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
51	0.001912	0.1324	stm2692	N/A	-10.31	0.546971	162 -- 173	130 -- 141	putative HlyD family secretion protein		_____________161__________174\n_____________\|____________\|\n5'-GUU...CCGUC____________AUGAA...CGU-3'\n______________GGGAGUGGAAAA\n______________\|\|:\|\|\|\|:\|\|\|\|\n______________CCUUCACUUUUU\n3'-UUU...CAUGU____________CCCAU...UCA-5'\n_____________\|____________\|\n_____________142__________129\n	166 -- 172	131 -- 137	-15.3652 kcal/mol	2.02429 kcal/mol	2.83702 kcal/mol	161 174@LB@ \| \|@LB@5'-GUU...CCGUC AUGAA...CGU-3'@LB@ GGGAGUGGAAAA@LB@ \|\|:\|\|\|\|:\|\|\|\|@LB@ CCUUCACUUUUU@LB@3'-UUU...CAUGU CCCAU...UCA-5'@LB@ \| \|@LB@ 142 129@LB@@LB@@LB@Energy -10.31 kcal/mol@LB@Hybridization Energy -15.3652 kcal/mol@LB@Unfolding Energy - mRNA 2.02429 kcal/mol@LB@Unfolding Energy - sRNA 2.83702 kcal/mol@LB@@LB@Position - mRNA 162 -- 173@LB@Position - sRNA 130 -- 141@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 131 -- 137@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@
53	0.002045	0.1363	stm1876	holE	-16.46	0.068295	21 -- 75	31 -- 90	DNA polymerase III subunit theta		_____________20__________________________________________76\n_____________\|___________________________________________\|\n5'-CGU...UGCCA_______GUAA___UA___________G___C__A________AUAUU...UGC-3'\n______________GC_AGCA____AGC__AACGUCGCGAU_GUG_AG__AGAAGCC\n______________\|\|_\|:\|\|____\|:\|__\|\|\|:\|\|:\|:\|:_\|\|:_\|\|__\|:\|\|\|\|\|\n______________CG_UUGU____UUG__UUGUAGUGUUG_CAU_UC__UUUUCGG\n3'-UUU...GUUAA__U____GUUG___UG___________G______GG_______GUAGU...UCA-5'\n_____________\|___________________________________________\|\n_____________91__________________________________________30\n	55 -- 61	49 -- 55	-35.8289 kcal/mol	10.2843 kcal/mol	15.2217 kcal/mol	20 76@LB@ \| \|@LB@5'-CGU...UGCCA GUAA UA G C A AUAUU...UGC-3'@LB@ GC AGCA AGC AACGUCGCGAU GUG AG AGAAGCC@LB@ \|\| \|:\|\| \|:\| \|\|\|:\|\|:\|:\|: \|\|: \|\| \|:\|\|\|\|\|@LB@ CG UUGU UUG UUGUAGUGUUG CAU UC UUUUCGG@LB@3'-UUU...GUUAA U GUUG UG G GG GUAGU...UCA-5'@LB@ \| \|@LB@ 91 30@LB@@LB@@LB@Energy -16.46 kcal/mol@LB@Hybridization Energy -35.8289 kcal/mol@LB@Unfolding Energy - mRNA 10.2843 kcal/mol@LB@Unfolding Energy - sRNA 15.2217 kcal/mol@LB@@LB@Position - mRNA 21 -- 75@LB@Position - sRNA 31 -- 90@LB@Position Seed - mRNA 55 -- 61@LB@Position Seed - sRNA 49 -- 55@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@
55	0.002114	0.1363	stm0887	artJ	-12.89	0.249853	160 -- 177	72 -- 90	arginine ABC transporter substrate-binding protein		_____________159_________________178\n_____________\|___________________\|\n5'-AUG...AUGCC___________________CAUAA...CGU-3'\n______________GCAGACACGGC_GCAUAAU\n______________\|\|\|:\|\|\|\|::\|_:\|\|:\|\|:\n______________CGUUUGUGUUG_UGUGUUG\n3'-UUU...GUUAA___________U_______UAGUG...UCA-5'\n_____________\|___________________\|\n_____________91__________________71\n	171 -- 177	72 -- 78	-21.0424 kcal/mol	4.03353 kcal/mol	3.80362 kcal/mol	159 178@LB@ \| \|@LB@5'-AUG...AUGCC CAUAA...CGU-3'@LB@ GCAGACACGGC GCAUAAU@LB@ \|\|\|:\|\|\|\|::\| :\|\|:\|\|:@LB@ CGUUUGUGUUG UGUGUUG@LB@3'-UUU...GUUAA U UAGUG...UCA-5'@LB@ \| \|@LB@ 91 71@LB@@LB@@LB@Energy -12.89 kcal/mol@LB@Hybridization Energy -21.0424 kcal/mol@LB@Unfolding Energy - mRNA 4.03353 kcal/mol@LB@Unfolding Energy - sRNA 3.80362 kcal/mol@LB@@LB@Position - mRNA 160 -- 177@LB@Position - sRNA 72 -- 90@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 72 -- 78@LB@
56	0.002144	0.1363	pslt006	repA	-15.36	0.103288	219 -- 279	36 -- 87	DNA replication		_____________218_____________________280\n_____________\|_______________________\|\n5'-ACU...ACACC_______UGUU____U_______CGACA...CCC-3'\n______________CGAACAC_____CAC__CAUUAC\n______________\|:\|\|\|\|\|_____\|\|\|__\|\|\|:\|\|\n______________GUUUGUG_____GUG__GUAGUG\n3'-UUU...UUAAC_______UUGUU___UU______UUGGC...UCA-5'\n_____________\|_______________________\|\n_____________88______________________35\n	225 -- 231	83 -- 89	-15.7114 kcal/mol	3.78124 kcal/mol	5.66809 kcal/mol	218 280@LB@ \| \|@LB@5'-ACU...ACACC UGUU U CGACA...CCC-3'@LB@ CGAACAC CAC CAUUAC@LB@ \|:\|\|\|\|\| \|\|\| \|\|\|:\|\|@LB@ GUUUGUG GUG GUAGUG@LB@3'-UUU...UUAAC UUGUU UU UUGGC...UCA-5'@LB@ \| \|@LB@ 88 35@LB@@LB@@LB@Energy -15.36 kcal/mol@LB@Hybridization Energy -15.7114 kcal/mol@LB@Unfolding Energy - mRNA 3.78124 kcal/mol@LB@Unfolding Energy - sRNA 5.66809 kcal/mol@LB@@LB@Position - mRNA 219 -- 279@LB@Position - sRNA 36 -- 87@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 83 -- 89@LB@
57	0.002298	0.14	stm3921	wecC	-19.39	0.022107	89 -- 132	46 -- 91	UDP-N-acetyl-D-mannosamine dehydrogenase		_____________88_____________________________________133\n_____________\|______________________________________\|\n5'-ACC...GCGUC___U__________AAAUG____________A______GCGCC...AUA-3'\n______________UGC__GCACGACGA_____AAUAUCA_AACC_UGAGCC\n______________\|\|\|__:\|\|\|:\|\|:\|_____\|\|:\|\|\|\|_\|\|\|\|_\|:\|\|\|\|\n______________ACG__UGUGUUGUU_____UUGUAGU_UUGG_AUUCGG\n3'-UUU...GGUUA___UU_________GUG_________G____C______UUUUC...UCA-5'\n_____________\|______________________________________\|\n_____________92_____________________________________45\n	107 -- 113	68 -- 74	-32.9193 kcal/mol	8.51619 kcal/mol	11.8308 kcal/mol	88 133@LB@ \| \|@LB@5'-ACC...GCGUC U AAAUG A GCGCC...AUA-3'@LB@ UGC GCACGACGA AAUAUCA AACC UGAGCC@LB@ \|\|\| :\|\|\|:\|\|:\| \|\|:\|\|\|\| \|\|\|\| \|:\|\|\|\|@LB@ ACG UGUGUUGUU UUGUAGU UUGG AUUCGG@LB@3'-UUU...GGUUA UU GUG G C UUUUC...UCA-5'@LB@ \| \|@LB@ 92 45@LB@@LB@@LB@Energy -19.39 kcal/mol@LB@Hybridization Energy -32.9193 kcal/mol@LB@Unfolding Energy - mRNA 8.51619 kcal/mol@LB@Unfolding Energy - sRNA 11.8308 kcal/mol@LB@@LB@Position - mRNA 89 -- 132@LB@Position - sRNA 46 -- 91@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 68 -- 74@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@
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@
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@

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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