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
138	0.007086	0.182	stm0624	citC	-16.00	0.081371	136 -- 192	38 -- 93	[citrate (pro-3S)-lyase] ligase	stm0058	_____________135___________________________193\n_____________\|_____________________________\|\n5'-AAA...AUCAA________________________A____GAAAA...AUA-3'\n______________GUUGC_AACACA___GCGCAACAU_UACA\n______________:\|\|\|\|_\|\|\|\|\|\|___:\|:\|\|\|\|\|\|_:\|\|\|\n______________UAACG_UUGUGU___UGUGUUGUA_GUGU\n3'-UUU...CUGGU_____U______UGU______________UGGCA...UCA-5'\n_____________\|_____________________________\|\n_____________94____________________________37\n	149 -- 155	70 -- 76	-24.6588 kcal/mol	7.05918 kcal/mol	6.32558 kcal/mol	135 193@LB@ \| \|@LB@5'-AAA...AUCAA A GAAAA...AUA-3'@LB@ GUUGC AACACA GCGCAACAU UACA@LB@ :\|\|\|\| \|\|\|\|\|\| :\|:\|\|\|\|\|\| :\|\|\|@LB@ UAACG UUGUGU UGUGUUGUA GUGU@LB@3'-UUU...CUGGU U UGU UGGCA...UCA-5'@LB@ \| \|@LB@ 94 37@LB@@LB@@LB@Energy -16.00 kcal/mol@LB@Hybridization Energy -24.6588 kcal/mol@LB@Unfolding Energy - mRNA 7.05918 kcal/mol@LB@Unfolding Energy - sRNA 6.32558 kcal/mol@LB@@LB@Position - mRNA 136 -- 192@LB@Position - sRNA 38 -- 93@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 70 -- 76@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@
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@
75	0.003517	0.1596	stm1214	ycfR	-14.36	0.148951	168 -- 212	35 -- 81	multiple stress resistance protein BhsA	stm0823	_____________167______________213\n_____________\|________________\|\n5'-AAA...ACCAC_________CA_____AUUCA...AAC-3'\n______________UUCUGGCUC___GAGU\n______________\|\|\|:\|\|\|\|\|___:\|\|\|\n______________AAGGCCGAG___UUCA\n3'-UUU...AAAGC_________UCC____-5'\n_____________\|_______________\|\n_____________82______________35\n	15 -- 21	8 -- 14	-15.9373 kcal/mol	4.12962 kcal/mol	4.82557 kcal/mol	167 213@LB@ \| \|@LB@5'-AAA...ACCAC CA AUUCA...AAC-3'@LB@ UUCUGGCUC GAGU@LB@ \|\|\|:\|\|\|\|\| :\|\|\|@LB@ AAGGCCGAG UUCA@LB@3'-UUU...AAAGC UCC -5'@LB@ \| \|@LB@ 82 35@LB@@LB@@LB@Energy -14.36 kcal/mol@LB@Hybridization Energy -15.9373 kcal/mol@LB@Unfolding Energy - mRNA 4.12962 kcal/mol@LB@Unfolding Energy - sRNA 4.82557 kcal/mol@LB@@LB@Position - mRNA 168 -- 212@LB@Position - sRNA 35 -- 81@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 8 -- 14@LB@
95	0.004301	0.1596	stm4114	pflD	-11.77	0.360092	46 -- 100	34 -- 88	formate C-acetyltransferase	stm0843	_____________45_____________________101\n_____________\|______________________\|\n5'-UUU...CGGUA_______C______________GAACA...AGA-3'\n______________AAACGCG_CGACGC__CAUUAU\n______________\|\|\|\|:\|:_\|:\|\|:\|__\|\|\|:\|:\n______________UUUGUGU_GUUGUG__GUAGUG\n3'-UUU...UAACG_______U______UU______UUGGC...UCA-5'\n_____________\|______________________\|\n_____________89_____________________33\n	46 -- 52	82 -- 88	-16.7675 kcal/mol	5.49067 kcal/mol	5.48747 kcal/mol	45 101@LB@ \| \|@LB@5'-UUU...CGGUA C GAACA...AGA-3'@LB@ AAACGCG CGACGC CAUUAU@LB@ \|\|\|\|:\|: \|:\|\|:\| \|\|\|:\|:@LB@ UUUGUGU GUUGUG GUAGUG@LB@3'-UUU...UAACG U UU UUGGC...UCA-5'@LB@ \| \|@LB@ 89 33@LB@@LB@@LB@Energy -11.77 kcal/mol@LB@Hybridization Energy -16.7675 kcal/mol@LB@Unfolding Energy - mRNA 5.49067 kcal/mol@LB@Unfolding Energy - sRNA 5.48747 kcal/mol@LB@@LB@Position - mRNA 46 -- 100@LB@Position - sRNA 34 -- 88@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 82 -- 88@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@
135	0.006796	0.1774	stm1044	sodC	-14.39	0.147293	208 -- 244	43 -- 78	Gifsy-2 prophage superoxide dismutase precursor (Cu-Zn)	stm1440 stm0924	_____________207__________245\n_____________\|____________\|\n5'-GAA...GCUUU____________CAGGG...CCA-3'\n______________GGUGGUCUCGCU\n______________\|\|\|:\|\|\|\|\|\|\|\|\n______________CCAUCAGAGCGA\n3'-UUU...UUUUC____________UGGCA...UCA-5'\n_____________\|____________\|\n_____________79___________42\n	78 -- 84	117 -- 123	-21.9622 kcal/mol	4.44224 kcal/mol	6.55795 kcal/mol	207 245@LB@ \| \|@LB@5'-GAA...GCUUU CAGGG...CCA-3'@LB@ GGUGGUCUCGCU@LB@ \|\|\|:\|\|\|\|\|\|\|\|@LB@ CCAUCAGAGCGA@LB@3'-UUU...UUUUC UGGCA...UCA-5'@LB@ \| \|@LB@ 79 42@LB@@LB@@LB@Energy -14.39 kcal/mol@LB@Hybridization Energy -21.9622 kcal/mol@LB@Unfolding Energy - mRNA 4.44224 kcal/mol@LB@Unfolding Energy - sRNA 6.55795 kcal/mol@LB@@LB@Position - mRNA 208 -- 244@LB@Position - sRNA 43 -- 78@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 117 -- 123@LB@
58	0.002307	0.14	stm2234	N/A	-13.92	0.174542	131 -- 196	38 -- 89	phage tail protein	stm2705 stm2233	_____________130______197\n_____________\|________\|\n5'-CUG...UACAC________AUCCA...CAG-3'\n______________CAGACAGG\n______________\|\|\|\|\|\|\|\|\n______________GUCUGUCC\n3'-UUU...UACCU________CAUUU...UCA-5'\n_____________\|________\|\n_____________90_______37\n	132 -- 138	153 -- 159	-13.9425 kcal/mol	2.61206 kcal/mol	2.72972 kcal/mol	130 197@LB@ \| \|@LB@5'-CUG...UACAC AUCCA...CAG-3'@LB@ CAGACAGG@LB@ \|\|\|\|\|\|\|\|@LB@ GUCUGUCC@LB@3'-UUU...UACCU CAUUU...UCA-5'@LB@ \| \|@LB@ 90 37@LB@@LB@@LB@Energy -13.92 kcal/mol@LB@Hybridization Energy -13.9425 kcal/mol@LB@Unfolding Energy - mRNA 2.61206 kcal/mol@LB@Unfolding Energy - sRNA 2.72972 kcal/mol@LB@@LB@Position - mRNA 131 -- 196@LB@Position - sRNA 38 -- 89@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 153 -- 159@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@
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@

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)

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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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