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
118	0.006444	0.1913	b0189	rof	-9.63	0.163299	226 -- 241	29 -- 45	modulator of Rho-dependent transcription termination	_____________225_______________242\n_____________\|_________________\|\n5'-AGG...AAUCA_________________UAAUC...GCG-3'\n______________AUUGUGAUGA_UUACGA\n______________\|\|\|:\|\|\|\|\|\|_\|\|\|\|:\|\n______________UAAUACUACU_AAUGUU\n3'-UUU...UUUAA__________C______CCCGU...GUG-5'\n_____________\|_________________\|\n_____________46________________28\n	229 -- 235	36 -- 42	-15.4032 kcal/mol	3.82623 kcal/mol	1.94966 kcal/mol	225 242@LB@ \| \|@LB@5'-AGG...AAUCA UAAUC...GCG-3'@LB@ AUUGUGAUGA UUACGA@LB@ \|\|\|:\|\|\|\|\|\| \|\|\|\|:\|@LB@ UAAUACUACU AAUGUU@LB@3'-UUU...UUUAA C CCCGU...GUG-5'@LB@ \| \|@LB@ 46 28@LB@@LB@@LB@Energy -9.63 kcal/mol@LB@Hybridization Energy -15.4032 kcal/mol@LB@Unfolding Energy - mRNA 3.82623 kcal/mol@LB@Unfolding Energy - sRNA 1.94966 kcal/mol@LB@@LB@Position - mRNA 226 -- 241@LB@Position - sRNA 29 -- 45@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 36 -- 42@LB@
9	0.0003241	0.1198	b1110	ycfJ	-9.50	0.172514	224 -- 251	52 -- 76	uncharacterized protein	_____________223__________________________252\n_____________\|____________________________\|\n5'-ACU...GCGGG_______AUU__U___GCA_________GGCGU...AAU-3'\n______________UAUCGGG___GG_GUC___GCUGCGCUG\n______________:\|:\|:\|\|___\|:_:\|\|___\|\|\|\|\|\|\|:\|\n______________GUGGUCC___CU_UAG___CGACGCGGC\n3'-UUU...CGGUU____________U___AAC_________AUUUA...GUG-5'\n_____________\|____________________________\|\n_____________77___________________________51\n	245 -- 251	52 -- 58	-26.6822 kcal/mol	7.91875 kcal/mol	9.26585 kcal/mol	223 252@LB@ \| \|@LB@5'-ACU...GCGGG AUU U GCA GGCGU...AAU-3'@LB@ UAUCGGG GG GUC GCUGCGCUG@LB@ :\|:\|:\|\| \|: :\|\| \|\|\|\|\|\|\|:\|@LB@ GUGGUCC CU UAG CGACGCGGC@LB@3'-UUU...CGGUU U AAC AUUUA...GUG-5'@LB@ \| \|@LB@ 77 51@LB@@LB@@LB@Energy -9.50 kcal/mol@LB@Hybridization Energy -26.6822 kcal/mol@LB@Unfolding Energy - mRNA 7.91875 kcal/mol@LB@Unfolding Energy - sRNA 9.26585 kcal/mol@LB@@LB@Position - mRNA 224 -- 251@LB@Position - sRNA 52 -- 76@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 52 -- 58@LB@
131	0.007315	0.1966	b3824	rhtB	-9.48	0.174149	77 -- 100	63 -- 87	homoserine homoserine lactone and S-methyl-methionine efflux pump	_____________76________________________101\n_____________\|_________________________\|\n5'-ACG...CUUUU______UGA_________U______GCCUC...ACC-3'\n______________UGCUGC___AACAUCGGG__AAUCU\n______________\|:\|\|\|\|___\|\|\|\|:\|:\|\|__\|\|\|\|\|\n______________AUGACG___UUGUGGUCC__UUAGA\n3'-UUU...CGCUU______CGG_________CU_____ACCGA...GUG-5'\n_____________\|_________________________\|\n_____________88________________________62\n	88 -- 94	70 -- 76	-24.9255 kcal/mol	8.06413 kcal/mol	7.38606 kcal/mol	76 101@LB@ \| \|@LB@5'-ACG...CUUUU UGA U GCCUC...ACC-3'@LB@ UGCUGC AACAUCGGG AAUCU@LB@ \|:\|\|\|\| \|\|\|\|:\|:\|\| \|\|\|\|\|@LB@ AUGACG UUGUGGUCC UUAGA@LB@3'-UUU...CGCUU CGG CU ACCGA...GUG-5'@LB@ \| \|@LB@ 88 62@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -24.9255 kcal/mol@LB@Unfolding Energy - mRNA 8.06413 kcal/mol@LB@Unfolding Energy - sRNA 7.38606 kcal/mol@LB@@LB@Position - mRNA 77 -- 100@LB@Position - sRNA 63 -- 87@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 70 -- 76@LB@
182	0.01083	0.2089	b0314	betT	-9.44	0.176432	217 -- 228	66 -- 77	choline transporter of high affinity	_____________216__________229\n_____________\|____________\|\n5'-UUC...UUCAC___G________AGGAC...UCC-3'\n______________ACA_CAGGGAAA\n______________\|\|\|_\|\|\|\|\|\|\|\|\n______________UGU_GUCCCUUU\n3'-UUU...GCGGU___G________AGAAC...GUG-5'\n_____________\|____________\|\n_____________78___________65\n	222 -- 228	66 -- 72	-15.8835 kcal/mol	1.82432 kcal/mol	4.61119 kcal/mol	216 229@LB@ \| \|@LB@5'-UUC...UUCAC G AGGAC...UCC-3'@LB@ ACA CAGGGAAA@LB@ \|\|\| \|\|\|\|\|\|\|\|@LB@ UGU GUCCCUUU@LB@3'-UUU...GCGGU G AGAAC...GUG-5'@LB@ \| \|@LB@ 78 65@LB@@LB@@LB@Energy -9.44 kcal/mol@LB@Hybridization Energy -15.8835 kcal/mol@LB@Unfolding Energy - mRNA 1.82432 kcal/mol@LB@Unfolding Energy - sRNA 4.61119 kcal/mol@LB@@LB@Position - mRNA 217 -- 228@LB@Position - sRNA 66 -- 77@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 66 -- 72@LB@
151	0.008943	0.2059	b1284	yciT	-9.40	0.179701	94 -- 109	63 -- 77	global regulator of transcription; DeoR family	_____________93_______________110\n_____________\|________________\|\n5'-GCA...CGAAG______U_________AACAA...CCA-3'\n______________GCACCG_GGGAGAUUU\n______________:\|\|\|\|:_\|\|\|\|:\|\|:\|\n______________UGUGGU_CCCUUUAGA\n3'-UUU...GCGGU________________ACCGA...GUG-5'\n_____________\|________________\|\n_____________78_______________62\n	103 -- 109	63 -- 69	-19.5221 kcal/mol	5.38652 kcal/mol	4.72953 kcal/mol	93 110@LB@ \| \|@LB@5'-GCA...CGAAG U AACAA...CCA-3'@LB@ GCACCG GGGAGAUUU@LB@ :\|\|\|\|: \|\|\|\|:\|\|:\|@LB@ UGUGGU CCCUUUAGA@LB@3'-UUU...GCGGU ACCGA...GUG-5'@LB@ \| \|@LB@ 78 62@LB@@LB@@LB@Energy -9.40 kcal/mol@LB@Hybridization Energy -19.5221 kcal/mol@LB@Unfolding Energy - mRNA 5.38652 kcal/mol@LB@Unfolding Energy - sRNA 4.72953 kcal/mol@LB@@LB@Position - mRNA 94 -- 109@LB@Position - sRNA 63 -- 77@LB@Position Seed - mRNA 103 -- 109@LB@Position Seed - sRNA 63 -- 69@LB@
99	0.005465	0.1855	b0767	pgl	-9.37	0.182441	275 -- 291	70 -- 86	6-phosphogluconolactonase	_____________274________________292\n_____________\|__________________\|\n5'-UCA...GGCGC____A_____________UUGUC...AUG-3'\n______________ACUG_CGCUGACA_CAGG\n______________\|\|\|\|_\|\|\|::\|\|\|_\|\|\|\|\n______________UGAC_GCGGUUGU_GUCC\n3'-UUU...GCUUA_____________G____CUUUA...GUG-5'\n_____________\|__________________\|\n_____________87_________________69\n	281 -- 287	75 -- 81	-21.4952 kcal/mol	4.85205 kcal/mol	7.27772 kcal/mol	274 292@LB@ \| \|@LB@5'-UCA...GGCGC A UUGUC...AUG-3'@LB@ ACUG CGCUGACA CAGG@LB@ \|\|\|\| \|\|\|::\|\|\| \|\|\|\|@LB@ UGAC GCGGUUGU GUCC@LB@3'-UUU...GCUUA G CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -9.37 kcal/mol@LB@Hybridization Energy -21.4952 kcal/mol@LB@Unfolding Energy - mRNA 4.85205 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 275 -- 291@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 75 -- 81@LB@
3	3.071e-06	0.003055	b2100	yegV	-9.35	0.183884	5 -- 14	51 -- 60	putative kinase	_____________4__________15\n_____________\|__________\|\n_______5'-AAUC__________CCUGU...CUU-3'\n______________GCUGCGCCGU\n______________\|\|\|\|\|\|\|\|\|\|\n______________CGACGCGGCA\n3'-UUU...AGAAC__________UUUAA...GUG-5'\n_____________\|__________\|\n_____________61_________50\n	8 -- 14	51 -- 57	-21.1769 kcal/mol	6.95722 kcal/mol	4.87294 kcal/mol	4 15@LB@ \| \|@LB@ 5'-AAUC CCUGU...CUU-3'@LB@ GCUGCGCCGU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CGACGCGGCA@LB@3'-UUU...AGAAC UUUAA...GUG-5'@LB@ \| \|@LB@ 61 50@LB@@LB@@LB@Energy -9.35 kcal/mol@LB@Hybridization Energy -21.1769 kcal/mol@LB@Unfolding Energy - mRNA 6.95722 kcal/mol@LB@Unfolding Energy - sRNA 4.87294 kcal/mol@LB@@LB@Position - mRNA 5 -- 14@LB@Position - sRNA 51 -- 60@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 51 -- 57@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@
88	0.004799	0.1855	b2213	ada	-9.32	0.185618	222 -- 245	63 -- 86	fused DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase	_____________221________________________246\n_____________\|__________________________\|\n5'-GGA...GCUUA____A__A__________C_______GUCUU...CCA-3'\n______________ACUG_CG_UCAACGCUGG___AAUCU\n______________\|\|\|\|_\|\|_:\|\|\|\|:\|::\|___\|\|\|\|\|\n______________UGAC_GC_GGUUGUGGUC___UUAGA\n3'-UUU...GCUUA__________________CCU_____ACCGA...GUG-5'\n_____________\|__________________________\|\n_____________87_________________________62\n	233 -- 239	71 -- 77	-21.7615 kcal/mol	5.05104 kcal/mol	7.38602 kcal/mol	221 246@LB@ \| \|@LB@5'-GGA...GCUUA A A C GUCUU...CCA-3'@LB@ ACUG CG UCAACGCUGG AAUCU@LB@ \|\|\|\| \|\| :\|\|\|\|:\|::\| \|\|\|\|\|@LB@ UGAC GC GGUUGUGGUC UUAGA@LB@3'-UUU...GCUUA CCU ACCGA...GUG-5'@LB@ \| \|@LB@ 87 62@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -21.7615 kcal/mol@LB@Unfolding Energy - mRNA 5.05104 kcal/mol@LB@Unfolding Energy - sRNA 7.38602 kcal/mol@LB@@LB@Position - mRNA 222 -- 245@LB@Position - sRNA 63 -- 86@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 71 -- 77@LB@
128	0.007127	0.1961	b0696	kdpC	-9.30	0.187437	90 -- 106	44 -- 60	potassium translocating ATPase subunit C	_____________89________________107\n_____________\|_________________\|\n5'-GCG...GCCAU____________C____GGAUU...GGU-3'\n______________GUUGCGCCGUAA_UUAU\n______________\|:\|\|\|\|\|\|\|\|\|\|_\|\|\|\|\n______________CGACGCGGCAUU_AAUA\n3'-UUU...AGAAC____________U____AUACU...GUG-5'\n_____________\|_________________\|\n_____________61________________43\n	95 -- 101	49 -- 55	-22.6138 kcal/mol	6.57247 kcal/mol	6.74006 kcal/mol	89 107@LB@ \| \|@LB@5'-GCG...GCCAU C GGAUU...GGU-3'@LB@ GUUGCGCCGUAA UUAU@LB@ \|:\|\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ CGACGCGGCAUU AAUA@LB@3'-UUU...AGAAC U AUACU...GUG-5'@LB@ \| \|@LB@ 61 43@LB@@LB@@LB@Energy -9.30 kcal/mol@LB@Hybridization Energy -22.6138 kcal/mol@LB@Unfolding Energy - mRNA 6.57247 kcal/mol@LB@Unfolding Energy - sRNA 6.74006 kcal/mol@LB@@LB@Position - mRNA 90 -- 106@LB@Position - sRNA 44 -- 60@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 49 -- 55@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)

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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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