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
14	0.0002233	0.05681	stm3843	trmE	-16.53	0.066478	207 -- 249	37 -- 85	tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE	_____________206______________250\n_____________\|________________\|\n5'-UGA...CAUGA________________UAUCG...CGC-3'\n______________GC___CAUAACGACAC\n______________\|\|___\|\|:\|\|\|:\|\|\|\|\n______________CG___GUGUUGUUGUG\n3'-UUU...GUUAA__UUU___________UUGUA...UCA-5'\n_____________\|________________\|\n_____________86_______________36\n	211 -- 217	75 -- 81	-15.3625 kcal/mol	2.22645 kcal/mol	3.72363 kcal/mol	206 250@LB@ \| \|@LB@5'-UGA...CAUGA UAUCG...CGC-3'@LB@ GC CAUAACGACAC@LB@ \|\| \|\|:\|\|\|:\|\|\|\|@LB@ CG GUGUUGUUGUG@LB@3'-UUU...GUUAA UUU UUGUA...UCA-5'@LB@ \| \|@LB@ 86 36@LB@@LB@@LB@Energy -16.53 kcal/mol@LB@Hybridization Energy -15.3625 kcal/mol@LB@Unfolding Energy - mRNA 2.22645 kcal/mol@LB@Unfolding Energy - sRNA 3.72363 kcal/mol@LB@@LB@Position - mRNA 207 -- 249@LB@Position - sRNA 37 -- 85@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 75 -- 81@LB@
94	0.0043	0.1596	stm3866	atpG	-16.85	0.058909	206 -- 253	35 -- 80	F0F1 ATP synthase subunit gamma	_____________205______________________254\n_____________\|________________________\|\n5'-GGU...CAAAA________AA_C______G_U___CGCCG...GUA-3'\n______________GAUCACUA__G_GAUGGA_A_GGU\n______________:\|\|\|\|\|\|\|__\|_\|\|::\|\|_\|_\|\|\|\n______________UUAGUGAU__C_CUGUCU_U_CCA\n3'-UUU...UGUAA________A_________G_C___UUUAC...UCA-5'\n_____________\|________________________\|\n_____________81_______________________34\n	258 -- 264	165 -- 171	-17.4899 kcal/mol	5.94142 kcal/mol	3.53572 kcal/mol	205 254@LB@ \| \|@LB@5'-GGU...CAAAA AA C G U CGCCG...GUA-3'@LB@ GAUCACUA G GAUGGA A GGU@LB@ :\|\|\|\|\|\|\| \| \|\|::\|\| \| \|\|\|@LB@ UUAGUGAU C CUGUCU U CCA@LB@3'-UUU...UGUAA A G C UUUAC...UCA-5'@LB@ \| \|@LB@ 81 34@LB@@LB@@LB@Energy -16.85 kcal/mol@LB@Hybridization Energy -17.4899 kcal/mol@LB@Unfolding Energy - mRNA 5.94142 kcal/mol@LB@Unfolding Energy - sRNA 3.53572 kcal/mol@LB@@LB@Position - mRNA 206 -- 253@LB@Position - sRNA 35 -- 80@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 165 -- 171@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@
196	0.01089	0.197	stm3904	ilvD	-14.14	0.161583	237 -- 253	179 -- 194	dihydroxy-acid dehydratase	_____________236___________254\n_____________\|_____________\|\n5'-CGA...UGAAG___AA________AGUAA...GCA-3'\n______________GGA__AGAUGGGG\n______________\|\|\|__\|\|\|::\|\|\|\n______________CCU__UCUGUCCC\n3'-UUU...UGAUA___G_________AUUUA...UCA-5'\n_____________\|_____________\|\n_____________195___________178\n	182 -- 188	152 -- 158	-15.6614 kcal/mol	1.17371 kcal/mol	3.10307 kcal/mol	236 254@LB@ \| \|@LB@5'-CGA...UGAAG AA AGUAA...GCA-3'@LB@ GGA AGAUGGGG@LB@ \|\|\| \|\|\|::\|\|\|@LB@ CCU UCUGUCCC@LB@3'-UUU...UGAUA G AUUUA...UCA-5'@LB@ \| \|@LB@ 195 178@LB@@LB@@LB@Energy -14.14 kcal/mol@LB@Hybridization Energy -15.6614 kcal/mol@LB@Unfolding Energy - mRNA 1.17371 kcal/mol@LB@Unfolding Energy - sRNA 3.10307 kcal/mol@LB@@LB@Position - mRNA 237 -- 253@LB@Position - sRNA 179 -- 194@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 152 -- 158@LB@
128	0.006467	0.1774	stm3907	N/A	-18.55	0.030594	118 -- 173	37 -- 89		_____________117__________________________174\n_____________\|____________________________\|\n5'-UCA...AAAAA____________ACCAGU______G___AAAAC...UUU-3'\n______________CAGACGCAACAA______CAGCAU_AUA\n______________\|\|:\|\|:\|\|\|\|\|\|______\|\|:\|\|\|_\|:\|\n______________GUUUGUGUUGUU______GUUGUA_UGU\n3'-UUU...UUAAC____________GU__________G___UGGCA...UCA-5'\n_____________\|____________________________\|\n_____________90___________________________36\n	123 -- 129	78 -- 84	-22.8944 kcal/mol	3.16008 kcal/mol	6.30461 kcal/mol	117 174@LB@ \| \|@LB@5'-UCA...AAAAA ACCAGU G AAAAC...UUU-3'@LB@ CAGACGCAACAA CAGCAU AUA@LB@ \|\|:\|\|:\|\|\|\|\|\| \|\|:\|\|\| \|:\|@LB@ GUUUGUGUUGUU GUUGUA UGU@LB@3'-UUU...UUAAC GU G UGGCA...UCA-5'@LB@ \| \|@LB@ 90 36@LB@@LB@@LB@Energy -18.55 kcal/mol@LB@Hybridization Energy -22.8944 kcal/mol@LB@Unfolding Energy - mRNA 3.16008 kcal/mol@LB@Unfolding Energy - sRNA 6.30461 kcal/mol@LB@@LB@Position - mRNA 118 -- 173@LB@Position - sRNA 37 -- 89@LB@Position Seed - mRNA 123 -- 129@LB@Position Seed - sRNA 78 -- 84@LB@
30	0.0007612	0.08814	stm3909	ilvC	-21.15	0.011132	166 -- 188	66 -- 89	ketol-acid reductoisomerase	_____________165_____________________189\n_____________\|_______________________\|\n5'-CCA...AACAA_______________________GGAGU...GCU-3'\n______________UAAGCGCGAC_ACACAACAUCAC\n______________:\|\|:\|:\|:\|\|_\|\|\|\|\|\|\|\|\|\|\|\|\n______________GUUUGUGUUG_UGUGUUGUAGUG\n3'-UUU...UUAAC__________U____________UUGGC...UCA-5'\n_____________\|_______________________\|\n_____________90______________________65\n	181 -- 187	67 -- 73	-29.859 kcal/mol	2.61707 kcal/mol	5.66809 kcal/mol	165 189@LB@ \| \|@LB@5'-CCA...AACAA GGAGU...GCU-3'@LB@ UAAGCGCGAC ACACAACAUCAC@LB@ :\|\|:\|:\|:\|\| \|\|\|\|\|\|\|\|\|\|\|\|@LB@ GUUUGUGUUG UGUGUUGUAGUG@LB@3'-UUU...UUAAC U UUGGC...UCA-5'@LB@ \| \|@LB@ 90 65@LB@@LB@@LB@Energy -21.15 kcal/mol@LB@Hybridization Energy -29.859 kcal/mol@LB@Unfolding Energy - mRNA 2.61707 kcal/mol@LB@Unfolding Energy - sRNA 5.66809 kcal/mol@LB@@LB@Position - mRNA 166 -- 188@LB@Position - sRNA 66 -- 89@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 67 -- 73@LB@
179	0.009806	0.1951	stm3912	rep	-13.00	0.240883	219 -- 287	22 -- 83	ATP-dependent DNA helicase Rep	_____________218__________________________288\n_____________\|____________________________\|\n5'-AGU...UCCCA____UUUAAAUCCC______________CUGUC...CCA-3'\n______________UGCG__________GGC_CAACAACACG\n______________\|\|\|:__________::\|_\|\|\|\|\|\|\|\|\|:\n______________ACGU__________UUG_GUUGUUGUGU\n3'-UUU...GGUUA_________________U__________UGUAG...UCA-5'\n_____________\|____________________________\|\n_____________84___________________________21\n	222 -- 228	74 -- 80	-15.5311 kcal/mol	3.54327 kcal/mol	3.73631 kcal/mol	218 288@LB@ \| \|@LB@5'-AGU...UCCCA UUUAAAUCCC CUGUC...CCA-3'@LB@ UGCG GGC CAACAACACG@LB@ \|\|\|: ::\| \|\|\|\|\|\|\|\|\|:@LB@ ACGU UUG GUUGUUGUGU@LB@3'-UUU...GGUUA U UGUAG...UCA-5'@LB@ \| \|@LB@ 84 21@LB@@LB@@LB@Energy -13.00 kcal/mol@LB@Hybridization Energy -15.5311 kcal/mol@LB@Unfolding Energy - mRNA 3.54327 kcal/mol@LB@Unfolding Energy - sRNA 3.73631 kcal/mol@LB@@LB@Position - mRNA 219 -- 287@LB@Position - sRNA 22 -- 83@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 74 -- 80@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@
68	0.003225	0.1596	stm3930	yifK	-15.10	0.113746	177 -- 247	44 -- 93	amino acid permease	_____________176____________________248\n_____________\|______________________\|\n5'-CUU...GAACC_______________UG_G___UUAUG...GCG-3'\n______________GUUGCAAACACGACA__A_GAU\n______________:\|\|\|\|\|\|\|\|\|\|:\|\|\|__\|_:\|:\n______________UAACGUUUGUGUUGU__U_UUG\n3'-UUU...CUGGU_______________UG_G___UAGUG...UCA-5'\n_____________\|______________________\|\n_____________94_____________________43\n	185 -- 191	79 -- 85	-22.6062 kcal/mol	5.26496 kcal/mol	3.80917 kcal/mol	176 248@LB@ \| \|@LB@5'-CUU...GAACC UG G UUAUG...GCG-3'@LB@ GUUGCAAACACGACA A GAU@LB@ :\|\|\|\|\|\|\|\|\|\|:\|\|\| \| :\|:@LB@ UAACGUUUGUGUUGU U UUG@LB@3'-UUU...CUGGU UG G UAGUG...UCA-5'@LB@ \| \|@LB@ 94 43@LB@@LB@@LB@Energy -15.10 kcal/mol@LB@Hybridization Energy -22.6062 kcal/mol@LB@Unfolding Energy - mRNA 5.26496 kcal/mol@LB@Unfolding Energy - sRNA 3.80917 kcal/mol@LB@@LB@Position - mRNA 177 -- 247@LB@Position - sRNA 44 -- 93@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 79 -- 85@LB@
173	0.009489	0.1945	stm3985	yigZ	-14.68	0.132642	77 -- 135	33 -- 90	YigZ family protein	_____________76___________________136\n_____________\|____________________\|\n5'-CGA...GUUCA________UU__________GAAAA...ACG-3'\n______________GCAAGCAC__CAAC_UGGCA\n______________\|\|\|\|:\|\|\|__\|\|\|\|_:::\|\|\n______________CGUUUGUG__GUUG_GUUGU\n3'-UUU...GUUAA________UU____U_____AGUGU...UCA-5'\n_____________\|____________________\|\n_____________91___________________32\n	78 -- 84	83 -- 89	-19.4869 kcal/mol	6.86655 kcal/mol	3.80671 kcal/mol	76 136@LB@ \| \|@LB@5'-CGA...GUUCA UU GAAAA...ACG-3'@LB@ GCAAGCAC CAAC UGGCA@LB@ \|\|\|\|:\|\|\| \|\|\|\| :::\|\|@LB@ CGUUUGUG GUUG GUUGU@LB@3'-UUU...GUUAA UU U AGUGU...UCA-5'@LB@ \| \|@LB@ 91 32@LB@@LB@@LB@Energy -14.68 kcal/mol@LB@Hybridization Energy -19.4869 kcal/mol@LB@Unfolding Energy - mRNA 6.86655 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 77 -- 135@LB@Position - sRNA 33 -- 90@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 83 -- 89@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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