 122	71 -- 77	-24.8461 kcal/mol	5.94354 kcal/mol	3.80671 kcal/mol	102 152@LB@ \| \|@LB@5'-GCG...UUUAA G GGCUU...UUC-3'@LB@ G AAACACGGCGAUACGGCA@LB@ \| \|\|\|\|\|\|::\|:\|:\|\|::\|\|@LB@ C UUUGUGUUGUUGUGUUGU@LB@3'-UUU...GUUAA G AGUGU...UCA-5'@LB@ \| \|@LB@ 91 32@LB@@LB@@LB@Energy -19.90 kcal/mol@LB@Hybridization Energy -24.8461 kcal/mol@LB@Unfolding Energy - mRNA 5.94354 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 103 -- 151@LB@Position - sRNA 33 -- 90@LB@Position Seed - mRNA 116 -- 122@LB@Position Seed - sRNA 71 -- 77@LB@
136	0.006805	0.1774	stm2812	N/A	-16.76	0.060981	84 -- 153	36 -- 90	MFS transporter		_____________83_____________________________________________154\n_____________\|______________________________________________\|\n5'-GGC...AUCCG__C________CUCUCCUCAAAGC______UU_______UC_____UCCCC...UGC-3'\n______________GC_AACGCAAU_____________GCACGA__CAUCACG__ACCGU\n______________\|\|_\|\|\|:\|\|\|:_____________:\|\|\|:\|__\|\|\|\|\|\|:__\|\|\|\|\|\n______________CG_UUGUGUUG_____________UGUGUU__GUAGUGU__UGGCA\n3'-UUU...GUUAA__U________U__________________________________UUCGG...UCA-5'\n_____________\|______________________________________________\|\n_____________91_____________________________________________35\n	116 -- 122	66 -- 72	-26.7431 kcal/mol	6.46375 kcal/mol	9.42239 kcal/mol	83 154@LB@ \| \|@LB@5'-GGC...AUCCG C CUCUCCUCAAAGC UU UC UCCCC...UGC-3'@LB@ GC AACGCAAU GCACGA CAUCACG ACCGU@LB@ \|\| \|\|\|:\|\|\|: :\|\|\|:\| \|\|\|\|\|\|: \|\|\|\|\|@LB@ CG UUGUGUUG UGUGUU GUAGUGU UGGCA@LB@3'-UUU...GUUAA U U UUCGG...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -16.76 kcal/mol@LB@Hybridization Energy -26.7431 kcal/mol@LB@Unfolding Energy - mRNA 6.46375 kcal/mol@LB@Unfolding Energy - sRNA 9.42239 kcal/mol@LB@@LB@Position - mRNA 84 -- 153@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 116 -- 122@LB@Position Seed - sRNA 66 -- 72@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@
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@

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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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

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