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
151	0.00796	0.1845	stm2365	folC	-10.71	0.491716	269 -- 300	50 -- 78	bifunctional tetrahydrofolate synthase/dihydrofolate synthase	_____________268__________301\n_____________\|____________\|\n5'-CCG...CGGCG____A_______UCUGA...AGC-3'\n______________CCGG_UCAGGAG\n______________\|\|\|\|_\|\|\|\|\|\|:\n______________GGCC_AGUCCUU\n3'-UUU...AGCAA____G_______CA-5'\n_____________\|____________\|\n_____________79___________49\n	115 -- 121	3 -- 9	-17.3652 kcal/mol	5.30633 kcal/mol	4.72771 kcal/mol	268 301@LB@ \| \|@LB@5'-CCG...CGGCG A UCUGA...AGC-3'@LB@ CCGG UCAGGAG@LB@ \|\|\|\| \|\|\|\|\|\|:@LB@ GGCC AGUCCUU@LB@3'-UUU...AGCAA G CA-5'@LB@ \| \|@LB@ 79 49@LB@@LB@@LB@Energy -10.71 kcal/mol@LB@Hybridization Energy -17.3652 kcal/mol@LB@Unfolding Energy - mRNA 5.30633 kcal/mol@LB@Unfolding Energy - sRNA 4.72771 kcal/mol@LB@@LB@Position - mRNA 269 -- 300@LB@Position - sRNA 50 -- 78@LB@Position Seed - mRNA 115 -- 121@LB@Position Seed - sRNA 3 -- 9@LB@
124	0.006123	0.1758	stm0794	bioB	-18.46	0.031660	1 -- 37	38 -- 79	biotin synthase	______________1________________38\n______________\|________________\|\n___________5'-_________________UUCGG...AGC-3'\n______________AAC_CAGC_UCGCAGCC\n______________\|\|\|_\|\|:\|_\|\|:\|\|:\|\|\n______________UUG_GUUG_AGUGUUGG\n3'-UUU...UGUUG___U____U________CAUUC...UCA-5'\n_____________\|_________________\|\n_____________80________________37\n	9 -- 15	63 -- 69	-17.7754 kcal/mol	2.27351 kcal/mol	6.48115 kcal/mol	1 38@LB@ \| \|@LB@ 5'- UUCGG...AGC-3'@LB@ AAC CAGC UCGCAGCC@LB@ \|\|\| \|\|:\| \|\|:\|\|:\|\|@LB@ UUG GUUG AGUGUUGG@LB@3'-UUU...UGUUG U U CAUUC...UCA-5'@LB@ \| \|@LB@ 80 37@LB@@LB@@LB@Energy -18.46 kcal/mol@LB@Hybridization Energy -17.7754 kcal/mol@LB@Unfolding Energy - mRNA 2.27351 kcal/mol@LB@Unfolding Energy - sRNA 6.48115 kcal/mol@LB@@LB@Position - mRNA 1 -- 37@LB@Position - sRNA 38 -- 79@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 63 -- 69@LB@
121	0.006021	0.1758	stm3903	ilvE	-13.34	0.214101	130 -- 170	39 -- 78	branched chain amino acid aminotransferase	_____________129__________________171\n_____________\|____________________\|\n5'-GGU...CCAGA___CU___C___U_______AAUCC...GUA-3'\n______________GCG___GC_ACA_CACAACA\n______________\|\|:___:\|_\|\|\|_\|\|\|\|\|\|\|\n______________CGU___UG_UGU_GUGUUGU\n3'-UUU...GUUAA___UUG__U___U_______AGUGU...UCA-5'\n_____________\|____________________\|\n_____________79___________________38\n	164 -- 170	71 -- 77	-14.4922 kcal/mol	2.12049 kcal/mol	3.80671 kcal/mol	129 171@LB@ \| \|@LB@5'-GGU...CCAGA CU C U AAUCC...GUA-3'@LB@ GCG GC ACA CACAACA@LB@ \|\|: :\| \|\|\| \|\|\|\|\|\|\|@LB@ CGU UG UGU GUGUUGU@LB@3'-UUU...GUUAA UUG U U AGUGU...UCA-5'@LB@ \| \|@LB@ 79 38@LB@@LB@@LB@Energy -13.34 kcal/mol@LB@Hybridization Energy -14.4922 kcal/mol@LB@Unfolding Energy - mRNA 2.12049 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 130 -- 170@LB@Position - sRNA 39 -- 78@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 71 -- 77@LB@
63	0.003024	0.1596	stm3563	livH	-16.49	0.067433	27 -- 175	36 -- 184	branched-chain amino acid ABC transporter permease LivH	_____________26_____________176\n_____________\|______________\|\n5'-GAU...GAAAU______________CGAUC...ACG-3'\n______________GGGA_UGAAAAAGG\n______________\|\|:\|_\|\|\|\|\|\|\|\|\|\n______________CCUU_ACUUUUUCC\n3'-UUU...CAUGU____C_________CAUCA...UCA-5'\n_____________\|______________\|\n_____________185____________35\n	65 -- 71	128 -- 134	-14.2251 kcal/mol	3.55711 kcal/mol	3.77758 kcal/mol	26 176@LB@ \| \|@LB@5'-GAU...GAAAU CGAUC...ACG-3'@LB@ GGGA UGAAAAAGG@LB@ \|\|:\| \|\|\|\|\|\|\|\|\|@LB@ CCUU ACUUUUUCC@LB@3'-UUU...CAUGU C CAUCA...UCA-5'@LB@ \| \|@LB@ 185 35@LB@@LB@@LB@Energy -16.49 kcal/mol@LB@Hybridization Energy -14.2251 kcal/mol@LB@Unfolding Energy - mRNA 3.55711 kcal/mol@LB@Unfolding Energy - sRNA 3.77758 kcal/mol@LB@@LB@Position - mRNA 27 -- 175@LB@Position - sRNA 36 -- 184@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 128 -- 134@LB@
5	6.363e-05	0.04123	stm0399	brnQ	-24.27	0.003272	169 -- 224	36 -- 81	branched-chain amino acid transport system II carrier protein	_____________168_______________________________________________________________225\n_____________\|_________________________________________________________________\|\n5'-AAC...UUUAA___U_________U________C_____G_A_____A__UUAU_A________UUAAAAU_____GAUAU...UCG-3'\n______________UGU___UACAACA_CAC__CAU_CACAG_C_GUAAG_CU____G_CCCAUCAG_______CGCGC\n______________\|\|:___:\|\|\|\|\|\|_\|\|\|__\|\|\|_\|\|\|\|:_\|_\|\|\|\|\|_\|:____\|_\|\|\|\|\|\|\|\|_______\|:\|\|\|\n______________ACG___GUGUUGU_GUG__GUA_GUGUU_G_CAUUC_GG____C_GGGUAGUC_______GUGCG\n3'-UUU...GGUUA___UUU_______U___UU_________G__________UUUU__________UU__________UAAGG...UCA-5'\n_____________\|_________________________________________________________________\|\n_____________82________________________________________________________________35\n	205 -- 211	44 -- 50	-45.9704 kcal/mol	7.09165 kcal/mol	22.503 kcal/mol	168 225@LB@ \| \|@LB@5'-AAC...UUUAA U U C G A A UUAU A UUAAAAU GAUAU...UCG-3'@LB@ UGU UACAACA CAC CAU CACAG C GUAAG CU G CCCAUCAG CGCGC@LB@ \|\|: :\|\|\|\|\|\| \|\|\| \|\|\| \|\|\|\|: \| \|\|\|\|\| \|: \| \|\|\|\|\|\|\|\| \|:\|\|\|@LB@ ACG GUGUUGU GUG GUA GUGUU G CAUUC GG C GGGUAGUC GUGCG@LB@3'-UUU...GGUUA UUU U UU G UUUU UU UAAGG...UCA-5'@LB@ \| \|@LB@ 82 35@LB@@LB@@LB@Energy -24.27 kcal/mol@LB@Hybridization Energy -45.9704 kcal/mol@LB@Unfolding Energy - mRNA 7.09165 kcal/mol@LB@Unfolding Energy - sRNA 22.503 kcal/mol@LB@@LB@Position - mRNA 169 -- 224@LB@Position - sRNA 36 -- 81@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 44 -- 50@LB@
42	0.001433	0.1215	stm1318	katE	-13.62	0.194137	191 -- 230	43 -- 82	catalase HPII	_____________190_________231\n_____________\|___________\|\n5'-GGC...UCUGC___________UCCCC...AUC-3'\n______________CGUUCCG_CUC\n______________\|\|\|\|\|\|\|_\|\|\|\n______________GCAAGGC_GAG\n3'-UUU...GAAAA_______C___UCCUUCA-5'\n_____________\|___________\|\n_____________83__________42\n	99 -- 105	12 -- 18	-14.968 kcal/mol	1.4568 kcal/mol	6.53351 kcal/mol	190 231@LB@ \| \|@LB@5'-GGC...UCUGC UCCCC...AUC-3'@LB@ CGUUCCG CUC@LB@ \|\|\|\|\|\|\| \|\|\|@LB@ GCAAGGC GAG@LB@3'-UUU...GAAAA C UCCUUCA-5'@LB@ \| \|@LB@ 83 42@LB@@LB@@LB@Energy -13.62 kcal/mol@LB@Hybridization Energy -14.968 kcal/mol@LB@Unfolding Energy - mRNA 1.4568 kcal/mol@LB@Unfolding Energy - sRNA 6.53351 kcal/mol@LB@@LB@Position - mRNA 191 -- 230@LB@Position - sRNA 43 -- 82@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 12 -- 18@LB@
44	0.001631	0.1267	stm1318	katE	-13.62	0.194137	191 -- 230	43 -- 82	catalase HPII	_____________190_________231\n_____________\|___________\|\n5'-GGC...UCUGC___________UCCCC...AUC-3'\n______________CGUUCCG_CUC\n______________\|\|\|\|\|\|\|_\|\|\|\n______________GCAAGGC_GAG\n3'-UUU...GAAAA_______C___UCCUUCA-5'\n_____________\|___________\|\n_____________83__________42\n	99 -- 105	12 -- 18	-14.968 kcal/mol	1.4568 kcal/mol	6.53351 kcal/mol	190 231@LB@ \| \|@LB@5'-GGC...UCUGC UCCCC...AUC-3'@LB@ CGUUCCG CUC@LB@ \|\|\|\|\|\|\| \|\|\|@LB@ GCAAGGC GAG@LB@3'-UUU...GAAAA C UCCUUCA-5'@LB@ \| \|@LB@ 83 42@LB@@LB@@LB@Energy -13.62 kcal/mol@LB@Hybridization Energy -14.968 kcal/mol@LB@Unfolding Energy - mRNA 1.4568 kcal/mol@LB@Unfolding Energy - sRNA 6.53351 kcal/mol@LB@@LB@Position - mRNA 191 -- 230@LB@Position - sRNA 43 -- 82@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 12 -- 18@LB@
60	0.002585	0.1534	stm0758	ybgR	-11.90	0.345594	235 -- 293	32 -- 91	cation transporter	_____________234_________________________294\n_____________\|___________________________\|\n5'-GGU...ACACC___CG___G__________U_______CUGCU...UCC-3'\n______________UGC__AAA_AUAAUAAUGC__CGUCGC\n______________\|\|\|__\|\|\|_\|:\|\|:\|\|::\|__\|:\|\|:\|\n______________ACG__UUU_UGUUGUUGUG__GUAGUG\n3'-UUU...GGUUA________G__________UU______UUGGC...UCA-5'\n_____________\|___________________________\|\n_____________92__________________________31\n	247 -- 253	75 -- 81	-19.147 kcal/mol	4.2306 kcal/mol	5.6854 kcal/mol	234 294@LB@ \| \|@LB@5'-GGU...ACACC CG G U CUGCU...UCC-3'@LB@ UGC AAA AUAAUAAUGC CGUCGC@LB@ \|\|\| \|\|\| \|:\|\|:\|\|::\| \|:\|\|:\|@LB@ ACG UUU UGUUGUUGUG GUAGUG@LB@3'-UUU...GGUUA G UU UUGGC...UCA-5'@LB@ \| \|@LB@ 92 31@LB@@LB@@LB@Energy -11.90 kcal/mol@LB@Hybridization Energy -19.147 kcal/mol@LB@Unfolding Energy - mRNA 4.2306 kcal/mol@LB@Unfolding Energy - sRNA 5.6854 kcal/mol@LB@@LB@Position - mRNA 235 -- 293@LB@Position - sRNA 32 -- 91@LB@Position Seed - mRNA 247 -- 253@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@
81	0.003764	0.1596	stm0121	ftsL	-18.45	0.031843	91 -- 225	48 -- 186	cell division protein FtsL	_____________90__________________226\n_____________\|___________________\|\n5'-CGU...UGCCG__________A________GAAAA...UGC-3'\n______________GGUGAAAAAG_GGUAG_CU\n______________:\|\|\|\|\|\|\|\|\|_\|\|\|\|\|_\|\|\n______________UCACUUUUUC_CCAUC_GA\n3'-UUU...GUCCU________________A__GCGAU...UCA-5'\n_____________\|___________________\|\n_____________187_________________47\n	133 -- 139	129 -- 135	-20.6582 kcal/mol	4.19087 kcal/mol	6.37024 kcal/mol	90 226@LB@ \| \|@LB@5'-CGU...UGCCG A GAAAA...UGC-3'@LB@ GGUGAAAAAG GGUAG CU@LB@ :\|\|\|\|\|\|\|\|\| \|\|\|\|\| \|\|@LB@ UCACUUUUUC CCAUC GA@LB@3'-UUU...GUCCU A GCGAU...UCA-5'@LB@ \| \|@LB@ 187 47@LB@@LB@@LB@Energy -18.45 kcal/mol@LB@Hybridization Energy -20.6582 kcal/mol@LB@Unfolding Energy - mRNA 4.19087 kcal/mol@LB@Unfolding Energy - sRNA 6.37024 kcal/mol@LB@@LB@Position - mRNA 91 -- 225@LB@Position - sRNA 48 -- 186@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 129 -- 135@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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