Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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_000913 Escherichia coli str. K-12 substr. MG1655

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
4	0.0001068	0.08442	b2069	yegD	-18.64	0.004982	22 -- 145	51 -- 187	Hsp70 chaperone family protein	_____________21_________________146\n_____________\|__________________\|\n5'-CAC...ACAUC__________A_______CGCUU...UGC-3'\n______________GCAUCUCCUU__UUCAUC\n______________\|\|\|:\|:\|\|\|\|__\|\|\|\|\|\|\n______________CGUGGGGGAA__AAGUAG\n3'-UUU...UACCC__________CG______-5'\n_____________\|_________________\|\n_____________188_______________51\n	72 -- 78	9 -- 15	-21.4418 kcal/mol	1.05479 kcal/mol	7.2533 kcal/mol	21 146@LB@ \| \|@LB@5'-CAC...ACAUC A CGCUU...UGC-3'@LB@ GCAUCUCCUU UUCAUC@LB@ \|\|\|:\|:\|\|\|\| \|\|\|\|\|\|@LB@ CGUGGGGGAA AAGUAG@LB@3'-UUU...UACCC CG -5'@LB@ \| \|@LB@ 188 51@LB@@LB@@LB@Energy -18.64 kcal/mol@LB@Hybridization Energy -21.4418 kcal/mol@LB@Unfolding Energy - mRNA 1.05479 kcal/mol@LB@Unfolding Energy - sRNA 7.2533 kcal/mol@LB@@LB@Position - mRNA 22 -- 145@LB@Position - sRNA 51 -- 187@LB@Position Seed - mRNA 72 -- 78@LB@Position Seed - sRNA 9 -- 15@LB@
153	0.01719	0.3749	b2997	hybO	-10.59	0.212773	44 -- 57	176 -- 189	hydrogenase 2 small subunit	_____________43_________________58\n_____________\|__________________\|\n5'-CUC...AUUAA______________CU__CCUUC...GCA-3'\n______________UUACACUAAUGCUU__UC\n______________\|\|\|\|\|\|:\|\|\|:\|\|:__\|\|\n______________AAUGUGGUUAUGAG__AG\n3'-UUU...ACUAA______________UC__UGUGU...UAG-5'\n_____________\|__________________\|\n_____________190________________175\n	51 -- 57	176 -- 182	-17.3647 kcal/mol	0.828093 kcal/mol	4.66778 kcal/mol	43 58@LB@ \| \|@LB@5'-CUC...AUUAA CU CCUUC...GCA-3'@LB@ UUACACUAAUGCUU UC@LB@ \|\|\|\|\|\|:\|\|\|:\|\|: \|\|@LB@ AAUGUGGUUAUGAG AG@LB@3'-UUU...ACUAA UC UGUGU...UAG-5'@LB@ \| \|@LB@ 190 175@LB@@LB@@LB@Energy -10.59 kcal/mol@LB@Hybridization Energy -17.3647 kcal/mol@LB@Unfolding Energy - mRNA 0.828093 kcal/mol@LB@Unfolding Energy - sRNA 4.66778 kcal/mol@LB@@LB@Position - mRNA 44 -- 57@LB@Position - sRNA 176 -- 189@LB@Position Seed - mRNA 51 -- 57@LB@Position Seed - sRNA 176 -- 182@LB@
14	0.00083	0.1886	b2721	hycE	-15.91	0.017607	169 -- 185	190 -- 205	hydrogenase 3 large subunit	_____________168_______________186\n_____________\|_________________\|\n5'-UUC...UCUCC__________C______AAAGA...UGA-3'\n______________UUGCUGGCGG_GUGAUU\n______________:\|\|\|\|\|\|\|\|\|_\|\|\|\|\|\|\n______________GACGACCGCC_CACUAA\n3'-UUU...UAUUA_________________AAUGU...UAG-5'\n_____________\|_________________\|\n_____________206_______________189\n	172 -- 178	196 -- 202	-26.9802 kcal/mol	6.4269 kcal/mol	9.06848 kcal/mol	168 186@LB@ \| \|@LB@5'-UUC...UCUCC C AAAGA...UGA-3'@LB@ UUGCUGGCGG GUGAUU@LB@ :\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GACGACCGCC CACUAA@LB@3'-UUU...UAUUA AAUGU...UAG-5'@LB@ \| \|@LB@ 206 189@LB@@LB@@LB@Energy -15.91 kcal/mol@LB@Hybridization Energy -26.9802 kcal/mol@LB@Unfolding Energy - mRNA 6.4269 kcal/mol@LB@Unfolding Energy - sRNA 9.06848 kcal/mol@LB@@LB@Position - mRNA 169 -- 185@LB@Position - sRNA 190 -- 205@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 196 -- 202@LB@
174	0.01972	0.3812	b0478	ybaL	-7.90	0.612018	5 -- 14	166 -- 176	inner membrane putative NAD(P)-binding transporter	_____________4___________15\n_____________\|___________\|\n_______5'-UUUA___________AAGCC...UGG-3'\n______________CAGUCGC_CAU\n______________\|\|\|\|\|:\|_\|\|\|\n______________GUCAGUG_GUA\n3'-UUU...UAUGA_______U___CUACG...UAG-5'\n_____________\|___________\|\n_____________177_________165\n	5 -- 11	170 -- 176	-11.743 kcal/mol	0.493889 kcal/mol	0.598087 kcal/mol	4 15@LB@ \| \|@LB@ 5'-UUUA AAGCC...UGG-3'@LB@ CAGUCGC CAU@LB@ \|\|\|\|\|:\| \|\|\|@LB@ GUCAGUG GUA@LB@3'-UUU...UAUGA U CUACG...UAG-5'@LB@ \| \|@LB@ 177 165@LB@@LB@@LB@Energy -7.90 kcal/mol@LB@Hybridization Energy -11.743 kcal/mol@LB@Unfolding Energy - mRNA 0.493889 kcal/mol@LB@Unfolding Energy - sRNA 0.598087 kcal/mol@LB@@LB@Position - mRNA 5 -- 14@LB@Position - sRNA 166 -- 176@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 170 -- 176@LB@
54	0.005402	0.3247	b3054	ygiF	-14.97	0.027422	5 -- 80	111 -- 177	inorganic triphosphatase	_____________4_______________________________________________________________________________81\n_____________\|_______________________________________________________________________________\|\n_______5'-GGCA_____GU___UAC_____AA___U______AUCAA_______CCUCUG___CA____U_G_______U___AA______CGCCC...CCG-3'\n______________UCAGU__CGC_____GCA__GCA__UCGAC_____UCGGAAU______UGU__GGUC_U_CCACUGC_UCA__CUUUUA\n______________\|\|\|\|\|__\|:\|_____\|\|\|__\|\|\|__\|\|:\|\|_____\|\|:\|\|\|\|______\|\|:__\|\|\|\|_\|_\|\|\|\|\|\|\|_\|\|\|__\|:\|\|:\|\n______________AGUCA__GUG_____CGU__CGU__AGUUG_____AGUCUUA______ACG__CCAG_A_GGUGACG_AGU__GGAAGU\n3'-UUU...UUAUG_____GU___UACUA___C____UC_____AA_________________________U_G_______U___CA______UCGUA...UAG-5'\n_____________\|_______________________________________________________________________________\|\n_____________178_____________________________________________________________________________110\n	62 -- 68	123 -- 129	-50.4846 kcal/mol	15.6316 kcal/mol	23.3828 kcal/mol	4 81@LB@ \| \|@LB@ 5'-GGCA GU UAC AA U AUCAA CCUCUG CA U G U AA CGCCC...CCG-3'@LB@ UCAGU CGC GCA GCA UCGAC UCGGAAU UGU GGUC U CCACUGC UCA CUUUUA@LB@ \|\|\|\|\| \|:\| \|\|\| \|\|\| \|\|:\|\| \|\|:\|\|\|\| \|\|: \|\|\|\| \| \|\|\|\|\|\|\| \|\|\| \|:\|\|:\|@LB@ AGUCA GUG CGU CGU AGUUG AGUCUUA ACG CCAG A GGUGACG AGU GGAAGU@LB@3'-UUU...UUAUG GU UACUA C UC AA U G U CA UCGUA...UAG-5'@LB@ \| \|@LB@ 178 110@LB@@LB@@LB@Energy -14.97 kcal/mol@LB@Hybridization Energy -50.4846 kcal/mol@LB@Unfolding Energy - mRNA 15.6316 kcal/mol@LB@Unfolding Energy - sRNA 23.3828 kcal/mol@LB@@LB@Position - mRNA 5 -- 80@LB@Position - sRNA 111 -- 177@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 123 -- 129@LB@
89	0.009985	0.3575	b0477	gsk	-9.51	0.338446	88 -- 115	123 -- 150	inosine/guanosine kinase	_____________87_____________116\n_____________\|______________\|\n5'-UUU...UCGCC_________AC___CCGUA...CUG-3'\n______________GCUCAGUUA__CAC\n______________:\|\|\|\|\|\|:\|__\|\|\|\n______________UGAGUCAGU__GUG\n3'-UUU...GGUUA______________UACUA...UAG-5'\n_____________\|______________\|\n_____________151____________122\n	175 -- 181	171 -- 177	-13.3754 kcal/mol	2.68541 kcal/mol	0.283892 kcal/mol	87 116@LB@ \| \|@LB@5'-UUU...UCGCC AC CCGUA...CUG-3'@LB@ GCUCAGUUA CAC@LB@ :\|\|\|\|\|\|:\| \|\|\|@LB@ UGAGUCAGU GUG@LB@3'-UUU...GGUUA UACUA...UAG-5'@LB@ \| \|@LB@ 151 122@LB@@LB@@LB@Energy -9.51 kcal/mol@LB@Hybridization Energy -13.3754 kcal/mol@LB@Unfolding Energy - mRNA 2.68541 kcal/mol@LB@Unfolding Energy - sRNA 0.283892 kcal/mol@LB@@LB@Position - mRNA 88 -- 115@LB@Position - sRNA 123 -- 150@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 171 -- 177@LB@
69	0.006739	0.3286	b2265	menF	-9.03	0.410924	65 -- 108	52 -- 101	isochorismate synthase 2	_____________64__________109\n_____________\|___________\|\n5'-ACU...CGGGU___________CUUUC...CUC-3'\n______________UAUCGAUAUUC\n______________:\|:\|:\|\|\|:\|\|\n______________GUGGUUAUGAG\n3'-UUU...AAAAU___________UCAGU...UAG-5'\n_____________\|___________\|\n_____________102_________51\n	285 -- 291	176 -- 182	-9.38108 kcal/mol	0.14396 kcal/mol	3.38772 kcal/mol	64 109@LB@ \| \|@LB@5'-ACU...CGGGU CUUUC...CUC-3'@LB@ UAUCGAUAUUC@LB@ :\|:\|:\|\|\|:\|\|@LB@ GUGGUUAUGAG@LB@3'-UUU...AAAAU UCAGU...UAG-5'@LB@ \| \|@LB@ 102 51@LB@@LB@@LB@Energy -9.03 kcal/mol@LB@Hybridization Energy -9.38108 kcal/mol@LB@Unfolding Energy - mRNA 0.14396 kcal/mol@LB@Unfolding Energy - sRNA 3.38772 kcal/mol@LB@@LB@Position - mRNA 65 -- 108@LB@Position - sRNA 52 -- 101@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 176 -- 182@LB@
152	0.0171	0.3749	b3605	lldD	-10.23	0.248595	212 -- 221	68 -- 77	L-lactate dehydrogenase FMN-linked	_____________211_______222\n_____________\|_________\|\n5'-UUU...GAAAA_________UAUUU...ACA-3'\n______________ACGCAUGAU\n______________\|\|:\|\|\|\|\|\|\n______________UGUGUACUA\n3'-UUU...GUCAG_________CGUCC...UAG-5'\n_____________\|_________\|\n_____________78________67\n	199 -- 205	163 -- 169	-11.1438 kcal/mol	1.00002 kcal/mol	4.14962 kcal/mol	211 222@LB@ \| \|@LB@5'-UUU...GAAAA UAUUU...ACA-3'@LB@ ACGCAUGAU@LB@ \|\|:\|\|\|\|\|\|@LB@ UGUGUACUA@LB@3'-UUU...GUCAG CGUCC...UAG-5'@LB@ \| \|@LB@ 78 67@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -11.1438 kcal/mol@LB@Unfolding Energy - mRNA 1.00002 kcal/mol@LB@Unfolding Energy - sRNA 4.14962 kcal/mol@LB@@LB@Position - mRNA 212 -- 221@LB@Position - sRNA 68 -- 77@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 163 -- 169@LB@
176	0.01994	0.3812	b2170	setB	-11.80	0.122017	181 -- 237	58 -- 116	lactose/glucose efflux system	_____________180____________238\n_____________\|______________\|\n5'-GCU...GAUCG______________AACUC...UGC-3'\n______________AC_CAG_CAUGCAU\n______________\|\|_\|\|\|_\|\|::\|\|\|\n______________UG_GUC_GUGUGUA\n3'-UUU...GGUUA__A___A_______CUACG...UAG-5'\n_____________\|______________\|\n_____________117____________57\n	200 -- 206	166 -- 172	-10.2756 kcal/mol	1.89616 kcal/mol	0.604817 kcal/mol	180 238@LB@ \| \|@LB@5'-GCU...GAUCG AACUC...UGC-3'@LB@ AC CAG CAUGCAU@LB@ \|\| \|\|\| \|\|::\|\|\|@LB@ UG GUC GUGUGUA@LB@3'-UUU...GGUUA A A CUACG...UAG-5'@LB@ \| \|@LB@ 117 57@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -10.2756 kcal/mol@LB@Unfolding Energy - mRNA 1.89616 kcal/mol@LB@Unfolding Energy - sRNA 0.604817 kcal/mol@LB@@LB@Position - mRNA 181 -- 237@LB@Position - sRNA 58 -- 116@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 166 -- 172@LB@
76	0.007832	0.3458	b1054	lpxL	-10.56	0.214918	224 -- 240	1 -- 17	lauryl-acyl carrier protein (ACP)-dependent acyltransferase	_____________223_______241\n_____________\|_________\|\n5'-AAA...CGCAC_________CGCGU...CCU-3'\n______________UGCUUCAUC\n______________\|\|\|\|\|\|\|\|\|\n______________ACGAAGUAG\n3'-UUU...GGGGA_________-5'\n_____________\|________\|\n_____________18_______1\n	234 -- 240	1 -- 7	-13.5925 kcal/mol	1.26369 kcal/mol	0.710349 kcal/mol	223 241@LB@ \| \|@LB@5'-AAA...CGCAC CGCGU...CCU-3'@LB@ UGCUUCAUC@LB@ \|\|\|\|\|\|\|\|\|@LB@ ACGAAGUAG@LB@3'-UUU...GGGGA -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -13.5925 kcal/mol@LB@Unfolding Energy - mRNA 1.26369 kcal/mol@LB@Unfolding Energy - sRNA 0.710349 kcal/mol@LB@@LB@Position - mRNA 224 -- 240@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 234 -- 240@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