Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
41	0.00828	0.5385	b2246	rhmT	-13.65	0.023999	257 -- 273	69 -- 86	putative L-rhamnonate transporter	_____________256________________274\n_____________\|__________________\|\n5'-ACG...AUUCC____________GCU___AUGUG...CGA-3'\n______________GUUUAUGUUGGC____GU\n______________\|\|\|:\|:\|\|\|\|\|\|____\|\|\n______________CAAGUGCAACCG____CA\n3'-CGC...GUUUU____________AAAU__AUAAG...AAG-5'\n_____________\|__________________\|\n_____________87_________________68\n	262 -- 268	75 -- 81	-18.6828 kcal/mol	4.45929 kcal/mol	0.568509 kcal/mol	256 274@LB@ \| \|@LB@5'-ACG...AUUCC GCU AUGUG...CGA-3'@LB@ GUUUAUGUUGGC GU@LB@ \|\|\|:\|:\|\|\|\|\|\| \|\|@LB@ CAAGUGCAACCG CA@LB@3'-CGC...GUUUU AAAU AUAAG...AAG-5'@LB@ \| \|@LB@ 87 68@LB@@LB@@LB@Energy -13.65 kcal/mol@LB@Hybridization Energy -18.6828 kcal/mol@LB@Unfolding Energy - mRNA 4.45929 kcal/mol@LB@Unfolding Energy - sRNA 0.568509 kcal/mol@LB@@LB@Position - mRNA 257 -- 273@LB@Position - sRNA 69 -- 86@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 75 -- 81@LB@
190	0.03345	0.5559	b4090	rpiB	-6.75	0.355761	259 -- 286	57 -- 78	ribose 5-phosphate isomerase B/allose 6-phosphate isomerase	_____________258__________________________287\n_____________\|____________________________\|\n5'-AAC...AAUAG____ACA________AGCG___C_____AGUGA...AAG-3'\n______________UGGC___UUUAGUUG____UGG_GUUGA\n______________\|\|\|\|___\|\|\|\|\|\|\|:____:\|:_\|\|\|\|\|\n______________ACCG___AAAUCAAU____GCU_CAACU\n3'-CGC...GUGCA_______________AA___________CUUUG...AAG-5'\n_____________\|____________________________\|\n_____________79___________________________56\n	267 -- 273	67 -- 73	-15.2709 kcal/mol	7.30632 kcal/mol	1.21856 kcal/mol	258 287@LB@ \| \|@LB@5'-AAC...AAUAG ACA AGCG C AGUGA...AAG-3'@LB@ UGGC UUUAGUUG UGG GUUGA@LB@ \|\|\|\| \|\|\|\|\|\|\|: :\|: \|\|\|\|\|@LB@ ACCG AAAUCAAU GCU CAACU@LB@3'-CGC...GUGCA AA CUUUG...AAG-5'@LB@ \| \|@LB@ 79 56@LB@@LB@@LB@Energy -6.75 kcal/mol@LB@Hybridization Energy -15.2709 kcal/mol@LB@Unfolding Energy - mRNA 7.30632 kcal/mol@LB@Unfolding Energy - sRNA 1.21856 kcal/mol@LB@@LB@Position - mRNA 259 -- 286@LB@Position - sRNA 57 -- 78@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 67 -- 73@LB@
130	0.02238	0.5385	b4365	yjjQ	-17.31	0.005324	260 -- 274	14 -- 28	putative transcriptional regulator	_____________259_____________275\n_____________\|_______________\|\n5'-AGG...CAAGC_______________CAUGA...AUG-3'\n______________AGGGUUAAAAGAGGU\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________UCCCAAUUUUCUCCA\n3'-CGC...GAAGU_______________CGGCG...AAG-5'\n_____________\|_______________\|\n_____________29______________13\n	268 -- 274	14 -- 20	-23.2971 kcal/mol	2.73817 kcal/mol	3.24497 kcal/mol	259 275@LB@ \| \|@LB@5'-AGG...CAAGC CAUGA...AUG-3'@LB@ AGGGUUAAAAGAGGU@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UCCCAAUUUUCUCCA@LB@3'-CGC...GAAGU CGGCG...AAG-5'@LB@ \| \|@LB@ 29 13@LB@@LB@@LB@Energy -17.31 kcal/mol@LB@Hybridization Energy -23.2971 kcal/mol@LB@Unfolding Energy - mRNA 2.73817 kcal/mol@LB@Unfolding Energy - sRNA 3.24497 kcal/mol@LB@@LB@Position - mRNA 260 -- 274@LB@Position - sRNA 14 -- 28@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 14 -- 20@LB@
152	0.02564	0.5485	b0887	cydD	-10.22	0.096853	263 -- 271	74 -- 82	glutathione/cysteine ABC transporter export permease/ATPase	_____________262_______272\n_____________\|_________\|\n5'-AUU...UCCCA_________GAAUA...UGA-3'\n______________ACGUUGGCU\n______________\|\|\|\|\|\|\|\|\|\n______________UGCAACCGA\n3'-CGC...UCAAG_________AAUCA...AAG-5'\n_____________\|_________\|\n_____________83________73\n	265 -- 271	74 -- 80	-15.056 kcal/mol	4.4924 kcal/mol	0.342466 kcal/mol	262 272@LB@ \| \|@LB@5'-AUU...UCCCA GAAUA...UGA-3'@LB@ ACGUUGGCU@LB@ \|\|\|\|\|\|\|\|\|@LB@ UGCAACCGA@LB@3'-CGC...UCAAG AAUCA...AAG-5'@LB@ \| \|@LB@ 83 73@LB@@LB@@LB@Energy -10.22 kcal/mol@LB@Hybridization Energy -15.056 kcal/mol@LB@Unfolding Energy - mRNA 4.4924 kcal/mol@LB@Unfolding Energy - sRNA 0.342466 kcal/mol@LB@@LB@Position - mRNA 263 -- 271@LB@Position - sRNA 74 -- 82@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 74 -- 80@LB@
133	0.02275	0.5385	b0177	bamA	-6.79	0.350358	265 -- 271	23 -- 29	BamABCDE complex OM biogenesis outer membrane pore-forming assembly factor	_____________264_____272\n_____________\|_______\|\n5'-CUG...UGCUG_______CGUAG...GCC-3'\n______________AAGGGUU\n______________\|\|\|\|\|\|\|\n______________UUCCCAA\n3'-CGC...UGAAG_______UUUUC...AAG-5'\n_____________\|_______\|\n_____________30______22\n	265 -- 271	23 -- 29	-7.93739 kcal/mol	1.09969 kcal/mol	0.0462613 kcal/mol	264 272@LB@ \| \|@LB@5'-CUG...UGCUG CGUAG...GCC-3'@LB@ AAGGGUU@LB@ \|\|\|\|\|\|\|@LB@ UUCCCAA@LB@3'-CGC...UGAAG UUUUC...AAG-5'@LB@ \| \|@LB@ 30 22@LB@@LB@@LB@Energy -6.79 kcal/mol@LB@Hybridization Energy -7.93739 kcal/mol@LB@Unfolding Energy - mRNA 1.09969 kcal/mol@LB@Unfolding Energy - sRNA 0.0462613 kcal/mol@LB@@LB@Position - mRNA 265 -- 271@LB@Position - sRNA 23 -- 29@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 23 -- 29@LB@
164	0.02889	0.5559	b1512	lsrR	-7.59	0.264791	265 -- 277	71 -- 84	lsr operon transcriptional repressor	_____________264____________278\n_____________\|______________\|\n5'-GCU...GCGGA______________CUAUC...AGA-3'\n______________UCGCG_UGGUUUUA\n______________\|\|:\|\|_\|\|\|:\|\|\|\|\n______________AGUGC_ACCGAAAU\n3'-CGC...UUUCA_____A________CAAUA...AAG-5'\n_____________\|______________\|\n_____________85_____________70\n	271 -- 277	71 -- 77	-14.8882 kcal/mol	6.73904 kcal/mol	0.5567 kcal/mol	264 278@LB@ \| \|@LB@5'-GCU...GCGGA CUAUC...AGA-3'@LB@ UCGCG UGGUUUUA@LB@ \|\|:\|\| \|\|\|:\|\|\|\|@LB@ AGUGC ACCGAAAU@LB@3'-CGC...UUUCA A CAAUA...AAG-5'@LB@ \| \|@LB@ 85 70@LB@@LB@@LB@Energy -7.59 kcal/mol@LB@Hybridization Energy -14.8882 kcal/mol@LB@Unfolding Energy - mRNA 6.73904 kcal/mol@LB@Unfolding Energy - sRNA 0.5567 kcal/mol@LB@@LB@Position - mRNA 265 -- 277@LB@Position - sRNA 71 -- 84@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 71 -- 77@LB@
165	0.02909	0.5559	b3283	yrdD	-9.69	0.119373	265 -- 285	52 -- 72	ssDNA-binding protein function unknown	_____________264___________________286\n_____________\|_____________________\|\n5'-AAC...UGAAC___________UCC_______ACGGU...UUG-3'\n______________UGGUUAUUCGA___GGGAAAC\n______________\|:\|\|\|\|\|\|\|\|\|___\|:\|\|\|\|\|\n______________AUCAAUAAGCU___CUCUUUG\n3'-CGC...CCGAA___________CAA_______AGAGC...AAG-5'\n_____________\|_____________________\|\n_____________73____________________51\n	279 -- 285	52 -- 58	-20.8466 kcal/mol	6.85358 kcal/mol	4.29991 kcal/mol	264 286@LB@ \| \|@LB@5'-AAC...UGAAC UCC ACGGU...UUG-3'@LB@ UGGUUAUUCGA GGGAAAC@LB@ \|:\|\|\|\|\|\|\|\|\| \|:\|\|\|\|\|@LB@ AUCAAUAAGCU CUCUUUG@LB@3'-CGC...CCGAA CAA AGAGC...AAG-5'@LB@ \| \|@LB@ 73 51@LB@@LB@@LB@Energy -9.69 kcal/mol@LB@Hybridization Energy -20.8466 kcal/mol@LB@Unfolding Energy - mRNA 6.85358 kcal/mol@LB@Unfolding Energy - sRNA 4.29991 kcal/mol@LB@@LB@Position - mRNA 265 -- 285@LB@Position - sRNA 52 -- 72@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 52 -- 58@LB@
92	0.01569	0.5385	b1246	oppD	-11.32	0.062179	266 -- 290	69 -- 90	oligopeptide ABC transporter ATPase	_____________265_______________________291\n_____________\|_________________________\|\n5'-AGC...AACGU_____A_______GUCAC_______ACCCC...ACG-3'\n______________GAAAG_UUUGCGU_____CUUUAGU\n______________:\|\|\|\|_\|\|::\|\|\|_____\|\|\|\|\|\|\|\n______________UUUUC_AAGUGCA_____GAAAUCA\n3'-CGC...AGGCG_____________ACC_________AUAAG...AAG-5'\n_____________\|_________________________\|\n_____________91________________________68\n	284 -- 290	69 -- 75	-14.6652 kcal/mol	2.76867 kcal/mol	0.572281 kcal/mol	265 291@LB@ \| \|@LB@5'-AGC...AACGU A GUCAC ACCCC...ACG-3'@LB@ GAAAG UUUGCGU CUUUAGU@LB@ :\|\|\|\| \|\|::\|\|\| \|\|\|\|\|\|\|@LB@ UUUUC AAGUGCA GAAAUCA@LB@3'-CGC...AGGCG ACC AUAAG...AAG-5'@LB@ \| \|@LB@ 91 68@LB@@LB@@LB@Energy -11.32 kcal/mol@LB@Hybridization Energy -14.6652 kcal/mol@LB@Unfolding Energy - mRNA 2.76867 kcal/mol@LB@Unfolding Energy - sRNA 0.572281 kcal/mol@LB@@LB@Position - mRNA 266 -- 290@LB@Position - sRNA 69 -- 90@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 69 -- 75@LB@
188	0.03339	0.5559	b3232	zapE	-6.91	0.336884	267 -- 282	15 -- 35	divisome ATPase	_____________266____________________283\n_____________\|______________________\|\n5'-AGG...CCGAC___G__________________CCGUC...AAA-3'\n______________GAC_UUCA______AAAAGAGG\n______________\|\|\|_\|\|\|\|______\|\|\|\|\|\|\|\|\n______________CUG_AAGU______UUUUCUCC\n3'-CGC...CGUCA________UCCCAA________ACGGC...AAG-5'\n_____________\|______________________\|\n_____________36_____________________14\n	276 -- 282	15 -- 21	-13.3674 kcal/mol	3.12995 kcal/mol	3.33058 kcal/mol	266 283@LB@ \| \|@LB@5'-AGG...CCGAC G CCGUC...AAA-3'@LB@ GAC UUCA AAAAGAGG@LB@ \|\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ CUG AAGU UUUUCUCC@LB@3'-CGC...CGUCA UCCCAA ACGGC...AAG-5'@LB@ \| \|@LB@ 36 14@LB@@LB@@LB@Energy -6.91 kcal/mol@LB@Hybridization Energy -13.3674 kcal/mol@LB@Unfolding Energy - mRNA 3.12995 kcal/mol@LB@Unfolding Energy - sRNA 3.33058 kcal/mol@LB@@LB@Position - mRNA 267 -- 282@LB@Position - sRNA 15 -- 35@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 15 -- 21@LB@
114	0.01931	0.5385	b1951	rcsA	-10.71	0.079523	269 -- 285	16 -- 29	transcriptional regulator of colanic acid capsular biosynthesis	_____________268_______________286\n_____________\|_________________\|\n5'-GUU...AGUAG__________AAA____AAAUC...UUG-3'\n______________AGGGGUUAAA___AGAG\n______________\|:\|\|\|\|\|\|\|\|___\|\|\|\|\n______________UUCCCAAUUU___UCUC\n3'-CGC...UGAAG_________________CACGG...AAG-5'\n_____________\|_________________\|\n_____________30________________15\n	272 -- 278	20 -- 26	-15.5636 kcal/mol	1.76121 kcal/mol	3.08831 kcal/mol	268 286@LB@ \| \|@LB@5'-GUU...AGUAG AAA AAAUC...UUG-3'@LB@ AGGGGUUAAA AGAG@LB@ \|:\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UUCCCAAUUU UCUC@LB@3'-CGC...UGAAG CACGG...AAG-5'@LB@ \| \|@LB@ 30 15@LB@@LB@@LB@Energy -10.71 kcal/mol@LB@Hybridization Energy -15.5636 kcal/mol@LB@Unfolding Energy - mRNA 1.76121 kcal/mol@LB@Unfolding Energy - sRNA 3.08831 kcal/mol@LB@@LB@Position - mRNA 269 -- 285@LB@Position - sRNA 16 -- 29@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 20 -- 26@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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