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
19	0.001698	0.2633	b2575	trmN	-12.50	0.088044	81 -- 92	14 -- 25	tRNA1(Val) (adenine(37)-N6)-methyltransferase	_____________80___________93\n_____________\|____________\|\n5'-ACC...UACAU__G_________GUAAU...GUA-3'\n______________CC_UGCUUCGUC\n______________\|\|_\|\|\|\|\|\|:\|\|\n______________GG_ACGAAGUAG\n3'-UUU...GUGGG__A_________-5'\n_____________\|___________\|\n_____________26__________14\n	222 -- 228	1 -- 7	-15.2724 kcal/mol	3.783 kcal/mol	1.04836 kcal/mol	80 93@LB@ \| \|@LB@5'-ACC...UACAU G GUAAU...GUA-3'@LB@ CC UGCUUCGUC@LB@ \|\| \|\|\|\|\|\|:\|\|@LB@ GG ACGAAGUAG@LB@3'-UUU...GUGGG A -5'@LB@ \| \|@LB@ 26 14@LB@@LB@@LB@Energy -12.50 kcal/mol@LB@Hybridization Energy -15.2724 kcal/mol@LB@Unfolding Energy - mRNA 3.783 kcal/mol@LB@Unfolding Energy - sRNA 1.04836 kcal/mol@LB@@LB@Position - mRNA 81 -- 92@LB@Position - sRNA 14 -- 25@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 1 -- 7@LB@
31	0.002426	0.2633	b2593	yfiH	-12.28	0.097562	144 -- 222	126 -- 203	UPF0124 family protein	_____________143___________________________________________________________________________223\n_____________\|_____________________________________________________________________________\|\n5'-CCA...AUUGA______GC______________AAGA_____AG_____________G____GG___U____AA__U_A_________AGUGG...CAC-3'\n______________GGUGAU___GCGCCGAU_UUCG____ACAUA__GAUG_____AAGU_GACU__UUA_GAGU__GC_G_UUGUCCCGC\n______________\|\|\|\|\|\|___:\|:\|\|:\|\|_:\|\|:____\|\|\|:\|__\|\|\|\|_____\|\|\|\|_:\|\|\|__\|:\|_\|\|:\|__\|\|_\|_\|::\|\|\|\|:\|\n______________CCACUA___UGUGGUUA_GAGU____UGUGU__CUAC_____UUCA_UUGA__AGU_CUUA__CG_C_AGUAGGGUG\n3'-UUU...ACCGC______AAA________U____CAG______A_____GUCCG____G____A_________A___C___________ACGUA...UAG-5'\n_____________\|_____________________________________________________________________________\|\n_____________204___________________________________________________________________________125\n	216 -- 222	126 -- 132	-51.0225 kcal/mol	17.9985 kcal/mol	20.5417 kcal/mol	143 223@LB@ \| \|@LB@5'-CCA...AUUGA GC AAGA AG G GG U AA U A AGUGG...CAC-3'@LB@ GGUGAU GCGCCGAU UUCG ACAUA GAUG AAGU GACU UUA GAGU GC G UUGUCCCGC@LB@ \|\|\|\|\|\| :\|:\|\|:\|\| :\|\|: \|\|\|:\| \|\|\|\| \|\|\|\| :\|\|\| \|:\| \|\|:\| \|\| \| \|::\|\|\|\|:\|@LB@ CCACUA UGUGGUUA GAGU UGUGU CUAC UUCA UUGA AGU CUUA CG C AGUAGGGUG@LB@3'-UUU...ACCGC AAA U CAG A GUCCG G A A C ACGUA...UAG-5'@LB@ \| \|@LB@ 204 125@LB@@LB@@LB@Energy -12.28 kcal/mol@LB@Hybridization Energy -51.0225 kcal/mol@LB@Unfolding Energy - mRNA 17.9985 kcal/mol@LB@Unfolding Energy - sRNA 20.5417 kcal/mol@LB@@LB@Position - mRNA 144 -- 222@LB@Position - sRNA 126 -- 203@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 126 -- 132@LB@
123	0.01344	0.3575	b2615	nadK	-10.03	0.271821	99 -- 122	57 -- 77	NAD kinase	_____________98____________123\n_____________\|_____________\|\n5'-CUC...CCCAC________AC___ACUGA...AAG-3'\n______________GGCACCCC__UGC\n______________\|\|\|\|\|\|\|\|__\|\|\|\n______________CCGUGGGG__ACG\n3'-UUU...GUACC________GA___AAGUAG-5'\n_____________\|_____________\|\n_____________78____________56\n	245 -- 251	12 -- 18	-21.986 kcal/mol	5.26387 kcal/mol	8.16826 kcal/mol	98 123@LB@ \| \|@LB@5'-CUC...CCCAC AC ACUGA...AAG-3'@LB@ GGCACCCC UGC@LB@ \|\|\|\|\|\|\|\| \|\|\|@LB@ CCGUGGGG ACG@LB@3'-UUU...GUACC GA AAGUAG-5'@LB@ \| \|@LB@ 78 56@LB@@LB@@LB@Energy -10.03 kcal/mol@LB@Hybridization Energy -21.986 kcal/mol@LB@Unfolding Energy - mRNA 5.26387 kcal/mol@LB@Unfolding Energy - sRNA 8.16826 kcal/mol@LB@@LB@Position - mRNA 99 -- 122@LB@Position - sRNA 57 -- 77@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 12 -- 18@LB@
88	0.009956	0.3575	b2672	ygaM	-12.38	0.093122	193 -- 231	56 -- 92	putative membrane-anchored DUF883 family ribosome-binding protein	_____________192______232\n_____________\|________\|\n5'-AAC...UGAAC________AGAAA...AGU-3'\n______________CUCAGUUA\n______________\|\|\|\|\|\|:\|\n______________GAGUCAGU\n3'-UUU...GUUAU________GUGUA...UAG-5'\n_____________\|________\|\n_____________93_______55\n	142 -- 148	171 -- 177	-10.1878 kcal/mol	1.87036 kcal/mol	0.207782 kcal/mol	192 232@LB@ \| \|@LB@5'-AAC...UGAAC AGAAA...AGU-3'@LB@ CUCAGUUA@LB@ \|\|\|\|\|\|:\|@LB@ GAGUCAGU@LB@3'-UUU...GUUAU GUGUA...UAG-5'@LB@ \| \|@LB@ 93 55@LB@@LB@@LB@Energy -12.38 kcal/mol@LB@Hybridization Energy -10.1878 kcal/mol@LB@Unfolding Energy - mRNA 1.87036 kcal/mol@LB@Unfolding Energy - sRNA 0.207782 kcal/mol@LB@@LB@Position - mRNA 193 -- 231@LB@Position - sRNA 56 -- 92@LB@Position Seed - mRNA 142 -- 148@LB@Position Seed - sRNA 171 -- 177@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@
190	0.02217	0.3833	b2754	ygbF	-10.33	0.238061	176 -- 225	124 -- 165	CRISPR adaptation ssRNA endonuclease	_____________175____________226\n_____________\|______________\|\n5'-UGG...AAAAU________GC____ACGAG...GUG-3'\n______________GUACCUCC__GCUU\n______________\|:\|\|\|:\|\|__\|\|\|\|\n______________CGUGGGGG__CGAA\n3'-UUU...UACCC________AA____GUAG-5'\n_____________\|______________\|\n_____________166____________123\n	232 -- 238	11 -- 17	-17.8256 kcal/mol	3.33543 kcal/mol	6.90657 kcal/mol	175 226@LB@ \| \|@LB@5'-UGG...AAAAU GC ACGAG...GUG-3'@LB@ GUACCUCC GCUU@LB@ \|:\|\|\|:\|\| \|\|\|\|@LB@ CGUGGGGG CGAA@LB@3'-UUU...UACCC AA GUAG-5'@LB@ \| \|@LB@ 166 123@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -17.8256 kcal/mol@LB@Unfolding Energy - mRNA 3.33543 kcal/mol@LB@Unfolding Energy - sRNA 6.90657 kcal/mol@LB@@LB@Position - mRNA 176 -- 225@LB@Position - sRNA 124 -- 165@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 11 -- 17@LB@
197	0.02355	0.3833	b2764	cysJ	-10.17	0.255883	3 -- 30	98 -- 123	sulfite reductase alpha subunit flavoprotein	_____________2________31\n_____________\|________\|\n5'-UUC...AACAG________ACUGG...UUG-3'\n______________CUUUGCUU\n______________\|:\|\|\|\|\|\|\n______________GGAACGAA\n3'-UUU...GUGGG________GUAG-5'\n_____________\|________\|\n_____________124______97\n	176 -- 182	5 -- 11	-8.59037 kcal/mol	0.881795 kcal/mol	1.04254 kcal/mol	2 31@LB@ \| \|@LB@5'-UUC...AACAG ACUGG...UUG-3'@LB@ CUUUGCUU@LB@ \|:\|\|\|\|\|\|@LB@ GGAACGAA@LB@3'-UUU...GUGGG GUAG-5'@LB@ \| \|@LB@ 124 97@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -8.59037 kcal/mol@LB@Unfolding Energy - mRNA 0.881795 kcal/mol@LB@Unfolding Energy - sRNA 1.04254 kcal/mol@LB@@LB@Position - mRNA 3 -- 30@LB@Position - sRNA 98 -- 123@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 5 -- 11@LB@
56	0.005619	0.3247	b2781	mazG	-9.54	0.334798	182 -- 193	141 -- 152	nucleoside triphosphate pyrophosphohydrolase	_____________181__________194\n_____________\|____________\|\n5'-UGA...ACCCG____________CAAUU...CGC-3'\n______________CAAUUUUCAGGA\n______________\|\|\|:\|\|\|\|\|\|:\|\n______________GUUGAAAGUCUU\n3'-UUU...GUUCA____________AACGC...UAG-5'\n_____________\|____________\|\n_____________153__________140\n	187 -- 193	141 -- 147	-13.182 kcal/mol	1.77322 kcal/mol	1.81388 kcal/mol	181 194@LB@ \| \|@LB@5'-UGA...ACCCG CAAUU...CGC-3'@LB@ CAAUUUUCAGGA@LB@ \|\|\|:\|\|\|\|\|\|:\|@LB@ GUUGAAAGUCUU@LB@3'-UUU...GUUCA AACGC...UAG-5'@LB@ \| \|@LB@ 153 140@LB@@LB@@LB@Energy -9.54 kcal/mol@LB@Hybridization Energy -13.182 kcal/mol@LB@Unfolding Energy - mRNA 1.77322 kcal/mol@LB@Unfolding Energy - sRNA 1.81388 kcal/mol@LB@@LB@Position - mRNA 182 -- 193@LB@Position - sRNA 141 -- 152@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 141 -- 147@LB@
78	0.008099	0.3458	b2810	csdA	-12.29	0.097398	132 -- 155	3 -- 23	cysteine sulfinate desulfinase	_____________131_______________156\n_____________\|_________________\|\n5'-CUU...GGUUA____U________A___AAGUG...AAG-3'\n______________GCAC_CUCCUUGU_UCA\n______________\|\|\|\|_\|:\|\|\|\|\|:_\|\|\|\n______________CGUG_GGGGAACG_AGU\n3'-UUU...UACCC_____________A___AG-5'\n_____________\|_________________\|\n_____________24________________2\n	145 -- 151	7 -- 13	-20.4088 kcal/mol	3.04417 kcal/mol	7.17675 kcal/mol	131 156@LB@ \| \|@LB@5'-CUU...GGUUA U A AAGUG...AAG-3'@LB@ GCAC CUCCUUGU UCA@LB@ \|\|\|\| \|:\|\|\|\|\|: \|\|\|@LB@ CGUG GGGGAACG AGU@LB@3'-UUU...UACCC A AG-5'@LB@ \| \|@LB@ 24 2@LB@@LB@@LB@Energy -12.29 kcal/mol@LB@Hybridization Energy -20.4088 kcal/mol@LB@Unfolding Energy - mRNA 3.04417 kcal/mol@LB@Unfolding Energy - sRNA 7.17675 kcal/mol@LB@@LB@Position - mRNA 132 -- 155@LB@Position - sRNA 3 -- 23@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 7 -- 13@LB@
103	0.0111	0.3575	b2821	ptrA	-11.45	0.143539	261 -- 295	141 -- 175	protease III	_____________260_______________________________________296\n_____________\|_________________________________________\|\n5'-GCU...GCACC___A_____G______AA____AU_______CGA_______AACCA-3'\n______________CUU_AGUCA_GCA_GA__CGGG__GG_CAGC___UUCAGGA\n______________\|\|:_\|\|\|\|\|_:\|\|_\|\|__\|:\|\|__:\|_\|\|:\|___\|\|\|\|\|:\|\n______________GAG_UCAGU_UGU_CU__GUCC__UC_GUUG___AAGUCUU\n3'-UUU...GUUAU_________G___A__AC____GU__A____A_________AACGC...UAG-5'\n_____________\|_________________________________________\|\n_____________176_______________________________________140\n	289 -- 295	141 -- 147	-30.7779 kcal/mol	8.8583 kcal/mol	8.83168 kcal/mol	260 296@LB@ \| \|@LB@5'-GCU...GCACC A G AA AU CGA AACCA-3'@LB@ CUU AGUCA GCA GA CGGG GG CAGC UUCAGGA@LB@ \|\|: \|\|\|\|\| :\|\| \|\| \|:\|\| :\| \|\|:\| \|\|\|\|\|:\|@LB@ GAG UCAGU UGU CU GUCC UC GUUG AAGUCUU@LB@3'-UUU...GUUAU G A AC GU A A AACGC...UAG-5'@LB@ \| \|@LB@ 176 140@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -30.7779 kcal/mol@LB@Unfolding Energy - mRNA 8.8583 kcal/mol@LB@Unfolding Energy - sRNA 8.83168 kcal/mol@LB@@LB@Position - mRNA 261 -- 295@LB@Position - sRNA 141 -- 175@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 141 -- 147@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