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
165	0.009721	0.2068	b1475	fdnH	-11.62	0.068172	63 -- 98	41 -- 76	formate dehydrogenase-N Fe-S (beta) subunit nitrate-inducible		_____________62_____________________________________99\n_____________\|______________________________________\|\n5'-CGC...CAAUC________CU___GA__G__U___G______G______AUCGC...UUA-3'\n______________CACUGGGG___UU__GG_UG_CGC_CGUAAA__GUUAU\n______________\|\|\|::\|\|\|___\|:__\|\|_\|\|_\|\|\|_\|\|\|\|\|\|__:\|\|\|\|\n______________GUGGUCCC___AG__CC_AC_GCG_GCAUUU__UAAUA\n3'-UUU...CGGUU________UUU__AA__G_____________AA_____CUACU...GUG-5'\n_____________\|______________________________________\|\n_____________77_____________________________________40\n	64 -- 70	69 -- 75	-31.0903 kcal/mol	10.1186 kcal/mol	9.35565 kcal/mol	62 99@LB@ \| \|@LB@5'-CGC...CAAUC CU GA G U G G AUCGC...UUA-3'@LB@ CACUGGGG UU GG UG CGC CGUAAA GUUAU@LB@ \|\|\|::\|\|\| \|: \|\| \|\| \|\|\| \|\|\|\|\|\| :\|\|\|\|@LB@ GUGGUCCC AG CC AC GCG GCAUUU UAAUA@LB@3'-UUU...CGGUU UUU AA G AA CUACU...GUG-5'@LB@ \| \|@LB@ 77 40@LB@@LB@@LB@Energy -11.62 kcal/mol@LB@Hybridization Energy -31.0903 kcal/mol@LB@Unfolding Energy - mRNA 10.1186 kcal/mol@LB@Unfolding Energy - sRNA 9.35565 kcal/mol@LB@@LB@Position - mRNA 63 -- 98@LB@Position - sRNA 41 -- 76@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 69 -- 75@LB@
150	0.008837	0.2059	b0453	ybaY	-11.57	0.069675	268 -- 294	71 -- 94	outer membrane lipoprotein		_____________267_________________________295\n_____________\|___________________________\|\n5'-AAG...UAAAA___________CA_A____________CUGCAA-3'\n______________GCGCGGAUAUU__G_CGCCAGCACCGG\n______________\|\|\|\|\|:\|\|\|:\|__\|_\|\|\|\|\|:\|\|\|\|:\|\n______________CGCGCUUAUGA__C_GCGGUUGUGGUC\n3'-UUU...CCCCA___________________________CCUUU...GUG-5'\n_____________\|___________________________\|\n_____________95__________________________70\n	283 -- 289	76 -- 82	-36.9875 kcal/mol	12.3701 kcal/mol	13.0144 kcal/mol	267 295@LB@ \| \|@LB@5'-AAG...UAAAA CA A CUGCAA-3'@LB@ GCGCGGAUAUU G CGCCAGCACCGG@LB@ \|\|\|\|\|:\|\|\|:\| \| \|\|\|\|\|:\|\|\|\|:\|@LB@ CGCGCUUAUGA C GCGGUUGUGGUC@LB@3'-UUU...CCCCA CCUUU...GUG-5'@LB@ \| \|@LB@ 95 70@LB@@LB@@LB@Energy -11.57 kcal/mol@LB@Hybridization Energy -36.9875 kcal/mol@LB@Unfolding Energy - mRNA 12.3701 kcal/mol@LB@Unfolding Energy - sRNA 13.0144 kcal/mol@LB@@LB@Position - mRNA 268 -- 294@LB@Position - sRNA 71 -- 94@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 76 -- 82@LB@
38	0.002093	0.1727	b1174	minE	-11.55	0.070176	37 -- 55	69 -- 87	cell division topological specificity factor		_____________36___________________56\n_____________\|____________________\|\n5'-AAC...AGUAU_________UCUA_______UGAAC...AUG-3'\n______________UGC_GCGCC____ACCAGGG\n______________\|:\|_\|\|\|\|\|____\|\|\|\|\|\|\|\n______________AUG_CGCGG____UGGUCCC\n3'-UUU...CGCUU___A_____UUG________UUUAG...GUG-5'\n_____________\|____________________\|\n_____________88___________________68\n	49 -- 55	69 -- 75	-25.7186 kcal/mol	6.79304 kcal/mol	7.3743 kcal/mol	36 56@LB@ \| \|@LB@5'-AAC...AGUAU UCUA UGAAC...AUG-3'@LB@ UGC GCGCC ACCAGGG@LB@ \|:\| \|\|\|\|\| \|\|\|\|\|\|\|@LB@ AUG CGCGG UGGUCCC@LB@3'-UUU...CGCUU A UUG UUUAG...GUG-5'@LB@ \| \|@LB@ 88 68@LB@@LB@@LB@Energy -11.55 kcal/mol@LB@Hybridization Energy -25.7186 kcal/mol@LB@Unfolding Energy - mRNA 6.79304 kcal/mol@LB@Unfolding Energy - sRNA 7.3743 kcal/mol@LB@@LB@Position - mRNA 37 -- 55@LB@Position - sRNA 69 -- 87@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 69 -- 75@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@
125	0.006795	0.1914	b3003	yghA	-11.52	0.071261	264 -- 274	70 -- 80	putative oxidoreductase	b2902	_____________263_________275\n_____________\|___________\|\n5'-AAC...AACAA___________CAUCC...UAC-3'\n______________CCGACGCCAGG\n______________\|\|:\|\|:\|\|\|\|\|\n______________GGUUGUGGUCC\n3'-UUU...GACGC___________CUUUA...GUG-5'\n_____________\|___________\|\n_____________81__________69\n	268 -- 274	70 -- 76	-20.3781 kcal/mol	2.1599 kcal/mol	6.70146 kcal/mol	263 275@LB@ \| \|@LB@5'-AAC...AACAA CAUCC...UAC-3'@LB@ CCGACGCCAGG@LB@ \|\|:\|\|:\|\|\|\|\|@LB@ GGUUGUGGUCC@LB@3'-UUU...GACGC CUUUA...GUG-5'@LB@ \| \|@LB@ 81 69@LB@@LB@@LB@Energy -11.52 kcal/mol@LB@Hybridization Energy -20.3781 kcal/mol@LB@Unfolding Energy - mRNA 2.1599 kcal/mol@LB@Unfolding Energy - sRNA 6.70146 kcal/mol@LB@@LB@Position - mRNA 264 -- 274@LB@Position - sRNA 70 -- 80@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 70 -- 76@LB@
168	0.009959	0.2071	b0727	sucB	-11.51	0.071542	30 -- 47	72 -- 88	dihydrolipoyltranssuccinase		_____________29_________________48\n_____________\|__________________\|\n5'-CAG...GCAUG_______A__________UUUCC...GUG-3'\n______________GUACUGC_GCCAGCAUCA\n______________:\|\|\|\|\|\|_\|\|\|\|:\|\|:\|\|\n______________UAUGACG_CGGUUGUGGU\n3'-UUU...GCGCU__________________CCCUU...GUG-5'\n_____________\|__________________\|\n_____________89_________________71\n	38 -- 44	75 -- 81	-25.7274 kcal/mol	6.97777 kcal/mol	7.24148 kcal/mol	29 48@LB@ \| \|@LB@5'-CAG...GCAUG A UUUCC...GUG-3'@LB@ GUACUGC GCCAGCAUCA@LB@ :\|\|\|\|\|\| \|\|\|\|:\|\|:\|\|@LB@ UAUGACG CGGUUGUGGU@LB@3'-UUU...GCGCU CCCUU...GUG-5'@LB@ \| \|@LB@ 89 71@LB@@LB@@LB@Energy -11.51 kcal/mol@LB@Hybridization Energy -25.7274 kcal/mol@LB@Unfolding Energy - mRNA 6.97777 kcal/mol@LB@Unfolding Energy - sRNA 7.24148 kcal/mol@LB@@LB@Position - mRNA 30 -- 47@LB@Position - sRNA 72 -- 88@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 75 -- 81@LB@
85	0.004761	0.1855	b2077	iceT	-11.46	0.073016	53 -- 74	64 -- 86	putative citrate/iron-citrate/zinc-citrate efflux transporter		_____________52______________________75\n_____________\|_______________________\|\n5'-CGG...UCGGA______G_______CU_______ACCAU...UUC-3'\n______________GCUGCG_CAAC_CC__GGGGAUC\n______________:\|\|\|\|\|_\|\|\|\|_\|\|__\|\|::\|\|\|\n______________UGACGC_GUUG_GG__CCUUUAG\n3'-UUU...GCUUA______G____U__UC_______AACCG...GUG-5'\n_____________\|_______________________\|\n_____________87______________________63\n	68 -- 74	64 -- 70	-29.0378 kcal/mol	10.1908 kcal/mol	7.38435 kcal/mol	52 75@LB@ \| \|@LB@5'-CGG...UCGGA G CU ACCAU...UUC-3'@LB@ GCUGCG CAAC CC GGGGAUC@LB@ :\|\|\|\|\| \|\|\|\| \|\| \|\|::\|\|\|@LB@ UGACGC GUUG GG CCUUUAG@LB@3'-UUU...GCUUA G U UC AACCG...GUG-5'@LB@ \| \|@LB@ 87 63@LB@@LB@@LB@Energy -11.46 kcal/mol@LB@Hybridization Energy -29.0378 kcal/mol@LB@Unfolding Energy - mRNA 10.1908 kcal/mol@LB@Unfolding Energy - sRNA 7.38435 kcal/mol@LB@@LB@Position - mRNA 53 -- 74@LB@Position - sRNA 64 -- 86@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 64 -- 70@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@
115	0.006085	0.1855	b3030	parE	-11.34	0.077071	10 -- 31	65 -- 86	DNA topoisomerase IV subunit B		_____________9______________________32\n_____________\|______________________\|\n5'-UUU...AUCUG_____UG_____GAC_______GAAGU...ACC-3'\n______________GCUGC__CAACA___GGGAGAU\n______________:\|\|\|\|__\|\|\|\|\|___\|\|\|\|:\|\|\n______________UGACG__GUUGU___CCCUUUA\n3'-UUU...GCUUA_____CG_____GGU_______GAACC...GUG-5'\n_____________\|______________________\|\n_____________87_____________________64\n	25 -- 31	65 -- 71	-24.4704 kcal/mol	5.74549 kcal/mol	7.38332 kcal/mol	9 32@LB@ \| \|@LB@5'-UUU...AUCUG UG GAC GAAGU...ACC-3'@LB@ GCUGC CAACA GGGAGAU@LB@ :\|\|\|\| \|\|\|\|\| \|\|\|\|:\|\|@LB@ UGACG GUUGU CCCUUUA@LB@3'-UUU...GCUUA CG GGU GAACC...GUG-5'@LB@ \| \|@LB@ 87 64@LB@@LB@@LB@Energy -11.34 kcal/mol@LB@Hybridization Energy -24.4704 kcal/mol@LB@Unfolding Energy - mRNA 5.74549 kcal/mol@LB@Unfolding Energy - sRNA 7.38332 kcal/mol@LB@@LB@Position - mRNA 10 -- 31@LB@Position - sRNA 65 -- 86@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 65 -- 71@LB@
181	0.0108	0.2089	b1683	sufB	-11.33	0.077347	153 -- 175	52 -- 74	component of SufBCD Fe-S cluster assembly scaffold		_____________152_______________________176\n_____________\|_________________________\|\n5'-GUU...AAAGC____AAU___UG__________G__AAAGC...AGC-3'\n______________CCAG___GAA____UGGCUGUG_CG\n______________\|\|\|\|___\|\|\|____\|\|\|\|\|\|:\|_\|\|\n______________GGUC___CUU____ACCGACGC_GC\n3'-UUU...GUUGU____C_____UAGA________G__AUUUA...GUG-5'\n_____________\|_________________________\|\n_____________75________________________51\n	166 -- 172	55 -- 61	-23.8546 kcal/mol	3.76094 kcal/mol	8.7601 kcal/mol	152 176@LB@ \| \|@LB@5'-GUU...AAAGC AAU UG G AAAGC...AGC-3'@LB@ CCAG GAA UGGCUGUG CG@LB@ \|\|\|\| \|\|\| \|\|\|\|\|\|:\| \|\|@LB@ GGUC CUU ACCGACGC GC@LB@3'-UUU...GUUGU C UAGA G AUUUA...GUG-5'@LB@ \| \|@LB@ 75 51@LB@@LB@@LB@Energy -11.33 kcal/mol@LB@Hybridization Energy -23.8546 kcal/mol@LB@Unfolding Energy - mRNA 3.76094 kcal/mol@LB@Unfolding Energy - sRNA 8.7601 kcal/mol@LB@@LB@Position - mRNA 153 -- 175@LB@Position - sRNA 52 -- 74@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 55 -- 61@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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