Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
55	0.002731	0.1727	b2480	bcp	-8.89	0.222722	156 -- 187	28 -- 56	peroxiredoxin; thiol peroxidase thioredoxin-dependent	_____________155_________________________________188\n_____________\|___________________________________\|\n5'-GAG...AUUAA______C_______CCCAAC_______________AUGGA...UUC-3'\n______________CGUCGU_AAUUAUU______AUGAUGA___ACAGG\n______________\|\|:\|\|\|_\|\|\|\|\|\|\|______\|\|\|\|\|\|\|___\|\|\|:\|\n______________GCGGCA_UUAAUAA______UACUACU___UGUUC\n3'-UUU...CCGAC______U____________________CAA_____CCGUG...GUG-5'\n_____________\|___________________________________\|\n_____________57__________________________________27\n	176 -- 182	36 -- 42	-21.7802 kcal/mol	6.3273 kcal/mol	6.56571 kcal/mol	155 188@LB@ \| \|@LB@5'-GAG...AUUAA C CCCAAC AUGGA...UUC-3'@LB@ CGUCGU AAUUAUU AUGAUGA ACAGG@LB@ \|\|:\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|:\|@LB@ GCGGCA UUAAUAA UACUACU UGUUC@LB@3'-UUU...CCGAC U CAA CCGUG...GUG-5'@LB@ \| \|@LB@ 57 27@LB@@LB@@LB@Energy -8.89 kcal/mol@LB@Hybridization Energy -21.7802 kcal/mol@LB@Unfolding Energy - mRNA 6.3273 kcal/mol@LB@Unfolding Energy - sRNA 6.56571 kcal/mol@LB@@LB@Position - mRNA 156 -- 187@LB@Position - sRNA 28 -- 56@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 36 -- 42@LB@
15	0.000767	0.1666	b2497	uraA	-16.56	0.007223	161 -- 232	28 -- 90	uracil permease	_____________160_________________________________________________________________________233\n_____________\|___________________________________________________________________________\|\n5'-AGC...UUUUU_____AA_____UAU_____AUAAUA___A___U___A__AU_AC________C_____CGG_______GA____ACCGC...UCC-3'\n______________GAGUA__GCGCC___AACAC______CAG_GGA_AAU_CU__G__GCGCCGUG___UAU___GGUGAGU___AAG\n______________\|\|:\|\|__\|\|\|\|\|___\|\|\|\|\|______\|\|\|_\|\|\|_\|\|\|_\|\|__\|__\|\|\|\|\|\|\|:___\|\|\|___\|:\|\|\|\|\|___\|\|\|\n______________CUUAU__CGCGG___UUGUG______GUC_CCU_UUA_GA__C__CGCGGCAU___AUA___CUACUCA___UUC\n3'-UUU...ACGCG_____GA_________________________________AC_GA________UUA___AUA_______AUG___CCGUG...GUG-5'\n_____________\|___________________________________________________________________________\|\n_____________91__________________________________________________________________________27\n	221 -- 227	34 -- 40	-48.784 kcal/mol	15.1604 kcal/mol	17.0677 kcal/mol	160 233@LB@ \| \|@LB@5'-AGC...UUUUU AA UAU AUAAUA A U A AU AC C CGG GA ACCGC...UCC-3'@LB@ GAGUA GCGCC AACAC CAG GGA AAU CU G GCGCCGUG UAU GGUGAGU AAG@LB@ \|\|:\|\| \|\|\|\|\| \|\|\|\|\| \|\|\| \|\|\| \|\|\| \|\| \| \|\|\|\|\|\|\|: \|\|\| \|:\|\|\|\|\| \|\|\|@LB@ CUUAU CGCGG UUGUG GUC CCU UUA GA C CGCGGCAU AUA CUACUCA UUC@LB@3'-UUU...ACGCG GA AC GA UUA AUA AUG CCGUG...GUG-5'@LB@ \| \|@LB@ 91 27@LB@@LB@@LB@Energy -16.56 kcal/mol@LB@Hybridization Energy -48.784 kcal/mol@LB@Unfolding Energy - mRNA 15.1604 kcal/mol@LB@Unfolding Energy - sRNA 17.0677 kcal/mol@LB@@LB@Position - mRNA 161 -- 232@LB@Position - sRNA 28 -- 90@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 34 -- 40@LB@
74	0.003792	0.1804	b2520	yfhM	-12.28	0.050623	263 -- 298	53 -- 91	bacterial alpha2-macroglobulin colonization factor ECAM; anti-host protease defense factor; periplasmic inner membrane-anchored lipoprotein	_____________262_____________________________________299\n_____________\|_______________________________________\|\n5'-CUC...AACAA___UA____________G___U____AAAGA________UU-3'\n______________CGA__AC_GCGCCAACA_CGG_GAAA_______UGCGCC\n______________\|\|\|__\|\|_\|\|\|\|\|\|\|\|\|_\|:\|_\|\|\|\|_______\|\|\|\|\|\|\n______________GCU__UG_CGCGGUUGU_GUC_CUUU_______ACGCGG\n3'-UUU...CACGC___UA__A_________G___C____AGAACCG______CAUUU...GUG-5'\n_____________\|_______________________________________\|\n_____________92______________________________________52\n	272 -- 278	75 -- 81	-39.9109 kcal/mol	10.9563 kcal/mol	16.677 kcal/mol	262 299@LB@ \| \|@LB@5'-CUC...AACAA UA G U AAAGA UU-3'@LB@ CGA AC GCGCCAACA CGG GAAA UGCGCC@LB@ \|\|\| \|\| \|\|\|\|\|\|\|\|\| \|:\| \|\|\|\| \|\|\|\|\|\|@LB@ GCU UG CGCGGUUGU GUC CUUU ACGCGG@LB@3'-UUU...CACGC UA A G C AGAACCG CAUUU...GUG-5'@LB@ \| \|@LB@ 92 52@LB@@LB@@LB@Energy -12.28 kcal/mol@LB@Hybridization Energy -39.9109 kcal/mol@LB@Unfolding Energy - mRNA 10.9563 kcal/mol@LB@Unfolding Energy - sRNA 16.677 kcal/mol@LB@@LB@Position - mRNA 263 -- 298@LB@Position - sRNA 53 -- 91@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 75 -- 81@LB@
21	0.001192	0.1727	b2526	hscA	-14.48	0.018641	235 -- 259	63 -- 88	DnaK-like molecular chaperone specific for IscU	_____________234________________________260\n_____________\|__________________________\|\n5'-AGC...UUUGA__________________C_UC____GGCGG...UGG-3'\n______________GUGCUGCGCC_GCAUCAG_G__GUCU\n______________:\|:\|\|\|\|\|\|\|_:\|\|:\|\|\|_\|__:\|\|\|\n______________UAUGACGCGG_UGUGGUC_C__UAGA\n3'-UUU...GCGCU__________U_______C_UU____ACCGA...GUG-5'\n_____________\|__________________________\|\n_____________89_________________________62\n	245 -- 251	71 -- 77	-31.0682 kcal/mol	9.20475 kcal/mol	7.38674 kcal/mol	234 260@LB@ \| \|@LB@5'-AGC...UUUGA C UC GGCGG...UGG-3'@LB@ GUGCUGCGCC GCAUCAG G GUCU@LB@ :\|:\|\|\|\|\|\|\| :\|\|:\|\|\| \| :\|\|\|@LB@ UAUGACGCGG UGUGGUC C UAGA@LB@3'-UUU...GCGCU U C UU ACCGA...GUG-5'@LB@ \| \|@LB@ 89 62@LB@@LB@@LB@Energy -14.48 kcal/mol@LB@Hybridization Energy -31.0682 kcal/mol@LB@Unfolding Energy - mRNA 9.20475 kcal/mol@LB@Unfolding Energy - sRNA 7.38674 kcal/mol@LB@@LB@Position - mRNA 235 -- 259@LB@Position - sRNA 63 -- 88@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 71 -- 77@LB@
124	0.006738	0.1913	b2533	suhB	-10.44	0.114821	158 -- 166	51 -- 59	inositol monophosphatase	_____________157_______167\n_____________\|_________\|\n5'-UUG...AUACU_________UUUCC...AGA-3'\n______________CUGCGCCGU\n______________\|\|\|\|\|\|\|\|\|\n______________GACGCGGCA\n3'-UUU...GAACC_________UUUAA...GUG-5'\n_____________\|_________\|\n_____________60________50\n	160 -- 166	51 -- 57	-17.2912 kcal/mol	2.02049 kcal/mol	4.83013 kcal/mol	157 167@LB@ \| \|@LB@5'-UUG...AUACU UUUCC...AGA-3'@LB@ CUGCGCCGU@LB@ \|\|\|\|\|\|\|\|\|@LB@ GACGCGGCA@LB@3'-UUU...GAACC UUUAA...GUG-5'@LB@ \| \|@LB@ 60 50@LB@@LB@@LB@Energy -10.44 kcal/mol@LB@Hybridization Energy -17.2912 kcal/mol@LB@Unfolding Energy - mRNA 2.02049 kcal/mol@LB@Unfolding Energy - sRNA 4.83013 kcal/mol@LB@@LB@Position - mRNA 158 -- 166@LB@Position - sRNA 51 -- 59@LB@Position Seed - mRNA 160 -- 166@LB@Position Seed - sRNA 51 -- 57@LB@
36	0.001988	0.1727	b2573	rpoE	-9.66	0.161217	247 -- 255	64 -- 72	RNA polymerase sigma E factor	_____________246_______256\n_____________\|_________\|\n5'-ACA...CCAGA_________AGAAA...UGG-3'\n______________AGGGAGAUC\n______________\|\|\|\|\|:\|\|\|\n______________UCCCUUUAG\n3'-UUU...UGUGG_________AACCG...GUG-5'\n_____________\|_________\|\n_____________73________63\n	249 -- 255	64 -- 70	-13.5601 kcal/mol	1.40253 kcal/mol	2.50058 kcal/mol	246 256@LB@ \| \|@LB@5'-ACA...CCAGA AGAAA...UGG-3'@LB@ AGGGAGAUC@LB@ \|\|\|\|\|:\|\|\|@LB@ UCCCUUUAG@LB@3'-UUU...UGUGG AACCG...GUG-5'@LB@ \| \|@LB@ 73 63@LB@@LB@@LB@Energy -9.66 kcal/mol@LB@Hybridization Energy -13.5601 kcal/mol@LB@Unfolding Energy - mRNA 1.40253 kcal/mol@LB@Unfolding Energy - sRNA 2.50058 kcal/mol@LB@@LB@Position - mRNA 247 -- 255@LB@Position - sRNA 64 -- 72@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 64 -- 70@LB@
64	0.003238	0.1727	b2578	eamB	-8.70	0.240388	240 -- 262	70 -- 85	cysteine and O-acetylserine exporter	_____________239_____________________263\n_____________\|_______________________\|\n5'-GUC...ACACC___AUUAC____AU_________ACCGA...CGC-3'\n______________CUG_____CGCU__GACGCCAGG\n______________\|\|\|_____\|\|\|:__:\|\|:\|\|\|\|\|\n______________GAC_____GCGG__UUGUGGUCC\n3'-UUU...CUUAU_______________________CUUUA...GUG-5'\n_____________\|_______________________\|\n_____________86______________________69\n	256 -- 262	70 -- 76	-20.6717 kcal/mol	4.69447 kcal/mol	7.27689 kcal/mol	239 263@LB@ \| \|@LB@5'-GUC...ACACC AUUAC AU ACCGA...CGC-3'@LB@ CUG CGCU GACGCCAGG@LB@ \|\|\| \|\|\|: :\|\|:\|\|\|\|\|@LB@ GAC GCGG UUGUGGUCC@LB@3'-UUU...CUUAU CUUUA...GUG-5'@LB@ \| \|@LB@ 86 69@LB@@LB@@LB@Energy -8.70 kcal/mol@LB@Hybridization Energy -20.6717 kcal/mol@LB@Unfolding Energy - mRNA 4.69447 kcal/mol@LB@Unfolding Energy - sRNA 7.27689 kcal/mol@LB@@LB@Position - mRNA 240 -- 262@LB@Position - sRNA 70 -- 85@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 70 -- 76@LB@
65	0.003263	0.1727	b2584	pka	-7.67	0.359085	49 -- 62	69 -- 82	protein lysine acetyltransferase	_____________48_____________63\n_____________\|______________\|\n5'-AGG...AUGGC__G___________CGGCG...GUA-3'\n______________CG_CGAUACCGGGG\n______________\|\|_\|:\|:\|\|\|:\|\|\|\n______________GC_GUUGUGGUCCC\n3'-UUU...AUGAC__G___________UUUAG...GUG-5'\n_____________\|______________\|\n_____________83_____________68\n	56 -- 62	69 -- 75	-21.7159 kcal/mol	7.18281 kcal/mol	6.85849 kcal/mol	48 63@LB@ \| \|@LB@5'-AGG...AUGGC G CGGCG...GUA-3'@LB@ CG CGAUACCGGGG@LB@ \|\| \|:\|:\|\|\|:\|\|\|@LB@ GC GUUGUGGUCCC@LB@3'-UUU...AUGAC G UUUAG...GUG-5'@LB@ \| \|@LB@ 83 68@LB@@LB@@LB@Energy -7.67 kcal/mol@LB@Hybridization Energy -21.7159 kcal/mol@LB@Unfolding Energy - mRNA 7.18281 kcal/mol@LB@Unfolding Energy - sRNA 6.85849 kcal/mol@LB@@LB@Position - mRNA 49 -- 62@LB@Position - sRNA 69 -- 82@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 69 -- 75@LB@
192	0.01187	0.2159	b2600	tyrA	-9.34	0.184498	136 -- 155	70 -- 86	fused chorismate mutase T/prephenate dehydrogenase	_____________135__________________156\n_____________\|____________________\|\n5'-UCG...GCCUU_______G__AUU_______AUCUG...UGG-3'\n______________GCUGCGU_AA___CAUCAGG\n______________:\|\|\|\|\|:_\|\|___\|\|:\|\|\|\|\n______________UGACGCG_UU___GUGGUCC\n3'-UUU...GCUUA_______G____________CUUUA...GUG-5'\n_____________\|____________________\|\n_____________87___________________69\n	149 -- 155	70 -- 76	-22.0981 kcal/mol	5.48162 kcal/mol	7.27772 kcal/mol	135 156@LB@ \| \|@LB@5'-UCG...GCCUU G AUU AUCUG...UGG-3'@LB@ GCUGCGU AA CAUCAGG@LB@ :\|\|\|\|\|: \|\| \|\|:\|\|\|\|@LB@ UGACGCG UU GUGGUCC@LB@3'-UUU...GCUUA G CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -22.0981 kcal/mol@LB@Unfolding Energy - mRNA 5.48162 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 136 -- 155@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 70 -- 76@LB@
154	0.009082	0.2059	b2676	nrdF	-13.94	0.023769	159 -- 176	53 -- 69	ribonucleoside-diphosphate reductase 2 beta subunit ferritin-like protein	_____________158________________177\n_____________\|__________________\|\n5'-AAG...GCACU______GAA_________UCCUG...CAG-3'\n______________GAAAUU___GGCUGCGUC\n______________\|\|\|\|\|:___\|\|\|\|\|\|\|:\|\n______________CUUUAG___CCGACGCGG\n3'-UUU...GGUCC______AA__________CAUUU...GUG-5'\n_____________\|__________________\|\n_____________70_________________52\n	170 -- 176	53 -- 59	-23.1658 kcal/mol	2.38862 kcal/mol	6.83371 kcal/mol	158 177@LB@ \| \|@LB@5'-AAG...GCACU GAA UCCUG...CAG-3'@LB@ GAAAUU GGCUGCGUC@LB@ \|\|\|\|\|: \|\|\|\|\|\|\|:\|@LB@ CUUUAG CCGACGCGG@LB@3'-UUU...GGUCC AA CAUUU...GUG-5'@LB@ \| \|@LB@ 70 52@LB@@LB@@LB@Energy -13.94 kcal/mol@LB@Hybridization Energy -23.1658 kcal/mol@LB@Unfolding Energy - mRNA 2.38862 kcal/mol@LB@Unfolding Energy - sRNA 6.83371 kcal/mol@LB@@LB@Position - mRNA 159 -- 176@LB@Position - sRNA 53 -- 69@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 53 -- 59@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