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
4	3.471e-06	0.003055	b2099	yegU	-19.38	0.001997	173 -- 198	64 -- 88	ADP-ribosylglycohydrolase family protein	_____________172________________________199\n_____________\|__________________________\|\n5'-GUG...UCGCG_______________AA_________AAAUG...CAC-3'\n______________AUAUUGCGUUGACAC__GGGGAAGUU\n______________\|\|\|:\|\|\|\|:::\|\|\|\|__:\|\|\|\|\|:\|:\n______________UAUGACGCGGUUGUG__UCCCUUUAG\n3'-UUU...GCGCU_______________G__________AACCG...GUG-5'\n_____________\|__________________________\|\n_____________89_________________________63\n	192 -- 198	64 -- 70	-32.1286 kcal/mol	5.35868 kcal/mol	7.38555 kcal/mol	172 199@LB@ \| \|@LB@5'-GUG...UCGCG AA AAAUG...CAC-3'@LB@ AUAUUGCGUUGACAC GGGGAAGUU@LB@ \|\|\|:\|\|\|\|:::\|\|\|\| :\|\|\|\|\|:\|:@LB@ UAUGACGCGGUUGUG UCCCUUUAG@LB@3'-UUU...GCGCU G AACCG...GUG-5'@LB@ \| \|@LB@ 89 63@LB@@LB@@LB@Energy -19.38 kcal/mol@LB@Hybridization Energy -32.1286 kcal/mol@LB@Unfolding Energy - mRNA 5.35868 kcal/mol@LB@Unfolding Energy - sRNA 7.38555 kcal/mol@LB@@LB@Position - mRNA 173 -- 198@LB@Position - sRNA 64 -- 88@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 64 -- 70@LB@
24	0.001457	0.1727	b0424	yajL	-16.26	0.008266	79 -- 97	64 -- 86	oxidative-stress-resistance chaperone	_____________78______________________98\n_____________\|_______________________\|\n5'-AGA...CGCGC_______________________GACUA...CCA-3'\n______________GCUGCGCCA_CACU___GAAAUC\n______________:\|\|\|\|\|\|\|\|_\|\|\|:___\|\|\|\|\|\|\n______________UGACGCGGU_GUGG___CUUUAG\n3'-UUU...GCUUA_________U____UCC______AACCG...GUG-5'\n_____________\|_______________________\|\n_____________87______________________63\n	81 -- 87	78 -- 84	-26.9283 kcal/mol	3.28429 kcal/mol	7.38435 kcal/mol	78 98@LB@ \| \|@LB@5'-AGA...CGCGC GACUA...CCA-3'@LB@ GCUGCGCCA CACU GAAAUC@LB@ :\|\|\|\|\|\|\|\| \|\|\|: \|\|\|\|\|\|@LB@ UGACGCGGU GUGG CUUUAG@LB@3'-UUU...GCUUA U UCC AACCG...GUG-5'@LB@ \| \|@LB@ 87 63@LB@@LB@@LB@Energy -16.26 kcal/mol@LB@Hybridization Energy -26.9283 kcal/mol@LB@Unfolding Energy - mRNA 3.28429 kcal/mol@LB@Unfolding Energy - sRNA 7.38435 kcal/mol@LB@@LB@Position - mRNA 79 -- 97@LB@Position - sRNA 64 -- 86@LB@Position Seed - mRNA 81 -- 87@LB@Position Seed - sRNA 78 -- 84@LB@
106	0.005731	0.1855	b0867	amiD	-15.82	0.010089	39 -- 60	64 -- 86	1 6-anhydro-N-acetylmuramyl-L-alanine amidase Zn-dependent; OM lipoprotein	_____________38_______________________61\n_____________\|________________________\|\n5'-GAU...AAAGA_______AA_______________GCCUU...CCC-3'\n______________ACUGCGU__AGCAC__GGGAGAUC\n______________\|\|\|\|\|\|:__\|:\|\|\|__\|\|\|\|:\|\|\|\n______________UGACGCG__UUGUG__CCCUUUAG\n3'-UUU...GCUUA_______G______GU________AACCG...GUG-5'\n_____________\|________________________\|\n_____________87_______________________63\n	54 -- 60	64 -- 70	-27.7093 kcal/mol	4.50209 kcal/mol	7.38435 kcal/mol	38 61@LB@ \| \|@LB@5'-GAU...AAAGA AA GCCUU...CCC-3'@LB@ ACUGCGU AGCAC GGGAGAUC@LB@ \|\|\|\|\|\|: \|:\|\|\| \|\|\|\|:\|\|\|@LB@ UGACGCG UUGUG CCCUUUAG@LB@3'-UUU...GCUUA G GU AACCG...GUG-5'@LB@ \| \|@LB@ 87 63@LB@@LB@@LB@Energy -15.82 kcal/mol@LB@Hybridization Energy -27.7093 kcal/mol@LB@Unfolding Energy - mRNA 4.50209 kcal/mol@LB@Unfolding Energy - sRNA 7.38435 kcal/mol@LB@@LB@Position - mRNA 39 -- 60@LB@Position - sRNA 64 -- 86@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 64 -- 70@LB@
34	0.001871	0.1727	b4485	ytfR	-15.36	0.012458	204 -- 227	64 -- 86	putative sugar ABC transporter ATPase	_____________203_______________________228\n_____________\|_________________________\|\n5'-CCU...CCAUG__GAC__A_________________CUCCG...GCC-3'\n______________AC___CG_CCAACACCA_GGAGAUC\n______________\|\|___\|\|_\|\|\|\|\|\|\|\|\|_\|\|\|:\|\|\|\n______________UG___GC_GGUUGUGGU_CCUUUAG\n3'-UUU...GCUUA__AC_____________C_______AACCG...GUG-5'\n_____________\|_________________________\|\n_____________87________________________63\n	221 -- 227	64 -- 70	-26.9267 kcal/mol	4.18191 kcal/mol	7.38435 kcal/mol	203 228@LB@ \| \|@LB@5'-CCU...CCAUG GAC A CUCCG...GCC-3'@LB@ AC CG CCAACACCA GGAGAUC@LB@ \|\| \|\| \|\|\|\|\|\|\|\|\| \|\|\|:\|\|\|@LB@ UG GC GGUUGUGGU CCUUUAG@LB@3'-UUU...GCUUA AC C AACCG...GUG-5'@LB@ \| \|@LB@ 87 63@LB@@LB@@LB@Energy -15.36 kcal/mol@LB@Hybridization Energy -26.9267 kcal/mol@LB@Unfolding Energy - mRNA 4.18191 kcal/mol@LB@Unfolding Energy - sRNA 7.38435 kcal/mol@LB@@LB@Position - mRNA 204 -- 227@LB@Position - sRNA 64 -- 86@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 64 -- 70@LB@
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@
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@
138	0.007886	0.2012	b3991	thiG	-13.21	0.033127	237 -- 259	64 -- 85	thiamine biosynthesis ThiGH complex subunit	_____________236______________________260\n_____________\|________________________\|\n5'-GCA...CACAU____UUA_________________CGCUU...CCG-3'\n______________CUGU___CCGGCA_CAGGGAAAUU\n______________\|\|\|:___\|\|::\|\|_\|\|\|\|\|\|\|\|\|:\n______________GACG___GGUUGU_GUCCCUUUAG\n3'-UUU...CUUAU____C________G__________AACCG...GUG-5'\n_____________\|________________________\|\n_____________86_______________________63\n	253 -- 259	64 -- 70	-25.8634 kcal/mol	5.26561 kcal/mol	7.38387 kcal/mol	236 260@LB@ \| \|@LB@5'-GCA...CACAU UUA CGCUU...CCG-3'@LB@ CUGU CCGGCA CAGGGAAAUU@LB@ \|\|\|: \|\|::\|\| \|\|\|\|\|\|\|\|\|:@LB@ GACG GGUUGU GUCCCUUUAG@LB@3'-UUU...CUUAU C G AACCG...GUG-5'@LB@ \| \|@LB@ 86 63@LB@@LB@@LB@Energy -13.21 kcal/mol@LB@Hybridization Energy -25.8634 kcal/mol@LB@Unfolding Energy - mRNA 5.26561 kcal/mol@LB@Unfolding Energy - sRNA 7.38387 kcal/mol@LB@@LB@Position - mRNA 237 -- 259@LB@Position - sRNA 64 -- 85@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 64 -- 70@LB@
50	0.002535	0.1727	b1879	flhA	-12.13	0.054078	218 -- 247	64 -- 89	putative flagellar export pore protein	_____________217______________________________248\n_____________\|________________________________\|\n5'-GCC...GCCGC___________U__CCGCAA___U________GACAC...CGA-3'\n______________GAUGCUGCGCC_GC______ACC___GAAAUC\n______________:\|\|:\|\|\|\|\|\|\|_:\|______\|\|\|___\|\|\|\|\|\|\n______________UUAUGACGCGG_UG______UGG___CUUUAG\n3'-UUU...CGCGC___________U___________UCC______AACCG...GUG-5'\n_____________\|________________________________\|\n_____________90_______________________________63\n	222 -- 228	79 -- 85	-26.8051 kcal/mol	6.79061 kcal/mol	7.88317 kcal/mol	217 248@LB@ \| \|@LB@5'-GCC...GCCGC U CCGCAA U GACAC...CGA-3'@LB@ GAUGCUGCGCC GC ACC GAAAUC@LB@ :\|\|:\|\|\|\|\|\|\| :\| \|\|\| \|\|\|\|\|\|@LB@ UUAUGACGCGG UG UGG CUUUAG@LB@3'-UUU...CGCGC U UCC AACCG...GUG-5'@LB@ \| \|@LB@ 90 63@LB@@LB@@LB@Energy -12.13 kcal/mol@LB@Hybridization Energy -26.8051 kcal/mol@LB@Unfolding Energy - mRNA 6.79061 kcal/mol@LB@Unfolding Energy - sRNA 7.88317 kcal/mol@LB@@LB@Position - mRNA 218 -- 247@LB@Position - sRNA 64 -- 89@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 79 -- 85@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@
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@

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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