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@
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@
173	0.01023	0.2071	b3297	rpsK	-11.54	0.070538	32 -- 43	48 -- 59	30S ribosomal subunit protein S11	_____________31___________44\n_____________\|____________\|\n5'-CGA...GUGAU____________AUCAG...CUA-3'\n______________CUGCGCCGUGAA\n______________\|\|\|\|\|\|\|\|\|:\|\|\n______________GACGCGGCAUUU\n3'-UUU...GAACC____________AAUAA...GUG-5'\n_____________\|____________\|\n_____________60___________47\n	37 -- 43	48 -- 54	-20.6796 kcal/mol	2.9935 kcal/mol	6.14631 kcal/mol	31 44@LB@ \| \|@LB@5'-CGA...GUGAU AUCAG...CUA-3'@LB@ CUGCGCCGUGAA@LB@ \|\|\|\|\|\|\|\|\|:\|\|@LB@ GACGCGGCAUUU@LB@3'-UUU...GAACC AAUAA...GUG-5'@LB@ \| \|@LB@ 60 47@LB@@LB@@LB@Energy -11.54 kcal/mol@LB@Hybridization Energy -20.6796 kcal/mol@LB@Unfolding Energy - mRNA 2.9935 kcal/mol@LB@Unfolding Energy - sRNA 6.14631 kcal/mol@LB@@LB@Position - mRNA 32 -- 43@LB@Position - sRNA 48 -- 59@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 48 -- 54@LB@
33	0.001709	0.1727	b0023	rpsT	-12.95	0.037339	65 -- 78	72 -- 85	30S ribosomal subunit protein S20	_____________64_____________79\n_____________\|______________\|\n5'-UGA...GAAUC________U_____CGUAA...AGA-3'\n______________CUGCGCCA_CACUA\n______________\|\|\|\|\|\|\|\|_\|\|\|:\|\n______________GACGCGGU_GUGGU\n3'-UUU...CUUAU________U_____CCCUU...GUG-5'\n_____________\|______________\|\n_____________86_____________71\n	66 -- 72	78 -- 84	-22.3173 kcal/mol	2.13275 kcal/mol	7.23443 kcal/mol	64 79@LB@ \| \|@LB@5'-UGA...GAAUC U CGUAA...AGA-3'@LB@ CUGCGCCA CACUA@LB@ \|\|\|\|\|\|\|\| \|\|\|:\|@LB@ GACGCGGU GUGGU@LB@3'-UUU...CUUAU U CCCUU...GUG-5'@LB@ \| \|@LB@ 86 71@LB@@LB@@LB@Energy -12.95 kcal/mol@LB@Hybridization Energy -22.3173 kcal/mol@LB@Unfolding Energy - mRNA 2.13275 kcal/mol@LB@Unfolding Energy - sRNA 7.23443 kcal/mol@LB@@LB@Position - mRNA 65 -- 78@LB@Position - sRNA 72 -- 85@LB@Position Seed - mRNA 66 -- 72@LB@Position Seed - sRNA 78 -- 84@LB@
29	0.001588	0.1727	b4371	rsmC	-11.43	0.073969	145 -- 160	74 -- 89	16S rRNA m(2)G1207 methyltransferase SAM-dependent	_____________144______________161\n_____________\|________________\|\n5'-AUC...UCGUC_____C__________AUGGC...UGC-3'\n______________GAUAC_GCGCCAACAU\n______________:\|\|\|\|_\|\|\|\|\|\|\|\|\|:\n______________UUAUG_CGCGGUUGUG\n3'-UUU...CGCGC_____A__________GUCCC...GUG-5'\n_____________\|________________\|\n_____________90_______________73\n	154 -- 160	74 -- 80	-22.1753 kcal/mol	3.46317 kcal/mol	7.27848 kcal/mol	144 161@LB@ \| \|@LB@5'-AUC...UCGUC C AUGGC...UGC-3'@LB@ GAUAC GCGCCAACAU@LB@ :\|\|\|\| \|\|\|\|\|\|\|\|\|:@LB@ UUAUG CGCGGUUGUG@LB@3'-UUU...CGCGC A GUCCC...GUG-5'@LB@ \| \|@LB@ 90 73@LB@@LB@@LB@Energy -11.43 kcal/mol@LB@Hybridization Energy -22.1753 kcal/mol@LB@Unfolding Energy - mRNA 3.46317 kcal/mol@LB@Unfolding Energy - sRNA 7.27848 kcal/mol@LB@@LB@Position - mRNA 145 -- 160@LB@Position - sRNA 74 -- 89@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 74 -- 80@LB@
42	0.002147	0.1727	b0082	rsmH	-13.18	0.033634	23 -- 49	70 -- 94	16S rRNA m(4)C1402 methyltransferase SAM-dependent	_____________22__________________________50\n_____________\|___________________________\|\n5'-UGG...UAAUC____C_________G____AU______CUGAC...GUC-3'\n______________GCGC_AGUACUGCG_CAAC__GCCGGG\n______________\|\|\|\|_\|:\|\|\|\|\|\|\|_\|\|\|\|__:\|\|:\|\|\n______________CGCG_UUAUGACGC_GUUG__UGGUCC\n3'-UUU...CCCCA____C_________G____________CUUUA...GUG-5'\n_____________\|___________________________\|\n_____________95__________________________69\n	30 -- 36	81 -- 87	-36.7334 kcal/mol	10.4772 kcal/mol	13.036 kcal/mol	22 50@LB@ \| \|@LB@5'-UGG...UAAUC C G AU CUGAC...GUC-3'@LB@ GCGC AGUACUGCG CAAC GCCGGG@LB@ \|\|\|\| \|:\|\|\|\|\|\|\| \|\|\|\| :\|\|:\|\|@LB@ CGCG UUAUGACGC GUUG UGGUCC@LB@3'-UUU...CCCCA C G CUUUA...GUG-5'@LB@ \| \|@LB@ 95 69@LB@@LB@@LB@Energy -13.18 kcal/mol@LB@Hybridization Energy -36.7334 kcal/mol@LB@Unfolding Energy - mRNA 10.4772 kcal/mol@LB@Unfolding Energy - sRNA 13.036 kcal/mol@LB@@LB@Position - mRNA 23 -- 49@LB@Position - sRNA 70 -- 94@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 81 -- 87@LB@
23	0.001421	0.1727	b1234	rssA	-12.55	0.044848	179 -- 192	61 -- 74	putative patatin-like family phospholipase	_____________178____________193\n_____________\|______________\|\n5'-GAU...GCAUU______________CGGGA...AAA-3'\n______________CCAGGGGAAUCUUG\n______________\|\|\|\|\|\|:\|\|\|\|\|\|\|\n______________GGUCCCUUUAGAAC\n3'-UUU...GUUGU______________CGACG...GUG-5'\n_____________\|______________\|\n_____________75_____________60\n	186 -- 192	61 -- 67	-22.3239 kcal/mol	6.14875 kcal/mol	3.62869 kcal/mol	178 193@LB@ \| \|@LB@5'-GAU...GCAUU CGGGA...AAA-3'@LB@ CCAGGGGAAUCUUG@LB@ \|\|\|\|\|\|:\|\|\|\|\|\|\|@LB@ GGUCCCUUUAGAAC@LB@3'-UUU...GUUGU CGACG...GUG-5'@LB@ \| \|@LB@ 75 60@LB@@LB@@LB@Energy -12.55 kcal/mol@LB@Hybridization Energy -22.3239 kcal/mol@LB@Unfolding Energy - mRNA 6.14875 kcal/mol@LB@Unfolding Energy - sRNA 3.62869 kcal/mol@LB@@LB@Position - mRNA 179 -- 192@LB@Position - sRNA 61 -- 74@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 61 -- 67@LB@
67	0.003373	0.1727	b0723	sdhA	-10.29	0.122560	175 -- 204	36 -- 70	succinate dehydrogenase flavoprotein subunit	_____________174_________________________________205\n_____________\|___________________________________\|\n5'-GGU...UUUAU___U____________G______GUG_________AAUUG...GUG-3'\n______________GGA__UC___GUUGUG_UGUGGG____UGUGAUGA\n______________\|\|\|__\|\|___\|:\|\|:\|_:\|\|:::____\|:\|\|\|\|\|\|\n______________CCU__AG___CGACGC_GCAUUU____AUACUACU\n3'-UUU...UGGUC___UU__AAC______G______AAUA________CAAUG...GUG-5'\n_____________\|___________________________________\|\n_____________71__________________________________35\n	198 -- 204	36 -- 42	-24.7755 kcal/mol	5.81881 kcal/mol	8.66537 kcal/mol	174 205@LB@ \| \|@LB@5'-GGU...UUUAU U G GUG AAUUG...GUG-3'@LB@ GGA UC GUUGUG UGUGGG UGUGAUGA@LB@ \|\|\| \|\| \|:\|\|:\| :\|\|::: \|:\|\|\|\|\|\|@LB@ CCU AG CGACGC GCAUUU AUACUACU@LB@3'-UUU...UGGUC UU AAC G AAUA CAAUG...GUG-5'@LB@ \| \|@LB@ 71 35@LB@@LB@@LB@Energy -10.29 kcal/mol@LB@Hybridization Energy -24.7755 kcal/mol@LB@Unfolding Energy - mRNA 5.81881 kcal/mol@LB@Unfolding Energy - sRNA 8.66537 kcal/mol@LB@@LB@Position - mRNA 175 -- 204@LB@Position - sRNA 36 -- 70@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 36 -- 42@LB@
178	0.01053	0.208	b3582	sgbU	-5.91	0.640260	169 -- 196	65 -- 84	putative L-xylulose 5-phosphate 3-epimerase	_____________168__________________________197\n_____________\|____________________________\|\n5'-UCU...UUCCA_____AAAU_______AUCU________GCGCG...UUG-3'\n______________UGCGC____CGACGCU____GGGGAGGU\n______________\|\|\|\|\|____\|:\|\|:\|:____:\|\|\|\|::\|\n______________ACGCG____GUUGUGG____UCCCUUUA\n3'-UUU...UUAUG____________________________GAACC...GUG-5'\n_____________\|____________________________\|\n_____________85___________________________64\n	190 -- 196	65 -- 71	-23.9168 kcal/mol	10.6467 kcal/mol	7.36194 kcal/mol	168 197@LB@ \| \|@LB@5'-UCU...UUCCA AAAU AUCU GCGCG...UUG-3'@LB@ UGCGC CGACGCU GGGGAGGU@LB@ \|\|\|\|\| \|:\|\|:\|: :\|\|\|\|::\|@LB@ ACGCG GUUGUGG UCCCUUUA@LB@3'-UUU...UUAUG GAACC...GUG-5'@LB@ \| \|@LB@ 85 64@LB@@LB@@LB@Energy -5.91 kcal/mol@LB@Hybridization Energy -23.9168 kcal/mol@LB@Unfolding Energy - mRNA 10.6467 kcal/mol@LB@Unfolding Energy - sRNA 7.36194 kcal/mol@LB@@LB@Position - mRNA 169 -- 196@LB@Position - sRNA 65 -- 84@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 65 -- 71@LB@
94	0.005015	0.1855	b2703	srlE	-7.35	0.404948	254 -- 271	70 -- 86	glucitol/sorbitol-specific enzyme IIB component of PTS	_____________253_________________272\n_____________\|___________________\|\n5'-GAA...CUUGA____AAA____________AAAAA...GUA-3'\n______________GCUG___GCC_ACGCCGGG\n______________:\|\|\|___\|\|\|_\|\|:\|\|:\|\|\n______________UGAC___CGG_UGUGGUCC\n3'-UUU...GCUUA____G_____U________CUUUA...GUG-5'\n_____________\|___________________\|\n_____________87__________________69\n	265 -- 271	70 -- 76	-23.089 kcal/mol	8.46506 kcal/mol	7.27772 kcal/mol	253 272@LB@ \| \|@LB@5'-GAA...CUUGA AAA AAAAA...GUA-3'@LB@ GCUG GCC ACGCCGGG@LB@ :\|\|\| \|\|\| \|\|:\|\|:\|\|@LB@ UGAC CGG UGUGGUCC@LB@3'-UUU...GCUUA G U CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -7.35 kcal/mol@LB@Hybridization Energy -23.089 kcal/mol@LB@Unfolding Energy - mRNA 8.46506 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 254 -- 271@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 70 -- 76@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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