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
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@
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@
59	0.002989	0.1727	b2713	hydN	-12.16	0.053402	276 -- 298	54 -- 76	formate dehydrogenase-H [4Fe-4S] ferredoxin subunit	b3573	_____________275______________________299\n_____________\|________________________\|\n5'-CUU...UUUCU_______A_____A___A______AU-3'\n______________CAUCAGG_AAAUC__GG_CUGUGC\n______________\|\|:\|\|\|\|_\|\|\|\|\|__\|\|_\|\|\|:\|\|\n______________GUGGUCC_UUUAG__CC_GACGCG\n3'-UUU...CGGUU_______C_____AA_________GCAUU...GUG-5'\n_____________\|________________________\|\n_____________77_______________________53\n	276 -- 282	70 -- 76	-25.5609 kcal/mol	4.47784 kcal/mol	8.92391 kcal/mol	275 299@LB@ \| \|@LB@5'-CUU...UUUCU A A A AU-3'@LB@ CAUCAGG AAAUC GG CUGUGC@LB@ \|\|:\|\|\|\| \|\|\|\|\| \|\| \|\|\|:\|\|@LB@ GUGGUCC UUUAG CC GACGCG@LB@3'-UUU...CGGUU C AA GCAUU...GUG-5'@LB@ \| \|@LB@ 77 53@LB@@LB@@LB@Energy -12.16 kcal/mol@LB@Hybridization Energy -25.5609 kcal/mol@LB@Unfolding Energy - mRNA 4.47784 kcal/mol@LB@Unfolding Energy - sRNA 8.92391 kcal/mol@LB@@LB@Position - mRNA 276 -- 298@LB@Position - sRNA 54 -- 76@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 70 -- 76@LB@
52	0.002619	0.1727	b2720	hycF	-12.75	0.040951	8 -- 55	44 -- 94	formate hydrogenlyase complex iron-sulfur protein		_____________7______________________________________________________56\n_____________\|______________________________________________________\|\n____5'-CGACCCU____UAC_________GG_________________CCGA_______CU______CGGUA...CAG-3'\n______________GCGC___AUGCUGCGC__CAACACC______GUUU____UGCGCCG__GAUUAU\n______________\|\|\|\|___\|\|:\|\|\|\|\|\|__\|\|\|\|\|\|\|______:\|:\|____\|\|\|\|\|\|\|__:\|\|\|\|\|\n______________CGCG___UAUGACGCG__GUUGUGG______UAGA____ACGCGGC__UUAAUA\n3'-UUU...CCCCA____CU___________________UCCCUU____ACCG_______AU______AUACU...GUG-5'\n_____________\|______________________________________________________\|\n_____________95_____________________________________________________43\n	41 -- 47	52 -- 58	-46.3174 kcal/mol	16.2176 kcal/mol	17.3533 kcal/mol	7 56@LB@ \| \|@LB@ 5'-CGACCCU UAC GG CCGA CU CGGUA...CAG-3'@LB@ GCGC AUGCUGCGC CAACACC GUUU UGCGCCG GAUUAU@LB@ \|\|\|\| \|\|:\|\|\|\|\|\| \|\|\|\|\|\|\| :\|:\| \|\|\|\|\|\|\| :\|\|\|\|\|@LB@ CGCG UAUGACGCG GUUGUGG UAGA ACGCGGC UUAAUA@LB@3'-UUU...CCCCA CU UCCCUU ACCG AU AUACU...GUG-5'@LB@ \| \|@LB@ 95 43@LB@@LB@@LB@Energy -12.75 kcal/mol@LB@Hybridization Energy -46.3174 kcal/mol@LB@Unfolding Energy - mRNA 16.2176 kcal/mol@LB@Unfolding Energy - sRNA 17.3533 kcal/mol@LB@@LB@Position - mRNA 8 -- 55@LB@Position - sRNA 44 -- 94@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 52 -- 58@LB@
103	0.005609	0.1855	b2912	fau	-11.92	0.059425	103 -- 124	64 -- 85	5-formyltetrahydrofolate cyclo-ligase family protein		_____________102____________________125\n_____________\|______________________\|\n5'-GAA...ACAGC_____G_______UC_______CCCUU...UGG-3'\n______________CUGCG_CGGCAUC__GGAGAUU\n______________\|\|\|\|\|_\|::\|\|:\|__\|\|\|:\|\|:\n______________GACGC_GUUGUGG__CCUUUAG\n3'-UUU...CUUAU_____G_______UC_______AACCG...GUG-5'\n_____________\|______________________\|\n_____________86_____________________63\n	118 -- 124	64 -- 70	-27.7471 kcal/mol	8.44142 kcal/mol	7.38387 kcal/mol	102 125@LB@ \| \|@LB@5'-GAA...ACAGC G UC CCCUU...UGG-3'@LB@ CUGCG CGGCAUC GGAGAUU@LB@ \|\|\|\|\| \|::\|\|:\| \|\|\|:\|\|:@LB@ GACGC GUUGUGG CCUUUAG@LB@3'-UUU...CUUAU G UC AACCG...GUG-5'@LB@ \| \|@LB@ 86 63@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -27.7471 kcal/mol@LB@Unfolding Energy - mRNA 8.44142 kcal/mol@LB@Unfolding Energy - sRNA 7.38387 kcal/mol@LB@@LB@Position - mRNA 103 -- 124@LB@Position - sRNA 64 -- 85@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 64 -- 70@LB@
126	0.006849	0.1914	b2930	yggF	-13.28	0.032133	176 -- 191	68 -- 83	fructose 1 6 bisphosphatase isozyme		_____________175______________192\n_____________\|________________\|\n5'-AUC...AUUUG________________GGCCG...GCC-3'\n______________GCGUUGAUAUCGGGGA\n______________\|\|\|:::\|:\|:\|:\|\|\|\|\n______________CGCGGUUGUGGUCCCU\n3'-UUU...UAUGA________________UUAGA...GUG-5'\n_____________\|________________\|\n_____________84_______________67\n	185 -- 191	68 -- 74	-24.7766 kcal/mol	4.1491 kcal/mol	7.34657 kcal/mol	175 192@LB@ \| \|@LB@5'-AUC...AUUUG GGCCG...GCC-3'@LB@ GCGUUGAUAUCGGGGA@LB@ \|\|\|:::\|:\|:\|:\|\|\|\|@LB@ CGCGGUUGUGGUCCCU@LB@3'-UUU...UAUGA UUAGA...GUG-5'@LB@ \| \|@LB@ 84 67@LB@@LB@@LB@Energy -13.28 kcal/mol@LB@Hybridization Energy -24.7766 kcal/mol@LB@Unfolding Energy - mRNA 4.1491 kcal/mol@LB@Unfolding Energy - sRNA 7.34657 kcal/mol@LB@@LB@Position - mRNA 176 -- 191@LB@Position - sRNA 68 -- 83@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 68 -- 74@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@
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@
97	0.005188	0.1855	b3060	ttdR	-16.80	0.006462	125 -- 147	67 -- 90	transcriptional activator of ttdABT	b1799	_____________124______________________148\n_____________\|________________________\|\n5'-UCC...AGAAU________________G_______UGGCA...CGC-3'\n______________GAAUAUUGCGCCAG_A_CAGGGAA\n______________\|\|\|\|\|:\|\|\|\|\|\|\|:_\|_\|\|\|\|\|\|\|\n______________CUUAUGACGCGGUU_U_GUCCCUU\n3'-UUU...ACGCG______________G_G_______UAGAA...GUG-5'\n_____________\|________________________\|\n_____________91_______________________66\n	141 -- 147	67 -- 73	-34.0784 kcal/mol	7.10756 kcal/mol	10.1694 kcal/mol	124 148@LB@ \| \|@LB@5'-UCC...AGAAU G UGGCA...CGC-3'@LB@ GAAUAUUGCGCCAG A CAGGGAA@LB@ \|\|\|\|\|:\|\|\|\|\|\|\|: \| \|\|\|\|\|\|\|@LB@ CUUAUGACGCGGUU U GUCCCUU@LB@3'-UUU...ACGCG G G UAGAA...GUG-5'@LB@ \| \|@LB@ 91 66@LB@@LB@@LB@Energy -16.80 kcal/mol@LB@Hybridization Energy -34.0784 kcal/mol@LB@Unfolding Energy - mRNA 7.10756 kcal/mol@LB@Unfolding Energy - sRNA 10.1694 kcal/mol@LB@@LB@Position - mRNA 125 -- 147@LB@Position - sRNA 67 -- 90@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 67 -- 73@LB@
149	0.008735	0.2059	b3088	alx	-8.37	0.274530	278 -- 288	25 -- 35	putative membrane-bound redox modulator		_____________277_________289\n_____________\|___________\|\n5'-GGG...CUGUU___________GUCGU...CAC-3'\n______________GUUGCAGGGGC\n______________\|\|\|:\|\|:\|\|\|\|\n______________CAAUGUUCCCG\n3'-UUU...CUACU___________UGUCG...GUG-5'\n_____________\|___________\|\n_____________36__________24\n	282 -- 288	25 -- 31	-18.295 kcal/mol	6.20791 kcal/mol	3.71635 kcal/mol	277 289@LB@ \| \|@LB@5'-GGG...CUGUU GUCGU...CAC-3'@LB@ GUUGCAGGGGC@LB@ \|\|\|:\|\|:\|\|\|\|@LB@ CAAUGUUCCCG@LB@3'-UUU...CUACU UGUCG...GUG-5'@LB@ \| \|@LB@ 36 24@LB@@LB@@LB@Energy -8.37 kcal/mol@LB@Hybridization Energy -18.295 kcal/mol@LB@Unfolding Energy - mRNA 6.20791 kcal/mol@LB@Unfolding Energy - sRNA 3.71635 kcal/mol@LB@@LB@Position - mRNA 278 -- 288@LB@Position - sRNA 25 -- 35@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 25 -- 31@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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