Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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	Additional homologs
27	0.0002115	0.02687	b2607	trmD	-14.32	0.001383	229 -- 258	48 -- 75	tRNA m(1)G37 methyltransferase SAM-dependent		_____________228____________________________259\n_____________\|______________________________\|\n5'-UCG...GUUUC___________C__G___U_A_________GGGUA...UCC-3'\n______________CUGAAAUGUUC_GC_CAA_U_CCGAUUACG\n______________\|\|:\|\|\|\|:\|\|\|_\|\|_\|\|\|_\|_\|\|\|\|\|\|\|\|\|\n______________GAUUUUAUAAG_CG_GUU_A_GGCUAAUGC\n3'-AUU...CCGCC___________U______U___________ACUUC...AUG-5'\n_____________\|______________________________\|\n_____________76_____________________________47\n	252 -- 258	48 -- 54	-28.476 kcal/mol	6.50272 kcal/mol	7.67232 kcal/mol	228 259@LB@ \| \|@LB@5'-UCG...GUUUC C G U A GGGUA...UCC-3'@LB@ CUGAAAUGUUC GC CAA U CCGAUUACG@LB@ \|\|:\|\|\|\|:\|\|\| \|\| \|\|\| \| \|\|\|\|\|\|\|\|\|@LB@ GAUUUUAUAAG CG GUU A GGCUAAUGC@LB@3'-AUU...CCGCC U U ACUUC...AUG-5'@LB@ \| \|@LB@ 76 47@LB@@LB@@LB@Energy -14.32 kcal/mol@LB@Hybridization Energy -28.476 kcal/mol@LB@Unfolding Energy - mRNA 6.50272 kcal/mol@LB@Unfolding Energy - sRNA 7.67232 kcal/mol@LB@@LB@Position - mRNA 229 -- 258@LB@Position - sRNA 48 -- 75@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 48 -- 54@LB@
82	0.001877	0.08053	b3199	lptC	-13.73	0.002422	95 -- 106	45 -- 56	periplasmic membrane-anchored LPS-binding protein; LPS export protein		_____________94___________107\n_____________\|____________\|\n5'-UAU...GCGCG____________CGCGC...UGG-3'\n______________CCGAUUACGUGA\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________GGCUAAUGCACU\n3'-AUU...GUUUA____________UCAUU...AUG-5'\n_____________\|____________\|\n_____________57___________44\n	100 -- 106	45 -- 51	-18.6784 kcal/mol	2.68909 kcal/mol	2.27945 kcal/mol	94 107@LB@ \| \|@LB@5'-UAU...GCGCG CGCGC...UGG-3'@LB@ CCGAUUACGUGA@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ GGCUAAUGCACU@LB@3'-AUU...GUUUA UCAUU...AUG-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -13.73 kcal/mol@LB@Hybridization Energy -18.6784 kcal/mol@LB@Unfolding Energy - mRNA 2.68909 kcal/mol@LB@Unfolding Energy - sRNA 2.27945 kcal/mol@LB@@LB@Position - mRNA 95 -- 106@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 45 -- 51@LB@
149	0.005967	0.1406	b0472	recR	-13.66	0.002580	134 -- 160	3 -- 29	gap repair protein		_____________133_________________________161\n_____________\|___________________________\|\n5'-GUG...AACGC___A____AAAAUG_____________CCGGA...UUC-3'\n______________AGA_AGAA______GCCUCUGUAUCCU\n______________\|\|\|_\|\|\|\|______:\|\|\|\|\|\|\|\|:\|\|\|\n______________UCU_UCUU______UGGAGACAUGGGA\n3'-AUU...GACUU___A____GUAGAA_____________UG-5'\n_____________\|___________________________\|\n_____________30__________________________2\n	154 -- 160	3 -- 9	-27.6106 kcal/mol	5.92472 kcal/mol	8.05021 kcal/mol	133 161@LB@ \| \|@LB@5'-GUG...AACGC A AAAAUG CCGGA...UUC-3'@LB@ AGA AGAA GCCUCUGUAUCCU@LB@ \|\|\| \|\|\|\| :\|\|\|\|\|\|\|\|:\|\|\|@LB@ UCU UCUU UGGAGACAUGGGA@LB@3'-AUU...GACUU A GUAGAA UG-5'@LB@ \| \|@LB@ 30 2@LB@@LB@@LB@Energy -13.66 kcal/mol@LB@Hybridization Energy -27.6106 kcal/mol@LB@Unfolding Energy - mRNA 5.92472 kcal/mol@LB@Unfolding Energy - sRNA 8.05021 kcal/mol@LB@@LB@Position - mRNA 134 -- 160@LB@Position - sRNA 3 -- 29@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 3 -- 9@LB@
80	0.001713	0.07533	b1343	dbpA	-13.62	0.002663	221 -- 243	1 -- 24	ATP-dependent RNA helicase specific for 23S rRNA		_____________220______________________244\n_____________\|________________________\|\n5'-ACG...ACCCU______________CC_____A__UCACG...CGC-3'\n______________GAAUGUUUUGCCUC___GCCC_AC\n______________\|\|\|::\|:\|\|:\|\|\|\|___:\|\|\|_\|\|\n______________CUUGUAGAAUGGAG___UGGG_UG\n3'-AUU...UCUAU______________ACA____A__-5'\n_____________\|_______________________\|\n_____________25______________________1\n	228 -- 234	11 -- 17	-24.5457 kcal/mol	2.92371 kcal/mol	8.02158 kcal/mol	220 244@LB@ \| \|@LB@5'-ACG...ACCCU CC A UCACG...CGC-3'@LB@ GAAUGUUUUGCCUC GCCC AC@LB@ \|\|\|::\|:\|\|:\|\|\|\| :\|\|\| \|\|@LB@ CUUGUAGAAUGGAG UGGG UG@LB@3'-AUU...UCUAU ACA A -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -13.62 kcal/mol@LB@Hybridization Energy -24.5457 kcal/mol@LB@Unfolding Energy - mRNA 2.92371 kcal/mol@LB@Unfolding Energy - sRNA 8.02158 kcal/mol@LB@@LB@Position - mRNA 221 -- 243@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 11 -- 17@LB@
94	0.002669	0.09947	b2659	csiD	-13.62	0.002680	28 -- 48	1 -- 21	carbon starvation protein		_____________27____________________49\n_____________\|_____________________\|\n5'-GUU...UGUCU__C________AA________GUUAA...UGG-3'\n______________CA_UUUGCCUU__UACCCUAC\n______________\|\|_:\|\|:\|\|\|:__\|\|\|\|\|\|\|\|\n______________GU_GAAUGGAG__AUGGGAUG\n3'-AUU...AUCUU__A________AC________-5'\n_____________\|____________________\|\n_____________22___________________1\n	42 -- 48	1 -- 7	-22.7197 kcal/mol	1.13457 kcal/mol	7.99195 kcal/mol	27 49@LB@ \| \|@LB@5'-GUU...UGUCU C AA GUUAA...UGG-3'@LB@ CA UUUGCCUU UACCCUAC@LB@ \|\| :\|\|:\|\|\|: \|\|\|\|\|\|\|\|@LB@ GU GAAUGGAG AUGGGAUG@LB@3'-AUU...AUCUU A AC -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -13.62 kcal/mol@LB@Hybridization Energy -22.7197 kcal/mol@LB@Unfolding Energy - mRNA 1.13457 kcal/mol@LB@Unfolding Energy - sRNA 7.99195 kcal/mol@LB@@LB@Position - mRNA 28 -- 48@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 1 -- 7@LB@
13	4.485e-05	0.01183	b0511	ybbW	-13.60	0.002717	173 -- 210	18 -- 58	putative allantoin transporter		_____________172________________________________________211\n_____________\|__________________________________________\|\n5'-UGG...ACGUU_______________AU____________UUU__________AGAGA...UUA-3'\n______________AUUCGA_UACGUGAA__UAAGAGG___GA___AUGGAACAUC\n______________\|\|:\|\|\|_\|\|\|\|\|\|\|\|__\|\|\|:\|\|\|___\|\|___\|\|:\|\|\|\|\|\|\|\n______________UAGGCU_AUGCACUU__AUUUUCC___CU___UAUCUUGUAG\n3'-AUU...CGGUU______A________C________AGA__UUC__________AAUGG...AUG-5'\n_____________\|__________________________________________\|\n_____________59_________________________________________17\n	204 -- 210	18 -- 24	-34.0515 kcal/mol	8.25655 kcal/mol	12.1809 kcal/mol	172 211@LB@ \| \|@LB@5'-UGG...ACGUU AU UUU AGAGA...UUA-3'@LB@ AUUCGA UACGUGAA UAAGAGG GA AUGGAACAUC@LB@ \|\|:\|\|\| \|\|\|\|\|\|\|\| \|\|\|:\|\|\| \|\| \|\|:\|\|\|\|\|\|\|@LB@ UAGGCU AUGCACUU AUUUUCC CU UAUCUUGUAG@LB@3'-AUU...CGGUU A C AGA UUC AAUGG...AUG-5'@LB@ \| \|@LB@ 59 17@LB@@LB@@LB@Energy -13.60 kcal/mol@LB@Hybridization Energy -34.0515 kcal/mol@LB@Unfolding Energy - mRNA 8.25655 kcal/mol@LB@Unfolding Energy - sRNA 12.1809 kcal/mol@LB@@LB@Position - mRNA 173 -- 210@LB@Position - sRNA 18 -- 58@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 18 -- 24@LB@
26	0.0002109	0.02687	b4122	fumB	-13.50	0.002989	276 -- 286	47 -- 57	anaerobic class I fumarate hydratase (fumarase B)	b1612	_____________275_________287\n_____________\|___________\|\n5'-UCC...UCACU___________UAGCG...ACU-3'\n______________UCCGAUUACGU\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________AGGCUAAUGCA\n3'-AUU...GGUUU___________CUUCA...AUG-5'\n_____________\|___________\|\n_____________58__________46\n	280 -- 286	47 -- 53	-16.5827 kcal/mol	1.51899 kcal/mol	1.56839 kcal/mol	275 287@LB@ \| \|@LB@5'-UCC...UCACU UAGCG...ACU-3'@LB@ UCCGAUUACGU@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ AGGCUAAUGCA@LB@3'-AUU...GGUUU CUUCA...AUG-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -13.50 kcal/mol@LB@Hybridization Energy -16.5827 kcal/mol@LB@Unfolding Energy - mRNA 1.51899 kcal/mol@LB@Unfolding Energy - sRNA 1.56839 kcal/mol@LB@@LB@Position - mRNA 276 -- 286@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 47 -- 53@LB@
90	0.002406	0.09404	b0551	quuD	-13.47	0.003063	177 -- 196	40 -- 58	DLP12 prophage; putative antitermination protein		_____________176__________________197\n_____________\|____________________\|\n5'-ACU...UUCUG________UU__________GUUGA...GAU-3'\n______________GUCUGAUU__UGUGGAGUAA\n______________:\|\|:\|\|\|\|__:\|\|\|:\|\|\|\|\|\n______________UAGGCUAA__GCACUUCAUU\n3'-AUU...CGGUU________U___________UUCCA...AUG-5'\n_____________\|____________________\|\n_____________59___________________39\n	190 -- 196	40 -- 46	-19.625 kcal/mol	2.82746 kcal/mol	3.34877 kcal/mol	176 197@LB@ \| \|@LB@5'-ACU...UUCUG UU GUUGA...GAU-3'@LB@ GUCUGAUU UGUGGAGUAA@LB@ :\|\|:\|\|\|\| :\|\|\|:\|\|\|\|\|@LB@ UAGGCUAA GCACUUCAUU@LB@3'-AUU...CGGUU U UUCCA...AUG-5'@LB@ \| \|@LB@ 59 39@LB@@LB@@LB@Energy -13.47 kcal/mol@LB@Hybridization Energy -19.625 kcal/mol@LB@Unfolding Energy - mRNA 2.82746 kcal/mol@LB@Unfolding Energy - sRNA 3.34877 kcal/mol@LB@@LB@Position - mRNA 177 -- 196@LB@Position - sRNA 40 -- 58@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 40 -- 46@LB@
21	0.0001601	0.02641	b2344	fadL	-13.31	0.003531	80 -- 135	1 -- 58	long-chain fatty acid outer membrane transporter		_____________79_________________________________________________________________136\n_____________\|__________________________________________________________________\|\n5'-UCC...AGCUG______CCUA___UCUCGCCACU________UUUCU____________________A_________ACUUC...UUU-3'\n______________GUCCGA____UAC___________GGUCUGA_____AAGAUG________UACCUC_G_ACCCUAC\n______________:\|\|\|\|\|____\|\|\|___________\|\|\|\|\|\|\|_____\|\|\|\|\|:________\|\|\|\|\|\|_\|_\|\|\|\|\|\|\|\n______________UAGGCU____AUG___________CCAGACU_____UUCUAU________AUGGAG_C_UGGGAUG\n3'-AUU...CGGUU______A______CACUUCAUUUU__________________CUUGUAGA______A_A_______-5'\n_____________\|_________________________________________________________________\|\n_____________59________________________________________________________________1\n	129 -- 135	1 -- 7	-38.7471 kcal/mol	12.7593 kcal/mol	12.7027 kcal/mol	79 136@LB@ \| \|@LB@5'-UCC...AGCUG CCUA UCUCGCCACU UUUCU A ACUUC...UUU-3'@LB@ GUCCGA UAC GGUCUGA AAGAUG UACCUC G ACCCUAC@LB@ :\|\|\|\|\| \|\|\| \|\|\|\|\|\|\| \|\|\|\|\|: \|\|\|\|\|\| \| \|\|\|\|\|\|\|@LB@ UAGGCU AUG CCAGACU UUCUAU AUGGAG C UGGGAUG@LB@3'-AUU...CGGUU A CACUUCAUUUU CUUGUAGA A A -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -13.31 kcal/mol@LB@Hybridization Energy -38.7471 kcal/mol@LB@Unfolding Energy - mRNA 12.7593 kcal/mol@LB@Unfolding Energy - sRNA 12.7027 kcal/mol@LB@@LB@Position - mRNA 80 -- 135@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 1 -- 7@LB@
99	0.00311	0.1096	b2801	fucP	-13.12	0.004165	162 -- 172	46 -- 56	L-fucose transporter		_____________161_________173\n_____________\|___________\|\n5'-AUG...CAUAA___________CUUAA...CAC-3'\n______________CCGAUUACGUG\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________GGCUAAUGCAC\n3'-AUU...GUUUA___________UUCAU...AUG-5'\n_____________\|___________\|\n_____________57__________45\n	166 -- 172	46 -- 52	-17.4041 kcal/mol	2.44124 kcal/mol	1.86194 kcal/mol	161 173@LB@ \| \|@LB@5'-AUG...CAUAA CUUAA...CAC-3'@LB@ CCGAUUACGUG@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ GGCUAAUGCAC@LB@3'-AUU...GUUUA UUCAU...AUG-5'@LB@ \| \|@LB@ 57 45@LB@@LB@@LB@Energy -13.12 kcal/mol@LB@Hybridization Energy -17.4041 kcal/mol@LB@Unfolding Energy - mRNA 2.44124 kcal/mol@LB@Unfolding Energy - sRNA 1.86194 kcal/mol@LB@@LB@Position - mRNA 162 -- 172@LB@Position - sRNA 46 -- 56@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 46 -- 52@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