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
115	0.005604	0.1728	stm0982	himD	-16.93	0.057154	154 -- 192	37 -- 75	integration host factor subunit beta	______________154________193\n______________\|__________\|\n___________5'-___________GGCUG...UGG-3'\n______________AACAACGCAAU\n______________\|\|\|\|\|\|:\|\|\|:\n______________UUGUUGUGUUG\n3'-UUU...UUGUG___________UAGUG...UCA-5'\n_____________\|___________\|\n_____________76__________36\n	5 -- 11	72 -- 78	-12.1177 kcal/mol	1.51678 kcal/mol	3.07616 kcal/mol	154 193@LB@ \| \|@LB@ 5'- GGCUG...UGG-3'@LB@ AACAACGCAAU@LB@ \|\|\|\|\|\|:\|\|\|:@LB@ UUGUUGUGUUG@LB@3'-UUU...UUGUG UAGUG...UCA-5'@LB@ \| \|@LB@ 76 36@LB@@LB@@LB@Energy -16.93 kcal/mol@LB@Hybridization Energy -12.1177 kcal/mol@LB@Unfolding Energy - mRNA 1.51678 kcal/mol@LB@Unfolding Energy - sRNA 3.07616 kcal/mol@LB@@LB@Position - mRNA 154 -- 192@LB@Position - sRNA 37 -- 75@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 72 -- 78@LB@
149	0.007892	0.1845	stm2071	hisG	-15.61	0.094042	166 -- 245	36 -- 100	ATP phosphoribosyltransferase	_____________165________________________246\n_____________\|__________________________\|\n5'-UUU...AGACC__UU________A________G____ACGCA...AUU-3'\n______________GG__CAGACAGG_UAA____A_AGGA\n______________\|\|__\|\|\|\|\|\|\|\|_\|\|\|____\|_\|\|\|\|\n______________CC__GUCUGUCC_AUU____U_UCCU\n3'-UUU...UGAUA__U_________C___UACA_G____UCACU...UCA-5'\n_____________\|__________________________\|\n_____________101________________________35\n	177 -- 183	153 -- 159	-19.7047 kcal/mol	3.01127 kcal/mol	3.70983 kcal/mol	165 246@LB@ \| \|@LB@5'-UUU...AGACC UU A G ACGCA...AUU-3'@LB@ GG CAGACAGG UAA A AGGA@LB@ \|\| \|\|\|\|\|\|\|\| \|\|\| \| \|\|\|\|@LB@ CC GUCUGUCC AUU U UCCU@LB@3'-UUU...UGAUA U C UACA G UCACU...UCA-5'@LB@ \| \|@LB@ 101 35@LB@@LB@@LB@Energy -15.61 kcal/mol@LB@Hybridization Energy -19.7047 kcal/mol@LB@Unfolding Energy - mRNA 3.01127 kcal/mol@LB@Unfolding Energy - sRNA 3.70983 kcal/mol@LB@@LB@Position - mRNA 166 -- 245@LB@Position - sRNA 36 -- 100@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 153 -- 159@LB@
45	0.001635	0.1267	stm2351	hisP	-13.82	0.180688	258 -- 282	115 -- 140	histidine and lysine/arginine/ornithine transport protein	_____________257__________________________283\n_____________\|____________________________\|\n5'-UAC...GUCAU______CU____________________AGGCC...AUG-3'\n______________GAAGUG__GAAAGGGGUA___UCGCUGC\n______________\|\|\|\|\|\|__:\|\|\|:\|\|\|\|\|___\|\|\|\|\|:\|\n______________CUUCAC__UUUUUCCCAU___AGCGAUG\n3'-UUU...AUGUC__________________CAG_______GCACC...UCA-5'\n_____________\|____________________________\|\n_____________141__________________________114\n	276 -- 282	115 -- 121	-29.6028 kcal/mol	6.54228 kcal/mol	8.52785 kcal/mol	257 283@LB@ \| \|@LB@5'-UAC...GUCAU CU AGGCC...AUG-3'@LB@ GAAGUG GAAAGGGGUA UCGCUGC@LB@ \|\|\|\|\|\| :\|\|\|:\|\|\|\|\| \|\|\|\|\|:\|@LB@ CUUCAC UUUUUCCCAU AGCGAUG@LB@3'-UUU...AUGUC CAG GCACC...UCA-5'@LB@ \| \|@LB@ 141 114@LB@@LB@@LB@Energy -13.82 kcal/mol@LB@Hybridization Energy -29.6028 kcal/mol@LB@Unfolding Energy - mRNA 6.54228 kcal/mol@LB@Unfolding Energy - sRNA 8.52785 kcal/mol@LB@@LB@Position - mRNA 258 -- 282@LB@Position - sRNA 115 -- 140@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 115 -- 121@LB@
122	0.00604	0.1758	stm2353	hisQ	-14.65	0.134227	190 -- 212	140 -- 163	amino acid ABC transporter permease	_____________189______________________213\n_____________\|________________________\|\n5'-GAU...CAACA________UGCAUGU_________UUUUC...UCG-3'\n______________GGACAGGC________UGUACGGG\n______________\|\|\|\|\|\|:\|________\|\|\|\|\|:\|\|\n______________CCUGUCUG________ACAUGUCC\n3'-UUU...UGAUA________UCCCAUUU________UUCAC...UCA-5'\n_____________\|________________________\|\n_____________164______________________139\n	206 -- 212	140 -- 146	-25.7393 kcal/mol	6.65037 kcal/mol	3.70771 kcal/mol	189 213@LB@ \| \|@LB@5'-GAU...CAACA UGCAUGU UUUUC...UCG-3'@LB@ GGACAGGC UGUACGGG@LB@ \|\|\|\|\|\|:\| \|\|\|\|\|:\|\|@LB@ CCUGUCUG ACAUGUCC@LB@3'-UUU...UGAUA UCCCAUUU UUCAC...UCA-5'@LB@ \| \|@LB@ 164 139@LB@@LB@@LB@Energy -14.65 kcal/mol@LB@Hybridization Energy -25.7393 kcal/mol@LB@Unfolding Energy - mRNA 6.65037 kcal/mol@LB@Unfolding Energy - sRNA 3.70771 kcal/mol@LB@@LB@Position - mRNA 190 -- 212@LB@Position - sRNA 140 -- 163@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 140 -- 146@LB@
127	0.006343	0.1774	stm1751	hns	-12.42	0.292757	1 -- 14	147 -- 162	transcriptional regulator	______________1_______________15\n______________\|_______________\|\n___________5'-________________AUCCC...UAG-3'\n______________GACAGAC__GGUGAGU\n______________\|\|\|\|\|\|\|__\|\|\|:\|:\|\n______________CUGUCUG__CCAUUUA\n3'-UUU...GAUAC_______UC_______CAUGU...UCA-5'\n_____________\|________________\|\n_____________163______________146\n	8 -- 14	147 -- 153	-17.2475 kcal/mol	3.56352 kcal/mol	3.32093 kcal/mol	1 15@LB@ \| \|@LB@ 5'- AUCCC...UAG-3'@LB@ GACAGAC GGUGAGU@LB@ \|\|\|\|\|\|\| \|\|\|:\|:\|@LB@ CUGUCUG CCAUUUA@LB@3'-UUU...GAUAC UC CAUGU...UCA-5'@LB@ \| \|@LB@ 163 146@LB@@LB@@LB@Energy -12.42 kcal/mol@LB@Hybridization Energy -17.2475 kcal/mol@LB@Unfolding Energy - mRNA 3.56352 kcal/mol@LB@Unfolding Energy - sRNA 3.32093 kcal/mol@LB@@LB@Position - mRNA 1 -- 14@LB@Position - sRNA 147 -- 162@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 147 -- 153@LB@
114	0.005594	0.1728	stm4557	holD	-13.75	0.185681	35 -- 94	141 -- 186	DNA polymerase III subunit psi	_____________34_____________________________________________95\n_____________\|______________________________________________\|\n5'-AGG...AAAUC__________C____CAAGACUUCACUUGC_________A______ACAUG...UUC-3'\n______________AUCACUGUGG_GCAG_______________CGGGGUAAA___GCAG\n______________\|\|\|\|\|\|:\|\|\|_:\|\|\|_______________\|:\|\|\|\|\|\|\|___:\|\|\|\n______________UAGUGAUACC_UGUC_______________GUCCCAUUU___UGUC\n3'-UUU...GUAAU_______________U_______________________ACA____CUUCA...UCA-5'\n_____________\|______________________________________________\|\n_____________187____________________________________________140\n	83 -- 89	148 -- 154	-31.7183 kcal/mol	12.8981 kcal/mol	5.60568 kcal/mol	34 95@LB@ \| \|@LB@5'-AGG...AAAUC C CAAGACUUCACUUGC A ACAUG...UUC-3'@LB@ AUCACUGUGG GCAG CGGGGUAAA GCAG@LB@ \|\|\|\|\|\|:\|\|\| :\|\|\| \|:\|\|\|\|\|\|\| :\|\|\|@LB@ UAGUGAUACC UGUC GUCCCAUUU UGUC@LB@3'-UUU...GUAAU U ACA CUUCA...UCA-5'@LB@ \| \|@LB@ 187 140@LB@@LB@@LB@Energy -13.75 kcal/mol@LB@Hybridization Energy -31.7183 kcal/mol@LB@Unfolding Energy - mRNA 12.8981 kcal/mol@LB@Unfolding Energy - sRNA 5.60568 kcal/mol@LB@@LB@Position - mRNA 35 -- 94@LB@Position - sRNA 141 -- 186@LB@Position Seed - mRNA 83 -- 89@LB@Position Seed - sRNA 148 -- 154@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@
85	0.003998	0.1596	stm1098	hpaC	-22.15	0.007534	132 -- 187	37 -- 90	4-hydroxyphenylacetate 3-monooxygenase reductase component	_____________131________________________________________188\n_____________\|__________________________________________\|\n5'-UAC...GUUUC___UUU__________G_________AU______GA______GCUGA...GCG-3'\n______________GCA___GCACAAUAAC_ACGACAUCA__CAACUG__UAAGCU\n______________\|\|\|___:\|\|\|\|\|:\|\|\|_\|\|:\|\|\|\|\|\|__\|\|\|\|:\|__\|\|\|\|\|:\n______________CGU___UGUGUUGUUG_UGUUGUAGU__GUUGGC__AUUCGG\n3'-UUU...GUUAA___U______________________________________UUUUC...UCA-5'\n_____________\|__________________________________________\|\n_____________91_________________________________________36\n	151 -- 157	68 -- 74	-38.4357 kcal/mol	7.30976 kcal/mol	11.8287 kcal/mol	131 188@LB@ \| \|@LB@5'-UAC...GUUUC UUU G AU GA GCUGA...GCG-3'@LB@ GCA GCACAAUAAC ACGACAUCA CAACUG UAAGCU@LB@ \|\|\| :\|\|\|\|\|:\|\|\| \|\|:\|\|\|\|\|\| \|\|\|\|:\| \|\|\|\|\|:@LB@ CGU UGUGUUGUUG UGUUGUAGU GUUGGC AUUCGG@LB@3'-UUU...GUUAA U UUUUC...UCA-5'@LB@ \| \|@LB@ 91 36@LB@@LB@@LB@Energy -22.15 kcal/mol@LB@Hybridization Energy -38.4357 kcal/mol@LB@Unfolding Energy - mRNA 7.30976 kcal/mol@LB@Unfolding Energy - sRNA 11.8287 kcal/mol@LB@@LB@Position - mRNA 132 -- 187@LB@Position - sRNA 37 -- 90@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 68 -- 74@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@
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@

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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