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	Additional homologs
84	0.004676	0.1855	b0526	cysS	-14.43	0.019007	256 -- 269	64 -- 77	cysteinyl-tRNA synthetase		_____________255____________270\n_____________\|______________\|\n5'-GCC...UAUUC______________GGCAU...ACG-3'\n______________ACGCCGGGGAAGUC\n______________\|\|:\|\|:\|\|\|\|\|:\|\|\n______________UGUGGUCCCUUUAG\n3'-UUU...GCGGU______________AACCG...GUG-5'\n_____________\|______________\|\n_____________78_____________63\n	263 -- 269	64 -- 70	-23.2043 kcal/mol	4.03864 kcal/mol	4.72709 kcal/mol	255 270@LB@ \| \|@LB@5'-GCC...UAUUC GGCAU...ACG-3'@LB@ ACGCCGGGGAAGUC@LB@ \|\|:\|\|:\|\|\|\|\|:\|\|@LB@ UGUGGUCCCUUUAG@LB@3'-UUU...GCGGU AACCG...GUG-5'@LB@ \| \|@LB@ 78 63@LB@@LB@@LB@Energy -14.43 kcal/mol@LB@Hybridization Energy -23.2043 kcal/mol@LB@Unfolding Energy - mRNA 4.03864 kcal/mol@LB@Unfolding Energy - sRNA 4.72709 kcal/mol@LB@@LB@Position - mRNA 256 -- 269@LB@Position - sRNA 64 -- 77@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 64 -- 70@LB@
49	0.00252	0.1727	b3452	ugpA	-14.40	0.019328	59 -- 78	52 -- 70	sn-glycerol-3-phosphate ABC transporter permease		_____________58___________________79\n_____________\|____________________\|\n5'-GAG...AGCGU_______AGUU_________CUUUG...CGG-3'\n______________GGAAAUC____GCUGCGCCG\n______________\|\|\|\|\|\|\|____\|\|\|\|\|\|\|\|\|\n______________CCUUUAG____CGACGCGGC\n3'-UUU...UGGUC_______AAC__________AUUUA...GUG-5'\n_____________\|____________________\|\n_____________71___________________51\n	72 -- 78	52 -- 58	-27.9409 kcal/mol	6.69662 kcal/mol	6.84683 kcal/mol	58 79@LB@ \| \|@LB@5'-GAG...AGCGU AGUU CUUUG...CGG-3'@LB@ GGAAAUC GCUGCGCCG@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ CCUUUAG CGACGCGGC@LB@3'-UUU...UGGUC AAC AUUUA...GUG-5'@LB@ \| \|@LB@ 71 51@LB@@LB@@LB@Energy -14.40 kcal/mol@LB@Hybridization Energy -27.9409 kcal/mol@LB@Unfolding Energy - mRNA 6.69662 kcal/mol@LB@Unfolding Energy - sRNA 6.84683 kcal/mol@LB@@LB@Position - mRNA 59 -- 78@LB@Position - sRNA 52 -- 70@LB@Position Seed - mRNA 72 -- 78@LB@Position Seed - sRNA 52 -- 58@LB@
54	0.002681	0.1727	b3201	lptB	-14.37	0.019597	275 -- 293	64 -- 82	lipopolysaccharide export ABC transporter ATPase		_____________274_________________294\n_____________\|___________________\|\n5'-UUC...CUGAC_______U___________GUCGGUC-3'\n______________CGUCAAC_CCGGGGAAAUU\n______________\|\|:\|\|\|\|_\|\|:\|\|\|\|\|\|\|:\n______________GCGGUUG_GGUCCCUUUAG\n3'-UUU...AUGAC_______U___________AACCG...GUG-5'\n_____________\|___________________\|\n_____________83__________________63\n	287 -- 293	64 -- 70	-27.6824 kcal/mol	6.24463 kcal/mol	7.07066 kcal/mol	274 294@LB@ \| \|@LB@5'-UUC...CUGAC U GUCGGUC-3'@LB@ CGUCAAC CCGGGGAAAUU@LB@ \|\|:\|\|\|\| \|\|:\|\|\|\|\|\|\|:@LB@ GCGGUUG GGUCCCUUUAG@LB@3'-UUU...AUGAC U AACCG...GUG-5'@LB@ \| \|@LB@ 83 63@LB@@LB@@LB@Energy -14.37 kcal/mol@LB@Hybridization Energy -27.6824 kcal/mol@LB@Unfolding Energy - mRNA 6.24463 kcal/mol@LB@Unfolding Energy - sRNA 7.07066 kcal/mol@LB@@LB@Position - mRNA 275 -- 293@LB@Position - sRNA 64 -- 82@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 64 -- 70@LB@
77	0.00398	0.182	b2411	ligA	-14.36	0.019662	79 -- 95	70 -- 86	DNA ligase NAD(+)-dependent		_____________78________________96\n_____________\|_________________\|\n5'-GCA...CAGAA_______G_________ACAUC...CUG-3'\n______________AUUGCGC_AGUACCAGG\n______________\|:\|\|\|\|\|_\|::\|\|\|\|\|\|\n______________UGACGCG_UUGUGGUCC\n3'-UUU...GCUUA_______G_________CUUUA...GUG-5'\n_____________\|_________________\|\n_____________87________________69\n	89 -- 95	70 -- 76	-25.4632 kcal/mol	3.82569 kcal/mol	7.27772 kcal/mol	78 96@LB@ \| \|@LB@5'-GCA...CAGAA G ACAUC...CUG-3'@LB@ AUUGCGC AGUACCAGG@LB@ \|:\|\|\|\|\| \|::\|\|\|\|\|\|@LB@ UGACGCG UUGUGGUCC@LB@3'-UUU...GCUUA G CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -14.36 kcal/mol@LB@Hybridization Energy -25.4632 kcal/mol@LB@Unfolding Energy - mRNA 3.82569 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 79 -- 95@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 70 -- 76@LB@
120	0.006631	0.1913	b0825	fsaA	-14.24	0.020734	15 -- 76	31 -- 86	fructose-6-phosphate aldolase 1	b3946	_____________14_____________________________________________________________77\n_____________\|______________________________________________________________\|\n5'-CUU...AUACG__C____G__________CC___A___G_CGAGUA______AAU____AAAAUCAU______CUCUC...CCG-3'\n______________AC_GUGC_GAUACCGGGG__AUC_UGG_U______GCGCUG___AUUG________AGUUGC\n______________\|\|_\|:\|\|_:\|:\|\|\|:\|\|\|__\|\|\|_\|\|\|_\|______\|\|\|\|:\|___\|\|\|:________\|\|\|\|:\|\n______________UG_CGCG_UUGUGGUCCC__UAG_ACC_A______CGCGGC___UAAU________UCAAUG\n3'-UUU...GCUUA__A____G__________UU___A___G_____________AUU____AAUACUAC______UUCCC...GUG-5'\n_____________\|______________________________________________________________\|\n_____________87_____________________________________________________________30\n	26 -- 32	69 -- 75	-46.4097 kcal/mol	15.1018 kcal/mol	17.0646 kcal/mol	14 77@LB@ \| \|@LB@5'-CUU...AUACG C G CC A G CGAGUA AAU AAAAUCAU CUCUC...CCG-3'@LB@ AC GUGC GAUACCGGGG AUC UGG U GCGCUG AUUG AGUUGC@LB@ \|\| \|:\|\| :\|:\|\|\|:\|\|\| \|\|\| \|\|\| \| \|\|\|\|:\| \|\|\|: \|\|\|\|:\|@LB@ UG CGCG UUGUGGUCCC UAG ACC A CGCGGC UAAU UCAAUG@LB@3'-UUU...GCUUA A G UU A G AUU AAUACUAC UUCCC...GUG-5'@LB@ \| \|@LB@ 87 30@LB@@LB@@LB@Energy -14.24 kcal/mol@LB@Hybridization Energy -46.4097 kcal/mol@LB@Unfolding Energy - mRNA 15.1018 kcal/mol@LB@Unfolding Energy - sRNA 17.0646 kcal/mol@LB@@LB@Position - mRNA 15 -- 76@LB@Position - sRNA 31 -- 86@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 69 -- 75@LB@
22	0.001393	0.1727	b0794	ybhF	-14.07	0.022426	148 -- 164	67 -- 84	putative ABC transporter ATPase		_____________147________________165\n_____________\|__________________\|\n5'-UAC...GAUGA__________________UGCCA...GUU-3'\n______________UGCGUU_ACGCCAGGGAA\n______________\|\|\|\|::_\|\|:\|\|\|\|\|\|\|\|\n______________ACGCGG_UGUGGUCCCUU\n3'-UUU...UUAUG______U___________UAGAA...GUG-5'\n_____________\|__________________\|\n_____________85_________________66\n	158 -- 164	67 -- 73	-27.705 kcal/mol	6.27905 kcal/mol	7.35473 kcal/mol	147 165@LB@ \| \|@LB@5'-UAC...GAUGA UGCCA...GUU-3'@LB@ UGCGUU ACGCCAGGGAA@LB@ \|\|\|\|:: \|\|:\|\|\|\|\|\|\|\|@LB@ ACGCGG UGUGGUCCCUU@LB@3'-UUU...UUAUG U UAGAA...GUG-5'@LB@ \| \|@LB@ 85 66@LB@@LB@@LB@Energy -14.07 kcal/mol@LB@Hybridization Energy -27.705 kcal/mol@LB@Unfolding Energy - mRNA 6.27905 kcal/mol@LB@Unfolding Energy - sRNA 7.35473 kcal/mol@LB@@LB@Position - mRNA 148 -- 164@LB@Position - sRNA 67 -- 84@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 67 -- 73@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@
196	0.01202	0.2159	b1729	ydjN	-13.87	0.024594	143 -- 155	72 -- 84	putative transporter		_____________142___________156\n_____________\|_____________\|\n5'-CAU...AAUCU_____________UGACU...UGC-3'\n______________UGCGCCAACACUA\n______________\|\|\|\|\|\|\|\|\|\|\|:\|\n______________ACGCGGUUGUGGU\n3'-UUU...UUAUG_____________CCCUU...GUG-5'\n_____________\|_____________\|\n_____________85____________71\n	149 -- 155	72 -- 78	-23.7045 kcal/mol	2.6326 kcal/mol	7.20328 kcal/mol	142 156@LB@ \| \|@LB@5'-CAU...AAUCU UGACU...UGC-3'@LB@ UGCGCCAACACUA@LB@ \|\|\|\|\|\|\|\|\|\|\|:\|@LB@ ACGCGGUUGUGGU@LB@3'-UUU...UUAUG CCCUU...GUG-5'@LB@ \| \|@LB@ 85 71@LB@@LB@@LB@Energy -13.87 kcal/mol@LB@Hybridization Energy -23.7045 kcal/mol@LB@Unfolding Energy - mRNA 2.6326 kcal/mol@LB@Unfolding Energy - sRNA 7.20328 kcal/mol@LB@@LB@Position - mRNA 143 -- 155@LB@Position - sRNA 72 -- 84@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 72 -- 78@LB@
156	0.009123	0.2059	b2683	ygaH	-13.79	0.025463	164 -- 213	27 -- 86	putative L-valine exporter norvaline resistance protein		_____________163______________________________________________________________214\n_____________\|________________________________________________________________\|\n5'-AUU...GCCUC_________________CAU________AAGGA_____C_________________C_______UUCUG...CAA-3'\n______________ACUGCGUUAAU_CCAGG____UC_UGGC_____GCGCC____________GAUGAG_UAUGAGG\n______________\|\|\|\|\|\|::\|\|:_\|\|\|\|\|____\|\|_\|\|\|\|_____\|\|\|\|\|____________\|\|\|\|\|\|_\|\|::\|\|\|\n______________UGACGCGGUUG_GGUCC____AG_ACCG_____CGCGG____________CUACUC_AUGUUCC\n3'-UUU...GCUUA___________U_____CUUU__A____A_________CAUUUAAUAAUA______A_______CGUGU...GUG-5'\n_____________\|________________________________________________________________\|\n_____________87_______________________________________________________________26\n	207 -- 213	27 -- 33	-50.2075 kcal/mol	19.3484 kcal/mol	17.0667 kcal/mol	163 214@LB@ \| \|@LB@5'-AUU...GCCUC CAU AAGGA C C UUCUG...CAA-3'@LB@ ACUGCGUUAAU CCAGG UC UGGC GCGCC GAUGAG UAUGAGG@LB@ \|\|\|\|\|\|::\|\|: \|\|\|\|\| \|\| \|\|\|\| \|\|\|\|\| \|\|\|\|\|\| \|\|::\|\|\|@LB@ UGACGCGGUUG GGUCC AG ACCG CGCGG CUACUC AUGUUCC@LB@3'-UUU...GCUUA U CUUU A A CAUUUAAUAAUA A CGUGU...GUG-5'@LB@ \| \|@LB@ 87 26@LB@@LB@@LB@Energy -13.79 kcal/mol@LB@Hybridization Energy -50.2075 kcal/mol@LB@Unfolding Energy - mRNA 19.3484 kcal/mol@LB@Unfolding Energy - sRNA 17.0667 kcal/mol@LB@@LB@Position - mRNA 164 -- 213@LB@Position - sRNA 27 -- 86@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 27 -- 33@LB@
32	0.001707	0.1727	b3606	trmL	-13.76	0.025837	263 -- 277	71 -- 85	tRNA Leu mC34 mU34 2'-O-methyltransferase SAM-dependent		_____________262_____________278\n_____________\|_______________\|\n5'-UAG...CGUCU_______________CUUUC...AAC-3'\n______________UUGCGCUAAUACCGG\n______________:\|\|\|\|\|:\|\|:\|\|\|:\|\n______________GACGCGGUUGUGGUC\n3'-UUU...CUUAU_______________CCUUU...GUG-5'\n_____________\|_______________\|\n_____________86______________70\n	271 -- 277	71 -- 77	-23.7581 kcal/mol	2.7368 kcal/mol	7.26103 kcal/mol	262 278@LB@ \| \|@LB@5'-UAG...CGUCU CUUUC...AAC-3'@LB@ UUGCGCUAAUACCGG@LB@ :\|\|\|\|\|:\|\|:\|\|\|:\|@LB@ GACGCGGUUGUGGUC@LB@3'-UUU...CUUAU CCUUU...GUG-5'@LB@ \| \|@LB@ 86 70@LB@@LB@@LB@Energy -13.76 kcal/mol@LB@Hybridization Energy -23.7581 kcal/mol@LB@Unfolding Energy - mRNA 2.7368 kcal/mol@LB@Unfolding Energy - sRNA 7.26103 kcal/mol@LB@@LB@Position - mRNA 263 -- 277@LB@Position - sRNA 71 -- 85@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 71 -- 77@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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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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