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
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@
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@
123	0.006073	0.1758	stm4355	yjeS	-17.69	0.042665	80 -- 140	31 -- 90	putative Fe-S protein	_____________79______________________________141\n_____________\|_______________________________\|\n_______5'-CGUU______________C________________AGUGU...UUA-3'\n______________GUUGC___CAUGAC_ACACAACA_C_CAGCC\n______________:\|\|\|\|___\|\|::\|\|_\|\|\|\|\|\|\|\|_\|_\|\|:\|\|\n______________UAACG___GUGUUG_UGUGUUGU_G_GUUGG\n3'-UUU...CUGGU_____UUU______U________A_U_____CAUUC...UCA-5'\n_____________\|_______________________________\|\n_____________91______________________________30\n	18 -- 24	71 -- 77	-27.2663 kcal/mol	5.13395 kcal/mol	8.62086 kcal/mol	79 141@LB@ \| \|@LB@ 5'-CGUU C AGUGU...UUA-3'@LB@ GUUGC CAUGAC ACACAACA C CAGCC@LB@ :\|\|\|\| \|\|::\|\| \|\|\|\|\|\|\|\| \| \|\|:\|\|@LB@ UAACG GUGUUG UGUGUUGU G GUUGG@LB@3'-UUU...CUGGU UUU U A U CAUUC...UCA-5'@LB@ \| \|@LB@ 91 30@LB@@LB@@LB@Energy -17.69 kcal/mol@LB@Hybridization Energy -27.2663 kcal/mol@LB@Unfolding Energy - mRNA 5.13395 kcal/mol@LB@Unfolding Energy - sRNA 8.62086 kcal/mol@LB@@LB@Position - mRNA 80 -- 140@LB@Position - sRNA 31 -- 90@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 71 -- 77@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@
125	0.006333	0.1774	stm3094	yggJ	-12.37	0.297521	35 -- 55	69 -- 89	putative cytoplasmic protein	_____________34____________________56\n_____________\|_____________________\|\n5'-GCG...GCCAA__________UUUU_______UGGGA...AGA-3'\n______________CAAACGCAGC____UAACGUC\n______________\|\|\|\|\|:\|\|:\|____:\|\|\|:\|\|\n______________GUUUGUGUUG____GUUGUAG\n3'-UUU...UUAAC__________UUGU_______UGUUG...UCA-5'\n_____________\|_____________________\|\n_____________90____________________68\n	49 -- 55	69 -- 75	-19.7914 kcal/mol	1.34113 kcal/mol	4.32311 kcal/mol	34 56@LB@ \| \|@LB@5'-GCG...GCCAA UUUU UGGGA...AGA-3'@LB@ CAAACGCAGC UAACGUC@LB@ \|\|\|\|\|:\|\|:\| :\|\|\|:\|\|@LB@ GUUUGUGUUG GUUGUAG@LB@3'-UUU...UUAAC UUGU UGUUG...UCA-5'@LB@ \| \|@LB@ 90 68@LB@@LB@@LB@Energy -12.37 kcal/mol@LB@Hybridization Energy -19.7914 kcal/mol@LB@Unfolding Energy - mRNA 1.34113 kcal/mol@LB@Unfolding Energy - sRNA 4.32311 kcal/mol@LB@@LB@Position - mRNA 35 -- 55@LB@Position - sRNA 69 -- 89@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 69 -- 75@LB@
126	0.006333	0.1774	stm1584	ansP	-14.21	0.157463	122 -- 184	36 -- 93	amino acid permease	_____________121_________________185\n_____________\|___________________\|\n5'-AUA...UGUCA________UAUAACA____ACGUA...GUC-3'\n______________GGACAGGC_______GGUA\n______________\|\|\|\|\|\|:\|_______\|\|\|\|\n______________CCUGUCUG_______CCAU\n3'-UUU...UGAUA________UC_________UUACA...UCA-5'\n_____________\|___________________\|\n_____________94__________________35\n	178 -- 184	156 -- 162	-15.5225 kcal/mol	4.18435 kcal/mol	3.12041 kcal/mol	121 185@LB@ \| \|@LB@5'-AUA...UGUCA UAUAACA ACGUA...GUC-3'@LB@ GGACAGGC GGUA@LB@ \|\|\|\|\|\|:\| \|\|\|\|@LB@ CCUGUCUG CCAU@LB@3'-UUU...UGAUA UC UUACA...UCA-5'@LB@ \| \|@LB@ 94 35@LB@@LB@@LB@Energy -14.21 kcal/mol@LB@Hybridization Energy -15.5225 kcal/mol@LB@Unfolding Energy - mRNA 4.18435 kcal/mol@LB@Unfolding Energy - sRNA 3.12041 kcal/mol@LB@@LB@Position - mRNA 122 -- 184@LB@Position - sRNA 36 -- 93@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 156 -- 162@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@
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@
129	0.006472	0.1774	stm0158	acnB	-11.80	0.356459	140 -- 172	33 -- 60	bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase	_____________139________________173\n_____________\|__________________\|\n5'-AUU...CUUUU_________G_U______UUAAA...UGC-3'\n______________UUGUAAACA_A_UAACAC\n______________\|\|\|:\|\|\|\|\|_\|_:\|\|\|\|\|\n______________AACGUUUGU_U_GUUGUG\n3'-UUU...UGGUU_________G_U______UUGUA...UCA-5'\n_____________\|__________________\|\n_____________61_________________32\n	48 -- 54	84 -- 90	-17.8051 kcal/mol	3.41045 kcal/mol	3.73018 kcal/mol	139 173@LB@ \| \|@LB@5'-AUU...CUUUU G U UUAAA...UGC-3'@LB@ UUGUAAACA A UAACAC@LB@ \|\|\|:\|\|\|\|\| \| :\|\|\|\|\|@LB@ AACGUUUGU U GUUGUG@LB@3'-UUU...UGGUU G U UUGUA...UCA-5'@LB@ \| \|@LB@ 61 32@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -17.8051 kcal/mol@LB@Unfolding Energy - mRNA 3.41045 kcal/mol@LB@Unfolding Energy - sRNA 3.73018 kcal/mol@LB@@LB@Position - mRNA 140 -- 172@LB@Position - sRNA 33 -- 60@LB@Position Seed - mRNA 48 -- 54@LB@Position Seed - sRNA 84 -- 90@LB@
130	0.00652	0.1774	stm4228	malF	-14.47	0.143021	162 -- 175	1 -- 15	maltose ABC transporter permease MalF	_____________161_____________176\n_____________\|_______________\|\n5'-AAC...ACAUC_______________UUCAA...UAA-3'\n______________UCCGGC_CAGGAAGU\n______________\|\|\|\|\|\|_\|\|\|\|\|\|\|\|\n______________AGGCCG_GUCCUUCA\n3'-UUU...AAGCA______A________-5'\n_____________\|______________\|\n_____________16_____________1\n	169 -- 175	1 -- 7	-25.2779 kcal/mol	6.67863 kcal/mol	4.81264 kcal/mol	161 176@LB@ \| \|@LB@5'-AAC...ACAUC UUCAA...UAA-3'@LB@ UCCGGC CAGGAAGU@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ AGGCCG GUCCUUCA@LB@3'-UUU...AAGCA A -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -14.47 kcal/mol@LB@Hybridization Energy -25.2779 kcal/mol@LB@Unfolding Energy - mRNA 6.67863 kcal/mol@LB@Unfolding Energy - sRNA 4.81264 kcal/mol@LB@@LB@Position - mRNA 162 -- 175@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 1 -- 7@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching