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
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@
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@
198	0.01217	0.2164	b1236	galU	-11.62	0.068156	187 -- 208	56 -- 74	glucose-1-phosphate uridylyltransferase	_____________186____________________209\n_____________\|______________________\|\n5'-CAA...ACAGU_____A______AAA_______CAUUA...UGC-3'\n______________CCAGG_GAAUUU___UGGCUGC\n______________\|\|\|\|\|_:\|\|\|:\|___\|\|\|\|\|\|\|\n______________GGUCC_UUUAGA___ACCGACG\n3'-UUU...GUUGU_____C________________CGGCA...GUG-5'\n_____________\|______________________\|\n_____________75_____________________55\n	202 -- 208	56 -- 62	-24.2568 kcal/mol	4.50323 kcal/mol	8.13729 kcal/mol	186 209@LB@ \| \|@LB@5'-CAA...ACAGU A AAA CAUUA...UGC-3'@LB@ CCAGG GAAUUU UGGCUGC@LB@ \|\|\|\|\| :\|\|\|:\| \|\|\|\|\|\|\|@LB@ GGUCC UUUAGA ACCGACG@LB@3'-UUU...GUUGU C CGGCA...GUG-5'@LB@ \| \|@LB@ 75 55@LB@@LB@@LB@Energy -11.62 kcal/mol@LB@Hybridization Energy -24.2568 kcal/mol@LB@Unfolding Energy - mRNA 4.50323 kcal/mol@LB@Unfolding Energy - sRNA 8.13729 kcal/mol@LB@@LB@Position - mRNA 187 -- 208@LB@Position - sRNA 56 -- 74@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 56 -- 62@LB@
73	0.003782	0.1804	b3560	glyQ	-10.80	0.098141	7 -- 31	51 -- 74	glycine tRNA synthetase alpha subunit	_____________6__________________________32\n_____________\|__________________________\|\n_____5'-ACAGUU____________A__AAA_____G__UAUAC...UGG-3'\n______________CCAGGGAAG_CU_UG___UGCGC_GU\n______________\|\|\|\|\|\|\|\|:_\|\|_\|\|___\|\|\|\|\|_\|\|\n______________GGUCCCUUU_GA_AC___ACGCG_CA\n3'-UUU...GUUGU_________A_____CG______G__UUUAA...GUG-5'\n_____________\|__________________________\|\n_____________75_________________________50\n	9 -- 15	66 -- 72	-27.2651 kcal/mol	7.67928 kcal/mol	8.78847 kcal/mol	6 32@LB@ \| \|@LB@ 5'-ACAGUU A AAA G UAUAC...UGG-3'@LB@ CCAGGGAAG CU UG UGCGC GU@LB@ \|\|\|\|\|\|\|\|: \|\| \|\| \|\|\|\|\| \|\|@LB@ GGUCCCUUU GA AC ACGCG CA@LB@3'-UUU...GUUGU A CG G UUUAA...GUG-5'@LB@ \| \|@LB@ 75 50@LB@@LB@@LB@Energy -10.80 kcal/mol@LB@Hybridization Energy -27.2651 kcal/mol@LB@Unfolding Energy - mRNA 7.67928 kcal/mol@LB@Unfolding Energy - sRNA 8.78847 kcal/mol@LB@@LB@Position - mRNA 7 -- 31@LB@Position - sRNA 51 -- 74@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 66 -- 72@LB@
184	0.01102	0.2089	b1033	ghrA	-10.56	0.108938	6 -- 15	64 -- 73	glyoxylate/hydroxypyruvate reductase A	_____________5__________16\n_____________\|__________\|\n______5'-UAAUU__________AUGAC...GCG-3'\n______________UAGGGAAAUC\n______________:\|\|\|\|\|\|\|\|\|\n______________GUCCCUUUAG\n3'-UUU...UUGUG__________AACCG...GUG-5'\n_____________\|__________\|\n_____________74_________63\n	9 -- 15	64 -- 70	-14.6499 kcal/mol	0.954451 kcal/mol	3.13463 kcal/mol	5 16@LB@ \| \|@LB@ 5'-UAAUU AUGAC...GCG-3'@LB@ UAGGGAAAUC@LB@ :\|\|\|\|\|\|\|\|\|@LB@ GUCCCUUUAG@LB@3'-UUU...UUGUG AACCG...GUG-5'@LB@ \| \|@LB@ 74 63@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -14.6499 kcal/mol@LB@Unfolding Energy - mRNA 0.954451 kcal/mol@LB@Unfolding Energy - sRNA 3.13463 kcal/mol@LB@@LB@Position - mRNA 6 -- 15@LB@Position - sRNA 64 -- 73@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 64 -- 70@LB@
61	0.003042	0.1727	b0104	guaC	-6.79	0.490983	117 -- 124	52 -- 59	GMP reductase	_____________116______125\n_____________\|________\|\n5'-AUG...CAGUC________CAUUG...GUC-3'\n______________UUGCGCCG\n______________:\|\|\|\|\|\|\|\n______________GACGCGGC\n3'-UUU...GAACC________AUUUA...GUG-5'\n_____________\|________\|\n_____________60_______51\n	118 -- 124	52 -- 58	-14.4979 kcal/mol	2.89251 kcal/mol	4.81798 kcal/mol	116 125@LB@ \| \|@LB@5'-AUG...CAGUC CAUUG...GUC-3'@LB@ UUGCGCCG@LB@ :\|\|\|\|\|\|\|@LB@ GACGCGGC@LB@3'-UUU...GAACC AUUUA...GUG-5'@LB@ \| \|@LB@ 60 51@LB@@LB@@LB@Energy -6.79 kcal/mol@LB@Hybridization Energy -14.4979 kcal/mol@LB@Unfolding Energy - mRNA 2.89251 kcal/mol@LB@Unfolding Energy - sRNA 4.81798 kcal/mol@LB@@LB@Position - mRNA 117 -- 124@LB@Position - sRNA 52 -- 59@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 52 -- 58@LB@
41	0.002142	0.1727	b2153	folE	-10.82	0.097170	217 -- 276	53 -- 121	GTP cyclohydrolase I	_____________216________________________________________________________________________277\n_____________\|__________________________________________________________________________\|\n5'-CUG...CAGUA______C__________CAU__AG__UUA_U________G____GA____________________________CGCCC...ACG-3'\n______________AAGAAG_GGCCCUGGUU___GA__CG___G_UGCGCGAG_ACUG____AACACC____________GCUGCGCC\n______________\|\|:\|\|:_\|:\|\|\|:\|\|:\|___\|\|__\|\|___\|_\|\|\|\|\|\|\|:_\|\|\|\|____\|\|\|\|\|\|____________\|\|\|\|\|\|\|\|\n______________UUUUUU_CUGGGGCCGA___CU__GC___C_ACGCGCUU_UGAC____UUGUGG____________CGACGCGG\n___________3'-______A__________U____G___C___C________A____GCGG______UCCCUUUAGAAC________CAUUU...GUG-5'\n______________\|_________________________________________________________________________\|\n______________121_______________________________________________________________________52\n	270 -- 276	53 -- 59	-62.0592 kcal/mol	19.5041 kcal/mol	31.7353 kcal/mol	216 277@LB@ \| \|@LB@5'-CUG...CAGUA C CAU AG UUA U G GA CGCCC...ACG-3'@LB@ AAGAAG GGCCCUGGUU GA CG G UGCGCGAG ACUG AACACC GCUGCGCC@LB@ \|\|:\|\|: \|:\|\|\|:\|\|:\| \|\| \|\| \| \|\|\|\|\|\|\|: \|\|\|\| \|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UUUUUU CUGGGGCCGA CU GC C ACGCGCUU UGAC UUGUGG CGACGCGG@LB@ 3'- A U G C C A GCGG UCCCUUUAGAAC CAUUU...GUG-5'@LB@ \| \|@LB@ 121 52@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -62.0592 kcal/mol@LB@Unfolding Energy - mRNA 19.5041 kcal/mol@LB@Unfolding Energy - sRNA 31.7353 kcal/mol@LB@@LB@Position - mRNA 217 -- 276@LB@Position - sRNA 53 -- 121@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 53 -- 59@LB@
129	0.007194	0.1964	b3401	hslO	-8.25	0.287762	98 -- 107	1 -- 10	heat shock protein Hsp33	_____________97_________108\n_____________\|__________\|\n5'-GCC...UUAAC__U_______CCGGA...AGA-3'\n______________CA_GCCGCAC\n______________\|\|_\|\|\|\|\|\|\|\n______________GU_CGGCGUG\n3'-UUU...AAAAA__C_______-5'\n_____________\|_________\|\n_____________11________1\n	101 -- 107	1 -- 7	-14.7655 kcal/mol	1.13179 kcal/mol	5.44172 kcal/mol	97 108@LB@ \| \|@LB@5'-GCC...UUAAC U CCGGA...AGA-3'@LB@ CA GCCGCAC@LB@ \|\| \|\|\|\|\|\|\|@LB@ GU CGGCGUG@LB@3'-UUU...AAAAA C -5'@LB@ \| \|@LB@ 11 1@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -14.7655 kcal/mol@LB@Unfolding Energy - mRNA 1.13179 kcal/mol@LB@Unfolding Energy - sRNA 5.44172 kcal/mol@LB@@LB@Position - mRNA 98 -- 107@LB@Position - sRNA 1 -- 10@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 1 -- 7@LB@
133	0.007533	0.1993	b2194	ccmH	-11.64	0.067570	191 -- 199	1 -- 9	heme lyase CcmH subunit	_____________190_______200\n_____________\|_________\|\n5'-CUG...UAAGG_________AAUGA...AGU-3'\n______________AGGCCGCAC\n______________\|\|\|\|\|\|\|\|\|\n______________UCCGGCGUG\n3'-UUU...AAAAG_________-5'\n_____________\|________\|\n_____________10_______1\n	193 -- 199	1 -- 7	-19.8862 kcal/mol	2.96679 kcal/mol	5.10726 kcal/mol	190 200@LB@ \| \|@LB@5'-CUG...UAAGG AAUGA...AGU-3'@LB@ AGGCCGCAC@LB@ \|\|\|\|\|\|\|\|\|@LB@ UCCGGCGUG@LB@3'-UUU...AAAAG -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -11.64 kcal/mol@LB@Hybridization Energy -19.8862 kcal/mol@LB@Unfolding Energy - mRNA 2.96679 kcal/mol@LB@Unfolding Energy - sRNA 5.10726 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 1 -- 7@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@

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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