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
99	0.005465	0.1855	b0767	pgl	-9.37	0.182441	275 -- 291	70 -- 86	6-phosphogluconolactonase	_____________274________________292\n_____________\|__________________\|\n5'-UCA...GGCGC____A_____________UUGUC...AUG-3'\n______________ACUG_CGCUGACA_CAGG\n______________\|\|\|\|_\|\|\|::\|\|\|_\|\|\|\|\n______________UGAC_GCGGUUGU_GUCC\n3'-UUU...GCUUA_____________G____CUUUA...GUG-5'\n_____________\|__________________\|\n_____________87_________________69\n	281 -- 287	75 -- 81	-21.4952 kcal/mol	4.85205 kcal/mol	7.27772 kcal/mol	274 292@LB@ \| \|@LB@5'-UCA...GGCGC A UUGUC...AUG-3'@LB@ ACUG CGCUGACA CAGG@LB@ \|\|\|\| \|\|\|::\|\|\| \|\|\|\|@LB@ UGAC GCGGUUGU GUCC@LB@3'-UUU...GCUUA G CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -9.37 kcal/mol@LB@Hybridization Energy -21.4952 kcal/mol@LB@Unfolding Energy - mRNA 4.85205 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 275 -- 291@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 75 -- 81@LB@
101	0.005473	0.1855	b1129	phoQ	-8.66	0.244665	211 -- 219	79 -- 87	sensory histidine kinase in two-component regulatory system with PhoP	_____________210_______220\n_____________\|_________\|\n5'-AUG...AAAAU_________UUUUU...GAA-3'\n______________UACUGCGUC\n______________\|\|\|\|\|\|\|:\|\n______________AUGACGCGG\n3'-UUU...CGCUU_________UUGUG...GUG-5'\n_____________\|_________\|\n_____________88________78\n	213 -- 219	79 -- 85	-14.7172 kcal/mol	1.01485 kcal/mol	5.0453 kcal/mol	210 220@LB@ \| \|@LB@5'-AUG...AAAAU UUUUU...GAA-3'@LB@ UACUGCGUC@LB@ \|\|\|\|\|\|\|:\|@LB@ AUGACGCGG@LB@3'-UUU...CGCUU UUGUG...GUG-5'@LB@ \| \|@LB@ 88 78@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -14.7172 kcal/mol@LB@Unfolding Energy - mRNA 1.01485 kcal/mol@LB@Unfolding Energy - sRNA 5.0453 kcal/mol@LB@@LB@Position - mRNA 211 -- 219@LB@Position - sRNA 79 -- 87@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 79 -- 85@LB@
65	0.003263	0.1727	b2584	pka	-7.67	0.359085	49 -- 62	69 -- 82	protein lysine acetyltransferase	_____________48_____________63\n_____________\|______________\|\n5'-AGG...AUGGC__G___________CGGCG...GUA-3'\n______________CG_CGAUACCGGGG\n______________\|\|_\|:\|:\|\|\|:\|\|\|\n______________GC_GUUGUGGUCCC\n3'-UUU...AUGAC__G___________UUUAG...GUG-5'\n_____________\|______________\|\n_____________83_____________68\n	56 -- 62	69 -- 75	-21.7159 kcal/mol	7.18281 kcal/mol	6.85849 kcal/mol	48 63@LB@ \| \|@LB@5'-AGG...AUGGC G CGGCG...GUA-3'@LB@ CG CGAUACCGGGG@LB@ \|\| \|:\|:\|\|\|:\|\|\|@LB@ GC GUUGUGGUCCC@LB@3'-UUU...AUGAC G UUUAG...GUG-5'@LB@ \| \|@LB@ 83 68@LB@@LB@@LB@Energy -7.67 kcal/mol@LB@Hybridization Energy -21.7159 kcal/mol@LB@Unfolding Energy - mRNA 7.18281 kcal/mol@LB@Unfolding Energy - sRNA 6.85849 kcal/mol@LB@@LB@Position - mRNA 49 -- 62@LB@Position - sRNA 69 -- 82@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 69 -- 75@LB@
72	0.00375	0.1804	b0386	proC	-10.69	0.102749	216 -- 233	53 -- 70	pyrroline-5-carboxylate reductase NAD(P)-binding	_____________215________________234\n_____________\|__________________\|\n5'-CAU...AAAUC__UUUUA_________G_AAUAU...GGG-3'\n______________GG_____UUGGCUGCG_C\n______________\|\|_____\|\|\|\|\|\|\|\|\|_\|\n______________CC_____AACCGACGC_G\n3'-UUU...UGGUC__UUUAG_________G_CAUUU...GUG-5'\n_____________\|__________________\|\n_____________71_________________52\n	225 -- 231	55 -- 61	-21.889 kcal/mol	4.36146 kcal/mol	6.83419 kcal/mol	215 234@LB@ \| \|@LB@5'-CAU...AAAUC UUUUA G AAUAU...GGG-3'@LB@ GG UUGGCUGCG C@LB@ \|\| \|\|\|\|\|\|\|\|\| \|@LB@ CC AACCGACGC G@LB@3'-UUU...UGGUC UUUAG G CAUUU...GUG-5'@LB@ \| \|@LB@ 71 52@LB@@LB@@LB@Energy -10.69 kcal/mol@LB@Hybridization Energy -21.889 kcal/mol@LB@Unfolding Energy - mRNA 4.36146 kcal/mol@LB@Unfolding Energy - sRNA 6.83419 kcal/mol@LB@@LB@Position - mRNA 216 -- 233@LB@Position - sRNA 53 -- 70@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 55 -- 61@LB@
177	0.01048	0.208	b2416	ptsI	-10.21	0.127224	180 -- 212	6 -- 36	PEP-protein phosphotransferase of PTS system (enzyme I)	_____________179________________________________213\n_____________\|__________________________________\|\n5'-GUG...AAAUC___C_____UAA____G___UA__A_________AUUUU...CCG-3'\n______________AGU_ACAAG___GGUA_GGU__UG__UUUCAGGC\n______________\|\|\|_\|\|\|\|\|___\|\|:\|_:\|:__\|\|__\|\|\|\|\|\|\|\|\n______________UCA_UGUUC___CCGU_UCG__AC__AAAGUCCG\n3'-UUU...ACUAC___A____________G___UG__AA________GCGUG-5'\n_____________\|__________________________________\|\n_____________37_________________________________5\n	206 -- 212	6 -- 12	-27.3223 kcal/mol	5.11839 kcal/mol	11.9979 kcal/mol	179 213@LB@ \| \|@LB@5'-GUG...AAAUC C UAA G UA A AUUUU...CCG-3'@LB@ AGU ACAAG GGUA GGU UG UUUCAGGC@LB@ \|\|\| \|\|\|\|\| \|\|:\| :\|: \|\| \|\|\|\|\|\|\|\|@LB@ UCA UGUUC CCGU UCG AC AAAGUCCG@LB@3'-UUU...ACUAC A G UG AA GCGUG-5'@LB@ \| \|@LB@ 37 5@LB@@LB@@LB@Energy -10.21 kcal/mol@LB@Hybridization Energy -27.3223 kcal/mol@LB@Unfolding Energy - mRNA 5.11839 kcal/mol@LB@Unfolding Energy - sRNA 11.9979 kcal/mol@LB@@LB@Position - mRNA 180 -- 212@LB@Position - sRNA 6 -- 36@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 6 -- 12@LB@
35	0.001921	0.1727	b1849	purT	-12.35	0.048961	166 -- 192	67 -- 88	phosphoribosylglycinamide formyltransferase 2	_____________165_________________________193\n_____________\|___________________________\|\n5'-UUU...CGUUU_________G__GAAUUA_________UAUUC...GUC-3'\n______________AUACUGCGC_CG______AUCAGGGGA\n______________\|\|\|\|\|\|\|\|\|_\|:______\|:\|\|\|\|\|:\|\n______________UAUGACGCG_GU______UGGUCCCUU\n3'-UUU...GCGCU____________UG_____________UAGAA...GUG-5'\n_____________\|___________________________\|\n_____________89__________________________66\n	186 -- 192	67 -- 73	-25.9621 kcal/mol	6.22738 kcal/mol	7.38319 kcal/mol	165 193@LB@ \| \|@LB@5'-UUU...CGUUU G GAAUUA UAUUC...GUC-3'@LB@ AUACUGCGC CG AUCAGGGGA@LB@ \|\|\|\|\|\|\|\|\| \|: \|:\|\|\|\|\|:\|@LB@ UAUGACGCG GU UGGUCCCUU@LB@3'-UUU...GCGCU UG UAGAA...GUG-5'@LB@ \| \|@LB@ 89 66@LB@@LB@@LB@Energy -12.35 kcal/mol@LB@Hybridization Energy -25.9621 kcal/mol@LB@Unfolding Energy - mRNA 6.22738 kcal/mol@LB@Unfolding Energy - sRNA 7.38319 kcal/mol@LB@@LB@Position - mRNA 166 -- 192@LB@Position - sRNA 67 -- 88@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 67 -- 73@LB@
2	1.572e-09	2.767e-06	b3749	rbsA	-20.95	0.000983	43 -- 64	65 -- 86	D-ribose ABC transporter ATPase	_____________42_____________________65\n_____________\|______________________\|\n5'-UAA...GAGCA_____AAA______________ACCAU...UGG-3'\n______________GCUGC___AACACCAGGGAAAU\n______________:\|\|\|\|___\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________UGACG___UUGUGGUCCCUUUA\n3'-UUU...GCUUA_____CGG______________GAACC...GUG-5'\n_____________\|______________________\|\n_____________87_____________________64\n	58 -- 64	65 -- 71	-31.8331 kcal/mol	3.49898 kcal/mol	7.38332 kcal/mol	42 65@LB@ \| \|@LB@5'-UAA...GAGCA AAA ACCAU...UGG-3'@LB@ GCUGC AACACCAGGGAAAU@LB@ :\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UGACG UUGUGGUCCCUUUA@LB@3'-UUU...GCUUA CGG GAACC...GUG-5'@LB@ \| \|@LB@ 87 64@LB@@LB@@LB@Energy -20.95 kcal/mol@LB@Hybridization Energy -31.8331 kcal/mol@LB@Unfolding Energy - mRNA 3.49898 kcal/mol@LB@Unfolding Energy - sRNA 7.38332 kcal/mol@LB@@LB@Position - mRNA 43 -- 64@LB@Position - sRNA 65 -- 86@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 65 -- 71@LB@
146	0.008611	0.2059	b3750	rbsC	-8.88	0.223197	137 -- 159	56 -- 77	D-ribose ABC transporter permease	_____________136_______________________160\n_____________\|_________________________\|\n5'-GAU...AGGCC_____________G_UAA_______CGCUG...UCU-3'\n______________AC_CCA_GGAAGU_U___UGGCUGC\n______________\|\|_\|\|\|_\|\|\|\|:\|_\|___\|\|\|\|\|\|\|\n______________UG_GGU_CCUUUA_A___ACCGACG\n3'-UUU...GCGGU__U___C______G___________CGGCA...GUG-5'\n_____________\|_________________________\|\n_____________78________________________55\n	153 -- 159	56 -- 62	-22.4095 kcal/mol	5.11916 kcal/mol	8.4081 kcal/mol	136 160@LB@ \| \|@LB@5'-GAU...AGGCC G UAA CGCUG...UCU-3'@LB@ AC CCA GGAAGU U UGGCUGC@LB@ \|\| \|\|\| \|\|\|\|:\| \| \|\|\|\|\|\|\|@LB@ UG GGU CCUUUA A ACCGACG@LB@3'-UUU...GCGGU U C G CGGCA...GUG-5'@LB@ \| \|@LB@ 78 55@LB@@LB@@LB@Energy -8.88 kcal/mol@LB@Hybridization Energy -22.4095 kcal/mol@LB@Unfolding Energy - mRNA 5.11916 kcal/mol@LB@Unfolding Energy - sRNA 8.4081 kcal/mol@LB@@LB@Position - mRNA 137 -- 159@LB@Position - sRNA 56 -- 77@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 56 -- 62@LB@
56	0.002848	0.1727	b0797	rhlE	-14.47	0.018687	57 -- 89	53 -- 82	ATP-dependent RNA helicase	_____________56_________________________________90\n_____________\|__________________________________\|\n5'-GAU...AGCAA______U_________U_____A__C________ACAAA...CUG-3'\n______________CGCCAG_CA_CAGGGA_AAUUU_UG_GCUGCGUC\n______________\|\|\|\|\|:_\|\|_\|\|\|\|\|\|_\|\|\|:\|_\|\|_\|\|\|\|\|\|:\|\n______________GCGGUU_GU_GUCCCU_UUAGA_AC_CGACGCGG\n3'-UUU...AUGAC_________G________________________CAUUU...GUG-5'\n_____________\|__________________________________\|\n_____________83_________________________________52\n	83 -- 89	53 -- 59	-38.8186 kcal/mol	7.89252 kcal/mol	16.4547 kcal/mol	56 90@LB@ \| \|@LB@5'-GAU...AGCAA U U A C ACAAA...CUG-3'@LB@ CGCCAG CA CAGGGA AAUUU UG GCUGCGUC@LB@ \|\|\|\|\|: \|\| \|\|\|\|\|\| \|\|\|:\| \|\| \|\|\|\|\|\|:\|@LB@ GCGGUU GU GUCCCU UUAGA AC CGACGCGG@LB@3'-UUU...AUGAC G CAUUU...GUG-5'@LB@ \| \|@LB@ 83 52@LB@@LB@@LB@Energy -14.47 kcal/mol@LB@Hybridization Energy -38.8186 kcal/mol@LB@Unfolding Energy - mRNA 7.89252 kcal/mol@LB@Unfolding Energy - sRNA 16.4547 kcal/mol@LB@@LB@Position - mRNA 57 -- 89@LB@Position - sRNA 53 -- 82@LB@Position Seed - mRNA 83 -- 89@LB@Position Seed - sRNA 53 -- 59@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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